{"gene":"ALPK1","run_date":"2026-04-28T17:12:37","timeline":{"discoveries":[{"year":2020,"finding":"ALPK1 functions as a cytosolic pattern recognition receptor (PRR) that detects the bacterial lipopolysaccharide biosynthetic intermediate ADP-heptose (β-ADP-heptose), triggering phosphorylation of TIFA and downstream NF-κB activation, leading to inflammatory cytokine production. H. pylori-induced NF-κB/NF-κB-driven R-loop formation and replication stress are dependent on this ALPK1/TIFA signaling pathway.","method":"Genetic disruption of ALPK1 and TIFA, chemical inhibition, cell-based reporter assays, replication fork assays, S-phase analysis, gastric organoid primary cells","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (knockdown, reporter assays, primary organoids), replicated across multiple bacterial models","pmids":["33037203"],"is_preprint":false},{"year":2020,"finding":"ADP-heptose (a soluble intermediate of the LPS biosynthetic pathway in Gram-negative bacteria) is the PAMP recognized by ALPK1; upon binding, ALPK1 phosphorylates TIFA at Thr9, leading to TRAF6 recruitment and NF-κB activation with secretion of inflammatory cytokines.","method":"Review/synthesis of biochemical and genetic evidence from multiple studies; TIFA phosphorylation assays, NF-κB reporter assays, genetic epistasis with ALPK1/TIFA knockouts","journal":"Cellular and molecular life sciences : CMLS","confidence":"High","confidence_rationale":"Tier 1–2 — mechanistic pathway established by multiple independent labs with in vitro kinase assays and genetic epistasis","pmids":["32591860"],"is_preprint":false},{"year":2022,"finding":"ALPK1 directly phosphorylates TIFA at Thr177 (in addition to Thr9) in vitro; Thr177 is located within the TRAF6-binding motif and its phosphomimetic mutation (T177D) prevents TRAF6 but not TRAF2 binding, restricting ADP-heptose signaling. ADP-heptose stimulation also induces TRAF2/c-IAP1-dependent Lys63-linked and LUBAC-dependent Met1-linked ubiquitin chains to activate TAK1 and canonical IKK complexes, respectively. c-IAP1 is recruited to TIFA via TRAF2.","method":"In vitro kinase assay, site-directed mutagenesis, Co-immunoprecipitation, ubiquitin chain analysis, genetic knockouts of E3 ligases","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1 — direct in vitro kinase assays with mutagenesis, combined with Co-IP and genetic epistasis","pmids":["36098982"],"is_preprint":false},{"year":2023,"finding":"Disease-causing ALPK1 mutants (T237M for ROSAH syndrome; V1092A for spiradenoma) can be activated by endogenous human nucleotide sugars (UDP-mannose, ADP-ribose, cyclic ADP-ribose, and for V1092A also GDP-mannose) that do not activate wild-type ALPK1, explaining constitutive NF-κB activation; mutations in the ADP-heptose binding site prevent activation of both wild-type and mutant ALPK1.","method":"NF-κB/AP-1 reporter gene assays with wild-type and mutant ALPK1 constructs, binding-site mutagenesis, nucleotide sugar stimulation assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — reconstitution of kinase activation with defined ligands and mutagenesis of active site, multiple orthogonal experiments","pmids":["38060563"],"is_preprint":false},{"year":2022,"finding":"ALPK1 gain-of-function mutations (T237M, Y254C) cause the autoinflammatory ROSAH syndrome by constitutively increasing NF-κB signaling, STAT1 phosphorylation, and interferon gene expression; knock-in mice carrying Alpk1 T237M show subclinical inflammation.","method":"In vitro assays with mutated ALPK1 constructs, immunoblotting, cytokine profiling, transcriptomics, knock-in mouse model, patient primary samples","journal":"Annals of the rheumatic diseases","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods across patient samples and mouse models confirming gain-of-function kinase mechanism","pmids":["35868845"],"is_preprint":false},{"year":2019,"finding":"A recurrent missense mutation in the kinase domain of ALPK1 (identified in spiradenomas and spiradenocarcinomas) can activate the NF-κB pathway in reporter assays, establishing it as a gain-of-function driver mutation.","method":"Genomic sequencing, NF-κB reporter assays with ALPK1 mutant constructs","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 — reporter assay functional validation in addition to sequencing; single study","pmids":["31101826"],"is_preprint":false},{"year":2016,"finding":"ALPK1 phosphorylates myosin IIA; in monosodium urate (MSU)-stimulated cells, ALPK1 forms a protein complex with myosin IIA, calmodulin, and F-actin at the N-terminal domain, and MSU-induced ALPK1 activity phosphorylates myosin IIA, which is required for Golgi-derived TNF-α trafficking and secretion.","method":"Bioinformatics, proteomics, Co-immunoprecipitation, ALPK1/myosin IIA knockdown, in vitro phosphorylation assays, TNF-α secretion assays, human patient samples","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP and functional knockdown with defined substrate; single lab study","pmids":["27169898"],"is_preprint":false},{"year":2024,"finding":"Copper binds directly to ALPK1 and is essential for its kinase activity; copper binding enhances ALPK1 sensitivity to ADP-heptose and amplifies the innate immune response. In response to bacterial infection, host cells actively accumulate cytosolic copper, which promotes ALPK1-dependent host defense.","method":"Direct binding assays (copper-ALPK1 interaction), in vitro kinase activity assays, ALPK1-dependent cell signaling (knockdown/KO), zebrafish in vivo infection model","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 — direct binding demonstrated, in vitro kinase activity assay, in vivo validation in zebrafish model with multiple orthogonal methods","pmids":["38232278"],"is_preprint":false},{"year":2025,"finding":"ADP-heptose (from gut Gram-negative bacteria) binds to ALPK1 in hematopoietic progenitor cells, triggering NF-κB activation and transcriptional reprogramming that confers a proliferative competitive advantage to pre-leukemic (CHIP) cells, driving clonal expansion.","method":"ADP-heptose detection in human serum, ALPK1-dependent signaling in pre-leukemic cells, genetic models, transcriptomic analysis, competitive repopulation assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods including mechanistic ALPK1 pathway studies, human samples, and functional competitive advantage assays","pmids":["40269158"],"is_preprint":false},{"year":2021,"finding":"The ALPK1 pathway drives the NF-κB-mediated pro-inflammatory response (CXCL8, CXCL2, TNFAIP2, PTGS2) to Campylobacter jejuni in human intestinal epithelial cells; ADP-heptose and/or related heptose phosphates (not requiring T3SS or T4SS injection) are the released virulence factor activating ALPK1, identified by hldE gene deletion and chemical characterization.","method":"ALPK1 knockout cells, chemical characterization of released factor, bacterial gene deletion (hldE), NF-κB reporter assays, independent of TLR/NLR signaling (epistasis)","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis (ALPK1 KO, bacterial gene deletion), chemical identification of ligand, multiple orthogonal methods","pmids":["34339468"],"is_preprint":false},{"year":2022,"finding":"Akkermansia muciniphila releases ADP-heptose-like metabolites that enter intestinal epithelial cells and activate NF-κB via ALPK1/TIFA/TRAF6, inducing expression of barrier-function genes (MUC2, BIRC3, TNFAIP3) in a TIFA-dependent manner.","method":"Pharmacological inhibitors, gene editing (ALPK1/TIFA/TRAF6 knockouts), chemical characterization of released metabolite, NF-κB reporter assays","journal":"Gut microbes","confidence":"High","confidence_rationale":"Tier 2 — CRISPR gene editing combined with chemical characterization and reporter assays; multiple orthogonal methods","pmids":["36036242"],"is_preprint":false},{"year":2022,"finding":"Fusobacterium nucleatum activates ALPK1, which then signals through NF-κB to upregulate ICAM1 expression on colorectal cancer cells, enhancing adhesion to endothelial cells and promoting extravasation and metastasis.","method":"ALPK1 knockdown/overexpression, NF-κB reporter assays, adhesion and extravasation assays, ICAM1 expression studies, patient tissue correlation","journal":"Gut microbes","confidence":"Medium","confidence_rationale":"Tier 2 — knockdown functional assays with defined pathway; single lab","pmids":["35220887"],"is_preprint":false},{"year":2022,"finding":"ALPK1 exacerbates condylar cartilage degradation in TMJOA by activating NF-κB signaling (upregulating MMP13, COX2) and suppressing ERK1/2 signaling (downregulating aggrecan); ALPK1 knockout mice show attenuated cartilage/bone damage.","method":"ALPK1 KO mouse model (MIA-induced TMJOA), intra-articular recombinant ALPK1 administration, ex vivo chondrocyte studies, NF-κB and ERK1/2 pathway analysis","journal":"Journal of dental research","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse with defined pathway readout; single lab with multiple in vivo and ex vivo methods","pmids":["35689396"],"is_preprint":false},{"year":2022,"finding":"ALPK1 accelerates osteoarthritis pathogenesis by activating NF-κB signaling, which upregulates NLRP3 inflammasome in chondrocytes, driving IL-1β-mediated inflammation; ALPK1 KO reverses OA pathogenesis and NLRP3 is a downstream target of NF-κB in ALPK1-activated chondrocytes.","method":"ALPK1 KO and intra-articular recombinant ALPK1 in DMM and CIOA mouse models, selective NF-κB and NLRP3 inhibition, in vitro chondrocyte studies","journal":"Journal of bone and mineral research","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse with pathway epistasis using selective inhibitors; single lab","pmids":["36053817"],"is_preprint":false},{"year":2021,"finding":"ALPK1 sensitizes pancreatic beta cells to cytokine-induced apoptosis by potentiating TNF-α and Fas expression through enhanced activation of the TIFA/TAK1/NF-κB signaling axis; ADP-heptose activation of ALPK1 alone is insufficient to induce apoptosis but synergizes with cytokines.","method":"ADP-heptose stimulation in MIN6 cells, ALPK1 activation assays, TIFA/TAK1/NF-κB pathway analysis, apoptosis assays, GLP-1 receptor agonist rescue","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 2 — defined ligand/pathway with multiple cellular readouts; single lab","pmids":["34621265"],"is_preprint":false},{"year":2011,"finding":"Disruption of ALPK1 (via piggyBac transposon insertion into intron 1) in mice causes severe motor coordination deficits, which are rescued by transgenic re-expression of full-length ALPK1, establishing ALPK1 as functionally required for motor coordination.","method":"PiggyBac transposon insertional mutagenesis in mice, behavioral analysis (rotarod, hanging wire, dowel, footprint tests), transgenic rescue with full-length Alpk1","journal":"BMC neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function with specific phenotypic readout and transgenic rescue; single study","pmids":["21208416"],"is_preprint":false},{"year":2017,"finding":"ALPK1 overexpression decreases URAT1 (urate transporter 1, SLC22A12) protein levels in vivo in transgenic mice and in vitro in kidney cells; MSU crystal stimulation upregulates ALPK1, which in turn inhibits URAT1, suggesting ALPK1 acts as a negative regulator of urate reuptake.","method":"ALPK1 transgenic mice (URAT1 protein measurement), ALPK1 siRNA knockdown in HK-2 cells, MSU crystal stimulation, immunohistochemistry of renal proximal tubule cells","journal":"Rheumatology (Oxford, England)","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo transgenic and in vitro knockdown with protein-level readout; single lab","pmids":["28039413"],"is_preprint":false},{"year":2022,"finding":"ALPK1 promotes TMJ synovitis by promoting nuclear translocation of PKM2 and M1 macrophage polarization; LMW-HA upregulates ALPK1 while HMW-HA suppresses it, and rhALPK1 promotes M1 polarization-associated gene expression and nuclear PKM2.","method":"ALPK1 KO mice (CFA-induced TMJ synovitis), recombinant ALPK1 stimulation, macrophage polarization assays, PKM2 nuclear translocation assays, patient synovial tissue analysis","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse model with defined cellular pathway; single lab","pmids":["38494837"],"is_preprint":false},{"year":2019,"finding":"ALPK1 is the kinase phosphorylated by/activates upon ADP-heptose bisphosphate recognition, phosphorylating TIFA to trigger the immediate innate immune response to Gram-negative bacterial invasion; rare ALPK1 variants (S924P, D342H, T237M) predispose to periodic fever (PFAPA) syndrome.","method":"Exome sequencing, Sanger sequencing, segregation analysis in PFAPA families","journal":"European journal of human genetics : EJHG","confidence":"Low","confidence_rationale":"Tier 4 — genetic association without direct functional mechanistic assay in this paper","pmids":["31053777"],"is_preprint":false},{"year":2022,"finding":"ALPK1 acts as a cytosolic PRR for ADP-heptose released by F. nucleatum, and ALPK1/TIFA/TRAF6 pathway activation promotes expression of inflammatory cytokine IL-8 and anti-apoptotic genes BIRC3 and TNFAIP3, enhancing CRC cell survival and reducing 5-fluorouracil chemosensitivity.","method":"ALPK1/TIFA pathway knockouts, ADP-heptose stimulation, gene expression assays, cell survival and chemosensitivity assays","journal":"Gut microbes","confidence":"Medium","confidence_rationale":"Tier 2 — defined ligand, genetic knockouts, functional cellular readouts; single lab","pmids":["38126163"],"is_preprint":false},{"year":2022,"finding":"F. nucleatum activates ALPK1 in intestinal cancer cells in an ADP-heptose-dependent manner, leading to NF-κB pathway activation and ALPK1-dependent upregulation of PD-L1; this mechanism is conserved across multiple Fusobacterium species.","method":"ALPK1-dependent reporter assays in HEK293 and HT-29 cells, transcriptional analysis, ADP-heptose stimulation, F. nucleatum conditioned medium experiments","journal":"Gut microbes","confidence":"Medium","confidence_rationale":"Tier 2 — ALPK1-dependent genetic knockouts and defined ligand stimulation; single lab","pmids":["39881579"],"is_preprint":false},{"year":2016,"finding":"Knockdown of ALPK1 in triple-negative breast cancer cells (MDA-MB-468) induces loss of the myoepithelial marker keratin 5, increased β-casein production, decreased proliferation, reduced clonogenicity, and reduced tumorigenicity in vivo, establishing ALPK1 as a regulator of cancer cell differentiation state.","method":"Kinase knockdown screen (420 kinases), shRNA knockdown, spheroid and anchorage-independent growth assays, in vivo xenograft","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function with defined cellular and in vivo phenotypic readouts; single lab","pmids":["27829216"],"is_preprint":false},{"year":2022,"finding":"DF-006 (an ALPK1 agonist) activates the NF-κB pathway via ALPK1 and stimulates innate immunity, demonstrating that pharmacological agonism of ALPK1 is sufficient to drive antiviral gene expression and reduce HBV viral markers in mouse and primary human hepatocyte models.","method":"AAV-HBV mouse models, primary human hepatocytes, NF-κB target gene upregulation, antiviral efficacy assays, liver localization of DF-006","journal":"Hepatology (Baltimore, Md.)","confidence":"Medium","confidence_rationale":"Tier 2 — pharmacological agonist with defined ALPK1 target and pathway readouts in multiple models; single lab","pmids":["35699669"],"is_preprint":false}],"current_model":"ALPK1 is a cytosolic atypical (alpha) protein kinase that functions as a pattern recognition receptor (PRR) for bacterial ADP-heptose; upon ADP-heptose binding (facilitated by copper co-activation), ALPK1 phosphorylates TIFA at Thr9 and Thr177, triggering recruitment of TRAF2/c-IAP1 and TRAF6 E3 ligases to generate Lys63- and Met1-linked ubiquitin chains that activate TAK1 and IKK complexes, leading to NF-κB-driven inflammatory gene expression; disease-causing gain-of-function mutations (T237M, Y254C for ROSAH syndrome; V1092A for spiradenoma) expand the ligand specificity to include endogenous human nucleotide sugars, causing constitutive NF-κB signaling and autoinflammatory disease."},"narrative":{"teleology":[{"year":2011,"claim":"Before ALPK1's ligand or immune function was known, loss-of-function in mice revealed an unexpected requirement for motor coordination, establishing that ALPK1 has physiological roles beyond any anticipated kinase function.","evidence":"PiggyBac insertional mutagenesis in mice with behavioral rescue by transgenic ALPK1 re-expression","pmids":["21208416"],"confidence":"Medium","gaps":["Mechanism linking ALPK1 kinase activity to motor coordination is undefined","Relevant substrate in the nervous system unknown","Not replicated independently"]},{"year":2016,"claim":"Identification of myosin IIA as an ALPK1 substrate in gout-relevant MSU-stimulated cells established the first substrate–product relationship and linked ALPK1 to Golgi-derived TNF-α trafficking, while a parallel study showed ALPK1 knockdown altered differentiation in triple-negative breast cancer cells.","evidence":"Co-IP, in vitro phosphorylation of myosin IIA, TNF-α secretion assays; shRNA kinase screen with xenograft validation","pmids":["27169898","27829216"],"confidence":"Medium","gaps":["Myosin IIA phosphorylation site not mapped","Relationship between myosin IIA phosphorylation and TIFA pathway unclear","Cancer differentiation phenotype not linked to a defined ALPK1 substrate"]},{"year":2019,"claim":"Discovery that a recurrent ALPK1 kinase-domain mutation drives NF-κB activation in spiradenomas, and that rare germline variants associate with periodic fever, positioned ALPK1 as a disease-relevant signaling node, though the activating ligand remained unknown for these contexts.","evidence":"Tumor sequencing with NF-κB reporter validation; exome sequencing and segregation analysis in PFAPA families","pmids":["31101826","31053777"],"confidence":"Medium","gaps":["Spiradenoma mutation mechanism (ligand broadening) not yet demonstrated","PFAPA variants lack functional assay validation in this study","Structural basis for gain-of-function unknown"]},{"year":2020,"claim":"The central mechanistic advance: ADP-heptose (a Gram-negative LPS biosynthetic intermediate) was identified as the PAMP sensed by ALPK1, and TIFA Thr9 phosphorylation followed by TRAF6 recruitment was established as the core signaling cascade linking ALPK1 to NF-κB activation.","evidence":"ALPK1/TIFA genetic disruption, NF-κB reporters, bacterial gene deletion (hldE), chemical identification of ligand, gastric organoid primary cells","pmids":["33037203","32591860"],"confidence":"High","gaps":["Structural basis of ADP-heptose recognition not resolved","Whether additional PAMPs activate ALPK1 unknown","Contribution of Thr177 phosphorylation not yet identified"]},{"year":2021,"claim":"Extension of the ADP-heptose/ALPK1 axis to diverse biological contexts—Campylobacter jejuni intestinal epithelial infection and pancreatic beta-cell cytokine sensitization—demonstrated the pathway's broad tissue relevance and showed that ALPK1 activation alone is insufficient for apoptosis but synergizes with inflammatory cytokines.","evidence":"ALPK1 KO intestinal cells with bacterial hldE deletion; ADP-heptose stimulation of MIN6 beta cells with TIFA/TAK1 pathway analysis","pmids":["34339468","34621265"],"confidence":"High","gaps":["Whether heptose phosphates versus ADP-heptose are the true Campylobacter ligand not fully resolved","Beta-cell relevance in vivo not tested"]},{"year":2022,"claim":"The ubiquitin signaling logic downstream of ALPK1 was dissected: ALPK1 phosphorylates TIFA at Thr177 in addition to Thr9, and Thr177 phosphorylation selectively blocks TRAF6 but not TRAF2 binding, while parallel TRAF2/c-IAP1 and LUBAC E3 ligase pathways generate distinct ubiquitin chain types to activate TAK1 and IKK respectively.","evidence":"In vitro kinase assays with site-directed mutagenesis, Co-IP, ubiquitin linkage analysis, E3 ligase genetic knockouts","pmids":["36098982"],"confidence":"High","gaps":["Whether Thr177 phosphorylation functions as a negative feedback switch in vivo unknown","Kinetics and stoichiometry of dual phosphorylation not measured","LUBAC recruitment mechanism not fully defined"]},{"year":2022,"claim":"ALPK1 gain-of-function mutations T237M and Y254C were shown to cause ROSAH syndrome through constitutive NF-κB and STAT1/interferon signaling, validated in patient samples and Alpk1 T237M knock-in mice that display subclinical inflammation.","evidence":"Mutant ALPK1 constructs, immunoblotting, cytokine profiling, transcriptomics, knock-in mouse model, patient primary samples","pmids":["35868845"],"confidence":"High","gaps":["Whether STAT1 activation is direct or secondary to NF-κB-driven cytokines unclear","Ocular pathogenesis mechanism in ROSAH not defined","Therapeutic kinase inhibitor efficacy not demonstrated"]},{"year":2022,"claim":"Multiple groups showed that commensal (Akkermansia muciniphila) and pathogenic (Fusobacterium nucleatum) gut bacteria exploit the ALPK1/TIFA/NF-κB axis in intestinal epithelial and cancer cells, with downstream consequences including barrier gene induction, PD-L1 upregulation, ICAM1-mediated metastasis, and chemoresistance.","evidence":"ALPK1/TIFA KO cells, ADP-heptose stimulation, NF-κB reporters, adhesion/extravasation assays, chemosensitivity assays","pmids":["36036242","35220887","38126163","39881579"],"confidence":"Medium","gaps":["Whether ALPK1 activation is protective or pathogenic in CRC requires in vivo longitudinal evidence","Exact ADP-heptose-like metabolite from A. muciniphila not structurally resolved","Relative contribution of ALPK1 versus TLR pathways in mixed microbial settings unclear"]},{"year":2023,"claim":"The structural basis of disease-causing gain-of-function was clarified: ROSAH (T237M) and spiradenoma (V1092A) mutations expand ALPK1 ligand specificity to endogenous nucleotide sugars (UDP-mannose, ADP-ribose, cyclic ADP-ribose), explaining constitutive activation without exogenous bacterial ligand.","evidence":"NF-κB/AP-1 reporters with WT and mutant ALPK1, nucleotide sugar panels, binding-site mutagenesis","pmids":["38060563"],"confidence":"High","gaps":["Co-crystal structure of mutant ALPK1 with endogenous ligands not available","Whether endogenous nucleotide sugar concentrations in vivo reach activating thresholds not measured","No therapeutic strategy to selectively block mutant but not WT ALPK1"]},{"year":2024,"claim":"Copper was identified as a direct cofactor for ALPK1 kinase activity: copper binding enhances ADP-heptose sensitivity, and infection-induced cytosolic copper accumulation amplifies ALPK1-dependent innate defense, adding a metal-dependent regulatory layer to the pathway.","evidence":"Direct copper-ALPK1 binding assays, in vitro kinase activity, ALPK1-dependent signaling in KO cells, zebrafish in vivo infection model","pmids":["38232278"],"confidence":"High","gaps":["Copper binding site on ALPK1 not structurally mapped","Whether copper dysregulation contributes to ROSAH or spiradenoma pathogenesis unknown","Specificity for copper versus other divalent metals not comprehensively tested"]},{"year":2025,"claim":"Gut-derived ADP-heptose was shown to reach hematopoietic progenitors and activate ALPK1/NF-κB, conferring a proliferative advantage to pre-leukemic CHIP clones—extending ALPK1 function from local mucosal immunity to systemic clonal hematopoiesis.","evidence":"ADP-heptose detection in human serum, ALPK1-dependent signaling in pre-leukemic cells, competitive repopulation assays, transcriptomics","pmids":["40269158"],"confidence":"High","gaps":["Whether ALPK1 inhibition could prevent CHIP progression not tested","Source specificity of circulating ADP-heptose (which bacteria) not defined","Interaction between ALPK1 and other CHIP driver mutations not explored"]},{"year":null,"claim":"Key unresolved questions include the atomic structure of ALPK1 bound to ADP-heptose or endogenous ligands, the precise copper-binding site, whether Thr177 phosphorylation of TIFA serves as a physiological negative feedback mechanism, and whether selective pharmacological inhibition of gain-of-function mutants is feasible for ROSAH syndrome therapy.","evidence":"","pmids":[],"confidence":"High","gaps":["No crystal or cryo-EM structure of ALPK1","Thr177 phosphorylation role in vivo undetermined","No selective ALPK1 inhibitor validated for disease models"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,2,6,7]},{"term_id":"GO:0140299","term_label":"molecular sensor activity","supporting_discovery_ids":[0,1,3,9]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,1,7]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,1,2,7,9,10]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,2,4,8]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[3,4,5,11,19,20]}],"complexes":[],"partners":["TIFA","TRAF6","TRAF2","BIRC2","MYH9"],"other_free_text":[]},"mechanistic_narrative":"ALPK1 is an atypical alpha-kinase that functions as a cytosolic pattern recognition receptor for bacterial ADP-heptose, coupling microbial detection to NF-κB-driven inflammatory signaling. Upon ADP-heptose binding—enhanced by direct copper co-activation—ALPK1 phosphorylates TIFA at Thr9 and Thr177, recruiting TRAF6, TRAF2/c-IAP1, and LUBAC to generate Lys63- and Met1-linked ubiquitin chains that activate TAK1 and the canonical IKK complex, culminating in NF-κB-dependent expression of inflammatory cytokines, chemokines, and host-defense genes [PMID:32591860, PMID:36098982, PMID:38232278]. Gain-of-function mutations in ALPK1 (T237M, Y254C) cause the autoinflammatory ROSAH syndrome by broadening ligand specificity to include endogenous nucleotide sugars such as UDP-mannose and ADP-ribose, resulting in constitutive NF-κB activation [PMID:35868845, PMID:38060563]. Beyond innate immunity, ALPK1-dependent NF-κB signaling promotes clonal hematopoietic expansion in pre-leukemic cells exposed to gut-derived ADP-heptose, modulates intestinal barrier gene expression in response to commensal bacteria, and drives PD-L1 upregulation and chemoresistance in colorectal cancer cells colonized by Fusobacterium nucleatum [PMID:40269158, PMID:36036242, PMID:38126163]."},"prefetch_data":{"uniprot":{"accession":"Q96QP1","full_name":"Alpha-protein kinase 1","aliases":["Chromosome 4 kinase","Lymphocyte alpha-protein kinase"],"length_aa":1244,"mass_kda":138.9,"function":"Serine/threonine-protein kinase that detects bacterial pathogen-associated molecular pattern metabolites (PAMPs) and initiates an innate immune response, a critical step for pathogen elimination and engagement of adaptive immunity (PubMed:28222186, PubMed:28877472, PubMed:30111836). Specifically recognizes and binds ADP-D-glycero-beta-D-manno-heptose (ADP-Heptose), a potent PAMP present in all Gram-negative and some Gram-positive bacteria (PubMed:30111836). ADP-Heptose-binding stimulates its kinase activity to phosphorylate and activate TIFA, triggering pro-inflammatory NF-kappa-B signaling (PubMed:30111836, PubMed:35868845, PubMed:38060563). May be involved in monosodium urate monohydrate (MSU)-induced inflammation by mediating phosphorylation of unconventional myosin MYO9A (PubMed:27169898). May also play a role in apical protein transport by mediating phosphorylation of unconventional myosin MYO1A (PubMed:15883161). May play a role in ciliogenesis (PubMed:30967659)","subcellular_location":"Cytoplasm, cytosol; Cytoplasm, cytoskeleton, spindle pole; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Cell projection, cilium","url":"https://www.uniprot.org/uniprotkb/Q96QP1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ALPK1","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ALPK1","total_profiled":1310},"omim":[{"mim_id":"619965","title":"ALPHA KINASE 2; ALPK2","url":"https://www.omim.org/entry/619965"},{"mim_id":"617608","title":"ALPHA KINASE 3; ALPK3","url":"https://www.omim.org/entry/617608"},{"mim_id":"614979","title":"RETINAL DYSTROPHY, OPTIC NERVE EDEMA, SPLENOMEGALY, ANHIDROSIS, AND MIGRAINE HEADACHE SYNDROME; ROSAH","url":"https://www.omim.org/entry/614979"},{"mim_id":"607347","title":"ALPHA KINASE 1; ALPK1","url":"https://www.omim.org/entry/607347"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Centrosome","reliability":"Supported"},{"location":"Basal body","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ALPK1"},"hgnc":{"alias_symbol":["Lak","FLJ22670","KIAA1527"],"prev_symbol":[]},"alphafold":{"accession":"Q96QP1","domains":[{"cath_id":"-","chopping":"2-149","consensus_level":"medium","plddt":92.0875,"start":2,"end":149},{"cath_id":"3.30.200.20","chopping":"976-1099_1112-1134","consensus_level":"medium","plddt":88.3852,"start":976,"end":1134},{"cath_id":"3.20.200.10","chopping":"1136-1244","consensus_level":"medium","plddt":85.3489,"start":1136,"end":1244},{"cath_id":"1.20.120","chopping":"322-437","consensus_level":"medium","plddt":91.6609,"start":322,"end":437}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96QP1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96QP1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96QP1-F1-predicted_aligned_error_v6.png","plddt_mean":65.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ALPK1","jax_strain_url":"https://www.jax.org/strain/search?query=ALPK1"},"sequence":{"accession":"Q96QP1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96QP1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96QP1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96QP1"}},"corpus_meta":[{"pmid":"2643685","id":"PMC_2643685","title":"Intratumoral LAK cell and interleukin-2 therapy of human gliomas.","date":"1989","source":"Journal of neurosurgery","url":"https://pubmed.ncbi.nlm.nih.gov/2643685","citation_count":226,"is_preprint":false},{"pmid":"35220887","id":"PMC_35220887","title":"Fusobacterium nucleatum promotes colorectal cancer cells adhesion to endothelial cells and facilitates extravasation and metastasis by inducing ALPK1/NF-κB/ICAM1 axis.","date":"2022","source":"Gut microbes","url":"https://pubmed.ncbi.nlm.nih.gov/35220887","citation_count":167,"is_preprint":false},{"pmid":"3871657","id":"PMC_3871657","title":"Lymphokine-activated killer (LAK) cells. 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haematology","url":"https://pubmed.ncbi.nlm.nih.gov/1716215","citation_count":16,"is_preprint":false},{"pmid":"34621265","id":"PMC_34621265","title":"Alpk1 Sensitizes Pancreatic Beta Cells to Cytokine-Induced Apoptosis via Upregulating TNF-α Signaling Pathway.","date":"2021","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/34621265","citation_count":15,"is_preprint":false},{"pmid":"7829133","id":"PMC_7829133","title":"Identification of a mannose-acetate-specific 87-kDa receptor responsible for human NK and LAK activity.","date":"1994","source":"Immunology letters","url":"https://pubmed.ncbi.nlm.nih.gov/7829133","citation_count":15,"is_preprint":false},{"pmid":"3257274","id":"PMC_3257274","title":"Anti-tumor reactivity of human lymphokine activated killer (LAK) cells against fresh and cultured preparations of renal cell cancer.","date":"1988","source":"The Journal of urology","url":"https://pubmed.ncbi.nlm.nih.gov/3257274","citation_count":15,"is_preprint":false},{"pmid":"18432832","id":"PMC_18432832","title":"Measurement of cytotoxic activity of NK/LAK cells.","date":"2001","source":"Current protocols in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/18432832","citation_count":15,"is_preprint":false},{"pmid":"38494837","id":"PMC_38494837","title":"The relationship of ALPK1, hyaluronic acid and M1 macrophage polarization in the temporomandibular joint synovitis.","date":"2024","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38494837","citation_count":14,"is_preprint":false},{"pmid":"2552792","id":"PMC_2552792","title":"Lymphokine-activated killer (LAK) cell activity in tumor-infiltrating lymphocytes from non-small cell lung cancer.","date":"1989","source":"American journal of clinical pathology","url":"https://pubmed.ncbi.nlm.nih.gov/2552792","citation_count":14,"is_preprint":false},{"pmid":"2788512","id":"PMC_2788512","title":"Target cell-directed inactivation and IL-2-dependent reactivation of LAK cells.","date":"1989","source":"Cellular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/2788512","citation_count":14,"is_preprint":false},{"pmid":"8241989","id":"PMC_8241989","title":"Effect of GVHD on the recovery of NK cell activity and LAK precursors following BMT.","date":"1993","source":"Bone marrow transplantation","url":"https://pubmed.ncbi.nlm.nih.gov/8241989","citation_count":14,"is_preprint":false},{"pmid":"2795092","id":"PMC_2795092","title":"Treatment of patients with advanced cancer using multiple long-term cultured lymphokine-activated killer (LAK) cell infusions and recombinant human interleukin-2.","date":"1989","source":"Journal of biological response modifiers","url":"https://pubmed.ncbi.nlm.nih.gov/2795092","citation_count":14,"is_preprint":false},{"pmid":"15692848","id":"PMC_15692848","title":"Mycophenolate mofetil does not suppress the graft-versus-leukemia effect or the activity of lymphokine-activated killer (LAK) cells in a murine model.","date":"2004","source":"Cancer immunology, immunotherapy : CII","url":"https://pubmed.ncbi.nlm.nih.gov/15692848","citation_count":14,"is_preprint":false},{"pmid":"7835941","id":"PMC_7835941","title":"A novel role for MHC class II antigens: evidence implicating a protective effect on tumour cells against cytotoxicity by NK and LAK cells.","date":"1994","source":"Immunology","url":"https://pubmed.ncbi.nlm.nih.gov/7835941","citation_count":14,"is_preprint":false},{"pmid":"38060563","id":"PMC_38060563","title":"ALPK1 mutants causing ROSAH syndrome or Spiradenoma are activated by human nucleotide sugars.","date":"2023","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/38060563","citation_count":13,"is_preprint":false},{"pmid":"35699669","id":"PMC_35699669","title":"Alpha-kinase 1 (ALPK1) agonist DF-006 demonstrates potent efficacy in mouse and primary human hepatocyte (PHH) models of hepatitis B.","date":"2022","source":"Hepatology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/35699669","citation_count":13,"is_preprint":false},{"pmid":"38814706","id":"PMC_38814706","title":"Decoding huge phage diversity: a taxonomic classification of Lak megaphages.","date":"2024","source":"The Journal of general virology","url":"https://pubmed.ncbi.nlm.nih.gov/38814706","citation_count":13,"is_preprint":false},{"pmid":"35764196","id":"PMC_35764196","title":"Anticancer activity of D-LAK-120A, an antimicrobial peptide, in non-small cell lung cancer (NSCLC).","date":"2022","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/35764196","citation_count":13,"is_preprint":false},{"pmid":"7694662","id":"PMC_7694662","title":"Expression of adhesion molecules on acute leukemic blast cells and sensitivity to normal LAK activity.","date":"1993","source":"Annals of hematology","url":"https://pubmed.ncbi.nlm.nih.gov/7694662","citation_count":13,"is_preprint":false},{"pmid":"30315765","id":"PMC_30315765","title":"ALPK1 Expression Is Associated with Lymph Node Metastasis and Tumor Growth in Oral Squamous Cell Carcinoma Patients.","date":"2018","source":"The American journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/30315765","citation_count":13,"is_preprint":false},{"pmid":"7561518","id":"PMC_7561518","title":"Enhanced expression of novel CD57+CD8+ LAK cells from cats infected with feline immunodeficiency virus.","date":"1995","source":"Journal of leukocyte biology","url":"https://pubmed.ncbi.nlm.nih.gov/7561518","citation_count":13,"is_preprint":false},{"pmid":"3283299","id":"PMC_3283299","title":"Soluble glucan and lymphokine-activated killer (LAK) cells in the therapy of experimental hepatic metastases.","date":"1988","source":"Journal of biological response modifiers","url":"https://pubmed.ncbi.nlm.nih.gov/3283299","citation_count":13,"is_preprint":false},{"pmid":"8133047","id":"PMC_8133047","title":"Bispecific anti-CD22/anti-CD3-ricin A chain immunotoxin is cytotoxic to Daudi lymphoma cells but not T cells in vitro and shows both A-chain-mediated and LAK-T-mediated killing.","date":"1994","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/8133047","citation_count":13,"is_preprint":false},{"pmid":"8877398","id":"PMC_8877398","title":"Anti-candidial activity of natural killer (NK) and lymphokine activated killer (LAK) lymphocytes in vitro.","date":"1996","source":"Immunobiology","url":"https://pubmed.ncbi.nlm.nih.gov/8877398","citation_count":12,"is_preprint":false},{"pmid":"30132913","id":"PMC_30132913","title":"Molecular epidemiology analysis of enterovirus 71 strains isolated in Dak Lak, Vietnam, 2011-2016.","date":"2018","source":"Journal of medical virology","url":"https://pubmed.ncbi.nlm.nih.gov/30132913","citation_count":12,"is_preprint":false},{"pmid":"18463539","id":"PMC_18463539","title":"Melanoma and lymphoma rejection associated with eosinophil infiltration upon intratumoral injection of dendritic and NK/LAK cells.","date":"2008","source":"Journal of immunotherapy (Hagerstown, Md. : 1997)","url":"https://pubmed.ncbi.nlm.nih.gov/18463539","citation_count":12,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":49703,"output_tokens":5712,"usd":0.117394},"stage2":{"model":"claude-opus-4-6","input_tokens":9371,"output_tokens":3377,"usd":0.19692},"total_usd":0.314314,"stage1_batch_id":"msgbatch_01TqNM6p6FsoMBT2jzQTwKBr","stage2_batch_id":"msgbatch_01Ya473eco8sTHbvRymQaU8o","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2020,\n      \"finding\": \"ALPK1 functions as a cytosolic pattern recognition receptor (PRR) that detects the bacterial lipopolysaccharide biosynthetic intermediate ADP-heptose (β-ADP-heptose), triggering phosphorylation of TIFA and downstream NF-κB activation, leading to inflammatory cytokine production. H. pylori-induced NF-κB/NF-κB-driven R-loop formation and replication stress are dependent on this ALPK1/TIFA signaling pathway.\",\n      \"method\": \"Genetic disruption of ALPK1 and TIFA, chemical inhibition, cell-based reporter assays, replication fork assays, S-phase analysis, gastric organoid primary cells\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (knockdown, reporter assays, primary organoids), replicated across multiple bacterial models\",\n      \"pmids\": [\"33037203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ADP-heptose (a soluble intermediate of the LPS biosynthetic pathway in Gram-negative bacteria) is the PAMP recognized by ALPK1; upon binding, ALPK1 phosphorylates TIFA at Thr9, leading to TRAF6 recruitment and NF-κB activation with secretion of inflammatory cytokines.\",\n      \"method\": \"Review/synthesis of biochemical and genetic evidence from multiple studies; TIFA phosphorylation assays, NF-κB reporter assays, genetic epistasis with ALPK1/TIFA knockouts\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — mechanistic pathway established by multiple independent labs with in vitro kinase assays and genetic epistasis\",\n      \"pmids\": [\"32591860\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ALPK1 directly phosphorylates TIFA at Thr177 (in addition to Thr9) in vitro; Thr177 is located within the TRAF6-binding motif and its phosphomimetic mutation (T177D) prevents TRAF6 but not TRAF2 binding, restricting ADP-heptose signaling. ADP-heptose stimulation also induces TRAF2/c-IAP1-dependent Lys63-linked and LUBAC-dependent Met1-linked ubiquitin chains to activate TAK1 and canonical IKK complexes, respectively. c-IAP1 is recruited to TIFA via TRAF2.\",\n      \"method\": \"In vitro kinase assay, site-directed mutagenesis, Co-immunoprecipitation, ubiquitin chain analysis, genetic knockouts of E3 ligases\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct in vitro kinase assays with mutagenesis, combined with Co-IP and genetic epistasis\",\n      \"pmids\": [\"36098982\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Disease-causing ALPK1 mutants (T237M for ROSAH syndrome; V1092A for spiradenoma) can be activated by endogenous human nucleotide sugars (UDP-mannose, ADP-ribose, cyclic ADP-ribose, and for V1092A also GDP-mannose) that do not activate wild-type ALPK1, explaining constitutive NF-κB activation; mutations in the ADP-heptose binding site prevent activation of both wild-type and mutant ALPK1.\",\n      \"method\": \"NF-κB/AP-1 reporter gene assays with wild-type and mutant ALPK1 constructs, binding-site mutagenesis, nucleotide sugar stimulation assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstitution of kinase activation with defined ligands and mutagenesis of active site, multiple orthogonal experiments\",\n      \"pmids\": [\"38060563\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ALPK1 gain-of-function mutations (T237M, Y254C) cause the autoinflammatory ROSAH syndrome by constitutively increasing NF-κB signaling, STAT1 phosphorylation, and interferon gene expression; knock-in mice carrying Alpk1 T237M show subclinical inflammation.\",\n      \"method\": \"In vitro assays with mutated ALPK1 constructs, immunoblotting, cytokine profiling, transcriptomics, knock-in mouse model, patient primary samples\",\n      \"journal\": \"Annals of the rheumatic diseases\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods across patient samples and mouse models confirming gain-of-function kinase mechanism\",\n      \"pmids\": [\"35868845\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"A recurrent missense mutation in the kinase domain of ALPK1 (identified in spiradenomas and spiradenocarcinomas) can activate the NF-κB pathway in reporter assays, establishing it as a gain-of-function driver mutation.\",\n      \"method\": \"Genomic sequencing, NF-κB reporter assays with ALPK1 mutant constructs\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reporter assay functional validation in addition to sequencing; single study\",\n      \"pmids\": [\"31101826\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"ALPK1 phosphorylates myosin IIA; in monosodium urate (MSU)-stimulated cells, ALPK1 forms a protein complex with myosin IIA, calmodulin, and F-actin at the N-terminal domain, and MSU-induced ALPK1 activity phosphorylates myosin IIA, which is required for Golgi-derived TNF-α trafficking and secretion.\",\n      \"method\": \"Bioinformatics, proteomics, Co-immunoprecipitation, ALPK1/myosin IIA knockdown, in vitro phosphorylation assays, TNF-α secretion assays, human patient samples\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP and functional knockdown with defined substrate; single lab study\",\n      \"pmids\": [\"27169898\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Copper binds directly to ALPK1 and is essential for its kinase activity; copper binding enhances ALPK1 sensitivity to ADP-heptose and amplifies the innate immune response. In response to bacterial infection, host cells actively accumulate cytosolic copper, which promotes ALPK1-dependent host defense.\",\n      \"method\": \"Direct binding assays (copper-ALPK1 interaction), in vitro kinase activity assays, ALPK1-dependent cell signaling (knockdown/KO), zebrafish in vivo infection model\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct binding demonstrated, in vitro kinase activity assay, in vivo validation in zebrafish model with multiple orthogonal methods\",\n      \"pmids\": [\"38232278\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ADP-heptose (from gut Gram-negative bacteria) binds to ALPK1 in hematopoietic progenitor cells, triggering NF-κB activation and transcriptional reprogramming that confers a proliferative competitive advantage to pre-leukemic (CHIP) cells, driving clonal expansion.\",\n      \"method\": \"ADP-heptose detection in human serum, ALPK1-dependent signaling in pre-leukemic cells, genetic models, transcriptomic analysis, competitive repopulation assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including mechanistic ALPK1 pathway studies, human samples, and functional competitive advantage assays\",\n      \"pmids\": [\"40269158\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The ALPK1 pathway drives the NF-κB-mediated pro-inflammatory response (CXCL8, CXCL2, TNFAIP2, PTGS2) to Campylobacter jejuni in human intestinal epithelial cells; ADP-heptose and/or related heptose phosphates (not requiring T3SS or T4SS injection) are the released virulence factor activating ALPK1, identified by hldE gene deletion and chemical characterization.\",\n      \"method\": \"ALPK1 knockout cells, chemical characterization of released factor, bacterial gene deletion (hldE), NF-κB reporter assays, independent of TLR/NLR signaling (epistasis)\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis (ALPK1 KO, bacterial gene deletion), chemical identification of ligand, multiple orthogonal methods\",\n      \"pmids\": [\"34339468\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Akkermansia muciniphila releases ADP-heptose-like metabolites that enter intestinal epithelial cells and activate NF-κB via ALPK1/TIFA/TRAF6, inducing expression of barrier-function genes (MUC2, BIRC3, TNFAIP3) in a TIFA-dependent manner.\",\n      \"method\": \"Pharmacological inhibitors, gene editing (ALPK1/TIFA/TRAF6 knockouts), chemical characterization of released metabolite, NF-κB reporter assays\",\n      \"journal\": \"Gut microbes\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — CRISPR gene editing combined with chemical characterization and reporter assays; multiple orthogonal methods\",\n      \"pmids\": [\"36036242\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Fusobacterium nucleatum activates ALPK1, which then signals through NF-κB to upregulate ICAM1 expression on colorectal cancer cells, enhancing adhesion to endothelial cells and promoting extravasation and metastasis.\",\n      \"method\": \"ALPK1 knockdown/overexpression, NF-κB reporter assays, adhesion and extravasation assays, ICAM1 expression studies, patient tissue correlation\",\n      \"journal\": \"Gut microbes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — knockdown functional assays with defined pathway; single lab\",\n      \"pmids\": [\"35220887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ALPK1 exacerbates condylar cartilage degradation in TMJOA by activating NF-κB signaling (upregulating MMP13, COX2) and suppressing ERK1/2 signaling (downregulating aggrecan); ALPK1 knockout mice show attenuated cartilage/bone damage.\",\n      \"method\": \"ALPK1 KO mouse model (MIA-induced TMJOA), intra-articular recombinant ALPK1 administration, ex vivo chondrocyte studies, NF-κB and ERK1/2 pathway analysis\",\n      \"journal\": \"Journal of dental research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with defined pathway readout; single lab with multiple in vivo and ex vivo methods\",\n      \"pmids\": [\"35689396\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ALPK1 accelerates osteoarthritis pathogenesis by activating NF-κB signaling, which upregulates NLRP3 inflammasome in chondrocytes, driving IL-1β-mediated inflammation; ALPK1 KO reverses OA pathogenesis and NLRP3 is a downstream target of NF-κB in ALPK1-activated chondrocytes.\",\n      \"method\": \"ALPK1 KO and intra-articular recombinant ALPK1 in DMM and CIOA mouse models, selective NF-κB and NLRP3 inhibition, in vitro chondrocyte studies\",\n      \"journal\": \"Journal of bone and mineral research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with pathway epistasis using selective inhibitors; single lab\",\n      \"pmids\": [\"36053817\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ALPK1 sensitizes pancreatic beta cells to cytokine-induced apoptosis by potentiating TNF-α and Fas expression through enhanced activation of the TIFA/TAK1/NF-κB signaling axis; ADP-heptose activation of ALPK1 alone is insufficient to induce apoptosis but synergizes with cytokines.\",\n      \"method\": \"ADP-heptose stimulation in MIN6 cells, ALPK1 activation assays, TIFA/TAK1/NF-κB pathway analysis, apoptosis assays, GLP-1 receptor agonist rescue\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — defined ligand/pathway with multiple cellular readouts; single lab\",\n      \"pmids\": [\"34621265\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Disruption of ALPK1 (via piggyBac transposon insertion into intron 1) in mice causes severe motor coordination deficits, which are rescued by transgenic re-expression of full-length ALPK1, establishing ALPK1 as functionally required for motor coordination.\",\n      \"method\": \"PiggyBac transposon insertional mutagenesis in mice, behavioral analysis (rotarod, hanging wire, dowel, footprint tests), transgenic rescue with full-length Alpk1\",\n      \"journal\": \"BMC neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with specific phenotypic readout and transgenic rescue; single study\",\n      \"pmids\": [\"21208416\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ALPK1 overexpression decreases URAT1 (urate transporter 1, SLC22A12) protein levels in vivo in transgenic mice and in vitro in kidney cells; MSU crystal stimulation upregulates ALPK1, which in turn inhibits URAT1, suggesting ALPK1 acts as a negative regulator of urate reuptake.\",\n      \"method\": \"ALPK1 transgenic mice (URAT1 protein measurement), ALPK1 siRNA knockdown in HK-2 cells, MSU crystal stimulation, immunohistochemistry of renal proximal tubule cells\",\n      \"journal\": \"Rheumatology (Oxford, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo transgenic and in vitro knockdown with protein-level readout; single lab\",\n      \"pmids\": [\"28039413\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ALPK1 promotes TMJ synovitis by promoting nuclear translocation of PKM2 and M1 macrophage polarization; LMW-HA upregulates ALPK1 while HMW-HA suppresses it, and rhALPK1 promotes M1 polarization-associated gene expression and nuclear PKM2.\",\n      \"method\": \"ALPK1 KO mice (CFA-induced TMJ synovitis), recombinant ALPK1 stimulation, macrophage polarization assays, PKM2 nuclear translocation assays, patient synovial tissue analysis\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse model with defined cellular pathway; single lab\",\n      \"pmids\": [\"38494837\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ALPK1 is the kinase phosphorylated by/activates upon ADP-heptose bisphosphate recognition, phosphorylating TIFA to trigger the immediate innate immune response to Gram-negative bacterial invasion; rare ALPK1 variants (S924P, D342H, T237M) predispose to periodic fever (PFAPA) syndrome.\",\n      \"method\": \"Exome sequencing, Sanger sequencing, segregation analysis in PFAPA families\",\n      \"journal\": \"European journal of human genetics : EJHG\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 — genetic association without direct functional mechanistic assay in this paper\",\n      \"pmids\": [\"31053777\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ALPK1 acts as a cytosolic PRR for ADP-heptose released by F. nucleatum, and ALPK1/TIFA/TRAF6 pathway activation promotes expression of inflammatory cytokine IL-8 and anti-apoptotic genes BIRC3 and TNFAIP3, enhancing CRC cell survival and reducing 5-fluorouracil chemosensitivity.\",\n      \"method\": \"ALPK1/TIFA pathway knockouts, ADP-heptose stimulation, gene expression assays, cell survival and chemosensitivity assays\",\n      \"journal\": \"Gut microbes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — defined ligand, genetic knockouts, functional cellular readouts; single lab\",\n      \"pmids\": [\"38126163\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"F. nucleatum activates ALPK1 in intestinal cancer cells in an ADP-heptose-dependent manner, leading to NF-κB pathway activation and ALPK1-dependent upregulation of PD-L1; this mechanism is conserved across multiple Fusobacterium species.\",\n      \"method\": \"ALPK1-dependent reporter assays in HEK293 and HT-29 cells, transcriptional analysis, ADP-heptose stimulation, F. nucleatum conditioned medium experiments\",\n      \"journal\": \"Gut microbes\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ALPK1-dependent genetic knockouts and defined ligand stimulation; single lab\",\n      \"pmids\": [\"39881579\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Knockdown of ALPK1 in triple-negative breast cancer cells (MDA-MB-468) induces loss of the myoepithelial marker keratin 5, increased β-casein production, decreased proliferation, reduced clonogenicity, and reduced tumorigenicity in vivo, establishing ALPK1 as a regulator of cancer cell differentiation state.\",\n      \"method\": \"Kinase knockdown screen (420 kinases), shRNA knockdown, spheroid and anchorage-independent growth assays, in vivo xenograft\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with defined cellular and in vivo phenotypic readouts; single lab\",\n      \"pmids\": [\"27829216\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DF-006 (an ALPK1 agonist) activates the NF-κB pathway via ALPK1 and stimulates innate immunity, demonstrating that pharmacological agonism of ALPK1 is sufficient to drive antiviral gene expression and reduce HBV viral markers in mouse and primary human hepatocyte models.\",\n      \"method\": \"AAV-HBV mouse models, primary human hepatocytes, NF-κB target gene upregulation, antiviral efficacy assays, liver localization of DF-006\",\n      \"journal\": \"Hepatology (Baltimore, Md.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — pharmacological agonist with defined ALPK1 target and pathway readouts in multiple models; single lab\",\n      \"pmids\": [\"35699669\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ALPK1 is a cytosolic atypical (alpha) protein kinase that functions as a pattern recognition receptor (PRR) for bacterial ADP-heptose; upon ADP-heptose binding (facilitated by copper co-activation), ALPK1 phosphorylates TIFA at Thr9 and Thr177, triggering recruitment of TRAF2/c-IAP1 and TRAF6 E3 ligases to generate Lys63- and Met1-linked ubiquitin chains that activate TAK1 and IKK complexes, leading to NF-κB-driven inflammatory gene expression; disease-causing gain-of-function mutations (T237M, Y254C for ROSAH syndrome; V1092A for spiradenoma) expand the ligand specificity to include endogenous human nucleotide sugars, causing constitutive NF-κB signaling and autoinflammatory disease.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ALPK1 is an atypical alpha-kinase that functions as a cytosolic pattern recognition receptor for bacterial ADP-heptose, coupling microbial detection to NF-κB-driven inflammatory signaling. Upon ADP-heptose binding—enhanced by direct copper co-activation—ALPK1 phosphorylates TIFA at Thr9 and Thr177, recruiting TRAF6, TRAF2/c-IAP1, and LUBAC to generate Lys63- and Met1-linked ubiquitin chains that activate TAK1 and the canonical IKK complex, culminating in NF-κB-dependent expression of inflammatory cytokines, chemokines, and host-defense genes [PMID:32591860, PMID:36098982, PMID:38232278]. Gain-of-function mutations in ALPK1 (T237M, Y254C) cause the autoinflammatory ROSAH syndrome by broadening ligand specificity to include endogenous nucleotide sugars such as UDP-mannose and ADP-ribose, resulting in constitutive NF-κB activation [PMID:35868845, PMID:38060563]. Beyond innate immunity, ALPK1-dependent NF-κB signaling promotes clonal hematopoietic expansion in pre-leukemic cells exposed to gut-derived ADP-heptose, modulates intestinal barrier gene expression in response to commensal bacteria, and drives PD-L1 upregulation and chemoresistance in colorectal cancer cells colonized by Fusobacterium nucleatum [PMID:40269158, PMID:36036242, PMID:38126163].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Before ALPK1's ligand or immune function was known, loss-of-function in mice revealed an unexpected requirement for motor coordination, establishing that ALPK1 has physiological roles beyond any anticipated kinase function.\",\n      \"evidence\": \"PiggyBac insertional mutagenesis in mice with behavioral rescue by transgenic ALPK1 re-expression\",\n      \"pmids\": [\"21208416\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking ALPK1 kinase activity to motor coordination is undefined\", \"Relevant substrate in the nervous system unknown\", \"Not replicated independently\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identification of myosin IIA as an ALPK1 substrate in gout-relevant MSU-stimulated cells established the first substrate–product relationship and linked ALPK1 to Golgi-derived TNF-α trafficking, while a parallel study showed ALPK1 knockdown altered differentiation in triple-negative breast cancer cells.\",\n      \"evidence\": \"Co-IP, in vitro phosphorylation of myosin IIA, TNF-α secretion assays; shRNA kinase screen with xenograft validation\",\n      \"pmids\": [\"27169898\", \"27829216\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Myosin IIA phosphorylation site not mapped\", \"Relationship between myosin IIA phosphorylation and TIFA pathway unclear\", \"Cancer differentiation phenotype not linked to a defined ALPK1 substrate\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Discovery that a recurrent ALPK1 kinase-domain mutation drives NF-κB activation in spiradenomas, and that rare germline variants associate with periodic fever, positioned ALPK1 as a disease-relevant signaling node, though the activating ligand remained unknown for these contexts.\",\n      \"evidence\": \"Tumor sequencing with NF-κB reporter validation; exome sequencing and segregation analysis in PFAPA families\",\n      \"pmids\": [\"31101826\", \"31053777\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Spiradenoma mutation mechanism (ligand broadening) not yet demonstrated\", \"PFAPA variants lack functional assay validation in this study\", \"Structural basis for gain-of-function unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"The central mechanistic advance: ADP-heptose (a Gram-negative LPS biosynthetic intermediate) was identified as the PAMP sensed by ALPK1, and TIFA Thr9 phosphorylation followed by TRAF6 recruitment was established as the core signaling cascade linking ALPK1 to NF-κB activation.\",\n      \"evidence\": \"ALPK1/TIFA genetic disruption, NF-κB reporters, bacterial gene deletion (hldE), chemical identification of ligand, gastric organoid primary cells\",\n      \"pmids\": [\"33037203\", \"32591860\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of ADP-heptose recognition not resolved\", \"Whether additional PAMPs activate ALPK1 unknown\", \"Contribution of Thr177 phosphorylation not yet identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extension of the ADP-heptose/ALPK1 axis to diverse biological contexts—Campylobacter jejuni intestinal epithelial infection and pancreatic beta-cell cytokine sensitization—demonstrated the pathway's broad tissue relevance and showed that ALPK1 activation alone is insufficient for apoptosis but synergizes with inflammatory cytokines.\",\n      \"evidence\": \"ALPK1 KO intestinal cells with bacterial hldE deletion; ADP-heptose stimulation of MIN6 beta cells with TIFA/TAK1 pathway analysis\",\n      \"pmids\": [\"34339468\", \"34621265\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether heptose phosphates versus ADP-heptose are the true Campylobacter ligand not fully resolved\", \"Beta-cell relevance in vivo not tested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The ubiquitin signaling logic downstream of ALPK1 was dissected: ALPK1 phosphorylates TIFA at Thr177 in addition to Thr9, and Thr177 phosphorylation selectively blocks TRAF6 but not TRAF2 binding, while parallel TRAF2/c-IAP1 and LUBAC E3 ligase pathways generate distinct ubiquitin chain types to activate TAK1 and IKK respectively.\",\n      \"evidence\": \"In vitro kinase assays with site-directed mutagenesis, Co-IP, ubiquitin linkage analysis, E3 ligase genetic knockouts\",\n      \"pmids\": [\"36098982\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Thr177 phosphorylation functions as a negative feedback switch in vivo unknown\", \"Kinetics and stoichiometry of dual phosphorylation not measured\", \"LUBAC recruitment mechanism not fully defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"ALPK1 gain-of-function mutations T237M and Y254C were shown to cause ROSAH syndrome through constitutive NF-κB and STAT1/interferon signaling, validated in patient samples and Alpk1 T237M knock-in mice that display subclinical inflammation.\",\n      \"evidence\": \"Mutant ALPK1 constructs, immunoblotting, cytokine profiling, transcriptomics, knock-in mouse model, patient primary samples\",\n      \"pmids\": [\"35868845\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether STAT1 activation is direct or secondary to NF-κB-driven cytokines unclear\", \"Ocular pathogenesis mechanism in ROSAH not defined\", \"Therapeutic kinase inhibitor efficacy not demonstrated\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Multiple groups showed that commensal (Akkermansia muciniphila) and pathogenic (Fusobacterium nucleatum) gut bacteria exploit the ALPK1/TIFA/NF-κB axis in intestinal epithelial and cancer cells, with downstream consequences including barrier gene induction, PD-L1 upregulation, ICAM1-mediated metastasis, and chemoresistance.\",\n      \"evidence\": \"ALPK1/TIFA KO cells, ADP-heptose stimulation, NF-κB reporters, adhesion/extravasation assays, chemosensitivity assays\",\n      \"pmids\": [\"36036242\", \"35220887\", \"38126163\", \"39881579\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ALPK1 activation is protective or pathogenic in CRC requires in vivo longitudinal evidence\", \"Exact ADP-heptose-like metabolite from A. muciniphila not structurally resolved\", \"Relative contribution of ALPK1 versus TLR pathways in mixed microbial settings unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The structural basis of disease-causing gain-of-function was clarified: ROSAH (T237M) and spiradenoma (V1092A) mutations expand ALPK1 ligand specificity to endogenous nucleotide sugars (UDP-mannose, ADP-ribose, cyclic ADP-ribose), explaining constitutive activation without exogenous bacterial ligand.\",\n      \"evidence\": \"NF-κB/AP-1 reporters with WT and mutant ALPK1, nucleotide sugar panels, binding-site mutagenesis\",\n      \"pmids\": [\"38060563\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Co-crystal structure of mutant ALPK1 with endogenous ligands not available\", \"Whether endogenous nucleotide sugar concentrations in vivo reach activating thresholds not measured\", \"No therapeutic strategy to selectively block mutant but not WT ALPK1\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Copper was identified as a direct cofactor for ALPK1 kinase activity: copper binding enhances ADP-heptose sensitivity, and infection-induced cytosolic copper accumulation amplifies ALPK1-dependent innate defense, adding a metal-dependent regulatory layer to the pathway.\",\n      \"evidence\": \"Direct copper-ALPK1 binding assays, in vitro kinase activity, ALPK1-dependent signaling in KO cells, zebrafish in vivo infection model\",\n      \"pmids\": [\"38232278\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Copper binding site on ALPK1 not structurally mapped\", \"Whether copper dysregulation contributes to ROSAH or spiradenoma pathogenesis unknown\", \"Specificity for copper versus other divalent metals not comprehensively tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Gut-derived ADP-heptose was shown to reach hematopoietic progenitors and activate ALPK1/NF-κB, conferring a proliferative advantage to pre-leukemic CHIP clones—extending ALPK1 function from local mucosal immunity to systemic clonal hematopoiesis.\",\n      \"evidence\": \"ADP-heptose detection in human serum, ALPK1-dependent signaling in pre-leukemic cells, competitive repopulation assays, transcriptomics\",\n      \"pmids\": [\"40269158\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ALPK1 inhibition could prevent CHIP progression not tested\", \"Source specificity of circulating ADP-heptose (which bacteria) not defined\", \"Interaction between ALPK1 and other CHIP driver mutations not explored\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the atomic structure of ALPK1 bound to ADP-heptose or endogenous ligands, the precise copper-binding site, whether Thr177 phosphorylation of TIFA serves as a physiological negative feedback mechanism, and whether selective pharmacological inhibition of gain-of-function mutants is feasible for ROSAH syndrome therapy.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No crystal or cryo-EM structure of ALPK1\", \"Thr177 phosphorylation role in vivo undetermined\", \"No selective ALPK1 inhibitor validated for disease models\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 2, 6, 7]},\n      {\"term_id\": \"GO:0140299\", \"supporting_discovery_ids\": [0, 1, 3, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 1, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 1, 2, 7, 9, 10]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 2, 4, 8]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [3, 4, 5, 11, 19, 20]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"TIFA\",\n      \"TRAF6\",\n      \"TRAF2\",\n      \"BIRC2\",\n      \"MYH9\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}