{"gene":"MPP4","run_date":"2026-06-10T02:59:51","timeline":{"discoveries":[{"year":2001,"finding":"MPP4 is a retina-specific member of the p55 subfamily of MAGUK proteins, containing a single PDZ domain, SH3 domain, and guanylate kinase-like (GUK) domain, with 637 amino acids encoded by a gene on chromosome 2q31-33.","method":"Full-length cDNA cloning, sequence alignment to protein databases, genomic organization analysis","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — molecular cloning with domain characterization, single lab, limited functional follow-up in this paper","pmids":["11414766"],"is_preprint":false},{"year":2003,"finding":"MPP4 protein localizes to the connecting cilia and synaptic terminals of cone and rod photoreceptors in bovine and porcine retina, suggesting roles at membrane-cytoskeleton interfaces in distinct structural and functional compartments.","method":"Immunofluorescence microscopy on mammalian retina sections using affinity-purified anti-MPP4 antibodies; Western blot of retinal extracts and transfected 293-Ebna cells","journal":"Investigative ophthalmology & visual science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct protein localization by immunofluorescence with antibody specificity validated by transfected cells; single lab","pmids":["14638699"],"is_preprint":false},{"year":2003,"finding":"Mouse Mpp4 mRNA is expressed postnatally (not embryonically) and is exclusively localized to photoreceptor cells in the retina; Mpp4 protein localizes specifically to rod (but not cone) photoreceptor synaptic terminals.","method":"Microarray expression analysis, quantitative RT-PCR, in situ hybridization, immunofluorescence on retinal sections including cone-specific GFP transgenic mice","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (microarray, qRT-PCR, ISH, immunofluorescence) in single lab establishing localization","pmids":["12859944"],"is_preprint":false},{"year":2004,"finding":"MPP4 associates with the CRB1 protein complex at the outer limiting membrane (OLM) of the retina, co-localizing with Crb1, Mupp1, and Pals1/Mpp5.","method":"Immunohistochemistry and co-immunoprecipitation in mouse retina; confocal microscopy","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — co-localization and co-immunoprecipitation in tissue context; replicated across multiple papers","pmids":["15316081"],"is_preprint":false},{"year":2005,"finding":"MPP4 is recruited to the CRB1 complex through direct interaction with MPP5 (PALS1); MPP4 and MPP5 co-localize at the OLM in human and mouse retina. Yeast two-hybrid and GST pull-down identified the direct MPP4–MPP5 interaction, and 3D homology modeling suggested a mechanism regulating recruitment of homo- and heterodimers of MPP4 and MPP5 to the complex.","method":"Yeast two-hybrid screening, GST pull-down assay, co-immunoprecipitation, immunohistochemistry, immunoelectron microscopy, 3D homology modeling","journal":"Investigative ophthalmology & visual science","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (yeast two-hybrid, GST pull-down, Co-IP, structural modeling) establishing direct protein interaction","pmids":["15914641"],"is_preprint":false},{"year":2005,"finding":"MPP4 directly interacts with Veli proteins (Veli1, Veli2, Veli3) via L27 heterodimerization in vitro, and co-localizes with Veli3 at photoreceptor synaptic terminals in the outer plexiform layer; MPP5 and MPP4 associate with Veli3 at distinct intercellular junctions in the retina.","method":"In vitro L27 heterodimerization assay, immunofluorescence microscopy, specific polyclonal and monoclonal antibody generation","journal":"The Journal of comparative neurology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro reconstitution of L27 domain interaction plus immunofluorescence colocalization, corroborated by subsequent studies","pmids":["15558731"],"is_preprint":false},{"year":2006,"finding":"In Mpp4 knockout mice, Psd95 is lost from presynaptic membranes of rods and cones, and total retinal Psd95 protein levels are significantly reduced (suggesting Mpp4 is involved in Psd95 turnover). Veli3 protein levels are unchanged but its correct presynaptic localization depends on Mpp4. Loss of Mpp4 only sporadically causes photoreceptor displacement without changing the Crb complex at the OLM.","method":"Mpp4 knockout mouse analysis, immunohistochemistry, Western blot, scanning laser ophthalmoscopy, electroretinography","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean knockout mouse with multiple orthogonal readouts (IHC, Western, ERG, ophthalmoscopy); replicated in subsequent studies","pmids":["16520334"],"is_preprint":false},{"year":2006,"finding":"MPP3 and MPP4 co-localize with DLG1 at the outer plexiform layer, and mouse Dlg1 forms separate complexes with Mpp3 and Mpp4 in vivo.","method":"Co-immunoprecipitation from mouse retina, immunohistochemistry, confocal microscopy","journal":"The FEBS journal","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — reciprocal Co-IP from tissue demonstrating distinct complexes; single lab","pmids":["16519681"],"is_preprint":false},{"year":2007,"finding":"Mpp4 organizes a presynaptic protein complex at rod photoreceptor synaptic terminals that includes plasma membrane Ca2+-ATPases (PMCAs), Veli3, and PSD95. In Mpp4 knockout mice, PMCAs are lost from rod presynaptic membranes, synaptic ribbons are enlarged (indicative of elevated Ca2+), SERCA2 is increased, and IP3RII distribution is shifted away from synaptic terminals. Synaptic transmission to second-order neurons is maintained but reduced in amplitude.","method":"Mpp4 knockout mouse, immunofluorescence, co-immunoprecipitation, Western blot, electroretinography","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — knockout mouse with multiple orthogonal mechanistic readouts; Co-IP demonstrating complex membership; corroborated by independent lab","pmids":["17341488"],"is_preprint":false},{"year":2008,"finding":"Immunoaffinity purification of the MPP4-associated protein complex from retina identified: previously known components Veli3 and Psd95-beta (interaction mediated by N-terminal L27 domains of MPP4 and PSD95beta), and novel associated proteins recoverin and Hsc70.","method":"Immunoaffinity chromatography with anti-MPP4 monoclonal antibody, 2D electrophoresis, mass spectrometry","journal":"Experimental eye research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proteomic immunoaffinity approach identified complex components; single lab, MS-based identification","pmids":["18955048"],"is_preprint":false},{"year":2009,"finding":"MPP4 is required for the membrane localization of TMEM16B at photoreceptor ribbon synapses; TMEM16B is absent from photoreceptor membranes in MPP4-deficient mice. TMEM16B co-localizes with PSD95, VELI3, and MPP4 at ribbon synapses and contains a PDZ class I binding motif capable of interacting with PSD95.","method":"Immunohistochemistry and immunofluorescence in MPP4-deficient mice; co-localization analysis; PDZ binding motif analysis","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — knockout mouse demonstrating MPP4-dependent membrane recruitment of TMEM16B; corroborated by localization studies","pmids":["19474308"],"is_preprint":false},{"year":2009,"finding":"MPP4 and PSD95beta are both essential for correct localization of PMCA at the presynaptic plasma membrane of photoreceptors. MPP4 deficiency causes loss of both PMCA and PSD95 from the photoreceptor synapse; truncation of MPP4's C-terminal part causes loss of PSD95 and mislocalization of PMCA. PSD95beta (not PSD95alpha) can restore plasma membrane localization of MPP4 and PMCA1 in Mpp4 mutant primary retinal explants.","method":"Mpp4 and Psd95 mutant mice, lentiviral molecular replacement in primary retinal explants, immunofluorescence microscopy","journal":"Molecular and cellular neurosciences","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — knockout mice combined with lentiviral rescue experiments in primary retinal explants; multiple orthogonal approaches; identifies isoform-specific (PSD95beta) requirement","pmids":["19233278"],"is_preprint":false},{"year":2018,"finding":"CRX transcription factor controls presynaptic active zone formation in photoreceptors; MPP4 is among the CRX target genes whose expression is aberrant in Crx-mutant retinas, linking CRX-dependent transcriptional control to MPP4-containing presynaptic scaffold assembly.","method":"Immunohistochemistry of Crx mutant mouse retinas; integrated analysis with CRX- and NRL-ChIP-Seq data and retinal transcriptomics","journal":"Human molecular genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — MPP4 identified as aberrantly expressed in Crx mutants by IHC; no direct mechanistic experiment on MPP4 itself in this study","pmids":["30084954"],"is_preprint":false}],"current_model":"MPP4 (DLG6) is a retina-specific MAGUK scaffolding protein localized to the presynaptic plasma membrane of rod photoreceptor synaptic terminals and (with MPP5) to the outer limiting membrane; it is recruited to the CRB1 complex via direct L27-domain-mediated interaction with MPP5, directly interacts with Veli proteins (Veli1/2/3) via L27 heterodimerization, and organizes a presynaptic protein complex containing PSD95beta (via L27 interaction), Veli3, plasma membrane Ca2+-ATPases (PMCAs), and TMEM16B, thereby regulating calcium homeostasis and neurotransmitter release at the photoreceptor ribbon synapse."},"narrative":{"mechanistic_narrative":"MPP4 (DLG6) is a retina-specific p55-subfamily MAGUK scaffolding protein that organizes a presynaptic protein complex at rod photoreceptor ribbon synapses to control calcium homeostasis and neurotransmitter release [PMID:11414766, PMID:17341488]. It localizes to photoreceptor synaptic terminals and to the outer limiting membrane, where it is recruited into the CRB1 complex through a direct L27-domain interaction with MPP5/PALS1 [PMID:15316081, PMID:15914641]. Through L27 heterodimerization MPP4 binds Veli proteins (Veli1/2/3) and PSD95beta, building a presynaptic scaffold whose assembly MPP4 nucleates [PMID:15558731, PMID:18955048]. Knockout and molecular-replacement studies establish MPP4 as essential for membrane recruitment of downstream synaptic components: loss of Mpp4 removes PSD95 and plasma membrane Ca2+-ATPases (PMCAs) from presynaptic membranes, mislocalizes Veli3 and TMEM16B, enlarges synaptic ribbons consistent with elevated Ca2+, and reduces the amplitude of synaptic transmission to second-order neurons [PMID:16520334, PMID:17341488, PMID:19474308, PMID:19233278]. PSD95beta specifically restores plasma membrane targeting of MPP4 and PMCA in Mpp4-mutant explants, defining an isoform-specific scaffolding requirement [PMID:19233278].","teleology":[{"year":2001,"claim":"Established the molecular identity of MPP4 as a retina-restricted MAGUK, defining the domain architecture (PDZ, SH3, GUK) that would later explain its scaffolding behavior.","evidence":"Full-length cDNA cloning, sequence alignment, and genomic organization analysis","pmids":["11414766"],"confidence":"Medium","gaps":["No functional or interaction data in this report","Cellular localization not resolved"]},{"year":2003,"claim":"Localized MPP4 protein to photoreceptor synaptic terminals (and connecting cilia), placing the scaffold at specific membrane-cytoskeleton compartments and restricting its action to rod synaptic terminals.","evidence":"Immunofluorescence on mammalian retina, in situ hybridization, qRT-PCR, and microarray expression analysis","pmids":["14638699","12859944"],"confidence":"Medium","gaps":["No binding partners identified","Functional role at terminals not tested"]},{"year":2004,"claim":"Connected MPP4 to a defined retinal scaffold by showing its association with the CRB1 complex at the outer limiting membrane, embedding MPP4 in an established polarity/junction module.","evidence":"Co-immunoprecipitation and confocal immunohistochemistry in mouse retina","pmids":["15316081"],"confidence":"Medium","gaps":["Direct versus indirect association not distinguished","Recruitment mechanism unknown"]},{"year":2005,"claim":"Defined the molecular mechanism of MPP4 recruitment, showing a direct MPP5/PALS1 interaction recruits MPP4 to the CRB1 complex and direct L27 heterodimerization with Veli proteins anchors it at synaptic terminals.","evidence":"Yeast two-hybrid, GST pull-down, Co-IP, in vitro L27 heterodimerization, immunoelectron microscopy, and 3D homology modeling","pmids":["15914641","15558731"],"confidence":"High","gaps":["Stoichiometry of homo/heterodimers in vivo not resolved","Functional consequence of these interactions not yet tested"]},{"year":2006,"claim":"Demonstrated MPP4 is functionally required for presynaptic organization in vivo, since Mpp4 loss depletes PSD95 from presynaptic membranes and mislocalizes Veli3 without disrupting the OLM Crb complex.","evidence":"Mpp4 knockout mouse with immunohistochemistry, Western blot, ERG, and ophthalmoscopy; reciprocal Co-IP of Dlg1 complexes","pmids":["16520334","16519681"],"confidence":"High","gaps":["Mechanism of PSD95 turnover/stabilization not defined","Why OLM Crb complex is spared not explained"]},{"year":2007,"claim":"Established the physiological output of the MPP4 scaffold by linking it to calcium handling, showing the complex contains PMCAs and that Mpp4 loss removes PMCAs, enlarges ribbons, and reduces synaptic transmission.","evidence":"Mpp4 knockout mouse with immunofluorescence, Co-IP, Western blot, and electroretinography","pmids":["17341488"],"confidence":"High","gaps":["Direct measurement of presynaptic Ca2+ dynamics not performed","Causal chain from PMCA loss to ribbon enlargement inferred"]},{"year":2008,"claim":"Refined complex composition by immunoaffinity proteomics, confirming L27-mediated PSD95beta and Veli3 membership and adding recoverin and Hsc70 as associated proteins.","evidence":"Anti-MPP4 immunoaffinity chromatography, 2D electrophoresis, and mass spectrometry from retina","pmids":["18955048"],"confidence":"Medium","gaps":["Roles of recoverin and Hsc70 in the complex untested","Direct versus indirect associations not resolved by MS"]},{"year":2009,"claim":"Extended the scaffold's recruitment role to the calcium-activated channel TMEM16B and pinned PMCA targeting to a specific PSD95beta isoform, defining MPP4 as the apical organizer of presynaptic membrane protein localization.","evidence":"MPP4-deficient mice with immunohistochemistry; lentiviral molecular replacement in retinal explants; PDZ binding motif analysis","pmids":["19474308","19233278"],"confidence":"High","gaps":["Functional consequence of TMEM16B mislocalization on transmission not measured","Structural basis of PSD95beta isoform specificity unknown"]},{"year":2018,"claim":"Placed MPP4 within transcriptional control of synapse formation by identifying it as a CRX target gene whose expression is altered in Crx-mutant retinas.","evidence":"Immunohistochemistry of Crx mutant retinas integrated with CRX/NRL ChIP-Seq and transcriptomics","pmids":["30084954"],"confidence":"Low","gaps":["No direct mechanistic experiment on MPP4 in this study","Direct CRX regulation of the MPP4 promoter not validated"]},{"year":null,"claim":"Whether MPP4 dysfunction causes human retinal disease, and how the scaffold quantitatively governs presynaptic Ca2+ dynamics and neurotransmission, remain open.","evidence":"","pmids":[],"confidence":"Low","gaps":["No timeline evidence of a causative human Mendelian mutation","Direct presynaptic Ca2+ imaging in Mpp4-null synapses not reported","Structural model of the assembled scaffold absent"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[4,5,9,11]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[1,2,8,11]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[8,10]}],"complexes":["CRB1 complex","MPP4 presynaptic scaffold (MPP4-PSD95beta-Veli3-PMCA-TMEM16B)"],"partners":["MPP5","VELI3","DLG4","MPP3","DLG1","CRB1","TMEM16B","ATP2B1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96JB8","full_name":"MAGUK p55 subfamily member 4","aliases":["Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 5 protein","Discs large homolog 6"],"length_aa":637,"mass_kda":72.8,"function":"May play a role in retinal photoreceptors development","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q96JB8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/MPP4","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/MPP4","total_profiled":1310},"omim":[{"mim_id":"619030","title":"SKELETAL MUSCLE GLYCOGEN CONTENT AND METABOLISM QUANTITATIVE TRAIT LOCUS; SMGMQTL","url":"https://www.omim.org/entry/619030"},{"mim_id":"612332","title":"LIN7 HOMOLOG C, CRUMBS CELL POLARITY COMPLEX COMPONENT; LIN7C","url":"https://www.omim.org/entry/612332"},{"mim_id":"606575","title":"MEMBRANE PROTEIN, PALMITOYLATED 4; MPP4","url":"https://www.omim.org/entry/606575"},{"mim_id":"604976","title":"PROTEIN KINASE, AMP-ACTIVATED, NONCATALYTIC, GAMMA-3; PRKAG3","url":"https://www.omim.org/entry/604976"},{"mim_id":"603182","title":"INTERLEUKIN ENHANCER-BINDING FACTOR 3; ILF3","url":"https://www.omim.org/entry/603182"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Actin filaments","reliability":"Additional"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"retina","ntpm":265.2}],"url":"https://www.proteinatlas.org/search/MPP4"},"hgnc":{"alias_symbol":[],"prev_symbol":["DLG6"]},"alphafold":{"accession":"Q96JB8","domains":[{"cath_id":"-","chopping":"88-132","consensus_level":"medium","plddt":88.902,"start":88,"end":132},{"cath_id":"2.30.42.10","chopping":"154-233","consensus_level":"high","plddt":89.1489,"start":154,"end":233},{"cath_id":"2.30.30.40","chopping":"246-317","consensus_level":"high","plddt":89.0076,"start":246,"end":317},{"cath_id":"3.40.50.300","chopping":"382-390_422-630","consensus_level":"medium","plddt":88.036,"start":382,"end":630}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JB8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JB8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JB8-F1-predicted_aligned_error_v6.png","plddt_mean":76.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MPP4","jax_strain_url":"https://www.jax.org/strain/search?query=MPP4"},"sequence":{"accession":"Q96JB8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96JB8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96JB8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JB8"}},"corpus_meta":[{"pmid":"15316081","id":"PMC_15316081","title":"Crumbs 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medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37910046","citation_count":8,"is_preprint":false},{"pmid":"24008227","id":"PMC_24008227","title":"Simultaneous expression of the bacterial Dictyoglomus thermophilum xynB gene under three different Trichoderma reesei promoters.","date":"2013","source":"New biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/24008227","citation_count":8,"is_preprint":false},{"pmid":"20231810","id":"PMC_20231810","title":"Identification of a novel peptide derived from the M-phase phosphoprotein 11 (MPP11) leukemic antigen recognized by human CD8+ cytotoxic T lymphocytes.","date":"2010","source":"Hematology/oncology and stem cell therapy","url":"https://pubmed.ncbi.nlm.nih.gov/20231810","citation_count":7,"is_preprint":false},{"pmid":"18955048","id":"PMC_18955048","title":"Proteomic analysis of the membrane palmitoylated protein-4 (MPP4)-associated protein complex in the retina.","date":"2008","source":"Experimental eye research","url":"https://pubmed.ncbi.nlm.nih.gov/18955048","citation_count":5,"is_preprint":false},{"pmid":"35402296","id":"PMC_35402296","title":"Oral Trypanosoma cruzi Acute Infection in Mice Targets Primary Lymphoid Organs and Triggers Extramedullary Hematopoiesis.","date":"2022","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/35402296","citation_count":5,"is_preprint":false},{"pmid":"39471249","id":"PMC_39471249","title":"CXCR4 signaling determines the fate of hematopoietic multipotent progenitors by stimulating mTOR activity and mitochondrial metabolism.","date":"2024","source":"Science signaling","url":"https://pubmed.ncbi.nlm.nih.gov/39471249","citation_count":4,"is_preprint":false},{"pmid":"35402845","id":"PMC_35402845","title":"Lymphoid-biased hematopoietic stem cells and myeloid-biased hematopoietic progenitor cells have radioprotection activity.","date":"2021","source":"Blood science (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/35402845","citation_count":3,"is_preprint":false},{"pmid":"40316244","id":"PMC_40316244","title":"Distinct transcriptional changes in hematopoietic progenitor subsets on LPS-induced emergency granulopoiesis.","date":"2025","source":"Experimental hematology","url":"https://pubmed.ncbi.nlm.nih.gov/40316244","citation_count":2,"is_preprint":false},{"pmid":"39555063","id":"PMC_39555063","title":"WBP1L regulates hematopoietic stem cell function and T cell development.","date":"2024","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/39555063","citation_count":1,"is_preprint":false},{"pmid":"40791535","id":"PMC_40791535","title":"Functional Comparison to Ezh2 Reveals PRC2-Independent Functions of Jarid2 in Hematopoietic Stem Cell Lineage Commitment.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40791535","citation_count":1,"is_preprint":false},{"pmid":"37356954","id":"PMC_37356954","title":"[Chronic Injury of Mice Bone Marrow Multipotent Hematopoietic Progenitor Cells Induced by Ionizing Radiation].","date":"2023","source":"Zhongguo shi yan xue ye xue za zhi","url":"https://pubmed.ncbi.nlm.nih.gov/37356954","citation_count":0,"is_preprint":false},{"pmid":"39114548","id":"PMC_39114548","title":"An Investigation of the Inflammatory Landscape in the Brain and Bone Marrow of the APP/PS1 Mouse.","date":"2024","source":"Journal of Alzheimer's disease reports","url":"https://pubmed.ncbi.nlm.nih.gov/39114548","citation_count":0,"is_preprint":false},{"pmid":"41650958","id":"PMC_41650958","title":"Comparison with Ezh2 reveals the PRC2-dependent functions of Jarid2 in hematopoietic stem Cell lineage commitment.","date":"2026","source":"Stem cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/41650958","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":26100,"output_tokens":3683,"usd":0.066772,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10703,"output_tokens":3124,"usd":0.065808,"stage2_stop_reason":"end_turn"},"total_usd":0.13258,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"Looking at the corpus, I need to distinguish between:\n1. **MPP4 (retinal MAGUK protein)** - membrane palmitoylated protein 4, a retina-specific scaffolding protein (MAGUK family), the canonical gene being queried\n2. **MPP4 (hematopoietic progenitor)** - lymphoid-primed multipotent progenitor 4, a cell population (NOT a protein gene)\n3. **MPP4 (imaging biomarker)** - mean of positive pixels, a radiology metric\n4. **MPP4/ILF3/NF90/DRBP76/TCP80** - there appears to be a naming collision where \"MPP4\" was used as an alias for what is actually ILF3/NF90 (M-phase phosphoprotein)\n\nThe canonical MPP4 gene (HGNC alias DLG6) is the retinal MAGUK scaffolding protein. Papers 4, 7, 8, 16, 27 describe ILF3/NF90 which was historically called \"MPP4\" as M-phase phosphoprotein — this is a different gene (ILF3), not DLG6/MPP4. I will exclude those.\n\nPapers about hematopoietic MPP4 progenitor populations (5, 11, 15, 19, 28, 31-35, 39-47) are about a cell type, not the MPP4 protein gene. Exclude.\n\nPapers 3, 12, 18, 20-22, 29, 36, 37 are clearly unrelated. Exclude.\n\nRelevant papers: 1, 2, 9, 10, 13, 14, 17, 23, 24, 25, 26, 30, 38, 6\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"MPP4 is a retina-specific member of the p55 subfamily of MAGUK proteins, containing a single PDZ domain, SH3 domain, and guanylate kinase-like (GUK) domain, with 637 amino acids encoded by a gene on chromosome 2q31-33.\",\n      \"method\": \"Full-length cDNA cloning, sequence alignment to protein databases, genomic organization analysis\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — molecular cloning with domain characterization, single lab, limited functional follow-up in this paper\",\n      \"pmids\": [\"11414766\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"MPP4 protein localizes to the connecting cilia and synaptic terminals of cone and rod photoreceptors in bovine and porcine retina, suggesting roles at membrane-cytoskeleton interfaces in distinct structural and functional compartments.\",\n      \"method\": \"Immunofluorescence microscopy on mammalian retina sections using affinity-purified anti-MPP4 antibodies; Western blot of retinal extracts and transfected 293-Ebna cells\",\n      \"journal\": \"Investigative ophthalmology & visual science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct protein localization by immunofluorescence with antibody specificity validated by transfected cells; single lab\",\n      \"pmids\": [\"14638699\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Mouse Mpp4 mRNA is expressed postnatally (not embryonically) and is exclusively localized to photoreceptor cells in the retina; Mpp4 protein localizes specifically to rod (but not cone) photoreceptor synaptic terminals.\",\n      \"method\": \"Microarray expression analysis, quantitative RT-PCR, in situ hybridization, immunofluorescence on retinal sections including cone-specific GFP transgenic mice\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (microarray, qRT-PCR, ISH, immunofluorescence) in single lab establishing localization\",\n      \"pmids\": [\"12859944\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"MPP4 associates with the CRB1 protein complex at the outer limiting membrane (OLM) of the retina, co-localizing with Crb1, Mupp1, and Pals1/Mpp5.\",\n      \"method\": \"Immunohistochemistry and co-immunoprecipitation in mouse retina; confocal microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — co-localization and co-immunoprecipitation in tissue context; replicated across multiple papers\",\n      \"pmids\": [\"15316081\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"MPP4 is recruited to the CRB1 complex through direct interaction with MPP5 (PALS1); MPP4 and MPP5 co-localize at the OLM in human and mouse retina. Yeast two-hybrid and GST pull-down identified the direct MPP4–MPP5 interaction, and 3D homology modeling suggested a mechanism regulating recruitment of homo- and heterodimers of MPP4 and MPP5 to the complex.\",\n      \"method\": \"Yeast two-hybrid screening, GST pull-down assay, co-immunoprecipitation, immunohistochemistry, immunoelectron microscopy, 3D homology modeling\",\n      \"journal\": \"Investigative ophthalmology & visual science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (yeast two-hybrid, GST pull-down, Co-IP, structural modeling) establishing direct protein interaction\",\n      \"pmids\": [\"15914641\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"MPP4 directly interacts with Veli proteins (Veli1, Veli2, Veli3) via L27 heterodimerization in vitro, and co-localizes with Veli3 at photoreceptor synaptic terminals in the outer plexiform layer; MPP5 and MPP4 associate with Veli3 at distinct intercellular junctions in the retina.\",\n      \"method\": \"In vitro L27 heterodimerization assay, immunofluorescence microscopy, specific polyclonal and monoclonal antibody generation\",\n      \"journal\": \"The Journal of comparative neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro reconstitution of L27 domain interaction plus immunofluorescence colocalization, corroborated by subsequent studies\",\n      \"pmids\": [\"15558731\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"In Mpp4 knockout mice, Psd95 is lost from presynaptic membranes of rods and cones, and total retinal Psd95 protein levels are significantly reduced (suggesting Mpp4 is involved in Psd95 turnover). Veli3 protein levels are unchanged but its correct presynaptic localization depends on Mpp4. Loss of Mpp4 only sporadically causes photoreceptor displacement without changing the Crb complex at the OLM.\",\n      \"method\": \"Mpp4 knockout mouse analysis, immunohistochemistry, Western blot, scanning laser ophthalmoscopy, electroretinography\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean knockout mouse with multiple orthogonal readouts (IHC, Western, ERG, ophthalmoscopy); replicated in subsequent studies\",\n      \"pmids\": [\"16520334\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"MPP3 and MPP4 co-localize with DLG1 at the outer plexiform layer, and mouse Dlg1 forms separate complexes with Mpp3 and Mpp4 in vivo.\",\n      \"method\": \"Co-immunoprecipitation from mouse retina, immunohistochemistry, confocal microscopy\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — reciprocal Co-IP from tissue demonstrating distinct complexes; single lab\",\n      \"pmids\": [\"16519681\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Mpp4 organizes a presynaptic protein complex at rod photoreceptor synaptic terminals that includes plasma membrane Ca2+-ATPases (PMCAs), Veli3, and PSD95. In Mpp4 knockout mice, PMCAs are lost from rod presynaptic membranes, synaptic ribbons are enlarged (indicative of elevated Ca2+), SERCA2 is increased, and IP3RII distribution is shifted away from synaptic terminals. Synaptic transmission to second-order neurons is maintained but reduced in amplitude.\",\n      \"method\": \"Mpp4 knockout mouse, immunofluorescence, co-immunoprecipitation, Western blot, electroretinography\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — knockout mouse with multiple orthogonal mechanistic readouts; Co-IP demonstrating complex membership; corroborated by independent lab\",\n      \"pmids\": [\"17341488\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Immunoaffinity purification of the MPP4-associated protein complex from retina identified: previously known components Veli3 and Psd95-beta (interaction mediated by N-terminal L27 domains of MPP4 and PSD95beta), and novel associated proteins recoverin and Hsc70.\",\n      \"method\": \"Immunoaffinity chromatography with anti-MPP4 monoclonal antibody, 2D electrophoresis, mass spectrometry\",\n      \"journal\": \"Experimental eye research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proteomic immunoaffinity approach identified complex components; single lab, MS-based identification\",\n      \"pmids\": [\"18955048\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"MPP4 is required for the membrane localization of TMEM16B at photoreceptor ribbon synapses; TMEM16B is absent from photoreceptor membranes in MPP4-deficient mice. TMEM16B co-localizes with PSD95, VELI3, and MPP4 at ribbon synapses and contains a PDZ class I binding motif capable of interacting with PSD95.\",\n      \"method\": \"Immunohistochemistry and immunofluorescence in MPP4-deficient mice; co-localization analysis; PDZ binding motif analysis\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — knockout mouse demonstrating MPP4-dependent membrane recruitment of TMEM16B; corroborated by localization studies\",\n      \"pmids\": [\"19474308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"MPP4 and PSD95beta are both essential for correct localization of PMCA at the presynaptic plasma membrane of photoreceptors. MPP4 deficiency causes loss of both PMCA and PSD95 from the photoreceptor synapse; truncation of MPP4's C-terminal part causes loss of PSD95 and mislocalization of PMCA. PSD95beta (not PSD95alpha) can restore plasma membrane localization of MPP4 and PMCA1 in Mpp4 mutant primary retinal explants.\",\n      \"method\": \"Mpp4 and Psd95 mutant mice, lentiviral molecular replacement in primary retinal explants, immunofluorescence microscopy\",\n      \"journal\": \"Molecular and cellular neurosciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — knockout mice combined with lentiviral rescue experiments in primary retinal explants; multiple orthogonal approaches; identifies isoform-specific (PSD95beta) requirement\",\n      \"pmids\": [\"19233278\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CRX transcription factor controls presynaptic active zone formation in photoreceptors; MPP4 is among the CRX target genes whose expression is aberrant in Crx-mutant retinas, linking CRX-dependent transcriptional control to MPP4-containing presynaptic scaffold assembly.\",\n      \"method\": \"Immunohistochemistry of Crx mutant mouse retinas; integrated analysis with CRX- and NRL-ChIP-Seq data and retinal transcriptomics\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — MPP4 identified as aberrantly expressed in Crx mutants by IHC; no direct mechanistic experiment on MPP4 itself in this study\",\n      \"pmids\": [\"30084954\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MPP4 (DLG6) is a retina-specific MAGUK scaffolding protein localized to the presynaptic plasma membrane of rod photoreceptor synaptic terminals and (with MPP5) to the outer limiting membrane; it is recruited to the CRB1 complex via direct L27-domain-mediated interaction with MPP5, directly interacts with Veli proteins (Veli1/2/3) via L27 heterodimerization, and organizes a presynaptic protein complex containing PSD95beta (via L27 interaction), Veli3, plasma membrane Ca2+-ATPases (PMCAs), and TMEM16B, thereby regulating calcium homeostasis and neurotransmitter release at the photoreceptor ribbon synapse.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"MPP4 (DLG6) is a retina-specific p55-subfamily MAGUK scaffolding protein that organizes a presynaptic protein complex at rod photoreceptor ribbon synapses to control calcium homeostasis and neurotransmitter release [#0, #8]. It localizes to photoreceptor synaptic terminals and to the outer limiting membrane, where it is recruited into the CRB1 complex through a direct L27-domain interaction with MPP5/PALS1 [#3, #4]. Through L27 heterodimerization MPP4 binds Veli proteins (Veli1/2/3) and PSD95beta, building a presynaptic scaffold whose assembly MPP4 nucleates [#5, #9]. Knockout and molecular-replacement studies establish MPP4 as essential for membrane recruitment of downstream synaptic components: loss of Mpp4 removes PSD95 and plasma membrane Ca2+-ATPases (PMCAs) from presynaptic membranes, mislocalizes Veli3 and TMEM16B, enlarges synaptic ribbons consistent with elevated Ca2+, and reduces the amplitude of synaptic transmission to second-order neurons [#6, #8, #10, #11]. PSD95beta specifically restores plasma membrane targeting of MPP4 and PMCA in Mpp4-mutant explants, defining an isoform-specific scaffolding requirement [#11].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established the molecular identity of MPP4 as a retina-restricted MAGUK, defining the domain architecture (PDZ, SH3, GUK) that would later explain its scaffolding behavior.\",\n      \"evidence\": \"Full-length cDNA cloning, sequence alignment, and genomic organization analysis\",\n      \"pmids\": [\"11414766\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional or interaction data in this report\", \"Cellular localization not resolved\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Localized MPP4 protein to photoreceptor synaptic terminals (and connecting cilia), placing the scaffold at specific membrane-cytoskeleton compartments and restricting its action to rod synaptic terminals.\",\n      \"evidence\": \"Immunofluorescence on mammalian retina, in situ hybridization, qRT-PCR, and microarray expression analysis\",\n      \"pmids\": [\"14638699\", \"12859944\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No binding partners identified\", \"Functional role at terminals not tested\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Connected MPP4 to a defined retinal scaffold by showing its association with the CRB1 complex at the outer limiting membrane, embedding MPP4 in an established polarity/junction module.\",\n      \"evidence\": \"Co-immunoprecipitation and confocal immunohistochemistry in mouse retina\",\n      \"pmids\": [\"15316081\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus indirect association not distinguished\", \"Recruitment mechanism unknown\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Defined the molecular mechanism of MPP4 recruitment, showing a direct MPP5/PALS1 interaction recruits MPP4 to the CRB1 complex and direct L27 heterodimerization with Veli proteins anchors it at synaptic terminals.\",\n      \"evidence\": \"Yeast two-hybrid, GST pull-down, Co-IP, in vitro L27 heterodimerization, immunoelectron microscopy, and 3D homology modeling\",\n      \"pmids\": [\"15914641\", \"15558731\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of homo/heterodimers in vivo not resolved\", \"Functional consequence of these interactions not yet tested\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Demonstrated MPP4 is functionally required for presynaptic organization in vivo, since Mpp4 loss depletes PSD95 from presynaptic membranes and mislocalizes Veli3 without disrupting the OLM Crb complex.\",\n      \"evidence\": \"Mpp4 knockout mouse with immunohistochemistry, Western blot, ERG, and ophthalmoscopy; reciprocal Co-IP of Dlg1 complexes\",\n      \"pmids\": [\"16520334\", \"16519681\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of PSD95 turnover/stabilization not defined\", \"Why OLM Crb complex is spared not explained\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Established the physiological output of the MPP4 scaffold by linking it to calcium handling, showing the complex contains PMCAs and that Mpp4 loss removes PMCAs, enlarges ribbons, and reduces synaptic transmission.\",\n      \"evidence\": \"Mpp4 knockout mouse with immunofluorescence, Co-IP, Western blot, and electroretinography\",\n      \"pmids\": [\"17341488\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct measurement of presynaptic Ca2+ dynamics not performed\", \"Causal chain from PMCA loss to ribbon enlargement inferred\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Refined complex composition by immunoaffinity proteomics, confirming L27-mediated PSD95beta and Veli3 membership and adding recoverin and Hsc70 as associated proteins.\",\n      \"evidence\": \"Anti-MPP4 immunoaffinity chromatography, 2D electrophoresis, and mass spectrometry from retina\",\n      \"pmids\": [\"18955048\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Roles of recoverin and Hsc70 in the complex untested\", \"Direct versus indirect associations not resolved by MS\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Extended the scaffold's recruitment role to the calcium-activated channel TMEM16B and pinned PMCA targeting to a specific PSD95beta isoform, defining MPP4 as the apical organizer of presynaptic membrane protein localization.\",\n      \"evidence\": \"MPP4-deficient mice with immunohistochemistry; lentiviral molecular replacement in retinal explants; PDZ binding motif analysis\",\n      \"pmids\": [\"19474308\", \"19233278\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of TMEM16B mislocalization on transmission not measured\", \"Structural basis of PSD95beta isoform specificity unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Placed MPP4 within transcriptional control of synapse formation by identifying it as a CRX target gene whose expression is altered in Crx-mutant retinas.\",\n      \"evidence\": \"Immunohistochemistry of Crx mutant retinas integrated with CRX/NRL ChIP-Seq and transcriptomics\",\n      \"pmids\": [\"30084954\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct mechanistic experiment on MPP4 in this study\", \"Direct CRX regulation of the MPP4 promoter not validated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether MPP4 dysfunction causes human retinal disease, and how the scaffold quantitatively governs presynaptic Ca2+ dynamics and neurotransmission, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No timeline evidence of a causative human Mendelian mutation\", \"Direct presynaptic Ca2+ imaging in Mpp4-null synapses not reported\", \"Structural model of the assembled scaffold absent\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [4, 5, 9, 11]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [1, 2, 8, 11]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [8, 10]}\n    ],\n    \"complexes\": [\n      \"CRB1 complex\",\n      \"MPP4 presynaptic scaffold (MPP4-PSD95beta-Veli3-PMCA-TMEM16B)\"\n    ],\n    \"partners\": [\n      \"MPP5\",\n      \"VELI3\",\n      \"DLG4\",\n      \"MPP3\",\n      \"DLG1\",\n      \"CRB1\",\n      \"TMEM16B\",\n      \"ATP2B1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":4,"faith_total":5,"faith_pct":80.0}}