{"gene":"NEIL2","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2003,"finding":"NEIL2 has a unique preference for excising oxidized base lesions from DNA bubble structures (single-stranded/bubble DNA), in contrast to NTH1 and OGG1 which are only active with duplex DNA. NEIL2 shows higher affinity for bubble structures of both damaged and undamaged DNA relative to duplex, suggesting preferential involvement in repair during transcription and/or replication.","method":"In vitro DNA glycosylase assays with bubble, single-stranded, and duplex DNA substrates containing oxidized bases; affinity binding studies","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro biochemical reconstitution with defined substrates, replicated across multiple subsequent studies","pmids":["14522990"],"is_preprint":false},{"year":2004,"finding":"The transcriptional coactivator p300 stably interacts with and acetylates NEIL2. Lys49 and Lys153 are the major acetylation sites. Acetylation of Lys49 (conserved among Nei orthologs), or its mutation to Arg, inactivates both base excision and AP lyase activities of NEIL2; acetylation of Lys153 has no effect. Reversible acetylation of Lys49 thus regulates NEIL2 repair activity in vivo.","method":"Co-immunoprecipitation, in vitro acetylation assay with p300, site-directed mutagenesis, in vivo and in vitro activity assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro acetylation assay with mutagenesis and functional readout, single lab with multiple orthogonal methods","pmids":["15175427"],"is_preprint":false},{"year":2004,"finding":"NEIL2 contains a zinc finger motif with a CHCC (Cys-X2-His-X16-Cys-X2-Cys) motif near its C-terminus. Individual mutations of Cys-291, His-295, Cys-315, and Cys-318 inactivate the enzyme by abolishing DNA binding. H295A and C318S mutants lack bound zinc and show significant secondary structure changes. Arg-310, in the zinc-binding pocket, is critical for activity. The zinc finger motif is essential for NEIL2 structural integrity and enzyme activity.","method":"ICP mass spectrometry (zinc quantification), site-directed mutagenesis, CD spectra analysis, molecular modeling, in vitro activity assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — multiple orthogonal methods (metal quantification, mutagenesis, CD spectroscopy, activity assays) in a single study","pmids":["15339932"],"is_preprint":false},{"year":2005,"finding":"NEIL1 and NEIL2 recognize and cleave DNA containing guanidinohydantoin (Gh)/iminoallantoin (Ia) and spiroiminodihydantoin (Sp) lesions (further oxidation products of 8-oxoguanine) via beta- and delta-elimination mechanism. NEIL2 shows little cleavage activity against Sp in duplex DNA but binds and recognizes it (shown by DNA trapping studies). Both enzymes excise Gh/Ia opposite all four natural bases in double-stranded DNA.","method":"In vitro DNA glycosylase cleavage assays with defined damaged substrates (single-stranded and duplex DNA), DNA trapping studies","journal":"DNA repair","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with defined substrates and multiple lesion types, single lab","pmids":["15533836"],"is_preprint":false},{"year":2006,"finding":"NEIL2-initiated repair of 5-hydroxyuracil (5-OHU) requires polynucleotide kinase (PNK) rather than APE1 to remove the 3'-phosphate terminus generated after strand cleavage. NEIL2 stably interacts with BER proteins DNA polymerase beta (Pol beta), DNA ligase IIIalpha (Lig IIIalpha), and XRCC1 (but not APE1). The essential N-terminal segment of NEIL2 mediates these interactions (unlike NEIL1 which uses its C-terminal region). A complex containing NEIL2, PNK, Pol beta, Lig IIIalpha, and XRCC1 can be isolated from human cells and is competent for repair of 5-OHU in plasmid DNA.","method":"In vitro repair assay with 5-OHU substrate, co-immunoprecipitation from human cells, domain mapping of protein-protein interactions, reconstituted repair assay in plasmid DNA","journal":"DNA repair","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — reconstituted repair assay, reciprocal Co-IP, domain mapping, and functional assay in single study","pmids":["16982218"],"is_preprint":false},{"year":2007,"finding":"Y box-binding protein (YB-1) is a stably interacting partner of NEIL2 (identified by mass spectrometry of NEIL2 immunocomplex). YB-1 stimulates NEIL2 base excision activity ~7-fold. YB-1 also interacts with DNA ligase IIIalpha and DNA polymerase beta, forming a large multiprotein complex. YB-1 normally cytoplasmic translocates to the nucleus during UVA-induced oxidative stress, concomitantly increasing its association with and activation of NEIL2. NEIL2-initiated base excision activity is significantly reduced in YB-1-depleted cells.","method":"Mass spectrometry of NEIL2 immunocomplex, co-immunoprecipitation, in vitro stimulation assay, YB-1 siRNA knockdown, nuclear/cytoplasmic fractionation, UVA treatment","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — MS identification of interactor, Co-IP validation, functional stimulation assay, siRNA knockdown with activity readout, single lab","pmids":["17686777"],"is_preprint":false},{"year":2006,"finding":"Recombinant NEIL2 purified from E. coli has biochemically characterized DNA glycosylase/AP lyase activity with unique preference for bubble or single-stranded DNA substrates over duplex DNA, unlike NTH1 and OGG1. NEIL2 and NEIL1 are distinct mammalian orthologs of E. coli Nei and Fpg in reaction mechanism.","method":"Purification of recombinant protein from E. coli, in vitro DNA glycosylase assays with bubble, single-stranded, and duplex DNA substrates","journal":"Methods in enzymology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution, consistent with and confirmatory of prior findings","pmids":["16793361"],"is_preprint":false},{"year":2005,"finding":"Murine NEIL2 (mNEIL2) associates with microtubules in situ and in vitro. Purified recombinant mNEIL2 co-precipitates with microtubules and associates with the microtubule network during interphase and with the spindle assembly at mitosis, as shown by in situ localization, microtubule co-precipitation, and site-directed photochemical experiments.","method":"In situ localization with fluorochrome-conjugated recombinant protein, microtubule co-precipitation, site-directed photochemical crosslinking","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-precipitation and in situ localization with recombinant protein, functional significance of microtubule association is unclear, single lab","pmids":["15725623"],"is_preprint":false},{"year":2010,"finding":"Pyridoxal-5'-phosphate (PLP) inhibits NEIL2 specifically among six bifunctional DNA repair glycosylases tested. Inhibition is through Schiff base formation between PLP and Lys50 of NEIL2, abolishing DNA binding. The beta2/beta3 loop where Lys50 is located is important for DNA binding and likely lies next to a phosphate-binding site.","method":"Enzyme inhibition assay, LC/nanoESI-MS/MS identification of modified residue, DNA binding assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1-2 / Weak — in vitro biochemical assay with MS identification of modification site, but single lab and single study","pmids":["20175991"],"is_preprint":false},{"year":2011,"finding":"NEIL2 is present in purified human mitochondrial extracts and co-localizes with the mitochondrion-specific protein MT-CO2 by confocal microscopy. ChIP analysis shows NEIL2 associates with mitochondrial genes MT-CO2 and MT-CO3, and with mitochondrial DNA polymerase gamma. Individual depletion of NEIL2 in HEK293 cells causes increased levels of oxidized bases in the mitochondrial genome, demonstrating NEIL2's role in mitochondrial genome maintenance.","method":"Mitochondrial extract purification, confocal microscopy, chromatin immunoprecipitation, proximity ligation assay, NEIL2 siRNA knockdown with mt-DNA damage quantification","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (fractionation, confocal, ChIP, PLA, siRNA knockdown with functional readout) in single lab","pmids":["22130663"],"is_preprint":false},{"year":2012,"finding":"Depletion of NEIL2 causes a 6-7-fold increase in spontaneous mutation frequency in the HPRT gene. The NEIL2 variant R257L has modestly decreased DNA glycosylase activity, but shows ~5-fold decreased repair in reconstituted BER assays due to lower affinity for Pol beta and other repair proteins. Cells expressing R257L show increased endogenous DNA damage relative to WT.","method":"siRNA depletion with HPRT mutation assay, reconstituted BER assay, biochemical characterization of variant proteins, protein-protein interaction assays","journal":"DNA repair","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — reconstituted repair assay, mutation frequency measurement, multiple orthogonal methods, single lab","pmids":["22497777"],"is_preprint":false},{"year":2014,"finding":"Cockayne Syndrome B (CSB) protein physically interacts with NEIL2 independently of DNA. CSB stimulates NEIL2 glycosylase activity on 5-hydroxyuracil lesion in a DNA bubble substrate and also stimulates a novel NEIL2 activity toward 4,6-diamino-5-formamidopyrimidine (FapyA). Immunofluorescence shows increased cytoplasmic co-localization of CSB and NEIL2 after oxidative stress. Stalling transcription with alpha-amanitin increases CSB-NEIL2 co-localization. CSB knockdown reduces NEIL2-dependent incision activity in whole cell extracts.","method":"Co-immunoprecipitation with recombinant proteins and cell extracts (DNA-independent), in vitro stimulation assay, immunofluorescence, transcription stalling with alpha-amanitin, siRNA knockdown with activity readout","journal":"Mechanisms of ageing and development","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — multiple orthogonal methods (reciprocal Co-IP, stimulation assay, immunofluorescence, knockdown), single lab","pmids":["24406253"],"is_preprint":false},{"year":2015,"finding":"Neil2-null mice accumulate oxidized DNA bases preferentially in transcriptionally active (transcribed) genomic sequences. In vivo immunopulldown from mouse tissue shows NEIL2 associates with RNA polymerase II, Cockayne syndrome group B protein (CSB), and TFIIH. ChIP from mouse tissue demonstrates co-occupancy of NEIL2 and RNA Pol II exclusively on transcribed genes. Neil2-null mouse embryonic fibroblasts show increased telomere loss and genomic instability. Neil2-null mice are more responsive to inflammatory agents, producing higher levels of inflammatory genes.","method":"Neil2-null mouse generation, co-immunoprecipitation from mouse tissue, ChIP from mouse tissue, LA-QPCR for oxidative DNA damage in transcribed regions, telomere FISH","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — knockout mouse model with multiple orthogonal in vivo and biochemical methods, replicated across multiple assays","pmids":["26245904"],"is_preprint":false},{"year":2019,"finding":"Depletion of NEIL1 and NEIL2 in Xenopus embryos and differentiating mouse ESCs causes a defect in cranial neural crest cell (cNCC) development via oxidative stress-induced TP53-dependent DNA damage response. Neil-deficiency causes oxidative damage specifically to mitochondrial DNA, triggering TP53-mediated intrinsic apoptosis. Epistasis with Tdg-deficient mESCs shows the cNCC defect is NOT due to impaired epigenetic DNA demethylation.","method":"Xenopus embryo knockdown, mouse ESC differentiation with NEIL KO, epistasis experiments with Tdg KO, TP53 inhibitor rescue, mitochondrial DNA damage assays","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple model systems, epistasis experiments, rescue experiments, single lab with multiple orthogonal methods","pmids":["31566562"],"is_preprint":false},{"year":2020,"finding":"Crystal structure of mammalian NEIL2 (opossum Monodelphis domestica) reveals an unusual 'open' conformation not seen in NEIL1 or NEIL3. Combined crystallographic and solution-scattering (SAXS) studies show NEIL2 is conformationally dynamic, predicted to adopt a 'closed' conformation upon substrate binding. Three cancer variants (S140N, G230W, G303R) were biochemically characterized.","method":"X-ray crystallography (crystal structure), small-angle X-ray scattering (SAXS), biochemical characterization of cancer variants","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure plus solution scattering, multiple orthogonal structural methods, single lab","pmids":["32846144"],"is_preprint":false},{"year":2021,"finding":"NEIL2 has a non-canonical function as a direct suppressor of NF-κB signaling. NEIL2 directly interacts with the Rel homology region of RelA (p65), blocking NF-κB binding to target gene promoters and repressing proinflammatory gene expression (Cxcl1, Cxcl2, Cxcl10, Il6, Tnfa). Neil2-null mice show significantly higher expression of proinflammatory genes. Intrapulmonary delivery of purified recombinant NEIL2 decreases NF-κB-DNA binding and reduces proinflammatory gene expression and neutrophil recruitment.","method":"Co-immunoprecipitation, ChIP, electrophoretic mobility shift assay (EMSA), Neil2-null mouse model, intrapulmonary administration of recombinant NEIL2 protein","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, ChIP, EMSA, in vivo rescue with recombinant protein), single lab","pmids":["33932404"],"is_preprint":false},{"year":2021,"finding":"NEIL2 conformation in solution is predominantly 'open'; its large N-terminal insert (absent from other DNA glycosylases) is unstructured in solution. HDX-MS combined with homology modeling and MD simulations shows NEIL2 is a conformationally flexible protein, consistent with its role in repair of non-canonical DNA structures and protein-protein interactions.","method":"Hydrogen/deuterium exchange mass spectrometry (HDX-MS), homology modeling, molecular dynamics simulations","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — HDX-MS with computational support, single lab, no functional validation of structural findings","pmids":["34757057"],"is_preprint":false},{"year":2021,"finding":"In cells depleted of OGG1 or treated with OGG1 inhibitor TH5487, NEIL2 accumulation at DNA damage sites is prolonged and NEIL2 retention at damaged chromatin is increased. NEIL2-depleted cells oxidatively stressed with OGG1 also inhibited show excessive genomic 8-oxoG accumulation, indicating NEIL2 serves as a backup BER enzyme for OGG1.","method":"Live cell imaging of NEIL2 recruitment kinetics, chromatin fractionation, siRNA depletion, pharmacological OGG1 inhibition, immunofluorescence for 8-oxoG","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — live imaging and chromatin binding assays, single lab, limited mechanistic depth","pmids":["33925271"],"is_preprint":false},{"year":2022,"finding":"NEIL2 polymorphic variant P304T (Pro304 in the beta-turn of the zinc finger motif) has ~5-fold reduced catalytic efficiency (kcat/KM) compared to wild-type, lower DNA affinity, and reduced proficiency in removing damaged bases from single-stranded and bubble-containing DNA. R103W variant is much less affected.","method":"Biochemical characterization of recombinant variant proteins, steady-state kinetics, DNA binding assays","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biochemical characterization with kinetics, single lab, single study","pmids":["35216329"],"is_preprint":false},{"year":2023,"finding":"NEIL2 directly binds to the 5'-UTR of SARS-CoV-2 genomic RNA and blocks viral protein synthesis. Delivery of recombinant NEIL2 into ACE2-expressing cells decreases expression of proinflammatory genes, viral E-gene expression, and lowers yield of viral progeny.","method":"RNA binding assay (NEIL2 binding to 5'-UTR of viral RNA), recombinant NEIL2 delivery into cells, measurement of viral replication and proinflammatory gene expression","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — novel mechanistic finding (RNA binding), functional rescue assay, single lab, single study; mechanistic detail of RNA binding is limited in abstract","pmids":["38071370"],"is_preprint":false},{"year":2023,"finding":"Crystal structure of mammalian NEIL2 in complex with an abasic site analog-containing DNA duplex at 2.08 Å reveals a large interdomain conformational shift upon DNA binding compared to the unliganded structure, with local changes in C-terminal zinc finger and N-terminal void-filling loop required to position the enzyme on DNA. Biochemical analysis shows NEIL2 has a significant preference for its lyase activity, particularly relevant for abasic sites. Detailed substrate range characterization confirms preference for oxidized cytosine products and abasic sites.","method":"X-ray crystallography (liganded structure at 2.08 Å), comparison with unliganded structure, biochemical assays with array of oxidized base lesions","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with substrate analog plus biochemical characterization, multiple orthogonal approaches in single study","pmids":["37971311"],"is_preprint":false},{"year":2023,"finding":"NEIL2 is phosphorylated by CDK5 and PKC in vitro and in SH-SY5Y neuroblastoma cells. Phosphorylation by PKC causes a substantial reduction in NEIL2 repair activity. CDK5 phosphorylation does not directly alter enzymatic activity. NEIL2 undergoes rapid dephosphorylation in response to oxidative stress in SH-SY5Y cells, indicating phosphorylation is an important modulator of NEIL2 function during oxidative stress.","method":"In vitro kinase assays with CDK5 and PKC, in vivo phosphorylation in SH-SY5Y cells, DNA repair activity assay after phosphorylation, oxidative stress treatment with phosphorylation status monitoring","journal":"Antioxidants","confidence":"Medium","confidence_rationale":"Tier 1-2 / Weak — in vitro and in vivo phosphorylation with functional activity readout, single lab, single study","pmids":["36829914"],"is_preprint":false},{"year":2019,"finding":"Sirt3 deacetylates NEIL2 (along with NEIL1, OGG1, MUTYH, APE1, and LIG3) in colorectal cancer cells, modulating mitochondrial BER activity; NEIL2 is identified as a substrate for Sirt3-mediated deacetylation.","method":"Deacetylation assay with Sirt3 and NEIL2 as substrate","journal":"Polski przeglad chirurgiczny","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single assay, limited methodological detail in abstract, single study covering multiple proteins","pmids":["32312920"],"is_preprint":false}],"current_model":"NEIL2 is a bifunctional DNA glycosylase/AP lyase of the Fpg/Nei family that initiates base excision repair (BER) of oxidized base lesions—particularly oxidized cytosines, formamidopyrimidines, and abasic sites—with a unique preference for bubble and single-stranded DNA substrates, implicating it in transcription-coupled repair; it assembles into an APE1-independent repair complex with PNK, Pol beta, Lig IIIalpha, and XRCC1 (stimulated by YB-1 under oxidative stress and by CSB during transcription), is regulated by p300-mediated acetylation of Lys49 and by PKC/CDK5-mediated phosphorylation, requires a structural zinc finger (CHCC motif) for DNA binding and catalytic integrity, localizes to both nuclear and mitochondrial compartments to protect both genomes, and exerts non-canonical roles including direct binding to the RelA Rel homology domain to suppress NF-κB-driven inflammation and binding to the 5'-UTR of SARS-CoV-2 RNA to block viral protein synthesis."},"narrative":{"mechanistic_narrative":"NEIL2 is a bifunctional DNA glycosylase/AP lyase of the Fpg/Nei family that initiates base excision repair (BER) of oxidized base lesions, with a distinctive preference for excising damage from DNA bubble and single-stranded substrates rather than duplex DNA, implicating it in repair coupled to transcription and replication [PMID:14522990, PMID:16793361]. Its substrate range spans oxidized cytosines, hydantoin lesions (Gh/Ia and Sp), 5-hydroxyuracil, formamidopyrimidines, and abasic sites, with biochemical and structural analysis revealing a strong bias toward its lyase activity at abasic sites [PMID:15533836, PMID:37971311]. Catalysis and DNA binding depend on a structural C-terminal CHCC zinc finger, and crystallographic and solution studies show NEIL2 is conformationally dynamic, shifting from an 'open' unliganded state to a 'closed' state that positions the enzyme on DNA [PMID:15339932, PMID:32846144, PMID:37971311]. NEIL2 organizes an APE1-independent repair complex: after strand cleavage it requires polynucleotide kinase (PNK) to process the 3'-phosphate, and its N-terminal segment mediates stable interactions with Pol beta, Lig IIIalpha, and XRCC1 to complete repair [PMID:16982218]. This complex is stimulated by YB-1, which translocates to the nucleus and activates NEIL2 under oxidative stress, and by Cockayne syndrome B protein (CSB), which links NEIL2 to transcription-coupled repair [PMID:17686777, PMID:24406253]. Consistent with a transcription-associated role, NEIL2 co-occupies transcribed genes with RNA polymerase II, CSB, and TFIIH, and Neil2-null mice accumulate oxidative damage preferentially in transcribed sequences and show telomere loss and genomic instability [PMID:26245904]. NEIL2 also localizes to mitochondria, associating with mitochondrial genes and Pol gamma to protect the mitochondrial genome, loss of which triggers TP53-dependent apoptosis during neural crest development [PMID:22130663, PMID:31566562]. Activity is tuned by post-translational modification, including inactivating p300-mediated acetylation of Lys49 and PKC-mediated phosphorylation that suppresses repair [PMID:15175427, PMID:36829914]. Beyond repair, NEIL2 exerts non-canonical functions: it directly binds the Rel homology region of RelA (p65) to block NF-κB promoter binding and suppress proinflammatory gene expression, and it binds the SARS-CoV-2 5'-UTR to block viral protein synthesis [PMID:33932404, PMID:38071370].","teleology":[{"year":2003,"claim":"Established that NEIL2 has a substrate preference distinct from other oxidized-base glycosylases, defining its niche in repair of non-duplex DNA structures arising during transcription and replication.","evidence":"In vitro glycosylase and affinity assays comparing bubble, single-stranded, and duplex substrates","pmids":["14522990"],"confidence":"High","gaps":["Did not establish which cellular processes generate the bubble substrates NEIL2 acts on","In vivo relevance of the bubble preference not yet demonstrated"]},{"year":2004,"claim":"Identified acetylation by p300 at Lys49 as a reversible switch that inactivates NEIL2, providing a mechanism for regulating repair activity in vivo.","evidence":"Co-IP, in vitro p300 acetylation, site-directed mutagenesis with activity readout","pmids":["15175427"],"confidence":"High","gaps":["Deacetylase counteracting p300 not identified in this study","Physiological stimuli controlling Lys49 acetylation not defined"]},{"year":2004,"claim":"Defined the C-terminal CHCC zinc finger as essential for DNA binding, structural integrity, and catalysis, explaining the structural basis of NEIL2 activity.","evidence":"Zinc quantification, mutagenesis, CD spectroscopy, molecular modeling, activity assays","pmids":["15339932"],"confidence":"High","gaps":["High-resolution structure of the zinc finger not yet available at this stage","How the zinc finger contributes to bubble-substrate recognition unresolved"]},{"year":2006,"claim":"Showed NEIL2 nucleates an APE1-independent BER pathway requiring PNK for 3'-end processing and assembling Pol beta, Lig IIIalpha, and XRCC1 via its N-terminus, distinguishing its repair route from NEIL1.","evidence":"Reconstituted repair of 5-OHU, reciprocal Co-IP from human cells, domain mapping","pmids":["16982218"],"confidence":"High","gaps":["Stoichiometry and assembly order of the complex not defined","Whether the complex is preformed or damage-induced not resolved"]},{"year":2007,"claim":"Identified YB-1 as a stress-responsive activator that translocates to the nucleus and stimulates NEIL2-initiated repair, linking oxidative stress signaling to NEIL2 function.","evidence":"MS of NEIL2 immunocomplex, Co-IP, in vitro stimulation, siRNA knockdown, fractionation under UVA","pmids":["17686777"],"confidence":"High","gaps":["Mechanism by which YB-1 stimulates excision not defined","Signaling pathway driving YB-1 nuclear translocation not mapped"]},{"year":2011,"claim":"Demonstrated NEIL2 localizes to mitochondria and maintains the mitochondrial genome, extending its protective role beyond the nucleus.","evidence":"Mitochondrial fractionation, confocal co-localization, ChIP, PLA, siRNA with mtDNA damage readout","pmids":["22130663"],"confidence":"High","gaps":["Mitochondrial import mechanism not defined","Mitochondrial BER partners of NEIL2 not fully enumerated"]},{"year":2012,"claim":"Linked NEIL2 loss to elevated spontaneous mutation and showed the R257L variant impairs repair by weakening interaction with Pol beta, connecting protein-protein contacts to genome stability.","evidence":"siRNA depletion with HPRT mutation assay, reconstituted BER, variant biochemistry","pmids":["22497777"],"confidence":"High","gaps":["Frequency and clinical significance of R257L in populations not addressed","Structural basis of reduced Pol beta affinity not determined"]},{"year":2014,"claim":"Established CSB as a DNA-independent NEIL2 partner that stimulates its glycosylase activity and links NEIL2 to transcription-coupled repair.","evidence":"Reciprocal Co-IP, in vitro stimulation, immunofluorescence under stress and transcription stalling, knockdown","pmids":["24406253"],"confidence":"High","gaps":["Mechanism of CSB-mediated stimulation not defined","Cytoplasmic co-localization significance unclear"]},{"year":2015,"claim":"Demonstrated in vivo that NEIL2 associates with the transcription machinery (RNA Pol II, CSB, TFIIH) and preferentially repairs transcribed genes, with loss causing telomere instability.","evidence":"Neil2-null mice, tissue Co-IP and ChIP, LA-QPCR for transcribed-region damage, telomere FISH","pmids":["26245904"],"confidence":"High","gaps":["How NEIL2 is recruited specifically to active genes not resolved","Mechanism connecting NEIL2 loss to telomere attrition not defined"]},{"year":2019,"claim":"Showed NEIL-dependent mitochondrial genome protection is required for cranial neural crest development via prevention of TP53-driven apoptosis, independent of epigenetic demethylation.","evidence":"Xenopus and mouse ESC knockdown/KO, Tdg epistasis, TP53 inhibitor rescue, mtDNA damage assays","pmids":["31566562"],"confidence":"High","gaps":["Relative contributions of NEIL1 vs NEIL2 not fully separated","Whether the requirement is mitochondrial-genome-specific in all lineages unclear"]},{"year":2020,"claim":"Provided the first mammalian NEIL2 crystal structure, revealing an unusual open conformation and conformational dynamics predicted to close on substrate.","evidence":"X-ray crystallography and SAXS, biochemical characterization of cancer variants","pmids":["32846144"],"confidence":"High","gaps":["Liganded conformation not yet captured at this stage","Functional consequence of dynamics not directly tested"]},{"year":2021,"claim":"Defined a non-canonical anti-inflammatory function: NEIL2 directly binds the RelA Rel homology region to block NF-κB promoter binding and suppress proinflammatory genes.","evidence":"Co-IP, ChIP, EMSA, Neil2-null mice, intrapulmonary recombinant NEIL2 rescue","pmids":["33932404"],"confidence":"High","gaps":["Whether this function requires catalytic activity not resolved","Structural detail of the NEIL2-RelA interface not determined"]},{"year":2021,"claim":"Characterized NEIL2 as intrinsically flexible with a disordered N-terminal insert, supporting its capacity for protein-protein interactions and non-canonical substrate engagement.","evidence":"HDX-MS, homology modeling, MD simulations","pmids":["34757057"],"confidence":"Medium","gaps":["No functional validation of the structural dynamics","Single lab, computational support only"]},{"year":2021,"claim":"Positioned NEIL2 as a backup glycosylase for OGG1, with prolonged NEIL2 retention at damage when OGG1 is absent or inhibited.","evidence":"Live-cell recruitment imaging, chromatin fractionation, siRNA, OGG1 inhibition, 8-oxoG immunofluorescence","pmids":["33925271"],"confidence":"Medium","gaps":["Single lab with limited mechanistic depth","Quantitative division of labor between OGG1 and NEIL2 not defined"]},{"year":2022,"claim":"Showed the zinc-finger beta-turn variant P304T markedly reduces NEIL2 catalytic efficiency and DNA affinity, linking specific residues to functional integrity.","evidence":"Steady-state kinetics and DNA binding of recombinant variants","pmids":["35216329"],"confidence":"Medium","gaps":["Single in vitro study without cellular validation","Disease association of P304T not established"]},{"year":2023,"claim":"Captured the liganded NEIL2 structure, revealing a large interdomain shift on DNA binding and confirming a strong preference for lyase activity at abasic sites.","evidence":"X-ray crystallography of abasic-analog DNA complex at 2.08 Å, comparison with apo structure, biochemical assays","pmids":["37971311"],"confidence":"High","gaps":["Structure with a bona fide oxidized-base substrate not solved","How the open→closed transition is triggered in bubble DNA unresolved"]},{"year":2023,"claim":"Identified PKC and CDK5 phosphorylation as modulators of NEIL2, with PKC reducing repair activity and stress-induced dephosphorylation restoring function.","evidence":"In vitro kinase assays, in-cell phosphorylation in SH-SY5Y, activity assays, oxidative stress monitoring","pmids":["36829914"],"confidence":"Medium","gaps":["Phosphorylation sites not mapped","Phosphatase responsible for stress-induced dephosphorylation not identified"]},{"year":2023,"claim":"Revealed an antiviral role: NEIL2 binds the SARS-CoV-2 5'-UTR to block viral protein synthesis and reduce viral yield and inflammation.","evidence":"RNA binding assay, recombinant NEIL2 delivery, viral replication and proinflammatory gene readouts","pmids":["38071370"],"confidence":"Medium","gaps":["Structural basis and sequence specificity of RNA binding not defined","Whether this reflects a general RNA-binding capacity unknown"]},{"year":null,"claim":"How NEIL2's repair, transcription-coupling, anti-inflammatory, and antiviral functions are coordinated and selectively engaged in vivo remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model integrating catalytic and non-canonical functions","Recruitment mechanism to active genes and to RelA/RNA targets not mechanistically connected","No human disease causation established despite multiple characterized variants"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140097","term_label":"catalytic activity, acting on DNA","supporting_discovery_ids":[0,3,4,6,20]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[2,18,20]},{"term_id":"GO:0016829","term_label":"lyase activity","supporting_discovery_ids":[3,20]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[19]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[15]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5,12]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[9,13]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0,4,6,12,20]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[15,19]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[5,11,17,21]}],"complexes":["NEIL2-PNK-Pol beta-Lig IIIalpha-XRCC1 BER complex"],"partners":["PNKP","POLB","LIG3","XRCC1","YBX1","ERCC6","EP300","RELA"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q969S2","full_name":"Endonuclease 8-like 2","aliases":["DNA glycosylase/AP lyase Neil2","DNA-(apurinic or apyrimidinic site) lyase Neil2","Endonuclease VIII-like 2","Nei homolog 2","NEH2","Nei-like protein 2"],"length_aa":332,"mass_kda":36.8,"function":"Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Has DNA glycosylase activity towards 5-hydroxyuracil and other oxidized derivatives of cytosine with a preference for mismatched double-stranded DNA (DNA bubbles). Has low or no DNA glycosylase activity towards thymine glycol, 2-hydroxyadenine, hypoxanthine and 8-oxoguanine. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q969S2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NEIL2","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/NEIL2","total_profiled":1310},"omim":[{"mim_id":"608933","title":"ENDONUCLEASE VIII-LIKE 2; NEIL2","url":"https://www.omim.org/entry/608933"},{"mim_id":"608844","title":"NEI-LIKE DNA GLYCOSYLASE 1; NEIL1","url":"https://www.omim.org/entry/608844"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NEIL2"},"hgnc":{"alias_symbol":["NEH2","FLJ31644","MGC2832","MGC4505"],"prev_symbol":[]},"alphafold":{"accession":"Q969S2","domains":[{"cath_id":"3.20.190.10","chopping":"3-59_128-184","consensus_level":"high","plddt":93.7905,"start":3,"end":184},{"cath_id":"1.10.8.50","chopping":"192-313","consensus_level":"high","plddt":96.6444,"start":192,"end":313}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q969S2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q969S2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q969S2-F1-predicted_aligned_error_v6.png","plddt_mean":81.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NEIL2","jax_strain_url":"https://www.jax.org/strain/search?query=NEIL2"},"sequence":{"accession":"Q969S2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q969S2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q969S2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q969S2"}},"corpus_meta":[{"pmid":"9887101","id":"PMC_9887101","title":"Keap1 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NEIL2 shows higher affinity for bubble structures of both damaged and undamaged DNA relative to duplex, suggesting preferential involvement in repair during transcription and/or replication.\",\n      \"method\": \"In vitro DNA glycosylase assays with bubble, single-stranded, and duplex DNA substrates containing oxidized bases; affinity binding studies\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro biochemical reconstitution with defined substrates, replicated across multiple subsequent studies\",\n      \"pmids\": [\"14522990\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"The transcriptional coactivator p300 stably interacts with and acetylates NEIL2. Lys49 and Lys153 are the major acetylation sites. Acetylation of Lys49 (conserved among Nei orthologs), or its mutation to Arg, inactivates both base excision and AP lyase activities of NEIL2; acetylation of Lys153 has no effect. Reversible acetylation of Lys49 thus regulates NEIL2 repair activity in vivo.\",\n      \"method\": \"Co-immunoprecipitation, in vitro acetylation assay with p300, site-directed mutagenesis, in vivo and in vitro activity assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro acetylation assay with mutagenesis and functional readout, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"15175427\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"NEIL2 contains a zinc finger motif with a CHCC (Cys-X2-His-X16-Cys-X2-Cys) motif near its C-terminus. Individual mutations of Cys-291, His-295, Cys-315, and Cys-318 inactivate the enzyme by abolishing DNA binding. H295A and C318S mutants lack bound zinc and show significant secondary structure changes. Arg-310, in the zinc-binding pocket, is critical for activity. The zinc finger motif is essential for NEIL2 structural integrity and enzyme activity.\",\n      \"method\": \"ICP mass spectrometry (zinc quantification), site-directed mutagenesis, CD spectra analysis, molecular modeling, in vitro activity assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple orthogonal methods (metal quantification, mutagenesis, CD spectroscopy, activity assays) in a single study\",\n      \"pmids\": [\"15339932\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"NEIL1 and NEIL2 recognize and cleave DNA containing guanidinohydantoin (Gh)/iminoallantoin (Ia) and spiroiminodihydantoin (Sp) lesions (further oxidation products of 8-oxoguanine) via beta- and delta-elimination mechanism. NEIL2 shows little cleavage activity against Sp in duplex DNA but binds and recognizes it (shown by DNA trapping studies). Both enzymes excise Gh/Ia opposite all four natural bases in double-stranded DNA.\",\n      \"method\": \"In vitro DNA glycosylase cleavage assays with defined damaged substrates (single-stranded and duplex DNA), DNA trapping studies\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with defined substrates and multiple lesion types, single lab\",\n      \"pmids\": [\"15533836\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"NEIL2-initiated repair of 5-hydroxyuracil (5-OHU) requires polynucleotide kinase (PNK) rather than APE1 to remove the 3'-phosphate terminus generated after strand cleavage. NEIL2 stably interacts with BER proteins DNA polymerase beta (Pol beta), DNA ligase IIIalpha (Lig IIIalpha), and XRCC1 (but not APE1). The essential N-terminal segment of NEIL2 mediates these interactions (unlike NEIL1 which uses its C-terminal region). A complex containing NEIL2, PNK, Pol beta, Lig IIIalpha, and XRCC1 can be isolated from human cells and is competent for repair of 5-OHU in plasmid DNA.\",\n      \"method\": \"In vitro repair assay with 5-OHU substrate, co-immunoprecipitation from human cells, domain mapping of protein-protein interactions, reconstituted repair assay in plasmid DNA\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — reconstituted repair assay, reciprocal Co-IP, domain mapping, and functional assay in single study\",\n      \"pmids\": [\"16982218\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Y box-binding protein (YB-1) is a stably interacting partner of NEIL2 (identified by mass spectrometry of NEIL2 immunocomplex). YB-1 stimulates NEIL2 base excision activity ~7-fold. YB-1 also interacts with DNA ligase IIIalpha and DNA polymerase beta, forming a large multiprotein complex. YB-1 normally cytoplasmic translocates to the nucleus during UVA-induced oxidative stress, concomitantly increasing its association with and activation of NEIL2. NEIL2-initiated base excision activity is significantly reduced in YB-1-depleted cells.\",\n      \"method\": \"Mass spectrometry of NEIL2 immunocomplex, co-immunoprecipitation, in vitro stimulation assay, YB-1 siRNA knockdown, nuclear/cytoplasmic fractionation, UVA treatment\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS identification of interactor, Co-IP validation, functional stimulation assay, siRNA knockdown with activity readout, single lab\",\n      \"pmids\": [\"17686777\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Recombinant NEIL2 purified from E. coli has biochemically characterized DNA glycosylase/AP lyase activity with unique preference for bubble or single-stranded DNA substrates over duplex DNA, unlike NTH1 and OGG1. NEIL2 and NEIL1 are distinct mammalian orthologs of E. coli Nei and Fpg in reaction mechanism.\",\n      \"method\": \"Purification of recombinant protein from E. coli, in vitro DNA glycosylase assays with bubble, single-stranded, and duplex DNA substrates\",\n      \"journal\": \"Methods in enzymology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution, consistent with and confirmatory of prior findings\",\n      \"pmids\": [\"16793361\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Murine NEIL2 (mNEIL2) associates with microtubules in situ and in vitro. Purified recombinant mNEIL2 co-precipitates with microtubules and associates with the microtubule network during interphase and with the spindle assembly at mitosis, as shown by in situ localization, microtubule co-precipitation, and site-directed photochemical experiments.\",\n      \"method\": \"In situ localization with fluorochrome-conjugated recombinant protein, microtubule co-precipitation, site-directed photochemical crosslinking\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-precipitation and in situ localization with recombinant protein, functional significance of microtubule association is unclear, single lab\",\n      \"pmids\": [\"15725623\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Pyridoxal-5'-phosphate (PLP) inhibits NEIL2 specifically among six bifunctional DNA repair glycosylases tested. Inhibition is through Schiff base formation between PLP and Lys50 of NEIL2, abolishing DNA binding. The beta2/beta3 loop where Lys50 is located is important for DNA binding and likely lies next to a phosphate-binding site.\",\n      \"method\": \"Enzyme inhibition assay, LC/nanoESI-MS/MS identification of modified residue, DNA binding assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Weak — in vitro biochemical assay with MS identification of modification site, but single lab and single study\",\n      \"pmids\": [\"20175991\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"NEIL2 is present in purified human mitochondrial extracts and co-localizes with the mitochondrion-specific protein MT-CO2 by confocal microscopy. ChIP analysis shows NEIL2 associates with mitochondrial genes MT-CO2 and MT-CO3, and with mitochondrial DNA polymerase gamma. Individual depletion of NEIL2 in HEK293 cells causes increased levels of oxidized bases in the mitochondrial genome, demonstrating NEIL2's role in mitochondrial genome maintenance.\",\n      \"method\": \"Mitochondrial extract purification, confocal microscopy, chromatin immunoprecipitation, proximity ligation assay, NEIL2 siRNA knockdown with mt-DNA damage quantification\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (fractionation, confocal, ChIP, PLA, siRNA knockdown with functional readout) in single lab\",\n      \"pmids\": [\"22130663\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Depletion of NEIL2 causes a 6-7-fold increase in spontaneous mutation frequency in the HPRT gene. The NEIL2 variant R257L has modestly decreased DNA glycosylase activity, but shows ~5-fold decreased repair in reconstituted BER assays due to lower affinity for Pol beta and other repair proteins. Cells expressing R257L show increased endogenous DNA damage relative to WT.\",\n      \"method\": \"siRNA depletion with HPRT mutation assay, reconstituted BER assay, biochemical characterization of variant proteins, protein-protein interaction assays\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — reconstituted repair assay, mutation frequency measurement, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"22497777\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Cockayne Syndrome B (CSB) protein physically interacts with NEIL2 independently of DNA. CSB stimulates NEIL2 glycosylase activity on 5-hydroxyuracil lesion in a DNA bubble substrate and also stimulates a novel NEIL2 activity toward 4,6-diamino-5-formamidopyrimidine (FapyA). Immunofluorescence shows increased cytoplasmic co-localization of CSB and NEIL2 after oxidative stress. Stalling transcription with alpha-amanitin increases CSB-NEIL2 co-localization. CSB knockdown reduces NEIL2-dependent incision activity in whole cell extracts.\",\n      \"method\": \"Co-immunoprecipitation with recombinant proteins and cell extracts (DNA-independent), in vitro stimulation assay, immunofluorescence, transcription stalling with alpha-amanitin, siRNA knockdown with activity readout\",\n      \"journal\": \"Mechanisms of ageing and development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — multiple orthogonal methods (reciprocal Co-IP, stimulation assay, immunofluorescence, knockdown), single lab\",\n      \"pmids\": [\"24406253\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Neil2-null mice accumulate oxidized DNA bases preferentially in transcriptionally active (transcribed) genomic sequences. In vivo immunopulldown from mouse tissue shows NEIL2 associates with RNA polymerase II, Cockayne syndrome group B protein (CSB), and TFIIH. ChIP from mouse tissue demonstrates co-occupancy of NEIL2 and RNA Pol II exclusively on transcribed genes. Neil2-null mouse embryonic fibroblasts show increased telomere loss and genomic instability. Neil2-null mice are more responsive to inflammatory agents, producing higher levels of inflammatory genes.\",\n      \"method\": \"Neil2-null mouse generation, co-immunoprecipitation from mouse tissue, ChIP from mouse tissue, LA-QPCR for oxidative DNA damage in transcribed regions, telomere FISH\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — knockout mouse model with multiple orthogonal in vivo and biochemical methods, replicated across multiple assays\",\n      \"pmids\": [\"26245904\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Depletion of NEIL1 and NEIL2 in Xenopus embryos and differentiating mouse ESCs causes a defect in cranial neural crest cell (cNCC) development via oxidative stress-induced TP53-dependent DNA damage response. Neil-deficiency causes oxidative damage specifically to mitochondrial DNA, triggering TP53-mediated intrinsic apoptosis. Epistasis with Tdg-deficient mESCs shows the cNCC defect is NOT due to impaired epigenetic DNA demethylation.\",\n      \"method\": \"Xenopus embryo knockdown, mouse ESC differentiation with NEIL KO, epistasis experiments with Tdg KO, TP53 inhibitor rescue, mitochondrial DNA damage assays\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple model systems, epistasis experiments, rescue experiments, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"31566562\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Crystal structure of mammalian NEIL2 (opossum Monodelphis domestica) reveals an unusual 'open' conformation not seen in NEIL1 or NEIL3. Combined crystallographic and solution-scattering (SAXS) studies show NEIL2 is conformationally dynamic, predicted to adopt a 'closed' conformation upon substrate binding. Three cancer variants (S140N, G230W, G303R) were biochemically characterized.\",\n      \"method\": \"X-ray crystallography (crystal structure), small-angle X-ray scattering (SAXS), biochemical characterization of cancer variants\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure plus solution scattering, multiple orthogonal structural methods, single lab\",\n      \"pmids\": [\"32846144\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NEIL2 has a non-canonical function as a direct suppressor of NF-κB signaling. NEIL2 directly interacts with the Rel homology region of RelA (p65), blocking NF-κB binding to target gene promoters and repressing proinflammatory gene expression (Cxcl1, Cxcl2, Cxcl10, Il6, Tnfa). Neil2-null mice show significantly higher expression of proinflammatory genes. Intrapulmonary delivery of purified recombinant NEIL2 decreases NF-κB-DNA binding and reduces proinflammatory gene expression and neutrophil recruitment.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, electrophoretic mobility shift assay (EMSA), Neil2-null mouse model, intrapulmonary administration of recombinant NEIL2 protein\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, ChIP, EMSA, in vivo rescue with recombinant protein), single lab\",\n      \"pmids\": [\"33932404\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NEIL2 conformation in solution is predominantly 'open'; its large N-terminal insert (absent from other DNA glycosylases) is unstructured in solution. HDX-MS combined with homology modeling and MD simulations shows NEIL2 is a conformationally flexible protein, consistent with its role in repair of non-canonical DNA structures and protein-protein interactions.\",\n      \"method\": \"Hydrogen/deuterium exchange mass spectrometry (HDX-MS), homology modeling, molecular dynamics simulations\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — HDX-MS with computational support, single lab, no functional validation of structural findings\",\n      \"pmids\": [\"34757057\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In cells depleted of OGG1 or treated with OGG1 inhibitor TH5487, NEIL2 accumulation at DNA damage sites is prolonged and NEIL2 retention at damaged chromatin is increased. NEIL2-depleted cells oxidatively stressed with OGG1 also inhibited show excessive genomic 8-oxoG accumulation, indicating NEIL2 serves as a backup BER enzyme for OGG1.\",\n      \"method\": \"Live cell imaging of NEIL2 recruitment kinetics, chromatin fractionation, siRNA depletion, pharmacological OGG1 inhibition, immunofluorescence for 8-oxoG\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — live imaging and chromatin binding assays, single lab, limited mechanistic depth\",\n      \"pmids\": [\"33925271\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NEIL2 polymorphic variant P304T (Pro304 in the beta-turn of the zinc finger motif) has ~5-fold reduced catalytic efficiency (kcat/KM) compared to wild-type, lower DNA affinity, and reduced proficiency in removing damaged bases from single-stranded and bubble-containing DNA. R103W variant is much less affected.\",\n      \"method\": \"Biochemical characterization of recombinant variant proteins, steady-state kinetics, DNA binding assays\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biochemical characterization with kinetics, single lab, single study\",\n      \"pmids\": [\"35216329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NEIL2 directly binds to the 5'-UTR of SARS-CoV-2 genomic RNA and blocks viral protein synthesis. Delivery of recombinant NEIL2 into ACE2-expressing cells decreases expression of proinflammatory genes, viral E-gene expression, and lowers yield of viral progeny.\",\n      \"method\": \"RNA binding assay (NEIL2 binding to 5'-UTR of viral RNA), recombinant NEIL2 delivery into cells, measurement of viral replication and proinflammatory gene expression\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — novel mechanistic finding (RNA binding), functional rescue assay, single lab, single study; mechanistic detail of RNA binding is limited in abstract\",\n      \"pmids\": [\"38071370\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Crystal structure of mammalian NEIL2 in complex with an abasic site analog-containing DNA duplex at 2.08 Å reveals a large interdomain conformational shift upon DNA binding compared to the unliganded structure, with local changes in C-terminal zinc finger and N-terminal void-filling loop required to position the enzyme on DNA. Biochemical analysis shows NEIL2 has a significant preference for its lyase activity, particularly relevant for abasic sites. Detailed substrate range characterization confirms preference for oxidized cytosine products and abasic sites.\",\n      \"method\": \"X-ray crystallography (liganded structure at 2.08 Å), comparison with unliganded structure, biochemical assays with array of oxidized base lesions\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with substrate analog plus biochemical characterization, multiple orthogonal approaches in single study\",\n      \"pmids\": [\"37971311\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"NEIL2 is phosphorylated by CDK5 and PKC in vitro and in SH-SY5Y neuroblastoma cells. Phosphorylation by PKC causes a substantial reduction in NEIL2 repair activity. CDK5 phosphorylation does not directly alter enzymatic activity. NEIL2 undergoes rapid dephosphorylation in response to oxidative stress in SH-SY5Y cells, indicating phosphorylation is an important modulator of NEIL2 function during oxidative stress.\",\n      \"method\": \"In vitro kinase assays with CDK5 and PKC, in vivo phosphorylation in SH-SY5Y cells, DNA repair activity assay after phosphorylation, oxidative stress treatment with phosphorylation status monitoring\",\n      \"journal\": \"Antioxidants\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Weak — in vitro and in vivo phosphorylation with functional activity readout, single lab, single study\",\n      \"pmids\": [\"36829914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Sirt3 deacetylates NEIL2 (along with NEIL1, OGG1, MUTYH, APE1, and LIG3) in colorectal cancer cells, modulating mitochondrial BER activity; NEIL2 is identified as a substrate for Sirt3-mediated deacetylation.\",\n      \"method\": \"Deacetylation assay with Sirt3 and NEIL2 as substrate\",\n      \"journal\": \"Polski przeglad chirurgiczny\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single assay, limited methodological detail in abstract, single study covering multiple proteins\",\n      \"pmids\": [\"32312920\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NEIL2 is a bifunctional DNA glycosylase/AP lyase of the Fpg/Nei family that initiates base excision repair (BER) of oxidized base lesions—particularly oxidized cytosines, formamidopyrimidines, and abasic sites—with a unique preference for bubble and single-stranded DNA substrates, implicating it in transcription-coupled repair; it assembles into an APE1-independent repair complex with PNK, Pol beta, Lig IIIalpha, and XRCC1 (stimulated by YB-1 under oxidative stress and by CSB during transcription), is regulated by p300-mediated acetylation of Lys49 and by PKC/CDK5-mediated phosphorylation, requires a structural zinc finger (CHCC motif) for DNA binding and catalytic integrity, localizes to both nuclear and mitochondrial compartments to protect both genomes, and exerts non-canonical roles including direct binding to the RelA Rel homology domain to suppress NF-κB-driven inflammation and binding to the 5'-UTR of SARS-CoV-2 RNA to block viral protein synthesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NEIL2 is a bifunctional DNA glycosylase/AP lyase of the Fpg/Nei family that initiates base excision repair (BER) of oxidized base lesions, with a distinctive preference for excising damage from DNA bubble and single-stranded substrates rather than duplex DNA, implicating it in repair coupled to transcription and replication [#0, #6]. Its substrate range spans oxidized cytosines, hydantoin lesions (Gh/Ia and Sp), 5-hydroxyuracil, formamidopyrimidines, and abasic sites, with biochemical and structural analysis revealing a strong bias toward its lyase activity at abasic sites [#3, #20]. Catalysis and DNA binding depend on a structural C-terminal CHCC zinc finger, and crystallographic and solution studies show NEIL2 is conformationally dynamic, shifting from an 'open' unliganded state to a 'closed' state that positions the enzyme on DNA [#2, #14, #20]. NEIL2 organizes an APE1-independent repair complex: after strand cleavage it requires polynucleotide kinase (PNK) to process the 3'-phosphate, and its N-terminal segment mediates stable interactions with Pol beta, Lig IIIalpha, and XRCC1 to complete repair [#4]. This complex is stimulated by YB-1, which translocates to the nucleus and activates NEIL2 under oxidative stress, and by Cockayne syndrome B protein (CSB), which links NEIL2 to transcription-coupled repair [#5, #11]. Consistent with a transcription-associated role, NEIL2 co-occupies transcribed genes with RNA polymerase II, CSB, and TFIIH, and Neil2-null mice accumulate oxidative damage preferentially in transcribed sequences and show telomere loss and genomic instability [#12]. NEIL2 also localizes to mitochondria, associating with mitochondrial genes and Pol gamma to protect the mitochondrial genome, loss of which triggers TP53-dependent apoptosis during neural crest development [#9, #13]. Activity is tuned by post-translational modification, including inactivating p300-mediated acetylation of Lys49 and PKC-mediated phosphorylation that suppresses repair [#1, #21]. Beyond repair, NEIL2 exerts non-canonical functions: it directly binds the Rel homology region of RelA (p65) to block NF-\\u03baB promoter binding and suppress proinflammatory gene expression, and it binds the SARS-CoV-2 5'-UTR to block viral protein synthesis [#15, #19].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Established that NEIL2 has a substrate preference distinct from other oxidized-base glycosylases, defining its niche in repair of non-duplex DNA structures arising during transcription and replication.\",\n      \"evidence\": \"In vitro glycosylase and affinity assays comparing bubble, single-stranded, and duplex substrates\",\n      \"pmids\": [\"14522990\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish which cellular processes generate the bubble substrates NEIL2 acts on\", \"In vivo relevance of the bubble preference not yet demonstrated\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Identified acetylation by p300 at Lys49 as a reversible switch that inactivates NEIL2, providing a mechanism for regulating repair activity in vivo.\",\n      \"evidence\": \"Co-IP, in vitro p300 acetylation, site-directed mutagenesis with activity readout\",\n      \"pmids\": [\"15175427\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Deacetylase counteracting p300 not identified in this study\", \"Physiological stimuli controlling Lys49 acetylation not defined\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Defined the C-terminal CHCC zinc finger as essential for DNA binding, structural integrity, and catalysis, explaining the structural basis of NEIL2 activity.\",\n      \"evidence\": \"Zinc quantification, mutagenesis, CD spectroscopy, molecular modeling, activity assays\",\n      \"pmids\": [\"15339932\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"High-resolution structure of the zinc finger not yet available at this stage\", \"How the zinc finger contributes to bubble-substrate recognition unresolved\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Showed NEIL2 nucleates an APE1-independent BER pathway requiring PNK for 3'-end processing and assembling Pol beta, Lig IIIalpha, and XRCC1 via its N-terminus, distinguishing its repair route from NEIL1.\",\n      \"evidence\": \"Reconstituted repair of 5-OHU, reciprocal Co-IP from human cells, domain mapping\",\n      \"pmids\": [\"16982218\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and assembly order of the complex not defined\", \"Whether the complex is preformed or damage-induced not resolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identified YB-1 as a stress-responsive activator that translocates to the nucleus and stimulates NEIL2-initiated repair, linking oxidative stress signaling to NEIL2 function.\",\n      \"evidence\": \"MS of NEIL2 immunocomplex, Co-IP, in vitro stimulation, siRNA knockdown, fractionation under UVA\",\n      \"pmids\": [\"17686777\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which YB-1 stimulates excision not defined\", \"Signaling pathway driving YB-1 nuclear translocation not mapped\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Demonstrated NEIL2 localizes to mitochondria and maintains the mitochondrial genome, extending its protective role beyond the nucleus.\",\n      \"evidence\": \"Mitochondrial fractionation, confocal co-localization, ChIP, PLA, siRNA with mtDNA damage readout\",\n      \"pmids\": [\"22130663\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mitochondrial import mechanism not defined\", \"Mitochondrial BER partners of NEIL2 not fully enumerated\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Linked NEIL2 loss to elevated spontaneous mutation and showed the R257L variant impairs repair by weakening interaction with Pol beta, connecting protein-protein contacts to genome stability.\",\n      \"evidence\": \"siRNA depletion with HPRT mutation assay, reconstituted BER, variant biochemistry\",\n      \"pmids\": [\"22497777\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Frequency and clinical significance of R257L in populations not addressed\", \"Structural basis of reduced Pol beta affinity not determined\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Established CSB as a DNA-independent NEIL2 partner that stimulates its glycosylase activity and links NEIL2 to transcription-coupled repair.\",\n      \"evidence\": \"Reciprocal Co-IP, in vitro stimulation, immunofluorescence under stress and transcription stalling, knockdown\",\n      \"pmids\": [\"24406253\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of CSB-mediated stimulation not defined\", \"Cytoplasmic co-localization significance unclear\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrated in vivo that NEIL2 associates with the transcription machinery (RNA Pol II, CSB, TFIIH) and preferentially repairs transcribed genes, with loss causing telomere instability.\",\n      \"evidence\": \"Neil2-null mice, tissue Co-IP and ChIP, LA-QPCR for transcribed-region damage, telomere FISH\",\n      \"pmids\": [\"26245904\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How NEIL2 is recruited specifically to active genes not resolved\", \"Mechanism connecting NEIL2 loss to telomere attrition not defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showed NEIL-dependent mitochondrial genome protection is required for cranial neural crest development via prevention of TP53-driven apoptosis, independent of epigenetic demethylation.\",\n      \"evidence\": \"Xenopus and mouse ESC knockdown/KO, Tdg epistasis, TP53 inhibitor rescue, mtDNA damage assays\",\n      \"pmids\": [\"31566562\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contributions of NEIL1 vs NEIL2 not fully separated\", \"Whether the requirement is mitochondrial-genome-specific in all lineages unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Provided the first mammalian NEIL2 crystal structure, revealing an unusual open conformation and conformational dynamics predicted to close on substrate.\",\n      \"evidence\": \"X-ray crystallography and SAXS, biochemical characterization of cancer variants\",\n      \"pmids\": [\"32846144\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Liganded conformation not yet captured at this stage\", \"Functional consequence of dynamics not directly tested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined a non-canonical anti-inflammatory function: NEIL2 directly binds the RelA Rel homology region to block NF-\\u03baB promoter binding and suppress proinflammatory genes.\",\n      \"evidence\": \"Co-IP, ChIP, EMSA, Neil2-null mice, intrapulmonary recombinant NEIL2 rescue\",\n      \"pmids\": [\"33932404\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether this function requires catalytic activity not resolved\", \"Structural detail of the NEIL2-RelA interface not determined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Characterized NEIL2 as intrinsically flexible with a disordered N-terminal insert, supporting its capacity for protein-protein interactions and non-canonical substrate engagement.\",\n      \"evidence\": \"HDX-MS, homology modeling, MD simulations\",\n      \"pmids\": [\"34757057\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional validation of the structural dynamics\", \"Single lab, computational support only\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Positioned NEIL2 as a backup glycosylase for OGG1, with prolonged NEIL2 retention at damage when OGG1 is absent or inhibited.\",\n      \"evidence\": \"Live-cell recruitment imaging, chromatin fractionation, siRNA, OGG1 inhibition, 8-oxoG immunofluorescence\",\n      \"pmids\": [\"33925271\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab with limited mechanistic depth\", \"Quantitative division of labor between OGG1 and NEIL2 not defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showed the zinc-finger beta-turn variant P304T markedly reduces NEIL2 catalytic efficiency and DNA affinity, linking specific residues to functional integrity.\",\n      \"evidence\": \"Steady-state kinetics and DNA binding of recombinant variants\",\n      \"pmids\": [\"35216329\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single in vitro study without cellular validation\", \"Disease association of P304T not established\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Captured the liganded NEIL2 structure, revealing a large interdomain shift on DNA binding and confirming a strong preference for lyase activity at abasic sites.\",\n      \"evidence\": \"X-ray crystallography of abasic-analog DNA complex at 2.08 \\u00c5, comparison with apo structure, biochemical assays\",\n      \"pmids\": [\"37971311\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure with a bona fide oxidized-base substrate not solved\", \"How the open\\u2192closed transition is triggered in bubble DNA unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified PKC and CDK5 phosphorylation as modulators of NEIL2, with PKC reducing repair activity and stress-induced dephosphorylation restoring function.\",\n      \"evidence\": \"In vitro kinase assays, in-cell phosphorylation in SH-SY5Y, activity assays, oxidative stress monitoring\",\n      \"pmids\": [\"36829914\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phosphorylation sites not mapped\", \"Phosphatase responsible for stress-induced dephosphorylation not identified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed an antiviral role: NEIL2 binds the SARS-CoV-2 5'-UTR to block viral protein synthesis and reduce viral yield and inflammation.\",\n      \"evidence\": \"RNA binding assay, recombinant NEIL2 delivery, viral replication and proinflammatory gene readouts\",\n      \"pmids\": [\"38071370\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis and sequence specificity of RNA binding not defined\", \"Whether this reflects a general RNA-binding capacity unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NEIL2's repair, transcription-coupling, anti-inflammatory, and antiviral functions are coordinated and selectively engaged in vivo remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model integrating catalytic and non-canonical functions\", \"Recruitment mechanism to active genes and to RelA/RNA targets not mechanistically connected\", \"No human disease causation established despite multiple characterized variants\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140097\", \"supporting_discovery_ids\": [0, 3, 4, 6, 20]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [2, 18, 20]},\n      {\"term_id\": \"GO:0016829\", \"supporting_discovery_ids\": [3, 20]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [19]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5, 12]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [9, 13]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0, 4, 6, 12, 20]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [15, 19]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [5, 11, 17, 21]}\n    ],\n    \"complexes\": [\"NEIL2-PNK-Pol beta-Lig IIIalpha-XRCC1 BER complex\"],\n    \"partners\": [\"PNKP\", \"POLB\", \"LIG3\", \"XRCC1\", \"YBX1\", \"ERCC6\", \"EP300\", \"RELA\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":9,"faith_total":9,"faith_pct":100.0}}