{"gene":"MS4A4A","run_date":"2026-06-10T02:59:51","timeline":{"discoveries":[{"year":2019,"finding":"MS4A4A physically interacts and colocalizes with the β-glucan receptor dectin-1 in lipid rafts of macrophages; Ms4a4a-deficient macrophages show defective dectin-1 signaling and defective production of effector molecules in response to dectin-1 ligands, placing MS4A4A upstream of dectin-1-dependent activation and NK cell-mediated metastasis control.","method":"Co-localization/interaction studies in lipid rafts, Ms4a4a-deficient macrophage functional assays (signaling readouts, effector molecule production), in vivo tumor metastasis models with genetic knockout","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-localization, genetic KO with defined cellular and in vivo phenotype, multiple orthogonal methods in a single rigorous study","pmids":["31263276"],"is_preprint":false},{"year":2020,"finding":"In human mast cells, MS4A4A promotes phosphorylation of PLCγ1, calcium flux, and degranulation in response to IgE-mediated FcεRI crosslinking; MS4A4A interacts with caveolin-1 and facilitates recruitment of FcεRI and KIT into lipid rafts; MS4A4A also regulates Orai1-mediated store-operated Ca2+ entry (SOCE) downstream of Ca2+ store release.","method":"siRNA knockdown in human mast cells, phosphorylation assays (western blot), calcium flux measurements, degranulation assays, co-immunoprecipitation with caveolin-1, lipid raft fractionation","journal":"Cellular signalling","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, multiple functional readouts (phosphorylation, Ca2+ flux, degranulation, lipid raft recruitment), single lab with orthogonal methods","pmids":["32240745"],"is_preprint":false},{"year":2020,"finding":"MS4A4A regulates expression of arginase 1 in macrophages under IL-4 stimulation and regulates eosinophil infiltration during lung allergic inflammation (house dust mite model) in mice.","method":"Ms4a4a-deficient mice, in vitro macrophage stimulation with IL-4, in vivo intranasal house dust mite challenge model with cellular readouts","journal":"European journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic KO with defined cellular phenotype, single lab, limited mechanistic detail in abstract","pmids":["32589266"],"is_preprint":false},{"year":2023,"finding":"MS4A4A promotes M2 polarization of macrophages by activating the PI3K/AKT and JAK/STAT6 signaling pathways; MS4A4A blockade in vivo reshapes the tumor immune microenvironment by reducing M2-TAM infiltration and increasing effector CD8+ T-cell infiltration.","method":"RNA sequencing, western blot analysis, flow cytometry, in vivo murine subcutaneous and orthotopic tumor models with MS4A4A inhibition and anti-MS4A4A monoclonal antibody treatment","journal":"Gut","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and antibody-mediated KO with multiple in vitro and in vivo readouts, signaling pathway identified by western blot, single lab","pmids":["37507218"],"is_preprint":false},{"year":2025,"finding":"MS4A4A interacts with MS4A6A and protects it from degradation; MS4A6A in turn forms a complex with and blocks the co-receptor DAP12, which modulates levels and signaling of TREM2 and other receptors; thereby MS4A4A and MS4A6A cooperatively act as post-transcriptional negative regulators of both transmembrane and soluble TREM2 and of microglial viability, phagocytosis, and lysosomal function.","method":"CRISPR knockout and overexpression of MS4A4A in macrophages/microglia, MS4A4A-degrading antibodies, co-immunoprecipitation (MS4A4A–MS4A6A and MS4A6A–DAP12 complexes), non-human primate and mouse amyloid pathology models, flow cytometry, functional phagocytosis/lysosomal assays","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — protein-protein interaction by Co-IP, CRISPR KO and OE, degrading antibody, multiple model systems (NHP, mouse, human microglia), multiple orthogonal functional readouts","pmids":["41435829"],"is_preprint":false},{"year":2025,"finding":"Ms4a4a deletion in a 5xFAD mouse model reduces steady-state amyloid-β levels, shortens Aβ half-life in brain interstitial fluid, increases plaque compaction, and reduces overall plaque burden; microglia lacking Ms4a4a are more pro-inflammatory and produce elevated MMP-9, which may facilitate Aβ degradation.","method":"Ms4a4a knockout in 5xFAD mice, brain interstitial fluid Aβ half-life measurement, plaque burden quantification, microglial inflammatory profiling, MMP-9 measurement (mouse and human CSF)","journal":"Alzheimer's & dementia","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with multiple in vivo readouts, corroborated by human CSF data, single lab","pmids":["40843775"],"is_preprint":false},{"year":2025,"finding":"Ms4a4a deletion impairs microglial phagocytosis, diminishes calcium influx, and disrupts mitochondrial metabolic fitness; the cytosolic fragment of Ms4a4a is anchored to cytoskeletal components, supporting its role in mediating phagocytosis; induction of Ms4a4a via central LNP-Il4 delivery alleviates seizure conditions in an AD mouse model.","method":"Ms4a4a knockout mouse model, microglial phagocytosis assays, calcium influx measurements, mitochondrial metabolic assays, cytoskeletal anchoring experiments, in vivo LNP-IL-4 delivery with seizure readout","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with multiple mechanistic readouts (phagocytosis, calcium, mitochondria, cytoskeletal anchoring) and rescue experiment, single lab","pmids":["40349168"],"is_preprint":false},{"year":2025,"finding":"In a mouse model of arthritis, Ms4a4a deletion does not alter disease course but is associated with enhanced therapeutic response specifically to corticosteroids; corticosteroids enhance expression of MS4A4A and FcγR3 in macrophages in vitro and in vivo, suggesting MS4A4A upregulation by corticosteroids counteracts their therapeutic activity.","method":"Ms4a4a-deficient mice in experimental arthritis model, in vitro corticosteroid treatment of human and murine macrophages, immunohistochemistry, RNA sequencing","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with defined in vivo phenotypic readout plus in vitro mechanistic follow-up, single lab","pmids":["40924449"],"is_preprint":false},{"year":2026,"finding":"MS4A4A regulates macrophage M2 polarization through NF-κB and JAK-STAT6 signaling pathways; macrophages overexpressing MS4A4A promote glioma cell proliferation, invasion, and temozolomide resistance in vitro and in vivo; targeting the MS4A4A/NF-κB/STAT6 axis improves outcomes in a glioma mouse model.","method":"MS4A4A knockdown and overexpression in macrophages, western blot for NF-κB and STAT6 pathway components, co-culture invasion/proliferation assays, in vivo subcutaneous and orthotopic glioma mouse models","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gain- and loss-of-function with multiple in vitro and in vivo readouts and signaling pathway identification, single lab","pmids":["42056558"],"is_preprint":false},{"year":2017,"finding":"MS4A4A protein is localized to the plasma membrane in monocytes; it is expressed in M2 (IL-4-polarized) macrophages but not M1 (IFN-γ/LPS-activated) macrophages; it is induced during monocyte-to-macrophage differentiation and absent in immature/precursor myeloid cells and healthy B lymphocytes but present in plasma cells.","method":"Monoclonal antibody generation against extracellular epitopes, flow cytometry of human peripheral blood, in vitro monocyte differentiation assays","journal":"Immunology and cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct protein-level localization by validated monoclonal antibodies and flow cytometry across multiple cell types, single lab","pmids":["28303902"],"is_preprint":false}],"current_model":"MS4A4A is a plasma membrane tetraspan protein selectively expressed in macrophage-lineage cells and microglia that functions as a lipid-raft scaffold organizing signaling complexes: it interacts with dectin-1 to support β-glucan-dependent macrophage activation, interacts with caveolin-1 to recruit FcεRI and KIT into lipid rafts and promote PLCγ1/SOCE/degranulation in mast cells, interacts with and stabilizes MS4A6A which in turn blocks DAP12 to post-transcriptionally suppress TREM2 levels and microglial phagocytosis/lysosomal function, and promotes M2 macrophage polarization via PI3K/AKT and NF-κB/JAK-STAT6 signaling pathways; additionally, its cytosolic domain anchors to the cytoskeleton to support microglial phagocytosis and calcium influx."},"narrative":{"mechanistic_narrative":"MS4A4A is a plasma-membrane tetraspan protein selectively expressed in macrophage-lineage cells, induced during monocyte-to-macrophage differentiation and restricted to M2 (IL-4-polarized) rather than M1 macrophages [PMID:28303902]. It functions as a lipid-raft scaffold that organizes receptor signaling complexes: it physically interacts and colocalizes with the β-glucan receptor dectin-1 in macrophage lipid rafts and is required for dectin-1-dependent activation, with its loss impairing effector molecule production and NK cell-mediated control of metastasis [PMID:31263276]. In mast cells, MS4A4A interacts with caveolin-1 to recruit FcεRI and KIT into lipid rafts, driving PLCγ1 phosphorylation, Orai1-mediated store-operated calcium entry, and degranulation [PMID:32240745]. MS4A4A promotes M2 macrophage polarization through PI3K/AKT and JAK/STAT6 signaling [PMID:37507218] as well as NF-κB/STAT6 signaling, and macrophage MS4A4A drives a pro-tumoral microenvironment in liver cancer and glioma [PMID:37507218, PMID:42056558]. In microglia, MS4A4A interacts with and stabilizes MS4A6A, which complexes with and blocks DAP12 to post-transcriptionally suppress TREM2 levels and thereby limit microglial phagocytosis and lysosomal function [PMID:41435829]; consistent with this, its cytosolic fragment anchors to cytoskeletal components to support phagocytosis, calcium influx, and mitochondrial fitness [PMID:40349168]. In amyloid pathology models, Ms4a4a deletion lowers steady-state amyloid-β and plaque burden while rendering microglia more pro-inflammatory [PMID:40843775].","teleology":[{"year":2017,"claim":"Established where MS4A4A protein resides and which myeloid states express it, defining it as a differentiation- and polarization-restricted plasma-membrane marker.","evidence":"Monoclonal antibodies against extracellular epitopes with flow cytometry of human blood and in vitro monocyte differentiation","pmids":["28303902"],"confidence":"Medium","gaps":["No molecular function assigned at this stage","Mechanism of M2-restricted induction not defined"]},{"year":2019,"claim":"Showed MS4A4A acts upstream of an innate immune receptor, answering how a tetraspan scaffold contributes to macrophage activation by partnering with dectin-1 in lipid rafts.","evidence":"Lipid-raft co-localization/interaction, Ms4a4a-deficient macrophage signaling and effector assays, in vivo metastasis models with genetic KO","pmids":["31263276"],"confidence":"High","gaps":["Direct binding interface with dectin-1 not mapped","Whether MS4A4A organizes other receptors not addressed here"]},{"year":2020,"claim":"Extended the raft-scaffold model beyond macrophages, showing MS4A4A recruits FcεRI/KIT via caveolin-1 to drive PLCγ1/SOCE-dependent mast cell degranulation.","evidence":"siRNA knockdown in human mast cells, phosphorylation/Ca2+/degranulation assays, caveolin-1 Co-IP, lipid raft fractionation","pmids":["32240745"],"confidence":"High","gaps":["Knockdown rather than genetic KO","Stoichiometry of MS4A4A–caveolin-1–receptor complexes unresolved"]},{"year":2020,"claim":"Linked MS4A4A to type-2 inflammation in vivo, showing it controls IL-4-induced arginase 1 and allergic eosinophil infiltration.","evidence":"Ms4a4a-deficient mice, IL-4 macrophage stimulation, house dust mite intranasal challenge","pmids":["32589266"],"confidence":"Medium","gaps":["Molecular link between MS4A4A and arginase 1 regulation unclear","Limited mechanistic detail"]},{"year":2023,"claim":"Defined the intracellular signaling output of MS4A4A in tumor-associated macrophages, implicating PI3K/AKT and JAK/STAT6 in M2 polarization and validating MS4A4A as an antibody-targetable node.","evidence":"RNA-seq, western blot, flow cytometry, murine tumor models with MS4A4A inhibition and anti-MS4A4A antibody","pmids":["37507218"],"confidence":"Medium","gaps":["How MS4A4A engages PI3K/AKT and JAK/STAT6 mechanistically not shown","Single lab"]},{"year":2025,"claim":"Uncovered an intracellular regulatory circuit, showing MS4A4A stabilizes MS4A6A, which blocks DAP12 to post-transcriptionally suppress TREM2 and constrain microglial function.","evidence":"CRISPR KO/OE, degrading antibodies, MS4A4A–MS4A6A and MS4A6A–DAP12 Co-IP, NHP/mouse amyloid models, phagocytosis/lysosomal assays","pmids":["41435829"],"confidence":"High","gaps":["Mechanism by which MS4A6A degrades/blocks DAP12 not fully defined","Direct vs indirect effect on TREM2 turnover"]},{"year":2025,"claim":"Connected MS4A4A's microglial role to cellular machinery, showing its cytosolic fragment anchors to the cytoskeleton to support phagocytosis, calcium influx, and mitochondrial fitness.","evidence":"Ms4a4a KO mouse, phagocytosis/calcium/mitochondrial assays, cytoskeletal anchoring experiments, LNP-IL-4 rescue in AD seizure model","pmids":["40349168"],"confidence":"Medium","gaps":["Cytoskeletal binding partners not identified","Causal chain from cytoskeleton to calcium/mitochondria unresolved"]},{"year":2025,"claim":"Demonstrated functional consequence of MS4A4A loss on amyloid handling, showing deletion lowers Aβ and plaque burden while making microglia more pro-inflammatory.","evidence":"Ms4a4a KO in 5xFAD mice, Aβ half-life and plaque quantification, microglial inflammatory and MMP-9 profiling, human CSF corroboration","pmids":["40843775"],"confidence":"Medium","gaps":["Whether MMP-9 mechanistically drives Aβ clearance not proven","Single lab"]},{"year":2025,"claim":"Revealed a context where MS4A4A modulates drug response, showing its corticosteroid-induced upregulation counteracts therapeutic activity in arthritis.","evidence":"Ms4a4a-deficient mice in experimental arthritis, corticosteroid treatment of human/murine macrophages, IHC, RNA-seq","pmids":["40924449"],"confidence":"Medium","gaps":["Mechanism linking MS4A4A to corticosteroid resistance not defined","No effect on disease course alone"]},{"year":2026,"claim":"Reinforced the pro-tumoral macrophage role, implicating NF-κB/STAT6 signaling in MS4A4A-driven M2 polarization and glioma progression/temozolomide resistance.","evidence":"MS4A4A KD/OE in macrophages, western blot for NF-κB/STAT6, co-culture invasion/proliferation assays, glioma mouse models","pmids":["42056558"],"confidence":"Medium","gaps":["How MS4A4A activates NF-κB not shown","Reconciliation of multiple signaling axes (PI3K/AKT vs NF-κB) across tumor types"]},{"year":null,"claim":"The structural basis by which MS4A4A organizes raft receptor complexes and transmits signals to its multiple downstream pathways remains undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of MS4A4A or its receptor complexes","Direct binding interfaces with dectin-1, caveolin-1, MS4A6A not mapped","Unifying mechanism linking raft scaffolding to PI3K/AKT, JAK/STAT6, and NF-κB outputs unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,4]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[6]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,1,9]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,1,3]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,8]}],"complexes":[],"partners":["CLEC7A","CAV1","MS4A6A","FCER1A","KIT"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96JQ5","full_name":"Membrane-spanning 4-domains subfamily A member 4A","aliases":["CD20 antigen-like 1","Four-span transmembrane protein 1"],"length_aa":239,"mass_kda":25.4,"function":"May be involved in signal transduction as a component of a multimeric receptor complex","subcellular_location":"Membrane","url":"https://www.uniprot.org/uniprotkb/Q96JQ5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/MS4A4A","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/MS4A4A","total_profiled":1310},"omim":[{"mim_id":"608402","title":"MEMBRANE-SPANNING 4-DOMAINS, SUBFAMILY A, MEMBER 6E; MS4A6E","url":"https://www.omim.org/entry/608402"},{"mim_id":"608401","title":"MEMBRANE-SPANNING 4-DOMAINS, SUBFAMILY A, MEMBER 4E; MS4A4E","url":"https://www.omim.org/entry/608401"},{"mim_id":"606547","title":"MEMBRANE-SPANNING 4-DOMAINS, SUBFAMILY A, MEMBER 4A; MS4A4A","url":"https://www.omim.org/entry/606547"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"placenta","ntpm":59.3}],"url":"https://www.proteinatlas.org/search/MS4A4A"},"hgnc":{"alias_symbol":["CD20L1","MS4A7"],"prev_symbol":["MS4A4"]},"alphafold":{"accession":"Q96JQ5","domains":[{"cath_id":"-","chopping":"63-213","consensus_level":"high","plddt":87.9697,"start":63,"end":213}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JQ5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JQ5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JQ5-F1-predicted_aligned_error_v6.png","plddt_mean":73.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MS4A4A","jax_strain_url":"https://www.jax.org/strain/search?query=MS4A4A"},"sequence":{"accession":"Q96JQ5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96JQ5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96JQ5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JQ5"}},"corpus_meta":[{"pmid":"31263276","id":"PMC_31263276","title":"The macrophage tetraspan MS4A4A enhances dectin-1-dependent NK cell-mediated resistance to metastasis.","date":"2019","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/31263276","citation_count":120,"is_preprint":false},{"pmid":"37507218","id":"PMC_37507218","title":"Targeting MS4A4A on tumour-associated macrophages restores CD8+ T-cell-mediated antitumour immunity.","date":"2023","source":"Gut","url":"https://pubmed.ncbi.nlm.nih.gov/37507218","citation_count":114,"is_preprint":false},{"pmid":"28303902","id":"PMC_28303902","title":"MS4A4A: a novel cell surface marker for M2 macrophages and plasma cells.","date":"2017","source":"Immunology and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/28303902","citation_count":79,"is_preprint":false},{"pmid":"36798226","id":"PMC_36798226","title":"MS4A4A modifies the risk of Alzheimer disease by regulating lipid metabolism and immune response in a unique microglia state.","date":"2023","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36798226","citation_count":18,"is_preprint":false},{"pmid":"32240745","id":"PMC_32240745","title":"The FcεRIβ homologue, MS4A4A, promotes FcεRI signal transduction and store-operated Ca2+ entry in human mast cells.","date":"2020","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/32240745","citation_count":17,"is_preprint":false},{"pmid":"38997808","id":"PMC_38997808","title":"Targeting MS4A4A: A novel pathway to improve immunotherapy responses in glioblastoma.","date":"2024","source":"CNS neuroscience & therapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/38997808","citation_count":15,"is_preprint":false},{"pmid":"32589266","id":"PMC_32589266","title":"MS4A4A Regulates Arginase 1 Induction during Macrophage Polarization and Lung Inflammation in Mice.","date":"2020","source":"European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/32589266","citation_count":15,"is_preprint":false},{"pmid":"40349168","id":"PMC_40349168","title":"Microglial MS4A4A Protects against Epileptic Seizures in Alzheimer's Disease.","date":"2025","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/40349168","citation_count":5,"is_preprint":false},{"pmid":"41435829","id":"PMC_41435829","title":"The Alzheimer's disease risk genes MS4A4A and MS4A6A cooperate to negatively regulate TREM2 and microglia states.","date":"2025","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/41435829","citation_count":4,"is_preprint":false},{"pmid":"40843775","id":"PMC_40843775","title":"Ms4a4a deficiency ameliorates plaque pathology in a mouse model of amyloid accumulation.","date":"2025","source":"Alzheimer's & dementia : the journal of the Alzheimer's Association","url":"https://pubmed.ncbi.nlm.nih.gov/40843775","citation_count":3,"is_preprint":false},{"pmid":"40924449","id":"PMC_40924449","title":"Synovial MS4A4A correlates with inflammation and counteracts response to corticosteroids in arthritis.","date":"2025","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/40924449","citation_count":2,"is_preprint":false},{"pmid":"41955527","id":"PMC_41955527","title":"Expression of MS4A4A on synovial infiltrating macrophages is a hallmark of rheumatoid arthritis and reflects disease severity.","date":"2026","source":"Immunological medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41955527","citation_count":0,"is_preprint":false},{"pmid":"42056558","id":"PMC_42056558","title":"MS4A4A promotes macrophages M2 polarization via NF-κB /JAK-STAT6 axis, resulting GBM malignant progression.","date":"2026","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/42056558","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.06.641917","title":"<i>Ms4a4a</i>  deficiency ameliorates plaque pa thology in a mouse model of amyloid accumulation","date":"2025-03-10","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.06.641917","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.11.23.625001","title":"The Alzheimer’s Disease Risk Genes MS4A4A And MS4A6A Cooperate to Negatively Regulate Trem2 and Microglia states","date":"2024-11-24","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.23.625001","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.08.27.672693","title":"Sex and regional effects of  <i>Bacteroides</i>  in the gut","date":"2025-08-27","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.27.672693","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10263,"output_tokens":2881,"usd":0.037002,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10235,"output_tokens":3552,"usd":0.069987,"stage2_stop_reason":"end_turn"},"total_usd":0.106989,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"MS4A4A physically interacts and colocalizes with the β-glucan receptor dectin-1 in lipid rafts of macrophages; Ms4a4a-deficient macrophages show defective dectin-1 signaling and defective production of effector molecules in response to dectin-1 ligands, placing MS4A4A upstream of dectin-1-dependent activation and NK cell-mediated metastasis control.\",\n      \"method\": \"Co-localization/interaction studies in lipid rafts, Ms4a4a-deficient macrophage functional assays (signaling readouts, effector molecule production), in vivo tumor metastasis models with genetic knockout\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-localization, genetic KO with defined cellular and in vivo phenotype, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"31263276\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In human mast cells, MS4A4A promotes phosphorylation of PLCγ1, calcium flux, and degranulation in response to IgE-mediated FcεRI crosslinking; MS4A4A interacts with caveolin-1 and facilitates recruitment of FcεRI and KIT into lipid rafts; MS4A4A also regulates Orai1-mediated store-operated Ca2+ entry (SOCE) downstream of Ca2+ store release.\",\n      \"method\": \"siRNA knockdown in human mast cells, phosphorylation assays (western blot), calcium flux measurements, degranulation assays, co-immunoprecipitation with caveolin-1, lipid raft fractionation\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, multiple functional readouts (phosphorylation, Ca2+ flux, degranulation, lipid raft recruitment), single lab with orthogonal methods\",\n      \"pmids\": [\"32240745\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"MS4A4A regulates expression of arginase 1 in macrophages under IL-4 stimulation and regulates eosinophil infiltration during lung allergic inflammation (house dust mite model) in mice.\",\n      \"method\": \"Ms4a4a-deficient mice, in vitro macrophage stimulation with IL-4, in vivo intranasal house dust mite challenge model with cellular readouts\",\n      \"journal\": \"European journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic KO with defined cellular phenotype, single lab, limited mechanistic detail in abstract\",\n      \"pmids\": [\"32589266\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MS4A4A promotes M2 polarization of macrophages by activating the PI3K/AKT and JAK/STAT6 signaling pathways; MS4A4A blockade in vivo reshapes the tumor immune microenvironment by reducing M2-TAM infiltration and increasing effector CD8+ T-cell infiltration.\",\n      \"method\": \"RNA sequencing, western blot analysis, flow cytometry, in vivo murine subcutaneous and orthotopic tumor models with MS4A4A inhibition and anti-MS4A4A monoclonal antibody treatment\",\n      \"journal\": \"Gut\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and antibody-mediated KO with multiple in vitro and in vivo readouts, signaling pathway identified by western blot, single lab\",\n      \"pmids\": [\"37507218\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"MS4A4A interacts with MS4A6A and protects it from degradation; MS4A6A in turn forms a complex with and blocks the co-receptor DAP12, which modulates levels and signaling of TREM2 and other receptors; thereby MS4A4A and MS4A6A cooperatively act as post-transcriptional negative regulators of both transmembrane and soluble TREM2 and of microglial viability, phagocytosis, and lysosomal function.\",\n      \"method\": \"CRISPR knockout and overexpression of MS4A4A in macrophages/microglia, MS4A4A-degrading antibodies, co-immunoprecipitation (MS4A4A–MS4A6A and MS4A6A–DAP12 complexes), non-human primate and mouse amyloid pathology models, flow cytometry, functional phagocytosis/lysosomal assays\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — protein-protein interaction by Co-IP, CRISPR KO and OE, degrading antibody, multiple model systems (NHP, mouse, human microglia), multiple orthogonal functional readouts\",\n      \"pmids\": [\"41435829\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Ms4a4a deletion in a 5xFAD mouse model reduces steady-state amyloid-β levels, shortens Aβ half-life in brain interstitial fluid, increases plaque compaction, and reduces overall plaque burden; microglia lacking Ms4a4a are more pro-inflammatory and produce elevated MMP-9, which may facilitate Aβ degradation.\",\n      \"method\": \"Ms4a4a knockout in 5xFAD mice, brain interstitial fluid Aβ half-life measurement, plaque burden quantification, microglial inflammatory profiling, MMP-9 measurement (mouse and human CSF)\",\n      \"journal\": \"Alzheimer's & dementia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with multiple in vivo readouts, corroborated by human CSF data, single lab\",\n      \"pmids\": [\"40843775\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Ms4a4a deletion impairs microglial phagocytosis, diminishes calcium influx, and disrupts mitochondrial metabolic fitness; the cytosolic fragment of Ms4a4a is anchored to cytoskeletal components, supporting its role in mediating phagocytosis; induction of Ms4a4a via central LNP-Il4 delivery alleviates seizure conditions in an AD mouse model.\",\n      \"method\": \"Ms4a4a knockout mouse model, microglial phagocytosis assays, calcium influx measurements, mitochondrial metabolic assays, cytoskeletal anchoring experiments, in vivo LNP-IL-4 delivery with seizure readout\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with multiple mechanistic readouts (phagocytosis, calcium, mitochondria, cytoskeletal anchoring) and rescue experiment, single lab\",\n      \"pmids\": [\"40349168\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In a mouse model of arthritis, Ms4a4a deletion does not alter disease course but is associated with enhanced therapeutic response specifically to corticosteroids; corticosteroids enhance expression of MS4A4A and FcγR3 in macrophages in vitro and in vivo, suggesting MS4A4A upregulation by corticosteroids counteracts their therapeutic activity.\",\n      \"method\": \"Ms4a4a-deficient mice in experimental arthritis model, in vitro corticosteroid treatment of human and murine macrophages, immunohistochemistry, RNA sequencing\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with defined in vivo phenotypic readout plus in vitro mechanistic follow-up, single lab\",\n      \"pmids\": [\"40924449\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"MS4A4A regulates macrophage M2 polarization through NF-κB and JAK-STAT6 signaling pathways; macrophages overexpressing MS4A4A promote glioma cell proliferation, invasion, and temozolomide resistance in vitro and in vivo; targeting the MS4A4A/NF-κB/STAT6 axis improves outcomes in a glioma mouse model.\",\n      \"method\": \"MS4A4A knockdown and overexpression in macrophages, western blot for NF-κB and STAT6 pathway components, co-culture invasion/proliferation assays, in vivo subcutaneous and orthotopic glioma mouse models\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gain- and loss-of-function with multiple in vitro and in vivo readouts and signaling pathway identification, single lab\",\n      \"pmids\": [\"42056558\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"MS4A4A protein is localized to the plasma membrane in monocytes; it is expressed in M2 (IL-4-polarized) macrophages but not M1 (IFN-γ/LPS-activated) macrophages; it is induced during monocyte-to-macrophage differentiation and absent in immature/precursor myeloid cells and healthy B lymphocytes but present in plasma cells.\",\n      \"method\": \"Monoclonal antibody generation against extracellular epitopes, flow cytometry of human peripheral blood, in vitro monocyte differentiation assays\",\n      \"journal\": \"Immunology and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct protein-level localization by validated monoclonal antibodies and flow cytometry across multiple cell types, single lab\",\n      \"pmids\": [\"28303902\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MS4A4A is a plasma membrane tetraspan protein selectively expressed in macrophage-lineage cells and microglia that functions as a lipid-raft scaffold organizing signaling complexes: it interacts with dectin-1 to support β-glucan-dependent macrophage activation, interacts with caveolin-1 to recruit FcεRI and KIT into lipid rafts and promote PLCγ1/SOCE/degranulation in mast cells, interacts with and stabilizes MS4A6A which in turn blocks DAP12 to post-transcriptionally suppress TREM2 levels and microglial phagocytosis/lysosomal function, and promotes M2 macrophage polarization via PI3K/AKT and NF-κB/JAK-STAT6 signaling pathways; additionally, its cytosolic domain anchors to the cytoskeleton to support microglial phagocytosis and calcium influx.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"MS4A4A is a plasma-membrane tetraspan protein selectively expressed in macrophage-lineage cells, induced during monocyte-to-macrophage differentiation and restricted to M2 (IL-4-polarized) rather than M1 macrophages [#9]. It functions as a lipid-raft scaffold that organizes receptor signaling complexes: it physically interacts and colocalizes with the \\u03b2-glucan receptor dectin-1 in macrophage lipid rafts and is required for dectin-1-dependent activation, with its loss impairing effector molecule production and NK cell-mediated control of metastasis [#0]. In mast cells, MS4A4A interacts with caveolin-1 to recruit Fc\\u03b5RI and KIT into lipid rafts, driving PLC\\u03b31 phosphorylation, Orai1-mediated store-operated calcium entry, and degranulation [#1]. MS4A4A promotes M2 macrophage polarization through PI3K/AKT and JAK/STAT6 signaling [#3] as well as NF-\\u03baB/STAT6 signaling, and macrophage MS4A4A drives a pro-tumoral microenvironment in liver cancer and glioma [#3, #8]. In microglia, MS4A4A interacts with and stabilizes MS4A6A, which complexes with and blocks DAP12 to post-transcriptionally suppress TREM2 levels and thereby limit microglial phagocytosis and lysosomal function [#4]; consistent with this, its cytosolic fragment anchors to cytoskeletal components to support phagocytosis, calcium influx, and mitochondrial fitness [#6]. In amyloid pathology models, Ms4a4a deletion lowers steady-state amyloid-\\u03b2 and plaque burden while rendering microglia more pro-inflammatory [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Established where MS4A4A protein resides and which myeloid states express it, defining it as a differentiation- and polarization-restricted plasma-membrane marker.\",\n      \"evidence\": \"Monoclonal antibodies against extracellular epitopes with flow cytometry of human blood and in vitro monocyte differentiation\",\n      \"pmids\": [\"28303902\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No molecular function assigned at this stage\", \"Mechanism of M2-restricted induction not defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showed MS4A4A acts upstream of an innate immune receptor, answering how a tetraspan scaffold contributes to macrophage activation by partnering with dectin-1 in lipid rafts.\",\n      \"evidence\": \"Lipid-raft co-localization/interaction, Ms4a4a-deficient macrophage signaling and effector assays, in vivo metastasis models with genetic KO\",\n      \"pmids\": [\"31263276\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct binding interface with dectin-1 not mapped\", \"Whether MS4A4A organizes other receptors not addressed here\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended the raft-scaffold model beyond macrophages, showing MS4A4A recruits Fc\\u03b5RI/KIT via caveolin-1 to drive PLC\\u03b31/SOCE-dependent mast cell degranulation.\",\n      \"evidence\": \"siRNA knockdown in human mast cells, phosphorylation/Ca2+/degranulation assays, caveolin-1 Co-IP, lipid raft fractionation\",\n      \"pmids\": [\"32240745\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Knockdown rather than genetic KO\", \"Stoichiometry of MS4A4A\\u2013caveolin-1\\u2013receptor complexes unresolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Linked MS4A4A to type-2 inflammation in vivo, showing it controls IL-4-induced arginase 1 and allergic eosinophil infiltration.\",\n      \"evidence\": \"Ms4a4a-deficient mice, IL-4 macrophage stimulation, house dust mite intranasal challenge\",\n      \"pmids\": [\"32589266\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular link between MS4A4A and arginase 1 regulation unclear\", \"Limited mechanistic detail\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined the intracellular signaling output of MS4A4A in tumor-associated macrophages, implicating PI3K/AKT and JAK/STAT6 in M2 polarization and validating MS4A4A as an antibody-targetable node.\",\n      \"evidence\": \"RNA-seq, western blot, flow cytometry, murine tumor models with MS4A4A inhibition and anti-MS4A4A antibody\",\n      \"pmids\": [\"37507218\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How MS4A4A engages PI3K/AKT and JAK/STAT6 mechanistically not shown\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Uncovered an intracellular regulatory circuit, showing MS4A4A stabilizes MS4A6A, which blocks DAP12 to post-transcriptionally suppress TREM2 and constrain microglial function.\",\n      \"evidence\": \"CRISPR KO/OE, degrading antibodies, MS4A4A\\u2013MS4A6A and MS4A6A\\u2013DAP12 Co-IP, NHP/mouse amyloid models, phagocytosis/lysosomal assays\",\n      \"pmids\": [\"41435829\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which MS4A6A degrades/blocks DAP12 not fully defined\", \"Direct vs indirect effect on TREM2 turnover\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected MS4A4A's microglial role to cellular machinery, showing its cytosolic fragment anchors to the cytoskeleton to support phagocytosis, calcium influx, and mitochondrial fitness.\",\n      \"evidence\": \"Ms4a4a KO mouse, phagocytosis/calcium/mitochondrial assays, cytoskeletal anchoring experiments, LNP-IL-4 rescue in AD seizure model\",\n      \"pmids\": [\"40349168\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cytoskeletal binding partners not identified\", \"Causal chain from cytoskeleton to calcium/mitochondria unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated functional consequence of MS4A4A loss on amyloid handling, showing deletion lowers A\\u03b2 and plaque burden while making microglia more pro-inflammatory.\",\n      \"evidence\": \"Ms4a4a KO in 5xFAD mice, A\\u03b2 half-life and plaque quantification, microglial inflammatory and MMP-9 profiling, human CSF corroboration\",\n      \"pmids\": [\"40843775\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether MMP-9 mechanistically drives A\\u03b2 clearance not proven\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealed a context where MS4A4A modulates drug response, showing its corticosteroid-induced upregulation counteracts therapeutic activity in arthritis.\",\n      \"evidence\": \"Ms4a4a-deficient mice in experimental arthritis, corticosteroid treatment of human/murine macrophages, IHC, RNA-seq\",\n      \"pmids\": [\"40924449\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking MS4A4A to corticosteroid resistance not defined\", \"No effect on disease course alone\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Reinforced the pro-tumoral macrophage role, implicating NF-\\u03baB/STAT6 signaling in MS4A4A-driven M2 polarization and glioma progression/temozolomide resistance.\",\n      \"evidence\": \"MS4A4A KD/OE in macrophages, western blot for NF-\\u03baB/STAT6, co-culture invasion/proliferation assays, glioma mouse models\",\n      \"pmids\": [\"42056558\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How MS4A4A activates NF-\\u03baB not shown\", \"Reconciliation of multiple signaling axes (PI3K/AKT vs NF-\\u03baB) across tumor types\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis by which MS4A4A organizes raft receptor complexes and transmits signals to its multiple downstream pathways remains undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of MS4A4A or its receptor complexes\", \"Direct binding interfaces with dectin-1, caveolin-1, MS4A6A not mapped\", \"Unifying mechanism linking raft scaffolding to PI3K/AKT, JAK/STAT6, and NF-\\u03baB outputs unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 1, 9]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 8]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CLEC7A\", \"CAV1\", \"MS4A6A\", \"FCER1A\", \"KIT\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}