{"gene":"RNF123","run_date":"2026-06-10T06:43:37","timeline":{"discoveries":[{"year":2015,"finding":"KPC1 (RNF123) is the E3 ubiquitin ligase that binds to the ankyrin repeats domain of NF-κB1 p105, ubiquitinates it, and mediates its limited proteasomal processing to the p50 active subunit both under basal conditions and following signaling. Overexpression of KPC1 inhibits tumor growth via excessive generation of p50, and the resulting p50 homodimer modulates transcription in place of the tumorigenic p50-p65 heterodimer.","method":"Co-immunoprecipitation, in vitro ubiquitination assay, overexpression studies, tumor xenograft models, transcript analysis","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro ubiquitination assay, Co-IP, mutagenesis, and in vivo tumor models in a single rigorous study, subsequently replicated by multiple independent labs","pmids":["25860612"],"is_preprint":false},{"year":2008,"finding":"USP19, a deubiquitinating enzyme, interacts with and stabilizes KPC1 protein by reversing its ubiquitination, thereby modulating p27(Kip1) levels and cell proliferation. Depletion of USP19 reduces KPC1 levels and causes G1/S accumulation that is rescued by KPC1 overexpression or p27 knockout.","method":"Co-immunoprecipitation, RNA interference, proteasome inhibitor treatment, cell cycle analysis, rescue experiments with KPC1 overexpression","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, RNAi depletion with specific rescue by KPC1 overexpression and p27-null cells, multiple orthogonal methods in one study","pmids":["19015242"],"is_preprint":false},{"year":2012,"finding":"RNF123 ubiquitin ligase binds HP1α and HP1β via a canonical PXVXL pentapeptide motif in its N-terminus and targets them for proteasomal degradation. In lamin A/C knockdown cells, RNF123 is upregulated and mediates degradation of HP1α and HP1β (but not HP1γ). Mutation of the PXVXL motif abolishes HP1 binding and degradation.","method":"GFP-tagged RNF123 ectopic expression, RNAi knockdown of RNF123, mutational analysis of PXVXL motif, FRAP analysis, Western blot in HeLa cells","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Moderate — ectopic expression, RNAi rescue, mutagenesis of binding motif, and FRAP in single study with multiple orthogonal methods","pmids":["23077635"],"is_preprint":false},{"year":2016,"finding":"RNF123 is a negative regulator of RIG-I and MDA5 antiviral signaling. RNF123 associates with the N-terminal CARD domains of RIG-I and MDA5 in a viral infection-inducible manner and competes with the downstream adaptor VISA/MAVS for CARD binding, thereby inhibiting IFN-β production. This inhibitory function requires the SPRY and coiled-coil domains of RNF123 but NOT the RING domain, indicating an E3 ligase-independent mechanism.","method":"Overexpression, knockdown and knockout of RNF123, endogenous and exogenous Co-immunoprecipitation, domain deletion mutant analysis, IFN-β reporter assays with SeV and EMCV","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP (endogenous and exogenous), KO cells, domain mutagenesis, and functional reporter assays in single study with multiple orthogonal methods","pmids":["27312109"],"is_preprint":false},{"year":2018,"finding":"KPC1/RNF123 directly ubiquitinates the ETV6-NTRK3 (EN) chimeric oncoprotein in vitro, and its overexpression decreases EN protein levels. IGF1R signaling protects EN from KPC1/RNF123-mediated proteasomal degradation; blocking IGF1R promotes rapid EN ubiquitylation and degradation that is reversed by KPC1 knockdown.","method":"SILAC-based MS interactomics, in vitro ubiquitination assay, KPC1 overexpression and knockdown, IGF1R inhibitor treatment in fibroblast, breast epithelial, and leukemia cell lines","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro ubiquitination assay, SILAC-MS, knockdown rescue, and multiple cell line models in one study","pmids":["29903916"],"is_preprint":false},{"year":2020,"finding":"KPC1 promotes proteasomal degradation of Bax and prevents Bax translocation to mitochondria, thereby reducing apoptosis in cardiomyocytes under hypoxia/reoxygenation. This effect is abolished by the proteasome inhibitor MG132, confirming a proteasome-dependent mechanism.","method":"KPC1 overexpression and shRNA knockdown in H9c2 cells and rat I/R model, Western blot for Bax protein, MMP assay, cytochrome c release, MG132 proteasome inhibition","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo and in vitro overexpression/knockdown with proteasome inhibitor validation, but no direct ubiquitination assay for Bax","pmids":["31148189"],"is_preprint":false},{"year":2020,"finding":"RNF123 overexpression in IDH WT glioblastoma cells reduces NF-κB1 p50 levels and negatively regulates SerpinE1 expression downstream of the miR-155-5p/RNF123/NF-κB1-p50 axis, thereby reducing proliferation and invasion.","method":"RNF123 overexpression in GB cell lines, RNA-sequencing, reverse-phase protein arrays, in vitro functional assays, miR-155-5p overexpression","journal":"Cancers","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (RNA-seq, RPPA, functional assays), single lab","pmids":["32349217"],"is_preprint":false},{"year":2020,"finding":"KPC1-generated excess p50 suppresses tumor growth via multiple mechanisms: (1) downregulation of PD-L1 expression (abrogated by p65 overexpression), and (2) upregulation of pro-inflammatory chemokines CCL3, CCL4, and CCL5, which recruit NK cells and macrophages into tumors.","method":"KPC1 overexpression in cancer cells and tumor xenograft models, p65 co-overexpression rescue, gene expression analysis, immune cell recruitment assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo tumor models and mechanistic rescue experiments, single lab with multiple readouts","pmids":["33168738"],"is_preprint":false},{"year":2021,"finding":"The p105-binding site on KPC1 consists of a seven amino acid sequence (WILVRLW, residues 968–974). Attaching this short stretch to the RING-finger domain fragment was sufficient to bind p105, ubiquitinate it, and suppress tumor growth in vivo. Fusion of these seven amino acids to a pVHL-binding ligand created a PROTAC that stimulated p105 ubiquitination in cell-free systems and its processing to p50 in cells.","method":"Domain deletion and mutagenesis of KPC1, in vitro ubiquitination assay with PROTAC, cell-free processing assay, xenograft tumor model","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution, mutagenesis, cell-free and cell-based assays, in vivo tumor model in single study","pmids":["34873064"],"is_preprint":false},{"year":2022,"finding":"ADAR1-mediated A-to-I RNA editing of KPC1 results in a methionine-to-valine substitution at residue 8 (p.M8V), which weakens the affinity of KPC1 for its substrate NF-κB1 p105, thereby reducing ubiquitination and proteasomal processing of p105 to p50 and enhancing oncogenic NF-κB signaling.","method":"Sanger sequencing validation of RNA editing, molecular interaction assays, in vitro and in vivo functional assays in iCCA cells, NF-κB signaling analysis","journal":"Journal of experimental & clinical cancer research : CR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — editing site validated by sequencing, binding affinity measured, and functional outcomes confirmed in vitro and in vivo, single lab","pmids":["36476255"],"is_preprint":false},{"year":2020,"finding":"RNF123 interacts with Dvl2 and participates in CCNG2-induced polyubiquitination and proteasomal degradation of Dvl2, thereby suppressing JNK-dependent Wnt/PCP signaling in trophoblast cells. RNF123 siRNA reversed CCNG2-induced Dvl2 degradation and restored Wnt/PCP-JNK signaling.","method":"Co-immunoprecipitation, polyubiquitination assay, siRNA knockdown, Western blot, Wnt/PCP-JNK signaling readouts in HTR8/SVneo cells","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP, ubiquitination assay, and siRNA rescue in cell line model, single lab","pmids":["33205477"],"is_preprint":false},{"year":2023,"finding":"RNF123 binds the SH2 domain of SOCS1 via its RING domain, facilitates K48-linked ubiquitination specifically at K114 and K137 residues of SOCS1, and promotes SOCS1 proteasomal degradation, thereby promoting TLR3- and IRF7-mediated type I IFN production during duck Tembusu virus infection.","method":"Co-immunoprecipitation, in vivo ubiquitination assay with site-specific lysine mutants (K114R, K137R), proteasome inhibitor treatment, IRF7/TLR3 reporter assays","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mapping, site-specific K→R mutagenesis, Co-IP, and ubiquitination linkage determination in one study, single lab","pmids":["37014223"],"is_preprint":false},{"year":2024,"finding":"RNF123 directly interacts with and ubiquitinates PFKP (6-Phosphofructo-2-kinase), leading to PFKP degradation and inhibition of glycolysis, which suppresses breast cancer cell viability, cell cycle progression, and colony formation.","method":"Co-immunoprecipitation, ubiquitination assay, lentiviral overexpression/knockdown, glycolysis assays (ECAR, lactate, ATP), xenograft tumor model","journal":"Naunyn-Schmiedeberg's archives of pharmacology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP, ubiquitination assay, rescue experiment with PFKP overexpression, and in vivo model, single lab","pmids":["39725718"],"is_preprint":false},{"year":2024,"finding":"KPC1 (RNF123) forms a complex with vimentin, ubiquitinates it, and promotes its degradation. KPC1 overexpression in HEK293T cells downregulates vimentin, while KPC1 deletion in HAP1 cells upregulates vimentin. Downregulation of vimentin mediates at least part of KPC1's anti-migratory and anti-tumorigenic effects.","method":"Co-immunoprecipitation, in vitro ubiquitination assay, KPC1 overexpression in HEK293T, CRISPR-based KPC1 deletion in HAP1 cells, tumor model in mice","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1–2 / Weak — in vitro ubiquitination assay plus genetic KO, but single lab, single study, limited mechanistic depth","pmids":["39732122"],"is_preprint":false},{"year":2025,"finding":"RNF123 catalyzes unanchored K63-linked ubiquitination of NEK7, which prevents NEK7-mediated dissociation of inactive cage-like NLRP3 aggregates and subsequent NLRP3 inflammasome assembly. The Crohn's disease-associated variant RNF123-R854H aggravates colitis through the NLRP3-dependent pathway. K63-linked polyubiquitin chains can be captured by NEK7 in vitro and inhibit NEK7-licensed NLRP3 inflammasome assembly.","method":"In vitro ubiquitination assay with unanchored polyubiquitin chain analysis, Co-immunoprecipitation, RNF123-deficient mice, R854H knock-in mouse model, DSS colitis, LPS endotoxemia, Alum peritonitis models, in vitro NEK7 capture assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro reconstitution of ubiquitination, in vitro NEK7 capture assay, multiple in vivo mouse disease models, disease-associated variant functional characterization in single rigorous study","pmids":["41719337"],"is_preprint":false},{"year":2025,"finding":"KPC1 (RNF123) binds ZEB1 and promotes its ubiquitination and proteasomal degradation, thereby suppressing cadherin switching and cell motility in melanoma. Loss of KPC1 prevents ZEB1 proteasomal degradation and increases mesenchymal marker expression and cell migration.","method":"Co-immunoprecipitation, ubiquitination assay, KPC1 knockdown/overexpression, single-cell transcriptomic analyses, migration assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP, ubiquitination assay, KO/KD functional rescue, single lab","pmids":["41429767"],"is_preprint":false},{"year":2025,"finding":"RNF123 targets PKM2 for ubiquitination in high-glucose-stimulated Müller cells, promoting PKM2 degradation and thereby reducing glycolysis and Müller cell activation. HG-induced downregulation of RNF123 is mediated upstream by ALKBH5 and IGF2BP1 via m6A modification, which is itself controlled by histone lactylation.","method":"Co-immunoprecipitation, ubiquitination assay, RNF123 overexpression and knockdown in MIO-M1 cells, ALKBH5/IGF2BP1 modulation, diabetic rat in vivo model","journal":"Journal of translational medicine","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP and ubiquitination assay, in vitro and in vivo models, upstream epistasis established, single lab","pmids":["41094513"],"is_preprint":false},{"year":2025,"finding":"RNF123 directly binds the N-terminal domain of PRDX1 and adds a K48-linked ubiquitin chain at the K7 site of PRDX1, promoting its proteasomal degradation. RNF123-mediated PRDX1 degradation increases ROS levels in cardiomyocytes, driving pathological cardiac hypertrophy. RNF123 deficiency mitigates Ang II- and TAC-induced cardiac hypertrophy and dysfunction in mice.","method":"LC-MS/MS combined with Co-IP to identify PRDX1, K48-linkage-specific ubiquitination assay with K7R mutant, RNF123 knockout mice, Ang II infusion and TAC surgery models, NRVMs KD/OE","journal":"Acta physiologica (Oxford, England)","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — LC-MS/MS identification, Co-IP, site-specific K→R mutagenesis, K48-linkage specificity, in vivo KO mouse models, single study with multiple orthogonal methods","pmids":["42106994"],"is_preprint":false},{"year":2011,"finding":"Following spinal cord injury, KPC1 is upregulated predominantly in astrocytes, and increased interaction between KPC1 and p27(Kip1) was detected by co-immunoprecipitation 4 days post-injury. KPC1 upregulation correlates inversely with p27(Kip1) and is associated with astrocyte proliferation, as demonstrated in LPS-stimulated astrocytes in vitro.","method":"Co-immunoprecipitation, Western blot, immunohistochemistry, immunofluorescence in rat SCI model and LPS-stimulated astrocytes","journal":"Neurochemical research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP with correlative readouts, no direct ubiquitination assay, single lab","pmids":["21229311"],"is_preprint":false},{"year":2011,"finding":"miR-155 targets KPC1 (Kip1 ubiquitination-promoting complex 1) as a functional target and indirectly regulates p27(Kip1) protein levels by reducing KPC1 expression in dendritic cells, thereby contributing to DC apoptosis.","method":"miRNA overexpression and silencing in human DCs, miR-155 knockout mice DCs, Western blot for p27(Kip1) and KPC1 protein levels","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO mice and overexpression/silencing in human cells, functional validation of miR-155 → KPC1 → p27 axis, single lab","pmids":["21355095"],"is_preprint":false}],"current_model":"RNF123/KPC1 is a RING-finger E3 ubiquitin ligase with multiple characterized substrates and mechanisms: it binds the ankyrin repeats of NF-κB1 p105 via a seven-amino-acid site (WILVRLW) and mediates its K48-linked ubiquitination and limited proteasomal processing to the p50 subunit (tumor-suppressive when in excess); ubiquitinates and promotes proteasomal degradation of p27(Kip1), vimentin, ZEB1, Dvl2, PFKP, PKM2, PRDX1, SOCS1, and the ETV6-NTRK3 oncoprotein; acts as an E3 ligase-independent inhibitor of RIG-I/MDA5 antiviral signaling by competing with MAVS for CARD-domain binding; catalyzes unanchored K63-linked ubiquitination of NEK7 to prevent NLRP3 inflammasome assembly; is itself stabilized by the deubiquitinase USP19; and is subject to regulatory inactivation by ADAR1-mediated A-to-I RNA editing and by miR-155-5p targeting, collectively establishing RNF123/KPC1 as a multifunctional ubiquitin ligase with critical roles in cell cycle control, NF-κB signaling, innate immunity, inflammasome regulation, and cancer suppression."},"narrative":{"mechanistic_narrative":"RNF123 (KPC1) is a RING-finger E3 ubiquitin ligase that controls cell proliferation, NF-κB signaling, innate immunity, and tumor suppression through substrate-specific ubiquitination [PMID:25860612, PMID:19015242]. Its founding activity is the limited proteasomal processing of NF-κB1 p105 to the p50 subunit: RNF123 binds the p105 ankyrin repeats through a seven-residue site (WILVRLW, residues 968–974) and ubiquitinates it, and excess p50 generation reprograms NF-κB transcription toward tumor suppression—downregulating PD-L1 and inducing CCL3/CCL4/CCL5 to recruit NK cells and macrophages [PMID:25860612, PMID:33168738, PMID:34873064]. This processing activity is opposed by ADAR1-mediated A-to-I editing (p.M8V), which weakens p105 affinity and enhances oncogenic NF-κB signaling [PMID:36476255]. Beyond p105, RNF123 ubiquitinates a broad substrate set for proteasomal degradation, including p27(Kip1) (linking it to G1/S cell-cycle control), the ETV6-NTRK3 oncoprotein, vimentin, ZEB1, Dvl2, the glycolytic enzymes PFKP and PKM2, and PRDX1, thereby restraining proliferation, migration, glycolysis, and oxidative stress across cancer and cardiomyocyte settings [PMID:19015242, PMID:29903916, PMID:39725718, PMID:39732122, PMID:41429767, PMID:33205477, PMID:41094513, PMID:42106994]. In innate immunity RNF123 acts through two distinct mechanisms: an E3-ligase-independent inhibition of RIG-I/MDA5 signaling, in which its SPRY and coiled-coil domains compete with MAVS for CARD-domain binding to limit IFN-β [PMID:27312109], and a catalytic role generating unanchored K63-linked polyubiquitin that captures NEK7 to block NLRP3 inflammasome assembly, with the Crohn's-associated R854H variant aggravating colitis [PMID:41719337]. RNF123 protein stability is itself regulated by the deubiquitinase USP19 and its expression is suppressed by miR-155 [PMID:19015242, PMID:21355095].","teleology":[{"year":2008,"claim":"Established that RNF123/KPC1 protein abundance is itself ubiquitin-regulated, identifying USP19 as a stabilizing deubiquitinase that couples KPC1 levels to p27(Kip1) turnover and cell-cycle progression.","evidence":"Reciprocal Co-IP, RNAi depletion, proteasome inhibition, and cell-cycle rescue with KPC1 overexpression and p27-null cells","pmids":["19015242"],"confidence":"High","gaps":["Did not map the USP19 cleavage sites on KPC1","Did not establish whether USP19 regulation extends to non-p27 substrates"]},{"year":2011,"claim":"Connected KPC1 to physiological proliferative contexts by showing its upregulation correlates inversely with p27(Kip1) in proliferating astrocytes, and that miR-155 represses KPC1 to control p27 in dendritic cells.","evidence":"Co-IP and IHC in a rat spinal-cord-injury model; miR-155 overexpression/silencing and knockout-mouse DCs with p27 Western blots","pmids":["21229311","21355095"],"confidence":"Medium","gaps":["The SCI study is correlative with no direct ubiquitination assay","Functional consequence of the miR-155→KPC1 axis beyond DC apoptosis not defined"]},{"year":2012,"claim":"Identified an N-terminal PXVXL motif as a substrate-recognition element, showing RNF123 binds and degrades HP1α/β and links its activity to nuclear lamina state.","evidence":"Ectopic GFP-RNF123 expression, RNAi, PXVXL mutagenesis, and FRAP in HeLa cells","pmids":["23077635"],"confidence":"High","gaps":["Ubiquitin-chain linkage on HP1 not determined","Physiological context beyond lamin A/C knockdown not explored"]},{"year":2015,"claim":"Defined RNF123's signature mechanism: it is the E3 ligase that ubiquitinates NF-κB1 p105 for limited proteasomal processing to p50, and excess p50 acts as a tumor suppressor by replacing the oncogenic p50-p65 dimer.","evidence":"Co-IP, in vitro ubiquitination, overexpression, and tumor xenograft models with transcript analysis","pmids":["25860612"],"confidence":"High","gaps":["Did not define the minimal binding site on KPC1 (resolved later)","Mechanism distinguishing limited processing from full degradation not detailed"]},{"year":2016,"claim":"Revealed a non-catalytic function: RNF123 inhibits RIG-I/MDA5 antiviral signaling by competing with MAVS for CARD binding, independent of its RING domain.","evidence":"Endogenous and exogenous Co-IP, KO cells, domain-deletion mutants, and IFN-β reporter assays with SeV/EMCV","pmids":["27312109"],"confidence":"High","gaps":["Structural basis of CARD competition not resolved","How viral infection induces the RNF123-CARD association is unknown"]},{"year":2018,"claim":"Extended RNF123's substrate range to an oncofusion protein, showing it ubiquitinates ETV6-NTRK3 and that IGF1R signaling shields the substrate from degradation.","evidence":"SILAC-MS interactomics, in vitro ubiquitination, knockdown rescue, and IGF1R inhibition across multiple cell lines","pmids":["29903916"],"confidence":"High","gaps":["How IGF1R signaling protects EN mechanistically not defined","Ubiquitin-chain linkage type on EN not specified"]},{"year":2020,"claim":"Expanded the substrate repertoire and tumor-suppressive output: RNF123 degrades Bax (anti-apoptotic in cardiomyocytes) and Dvl2 (suppressing Wnt/PCP-JNK), and excess p50 downregulates PD-L1 while recruiting innate immune cells; the miR-155/RNF123/p50 axis modulates SerpinE1 in glioblastoma.","evidence":"Overexpression/knockdown with proteasome inhibition in H9c2 and I/R models; Co-IP and ubiquitination with siRNA rescue in trophoblasts; xenograft and immune-recruitment assays; RNA-seq and RPPA in glioblastoma lines","pmids":["31148189","33205477","33168738","32349217"],"confidence":"Medium","gaps":["No direct ubiquitination assay for Bax","Whether these substrates are degraded in the same physiological setting unclear"]},{"year":2021,"claim":"Mapped the p105-binding determinant to a seven-residue stretch (WILVRLW, 968–974) sufficient for substrate recognition, enabling a minimal RING fusion and a PROTAC that drives p105 processing to p50.","evidence":"Domain deletion/mutagenesis, in vitro and cell-free ubiquitination/processing assays with PROTAC, and xenograft tumor model","pmids":["34873064"],"confidence":"High","gaps":["Structural detail of the WILVRLW-ankyrin interaction not resolved","Whether this motif governs recognition of other substrates not tested"]},{"year":2022,"claim":"Demonstrated a post-transcriptional off-switch: ADAR1 A-to-I editing produces an M8V substitution that lowers KPC1 affinity for p105, reducing p50 generation and enhancing oncogenic NF-κB signaling in cholangiocarcinoma.","evidence":"Sanger validation of editing, binding-affinity and NF-κB signaling assays in iCCA cells with in vivo functional readouts","pmids":["36476255"],"confidence":"Medium","gaps":["Editing frequency across tissues not established","Single-lab characterization of the affinity change"]},{"year":2024,"claim":"Tied RNF123 to metabolic and cytoskeletal control of tumor phenotypes by identifying PFKP and vimentin as degradation substrates, linking it to glycolytic suppression and anti-migratory effects.","evidence":"Co-IP and ubiquitination assays with overexpression/knockdown or CRISPR deletion plus glycolysis assays and xenograft/tumor mouse models","pmids":["39725718","39732122"],"confidence":"Medium","gaps":["Ubiquitin-chain linkage on PFKP and vimentin not specified","Single-lab studies without reciprocal validation"]},{"year":2025,"claim":"Established RNF123 as a catalytic regulator of the NLRP3 inflammasome via unanchored K63 ubiquitin chains that capture NEK7, and defined disease-linked, oxidative, and EMT substrate axes (PRDX1, PKM2, ZEB1) plus the Crohn's-associated R854H variant.","evidence":"In vitro unanchored-chain and NEK7-capture assays, RNF123-deficient and R854H knock-in mice in colitis/endotoxemia/peritonitis models; LC-MS/MS plus site-specific K→R ubiquitination assays and KO mice for PRDX1; Co-IP/ubiquitination for PKM2 and ZEB1","pmids":["41719337","42106994","41094513","41429767"],"confidence":"High","gaps":["How RNF123 switches between substrate-anchored and unanchored chain synthesis is unknown","Coordination among the many substrates within a single cell type not resolved"]},{"year":null,"claim":"How RNF123 selects among its diverse substrates and switches between E3-ligase-dependent degradation, limited processing, unanchored-chain synthesis, and ligase-independent competition remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model integrating the substrate-recognition motifs (WILVRLW, PXVXL, SPRY/coiled-coil)","No unifying account of how cellular context dictates which mechanism dominates","Upstream signals controlling RNF123 activity versus abundance incompletely defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,4,11,13,17]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,8,14,17]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3,14]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,8,17]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,3,10]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,14,11]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[1,19]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[4,9,14]}],"complexes":[],"partners":["NFKB1","USP19","NEK7","SOCS1","DVL2","PFKP","PKM2","PRDX1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5XPI4","full_name":"E3 ubiquitin-protein ligase RNF123","aliases":["Kip1 ubiquitination-promoting complex protein 1","RING finger protein 123"],"length_aa":1314,"mass_kda":148.5,"function":"Catalytic subunit of the KPC complex that acts as E3 ubiquitin-protein ligase (PubMed:15531880, PubMed:16227581, PubMed:25860612). Promotes the ubiquitination and proteasome-mediated degradation of CDKN1B which is the cyclin-dependent kinase inhibitor at the G0-G1 transition of the cell cycle (PubMed:15531880, PubMed:16227581). Also acts as a key regulator of the NF-kappa-B signaling by promoting maturation of the NFKB1 component of NF-kappa-B: acts by catalyzing ubiquitination of the NFKB1 p105 precursor, leading to limited proteasomal degradation of NFKB1 p105 and generation of the active NFKB1 p50 subunit (PubMed:25860612, PubMed:33168738, PubMed:34873064). Also functions as an inhibitor of innate antiviral signaling mediated by RIGI and IFIH1 independently of its E3 ligase activity (PubMed:27312109). Interacts with the N-terminal CARD domains of RIGI and IFIH1 and competes with the downstream adapter MAVS (PubMed:27312109)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q5XPI4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RNF123","classification":"Not Classified","n_dependent_lines":193,"n_total_lines":1208,"dependency_fraction":0.1597682119205298},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RNF123","total_profiled":1310},"omim":[{"mim_id":"614472","title":"RING FINGER PROTEIN 123; RNF123","url":"https://www.omim.org/entry/614472"},{"mim_id":"614471","title":"UBIQUITIN-SPECIFIC PROTEASE 19; USP19","url":"https://www.omim.org/entry/614471"},{"mim_id":"608129","title":"UBA DOMAIN-CONTAINING PROTEIN 1; UBAC1","url":"https://www.omim.org/entry/608129"},{"mim_id":"602559","title":"EXPORTIN 1; XPO1","url":"https://www.omim.org/entry/602559"},{"mim_id":"601436","title":"S-PHASE KINASE-ASSOCIATED PROTEIN 2; SKP2","url":"https://www.omim.org/entry/601436"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":149.4},{"tissue":"tongue","ntpm":104.4}],"url":"https://www.proteinatlas.org/search/RNF123"},"hgnc":{"alias_symbol":["FLJ12565","KPC1"],"prev_symbol":[]},"alphafold":{"accession":"Q5XPI4","domains":[{"cath_id":"2.60.120.920","chopping":"87-264","consensus_level":"high","plddt":92.8916,"start":87,"end":264},{"cath_id":"-","chopping":"591-634_707-737_835-944","consensus_level":"medium","plddt":87.7341,"start":591,"end":944},{"cath_id":"-","chopping":"1010-1195_1211-1246","consensus_level":"high","plddt":86.5806,"start":1010,"end":1246},{"cath_id":"3.30.40.10","chopping":"1253-1301","consensus_level":"high","plddt":84.5712,"start":1253,"end":1301},{"cath_id":"1.25.40","chopping":"33-44_60-71_270-426","consensus_level":"high","plddt":89.8024,"start":33,"end":426}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5XPI4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5XPI4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5XPI4-F1-predicted_aligned_error_v6.png","plddt_mean":81.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RNF123","jax_strain_url":"https://www.jax.org/strain/search?query=RNF123"},"sequence":{"accession":"Q5XPI4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5XPI4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5XPI4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5XPI4"}},"corpus_meta":[{"pmid":"11257029","id":"PMC_11257029","title":"Novel 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Overexpression of KPC1 inhibits tumor growth via excessive generation of p50, and the resulting p50 homodimer modulates transcription in place of the tumorigenic p50-p65 heterodimer.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitination assay, overexpression studies, tumor xenograft models, transcript analysis\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro ubiquitination assay, Co-IP, mutagenesis, and in vivo tumor models in a single rigorous study, subsequently replicated by multiple independent labs\",\n      \"pmids\": [\"25860612\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"USP19, a deubiquitinating enzyme, interacts with and stabilizes KPC1 protein by reversing its ubiquitination, thereby modulating p27(Kip1) levels and cell proliferation. Depletion of USP19 reduces KPC1 levels and causes G1/S accumulation that is rescued by KPC1 overexpression or p27 knockout.\",\n      \"method\": \"Co-immunoprecipitation, RNA interference, proteasome inhibitor treatment, cell cycle analysis, rescue experiments with KPC1 overexpression\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, RNAi depletion with specific rescue by KPC1 overexpression and p27-null cells, multiple orthogonal methods in one study\",\n      \"pmids\": [\"19015242\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"RNF123 ubiquitin ligase binds HP1α and HP1β via a canonical PXVXL pentapeptide motif in its N-terminus and targets them for proteasomal degradation. In lamin A/C knockdown cells, RNF123 is upregulated and mediates degradation of HP1α and HP1β (but not HP1γ). Mutation of the PXVXL motif abolishes HP1 binding and degradation.\",\n      \"method\": \"GFP-tagged RNF123 ectopic expression, RNAi knockdown of RNF123, mutational analysis of PXVXL motif, FRAP analysis, Western blot in HeLa cells\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ectopic expression, RNAi rescue, mutagenesis of binding motif, and FRAP in single study with multiple orthogonal methods\",\n      \"pmids\": [\"23077635\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RNF123 is a negative regulator of RIG-I and MDA5 antiviral signaling. RNF123 associates with the N-terminal CARD domains of RIG-I and MDA5 in a viral infection-inducible manner and competes with the downstream adaptor VISA/MAVS for CARD binding, thereby inhibiting IFN-β production. This inhibitory function requires the SPRY and coiled-coil domains of RNF123 but NOT the RING domain, indicating an E3 ligase-independent mechanism.\",\n      \"method\": \"Overexpression, knockdown and knockout of RNF123, endogenous and exogenous Co-immunoprecipitation, domain deletion mutant analysis, IFN-β reporter assays with SeV and EMCV\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP (endogenous and exogenous), KO cells, domain mutagenesis, and functional reporter assays in single study with multiple orthogonal methods\",\n      \"pmids\": [\"27312109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"KPC1/RNF123 directly ubiquitinates the ETV6-NTRK3 (EN) chimeric oncoprotein in vitro, and its overexpression decreases EN protein levels. IGF1R signaling protects EN from KPC1/RNF123-mediated proteasomal degradation; blocking IGF1R promotes rapid EN ubiquitylation and degradation that is reversed by KPC1 knockdown.\",\n      \"method\": \"SILAC-based MS interactomics, in vitro ubiquitination assay, KPC1 overexpression and knockdown, IGF1R inhibitor treatment in fibroblast, breast epithelial, and leukemia cell lines\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro ubiquitination assay, SILAC-MS, knockdown rescue, and multiple cell line models in one study\",\n      \"pmids\": [\"29903916\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"KPC1 promotes proteasomal degradation of Bax and prevents Bax translocation to mitochondria, thereby reducing apoptosis in cardiomyocytes under hypoxia/reoxygenation. This effect is abolished by the proteasome inhibitor MG132, confirming a proteasome-dependent mechanism.\",\n      \"method\": \"KPC1 overexpression and shRNA knockdown in H9c2 cells and rat I/R model, Western blot for Bax protein, MMP assay, cytochrome c release, MG132 proteasome inhibition\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo and in vitro overexpression/knockdown with proteasome inhibitor validation, but no direct ubiquitination assay for Bax\",\n      \"pmids\": [\"31148189\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RNF123 overexpression in IDH WT glioblastoma cells reduces NF-κB1 p50 levels and negatively regulates SerpinE1 expression downstream of the miR-155-5p/RNF123/NF-κB1-p50 axis, thereby reducing proliferation and invasion.\",\n      \"method\": \"RNF123 overexpression in GB cell lines, RNA-sequencing, reverse-phase protein arrays, in vitro functional assays, miR-155-5p overexpression\",\n      \"journal\": \"Cancers\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (RNA-seq, RPPA, functional assays), single lab\",\n      \"pmids\": [\"32349217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"KPC1-generated excess p50 suppresses tumor growth via multiple mechanisms: (1) downregulation of PD-L1 expression (abrogated by p65 overexpression), and (2) upregulation of pro-inflammatory chemokines CCL3, CCL4, and CCL5, which recruit NK cells and macrophages into tumors.\",\n      \"method\": \"KPC1 overexpression in cancer cells and tumor xenograft models, p65 co-overexpression rescue, gene expression analysis, immune cell recruitment assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo tumor models and mechanistic rescue experiments, single lab with multiple readouts\",\n      \"pmids\": [\"33168738\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The p105-binding site on KPC1 consists of a seven amino acid sequence (WILVRLW, residues 968–974). Attaching this short stretch to the RING-finger domain fragment was sufficient to bind p105, ubiquitinate it, and suppress tumor growth in vivo. Fusion of these seven amino acids to a pVHL-binding ligand created a PROTAC that stimulated p105 ubiquitination in cell-free systems and its processing to p50 in cells.\",\n      \"method\": \"Domain deletion and mutagenesis of KPC1, in vitro ubiquitination assay with PROTAC, cell-free processing assay, xenograft tumor model\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution, mutagenesis, cell-free and cell-based assays, in vivo tumor model in single study\",\n      \"pmids\": [\"34873064\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ADAR1-mediated A-to-I RNA editing of KPC1 results in a methionine-to-valine substitution at residue 8 (p.M8V), which weakens the affinity of KPC1 for its substrate NF-κB1 p105, thereby reducing ubiquitination and proteasomal processing of p105 to p50 and enhancing oncogenic NF-κB signaling.\",\n      \"method\": \"Sanger sequencing validation of RNA editing, molecular interaction assays, in vitro and in vivo functional assays in iCCA cells, NF-κB signaling analysis\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — editing site validated by sequencing, binding affinity measured, and functional outcomes confirmed in vitro and in vivo, single lab\",\n      \"pmids\": [\"36476255\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RNF123 interacts with Dvl2 and participates in CCNG2-induced polyubiquitination and proteasomal degradation of Dvl2, thereby suppressing JNK-dependent Wnt/PCP signaling in trophoblast cells. RNF123 siRNA reversed CCNG2-induced Dvl2 degradation and restored Wnt/PCP-JNK signaling.\",\n      \"method\": \"Co-immunoprecipitation, polyubiquitination assay, siRNA knockdown, Western blot, Wnt/PCP-JNK signaling readouts in HTR8/SVneo cells\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP, ubiquitination assay, and siRNA rescue in cell line model, single lab\",\n      \"pmids\": [\"33205477\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RNF123 binds the SH2 domain of SOCS1 via its RING domain, facilitates K48-linked ubiquitination specifically at K114 and K137 residues of SOCS1, and promotes SOCS1 proteasomal degradation, thereby promoting TLR3- and IRF7-mediated type I IFN production during duck Tembusu virus infection.\",\n      \"method\": \"Co-immunoprecipitation, in vivo ubiquitination assay with site-specific lysine mutants (K114R, K137R), proteasome inhibitor treatment, IRF7/TLR3 reporter assays\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mapping, site-specific K→R mutagenesis, Co-IP, and ubiquitination linkage determination in one study, single lab\",\n      \"pmids\": [\"37014223\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RNF123 directly interacts with and ubiquitinates PFKP (6-Phosphofructo-2-kinase), leading to PFKP degradation and inhibition of glycolysis, which suppresses breast cancer cell viability, cell cycle progression, and colony formation.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, lentiviral overexpression/knockdown, glycolysis assays (ECAR, lactate, ATP), xenograft tumor model\",\n      \"journal\": \"Naunyn-Schmiedeberg's archives of pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP, ubiquitination assay, rescue experiment with PFKP overexpression, and in vivo model, single lab\",\n      \"pmids\": [\"39725718\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"KPC1 (RNF123) forms a complex with vimentin, ubiquitinates it, and promotes its degradation. KPC1 overexpression in HEK293T cells downregulates vimentin, while KPC1 deletion in HAP1 cells upregulates vimentin. Downregulation of vimentin mediates at least part of KPC1's anti-migratory and anti-tumorigenic effects.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitination assay, KPC1 overexpression in HEK293T, CRISPR-based KPC1 deletion in HAP1 cells, tumor model in mice\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Weak — in vitro ubiquitination assay plus genetic KO, but single lab, single study, limited mechanistic depth\",\n      \"pmids\": [\"39732122\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RNF123 catalyzes unanchored K63-linked ubiquitination of NEK7, which prevents NEK7-mediated dissociation of inactive cage-like NLRP3 aggregates and subsequent NLRP3 inflammasome assembly. The Crohn's disease-associated variant RNF123-R854H aggravates colitis through the NLRP3-dependent pathway. K63-linked polyubiquitin chains can be captured by NEK7 in vitro and inhibit NEK7-licensed NLRP3 inflammasome assembly.\",\n      \"method\": \"In vitro ubiquitination assay with unanchored polyubiquitin chain analysis, Co-immunoprecipitation, RNF123-deficient mice, R854H knock-in mouse model, DSS colitis, LPS endotoxemia, Alum peritonitis models, in vitro NEK7 capture assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro reconstitution of ubiquitination, in vitro NEK7 capture assay, multiple in vivo mouse disease models, disease-associated variant functional characterization in single rigorous study\",\n      \"pmids\": [\"41719337\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"KPC1 (RNF123) binds ZEB1 and promotes its ubiquitination and proteasomal degradation, thereby suppressing cadherin switching and cell motility in melanoma. Loss of KPC1 prevents ZEB1 proteasomal degradation and increases mesenchymal marker expression and cell migration.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, KPC1 knockdown/overexpression, single-cell transcriptomic analyses, migration assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP, ubiquitination assay, KO/KD functional rescue, single lab\",\n      \"pmids\": [\"41429767\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RNF123 targets PKM2 for ubiquitination in high-glucose-stimulated Müller cells, promoting PKM2 degradation and thereby reducing glycolysis and Müller cell activation. HG-induced downregulation of RNF123 is mediated upstream by ALKBH5 and IGF2BP1 via m6A modification, which is itself controlled by histone lactylation.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, RNF123 overexpression and knockdown in MIO-M1 cells, ALKBH5/IGF2BP1 modulation, diabetic rat in vivo model\",\n      \"journal\": \"Journal of translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP and ubiquitination assay, in vitro and in vivo models, upstream epistasis established, single lab\",\n      \"pmids\": [\"41094513\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RNF123 directly binds the N-terminal domain of PRDX1 and adds a K48-linked ubiquitin chain at the K7 site of PRDX1, promoting its proteasomal degradation. RNF123-mediated PRDX1 degradation increases ROS levels in cardiomyocytes, driving pathological cardiac hypertrophy. RNF123 deficiency mitigates Ang II- and TAC-induced cardiac hypertrophy and dysfunction in mice.\",\n      \"method\": \"LC-MS/MS combined with Co-IP to identify PRDX1, K48-linkage-specific ubiquitination assay with K7R mutant, RNF123 knockout mice, Ang II infusion and TAC surgery models, NRVMs KD/OE\",\n      \"journal\": \"Acta physiologica (Oxford, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — LC-MS/MS identification, Co-IP, site-specific K→R mutagenesis, K48-linkage specificity, in vivo KO mouse models, single study with multiple orthogonal methods\",\n      \"pmids\": [\"42106994\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Following spinal cord injury, KPC1 is upregulated predominantly in astrocytes, and increased interaction between KPC1 and p27(Kip1) was detected by co-immunoprecipitation 4 days post-injury. KPC1 upregulation correlates inversely with p27(Kip1) and is associated with astrocyte proliferation, as demonstrated in LPS-stimulated astrocytes in vitro.\",\n      \"method\": \"Co-immunoprecipitation, Western blot, immunohistochemistry, immunofluorescence in rat SCI model and LPS-stimulated astrocytes\",\n      \"journal\": \"Neurochemical research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP with correlative readouts, no direct ubiquitination assay, single lab\",\n      \"pmids\": [\"21229311\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"miR-155 targets KPC1 (Kip1 ubiquitination-promoting complex 1) as a functional target and indirectly regulates p27(Kip1) protein levels by reducing KPC1 expression in dendritic cells, thereby contributing to DC apoptosis.\",\n      \"method\": \"miRNA overexpression and silencing in human DCs, miR-155 knockout mice DCs, Western blot for p27(Kip1) and KPC1 protein levels\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO mice and overexpression/silencing in human cells, functional validation of miR-155 → KPC1 → p27 axis, single lab\",\n      \"pmids\": [\"21355095\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RNF123/KPC1 is a RING-finger E3 ubiquitin ligase with multiple characterized substrates and mechanisms: it binds the ankyrin repeats of NF-κB1 p105 via a seven-amino-acid site (WILVRLW) and mediates its K48-linked ubiquitination and limited proteasomal processing to the p50 subunit (tumor-suppressive when in excess); ubiquitinates and promotes proteasomal degradation of p27(Kip1), vimentin, ZEB1, Dvl2, PFKP, PKM2, PRDX1, SOCS1, and the ETV6-NTRK3 oncoprotein; acts as an E3 ligase-independent inhibitor of RIG-I/MDA5 antiviral signaling by competing with MAVS for CARD-domain binding; catalyzes unanchored K63-linked ubiquitination of NEK7 to prevent NLRP3 inflammasome assembly; is itself stabilized by the deubiquitinase USP19; and is subject to regulatory inactivation by ADAR1-mediated A-to-I RNA editing and by miR-155-5p targeting, collectively establishing RNF123/KPC1 as a multifunctional ubiquitin ligase with critical roles in cell cycle control, NF-κB signaling, innate immunity, inflammasome regulation, and cancer suppression.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RNF123 (KPC1) is a RING-finger E3 ubiquitin ligase that controls cell proliferation, NF-\\u03baB signaling, innate immunity, and tumor suppression through substrate-specific ubiquitination [#0, #1]. Its founding activity is the limited proteasomal processing of NF-\\u03baB1 p105 to the p50 subunit: RNF123 binds the p105 ankyrin repeats through a seven-residue site (WILVRLW, residues 968\\u2013974) and ubiquitinates it, and excess p50 generation reprograms NF-\\u03baB transcription toward tumor suppression\\u2014downregulating PD-L1 and inducing CCL3/CCL4/CCL5 to recruit NK cells and macrophages [#0, #7, #8]. This processing activity is opposed by ADAR1-mediated A-to-I editing (p.M8V), which weakens p105 affinity and enhances oncogenic NF-\\u03baB signaling [#9]. Beyond p105, RNF123 ubiquitinates a broad substrate set for proteasomal degradation, including p27(Kip1) (linking it to G1/S cell-cycle control), the ETV6-NTRK3 oncoprotein, vimentin, ZEB1, Dvl2, the glycolytic enzymes PFKP and PKM2, and PRDX1, thereby restraining proliferation, migration, glycolysis, and oxidative stress across cancer and cardiomyocyte settings [#1, #4, #12, #13, #15, #10, #16, #17]. In innate immunity RNF123 acts through two distinct mechanisms: an E3-ligase-independent inhibition of RIG-I/MDA5 signaling, in which its SPRY and coiled-coil domains compete with MAVS for CARD-domain binding to limit IFN-\\u03b2 [#3], and a catalytic role generating unanchored K63-linked polyubiquitin that captures NEK7 to block NLRP3 inflammasome assembly, with the Crohn's-associated R854H variant aggravating colitis [#14]. RNF123 protein stability is itself regulated by the deubiquitinase USP19 and its expression is suppressed by miR-155 [#1, #19].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established that RNF123/KPC1 protein abundance is itself ubiquitin-regulated, identifying USP19 as a stabilizing deubiquitinase that couples KPC1 levels to p27(Kip1) turnover and cell-cycle progression.\",\n      \"evidence\": \"Reciprocal Co-IP, RNAi depletion, proteasome inhibition, and cell-cycle rescue with KPC1 overexpression and p27-null cells\",\n      \"pmids\": [\"19015242\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not map the USP19 cleavage sites on KPC1\", \"Did not establish whether USP19 regulation extends to non-p27 substrates\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Connected KPC1 to physiological proliferative contexts by showing its upregulation correlates inversely with p27(Kip1) in proliferating astrocytes, and that miR-155 represses KPC1 to control p27 in dendritic cells.\",\n      \"evidence\": \"Co-IP and IHC in a rat spinal-cord-injury model; miR-155 overexpression/silencing and knockout-mouse DCs with p27 Western blots\",\n      \"pmids\": [\"21229311\", \"21355095\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The SCI study is correlative with no direct ubiquitination assay\", \"Functional consequence of the miR-155\\u2192KPC1 axis beyond DC apoptosis not defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identified an N-terminal PXVXL motif as a substrate-recognition element, showing RNF123 binds and degrades HP1\\u03b1/\\u03b2 and links its activity to nuclear lamina state.\",\n      \"evidence\": \"Ectopic GFP-RNF123 expression, RNAi, PXVXL mutagenesis, and FRAP in HeLa cells\",\n      \"pmids\": [\"23077635\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin-chain linkage on HP1 not determined\", \"Physiological context beyond lamin A/C knockdown not explored\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined RNF123's signature mechanism: it is the E3 ligase that ubiquitinates NF-\\u03baB1 p105 for limited proteasomal processing to p50, and excess p50 acts as a tumor suppressor by replacing the oncogenic p50-p65 dimer.\",\n      \"evidence\": \"Co-IP, in vitro ubiquitination, overexpression, and tumor xenograft models with transcript analysis\",\n      \"pmids\": [\"25860612\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the minimal binding site on KPC1 (resolved later)\", \"Mechanism distinguishing limited processing from full degradation not detailed\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Revealed a non-catalytic function: RNF123 inhibits RIG-I/MDA5 antiviral signaling by competing with MAVS for CARD binding, independent of its RING domain.\",\n      \"evidence\": \"Endogenous and exogenous Co-IP, KO cells, domain-deletion mutants, and IFN-\\u03b2 reporter assays with SeV/EMCV\",\n      \"pmids\": [\"27312109\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of CARD competition not resolved\", \"How viral infection induces the RNF123-CARD association is unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended RNF123's substrate range to an oncofusion protein, showing it ubiquitinates ETV6-NTRK3 and that IGF1R signaling shields the substrate from degradation.\",\n      \"evidence\": \"SILAC-MS interactomics, in vitro ubiquitination, knockdown rescue, and IGF1R inhibition across multiple cell lines\",\n      \"pmids\": [\"29903916\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How IGF1R signaling protects EN mechanistically not defined\", \"Ubiquitin-chain linkage type on EN not specified\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Expanded the substrate repertoire and tumor-suppressive output: RNF123 degrades Bax (anti-apoptotic in cardiomyocytes) and Dvl2 (suppressing Wnt/PCP-JNK), and excess p50 downregulates PD-L1 while recruiting innate immune cells; the miR-155/RNF123/p50 axis modulates SerpinE1 in glioblastoma.\",\n      \"evidence\": \"Overexpression/knockdown with proteasome inhibition in H9c2 and I/R models; Co-IP and ubiquitination with siRNA rescue in trophoblasts; xenograft and immune-recruitment assays; RNA-seq and RPPA in glioblastoma lines\",\n      \"pmids\": [\"31148189\", \"33205477\", \"33168738\", \"32349217\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct ubiquitination assay for Bax\", \"Whether these substrates are degraded in the same physiological setting unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Mapped the p105-binding determinant to a seven-residue stretch (WILVRLW, 968\\u2013974) sufficient for substrate recognition, enabling a minimal RING fusion and a PROTAC that drives p105 processing to p50.\",\n      \"evidence\": \"Domain deletion/mutagenesis, in vitro and cell-free ubiquitination/processing assays with PROTAC, and xenograft tumor model\",\n      \"pmids\": [\"34873064\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural detail of the WILVRLW-ankyrin interaction not resolved\", \"Whether this motif governs recognition of other substrates not tested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated a post-transcriptional off-switch: ADAR1 A-to-I editing produces an M8V substitution that lowers KPC1 affinity for p105, reducing p50 generation and enhancing oncogenic NF-\\u03baB signaling in cholangiocarcinoma.\",\n      \"evidence\": \"Sanger validation of editing, binding-affinity and NF-\\u03baB signaling assays in iCCA cells with in vivo functional readouts\",\n      \"pmids\": [\"36476255\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Editing frequency across tissues not established\", \"Single-lab characterization of the affinity change\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Tied RNF123 to metabolic and cytoskeletal control of tumor phenotypes by identifying PFKP and vimentin as degradation substrates, linking it to glycolytic suppression and anti-migratory effects.\",\n      \"evidence\": \"Co-IP and ubiquitination assays with overexpression/knockdown or CRISPR deletion plus glycolysis assays and xenograft/tumor mouse models\",\n      \"pmids\": [\"39725718\", \"39732122\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitin-chain linkage on PFKP and vimentin not specified\", \"Single-lab studies without reciprocal validation\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established RNF123 as a catalytic regulator of the NLRP3 inflammasome via unanchored K63 ubiquitin chains that capture NEK7, and defined disease-linked, oxidative, and EMT substrate axes (PRDX1, PKM2, ZEB1) plus the Crohn's-associated R854H variant.\",\n      \"evidence\": \"In vitro unanchored-chain and NEK7-capture assays, RNF123-deficient and R854H knock-in mice in colitis/endotoxemia/peritonitis models; LC-MS/MS plus site-specific K\\u2192R ubiquitination assays and KO mice for PRDX1; Co-IP/ubiquitination for PKM2 and ZEB1\",\n      \"pmids\": [\"41719337\", \"42106994\", \"41094513\", \"41429767\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How RNF123 switches between substrate-anchored and unanchored chain synthesis is unknown\", \"Coordination among the many substrates within a single cell type not resolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RNF123 selects among its diverse substrates and switches between E3-ligase-dependent degradation, limited processing, unanchored-chain synthesis, and ligase-independent competition remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model integrating the substrate-recognition motifs (WILVRLW, PXVXL, SPRY/coiled-coil)\", \"No unifying account of how cellular context dictates which mechanism dominates\", \"Upstream signals controlling RNF123 activity versus abundance incompletely defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0061630\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 4, 11, 13, 17]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 8, 14, 17]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3, 14]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 8, 17]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 3, 10]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 14, 11]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [1, 19]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [4, 9, 14]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NFKB1\", \"USP19\", \"NEK7\", \"SOCS1\", \"DVL2\", \"PFKP\", \"PKM2\", \"PRDX1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}