{"gene":"NLRP3","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2006,"finding":"NALP3 (NLRP3) forms a caspase-1-activating inflammasome complex with ASC that is required for monosodium urate (MSU) and calcium pyrophosphate dihydrate (CPPD) crystal-induced IL-1β and IL-18 maturation; macrophages deficient in NALP3, ASC, or caspase-1 are defective in crystal-induced IL-1β activation, and inflammasome-deficient mice show impaired neutrophil influx in crystal-induced peritonitis.","method":"Genetic knockout (NALP3-/-, ASC-/-, caspase-1-/- mice), in vivo peritonitis model, IL-1β/IL-18 secretion assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple KO models with defined cellular and in vivo phenotypes, replicated across inflammasome components","pmids":["16407889"],"is_preprint":false},{"year":2006,"finding":"Cryopyrin (NLRP3/Nalp3) and ASC are essential components of the inflammasome required for caspase-1 activation and IL-1β/IL-18 production in response to bacterial RNA and imidazoquinoline compounds (R837, R848); NLRP3 deficiency did not affect TNF-α, IL-6, NF-κB, or MAPK activation, demonstrating a specific role in caspase-1 activation distinct from TLR signaling.","method":"Cryopyrin-deficient macrophages, cytokine secretion assays, NF-κB/MAPK activation assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO with multiple orthogonal readouts, replicated in two independent 2006 Nature papers","pmids":["16407888"],"is_preprint":false},{"year":2006,"finding":"NALP3 is essential for ATP-driven caspase-1 activation in LPS-stimulated macrophages and for secretion of IL-1α, IL-1β, and IL-18; NALP3 is not required for caspase-1 activation by Salmonella typhimurium, revealing stimulus-specific inflammasome assembly.","method":"NALP3-deficient and ASC-deficient mice, ATP stimulation of LPS-primed macrophages, contact hypersensitivity model in vivo","journal":"Immunity","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO with defined cellular phenotype and in vivo model, multiple cytokine readouts","pmids":["16546100"],"is_preprint":false},{"year":2008,"finding":"NALP3 inflammasome activation by silica crystals and aluminum salts requires phagocytosis of the crystals, followed by lysosomal damage/rupture; inhibition of phagosomal acidification or cathepsin B activity impaired NALP3 activation, identifying lysosomal damage as an endogenous danger signal sensed by NALP3.","method":"Crystal phagocytosis assays, lysosomal disruption experiments, cathepsin B inhibition, macrophage IL-1β secretion assays, NALP3-deficient cells","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple pharmacological and genetic interventions, mechanistic pathway established with orthogonal methods","pmids":["18604214"],"is_preprint":false},{"year":2010,"finding":"Depletion of autophagic proteins LC3B and beclin 1 enhances NLRP3 inflammasome activation (caspase-1 activation, IL-1β/IL-18 secretion) by promoting accumulation of dysfunctional mitochondria and cytosolic translocation of mitochondrial DNA (mtDNA); cytosolic mtDNA release depended on the NLRP3 inflammasome and mitochondrial ROS, and cytosolic mtDNA contributed to IL-1β/IL-18 secretion.","method":"LC3B/beclin-1 knockdown macrophages, LC3B-deficient mice, mtDNA cytosolic fractionation, ROS measurement, sepsis models","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO and KD with multiple orthogonal readouts including in vivo models","pmids":["21151103"],"is_preprint":false},{"year":2011,"finding":"Crystal structure of the NALP3 pyrin domain (PYD) resolved at 1.7-Å resolution reveals a canonical six-helical bundle fold with a homodimeric interface, conserved surface residues implicated in ASC interaction, and an unexpected disulfide bond between Cys-8 and Cys-108 that may regulate NALP3 activity via redox potential.","method":"X-ray crystallography (1.7-Å resolution), structural and sequence analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with functional inference from structural analysis, single study","pmids":["21880711"],"is_preprint":false},{"year":2013,"finding":"Activated ASC pyroptosome co-localizes with NLRP3 and caspase-1 in the cytoplasm but does not co-localize with mitochondria or seven other organelles tested in mouse peritoneal macrophages, establishing the cytoplasm (rather than specific organelles) as the site of NLRP3 inflammasome assembly under ATP, nigericin, or MSU stimulation.","method":"Confocal microscopy co-localization in primary macrophages, multiple organelle markers tested","journal":"Protein & cell","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization by confocal imaging, single lab, multiple stimuli tested","pmids":["23609011"],"is_preprint":false},{"year":2014,"finding":"Aryl hydrocarbon receptor (AhR) binds to the xenobiotic response element (XRE) in the NLRP3 promoter and directly inhibits NLRP3 transcription; AhR activation reduces NLRP3 protein level, caspase-1 activation, and IL-1β secretion, while AhR siRNA knockdown has opposite effects.","method":"ChIP assay (AhR binding to NLRP3 promoter XRE), siRNA knockdown, IL-1β/caspase-1 assays, in vivo alum peritonitis model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Moderate — ChIP demonstrating direct promoter binding plus functional KD/OE experiments with defined readouts","pmids":["25141024"],"is_preprint":false},{"year":2015,"finding":"NLRP3-activated caspase-1 cleaves the glucocorticoid receptor, diminishing glucocorticoid-induced transcriptional responses and increasing glucocorticoid resistance in acute lymphoblastic leukemia cells; knockdown or inhibition of CASP1 increased glucocorticoid receptor levels and mitigated resistance.","method":"CASP1 overexpression/knockdown, glucocorticoid receptor cleavage assays, transcriptional response assays, methylation analysis of CASP1/NLRP3 promoters in 444 patient samples","journal":"Nature genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mechanistic cleavage assay plus KD rescue in human cells; NLRP3 role inferred through CASP1 activation","pmids":["25938942"],"is_preprint":false},{"year":2016,"finding":"NLRP3 physically associates with NLRC4 via the NLRC4 NACHT domain in macrophages during Salmonella infection or flagellin transfection; when NLRC4 phosphorylation at S533 is ablated (S533A mutant), NLRP3 is recruited to compensate for caspase-1 activation, and the double KO (NLRC4 S533A/Nlrp3-/-) phenocopies NLRC4-/- cells, demonstrating functional overlap between the two inflammasome scaffolds.","method":"Co-immunoprecipitation, bone marrow-derived macrophages from Nlrc4(S533A/S533A) and Nlrp3-/- mice, Salmonella infection/flagellin transfection, caspase-1 activation assays","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP plus genetic epistasis with double mutant, defined phenotypic readout","pmids":["27139490"],"is_preprint":false},{"year":2017,"finding":"E3 ubiquitin ligase ARIH2 interacts with NLRP3 via its NACHT domain (aa 220-575) and ubiquitinates NLRP3 via K48- and K63-linked chains using its RING2 domain; ARIH2 deletion by CRISPR/Cas9 inhibits NLRP3 ubiquitination and promotes inflammasome activation, while ARIH2 overexpression promotes ubiquitination and inhibits activation.","method":"Co-IP, CRISPR/Cas9 deletion, ubiquitin linkage mutants, IL-1β/ASC oligomerization assays","journal":"Journal of immunology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — Co-IP defining binding domain, CRISPR KO and OE with reciprocal phenotypes, ubiquitin linkage mutagenesis","pmids":["29021376"],"is_preprint":false},{"year":2019,"finding":"Human NLRP3 is expressed as two major isoforms by alternative splicing: full-length and a variant lacking exon 5; the NLRP3 Δexon5 isoform lacks the interaction surface for NEK7 and is therefore inactive, establishing stochastic alternative splicing of LRR domain exons as a regulatory mechanism for NLRP3 activity.","method":"RT-PCR isoform identification, NEK7 interaction assays with Δexon5 mutant, functional activity assays","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — splice isoform characterization plus interaction domain mapping, single lab","pmids":["31324763"],"is_preprint":false},{"year":2019,"finding":"SUMO1 SUMOylates NLRP3 at Lys204 via the SUMO-conjugating enzyme UBC9, facilitating ASC oligomerization and inflammasome activation; SENP3 deSUMOylates NLRP3 to attenuate ASC recruitment, speck formation, inflammasome activation, and IL-1β secretion.","method":"Co-IP, SUMOylation site mutagenesis (K204), SENP3 overexpression/knockdown, ASC speck formation assays, IL-1β cleavage assays","journal":"FASEB journal","confidence":"High","confidence_rationale":"Tier 2 / Moderate — site-specific mutagenesis identifying K204, writer (UBC9/SUMO1) and eraser (SENP3) identified, functional readouts","pmids":["31914638"],"is_preprint":false},{"year":2020,"finding":"AKT kinase associates with NLRP3 and phosphorylates it at Ser5, limiting NLRP3 oligomerization; this S5 phosphorylation also stabilizes NLRP3 by reducing K496 ubiquitination and proteasome-mediated degradation by E3 ligase Trim31. Pharmacological AKT manipulation reciprocally modulates IL-1β production in vitro and in vivo.","method":"Co-IP (AKT-NLRP3), site-specific phosphorylation assays (S5 mutagenesis), ubiquitination assays (K496), Trim31 interaction, pharmacological AKT inhibition in vivo (LPS injection)","journal":"Journal of immunology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — kinase-substrate relationship established with mutagenesis, ubiquitination linkage defined, in vivo validation","pmids":["32929041"],"is_preprint":false},{"year":2020,"finding":"RACK1 (receptor for activated protein C kinase 1) is a component of the NLRP3 complex in macrophages; RACK1 interacts with NLRP3 and NEK7 (but not ASC), promotes the active conformation of NLRP3 induced by activating stimuli, and is required for subsequent inflammasome assembly, caspase-1 activation, and IL-1β release specifically downstream of NLRP3 (not NLRC4 or AIM2).","method":"Co-IP, RACK1 siRNA knockdown, caspase-1 activation and IL-1β release assays, specificity testing across multiple inflammasomes","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and KD with defined phenotype, single lab, specificity established by parallel inflammasome controls","pmids":["33207200"],"is_preprint":false},{"year":2020,"finding":"β-catenin physically interacts with NLRP3 and promotes the association between NLRP3 and ASC; siRNA or pharmacological suppression of β-catenin impairs NLRP3 inflammasome activation, and β-catenin inhibitor attenuates LPS-induced systemic inflammation in vivo.","method":"Co-IP, siRNA knockdown, pharmacological inhibition, in vivo LPS model, IL-1β/caspase-1 assays","journal":"Molecular immunology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP establishing interaction, KD and pharmacological inhibition with in vivo validation, single lab","pmids":["32244067"],"is_preprint":false},{"year":2021,"finding":"Full-length mouse NLRP3 forms a 12- to 16-mer double-ring cage oligomer held together by LRR-LRR interactions, with pyrin domains shielded within the assembly to prevent premature activation; this NLRP3 cage is predominantly membrane-localized. Structure-guided mutagenesis shows that double-ring cage formation is required for trans-Golgi network (TGN) dispersion (an early event in NLRP3 activation by many stimuli) and for inflammasome punctum formation, caspase-1 processing, and cell death.","method":"Cryo-EM structure of full-length mouse NLRP3, structure-guided mutagenesis, membrane fractionation, TGN dispersion assays, caspase-1 processing and cell death assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure combined with structure-guided mutagenesis and multiple functional readouts in a single rigorous study","pmids":["34861190"],"is_preprint":false},{"year":2021,"finding":"TRIM28 (E3 SUMO ligase) binds NLRP3 and promotes its SUMOylation by SUMO1, SUMO2, and SUMO3; this SUMOylation inhibits NLRP3 ubiquitination and proteasomal degradation, thereby stabilizing NLRP3 and facilitating inflammasome activation. Trim28 deficiency attenuates NLRP3 inflammasome activation in vitro and in vivo.","method":"Co-IP, SUMO modification assays, ubiquitination assays, Trim28 KO (in vitro and in vivo), caspase-1/IL-1β assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Moderate — writer identified (TRIM28), SUMOylation-ubiquitination crosstalk defined, KO with functional readouts in vivo","pmids":["34373456"],"is_preprint":false},{"year":2021,"finding":"YAP physically interacts with NLRP3 and maintains NLRP3 stability by blocking the association between NLRP3 and E3 ligase β-TrCP1; β-TrCP1 promotes NLRP3 proteasomal degradation via K27-linked ubiquitination at Lys380. YAP deficiency in myeloid cells attenuates LPS-induced systemic inflammation and MSU crystal-induced peritonitis.","method":"Co-IP (YAP-NLRP3, NLRP3-β-TrCP1), ubiquitination assays (K27, K380), myeloid-specific YAP KO mice, in vivo inflammation models","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple Co-IPs defining interaction partners, ubiquitination site identified, in vivo KO validation","pmids":["33976226"],"is_preprint":false},{"year":2021,"finding":"BRISC complex (containing BRCC3 metalloprotease) mediates deubiquitination of NLRP3, which is required for efficient NLRP3 inflammasome activation; thiolutin (JAMM domain metalloprotease inhibitor) blocks BRISC-mediated NLRP3 deubiquitination and suppresses NLRP3 inflammasome activation across canonical, noncanonical, alternative, and transcription-independent pathways at nanomolar concentrations.","method":"BRISC/BRCC3 inhibition by thiolutin, NLRP3 ubiquitination assays, multiple NLRP3 activation pathway assays, in vivo models (sepsis, peritonitis, EAE, CAPS, NAFLD)","journal":"Science immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — specific deubiquitinase complex identified, pharmacological and mechanistic validation across multiple pathways and in vivo models","pmids":["33931568"],"is_preprint":false},{"year":2021,"finding":"UAF1/USP1 deubiquitinase complex selectively removes K48-linked polyubiquitination from NLRP3, suppressing its proteasomal degradation and enhancing cellular NLRP3 levels required for inflammasome assembly; UAF1/USP12 and UAF1/USP46 complexes additionally promote NF-κB activation to enhance NLRP3 transcription. Uaf1 deficiency attenuates NLRP3 inflammasome activation in vitro and in vivo.","method":"Co-IP, K48-linked ubiquitination assays, deubiquitinase activity assays, Uaf1 KD (in vitro and in vivo), IL-1β secretion assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Moderate — specific deubiquitinase complex identified, ubiquitin linkage specificity established, in vivo validation","pmids":["33247121"],"is_preprint":false},{"year":2021,"finding":"USP5 deubiquitinase attenuates NLRP3 inflammasome activation by promoting autophagic degradation of NLRP3; USP5 deficiency or overexpression reciprocally modulates NLRP3 protein levels and inflammasome activation.","method":"USP5 KD/OE, co-IP, autophagy flux assays, NLRP3 degradation assays, IL-1β/caspase-1 assays","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — deubiquitinase-autophagy link established by KD/OE, single lab","pmids":["34486483"],"is_preprint":false},{"year":2022,"finding":"E3 ubiquitin ligase gp78 mediates mixed ubiquitination of NLRP3, which inhibits NLRP3 inflammasome activation by suppressing NLRP3 oligomerization and subcellular translocation; Insig-1 (ER membrane protein) is required for the gp78-NLRP3 interaction and gp78-mediated NLRP3 ubiquitination. gp78 or Insig-1 deficiency in myeloid cells exacerbates NLRP3-dependent inflammation in vivo.","method":"Co-IP (gp78-NLRP3, gp78-Insig-1), ubiquitination assays, NLRP3 oligomerization assays, myeloid-specific KO mice, in vivo inflammation models","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 2 / Moderate — E3 ligase-substrate interaction defined, adaptor protein identified, in vivo KO validation","pmids":["35110683"],"is_preprint":false},{"year":2022,"finding":"USP22 deubiquitinase inhibits NLRP3 inflammasome activation by promoting ATG5-mediated macroautophagy/NLRP3 degradation; USP22 stabilizes ATG5 via decreasing K27- and K48-linked ubiquitination at Lys118. USP22 deficiency significantly increases alum-induced peritonitis and LPS-induced systemic inflammation in vivo.","method":"USP22 KD/KO, co-IP, ubiquitination assays (K27/K48-ATG5 K118), autophagy flux assays, in vivo models","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — indirect NLRP3 regulation via ATG5, ubiquitination sites defined, in vivo validation, single lab","pmids":["35900990"],"is_preprint":false},{"year":2022,"finding":"TRIM31 interacts with NLRP3 in retinal pigment epithelial cells and promotes NLRP3 ubiquitination, thereby inhibiting NLRP3 inflammasome activation and pyroptosis; TRIM31 knockdown phenocopies NLRP3 activation by ox-LDL.","method":"Co-IP, ubiquitination assays, TRIM31 KD/OE, NLRP3 inhibitor controls, IL-1β/caspase-1 assays","journal":"Cell biology international","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and ubiquitination assay in a single cell type, single lab","pmids":["32716108"],"is_preprint":false},{"year":2023,"finding":"NLRP3 is S-palmitoylated at the LRR domain by ZDHHC5; this palmitoylation promotes NLRP3 oligomerization, NLRP3-NEK7 interaction, and ASC aggregate formation, leading to caspase-1 activation, IL-1β/IL-18 release, and GSDMD cleavage. ABHD17A acts as the depalmitoylase for NLRP3, and a disease-associated NLRP3 mutation shows defective ABHD17A binding and hyper-palmitoylation. Zdhhc5-/- mice exhibit defective NLRP3 inflammasome activation in vivo.","method":"Acyl-RAC palmitoylation assay, ZDHHC5 KO/siRNA, site-specific mutagenesis (LRR palmitoylation site), NLRP3 oligomerization assays, NEK7 interaction assays, ASC speck formation, Zdhhc5-/- mice, ABHD17A depalmitoylase assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — palmitoylation writer (ZDHHC5) and eraser (ABHD17A) identified, site-specific mutagenesis, disease mutation functional characterization, in vivo KO validation","pmids":["38092000"],"is_preprint":false},{"year":2023,"finding":"NLRP3 binds non-oxidized mtDNA with much higher affinity (IC50 ~4 nM) than Ox-mtDNA (IC50 ~247 nM); the NLRP3 PYD domain mediates DNA binding and preferentially binds Ox-mtDNA; a NOMID/FCAS gain-of-function mutant shows higher affinity for Ox-mtDNA (IC50 ~8.1 nM). A structural model based on alignment to DNA glycosylases suggests a DNA-binding mechanism involving the PYD domain fold.","method":"In vitro DNA-binding assays (IC50 determination), domain deletion/truncation constructs, monoclonal antibody blocking assays, structural homology modeling","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro binding assay with mutants but structural model is computational; single study","pmids":["37253813"],"is_preprint":false},{"year":2023,"finding":"MARCH5 (mitochondria-associated E3 ubiquitin ligase) interacts with the NACHT domain of NLRP3 and promotes K27-linked polyubiquitination at K324 and K430 residues; this ubiquitination is required for NLRP3-NEK7 binding, NLRP3 oligomerization, and ASC speck formation. Myeloid-specific March5 cKO mice fail to secrete IL-1β/IL-18 and show attenuated LPS- or Pseudomonas-induced mortality.","method":"Co-IP (MARCH5-NLRP3 NACHT domain), K27-linked ubiquitination assays with K324A/K430A mutants, NEK7 binding assays, ASC speck assays, myeloid-specific March5 cKO mice, in vivo infection models","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — E3 ligase substrate sites precisely mapped by mutagenesis, ubiquitin linkage defined, domain of interaction mapped, in vivo conditional KO validation","pmids":["37575012"],"is_preprint":false},{"year":2024,"finding":"ZDHHC7 palmitoylates NLRP3 at Cys126, which is critical for NLRP3 inflammasome activation; Cys126 palmitoylation by ZDHHC7 promotes resting NLRP3 localization on the trans-Golgi network (TGN) and activated NLRP3 on dispersed TGN, enabling ASC recruitment and oligomerization. ZDHHC7 KO, pharmacological inhibition, or C126 mutation diminishes NLRP3 activation in macrophages and in vivo. ZDHHC12 has a terminating/opposing palmitoylation effect on NLRP3.","method":"Acyl-RAC palmitoylation assay, ZDHHC7 KO, C126 site mutagenesis, TGN localization by live imaging/immunofluorescence, ASC oligomerization assays, in vivo inflammasome models","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — palmitoylation site (C126) and writer (ZDHHC7) identified with mutagenesis, subcellular localization consequence demonstrated, in vivo validation","pmids":["38583156"],"is_preprint":false},{"year":2024,"finding":"Tau protein directly acetylates NLRP3 at K21, K22, and K24 within its PYD domain (via Tau's K18 domain acetyltransferase activity), inducing inflammasome activation in microglia; blocking the Tau-NLRP3 interaction with a designed peptide inhibits NLRP3 acetylation, inflammasome activation, microgliosis, and cognitive impairment in mice.","method":"In vitro acetylation assay (test-tube), co-IP, mass spectrometry (acetylation site identification), molecular docking, AAV-mediated Tau overexpression in mice, behavioral testing, PET/CT imaging, blocking peptide intervention","journal":"Clinical and translational medicine","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro acetyltransferase assay with site mapping by MS, in vivo AAV model with functional rescue by blocking peptide, single lab","pmids":["38488468"],"is_preprint":false},{"year":2024,"finding":"NLRP12 interacts with NLRP3 and inhibits human (but not murine) NLRP3-induced ASC inflammasome assembly; NLRP12 failed to nucleate ASC polymerization itself, and disease-associated NLRP12 mutants lost the ability to suppress NLRP3 inflammasome assembly. PBMCs from NLRP12-mutant patients showed increased IL-1β in response to NLRP3 stimulation.","method":"ASC polymerization/speck formation screen, Co-IP (NLRP12-NLRP3), NLRP12 disease mutant analysis, IL-1β assays in patient PBMCs, species specificity testing (human vs. murine NLRP3)","journal":"Science signaling","confidence":"High","confidence_rationale":"Tier 2 / Moderate — NLR screen, Co-IP, disease mutant functional testing, human patient validation with defined mechanism","pmids":["38261657"],"is_preprint":false},{"year":2014,"finding":"TXNIP (thioredoxin-interacting protein) activates the NALP3 inflammasome by directly interacting with NLRP3 in high-glucose-exposed podocytes; TXNIP knockdown impedes NLRP3 inflammasome activation and attenuates podocyte injury. Blocking NLRP3 inflammasome activation by NLRP3/ASC shRNA or caspase-1 inhibition prevents IL-1β production and podocyte injury under diabetic conditions.","method":"Co-IP (TXNIP-NLRP3), TXNIP/NLRP3/ASC shRNA knockdown, caspase-1 inhibition, in vivo diabetic nephropathy model, IL-1β assays","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP establishing TXNIP-NLRP3 interaction, KD rescue experiments, in vivo model","pmids":["25017793"],"is_preprint":false},{"year":2022,"finding":"CB1R (cannabinoid receptor 1) directly interacts with the NLRP3 inflammasome via amino acid residues 177-209; antipsychotics drive CB1R translocation to the cytoplasm where CB1R stabilizes the inflammasome. Cb1r KO significantly alleviates antipsychotic-induced cardiomyocyte pyroptosis and cardiotoxicity.","method":"Co-IP (CB1R-NLRP3, domain mapping 177-209), RNA sequencing, small-molecule screen, Cb1r KO mice, pyroptosis assays","journal":"Signal transduction and targeted therapy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with interaction domain mapped, KO validation in vivo, single lab","pmids":["35739093"],"is_preprint":false},{"year":2003,"finding":"3D modeling of the NLRP3 NBD domain reveals structural similarity to AAA+ ATPases; most CAPS/MWS/FCU-associated mutations cluster on one side of the NBD in a region predicted to mediate intermolecular contacts, suggesting that defects in nucleotide binding, hydrolysis, or protein oligomerization underlie NLRP3 functional dysregulation in autoinflammatory diseases.","method":"3D structural modeling of the NBD domain, mapping of known mutations onto the model, sequence/structural analysis","journal":"Blood","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational structural model only, no direct biochemical validation of mechanism","pmids":["14630794"],"is_preprint":false},{"year":2021,"finding":"NLRP3 activated by diverse stimuli triggers gasdermin D cleavage by caspase-1, releasing the pore-forming N-terminal domain that drives pyroptosis; the assembled NLRP3 inflammasome contributes not only to pyroptosis but also to apoptosis, necroptosis, and ferroptosis.","method":"Review summarizing experimental findings from multiple studies including loss-of-function and caspase-1 activation assays","journal":"Cellular & molecular immunology","confidence":"Low","confidence_rationale":"Tier 4 / Weak — review article, no new experimental data reported","pmids":["34321623"],"is_preprint":false},{"year":2018,"finding":"NLRP3 inflammasome activation requires intracellular copper; the copper chelator tetrathiomolybdate specifically inhibits canonical NLRP3 but not AIM2, NLRC4, or NLRP1 inflammasomes or NF-κB priming; the regulation involves copper at the active site of superoxide dismutase 1 (SOD1), and SOD1-deficient mice show impaired inflammasome function. In vivo copper depletion attenuated caspase-1-dependent inflammation.","method":"Copper chelation (tetrathiomolybdate), SOD1-deficient mice, multiple inflammasome specificity assays, in vivo endotoxic shock model","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pharmacological and genetic dissection of copper requirement, SOD1 KO mechanistic link, specificity established, single lab","pmids":["29358279"],"is_preprint":false},{"year":2024,"finding":"FXR inhibits NLRP3 activity by restraining its Ser295 phosphorylation in hepatic stellate cells; knockdown or knockout of NLRP3 relieves GCDCA-induced hepatic fibrosis, placing NLRP3 downstream of bile acid signaling via FXR-mediated phosphorylation control.","method":"NLRP3 knockdown/knockout, FXR overexpression, Western blotting for Ser295 phosphorylation, in vivo mouse liver fibrosis model with GCDCA","journal":"Hepatology international","confidence":"Low","confidence_rationale":"Tier 3 / Weak — phosphorylation detected by Western blot, FXR OE and NLRP3 KO rescue, single lab without kinase reconstitution","pmids":["38172440"],"is_preprint":false}],"current_model":"NLRP3 is a cytosolic pattern-recognition receptor that, upon sensing diverse PAMPs/DAMPs (including crystals, bacterial RNA, lysosomal damage, mtDNA, and metabolic signals), undergoes oligomerization into a 12–16-mer double-ring cage (membrane-localized, held by LRR-LRR interactions with shielded PYD domains) that disperses from the trans-Golgi network upon activation; NLRP3 then recruits the adaptor ASC via PYD-PYD interaction and procaspase-1 via ASC's CARD, forming the inflammasome complex that auto-activates caspase-1 to cleave pro-IL-1β, pro-IL-18, and gasdermin D (pyroptosis). NLRP3 activity is tightly controlled by post-translational modifications: stabilizing SUMOylation (TRIM28/SUMO1; UBC9/SUMO1 at K204, reversed by SENP3), activating palmitoylation (ZDHHC5 at LRR domain; ZDHHC7 at C126, enabling TGN localization, reversed by ABHD17A/ZDHHC12), inhibitory phosphorylation (AKT at S5, PKA/PKD at S295, JNK at S198), and multiple ubiquitination events—both activating (MARCH5 K27-Ub at K324/K430 enabling NEK7 binding; BRISC/BRCC3 deubiquitination permitting activation; UAF1/USP1 K48-deubiquitination stabilizing NLRP3) and inhibitory (ARIH2 K48/K63-Ub; β-TrCP1 K27-Ub at K380 blocked by YAP; gp78/Insig-1 ubiquitination; Trim31 K496-Ub). NLRP3 also binds mtDNA via its PYD domain, interacts with NLRC4 to cooperate in inflammasome signaling, is acetylated at PYD residues K21/K22/K24 by Tau (promoting microglial activation), and is transcriptionally regulated by AhR binding to its promoter XRE; gain-of-function mutations in the NACHT domain cluster at predicted oligomerization interfaces and cause cryopyrin-associated autoinflammatory diseases."},"narrative":{"mechanistic_narrative":"NLRP3 is a cytosolic pattern-recognition receptor that nucleates an ASC- and caspase-1-containing inflammasome to drive maturation of IL-1β and IL-18 in response to diverse danger signals including monosodium urate and CPPD crystals, bacterial RNA, imidazoquinolines, and ATP [PMID:16407889, PMID:16407888, PMID:16546100]. It senses these stimuli through convergent upstream events: phagocytosis-dependent lysosomal rupture and cathepsin B release from crystalline particulates [PMID:18604214], and accumulation of dysfunctional mitochondria with cytosolic mtDNA release driven by mitochondrial ROS [PMID:21151103], with NLRP3 directly binding mtDNA through its PYD domain [PMID:37253813]. Activated NLRP3 assembles a 12–16-mer double-ring cage held by LRR-LRR contacts with shielded pyrin domains; cage formation drives dispersion from the trans-Golgi network and is required for inflammasome punctum formation, caspase-1 processing, and cell death [PMID:34861190], with downstream caspase-1 cleaving gasdermin D to execute pyroptosis [PMID:34321623]. Inflammasome assembly proceeds via ASC nucleation and is supported by accessory partners including NEK7, RACK1, and β-catenin that promote the active conformation and ASC association [PMID:33207200, PMID:32244067], and NLRP3 can cooperate with the NLRC4 scaffold to drive caspase-1 activation during bacterial infection [PMID:27139490]. NLRP3 activity is governed by an extensive post-translational code: activating S-palmitoylation by ZDHHC5 at the LRR and by ZDHHC7 at Cys126 that controls TGN localization (reversed by ABHD17A/ZDHHC12) [PMID:38092000, PMID:38583156], stabilizing SUMOylation at Lys204 by UBC9/SUMO1 and by TRIM28 (erased by SENP3) [PMID:31914638, PMID:34373456], activating K27-linked ubiquitination by MARCH5 at K324/K430 that enables NEK7 binding [PMID:37575012], and stabilizing K48-deubiquitination by UAF1/USP1 and BRCC3/BRISC [PMID:33931568, PMID:33247121], counterbalanced by inhibitory AKT phosphorylation at Ser5 and multiple inhibitory ubiquitin ligases (ARIH2, β-TrCP1 at K380 antagonized by YAP, gp78/Insig-1) [PMID:32929041, PMID:29021376, PMID:33976226, PMID:35110683]. Transcriptionally, NLRP3 is directly repressed by AhR binding to a promoter XRE [PMID:25141024]. Structural modeling places gain-of-function mutations causing cryopyrin-associated autoinflammatory disease at NBD oligomerization interfaces [PMID:14630794].","teleology":[{"year":2006,"claim":"Established NLRP3 as the sensor component of a caspase-1-activating inflammasome, defining its core function as converting diverse danger signals into IL-1β/IL-18 maturation independently of TLR-driven NF-κB/MAPK signaling.","evidence":"Genetic knockouts (NALP3-/-, ASC-/-, caspase-1-/-) with crystal, bacterial RNA, imidazoquinoline, and ATP stimulation plus in vivo peritonitis and contact hypersensitivity models","pmids":["16407889","16407888","16546100"],"confidence":"High","gaps":["Did not resolve how chemically distinct stimuli converge on a single sensor","Stimulus-specificity (e.g. Salmonella independence) left the upstream sensing mechanism undefined"]},{"year":2008,"claim":"Resolved how particulate stimuli are sensed, showing crystals act indirectly via phagocytosis-driven lysosomal rupture and cathepsin B release rather than direct receptor binding.","evidence":"Crystal phagocytosis assays, lysosomal disruption, cathepsin B and acidification inhibition in NALP3-deficient macrophages","pmids":["18604214"],"confidence":"High","gaps":["The direct molecular link between cathepsin B and NLRP3 activation was not identified","Did not explain non-particulate (ATP/nigericin) activation"]},{"year":2010,"claim":"Identified mitochondrial damage and cytosolic mtDNA as an endogenous trigger linking autophagy quality control to inflammasome activation.","evidence":"LC3B/beclin-1 knockdown and LC3B-deficient macrophages, mtDNA cytosolic fractionation, ROS measurement, sepsis models","pmids":["21151103"],"confidence":"High","gaps":["Did not establish whether mtDNA binds NLRP3 directly","Mechanism of mtDNA cytosolic translocation incompletely defined"]},{"year":2011,"claim":"Provided the first atomic-resolution view of the PYD interaction module, revealing a redox-sensitive disulfide that could couple NLRP3 activity to cellular redox state.","evidence":"X-ray crystallography of the NALP3 PYD at 1.7 Å with structural/sequence analysis","pmids":["21880711"],"confidence":"High","gaps":["Functional role of the Cys8-Cys108 disulfide inferred but not tested","Full-length assembly context absent"]},{"year":2013,"claim":"Localized inflammasome assembly to the cytoplasm rather than a specific organelle, constraining models of where NLRP3/ASC/caspase-1 nucleation occurs.","evidence":"Confocal co-localization in primary macrophages against multiple organelle markers under ATP/nigericin/MSU","pmids":["23609011"],"confidence":"Medium","gaps":["Single-lab imaging without biochemical fractionation","Apparent tension with later TGN-dispersion model unresolved"]},{"year":2014,"claim":"Defined transcriptional control of NLRP3 by showing AhR directly represses its promoter, and identified a metabolic priming partner (TXNIP).","evidence":"ChIP for AhR binding to the NLRP3 promoter XRE with siRNA/overexpression; TXNIP-NLRP3 Co-IP and knockdown in diabetic nephropathy model","pmids":["25141024","25017793"],"confidence":"High","gaps":["TXNIP-NLRP3 interaction is single-lab and context-specific","How transcriptional repression integrates with post-translational control not addressed"]},{"year":2016,"claim":"Demonstrated cross-talk between inflammasome scaffolds, showing NLRP3 can be recruited to compensate for NLRC4 in caspase-1 activation during bacterial infection.","evidence":"Reciprocal Co-IP and genetic epistasis with Nlrc4(S533A) and Nlrp3-/- macrophages during Salmonella infection","pmids":["27139490"],"confidence":"High","gaps":["Physical architecture of a joint NLRP3-NLRC4 complex not resolved","Physiological contexts requiring cooperation unclear"]},{"year":2021,"claim":"Defined the resting and active higher-order architecture of NLRP3, establishing the double-ring cage with shielded PYDs and linking cage formation to TGN dispersion as a prerequisite for activation.","evidence":"Cryo-EM of full-length mouse NLRP3 with structure-guided mutagenesis, membrane fractionation, and TGN dispersion/caspase-1 readouts","pmids":["34861190"],"confidence":"High","gaps":["How specific stimuli release PYD shielding not mechanistically resolved","Conformational transition from cage to active inflammasome incompletely defined"]},{"year":2021,"claim":"Established ubiquitin removal as a licensing step for activation and SUMOylation as a competing stabilizing modification, building a PTM logic of NLRP3 control.","evidence":"BRISC/BRCC3 inhibition (thiolutin), UAF1/USP1 K48-deubiquitination, USP5 autophagic degradation, and TRIM28/SUMO1 plus YAP/β-TrCP1 K380 ubiquitination studies with KO and in vivo models","pmids":["33931568","33247121","34486483","34373456","33976226"],"confidence":"High","gaps":["Temporal ordering and hierarchy among competing PTMs unresolved","Some erasers/ligases validated in single labs"]},{"year":2023,"claim":"Identified palmitoylation and K27-ubiquitination as positive controls that govern TGN localization and NEK7-dependent oligomerization, mechanistically connecting lipid/ubiquitin marks to assembly.","evidence":"Acyl-RAC, ZDHHC5/ZDHHC7 KO and site mutagenesis (C126/LRR), ABHD17A depalmitoylase assays, and MARCH5 K27-Ub mapping at K324/K430 with conditional KO mice","pmids":["38092000","37575012","38583156"],"confidence":"High","gaps":["How palmitoylation, K27-Ub, and NEK7 recruitment are coordinated in time not resolved","Direct mtDNA-binding affinity model is computational (37253813)"]},{"year":2024,"claim":"Extended NLRP3 regulation into cell-type-specific and disease contexts, including Tau-mediated PYD acetylation in microglia and NLRP12 as a human-specific suppressor of NLRP3-driven ASC assembly.","evidence":"In vitro acetyltransferase assay with MS site mapping and AAV Tau model; ASC polymerization screen, Co-IP, and disease-mutant testing in patient PBMCs","pmids":["38488468","38261657"],"confidence":"High","gaps":["Species differences (human vs murine NLRP3 regulation by NLRP12) limit generalization","Acetylation work is single-lab"]},{"year":null,"claim":"How the dozens of identified PTMs, accessory partners, and localization cues are integrated into a single ordered activation pathway, and how individual stimuli select among them, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified temporal model of competing/cooperating PTMs","Direct stimulus-to-conformational-change coupling undefined","Structural basis of the active inflammasome (vs resting cage) not fully resolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[26]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,16]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[33]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[6]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[16,28]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[16]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,1,2]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[16,34]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[3,4]}],"complexes":["NLRP3 inflammasome"],"partners":["ASC","NEK7","NLRC4","MARCH5","ZDHHC7","RACK1","YAP","NLRP12"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96P20","full_name":"NACHT, LRR and PYD domains-containing protein 3","aliases":["Angiotensin/vasopressin receptor AII/AVP-like","Caterpiller protein 1.1","CLR1.1","Cold-induced autoinflammatory syndrome 1 protein","Cryopyrin","PYRIN-containing APAF1-like protein 1"],"length_aa":1036,"mass_kda":118.2,"function":"Sensor component of the NLRP3 inflammasome, which mediates inflammasome activation in response to defects in membrane integrity, leading to secretion of inflammatory cytokines IL1B and IL18 and pyroptosis (PubMed:16407889, PubMed:18403674, PubMed:18604214, PubMed:23582325, PubMed:25686105, PubMed:27929086, PubMed:28656979, PubMed:28847925, PubMed:30487600, PubMed:30612879, PubMed:31086327, PubMed:31086329, PubMed:31189953, PubMed:33231615, PubMed:34133077, PubMed:34341353, PubMed:34512673, PubMed:36442502, PubMed:40450990). In response to pathogens and other damage-associated signals that affect the integrity of membranes, initiates the formation of the inflammasome polymeric complex composed of NLRP3, CASP1 and PYCARD/ASC (PubMed:16407889, PubMed:18403674, PubMed:27432880, PubMed:28847925, PubMed:31189953, PubMed:33231615, PubMed:34133077, PubMed:34341353, PubMed:36142182, PubMed:36442502). Recruitment of pro-caspase-1 (proCASP1) to the NLRP3 inflammasome promotes caspase-1 (CASP1) activation, which subsequently cleaves and activates inflammatory cytokines IL1B and IL18 and gasdermin-D (GSDMD), promoting cytokine secretion and pyroptosis (PubMed:23582325, PubMed:28847925, PubMed:31189953, PubMed:33231615, PubMed:34133077, PubMed:34341353). Activation of NLRP3 inflammasome is also required for HMGB1 secretion; stimulating inflammatory responses (PubMed:22801494). Involved in the homeostatic wound healing response to tissue injury, a multistep cascade that guides neutrophil migration to necrotic sites while avoiding collateral damage of healthy tissues. ATP released from necrotic cells triggers activation of NLRP3 inflammasome through P2RX7 signaling leading to neutrophil adhesion to the vascular endothelium close to the injury site (By similarity). Under resting conditions, ADP-bound NLRP3 is autoinhibited (PubMed:35114687). NLRP3 activation stimuli include extracellular ATP, nigericin, reactive oxygen species, crystals of monosodium urate or cholesterol, amyloid-beta fibers, environmental or industrial particles and nanoparticles, such as asbestos, silica, aluminum salts, cytosolic dsRNA, etc (PubMed:16407889, PubMed:18403674, PubMed:18604214, PubMed:19414800, PubMed:23871209). Almost all stimuli trigger intracellular K(+) efflux (By similarity). These stimuli lead to membrane perturbation and activation of NLRP3 (By similarity). Upon activation, NLRP3 is transported to microtubule organizing center (MTOC), where it is unlocked by NEK7, leading to its relocalization to dispersed trans-Golgi network (dTGN) vesicle membranes and formation of an active inflammasome complex (PubMed:36442502, PubMed:39173637). Associates with dTGN vesicle membranes by binding to phosphatidylinositol 4-phosphate (PtdIns4P) (PubMed:30487600, PubMed:34554188). Shows ATPase activity (PubMed:17483456) Independently of inflammasome activation, regulates the differentiation of T helper 2 (Th2) cells and has a role in Th2 cell-dependent asthma and tumor growth (By similarity). During Th2 differentiation, required for optimal IRF4 binding to IL4 promoter and for IRF4-dependent IL4 transcription (By similarity). Binds to the consensus DNA sequence 5'-GRRGGNRGAG-3' (By similarity). May also participate in the transcription of IL5, IL13, GATA3, CCR3, CCR4 and MAF (By similarity)","subcellular_location":"Cytoplasm, cytosol; Inflammasome; Cytoplasm, cytoskeleton, microtubule organizing center; Golgi apparatus membrane; Endoplasmic reticulum; Mitochondrion; Secreted; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q96P20/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NLRP3","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/NLRP3","total_profiled":1310},"omim":[{"mim_id":"621395","title":"DEAD-BOX HELICASE 19A; DDX19A","url":"https://www.omim.org/entry/621395"},{"mim_id":"621348","title":"ZDHHC PALMITOYLTRANSFERASE 12; ZDHHC12","url":"https://www.omim.org/entry/621348"},{"mim_id":"621036","title":"ABHYDROLASE DOMAIN-CONTAINING PROTEIN 8; ABHD8","url":"https://www.omim.org/entry/621036"},{"mim_id":"620563","title":"UBIQUITIN-SPECIFIC PEPTIDASE 50; USP50","url":"https://www.omim.org/entry/620563"},{"mim_id":"619079","title":"INFLAMMATORY BOWEL DISEASE (CROHN DISEASE) 30; IBD30","url":"https://www.omim.org/entry/619079"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"bone marrow","ntpm":51.5}],"url":"https://www.proteinatlas.org/search/NLRP3"},"hgnc":{"alias_symbol":["AGTAVPRL","AII","AVP","FCAS","FCU","NALP3","PYPAF1","MWS","CLR1.1"],"prev_symbol":["C1orf7","CIAS1","DFNA34"]},"alphafold":{"accession":"Q96P20","domains":[{"cath_id":"1.10.533.10","chopping":"7-91","consensus_level":"high","plddt":86.14,"start":7,"end":91},{"cath_id":"3.40.50.300","chopping":"142-170_206-211_219-370","consensus_level":"high","plddt":86.9661,"start":142,"end":370},{"cath_id":"-","chopping":"384-438","consensus_level":"high","plddt":80.8005,"start":384,"end":438},{"cath_id":"-","chopping":"462-500_522-539_557-640","consensus_level":"high","plddt":82.6702,"start":462,"end":640},{"cath_id":"3.80.10.10","chopping":"965-1036","consensus_level":"medium","plddt":91.5085,"start":965,"end":1036}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96P20","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96P20-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96P20-F1-predicted_aligned_error_v6.png","plddt_mean":81.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NLRP3","jax_strain_url":"https://www.jax.org/strain/search?query=NLRP3"},"sequence":{"accession":"Q96P20","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96P20.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96P20/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96P20"}},"corpus_meta":[{"pmid":"16407889","id":"PMC_16407889","title":"Gout-associated uric acid crystals activate the NALP3 inflammasome.","date":"2006","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/16407889","citation_count":4166,"is_preprint":false},{"pmid":"21151103","id":"PMC_21151103","title":"Autophagy proteins regulate innate immune responses by inhibiting the release of mitochondrial DNA mediated by the NALP3 inflammasome.","date":"2010","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/21151103","citation_count":2561,"is_preprint":false},{"pmid":"18604214","id":"PMC_18604214","title":"Silica crystals and aluminum salts activate the NALP3 inflammasome through phagosomal destabilization.","date":"2008","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/18604214","citation_count":2428,"is_preprint":false},{"pmid":"34321623","id":"PMC_34321623","title":"NLRP3 inflammasome activation and cell death.","date":"2021","source":"Cellular & molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/34321623","citation_count":1237,"is_preprint":false},{"pmid":"16407888","id":"PMC_16407888","title":"Bacterial RNA and small antiviral compounds activate caspase-1 through cryopyrin/Nalp3.","date":"2006","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/16407888","citation_count":931,"is_preprint":false},{"pmid":"16546100","id":"PMC_16546100","title":"Critical role for NALP3/CIAS1/Cryopyrin in innate and adaptive immunity through its regulation of caspase-1.","date":"2006","source":"Immunity","url":"https://pubmed.ncbi.nlm.nih.gov/16546100","citation_count":808,"is_preprint":false},{"pmid":"26594174","id":"PMC_26594174","title":"NLRP3 inflammasome and its inhibitors: a review.","date":"2015","source":"Frontiers in pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/26594174","citation_count":720,"is_preprint":false},{"pmid":"24840700","id":"PMC_24840700","title":"Mechanism of NLRP3 inflammasome activation.","date":"2014","source":"Annals of the New York Academy of Sciences","url":"https://pubmed.ncbi.nlm.nih.gov/24840700","citation_count":604,"is_preprint":false},{"pmid":"31749805","id":"PMC_31749805","title":"Pharmacological Inhibitors of the NLRP3 Inflammasome.","date":"2019","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/31749805","citation_count":564,"is_preprint":false},{"pmid":"33163006","id":"PMC_33163006","title":"Interplay Between NLRP3 Inflammasome and Autophagy.","date":"2020","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/33163006","citation_count":516,"is_preprint":false},{"pmid":"32948742","id":"PMC_32948742","title":"NLRP3 inflammasome in endothelial dysfunction.","date":"2020","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/32948742","citation_count":412,"is_preprint":false},{"pmid":"28345767","id":"PMC_28345767","title":"NLRP3 inflammasome: Its regulation and involvement in atherosclerosis.","date":"2017","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/28345767","citation_count":378,"is_preprint":false},{"pmid":"32148650","id":"PMC_32148650","title":"NLRP3 Inflammasome and Inflammatory Diseases.","date":"2020","source":"Oxidative medicine and cellular longevity","url":"https://pubmed.ncbi.nlm.nih.gov/32148650","citation_count":294,"is_preprint":false},{"pmid":"29247992","id":"PMC_29247992","title":"Metabolic regulation of NLRP3.","date":"2018","source":"Immunological reviews","url":"https://pubmed.ncbi.nlm.nih.gov/29247992","citation_count":250,"is_preprint":false},{"pmid":"21388882","id":"PMC_21388882","title":"The Nlrp3 inflammasome: contributions to intestinal homeostasis.","date":"2011","source":"Trends in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/21388882","citation_count":242,"is_preprint":false},{"pmid":"14630794","id":"PMC_14630794","title":"Molecular basis of the spectral expression of CIAS1 mutations associated with phagocytic cell-mediated autoinflammatory disorders CINCA/NOMID, MWS, and FCU.","date":"2003","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/14630794","citation_count":228,"is_preprint":false},{"pmid":"34861190","id":"PMC_34861190","title":"NLRP3 cages revealed by full-length mouse NLRP3 structure control pathway activation.","date":"2021","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/34861190","citation_count":222,"is_preprint":false},{"pmid":"30288079","id":"PMC_30288079","title":"Spotlight on the NLRP3 inflammasome pathway.","date":"2018","source":"Journal of inflammation research","url":"https://pubmed.ncbi.nlm.nih.gov/30288079","citation_count":219,"is_preprint":false},{"pmid":"25141024","id":"PMC_25141024","title":"Aryl hydrocarbon receptor negatively regulates NLRP3 inflammasome activity by inhibiting NLRP3 transcription.","date":"2014","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/25141024","citation_count":191,"is_preprint":false},{"pmid":"30349539","id":"PMC_30349539","title":"Regulation of NLRP3 Inflammasome by Phosphorylation.","date":"2018","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/30349539","citation_count":189,"is_preprint":false},{"pmid":"36669831","id":"PMC_36669831","title":"Pharmacological Inhibition of the NLRP3 Inflammasome: Structure, Molecular Activation, and Inhibitor-NLRP3 Interaction.","date":"2023","source":"Pharmacological reviews","url":"https://pubmed.ncbi.nlm.nih.gov/36669831","citation_count":183,"is_preprint":false},{"pmid":"21880711","id":"PMC_21880711","title":"Crystal structure of NALP3 protein pyrin domain (PYD) and its implications in inflammasome assembly.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21880711","citation_count":167,"is_preprint":false},{"pmid":"22310372","id":"PMC_22310372","title":"Intrinsic properties and functional circuitry of the AII amacrine cell.","date":"2012","source":"Visual neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/22310372","citation_count":146,"is_preprint":false},{"pmid":"30268598","id":"PMC_30268598","title":"NLRP3 inflammasome activation in inflammaging.","date":"2018","source":"Seminars in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/30268598","citation_count":140,"is_preprint":false},{"pmid":"25938942","id":"PMC_25938942","title":"NALP3 inflammasome upregulation and CASP1 cleavage of the glucocorticoid receptor cause glucocorticoid resistance in leukemia cells.","date":"2015","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/25938942","citation_count":140,"is_preprint":false},{"pmid":"19664151","id":"PMC_19664151","title":"Expression and regulation of the NALP3 inflammasome complex in periodontal diseases.","date":"2009","source":"Clinical and experimental immunology","url":"https://pubmed.ncbi.nlm.nih.gov/19664151","citation_count":136,"is_preprint":false},{"pmid":"34373456","id":"PMC_34373456","title":"TRIM28 SUMOylates and stabilizes NLRP3 to facilitate inflammasome activation.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34373456","citation_count":135,"is_preprint":false},{"pmid":"33976226","id":"PMC_33976226","title":"YAP promotes the activation of NLRP3 inflammasome via blocking K27-linked polyubiquitination of NLRP3.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33976226","citation_count":134,"is_preprint":false},{"pmid":"27139490","id":"PMC_27139490","title":"NLRP3 recruitment by NLRC4 during Salmonella infection.","date":"2016","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/27139490","citation_count":124,"is_preprint":false},{"pmid":"38092000","id":"PMC_38092000","title":"ZDHHC5-mediated NLRP3 palmitoylation promotes NLRP3-NEK7 interaction and inflammasome activation.","date":"2023","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/38092000","citation_count":122,"is_preprint":false},{"pmid":"24876671","id":"PMC_24876671","title":"Chrysophanol inhibits NALP3 inflammasome activation and ameliorates cerebral ischemia/reperfusion in mice.","date":"2014","source":"Mediators of inflammation","url":"https://pubmed.ncbi.nlm.nih.gov/24876671","citation_count":122,"is_preprint":false},{"pmid":"29021376","id":"PMC_29021376","title":"ARIH2 Ubiquitinates NLRP3 and Negatively Regulates NLRP3 Inflammasome Activation in Macrophages.","date":"2017","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/29021376","citation_count":118,"is_preprint":false},{"pmid":"20079456","id":"PMC_20079456","title":"Nlrp3: an immune sensor of cellular stress and infection.","date":"2010","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/20079456","citation_count":115,"is_preprint":false},{"pmid":"34486483","id":"PMC_34486483","title":"USP5 attenuates NLRP3 inflammasome activation by promoting autophagic degradation of NLRP3.","date":"2021","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/34486483","citation_count":113,"is_preprint":false},{"pmid":"33247121","id":"PMC_33247121","title":"UAF1 deubiquitinase complexes facilitate NLRP3 inflammasome activation by promoting NLRP3 expression.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33247121","citation_count":112,"is_preprint":false},{"pmid":"22147977","id":"PMC_22147977","title":"Lipopolysaccharide induces and activates the Nalp3 inflammasome in the liver.","date":"2011","source":"World journal of gastroenterology","url":"https://pubmed.ncbi.nlm.nih.gov/22147977","citation_count":109,"is_preprint":false},{"pmid":"35952982","id":"PMC_35952982","title":"NLRP3 inflammasome in neurodegenerative disease.","date":"2022","source":"Translational research : the journal of laboratory and clinical medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35952982","citation_count":105,"is_preprint":false},{"pmid":"21128730","id":"PMC_21128730","title":"Gene silencing of NALP3 protects against liver ischemia-reperfusion injury in mice.","date":"2011","source":"Human gene therapy","url":"https://pubmed.ncbi.nlm.nih.gov/21128730","citation_count":105,"is_preprint":false},{"pmid":"31609412","id":"PMC_31609412","title":"Interaction between autophagy and the NLRP3 inflammasome.","date":"2019","source":"Acta biochimica et biophysica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/31609412","citation_count":102,"is_preprint":false},{"pmid":"23453445","id":"PMC_23453445","title":"Nalp3 inflammasome is activated and required for vascular smooth muscle cell calcification.","date":"2013","source":"International journal of cardiology","url":"https://pubmed.ncbi.nlm.nih.gov/23453445","citation_count":94,"is_preprint":false},{"pmid":"33255820","id":"PMC_33255820","title":"Inhibiting the NLRP3 Inflammasome.","date":"2020","source":"Molecules (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/33255820","citation_count":92,"is_preprint":false},{"pmid":"26237026","id":"PMC_26237026","title":"NLRP3 Inflammasome and Pathobiology in AMD.","date":"2015","source":"Journal of clinical medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26237026","citation_count":91,"is_preprint":false},{"pmid":"34882936","id":"PMC_34882936","title":"Licochalcone B specifically inhibits the NLRP3 inflammasome by disrupting NEK7-NLRP3 interaction.","date":"2021","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/34882936","citation_count":91,"is_preprint":false},{"pmid":"28652704","id":"PMC_28652704","title":"Rhein attenuates inflammation through inhibition of NF-κB and NALP3 inflammasome in vivo and in vitro.","date":"2017","source":"Drug design, development and therapy","url":"https://pubmed.ncbi.nlm.nih.gov/28652704","citation_count":91,"is_preprint":false},{"pmid":"19824913","id":"PMC_19824913","title":"Expression and function of the NALP3 inflammasome in rheumatoid synovium.","date":"2009","source":"Immunology","url":"https://pubmed.ncbi.nlm.nih.gov/19824913","citation_count":86,"is_preprint":false},{"pmid":"36299604","id":"PMC_36299604","title":"Corilagin Restrains NLRP3 Inflammasome Activation and Pyroptosis through the ROS/TXNIP/NLRP3 Pathway to Prevent Inflammation.","date":"2022","source":"Oxidative medicine and cellular longevity","url":"https://pubmed.ncbi.nlm.nih.gov/36299604","citation_count":82,"is_preprint":false},{"pmid":"35496273","id":"PMC_35496273","title":"Salidroside Ameliorates Depression by Suppressing NLRP3-Mediated Pyroptosis via P2X7/NF-κB/NLRP3 Signaling Pathway.","date":"2022","source":"Frontiers in pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/35496273","citation_count":82,"is_preprint":false},{"pmid":"34445484","id":"PMC_34445484","title":"NLRP3 Ubiquitination-A New Approach to Target NLRP3 Inflammasome Activation.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34445484","citation_count":80,"is_preprint":false},{"pmid":"32531835","id":"PMC_32531835","title":"Increasing complexity of NLRP3 inflammasome regulation.","date":"2020","source":"Journal of leukocyte biology","url":"https://pubmed.ncbi.nlm.nih.gov/32531835","citation_count":79,"is_preprint":false},{"pmid":"38583156","id":"PMC_38583156","title":"NLRP3 Cys126 palmitoylation by ZDHHC7 promotes inflammasome activation.","date":"2024","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/38583156","citation_count":78,"is_preprint":false},{"pmid":"29960001","id":"PMC_29960001","title":"Flavonoids interfere with NLRP3 inflammasome activation.","date":"2018","source":"Toxicology and applied pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/29960001","citation_count":78,"is_preprint":false},{"pmid":"33931568","id":"PMC_33931568","title":"Pharmacological targeting of NLRP3 deubiquitination for treatment of NLRP3-associated inflammatory diseases.","date":"2021","source":"Science immunology","url":"https://pubmed.ncbi.nlm.nih.gov/33931568","citation_count":74,"is_preprint":false},{"pmid":"25017793","id":"PMC_25017793","title":"Thioredoxin-interacting protein mediates NALP3 inflammasome activation in podocytes during diabetic nephropathy.","date":"2014","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/25017793","citation_count":72,"is_preprint":false},{"pmid":"35900990","id":"PMC_35900990","title":"USP22 suppresses the NLRP3 inflammasome by degrading NLRP3 via ATG5-dependent autophagy.","date":"2022","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/35900990","citation_count":69,"is_preprint":false},{"pmid":"32929041","id":"PMC_32929041","title":"AKT Regulates NLRP3 Inflammasome Activation by Phosphorylating NLRP3 Serine 5.","date":"2020","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/32929041","citation_count":68,"is_preprint":false},{"pmid":"12522564","id":"PMC_12522564","title":"Fine structure mapping of CIAS1: identification of an ancestral haplotype and a common FCAS mutation, L353P.","date":"2002","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/12522564","citation_count":67,"is_preprint":false},{"pmid":"31100298","id":"PMC_31100298","title":"MicroRNAs as important regulators of the NLRP3 inflammasome.","date":"2019","source":"Progress in biophysics and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/31100298","citation_count":65,"is_preprint":false},{"pmid":"33207200","id":"PMC_33207200","title":"RACK1 Mediates NLRP3 Inflammasome Activation by Promoting NLRP3 Active Conformation and Inflammasome Assembly.","date":"2020","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/33207200","citation_count":64,"is_preprint":false},{"pmid":"25496217","id":"PMC_25496217","title":"TLR4 and NALP3 inflammasome in the development of endothelial dysfunction in uraemia.","date":"2015","source":"European journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/25496217","citation_count":63,"is_preprint":false},{"pmid":"37670126","id":"PMC_37670126","title":"Targeting NLRP3 inflammasome for neurodegenerative disorders.","date":"2023","source":"Molecular psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/37670126","citation_count":62,"is_preprint":false},{"pmid":"31914638","id":"PMC_31914638","title":"SUMO1 SUMOylates and SENP3 deSUMOylates NLRP3 to orchestrate the inflammasome activation.","date":"2019","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/31914638","citation_count":59,"is_preprint":false},{"pmid":"35110683","id":"PMC_35110683","title":"Ubiquitination of NLRP3 by gp78/Insig-1 restrains NLRP3 inflammasome activation.","date":"2022","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/35110683","citation_count":57,"is_preprint":false},{"pmid":"31324763","id":"PMC_31324763","title":"Alternative splicing regulates stochastic NLRP3 activity.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31324763","citation_count":57,"is_preprint":false},{"pmid":"19579027","id":"PMC_19579027","title":"MEFV, TNF1rA, CARD15 and NLRP3 mutation analysis in PFAPA.","date":"2009","source":"Rheumatology international","url":"https://pubmed.ncbi.nlm.nih.gov/19579027","citation_count":56,"is_preprint":false},{"pmid":"36275641","id":"PMC_36275641","title":"NLRP3 inflammasome and NLRP3-related autoinflammatory diseases: From cryopyrin function to targeted therapies.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/36275641","citation_count":54,"is_preprint":false},{"pmid":"25461402","id":"PMC_25461402","title":"Methylsulfonylmethane inhibits NLRP3 inflammasome activation.","date":"2014","source":"Cytokine","url":"https://pubmed.ncbi.nlm.nih.gov/25461402","citation_count":52,"is_preprint":false},{"pmid":"17382568","id":"PMC_17382568","title":"ASC, Ipaf and Cryopyrin/Nalp3: bona fide intracellular adapters of the caspase-1 inflammasome.","date":"2007","source":"Microbes and infection","url":"https://pubmed.ncbi.nlm.nih.gov/17382568","citation_count":51,"is_preprint":false},{"pmid":"29358279","id":"PMC_29358279","title":"Copper Regulates the Canonical NLRP3 Inflammasome.","date":"2018","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/29358279","citation_count":51,"is_preprint":false},{"pmid":"34034975","id":"PMC_34034975","title":"NLRP3 inflammasomes that induce antitumor immunity.","date":"2021","source":"Trends in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/34034975","citation_count":48,"is_preprint":false},{"pmid":"33982766","id":"PMC_33982766","title":"NLRP3 inflammasome in sepsis (Review).","date":"2021","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/33982766","citation_count":47,"is_preprint":false},{"pmid":"20384614","id":"PMC_20384614","title":"Nod1, Nod2 and Nalp3 receptors, new potential targets in treatment of allergic rhinitis?","date":"2010","source":"Allergy","url":"https://pubmed.ncbi.nlm.nih.gov/20384614","citation_count":45,"is_preprint":false},{"pmid":"32973739","id":"PMC_32973739","title":"The NLRP3 Inflammasome and Its Role in T1DM.","date":"2020","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/32973739","citation_count":44,"is_preprint":false},{"pmid":"34861056","id":"PMC_34861056","title":"Reviewing the importance of TLR-NLRP3-pyroptosis pathway and mechanism of experimental NLRP3 inflammasome inhibitors.","date":"2021","source":"Scandinavian journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/34861056","citation_count":44,"is_preprint":false},{"pmid":"37253813","id":"PMC_37253813","title":"Differential Binding of NLRP3 to non-oxidized and Ox-mtDNA mediates NLRP3 Inflammasome Activation.","date":"2023","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/37253813","citation_count":43,"is_preprint":false},{"pmid":"28659178","id":"PMC_28659178","title":"Azithromycin decreases NALP3 mRNA stability in monocytes to limit inflammasome-dependent inflammation.","date":"2017","source":"Respiratory research","url":"https://pubmed.ncbi.nlm.nih.gov/28659178","citation_count":43,"is_preprint":false},{"pmid":"32171704","id":"PMC_32171704","title":"Chronic cerebral hypoperfusion activates AIM2 and NLRP3 inflammasome.","date":"2020","source":"Brain research","url":"https://pubmed.ncbi.nlm.nih.gov/32171704","citation_count":42,"is_preprint":false},{"pmid":"23609011","id":"PMC_23609011","title":"Cellular localization of NLRP3 inflammasome.","date":"2013","source":"Protein & cell","url":"https://pubmed.ncbi.nlm.nih.gov/23609011","citation_count":42,"is_preprint":false},{"pmid":"33202405","id":"PMC_33202405","title":"Role of NLRP3 Inflammasomes in Neuroinflammation Diseases.","date":"2020","source":"European neurology","url":"https://pubmed.ncbi.nlm.nih.gov/33202405","citation_count":40,"is_preprint":false},{"pmid":"37575012","id":"PMC_37575012","title":"MARCH5-dependent NLRP3 ubiquitination is required for mitochondrial NLRP3-NEK7 complex formation and NLRP3 inflammasome activation.","date":"2023","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/37575012","citation_count":40,"is_preprint":false},{"pmid":"26388856","id":"PMC_26388856","title":"Expression of dectin-1 and enhanced activation of NALP3 inflammasome are associated with resistance to paracoccidioidomycosis.","date":"2015","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/26388856","citation_count":40,"is_preprint":false},{"pmid":"38488468","id":"PMC_38488468","title":"Tau induces inflammasome activation and microgliosis through acetylating NLRP3.","date":"2024","source":"Clinical and translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38488468","citation_count":39,"is_preprint":false},{"pmid":"26131053","id":"PMC_26131053","title":"The NLRP3 inflammasome and stroke.","date":"2015","source":"International journal of clinical and experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/26131053","citation_count":39,"is_preprint":false},{"pmid":"32585073","id":"PMC_32585073","title":"Role of NLRP3 inflammasome in liver disease.","date":"2020","source":"Journal of digestive diseases","url":"https://pubmed.ncbi.nlm.nih.gov/32585073","citation_count":38,"is_preprint":false},{"pmid":"27249000","id":"PMC_27249000","title":"Goldfish Leptin-AI and Leptin-AII: Function and Central Mechanism in Feeding Control.","date":"2016","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/27249000","citation_count":37,"is_preprint":false},{"pmid":"34599154","id":"PMC_34599154","title":"Suppression of lncRNA NLRP3 inhibits NLRP3-triggered inflammatory responses in early acute lung injury.","date":"2021","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/34599154","citation_count":37,"is_preprint":false},{"pmid":"27187378","id":"PMC_27187378","title":"The Relationship between NALP3 and Autoinflammatory Syndromes.","date":"2016","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/27187378","citation_count":36,"is_preprint":false},{"pmid":"26037399","id":"PMC_26037399","title":"NALP3 inflammasome activation in protein misfolding diseases.","date":"2015","source":"Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/26037399","citation_count":36,"is_preprint":false},{"pmid":"32244067","id":"PMC_32244067","title":"β-catenin promotes NLRP3 inflammasome activation via increasing the association between NLRP3 and ASC.","date":"2020","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/32244067","citation_count":36,"is_preprint":false},{"pmid":"30844378","id":"PMC_30844378","title":"Effects of phosphorylation on the NLRP3 inflammasome.","date":"2019","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/30844378","citation_count":35,"is_preprint":false},{"pmid":"32716108","id":"PMC_32716108","title":"TRIM31 inhibits NLRP3 inflammasome and pyroptosis of retinal pigment epithelial cells through ubiquitination of NLRP3.","date":"2020","source":"Cell biology international","url":"https://pubmed.ncbi.nlm.nih.gov/32716108","citation_count":35,"is_preprint":false},{"pmid":"36238294","id":"PMC_36238294","title":"NLRP3: Role in ischemia/reperfusion injuries.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/36238294","citation_count":34,"is_preprint":false},{"pmid":"34639204","id":"PMC_34639204","title":"Research Progress of Mitochondrial Mechanism in NLRP3 Inflammasome Activation and Exercise Regulation of NLRP3 Inflammasome.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34639204","citation_count":34,"is_preprint":false},{"pmid":"38172440","id":"PMC_38172440","title":"Bile acids induce liver fibrosis through the NLRP3 inflammasome pathway and the mechanism of FXR inhibition of NLRP3 activation.","date":"2024","source":"Hepatology international","url":"https://pubmed.ncbi.nlm.nih.gov/38172440","citation_count":33,"is_preprint":false},{"pmid":"37849728","id":"PMC_37849728","title":"Natural products modulate NLRP3 in ulcerative colitis.","date":"2023","source":"Frontiers in pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/37849728","citation_count":33,"is_preprint":false},{"pmid":"29039099","id":"PMC_29039099","title":"Assessing NLRP3 Inflammasome Activation by Nanoparticles.","date":"2018","source":"Methods in molecular biology (Clifton, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/29039099","citation_count":33,"is_preprint":false},{"pmid":"36304814","id":"PMC_36304814","title":"Pyroptosis in NLRP3 inflammasome-related atherosclerosis.","date":"2022","source":"Cell stress","url":"https://pubmed.ncbi.nlm.nih.gov/36304814","citation_count":32,"is_preprint":false},{"pmid":"35739093","id":"PMC_35739093","title":"CB1R-stabilized NLRP3 inflammasome drives antipsychotics cardiotoxicity.","date":"2022","source":"Signal transduction and targeted therapy","url":"https://pubmed.ncbi.nlm.nih.gov/35739093","citation_count":32,"is_preprint":false},{"pmid":"38261657","id":"PMC_38261657","title":"NLRP12 interacts with NLRP3 to block the activation of the human NLRP3 inflammasome.","date":"2024","source":"Science signaling","url":"https://pubmed.ncbi.nlm.nih.gov/38261657","citation_count":32,"is_preprint":false},{"pmid":"33718366","id":"PMC_33718366","title":"Targeting the NLRP3 Inflammasome via BTK.","date":"2021","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/33718366","citation_count":32,"is_preprint":false},{"pmid":"8726686","id":"PMC_8726686","title":"Cardiac effects of AII. AT1A receptor signaling, desensitization, and internalization.","date":"1996","source":"Advances in experimental medicine and biology","url":"https://pubmed.ncbi.nlm.nih.gov/8726686","citation_count":32,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":47206,"output_tokens":10437,"usd":0.149087,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":20584,"output_tokens":4388,"usd":0.10631,"stage2_stop_reason":"end_turn"},"total_usd":0.255397,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"NALP3 (NLRP3) forms a caspase-1-activating inflammasome complex with ASC that is required for monosodium urate (MSU) and calcium pyrophosphate dihydrate (CPPD) crystal-induced IL-1β and IL-18 maturation; macrophages deficient in NALP3, ASC, or caspase-1 are defective in crystal-induced IL-1β activation, and inflammasome-deficient mice show impaired neutrophil influx in crystal-induced peritonitis.\",\n      \"method\": \"Genetic knockout (NALP3-/-, ASC-/-, caspase-1-/- mice), in vivo peritonitis model, IL-1β/IL-18 secretion assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple KO models with defined cellular and in vivo phenotypes, replicated across inflammasome components\",\n      \"pmids\": [\"16407889\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Cryopyrin (NLRP3/Nalp3) and ASC are essential components of the inflammasome required for caspase-1 activation and IL-1β/IL-18 production in response to bacterial RNA and imidazoquinoline compounds (R837, R848); NLRP3 deficiency did not affect TNF-α, IL-6, NF-κB, or MAPK activation, demonstrating a specific role in caspase-1 activation distinct from TLR signaling.\",\n      \"method\": \"Cryopyrin-deficient macrophages, cytokine secretion assays, NF-κB/MAPK activation assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO with multiple orthogonal readouts, replicated in two independent 2006 Nature papers\",\n      \"pmids\": [\"16407888\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"NALP3 is essential for ATP-driven caspase-1 activation in LPS-stimulated macrophages and for secretion of IL-1α, IL-1β, and IL-18; NALP3 is not required for caspase-1 activation by Salmonella typhimurium, revealing stimulus-specific inflammasome assembly.\",\n      \"method\": \"NALP3-deficient and ASC-deficient mice, ATP stimulation of LPS-primed macrophages, contact hypersensitivity model in vivo\",\n      \"journal\": \"Immunity\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO with defined cellular phenotype and in vivo model, multiple cytokine readouts\",\n      \"pmids\": [\"16546100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"NALP3 inflammasome activation by silica crystals and aluminum salts requires phagocytosis of the crystals, followed by lysosomal damage/rupture; inhibition of phagosomal acidification or cathepsin B activity impaired NALP3 activation, identifying lysosomal damage as an endogenous danger signal sensed by NALP3.\",\n      \"method\": \"Crystal phagocytosis assays, lysosomal disruption experiments, cathepsin B inhibition, macrophage IL-1β secretion assays, NALP3-deficient cells\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple pharmacological and genetic interventions, mechanistic pathway established with orthogonal methods\",\n      \"pmids\": [\"18604214\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Depletion of autophagic proteins LC3B and beclin 1 enhances NLRP3 inflammasome activation (caspase-1 activation, IL-1β/IL-18 secretion) by promoting accumulation of dysfunctional mitochondria and cytosolic translocation of mitochondrial DNA (mtDNA); cytosolic mtDNA release depended on the NLRP3 inflammasome and mitochondrial ROS, and cytosolic mtDNA contributed to IL-1β/IL-18 secretion.\",\n      \"method\": \"LC3B/beclin-1 knockdown macrophages, LC3B-deficient mice, mtDNA cytosolic fractionation, ROS measurement, sepsis models\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO and KD with multiple orthogonal readouts including in vivo models\",\n      \"pmids\": [\"21151103\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Crystal structure of the NALP3 pyrin domain (PYD) resolved at 1.7-Å resolution reveals a canonical six-helical bundle fold with a homodimeric interface, conserved surface residues implicated in ASC interaction, and an unexpected disulfide bond between Cys-8 and Cys-108 that may regulate NALP3 activity via redox potential.\",\n      \"method\": \"X-ray crystallography (1.7-Å resolution), structural and sequence analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with functional inference from structural analysis, single study\",\n      \"pmids\": [\"21880711\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Activated ASC pyroptosome co-localizes with NLRP3 and caspase-1 in the cytoplasm but does not co-localize with mitochondria or seven other organelles tested in mouse peritoneal macrophages, establishing the cytoplasm (rather than specific organelles) as the site of NLRP3 inflammasome assembly under ATP, nigericin, or MSU stimulation.\",\n      \"method\": \"Confocal microscopy co-localization in primary macrophages, multiple organelle markers tested\",\n      \"journal\": \"Protein & cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization by confocal imaging, single lab, multiple stimuli tested\",\n      \"pmids\": [\"23609011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Aryl hydrocarbon receptor (AhR) binds to the xenobiotic response element (XRE) in the NLRP3 promoter and directly inhibits NLRP3 transcription; AhR activation reduces NLRP3 protein level, caspase-1 activation, and IL-1β secretion, while AhR siRNA knockdown has opposite effects.\",\n      \"method\": \"ChIP assay (AhR binding to NLRP3 promoter XRE), siRNA knockdown, IL-1β/caspase-1 assays, in vivo alum peritonitis model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP demonstrating direct promoter binding plus functional KD/OE experiments with defined readouts\",\n      \"pmids\": [\"25141024\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"NLRP3-activated caspase-1 cleaves the glucocorticoid receptor, diminishing glucocorticoid-induced transcriptional responses and increasing glucocorticoid resistance in acute lymphoblastic leukemia cells; knockdown or inhibition of CASP1 increased glucocorticoid receptor levels and mitigated resistance.\",\n      \"method\": \"CASP1 overexpression/knockdown, glucocorticoid receptor cleavage assays, transcriptional response assays, methylation analysis of CASP1/NLRP3 promoters in 444 patient samples\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mechanistic cleavage assay plus KD rescue in human cells; NLRP3 role inferred through CASP1 activation\",\n      \"pmids\": [\"25938942\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"NLRP3 physically associates with NLRC4 via the NLRC4 NACHT domain in macrophages during Salmonella infection or flagellin transfection; when NLRC4 phosphorylation at S533 is ablated (S533A mutant), NLRP3 is recruited to compensate for caspase-1 activation, and the double KO (NLRC4 S533A/Nlrp3-/-) phenocopies NLRC4-/- cells, demonstrating functional overlap between the two inflammasome scaffolds.\",\n      \"method\": \"Co-immunoprecipitation, bone marrow-derived macrophages from Nlrc4(S533A/S533A) and Nlrp3-/- mice, Salmonella infection/flagellin transfection, caspase-1 activation assays\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP plus genetic epistasis with double mutant, defined phenotypic readout\",\n      \"pmids\": [\"27139490\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"E3 ubiquitin ligase ARIH2 interacts with NLRP3 via its NACHT domain (aa 220-575) and ubiquitinates NLRP3 via K48- and K63-linked chains using its RING2 domain; ARIH2 deletion by CRISPR/Cas9 inhibits NLRP3 ubiquitination and promotes inflammasome activation, while ARIH2 overexpression promotes ubiquitination and inhibits activation.\",\n      \"method\": \"Co-IP, CRISPR/Cas9 deletion, ubiquitin linkage mutants, IL-1β/ASC oligomerization assays\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP defining binding domain, CRISPR KO and OE with reciprocal phenotypes, ubiquitin linkage mutagenesis\",\n      \"pmids\": [\"29021376\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Human NLRP3 is expressed as two major isoforms by alternative splicing: full-length and a variant lacking exon 5; the NLRP3 Δexon5 isoform lacks the interaction surface for NEK7 and is therefore inactive, establishing stochastic alternative splicing of LRR domain exons as a regulatory mechanism for NLRP3 activity.\",\n      \"method\": \"RT-PCR isoform identification, NEK7 interaction assays with Δexon5 mutant, functional activity assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — splice isoform characterization plus interaction domain mapping, single lab\",\n      \"pmids\": [\"31324763\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SUMO1 SUMOylates NLRP3 at Lys204 via the SUMO-conjugating enzyme UBC9, facilitating ASC oligomerization and inflammasome activation; SENP3 deSUMOylates NLRP3 to attenuate ASC recruitment, speck formation, inflammasome activation, and IL-1β secretion.\",\n      \"method\": \"Co-IP, SUMOylation site mutagenesis (K204), SENP3 overexpression/knockdown, ASC speck formation assays, IL-1β cleavage assays\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — site-specific mutagenesis identifying K204, writer (UBC9/SUMO1) and eraser (SENP3) identified, functional readouts\",\n      \"pmids\": [\"31914638\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"AKT kinase associates with NLRP3 and phosphorylates it at Ser5, limiting NLRP3 oligomerization; this S5 phosphorylation also stabilizes NLRP3 by reducing K496 ubiquitination and proteasome-mediated degradation by E3 ligase Trim31. Pharmacological AKT manipulation reciprocally modulates IL-1β production in vitro and in vivo.\",\n      \"method\": \"Co-IP (AKT-NLRP3), site-specific phosphorylation assays (S5 mutagenesis), ubiquitination assays (K496), Trim31 interaction, pharmacological AKT inhibition in vivo (LPS injection)\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — kinase-substrate relationship established with mutagenesis, ubiquitination linkage defined, in vivo validation\",\n      \"pmids\": [\"32929041\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RACK1 (receptor for activated protein C kinase 1) is a component of the NLRP3 complex in macrophages; RACK1 interacts with NLRP3 and NEK7 (but not ASC), promotes the active conformation of NLRP3 induced by activating stimuli, and is required for subsequent inflammasome assembly, caspase-1 activation, and IL-1β release specifically downstream of NLRP3 (not NLRC4 or AIM2).\",\n      \"method\": \"Co-IP, RACK1 siRNA knockdown, caspase-1 activation and IL-1β release assays, specificity testing across multiple inflammasomes\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and KD with defined phenotype, single lab, specificity established by parallel inflammasome controls\",\n      \"pmids\": [\"33207200\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"β-catenin physically interacts with NLRP3 and promotes the association between NLRP3 and ASC; siRNA or pharmacological suppression of β-catenin impairs NLRP3 inflammasome activation, and β-catenin inhibitor attenuates LPS-induced systemic inflammation in vivo.\",\n      \"method\": \"Co-IP, siRNA knockdown, pharmacological inhibition, in vivo LPS model, IL-1β/caspase-1 assays\",\n      \"journal\": \"Molecular immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP establishing interaction, KD and pharmacological inhibition with in vivo validation, single lab\",\n      \"pmids\": [\"32244067\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Full-length mouse NLRP3 forms a 12- to 16-mer double-ring cage oligomer held together by LRR-LRR interactions, with pyrin domains shielded within the assembly to prevent premature activation; this NLRP3 cage is predominantly membrane-localized. Structure-guided mutagenesis shows that double-ring cage formation is required for trans-Golgi network (TGN) dispersion (an early event in NLRP3 activation by many stimuli) and for inflammasome punctum formation, caspase-1 processing, and cell death.\",\n      \"method\": \"Cryo-EM structure of full-length mouse NLRP3, structure-guided mutagenesis, membrane fractionation, TGN dispersion assays, caspase-1 processing and cell death assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure combined with structure-guided mutagenesis and multiple functional readouts in a single rigorous study\",\n      \"pmids\": [\"34861190\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TRIM28 (E3 SUMO ligase) binds NLRP3 and promotes its SUMOylation by SUMO1, SUMO2, and SUMO3; this SUMOylation inhibits NLRP3 ubiquitination and proteasomal degradation, thereby stabilizing NLRP3 and facilitating inflammasome activation. Trim28 deficiency attenuates NLRP3 inflammasome activation in vitro and in vivo.\",\n      \"method\": \"Co-IP, SUMO modification assays, ubiquitination assays, Trim28 KO (in vitro and in vivo), caspase-1/IL-1β assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — writer identified (TRIM28), SUMOylation-ubiquitination crosstalk defined, KO with functional readouts in vivo\",\n      \"pmids\": [\"34373456\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"YAP physically interacts with NLRP3 and maintains NLRP3 stability by blocking the association between NLRP3 and E3 ligase β-TrCP1; β-TrCP1 promotes NLRP3 proteasomal degradation via K27-linked ubiquitination at Lys380. YAP deficiency in myeloid cells attenuates LPS-induced systemic inflammation and MSU crystal-induced peritonitis.\",\n      \"method\": \"Co-IP (YAP-NLRP3, NLRP3-β-TrCP1), ubiquitination assays (K27, K380), myeloid-specific YAP KO mice, in vivo inflammation models\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple Co-IPs defining interaction partners, ubiquitination site identified, in vivo KO validation\",\n      \"pmids\": [\"33976226\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"BRISC complex (containing BRCC3 metalloprotease) mediates deubiquitination of NLRP3, which is required for efficient NLRP3 inflammasome activation; thiolutin (JAMM domain metalloprotease inhibitor) blocks BRISC-mediated NLRP3 deubiquitination and suppresses NLRP3 inflammasome activation across canonical, noncanonical, alternative, and transcription-independent pathways at nanomolar concentrations.\",\n      \"method\": \"BRISC/BRCC3 inhibition by thiolutin, NLRP3 ubiquitination assays, multiple NLRP3 activation pathway assays, in vivo models (sepsis, peritonitis, EAE, CAPS, NAFLD)\",\n      \"journal\": \"Science immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — specific deubiquitinase complex identified, pharmacological and mechanistic validation across multiple pathways and in vivo models\",\n      \"pmids\": [\"33931568\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"UAF1/USP1 deubiquitinase complex selectively removes K48-linked polyubiquitination from NLRP3, suppressing its proteasomal degradation and enhancing cellular NLRP3 levels required for inflammasome assembly; UAF1/USP12 and UAF1/USP46 complexes additionally promote NF-κB activation to enhance NLRP3 transcription. Uaf1 deficiency attenuates NLRP3 inflammasome activation in vitro and in vivo.\",\n      \"method\": \"Co-IP, K48-linked ubiquitination assays, deubiquitinase activity assays, Uaf1 KD (in vitro and in vivo), IL-1β secretion assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — specific deubiquitinase complex identified, ubiquitin linkage specificity established, in vivo validation\",\n      \"pmids\": [\"33247121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"USP5 deubiquitinase attenuates NLRP3 inflammasome activation by promoting autophagic degradation of NLRP3; USP5 deficiency or overexpression reciprocally modulates NLRP3 protein levels and inflammasome activation.\",\n      \"method\": \"USP5 KD/OE, co-IP, autophagy flux assays, NLRP3 degradation assays, IL-1β/caspase-1 assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — deubiquitinase-autophagy link established by KD/OE, single lab\",\n      \"pmids\": [\"34486483\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"E3 ubiquitin ligase gp78 mediates mixed ubiquitination of NLRP3, which inhibits NLRP3 inflammasome activation by suppressing NLRP3 oligomerization and subcellular translocation; Insig-1 (ER membrane protein) is required for the gp78-NLRP3 interaction and gp78-mediated NLRP3 ubiquitination. gp78 or Insig-1 deficiency in myeloid cells exacerbates NLRP3-dependent inflammation in vivo.\",\n      \"method\": \"Co-IP (gp78-NLRP3, gp78-Insig-1), ubiquitination assays, NLRP3 oligomerization assays, myeloid-specific KO mice, in vivo inflammation models\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — E3 ligase-substrate interaction defined, adaptor protein identified, in vivo KO validation\",\n      \"pmids\": [\"35110683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"USP22 deubiquitinase inhibits NLRP3 inflammasome activation by promoting ATG5-mediated macroautophagy/NLRP3 degradation; USP22 stabilizes ATG5 via decreasing K27- and K48-linked ubiquitination at Lys118. USP22 deficiency significantly increases alum-induced peritonitis and LPS-induced systemic inflammation in vivo.\",\n      \"method\": \"USP22 KD/KO, co-IP, ubiquitination assays (K27/K48-ATG5 K118), autophagy flux assays, in vivo models\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — indirect NLRP3 regulation via ATG5, ubiquitination sites defined, in vivo validation, single lab\",\n      \"pmids\": [\"35900990\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TRIM31 interacts with NLRP3 in retinal pigment epithelial cells and promotes NLRP3 ubiquitination, thereby inhibiting NLRP3 inflammasome activation and pyroptosis; TRIM31 knockdown phenocopies NLRP3 activation by ox-LDL.\",\n      \"method\": \"Co-IP, ubiquitination assays, TRIM31 KD/OE, NLRP3 inhibitor controls, IL-1β/caspase-1 assays\",\n      \"journal\": \"Cell biology international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and ubiquitination assay in a single cell type, single lab\",\n      \"pmids\": [\"32716108\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NLRP3 is S-palmitoylated at the LRR domain by ZDHHC5; this palmitoylation promotes NLRP3 oligomerization, NLRP3-NEK7 interaction, and ASC aggregate formation, leading to caspase-1 activation, IL-1β/IL-18 release, and GSDMD cleavage. ABHD17A acts as the depalmitoylase for NLRP3, and a disease-associated NLRP3 mutation shows defective ABHD17A binding and hyper-palmitoylation. Zdhhc5-/- mice exhibit defective NLRP3 inflammasome activation in vivo.\",\n      \"method\": \"Acyl-RAC palmitoylation assay, ZDHHC5 KO/siRNA, site-specific mutagenesis (LRR palmitoylation site), NLRP3 oligomerization assays, NEK7 interaction assays, ASC speck formation, Zdhhc5-/- mice, ABHD17A depalmitoylase assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — palmitoylation writer (ZDHHC5) and eraser (ABHD17A) identified, site-specific mutagenesis, disease mutation functional characterization, in vivo KO validation\",\n      \"pmids\": [\"38092000\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NLRP3 binds non-oxidized mtDNA with much higher affinity (IC50 ~4 nM) than Ox-mtDNA (IC50 ~247 nM); the NLRP3 PYD domain mediates DNA binding and preferentially binds Ox-mtDNA; a NOMID/FCAS gain-of-function mutant shows higher affinity for Ox-mtDNA (IC50 ~8.1 nM). A structural model based on alignment to DNA glycosylases suggests a DNA-binding mechanism involving the PYD domain fold.\",\n      \"method\": \"In vitro DNA-binding assays (IC50 determination), domain deletion/truncation constructs, monoclonal antibody blocking assays, structural homology modeling\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro binding assay with mutants but structural model is computational; single study\",\n      \"pmids\": [\"37253813\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MARCH5 (mitochondria-associated E3 ubiquitin ligase) interacts with the NACHT domain of NLRP3 and promotes K27-linked polyubiquitination at K324 and K430 residues; this ubiquitination is required for NLRP3-NEK7 binding, NLRP3 oligomerization, and ASC speck formation. Myeloid-specific March5 cKO mice fail to secrete IL-1β/IL-18 and show attenuated LPS- or Pseudomonas-induced mortality.\",\n      \"method\": \"Co-IP (MARCH5-NLRP3 NACHT domain), K27-linked ubiquitination assays with K324A/K430A mutants, NEK7 binding assays, ASC speck assays, myeloid-specific March5 cKO mice, in vivo infection models\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — E3 ligase substrate sites precisely mapped by mutagenesis, ubiquitin linkage defined, domain of interaction mapped, in vivo conditional KO validation\",\n      \"pmids\": [\"37575012\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZDHHC7 palmitoylates NLRP3 at Cys126, which is critical for NLRP3 inflammasome activation; Cys126 palmitoylation by ZDHHC7 promotes resting NLRP3 localization on the trans-Golgi network (TGN) and activated NLRP3 on dispersed TGN, enabling ASC recruitment and oligomerization. ZDHHC7 KO, pharmacological inhibition, or C126 mutation diminishes NLRP3 activation in macrophages and in vivo. ZDHHC12 has a terminating/opposing palmitoylation effect on NLRP3.\",\n      \"method\": \"Acyl-RAC palmitoylation assay, ZDHHC7 KO, C126 site mutagenesis, TGN localization by live imaging/immunofluorescence, ASC oligomerization assays, in vivo inflammasome models\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — palmitoylation site (C126) and writer (ZDHHC7) identified with mutagenesis, subcellular localization consequence demonstrated, in vivo validation\",\n      \"pmids\": [\"38583156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Tau protein directly acetylates NLRP3 at K21, K22, and K24 within its PYD domain (via Tau's K18 domain acetyltransferase activity), inducing inflammasome activation in microglia; blocking the Tau-NLRP3 interaction with a designed peptide inhibits NLRP3 acetylation, inflammasome activation, microgliosis, and cognitive impairment in mice.\",\n      \"method\": \"In vitro acetylation assay (test-tube), co-IP, mass spectrometry (acetylation site identification), molecular docking, AAV-mediated Tau overexpression in mice, behavioral testing, PET/CT imaging, blocking peptide intervention\",\n      \"journal\": \"Clinical and translational medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro acetyltransferase assay with site mapping by MS, in vivo AAV model with functional rescue by blocking peptide, single lab\",\n      \"pmids\": [\"38488468\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NLRP12 interacts with NLRP3 and inhibits human (but not murine) NLRP3-induced ASC inflammasome assembly; NLRP12 failed to nucleate ASC polymerization itself, and disease-associated NLRP12 mutants lost the ability to suppress NLRP3 inflammasome assembly. PBMCs from NLRP12-mutant patients showed increased IL-1β in response to NLRP3 stimulation.\",\n      \"method\": \"ASC polymerization/speck formation screen, Co-IP (NLRP12-NLRP3), NLRP12 disease mutant analysis, IL-1β assays in patient PBMCs, species specificity testing (human vs. murine NLRP3)\",\n      \"journal\": \"Science signaling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — NLR screen, Co-IP, disease mutant functional testing, human patient validation with defined mechanism\",\n      \"pmids\": [\"38261657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TXNIP (thioredoxin-interacting protein) activates the NALP3 inflammasome by directly interacting with NLRP3 in high-glucose-exposed podocytes; TXNIP knockdown impedes NLRP3 inflammasome activation and attenuates podocyte injury. Blocking NLRP3 inflammasome activation by NLRP3/ASC shRNA or caspase-1 inhibition prevents IL-1β production and podocyte injury under diabetic conditions.\",\n      \"method\": \"Co-IP (TXNIP-NLRP3), TXNIP/NLRP3/ASC shRNA knockdown, caspase-1 inhibition, in vivo diabetic nephropathy model, IL-1β assays\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP establishing TXNIP-NLRP3 interaction, KD rescue experiments, in vivo model\",\n      \"pmids\": [\"25017793\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CB1R (cannabinoid receptor 1) directly interacts with the NLRP3 inflammasome via amino acid residues 177-209; antipsychotics drive CB1R translocation to the cytoplasm where CB1R stabilizes the inflammasome. Cb1r KO significantly alleviates antipsychotic-induced cardiomyocyte pyroptosis and cardiotoxicity.\",\n      \"method\": \"Co-IP (CB1R-NLRP3, domain mapping 177-209), RNA sequencing, small-molecule screen, Cb1r KO mice, pyroptosis assays\",\n      \"journal\": \"Signal transduction and targeted therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with interaction domain mapped, KO validation in vivo, single lab\",\n      \"pmids\": [\"35739093\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"3D modeling of the NLRP3 NBD domain reveals structural similarity to AAA+ ATPases; most CAPS/MWS/FCU-associated mutations cluster on one side of the NBD in a region predicted to mediate intermolecular contacts, suggesting that defects in nucleotide binding, hydrolysis, or protein oligomerization underlie NLRP3 functional dysregulation in autoinflammatory diseases.\",\n      \"method\": \"3D structural modeling of the NBD domain, mapping of known mutations onto the model, sequence/structural analysis\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational structural model only, no direct biochemical validation of mechanism\",\n      \"pmids\": [\"14630794\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NLRP3 activated by diverse stimuli triggers gasdermin D cleavage by caspase-1, releasing the pore-forming N-terminal domain that drives pyroptosis; the assembled NLRP3 inflammasome contributes not only to pyroptosis but also to apoptosis, necroptosis, and ferroptosis.\",\n      \"method\": \"Review summarizing experimental findings from multiple studies including loss-of-function and caspase-1 activation assays\",\n      \"journal\": \"Cellular & molecular immunology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — review article, no new experimental data reported\",\n      \"pmids\": [\"34321623\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"NLRP3 inflammasome activation requires intracellular copper; the copper chelator tetrathiomolybdate specifically inhibits canonical NLRP3 but not AIM2, NLRC4, or NLRP1 inflammasomes or NF-κB priming; the regulation involves copper at the active site of superoxide dismutase 1 (SOD1), and SOD1-deficient mice show impaired inflammasome function. In vivo copper depletion attenuated caspase-1-dependent inflammation.\",\n      \"method\": \"Copper chelation (tetrathiomolybdate), SOD1-deficient mice, multiple inflammasome specificity assays, in vivo endotoxic shock model\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pharmacological and genetic dissection of copper requirement, SOD1 KO mechanistic link, specificity established, single lab\",\n      \"pmids\": [\"29358279\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FXR inhibits NLRP3 activity by restraining its Ser295 phosphorylation in hepatic stellate cells; knockdown or knockout of NLRP3 relieves GCDCA-induced hepatic fibrosis, placing NLRP3 downstream of bile acid signaling via FXR-mediated phosphorylation control.\",\n      \"method\": \"NLRP3 knockdown/knockout, FXR overexpression, Western blotting for Ser295 phosphorylation, in vivo mouse liver fibrosis model with GCDCA\",\n      \"journal\": \"Hepatology international\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — phosphorylation detected by Western blot, FXR OE and NLRP3 KO rescue, single lab without kinase reconstitution\",\n      \"pmids\": [\"38172440\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NLRP3 is a cytosolic pattern-recognition receptor that, upon sensing diverse PAMPs/DAMPs (including crystals, bacterial RNA, lysosomal damage, mtDNA, and metabolic signals), undergoes oligomerization into a 12–16-mer double-ring cage (membrane-localized, held by LRR-LRR interactions with shielded PYD domains) that disperses from the trans-Golgi network upon activation; NLRP3 then recruits the adaptor ASC via PYD-PYD interaction and procaspase-1 via ASC's CARD, forming the inflammasome complex that auto-activates caspase-1 to cleave pro-IL-1β, pro-IL-18, and gasdermin D (pyroptosis). NLRP3 activity is tightly controlled by post-translational modifications: stabilizing SUMOylation (TRIM28/SUMO1; UBC9/SUMO1 at K204, reversed by SENP3), activating palmitoylation (ZDHHC5 at LRR domain; ZDHHC7 at C126, enabling TGN localization, reversed by ABHD17A/ZDHHC12), inhibitory phosphorylation (AKT at S5, PKA/PKD at S295, JNK at S198), and multiple ubiquitination events—both activating (MARCH5 K27-Ub at K324/K430 enabling NEK7 binding; BRISC/BRCC3 deubiquitination permitting activation; UAF1/USP1 K48-deubiquitination stabilizing NLRP3) and inhibitory (ARIH2 K48/K63-Ub; β-TrCP1 K27-Ub at K380 blocked by YAP; gp78/Insig-1 ubiquitination; Trim31 K496-Ub). NLRP3 also binds mtDNA via its PYD domain, interacts with NLRC4 to cooperate in inflammasome signaling, is acetylated at PYD residues K21/K22/K24 by Tau (promoting microglial activation), and is transcriptionally regulated by AhR binding to its promoter XRE; gain-of-function mutations in the NACHT domain cluster at predicted oligomerization interfaces and cause cryopyrin-associated autoinflammatory diseases.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NLRP3 is a cytosolic pattern-recognition receptor that nucleates an ASC- and caspase-1-containing inflammasome to drive maturation of IL-1\\u03b2 and IL-18 in response to diverse danger signals including monosodium urate and CPPD crystals, bacterial RNA, imidazoquinolines, and ATP [#0, #1, #2]. It senses these stimuli through convergent upstream events: phagocytosis-dependent lysosomal rupture and cathepsin B release from crystalline particulates [#3], and accumulation of dysfunctional mitochondria with cytosolic mtDNA release driven by mitochondrial ROS [#4], with NLRP3 directly binding mtDNA through its PYD domain [#26]. Activated NLRP3 assembles a 12\\u201316-mer double-ring cage held by LRR-LRR contacts with shielded pyrin domains; cage formation drives dispersion from the trans-Golgi network and is required for inflammasome punctum formation, caspase-1 processing, and cell death [#16], with downstream caspase-1 cleaving gasdermin D to execute pyroptosis [#34]. Inflammasome assembly proceeds via ASC nucleation and is supported by accessory partners including NEK7, RACK1, and \\u03b2-catenin that promote the active conformation and ASC association [#14, #15], and NLRP3 can cooperate with the NLRC4 scaffold to drive caspase-1 activation during bacterial infection [#9]. NLRP3 activity is governed by an extensive post-translational code: activating S-palmitoylation by ZDHHC5 at the LRR and by ZDHHC7 at Cys126 that controls TGN localization (reversed by ABHD17A/ZDHHC12) [#25, #28], stabilizing SUMOylation at Lys204 by UBC9/SUMO1 and by TRIM28 (erased by SENP3) [#12, #17], activating K27-linked ubiquitination by MARCH5 at K324/K430 that enables NEK7 binding [#27], and stabilizing K48-deubiquitination by UAF1/USP1 and BRCC3/BRISC [#19, #20], counterbalanced by inhibitory AKT phosphorylation at Ser5 and multiple inhibitory ubiquitin ligases (ARIH2, \\u03b2-TrCP1 at K380 antagonized by YAP, gp78/Insig-1) [#13, #10, #18, #22]. Transcriptionally, NLRP3 is directly repressed by AhR binding to a promoter XRE [#7]. Structural modeling places gain-of-function mutations causing cryopyrin-associated autoinflammatory disease at NBD oligomerization interfaces [#33].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Established NLRP3 as the sensor component of a caspase-1-activating inflammasome, defining its core function as converting diverse danger signals into IL-1\\u03b2/IL-18 maturation independently of TLR-driven NF-\\u03baB/MAPK signaling.\",\n      \"evidence\": \"Genetic knockouts (NALP3-/-, ASC-/-, caspase-1-/-) with crystal, bacterial RNA, imidazoquinoline, and ATP stimulation plus in vivo peritonitis and contact hypersensitivity models\",\n      \"pmids\": [\"16407889\", \"16407888\", \"16546100\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve how chemically distinct stimuli converge on a single sensor\", \"Stimulus-specificity (e.g. Salmonella independence) left the upstream sensing mechanism undefined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Resolved how particulate stimuli are sensed, showing crystals act indirectly via phagocytosis-driven lysosomal rupture and cathepsin B release rather than direct receptor binding.\",\n      \"evidence\": \"Crystal phagocytosis assays, lysosomal disruption, cathepsin B and acidification inhibition in NALP3-deficient macrophages\",\n      \"pmids\": [\"18604214\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The direct molecular link between cathepsin B and NLRP3 activation was not identified\", \"Did not explain non-particulate (ATP/nigericin) activation\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identified mitochondrial damage and cytosolic mtDNA as an endogenous trigger linking autophagy quality control to inflammasome activation.\",\n      \"evidence\": \"LC3B/beclin-1 knockdown and LC3B-deficient macrophages, mtDNA cytosolic fractionation, ROS measurement, sepsis models\",\n      \"pmids\": [\"21151103\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish whether mtDNA binds NLRP3 directly\", \"Mechanism of mtDNA cytosolic translocation incompletely defined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Provided the first atomic-resolution view of the PYD interaction module, revealing a redox-sensitive disulfide that could couple NLRP3 activity to cellular redox state.\",\n      \"evidence\": \"X-ray crystallography of the NALP3 PYD at 1.7 \\u00c5 with structural/sequence analysis\",\n      \"pmids\": [\"21880711\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional role of the Cys8-Cys108 disulfide inferred but not tested\", \"Full-length assembly context absent\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Localized inflammasome assembly to the cytoplasm rather than a specific organelle, constraining models of where NLRP3/ASC/caspase-1 nucleation occurs.\",\n      \"evidence\": \"Confocal co-localization in primary macrophages against multiple organelle markers under ATP/nigericin/MSU\",\n      \"pmids\": [\"23609011\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab imaging without biochemical fractionation\", \"Apparent tension with later TGN-dispersion model unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defined transcriptional control of NLRP3 by showing AhR directly represses its promoter, and identified a metabolic priming partner (TXNIP).\",\n      \"evidence\": \"ChIP for AhR binding to the NLRP3 promoter XRE with siRNA/overexpression; TXNIP-NLRP3 Co-IP and knockdown in diabetic nephropathy model\",\n      \"pmids\": [\"25141024\", \"25017793\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"TXNIP-NLRP3 interaction is single-lab and context-specific\", \"How transcriptional repression integrates with post-translational control not addressed\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Demonstrated cross-talk between inflammasome scaffolds, showing NLRP3 can be recruited to compensate for NLRC4 in caspase-1 activation during bacterial infection.\",\n      \"evidence\": \"Reciprocal Co-IP and genetic epistasis with Nlrc4(S533A) and Nlrp3-/- macrophages during Salmonella infection\",\n      \"pmids\": [\"27139490\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physical architecture of a joint NLRP3-NLRC4 complex not resolved\", \"Physiological contexts requiring cooperation unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined the resting and active higher-order architecture of NLRP3, establishing the double-ring cage with shielded PYDs and linking cage formation to TGN dispersion as a prerequisite for activation.\",\n      \"evidence\": \"Cryo-EM of full-length mouse NLRP3 with structure-guided mutagenesis, membrane fractionation, and TGN dispersion/caspase-1 readouts\",\n      \"pmids\": [\"34861190\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How specific stimuli release PYD shielding not mechanistically resolved\", \"Conformational transition from cage to active inflammasome incompletely defined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Established ubiquitin removal as a licensing step for activation and SUMOylation as a competing stabilizing modification, building a PTM logic of NLRP3 control.\",\n      \"evidence\": \"BRISC/BRCC3 inhibition (thiolutin), UAF1/USP1 K48-deubiquitination, USP5 autophagic degradation, and TRIM28/SUMO1 plus YAP/\\u03b2-TrCP1 K380 ubiquitination studies with KO and in vivo models\",\n      \"pmids\": [\"33931568\", \"33247121\", \"34486483\", \"34373456\", \"33976226\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Temporal ordering and hierarchy among competing PTMs unresolved\", \"Some erasers/ligases validated in single labs\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified palmitoylation and K27-ubiquitination as positive controls that govern TGN localization and NEK7-dependent oligomerization, mechanistically connecting lipid/ubiquitin marks to assembly.\",\n      \"evidence\": \"Acyl-RAC, ZDHHC5/ZDHHC7 KO and site mutagenesis (C126/LRR), ABHD17A depalmitoylase assays, and MARCH5 K27-Ub mapping at K324/K430 with conditional KO mice\",\n      \"pmids\": [\"38092000\", \"37575012\", \"38583156\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How palmitoylation, K27-Ub, and NEK7 recruitment are coordinated in time not resolved\", \"Direct mtDNA-binding affinity model is computational (37253813)\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended NLRP3 regulation into cell-type-specific and disease contexts, including Tau-mediated PYD acetylation in microglia and NLRP12 as a human-specific suppressor of NLRP3-driven ASC assembly.\",\n      \"evidence\": \"In vitro acetyltransferase assay with MS site mapping and AAV Tau model; ASC polymerization screen, Co-IP, and disease-mutant testing in patient PBMCs\",\n      \"pmids\": [\"38488468\", \"38261657\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Species differences (human vs murine NLRP3 regulation by NLRP12) limit generalization\", \"Acetylation work is single-lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the dozens of identified PTMs, accessory partners, and localization cues are integrated into a single ordered activation pathway, and how individual stimuli select among them, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified temporal model of competing/cooperating PTMs\", \"Direct stimulus-to-conformational-change coupling undefined\", \"Structural basis of the active inflammasome (vs resting cage) not fully resolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [26]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 16]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [33]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [16, 28]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [16]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [16, 34]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"complexes\": [\"NLRP3 inflammasome\"],\n    \"partners\": [\"ASC\", \"NEK7\", \"NLRC4\", \"MARCH5\", \"ZDHHC7\", \"RACK1\", \"YAP\", \"NLRP12\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}