{"gene":"MTMR4","run_date":"2026-06-10T05:19:51","timeline":{"discoveries":[{"year":2010,"finding":"MTMR4, a FYVE domain-containing dual-specificity protein phosphatase, attenuates TGFβ signaling by directly dephosphorylating phosphorylated R-Smads (Smad2/3) at their C-terminal SXS motif in early endosomes. Endogenous MTMR4 co-immunoprecipitates with phosphorylated R-Smads; overexpression sequesters activated Smad3 in early endosomes, reducing nuclear translocation; catalytic-dead mutant (C407S) and siRNA knockdown both sustain Smad3 activation.","method":"Co-immunoprecipitation, overexpression/knockdown with phospho-Smad reporter assays, catalytic-dead point mutant (C407S), subcellular fractionation/imaging","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, catalytic-dead mutant, siRNA knockdown, subcellular localization with functional consequence, all in one study with multiple orthogonal methods","pmids":["20061380"],"is_preprint":false},{"year":2010,"finding":"MTMR4 localizes to early endosomes and Rab11/Sec15-positive recycling endosomes and functions as a PtdIns(3)P 3-phosphatase at the interface of early and recycling endosomes. MTMR4 knockdown or expression of catalytically inactive MTMR4(C407A) significantly increases the number of PtdIns(3)P-decorated endosomes. MTMR4 also regulates the subcellular distribution of Rab11 (away from the pericentriolar recycling compartment upon knockdown) and VAMP3 distribution, and overexpression delays transferrin exit from early endosomes.","method":"siRNA knockdown, catalytically inactive dominant-negative construct (C407A), live-cell imaging, PtdIns(3)P reporter assays, fluorescence microscopy of Rab11 and VAMP3","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (knockdown, dominant-negative, lipid reporter, organelle markers) in single rigorous study with clear functional readouts","pmids":["20736309"],"is_preprint":false},{"year":2009,"finding":"MTMR4 is a substrate of the ubiquitin E3 ligase Nedd4; the PY motif of MTMR4 binds to WW domains of Nedd4, the two proteins co-immunoprecipitate and co-localize to late endosomes, and Nedd4 ubiquitinates MTMR4.","method":"Co-immunoprecipitation, co-localization by fluorescence microscopy, ubiquitination assay, PY-motif interaction mapping","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-IP and co-localization with ubiquitination assay; single lab but two orthogonal methods (binding and ubiquitination)","pmids":["19125695"],"is_preprint":false},{"year":2012,"finding":"MTMR4 attenuates BMP signaling by associating with and dephosphorylating activated R-Smads in the cytoplasm. Transcriptional activation by BMPs is controlled by MTMR4 expression level and its phosphatase activity. In Drosophila, ectopic expression of MTMR4 or its homolog CG3632 genetically interacts with BMP/Dpp signaling in wing vein development, and MTMR4 can dephosphorylate Drosophila R-Smad Mad, affecting target gene expression.","method":"Co-immunoprecipitation, phosphatase activity assay, transcriptional reporter assays, Drosophila genetic epistasis (wing vein phenotype), in vivo overexpression","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro dephosphorylation assay, Co-IP, transcriptional reporters, and in vivo Drosophila genetic epistasis across multiple orthogonal methods","pmids":["23150675"],"is_preprint":false},{"year":2018,"finding":"MTMR4 localizes primarily to late endosomes and autophagosomes in A549 cells. MTMR4 knockdown impairs motility, fusion, and fission of PtdIns(3)P-enriched structures, decreases late endosomes, autophagosomes, and lysosomes, and enlarges PtdIns(3)P-enriched early and late endosomes. Under starvation, MTMR4 knockdown inhibits nuclear translocation of TFEB and reduces expression of lysosome-related genes, indicating MTMR4 is required for integrity of endocytic and autophagic pathways.","method":"siRNA knockdown, subcellular localization by fluorescence microscopy, PtdIns(3)P reporter assays, TFEB nuclear translocation assay, organelle dynamics (live imaging), gene expression analysis","journal":"Genes to cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown with multiple functional readouts (organelle dynamics, TFEB localization, gene expression) in a single lab study","pmids":["29962048"],"is_preprint":false},{"year":2019,"finding":"MTMR3 and MTMR4 together regulate STING trafficking by controlling PtdIns(3)P levels. In MTMR3/MTMR4 double-knockout macrophages, STING aberrantly accumulates in enlarged PtdIns(3)P-positive cytosolic puncta instead of trafficking normally from ER to Golgi, leading to enhanced IRF3 phosphorylation and increased type I interferon production after DNA stimulation or HSV-1 infection.","method":"CRISPR/Cas9 double-knockout, fluorescence microscopy of STING localization, IRF3 phosphorylation assay, interferon production assay, PtdIns(3)P reporter","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean double-KO with multiple mechanistic readouts; however MTMR4-specific contribution is not fully separated from MTMR3, single lab","pmids":["30944173"],"is_preprint":false},{"year":2019,"finding":"MTMR4 is dynamically recruited to phagosomes during phagocytosis, negatively regulates FcγR-mediated phagocytosis of IgG-opsonized particles, and controls the duration of PtdIns(3)P on phagosomal membranes. MTMR4 overexpression reduces and Mtmr4 siRNA increases cell-surface FcγR levels with altered pseudopodal F-actin. Mtmr4-knockdown macrophages show extended phagosomal PtdIns(3)P signaling and increased resistance to Mycobacterium marinum-induced phagosome arrest, with enhanced phagosome maturation to acidic compartments.","method":"siRNA knockdown, overexpression, live-cell fluorescence microscopy (phagosome recruitment), PtdIns(3)P reporter on phagosomes, phagocytosis assay (IgG-opsonized particles), Mycobacterium infection model, flow cytometry for FcγR surface levels","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (live recruitment, lipid reporter, phagocytosis assay, infection model, surface receptor quantification) with gain- and loss-of-function","pmids":["31543504"],"is_preprint":false},{"year":2016,"finding":"GFP-tagged MTMR4 is recruited to the Salmonella-containing vacuole (SCV). Depletion of MTMR4 decreases viable intracellular Salmonella by increasing the proportion of SCVs with compromised integrity, targeting them for autophagy-mediated bacterial killing, establishing a role for MTMR4 in PtdIns(3)P regulation required for SCV stability.","method":"GFP-MTMR4 recruitment by fluorescence microscopy, siRNA knockdown, bacterial viability assay, SCV integrity assay, autophagy marker co-localization","journal":"Frontiers in cellular and infection microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — localization with functional consequence (bacterial survival, SCV integrity), knockdown with defined readout, single lab study","pmids":["27625994"],"is_preprint":false},{"year":2021,"finding":"MTMR4 interacts with Nedd4L (an E3 ubiquitin ligase), and two MTMR4 SNVs (identified in asymptomatic LQTS patients) reduce Nedd4L activity, thereby decreasing ubiquitin-mediated degradation of ion channel proteins (KCNQ1 and hERG). CRISPR/Cas9 correction of these SNVs in iPSC-derived cardiomyocytes unmasked the LQTS arrhythmic phenotype, establishing a mechanistic link between MTMR4 variants, Nedd4L regulation, and channel protein stability.","method":"iPSC-derived cardiomyocytes, CRISPR/Cas9 correction of SNVs, Nedd4L activity assay, protein degradation/ubiquitination analysis, electrophysiology, whole-exome sequencing","journal":"Cardiovascular research","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — CRISPR correction with functional rescue, enzymatic activity assay, and protein degradation assay across multiple orthogonal methods in a single rigorous iPSC study","pmids":["32173736"],"is_preprint":false},{"year":2014,"finding":"The PH-GRAM domain of human MTMR4 was crystallized and diffracted to 3.20 Å resolution, providing initial structural data for this lipid-binding domain.","method":"X-ray crystallography (vapour-diffusion crystallization, synchrotron data collection to 3.20 Å)","journal":"Acta crystallographica. Section F, Structural biology communications","confidence":"Low","confidence_rationale":"Tier 1 / Weak — crystal structure reported as preliminary crystallographic analysis only, no functional validation described in abstract","pmids":["25195910"],"is_preprint":false}],"current_model":"MTMR4 is a FYVE domain-containing PtdIns(3)P 3-phosphatase that localizes to early endosomes, recycling endosomes, late endosomes, autophagosomes, and phagosomes, where it dephosphorylates PtdIns(3)P to control endosomal sorting, autophagosome and phagosome maturation, and STING trafficking; it also acts as a dual-specificity phosphatase that directly dephosphorylates activated R-Smads (Smad2/3 for TGFβ; BMP R-Smads) in the cytoplasm/early endosomes to terminate signaling, is itself targeted for ubiquitin-mediated degradation by Nedd4/Nedd4L through a PY-WW domain interaction, and loss of MTMR4 dysregulates TFEB nuclear translocation, phagocytic FcγR surface levels, and Salmonella-containing vacuole integrity."},"narrative":{"mechanistic_narrative":"MTMR4 is a FYVE domain-containing myotubularin-family PtdIns(3)P 3-phosphatase that controls phosphoinositide identity along the endocytic and autophagic pathways and serves as a negative regulator of TGFβ/BMP signaling [PMID:20061380, PMID:20736309]. Acting at the interface of early and recycling endosomes, MTMR4 dephosphorylates PtdIns(3)P, and its loss or catalytic inactivation (C407A/C407S) increases PtdIns(3)P-decorated endosomes, redistributes Rab11 and VAMP3, and delays endosomal cargo exit [PMID:20736309]; at late endosomes and autophagosomes it sustains organelle motility, fusion/fission dynamics, and starvation-induced TFEB nuclear translocation and lysosomal gene expression [PMID:29962048]. The same lipid-phosphatase activity governs membrane-trafficking events relevant to immunity and infection: with MTMR3 it regulates ER-to-Golgi STING trafficking to limit type I interferon output [PMID:30944173], it is recruited to phagosomes to time PtdIns(3)P decay and negatively regulate FcγR-mediated phagocytosis and phagosome maturation [PMID:31543504], and it localizes to the Salmonella-containing vacuole to maintain vacuolar integrity against autophagic killing [PMID:27625994]. As a dual-specificity phosphatase, MTMR4 also directly binds and dephosphorylates the C-terminal SXS motif of activated R-Smads in the cytoplasm and early endosomes, terminating both TGFβ (Smad2/3) and BMP signaling, a function conserved in Drosophila Dpp/Mad signaling [PMID:20061380, PMID:23150675]. MTMR4 is itself regulated by the Nedd4/Nedd4L ubiquitin ligases through a PY-motif/WW-domain interaction that drives its ubiquitination [PMID:19125695], and human MTMR4 variants that impair Nedd4L activity stabilize the cardiac ion channels KCNQ1 and hERG and modify a long-QT arrhythmic phenotype in iPSC-derived cardiomyocytes [PMID:32173736].","teleology":[{"year":2009,"claim":"Established that MTMR4 is not only an enzyme but also a regulated target, linking its turnover to a defined ubiquitin ligase via a PY-WW interaction.","evidence":"Co-IP, co-localization to late endosomes, ubiquitination assay, and PY-motif mapping with Nedd4","pmids":["19125695"],"confidence":"Medium","gaps":["Single lab; functional consequence of MTMR4 degradation on its phosphatase outputs not measured","Did not establish whether ubiquitination is degradative versus regulatory"]},{"year":2010,"claim":"Defined a non-lipid substrate for MTMR4, showing it terminates TGFβ signaling by directly dephosphorylating activated R-Smads in early endosomes.","evidence":"Reciprocal Co-IP with phospho-Smad, catalytic-dead C407S mutant, siRNA knockdown, and subcellular localization in mammalian cells","pmids":["20061380"],"confidence":"High","gaps":["In vitro direct dephosphorylation of purified Smad not shown in this study","Relationship between endosomal sequestration and catalytic activity not fully separated"]},{"year":2010,"claim":"Placed MTMR4 mechanistically as a PtdIns(3)P 3-phosphatase at the early/recycling endosome interface controlling endosomal sorting and recycling traffic.","evidence":"siRNA knockdown, catalytically inactive C407A dominant-negative, PtdIns(3)P reporter, and imaging of Rab11/VAMP3 and transferrin trafficking","pmids":["20736309"],"confidence":"High","gaps":["Did not reconcile lipid-phosphatase role with R-Smad dephosphorylation in the same system","In vivo physiological consequence not addressed"]},{"year":2012,"claim":"Extended the R-Smad-phosphatase function to BMP signaling and demonstrated conservation through Drosophila genetics, generalizing MTMR4 as a brake on multiple TGFβ-superfamily pathways.","evidence":"In vitro phosphatase assay, Co-IP, transcriptional reporters, and Drosophila wing-vein genetic epistasis with Dpp/Mad","pmids":["23150675"],"confidence":"High","gaps":["Endogenous loss-of-function phenotype in vertebrate development not established","Selectivity among R-Smad isoforms not quantified"]},{"year":2016,"claim":"Showed MTMR4 is co-opted at a pathogen-containing compartment, where its PtdIns(3)P regulation maintains Salmonella-containing vacuole integrity and protects bacteria from autophagy.","evidence":"GFP-MTMR4 recruitment imaging, siRNA knockdown, bacterial viability and SCV integrity assays, autophagy marker co-localization","pmids":["27625994"],"confidence":"Medium","gaps":["Direct demonstration of PtdIns(3)P turnover on the SCV not shown","Single lab; host pathway recruiting MTMR4 to the SCV unknown"]},{"year":2018,"claim":"Demonstrated MTMR4 is required for integrity of the endocytic-autophagic continuum, connecting its lipid-phosphatase activity to organelle dynamics and TFEB-driven lysosomal biogenesis.","evidence":"siRNA knockdown with live organelle dynamics imaging, PtdIns(3)P reporters, TFEB nuclear translocation, and lysosomal gene expression analysis","pmids":["29962048"],"confidence":"Medium","gaps":["Mechanism linking PtdIns(3)P control to TFEB regulation not resolved","Single cell line (A549); single lab"]},{"year":2019,"claim":"Connected MTMR4's PtdIns(3)P control to innate immunity by showing that, with MTMR3, it governs STING trafficking and tempers type I interferon responses.","evidence":"CRISPR/Cas9 MTMR3/MTMR4 double-knockout macrophages, STING localization imaging, IRF3 phosphorylation, interferon assays, PtdIns(3)P reporter","pmids":["30944173"],"confidence":"Medium","gaps":["MTMR4-specific contribution not separated from MTMR3","Single lab"]},{"year":2019,"claim":"Established MTMR4 as a dynamic phagosomal regulator that times PtdIns(3)P decay to set FcγR-mediated phagocytosis and phagosome maturation.","evidence":"Gain- and loss-of-function with live phagosome recruitment imaging, phagosomal PtdIns(3)P reporter, IgG-particle phagocytosis assay, Mycobacterium infection, and FcγR surface flow cytometry","pmids":["31543504"],"confidence":"High","gaps":["Mechanism coupling MTMR4 activity to surface FcγR levels not defined","Recruitment machinery to phagosomes not identified"]},{"year":2021,"claim":"Linked MTMR4 to human cardiac disease by showing that variants impairing its Nedd4L interaction stabilize KCNQ1/hERG and modify a long-QT arrhythmic phenotype.","evidence":"iPSC-derived cardiomyocytes with CRISPR/Cas9 SNV correction, Nedd4L activity assay, channel protein degradation analysis, electrophysiology, whole-exome sequencing","pmids":["32173736"],"confidence":"High","gaps":["Whether MTMR4 phosphatase activity contributes to channel regulation versus a purely Nedd4L-modulating role is unresolved","Mechanism by which MTMR4 variants alter Nedd4L activity not detailed"]},{"year":null,"claim":"How MTMR4's dual roles — lipid PtdIns(3)P phosphatase versus protein (R-Smad) phosphatase — are coordinated, and how its recruitment to distinct compartments (endosomes, phagosomes, SCV, STING puncta) is targeted, remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model connecting catalytic activity to substrate/compartment selection beyond a preliminary PH-GRAM crystal","Endogenous knockout/whole-organism phenotype not characterized in the corpus","Whether protein- and lipid-substrate functions are independent or coupled is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,1,3,4,6]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,3]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[1,9]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,3]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,1,2,4]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,3]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[4,6,7]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,3]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,4,5,6]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[4,7]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[5,6]}],"complexes":[],"partners":["NEDD4","NEDD4L","SMAD2","SMAD3","MTMR3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NYA4","full_name":"Phosphatidylinositol-3,5-bisphosphate 3-phosphatase MTMR4","aliases":["FYVE domain-containing dual specificity protein phosphatase 2","FYVE-DSP2","Myotubularin-related protein 4","Phosphatidylinositol-3,5-bisphosphate 3-phosphatase","Zinc finger FYVE domain-containing protein 11"],"length_aa":1195,"mass_kda":133.4,"function":"Lipid phosphatase that specifically dephosphorylates the D-3 position of phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate, generating phosphatidylinositol and phosphatidylinositol 5-phosphate (PubMed:11302699, PubMed:16787938, PubMed:20736309, PubMed:27625994, PubMed:29962048, PubMed:30944173). Decreases the levels of phosphatidylinositol 3-phosphate, a phospholipid found in cell membranes where it acts as key regulator of both cell signaling and intracellular membrane traffic, in a subset of endosomal membranes to negatively regulate both endocytic recycling and trafficking and/or maturation of endosomes toward lysosomes (PubMed:16787938, PubMed:20736309, PubMed:29962048). Through phosphatidylinositol 3-phosphate turnover in phagosome membranes regulates phagocytosis and phagosome maturation (PubMed:31543504). By decreasing phosphatidylinositol 3-monophosphate (PI3P) levels in immune cells it can also regulate the innate immune response (PubMed:30944173). Beside its lipid phosphatase activity, can also function as a molecular adapter to regulate midbody abscission during mitotic cytokinesis (PubMed:25659891). Can also negatively regulate TGF-beta and BMP signaling through Smad proteins dephosphorylation and retention in endosomes (PubMed:20061380, PubMed:23150675)","subcellular_location":"Early endosome membrane; Recycling endosome membrane; Late endosome membrane; Cytoplasmic vesicle, phagosome membrane","url":"https://www.uniprot.org/uniprotkb/Q9NYA4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/MTMR4","classification":"Not Classified","n_dependent_lines":93,"n_total_lines":1208,"dependency_fraction":0.07698675496688742},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/MTMR4","total_profiled":1310},"omim":[{"mim_id":"603559","title":"MYOTUBULARIN-RELATED PROTEIN 4; MTMR4","url":"https://www.omim.org/entry/603559"},{"mim_id":"603558","title":"MYOTUBULARIN-RELATED PROTEIN 3; MTMR3","url":"https://www.omim.org/entry/603558"},{"mim_id":"300415","title":"MYOTUBULARIN; MTM1","url":"https://www.omim.org/entry/300415"},{"mim_id":"300171","title":"MYOTUBULARIN-RELATED PROTEIN 1; MTMR1","url":"https://www.omim.org/entry/300171"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/MTMR4"},"hgnc":{"alias_symbol":["KIAA0647","ZFYVE11"],"prev_symbol":[]},"alphafold":{"accession":"Q9NYA4","domains":[{"cath_id":"2.30.29.30","chopping":"15-120","consensus_level":"high","plddt":92.0542,"start":15,"end":120},{"cath_id":"-","chopping":"154-266_304-572","consensus_level":"medium","plddt":93.2691,"start":154,"end":572},{"cath_id":"3.30.40.10","chopping":"1112-1193","consensus_level":"high","plddt":84.4379,"start":1112,"end":1193}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NYA4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NYA4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NYA4-F1-predicted_aligned_error_v6.png","plddt_mean":65.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MTMR4","jax_strain_url":"https://www.jax.org/strain/search?query=MTMR4"},"sequence":{"accession":"Q9NYA4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NYA4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NYA4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NYA4"}},"corpus_meta":[{"pmid":"20061380","id":"PMC_20061380","title":"MTMR4 attenuates transforming growth factor beta (TGFbeta) signaling by dephosphorylating R-Smads in endosomes.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20061380","citation_count":46,"is_preprint":false},{"pmid":"20736309","id":"PMC_20736309","title":"The myotubularin phosphatase MTMR4 regulates sorting from early endosomes.","date":"2010","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/20736309","citation_count":46,"is_preprint":false},{"pmid":"32173736","id":"PMC_32173736","title":"MTMR4 SNVs modulate ion channel degradation and clinical severity in congenital long QT syndrome: insights in the mechanism of action of protective modifier genes.","date":"2021","source":"Cardiovascular research","url":"https://pubmed.ncbi.nlm.nih.gov/32173736","citation_count":38,"is_preprint":false},{"pmid":"19125695","id":"PMC_19125695","title":"The inositol phosphatase MTMR4 is a novel target of the ubiquitin ligase Nedd4.","date":"2009","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/19125695","citation_count":21,"is_preprint":false},{"pmid":"30944173","id":"PMC_30944173","title":"PtdIns3P phosphatases MTMR3 and MTMR4 negatively regulate innate immune responses to DNA through modulating STING trafficking.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30944173","citation_count":18,"is_preprint":false},{"pmid":"23150675","id":"PMC_23150675","title":"Myotubularin-related protein 4 (MTMR4) attenuates BMP/Dpp signaling by dephosphorylation of Smad proteins.","date":"2012","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23150675","citation_count":18,"is_preprint":false},{"pmid":"29962048","id":"PMC_29962048","title":"MTMR4, a phosphoinositide-specific 3'-phosphatase, regulates TFEB activity and the endocytic and autophagic pathways.","date":"2018","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/29962048","citation_count":15,"is_preprint":false},{"pmid":"27625994","id":"PMC_27625994","title":"MTMR4 Is Required for the Stability of the Salmonella-Containing Vacuole.","date":"2016","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/27625994","citation_count":7,"is_preprint":false},{"pmid":"31543504","id":"PMC_31543504","title":"The myotubularin MTMR4 regulates phagosomal phosphatidylinositol 3-phosphate turnover and phagocytosis.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31543504","citation_count":5,"is_preprint":false},{"pmid":"42128250","id":"PMC_42128250","title":"MTMR4 variants have opposite gene-specific impact on life-threatening arrhythmic risk in type 1 and 2 long QT syndrome.","date":"2026","source":"European heart journal","url":"https://pubmed.ncbi.nlm.nih.gov/42128250","citation_count":0,"is_preprint":false},{"pmid":"25195910","id":"PMC_25195910","title":"Crystallization and preliminary X-ray crystallographic analysis of the PH-GRAM domain of human MTMR4.","date":"2014","source":"Acta crystallographica. Section F, Structural biology communications","url":"https://pubmed.ncbi.nlm.nih.gov/25195910","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7956,"output_tokens":3225,"usd":0.036122,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10536,"output_tokens":3752,"usd":0.07324,"stage2_stop_reason":"end_turn"},"total_usd":0.109362,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"MTMR4, a FYVE domain-containing dual-specificity protein phosphatase, attenuates TGFβ signaling by directly dephosphorylating phosphorylated R-Smads (Smad2/3) at their C-terminal SXS motif in early endosomes. Endogenous MTMR4 co-immunoprecipitates with phosphorylated R-Smads; overexpression sequesters activated Smad3 in early endosomes, reducing nuclear translocation; catalytic-dead mutant (C407S) and siRNA knockdown both sustain Smad3 activation.\",\n      \"method\": \"Co-immunoprecipitation, overexpression/knockdown with phospho-Smad reporter assays, catalytic-dead point mutant (C407S), subcellular fractionation/imaging\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, catalytic-dead mutant, siRNA knockdown, subcellular localization with functional consequence, all in one study with multiple orthogonal methods\",\n      \"pmids\": [\"20061380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"MTMR4 localizes to early endosomes and Rab11/Sec15-positive recycling endosomes and functions as a PtdIns(3)P 3-phosphatase at the interface of early and recycling endosomes. MTMR4 knockdown or expression of catalytically inactive MTMR4(C407A) significantly increases the number of PtdIns(3)P-decorated endosomes. MTMR4 also regulates the subcellular distribution of Rab11 (away from the pericentriolar recycling compartment upon knockdown) and VAMP3 distribution, and overexpression delays transferrin exit from early endosomes.\",\n      \"method\": \"siRNA knockdown, catalytically inactive dominant-negative construct (C407A), live-cell imaging, PtdIns(3)P reporter assays, fluorescence microscopy of Rab11 and VAMP3\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (knockdown, dominant-negative, lipid reporter, organelle markers) in single rigorous study with clear functional readouts\",\n      \"pmids\": [\"20736309\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"MTMR4 is a substrate of the ubiquitin E3 ligase Nedd4; the PY motif of MTMR4 binds to WW domains of Nedd4, the two proteins co-immunoprecipitate and co-localize to late endosomes, and Nedd4 ubiquitinates MTMR4.\",\n      \"method\": \"Co-immunoprecipitation, co-localization by fluorescence microscopy, ubiquitination assay, PY-motif interaction mapping\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-IP and co-localization with ubiquitination assay; single lab but two orthogonal methods (binding and ubiquitination)\",\n      \"pmids\": [\"19125695\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"MTMR4 attenuates BMP signaling by associating with and dephosphorylating activated R-Smads in the cytoplasm. Transcriptional activation by BMPs is controlled by MTMR4 expression level and its phosphatase activity. In Drosophila, ectopic expression of MTMR4 or its homolog CG3632 genetically interacts with BMP/Dpp signaling in wing vein development, and MTMR4 can dephosphorylate Drosophila R-Smad Mad, affecting target gene expression.\",\n      \"method\": \"Co-immunoprecipitation, phosphatase activity assay, transcriptional reporter assays, Drosophila genetic epistasis (wing vein phenotype), in vivo overexpression\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro dephosphorylation assay, Co-IP, transcriptional reporters, and in vivo Drosophila genetic epistasis across multiple orthogonal methods\",\n      \"pmids\": [\"23150675\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"MTMR4 localizes primarily to late endosomes and autophagosomes in A549 cells. MTMR4 knockdown impairs motility, fusion, and fission of PtdIns(3)P-enriched structures, decreases late endosomes, autophagosomes, and lysosomes, and enlarges PtdIns(3)P-enriched early and late endosomes. Under starvation, MTMR4 knockdown inhibits nuclear translocation of TFEB and reduces expression of lysosome-related genes, indicating MTMR4 is required for integrity of endocytic and autophagic pathways.\",\n      \"method\": \"siRNA knockdown, subcellular localization by fluorescence microscopy, PtdIns(3)P reporter assays, TFEB nuclear translocation assay, organelle dynamics (live imaging), gene expression analysis\",\n      \"journal\": \"Genes to cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown with multiple functional readouts (organelle dynamics, TFEB localization, gene expression) in a single lab study\",\n      \"pmids\": [\"29962048\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"MTMR3 and MTMR4 together regulate STING trafficking by controlling PtdIns(3)P levels. In MTMR3/MTMR4 double-knockout macrophages, STING aberrantly accumulates in enlarged PtdIns(3)P-positive cytosolic puncta instead of trafficking normally from ER to Golgi, leading to enhanced IRF3 phosphorylation and increased type I interferon production after DNA stimulation or HSV-1 infection.\",\n      \"method\": \"CRISPR/Cas9 double-knockout, fluorescence microscopy of STING localization, IRF3 phosphorylation assay, interferon production assay, PtdIns(3)P reporter\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean double-KO with multiple mechanistic readouts; however MTMR4-specific contribution is not fully separated from MTMR3, single lab\",\n      \"pmids\": [\"30944173\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"MTMR4 is dynamically recruited to phagosomes during phagocytosis, negatively regulates FcγR-mediated phagocytosis of IgG-opsonized particles, and controls the duration of PtdIns(3)P on phagosomal membranes. MTMR4 overexpression reduces and Mtmr4 siRNA increases cell-surface FcγR levels with altered pseudopodal F-actin. Mtmr4-knockdown macrophages show extended phagosomal PtdIns(3)P signaling and increased resistance to Mycobacterium marinum-induced phagosome arrest, with enhanced phagosome maturation to acidic compartments.\",\n      \"method\": \"siRNA knockdown, overexpression, live-cell fluorescence microscopy (phagosome recruitment), PtdIns(3)P reporter on phagosomes, phagocytosis assay (IgG-opsonized particles), Mycobacterium infection model, flow cytometry for FcγR surface levels\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (live recruitment, lipid reporter, phagocytosis assay, infection model, surface receptor quantification) with gain- and loss-of-function\",\n      \"pmids\": [\"31543504\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"GFP-tagged MTMR4 is recruited to the Salmonella-containing vacuole (SCV). Depletion of MTMR4 decreases viable intracellular Salmonella by increasing the proportion of SCVs with compromised integrity, targeting them for autophagy-mediated bacterial killing, establishing a role for MTMR4 in PtdIns(3)P regulation required for SCV stability.\",\n      \"method\": \"GFP-MTMR4 recruitment by fluorescence microscopy, siRNA knockdown, bacterial viability assay, SCV integrity assay, autophagy marker co-localization\",\n      \"journal\": \"Frontiers in cellular and infection microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — localization with functional consequence (bacterial survival, SCV integrity), knockdown with defined readout, single lab study\",\n      \"pmids\": [\"27625994\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"MTMR4 interacts with Nedd4L (an E3 ubiquitin ligase), and two MTMR4 SNVs (identified in asymptomatic LQTS patients) reduce Nedd4L activity, thereby decreasing ubiquitin-mediated degradation of ion channel proteins (KCNQ1 and hERG). CRISPR/Cas9 correction of these SNVs in iPSC-derived cardiomyocytes unmasked the LQTS arrhythmic phenotype, establishing a mechanistic link between MTMR4 variants, Nedd4L regulation, and channel protein stability.\",\n      \"method\": \"iPSC-derived cardiomyocytes, CRISPR/Cas9 correction of SNVs, Nedd4L activity assay, protein degradation/ubiquitination analysis, electrophysiology, whole-exome sequencing\",\n      \"journal\": \"Cardiovascular research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — CRISPR correction with functional rescue, enzymatic activity assay, and protein degradation assay across multiple orthogonal methods in a single rigorous iPSC study\",\n      \"pmids\": [\"32173736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The PH-GRAM domain of human MTMR4 was crystallized and diffracted to 3.20 Å resolution, providing initial structural data for this lipid-binding domain.\",\n      \"method\": \"X-ray crystallography (vapour-diffusion crystallization, synchrotron data collection to 3.20 Å)\",\n      \"journal\": \"Acta crystallographica. Section F, Structural biology communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 1 / Weak — crystal structure reported as preliminary crystallographic analysis only, no functional validation described in abstract\",\n      \"pmids\": [\"25195910\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MTMR4 is a FYVE domain-containing PtdIns(3)P 3-phosphatase that localizes to early endosomes, recycling endosomes, late endosomes, autophagosomes, and phagosomes, where it dephosphorylates PtdIns(3)P to control endosomal sorting, autophagosome and phagosome maturation, and STING trafficking; it also acts as a dual-specificity phosphatase that directly dephosphorylates activated R-Smads (Smad2/3 for TGFβ; BMP R-Smads) in the cytoplasm/early endosomes to terminate signaling, is itself targeted for ubiquitin-mediated degradation by Nedd4/Nedd4L through a PY-WW domain interaction, and loss of MTMR4 dysregulates TFEB nuclear translocation, phagocytic FcγR surface levels, and Salmonella-containing vacuole integrity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"MTMR4 is a FYVE domain-containing myotubularin-family PtdIns(3)P 3-phosphatase that controls phosphoinositide identity along the endocytic and autophagic pathways and serves as a negative regulator of TGFβ/BMP signaling [#0, #1]. Acting at the interface of early and recycling endosomes, MTMR4 dephosphorylates PtdIns(3)P, and its loss or catalytic inactivation (C407A/C407S) increases PtdIns(3)P-decorated endosomes, redistributes Rab11 and VAMP3, and delays endosomal cargo exit [#1]; at late endosomes and autophagosomes it sustains organelle motility, fusion/fission dynamics, and starvation-induced TFEB nuclear translocation and lysosomal gene expression [#4]. The same lipid-phosphatase activity governs membrane-trafficking events relevant to immunity and infection: with MTMR3 it regulates ER-to-Golgi STING trafficking to limit type I interferon output [#5], it is recruited to phagosomes to time PtdIns(3)P decay and negatively regulate FcγR-mediated phagocytosis and phagosome maturation [#6], and it localizes to the Salmonella-containing vacuole to maintain vacuolar integrity against autophagic killing [#7]. As a dual-specificity phosphatase, MTMR4 also directly binds and dephosphorylates the C-terminal SXS motif of activated R-Smads in the cytoplasm and early endosomes, terminating both TGFβ (Smad2/3) and BMP signaling, a function conserved in Drosophila Dpp/Mad signaling [#0, #3]. MTMR4 is itself regulated by the Nedd4/Nedd4L ubiquitin ligases through a PY-motif/WW-domain interaction that drives its ubiquitination [#2], and human MTMR4 variants that impair Nedd4L activity stabilize the cardiac ion channels KCNQ1 and hERG and modify a long-QT arrhythmic phenotype in iPSC-derived cardiomyocytes [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established that MTMR4 is not only an enzyme but also a regulated target, linking its turnover to a defined ubiquitin ligase via a PY-WW interaction.\",\n      \"evidence\": \"Co-IP, co-localization to late endosomes, ubiquitination assay, and PY-motif mapping with Nedd4\",\n      \"pmids\": [\"19125695\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; functional consequence of MTMR4 degradation on its phosphatase outputs not measured\", \"Did not establish whether ubiquitination is degradative versus regulatory\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined a non-lipid substrate for MTMR4, showing it terminates TGFβ signaling by directly dephosphorylating activated R-Smads in early endosomes.\",\n      \"evidence\": \"Reciprocal Co-IP with phospho-Smad, catalytic-dead C407S mutant, siRNA knockdown, and subcellular localization in mammalian cells\",\n      \"pmids\": [\"20061380\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vitro direct dephosphorylation of purified Smad not shown in this study\", \"Relationship between endosomal sequestration and catalytic activity not fully separated\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Placed MTMR4 mechanistically as a PtdIns(3)P 3-phosphatase at the early/recycling endosome interface controlling endosomal sorting and recycling traffic.\",\n      \"evidence\": \"siRNA knockdown, catalytically inactive C407A dominant-negative, PtdIns(3)P reporter, and imaging of Rab11/VAMP3 and transferrin trafficking\",\n      \"pmids\": [\"20736309\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not reconcile lipid-phosphatase role with R-Smad dephosphorylation in the same system\", \"In vivo physiological consequence not addressed\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Extended the R-Smad-phosphatase function to BMP signaling and demonstrated conservation through Drosophila genetics, generalizing MTMR4 as a brake on multiple TGFβ-superfamily pathways.\",\n      \"evidence\": \"In vitro phosphatase assay, Co-IP, transcriptional reporters, and Drosophila wing-vein genetic epistasis with Dpp/Mad\",\n      \"pmids\": [\"23150675\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Endogenous loss-of-function phenotype in vertebrate development not established\", \"Selectivity among R-Smad isoforms not quantified\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed MTMR4 is co-opted at a pathogen-containing compartment, where its PtdIns(3)P regulation maintains Salmonella-containing vacuole integrity and protects bacteria from autophagy.\",\n      \"evidence\": \"GFP-MTMR4 recruitment imaging, siRNA knockdown, bacterial viability and SCV integrity assays, autophagy marker co-localization\",\n      \"pmids\": [\"27625994\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct demonstration of PtdIns(3)P turnover on the SCV not shown\", \"Single lab; host pathway recruiting MTMR4 to the SCV unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrated MTMR4 is required for integrity of the endocytic-autophagic continuum, connecting its lipid-phosphatase activity to organelle dynamics and TFEB-driven lysosomal biogenesis.\",\n      \"evidence\": \"siRNA knockdown with live organelle dynamics imaging, PtdIns(3)P reporters, TFEB nuclear translocation, and lysosomal gene expression analysis\",\n      \"pmids\": [\"29962048\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking PtdIns(3)P control to TFEB regulation not resolved\", \"Single cell line (A549); single lab\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Connected MTMR4's PtdIns(3)P control to innate immunity by showing that, with MTMR3, it governs STING trafficking and tempers type I interferon responses.\",\n      \"evidence\": \"CRISPR/Cas9 MTMR3/MTMR4 double-knockout macrophages, STING localization imaging, IRF3 phosphorylation, interferon assays, PtdIns(3)P reporter\",\n      \"pmids\": [\"30944173\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"MTMR4-specific contribution not separated from MTMR3\", \"Single lab\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Established MTMR4 as a dynamic phagosomal regulator that times PtdIns(3)P decay to set FcγR-mediated phagocytosis and phagosome maturation.\",\n      \"evidence\": \"Gain- and loss-of-function with live phagosome recruitment imaging, phagosomal PtdIns(3)P reporter, IgG-particle phagocytosis assay, Mycobacterium infection, and FcγR surface flow cytometry\",\n      \"pmids\": [\"31543504\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism coupling MTMR4 activity to surface FcγR levels not defined\", \"Recruitment machinery to phagosomes not identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linked MTMR4 to human cardiac disease by showing that variants impairing its Nedd4L interaction stabilize KCNQ1/hERG and modify a long-QT arrhythmic phenotype.\",\n      \"evidence\": \"iPSC-derived cardiomyocytes with CRISPR/Cas9 SNV correction, Nedd4L activity assay, channel protein degradation analysis, electrophysiology, whole-exome sequencing\",\n      \"pmids\": [\"32173736\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether MTMR4 phosphatase activity contributes to channel regulation versus a purely Nedd4L-modulating role is unresolved\", \"Mechanism by which MTMR4 variants alter Nedd4L activity not detailed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How MTMR4's dual roles — lipid PtdIns(3)P phosphatase versus protein (R-Smad) phosphatase — are coordinated, and how its recruitment to distinct compartments (endosomes, phagosomes, SCV, STING puncta) is targeted, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model connecting catalytic activity to substrate/compartment selection beyond a preliminary PH-GRAM crystal\", \"Endogenous knockout/whole-organism phenotype not characterized in the corpus\", \"Whether protein- and lipid-substrate functions are independent or coupled is unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 1, 3, 4, 6]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [1, 9]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 1, 2, 4]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [4, 6, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 4, 5, 6]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [4, 7]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [5, 6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NEDD4\", \"NEDD4L\", \"SMAD2\", \"SMAD3\", \"MTMR3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}