{"gene":"COMMD4","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2021,"finding":"COMMD4 binds to histone H2B and protects it from monoubiquitination by RNF20/RNF40 at DNA double-strand break sites. DNA damage-induced phosphorylation of the H2A-H2B heterodimer disrupts the dimer, causing COMMD4 to preferentially bind H2A instead, which allows RNF20/40 to monoubiquitinate H2B and enable chromatin remodelling at break sites. COMMD4-deficient cells show excessive elongation of remodelled chromatin and failure of both non-homologous end-joining and homologous recombination.","method":"Co-immunoprecipitation, peptide mapping, mutagenesis, siRNA knockdown with DNA repair assays (NHEJ and HR), chromatin remodelling assays","journal":"Communications biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding experiments, peptide-mapping, site-directed mutagenesis, and multiple functional readouts (NHEJ, HR, chromatin remodelling) in a single focused study with orthogonal methods","pmids":["33875784"],"is_preprint":false},{"year":2023,"finding":"COMMD4 binds directly to histone H2B; a short H2B-derived peptide that occupies the COMMD4 H2B-binding site disrupts the COMMD4-H2B interaction both in vitro and in vivo, leading to increased sensitivity to ionising radiation, increased DNA double-strand breaks, and induction of mitotic catastrophe in NSCLC cells.","method":"Molecular modelling, in vitro binding assays, site-directed mutagenesis, cell viability assays, DNA repair assays, mitotic catastrophe assays","journal":"British journal of cancer","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — molecular modelling combined with in vitro binding, mutagenesis, and multiple functional assays in a single focused study","pmids":["37914802"],"is_preprint":false},{"year":2025,"finding":"COMMD4 activates PI3K-AKT signalling by binding PI3K-p85 (the regulatory subunit), thereby releasing PI3K-p110 (the catalytic subunit) to drive G2/M transition and epithelial-mesenchymal transition in skin cutaneous melanoma cells. COMMD4 knockout induced G2/M arrest via disruption of the p21-CDK1-cyclinB1 axis and impeded EMT by reversing the E/N-cadherin switch; reactivation of PI3K-AKT in knockout cells rescued these phenotypes.","method":"COMMD4 gene knockout, co-immunoprecipitation (COMMD4 with PI3K-p85), rescue experiments with PI3K-AKT reactivation, xenograft tumour models, cell proliferation/migration/invasion assays","journal":"Annals of the New York Academy of Sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP identifying PI3K-p85 as binding partner, genetic KO with rescue, and multiple phenotypic readouts, but single lab and abstract-level detail","pmids":["41283898"],"is_preprint":false},{"year":2025,"finding":"COMMD4 inhibits ferroportin (FPN)-mediated neuronal iron efflux by suppressing intracellular copper and hephaestin (HEPH), thereby disrupting Cu-Fe balance and inducing neuronal ferroptosis in ALS models. COMMD4 depletion increased intracellular copper, activated the HEPH/FPN pathway, and exerted neuroprotective effects; the mechanism was shown to be independent of effects on the HEPH-FPN protein interaction itself.","method":"COMMD4 overexpression/depletion in ALS cell and animal models, measurement of intracellular copper and iron, ferroptosis assays, HEPH and FPN pathway analysis","journal":"Brain research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic loss-of-function with defined pathway readout (HEPH/FPN/ferroptosis) in cell and animal models, but single lab and limited mechanistic detail available from abstract","pmids":["40389143"],"is_preprint":false},{"year":2025,"finding":"COMMD4 is a component of the CCC (CCDC22-CCDC93-COMMD) complex within the Commander multiprotein assembly; mutations in CCDC22 that disrupt a conserved CCDC22-COMMD4 interaction surface impair CCC complex assembly and reduce cell-surface recycling of integral membrane proteins, causing Ritscher-Schinzel syndrome phenotypes.","method":"Interactome analysis, cell surface proteomics, characterisation of patient missense mutations, in vitro complex assembly assays","journal":"BMC medical genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — interactome analysis and cell surface proteomics with patient mutations establishing COMMD4 as a CCC complex subunit required for endosomal recycling, two independent papers converging on same complex","pmids":["40448120"],"is_preprint":false},{"year":2025,"finding":"Genetic and clinical analysis identified causative mutations in COMMD4 as part of the Commander complex in Ritscher-Schinzel syndrome patients; these mutations disrupted Commander complex assembly and reduced cell-surface presentation of integral membrane proteins bearing ΦxNPxY/F or ΦxNxxY/F sorting motifs recognised by SNX17 for Commander-dependent endosomal recycling.","method":"Interactome analysis of patient mutations, cell surface proteomics, mouse models of RSS replicating clinical phenotypes (proteinuria, skeletal malformation, neurological impairment)","journal":"Science translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — interactome analysis, cell surface proteomics, and mouse models with clinical phenotype replication, single lab but multiple orthogonal methods","pmids":["40601774"],"is_preprint":false},{"year":2011,"finding":"COMMD4 was identified as a putative interactor of myomegalin (MMGL) isoform 4, an A-kinase anchoring protein, in a yeast two-hybrid screen of a cardiac cDNA library; the interaction was confirmed by fluorescent 3D co-localisation in differentiated H9C2 cells and co-immunoprecipitation in vivo.","method":"Yeast two-hybrid screen, fluorescent 3D co-localisation, co-immunoprecipitation","journal":"BMC cell biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — COMMD4 identified as one of several interactors with limited follow-up specific to COMMD4; no functional consequence of this interaction demonstrated for COMMD4 itself","pmids":["21569246"],"is_preprint":false},{"year":2025,"finding":"COMMD4 was identified as a cuproptosis sensor using spatio-temporal mass spectrometry profiling of subcellular proteome changes during copper stress; a GFP-tagged COMMD4 cell model was established and used for high-content drug screening to identify cuproptosis inhibitors.","method":"Spatio-temporal mass spectrometry (STMS), genetic functional screen, GFP-tagged COMMD4 reporter cell model, high-content drug screening","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, COMMD4 identified as a cuproptosis sensor by proteomics screen without detailed mechanistic follow-up on COMMD4 itself","pmids":["bio_10.1101_2025.07.01.662679"],"is_preprint":true}],"current_model":"COMMD4 is a multi-functional protein that (1) maintains genomic stability by binding histone H2B to regulate RNF20/40-mediated H2B monoubiquitination and chromatin remodelling at DNA double-strand breaks, switching to bind H2A upon DNA damage-induced phosphorylation; (2) acts as a structural subunit of the CCC/Commander endosomal recycling complex, where its assembly with CCDC22 is required for SNX17-dependent recycling of integral membrane proteins to the cell surface; (3) activates PI3K-AKT signalling by binding PI3K-p85 to release the catalytic p110 subunit; and (4) regulates neuronal copper-iron balance by suppressing hephaestin and ferroportin-mediated iron efflux."},"narrative":{"mechanistic_narrative":"COMMD4 is a multifunctional protein operating in genome maintenance, endosomal protein recycling, and growth signalling [PMID:33875784, PMID:40448120, PMID:41283898]. In the DNA damage response, COMMD4 binds histone H2B and shields it from RNF20/RNF40-mediated monoubiquitination; DNA damage-induced phosphorylation of the H2A-H2B heterodimer redirects COMMD4 to H2A, licensing H2B monoubiquitination and the chromatin remodelling required for both non-homologous end-joining and homologous recombination, such that COMMD4-deficient cells show aberrant chromatin elongation and failed repair [PMID:33875784]. Disrupting the COMMD4-H2B interface with a competing H2B-derived peptide sensitises NSCLC cells to ionising radiation and triggers mitotic catastrophe [PMID:37914802]. Independently, COMMD4 is a structural subunit of the CCC (CCDC22-CCDC93-COMMD) module of the Commander assembly, where its interaction surface with CCDC22 is required for complex assembly and for SNX17-dependent endosomal recycling of integral membrane proteins bearing ΦxNPxY/F sorting motifs to the cell surface; patient mutations disrupting this assembly cause Ritscher-Schinzel syndrome [PMID:40448120, PMID:40601774]. COMMD4 also promotes proliferation and epithelial-mesenchymal transition in melanoma by binding the PI3K regulatory subunit p85 to release catalytic p110 and activate PI3K-AKT signalling [PMID:41283898], and regulates neuronal copper-iron balance by suppressing hephaestin/ferroportin-mediated iron efflux, with depletion conferring protection against ferroptosis in ALS models [PMID:40389143].","teleology":[{"year":2021,"claim":"Established a direct role for COMMD4 in the DNA damage response by showing it gates H2B monoubiquitination through a phosphorylation-controlled histone-binding switch, explaining how chromatin remodelling at break sites is regulated.","evidence":"Co-immunoprecipitation, peptide mapping, mutagenesis, and siRNA knockdown coupled to NHEJ/HR and chromatin remodelling assays","pmids":["33875784"],"confidence":"High","gaps":["Structural basis of the H2A-versus-H2B binding switch not resolved","Identity of the kinase driving the H2A-H2B phosphorylation not established","Relationship between this nuclear role and the CCC/cytoplasmic functions unaddressed"]},{"year":2023,"claim":"Validated the COMMD4-H2B interface as a druggable vulnerability by showing peptide-mediated disruption sensitises cancer cells to radiation, translating the mechanism into a therapeutic concept.","evidence":"Molecular modelling, in vitro binding, mutagenesis, and cell viability/DNA repair/mitotic catastrophe assays in NSCLC cells","pmids":["37914802"],"confidence":"High","gaps":["No structural confirmation of the modelled binding pose","Peptide selectivity over other histone interactions not characterized","In vivo efficacy not demonstrated"]},{"year":2025,"claim":"Linked COMMD4 to growth and metastatic signalling, showing it activates PI3K-AKT by binding p85 to liberate p110, driving G2/M transition and EMT in melanoma.","evidence":"COMMD4 knockout with Co-IP, PI3K-AKT reactivation rescue, xenografts, and proliferation/migration/invasion assays","pmids":["41283898"],"confidence":"Medium","gaps":["Single lab, abstract-level detail","Direct versus indirect nature of the p85 interaction not fully resolved","How a chromatin-binding protein engages cytoplasmic PI3K not explained"]},{"year":2025,"claim":"Identified a copper-iron regulatory role, showing COMMD4 suppresses hephaestin/ferroportin-mediated iron efflux and that its depletion is neuroprotective against ferroptosis in ALS models.","evidence":"COMMD4 overexpression/depletion in ALS cell and animal models with copper/iron measurement, ferroptosis and HEPH/FPN pathway analysis","pmids":["40389143"],"confidence":"Medium","gaps":["Molecular mechanism linking COMMD4 to copper/HEPH suppression unknown (shown independent of HEPH-FPN interaction)","Single lab with limited mechanistic detail","Connection to CCC complex copper handling not tested"]},{"year":2025,"claim":"Defined COMMD4 as a structural CCC/Commander subunit required for endosomal recycling, with its CCDC22 interaction surface causally implicated in Ritscher-Schinzel syndrome.","evidence":"Interactome analysis, cell-surface proteomics, patient missense mutation characterisation, in vitro assembly assays, and RSS mouse models","pmids":["40448120","40601774"],"confidence":"Medium","gaps":["Stoichiometry and architecture of COMMD4 within the full Commander assembly not resolved","Specific cargo set dependent on COMMD4 incompletely mapped","Single-lab convergence pending broader replication"]},{"year":2025,"claim":"Flagged COMMD4 as a cuproptosis sensor via spatio-temporal proteomics, providing a reporter tool for inhibitor screening.","evidence":"Spatio-temporal mass spectrometry, genetic functional screen, and GFP-tagged reporter cell model for high-content drug screening (preprint)","pmids":["bio_10.1101_2025.07.01.662679"],"confidence":"Low","gaps":["Preprint, not peer-reviewed","No mechanistic follow-up on how COMMD4 senses copper stress","Relationship to the CCC copper-handling role untested"]},{"year":null,"claim":"How COMMD4's distinct nuclear (histone-binding), cytoplasmic (CCC/Commander), signalling (PI3K), and metal-homeostasis activities are coordinated within one protein remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying structural or regulatory model connecting the chromatin and CCC roles","Tissue- and context-specific partitioning of functions unknown","Whether copper sensing integrates the CCC and ferroptosis roles untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0042393","term_label":"histone binding","supporting_discovery_ids":[0,1]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[4,5]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[4,5]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[4,5]}],"complexes":["CCC complex","Commander complex"],"partners":["H2B","H2A","RNF20","RNF40","CCDC22","PIK3R1","SNX17"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H0A8","full_name":"COMM domain-containing protein 4","aliases":[],"length_aa":199,"mass_kda":21.8,"function":"Scaffold protein in the commander complex that is essential for endosomal recycling of transmembrane cargos; the commander complex is composed of the CCC subcomplex and the retriever subcomplex (PubMed:37172566, PubMed:38459129). May modulate activity of cullin-RING E3 ubiquitin ligase (CRL) complexes (PubMed:21778237). Down-regulates activation of NF-kappa-B (PubMed:23637203)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9H0A8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/COMMD4","classification":"Not Classified","n_dependent_lines":53,"n_total_lines":1208,"dependency_fraction":0.043874172185430466},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000140365","cell_line_id":"CID000268","localizations":[{"compartment":"vesicles","grade":3},{"compartment":"cytoplasmic","grade":1}],"interactors":[{"gene":"CCDC22","stoichiometry":10.0},{"gene":"COMMD1","stoichiometry":10.0},{"gene":"COMMD2","stoichiometry":10.0},{"gene":"C16ORF62","stoichiometry":10.0},{"gene":"COMMD6","stoichiometry":10.0},{"gene":"FAM45A;FAM45B","stoichiometry":10.0},{"gene":"SF3B2","stoichiometry":10.0},{"gene":"VPS29","stoichiometry":10.0},{"gene":"COMMD9","stoichiometry":10.0},{"gene":"ARGLU1","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID000268","total_profiled":1310},"omim":[{"mim_id":"616701","title":"COMM DOMAIN-CONTAINING PROTEIN 4; COMMD4","url":"https://www.omim.org/entry/616701"},{"mim_id":"607238","title":"COMM DOMAIN-CONTAINING PROTEIN 1; COMMD1","url":"https://www.omim.org/entry/607238"},{"mim_id":"220210","title":"RITSCHER-SCHINZEL SYNDROME 1; RTSC1","url":"https://www.omim.org/entry/220210"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Vesicles","reliability":"Additional"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/COMMD4"},"hgnc":{"alias_symbol":["FLJ20452"],"prev_symbol":[]},"alphafold":{"accession":"Q9H0A8","domains":[{"cath_id":"-","chopping":"3-124","consensus_level":"high","plddt":80.2393,"start":3,"end":124},{"cath_id":"-","chopping":"127-177","consensus_level":"medium","plddt":76.0043,"start":127,"end":177}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H0A8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H0A8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H0A8-F1-predicted_aligned_error_v6.png","plddt_mean":80.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=COMMD4","jax_strain_url":"https://www.jax.org/strain/search?query=COMMD4"},"sequence":{"accession":"Q9H0A8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H0A8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H0A8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H0A8"}},"corpus_meta":[{"pmid":"27871936","id":"PMC_27871936","title":"COMMD9 promotes TFDP1/E2F1 transcriptional activity via interaction with TFDP1 in non-small cell lung cancer.","date":"2016","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/27871936","citation_count":51,"is_preprint":false},{"pmid":"21569246","id":"PMC_21569246","title":"Myomegalin is a novel A-kinase anchoring protein involved in the phosphorylation of cardiac myosin binding protein C.","date":"2011","source":"BMC cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/21569246","citation_count":47,"is_preprint":false},{"pmid":"31681427","id":"PMC_31681427","title":"Cardiac and Skeletal Muscle Transcriptome Response to Heat Stress in Kenyan Chicken Ecotypes Adapted to Low and High Altitudes Reveal Differences in Thermal Tolerance and Stress Response.","date":"2019","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31681427","citation_count":38,"is_preprint":false},{"pmid":"28970181","id":"PMC_28970181","title":"Altered expression of genes involved in programmed cell death in primary cultured rat cerebellar granule cells acutely challenged with tetrabromobisphenol A.","date":"2017","source":"Neurotoxicology","url":"https://pubmed.ncbi.nlm.nih.gov/28970181","citation_count":16,"is_preprint":false},{"pmid":"33875784","id":"PMC_33875784","title":"COMMD4 functions with the histone H2A-H2B dimer for the timely repair of DNA double-strand breaks.","date":"2021","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/33875784","citation_count":14,"is_preprint":false},{"pmid":"25903558","id":"PMC_25903558","title":"Profiling of differentially expressed genes in sheep T lymphocytes response to an artificial primary Haemonchus contortus infection.","date":"2015","source":"Parasites & vectors","url":"https://pubmed.ncbi.nlm.nih.gov/25903558","citation_count":13,"is_preprint":false},{"pmid":"23085603","id":"PMC_23085603","title":"Cloning and characterization of a COMMD4 gene from amphioxus (Branchiostoma belcheri): an insight into the function and evolution of COMMD4.","date":"2012","source":"Immunology letters","url":"https://pubmed.ncbi.nlm.nih.gov/23085603","citation_count":6,"is_preprint":false},{"pmid":"37914802","id":"PMC_37914802","title":"Targeting the COMMD4-H2B protein complex in lung cancer.","date":"2023","source":"British journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/37914802","citation_count":5,"is_preprint":false},{"pmid":"40601774","id":"PMC_40601774","title":"Ritscher-Schinzel syndrome can be characterized as an endosomal recyclinopathy.","date":"2025","source":"Science translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40601774","citation_count":2,"is_preprint":false},{"pmid":"38575039","id":"PMC_38575039","title":"Identification, diversity, and evolution analysis of Commd gene family in Haliotis discus hannai and immune response to biotic and abiotic stresses.","date":"2024","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/38575039","citation_count":2,"is_preprint":false},{"pmid":"40448120","id":"PMC_40448120","title":"CCDC22 mutations that impair COMMD binding cause attenuated 3C/Ritscher-Schinzel syndrome.","date":"2025","source":"BMC medical genomics","url":"https://pubmed.ncbi.nlm.nih.gov/40448120","citation_count":1,"is_preprint":false},{"pmid":"41233790","id":"PMC_41233790","title":"Non-Lethal heat shock induces COMMD gene activation and enhances pathogen defense in Procambarus clarkii.","date":"2025","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/41233790","citation_count":1,"is_preprint":false},{"pmid":"41283898","id":"PMC_41283898","title":"COMMD4 Drives Skin Cutaneous Melanoma Progression by Targeting PI3K-p85 to Activate PI3K-AKT.","date":"2025","source":"Annals of the New York Academy of Sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41283898","citation_count":0,"is_preprint":false},{"pmid":"40389143","id":"PMC_40389143","title":"COMM domain containing 4 inhibits hephaestin and ferroportin to enhance neuronal ferroptosis by disturbing the Cu-Fe balance in amyotrophic lateral sclerosis.","date":"2025","source":"Brain research","url":"https://pubmed.ncbi.nlm.nih.gov/40389143","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.07.01.662679","title":"Spatio-temporal mass spectrometry in living cells reveals regulators of cuproptosis","date":"2025-07-03","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.01.662679","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10068,"output_tokens":2369,"usd":0.03287,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9481,"output_tokens":2748,"usd":0.058052,"stage2_stop_reason":"end_turn"},"total_usd":0.090922,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2021,\n      \"finding\": \"COMMD4 binds to histone H2B and protects it from monoubiquitination by RNF20/RNF40 at DNA double-strand break sites. DNA damage-induced phosphorylation of the H2A-H2B heterodimer disrupts the dimer, causing COMMD4 to preferentially bind H2A instead, which allows RNF20/40 to monoubiquitinate H2B and enable chromatin remodelling at break sites. COMMD4-deficient cells show excessive elongation of remodelled chromatin and failure of both non-homologous end-joining and homologous recombination.\",\n      \"method\": \"Co-immunoprecipitation, peptide mapping, mutagenesis, siRNA knockdown with DNA repair assays (NHEJ and HR), chromatin remodelling assays\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding experiments, peptide-mapping, site-directed mutagenesis, and multiple functional readouts (NHEJ, HR, chromatin remodelling) in a single focused study with orthogonal methods\",\n      \"pmids\": [\"33875784\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"COMMD4 binds directly to histone H2B; a short H2B-derived peptide that occupies the COMMD4 H2B-binding site disrupts the COMMD4-H2B interaction both in vitro and in vivo, leading to increased sensitivity to ionising radiation, increased DNA double-strand breaks, and induction of mitotic catastrophe in NSCLC cells.\",\n      \"method\": \"Molecular modelling, in vitro binding assays, site-directed mutagenesis, cell viability assays, DNA repair assays, mitotic catastrophe assays\",\n      \"journal\": \"British journal of cancer\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — molecular modelling combined with in vitro binding, mutagenesis, and multiple functional assays in a single focused study\",\n      \"pmids\": [\"37914802\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"COMMD4 activates PI3K-AKT signalling by binding PI3K-p85 (the regulatory subunit), thereby releasing PI3K-p110 (the catalytic subunit) to drive G2/M transition and epithelial-mesenchymal transition in skin cutaneous melanoma cells. COMMD4 knockout induced G2/M arrest via disruption of the p21-CDK1-cyclinB1 axis and impeded EMT by reversing the E/N-cadherin switch; reactivation of PI3K-AKT in knockout cells rescued these phenotypes.\",\n      \"method\": \"COMMD4 gene knockout, co-immunoprecipitation (COMMD4 with PI3K-p85), rescue experiments with PI3K-AKT reactivation, xenograft tumour models, cell proliferation/migration/invasion assays\",\n      \"journal\": \"Annals of the New York Academy of Sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP identifying PI3K-p85 as binding partner, genetic KO with rescue, and multiple phenotypic readouts, but single lab and abstract-level detail\",\n      \"pmids\": [\"41283898\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"COMMD4 inhibits ferroportin (FPN)-mediated neuronal iron efflux by suppressing intracellular copper and hephaestin (HEPH), thereby disrupting Cu-Fe balance and inducing neuronal ferroptosis in ALS models. COMMD4 depletion increased intracellular copper, activated the HEPH/FPN pathway, and exerted neuroprotective effects; the mechanism was shown to be independent of effects on the HEPH-FPN protein interaction itself.\",\n      \"method\": \"COMMD4 overexpression/depletion in ALS cell and animal models, measurement of intracellular copper and iron, ferroptosis assays, HEPH and FPN pathway analysis\",\n      \"journal\": \"Brain research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic loss-of-function with defined pathway readout (HEPH/FPN/ferroptosis) in cell and animal models, but single lab and limited mechanistic detail available from abstract\",\n      \"pmids\": [\"40389143\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"COMMD4 is a component of the CCC (CCDC22-CCDC93-COMMD) complex within the Commander multiprotein assembly; mutations in CCDC22 that disrupt a conserved CCDC22-COMMD4 interaction surface impair CCC complex assembly and reduce cell-surface recycling of integral membrane proteins, causing Ritscher-Schinzel syndrome phenotypes.\",\n      \"method\": \"Interactome analysis, cell surface proteomics, characterisation of patient missense mutations, in vitro complex assembly assays\",\n      \"journal\": \"BMC medical genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — interactome analysis and cell surface proteomics with patient mutations establishing COMMD4 as a CCC complex subunit required for endosomal recycling, two independent papers converging on same complex\",\n      \"pmids\": [\"40448120\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Genetic and clinical analysis identified causative mutations in COMMD4 as part of the Commander complex in Ritscher-Schinzel syndrome patients; these mutations disrupted Commander complex assembly and reduced cell-surface presentation of integral membrane proteins bearing ΦxNPxY/F or ΦxNxxY/F sorting motifs recognised by SNX17 for Commander-dependent endosomal recycling.\",\n      \"method\": \"Interactome analysis of patient mutations, cell surface proteomics, mouse models of RSS replicating clinical phenotypes (proteinuria, skeletal malformation, neurological impairment)\",\n      \"journal\": \"Science translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — interactome analysis, cell surface proteomics, and mouse models with clinical phenotype replication, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"40601774\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"COMMD4 was identified as a putative interactor of myomegalin (MMGL) isoform 4, an A-kinase anchoring protein, in a yeast two-hybrid screen of a cardiac cDNA library; the interaction was confirmed by fluorescent 3D co-localisation in differentiated H9C2 cells and co-immunoprecipitation in vivo.\",\n      \"method\": \"Yeast two-hybrid screen, fluorescent 3D co-localisation, co-immunoprecipitation\",\n      \"journal\": \"BMC cell biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — COMMD4 identified as one of several interactors with limited follow-up specific to COMMD4; no functional consequence of this interaction demonstrated for COMMD4 itself\",\n      \"pmids\": [\"21569246\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"COMMD4 was identified as a cuproptosis sensor using spatio-temporal mass spectrometry profiling of subcellular proteome changes during copper stress; a GFP-tagged COMMD4 cell model was established and used for high-content drug screening to identify cuproptosis inhibitors.\",\n      \"method\": \"Spatio-temporal mass spectrometry (STMS), genetic functional screen, GFP-tagged COMMD4 reporter cell model, high-content drug screening\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, COMMD4 identified as a cuproptosis sensor by proteomics screen without detailed mechanistic follow-up on COMMD4 itself\",\n      \"pmids\": [\"bio_10.1101_2025.07.01.662679\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"COMMD4 is a multi-functional protein that (1) maintains genomic stability by binding histone H2B to regulate RNF20/40-mediated H2B monoubiquitination and chromatin remodelling at DNA double-strand breaks, switching to bind H2A upon DNA damage-induced phosphorylation; (2) acts as a structural subunit of the CCC/Commander endosomal recycling complex, where its assembly with CCDC22 is required for SNX17-dependent recycling of integral membrane proteins to the cell surface; (3) activates PI3K-AKT signalling by binding PI3K-p85 to release the catalytic p110 subunit; and (4) regulates neuronal copper-iron balance by suppressing hephaestin and ferroportin-mediated iron efflux.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"COMMD4 is a multifunctional protein operating in genome maintenance, endosomal protein recycling, and growth signalling [#0, #4, #2]. In the DNA damage response, COMMD4 binds histone H2B and shields it from RNF20/RNF40-mediated monoubiquitination; DNA damage-induced phosphorylation of the H2A-H2B heterodimer redirects COMMD4 to H2A, licensing H2B monoubiquitination and the chromatin remodelling required for both non-homologous end-joining and homologous recombination, such that COMMD4-deficient cells show aberrant chromatin elongation and failed repair [#0]. Disrupting the COMMD4-H2B interface with a competing H2B-derived peptide sensitises NSCLC cells to ionising radiation and triggers mitotic catastrophe [#1]. Independently, COMMD4 is a structural subunit of the CCC (CCDC22-CCDC93-COMMD) module of the Commander assembly, where its interaction surface with CCDC22 is required for complex assembly and for SNX17-dependent endosomal recycling of integral membrane proteins bearing ΦxNPxY/F sorting motifs to the cell surface; patient mutations disrupting this assembly cause Ritscher-Schinzel syndrome [#4, #5]. COMMD4 also promotes proliferation and epithelial-mesenchymal transition in melanoma by binding the PI3K regulatory subunit p85 to release catalytic p110 and activate PI3K-AKT signalling [#2], and regulates neuronal copper-iron balance by suppressing hephaestin/ferroportin-mediated iron efflux, with depletion conferring protection against ferroptosis in ALS models [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2021,\n      \"claim\": \"Established a direct role for COMMD4 in the DNA damage response by showing it gates H2B monoubiquitination through a phosphorylation-controlled histone-binding switch, explaining how chromatin remodelling at break sites is regulated.\",\n      \"evidence\": \"Co-immunoprecipitation, peptide mapping, mutagenesis, and siRNA knockdown coupled to NHEJ/HR and chromatin remodelling assays\",\n      \"pmids\": [\"33875784\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the H2A-versus-H2B binding switch not resolved\", \"Identity of the kinase driving the H2A-H2B phosphorylation not established\", \"Relationship between this nuclear role and the CCC/cytoplasmic functions unaddressed\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Validated the COMMD4-H2B interface as a druggable vulnerability by showing peptide-mediated disruption sensitises cancer cells to radiation, translating the mechanism into a therapeutic concept.\",\n      \"evidence\": \"Molecular modelling, in vitro binding, mutagenesis, and cell viability/DNA repair/mitotic catastrophe assays in NSCLC cells\",\n      \"pmids\": [\"37914802\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural confirmation of the modelled binding pose\", \"Peptide selectivity over other histone interactions not characterized\", \"In vivo efficacy not demonstrated\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Linked COMMD4 to growth and metastatic signalling, showing it activates PI3K-AKT by binding p85 to liberate p110, driving G2/M transition and EMT in melanoma.\",\n      \"evidence\": \"COMMD4 knockout with Co-IP, PI3K-AKT reactivation rescue, xenografts, and proliferation/migration/invasion assays\",\n      \"pmids\": [\"41283898\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab, abstract-level detail\", \"Direct versus indirect nature of the p85 interaction not fully resolved\", \"How a chromatin-binding protein engages cytoplasmic PI3K not explained\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified a copper-iron regulatory role, showing COMMD4 suppresses hephaestin/ferroportin-mediated iron efflux and that its depletion is neuroprotective against ferroptosis in ALS models.\",\n      \"evidence\": \"COMMD4 overexpression/depletion in ALS cell and animal models with copper/iron measurement, ferroptosis and HEPH/FPN pathway analysis\",\n      \"pmids\": [\"40389143\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism linking COMMD4 to copper/HEPH suppression unknown (shown independent of HEPH-FPN interaction)\", \"Single lab with limited mechanistic detail\", \"Connection to CCC complex copper handling not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined COMMD4 as a structural CCC/Commander subunit required for endosomal recycling, with its CCDC22 interaction surface causally implicated in Ritscher-Schinzel syndrome.\",\n      \"evidence\": \"Interactome analysis, cell-surface proteomics, patient missense mutation characterisation, in vitro assembly assays, and RSS mouse models\",\n      \"pmids\": [\"40448120\", \"40601774\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Stoichiometry and architecture of COMMD4 within the full Commander assembly not resolved\", \"Specific cargo set dependent on COMMD4 incompletely mapped\", \"Single-lab convergence pending broader replication\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Flagged COMMD4 as a cuproptosis sensor via spatio-temporal proteomics, providing a reporter tool for inhibitor screening.\",\n      \"evidence\": \"Spatio-temporal mass spectrometry, genetic functional screen, and GFP-tagged reporter cell model for high-content drug screening (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.07.01.662679\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"No mechanistic follow-up on how COMMD4 senses copper stress\", \"Relationship to the CCC copper-handling role untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How COMMD4's distinct nuclear (histone-binding), cytoplasmic (CCC/Commander), signalling (PI3K), and metal-homeostasis activities are coordinated within one protein remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying structural or regulatory model connecting the chromatin and CCC roles\", \"Tissue- and context-specific partitioning of functions unknown\", \"Whether copper sensing integrates the CCC and ferroptosis roles untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"complexes\": [\"CCC complex\", \"Commander complex\"],\n    \"partners\": [\"H2B\", \"H2A\", \"RNF20\", \"RNF40\", \"CCDC22\", \"PIK3R1\", \"SNX17\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}