{"gene":"IFITM3","run_date":"2026-04-28T18:06:53","timeline":{"discoveries":[{"year":2010,"finding":"IFITM3 antiviral activity is post-translationally regulated by S-palmitoylation on membrane-proximal cysteines, which controls its clustering in membrane compartments and its antiviral activity against influenza virus.","method":"Chemical reporter-based palmitoylome profiling, site-directed mutagenesis of cysteine residues, influenza virus infection assays","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods (chemical proteomics, mutagenesis, functional antiviral assays) in a single study","pmids":["20601941"],"is_preprint":false},{"year":2012,"finding":"IFITM3 is essential for defending the host against influenza A virus in vivo; knockout mice develop fulminant viral pneumonia with a normally low-pathogenicity virus, and protection is rescued by re-introduction of Ifitm3.","method":"Knockout mouse model, viral challenge, in vitro complementation","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined phenotype, rescue experiment, replicated in vitro and in vivo","pmids":["22446628"],"is_preprint":false},{"year":2012,"finding":"IFITM3 localizes to endolysosomes and prevents endocytosed virus particles from accessing the host cytoplasm; S-palmitoylation enhances membrane affinity and antiviral activity, while lysine ubiquitination decreases endolysosomal localization and antiviral activity. IFITM3 is proposed to adopt an intramembrane topology with both N and C termini facing the cytoplasm.","method":"Fluorescence imaging, cellular fractionation, N-linked glycosylation site insertion, protein lipidation mapping, mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods (imaging, fractionation, topology mapping, mutagenesis) with functional readouts","pmids":["22511783"],"is_preprint":false},{"year":2012,"finding":"The N-terminal 21-amino-acid region of IFITM3 is required for its endosomal localization and antiviral activity against pH-dependent viruses (influenza A); deletion of this region relocates IFITM3 to the cell periphery, abolishing restriction of pH-dependent viruses but not HIV-1.","method":"Deletion mutagenesis, subcellular localization imaging, viral infection assays","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 2 — mutagenesis linked to localization and function with multiple viral systems","pmids":["23055554"],"is_preprint":false},{"year":2013,"finding":"IFITM3 interacts with VAPA and prevents its association with OSBP, thereby disrupting intracellular cholesterol homeostasis; this induces cholesterol accumulation in multivesicular bodies and late endosomes, inhibiting fusion of virion-containing intraluminal vesicles with endosomal membranes and blocking virus release into the cytosol.","method":"Co-immunoprecipitation, ectopic expression/depletion of VAPA, cholesterol localization assays, viral entry assays","journal":"Cell host & microbe","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, genetic manipulation (depletion/overexpression), mechanistic functional readouts","pmids":["23601107"],"is_preprint":false},{"year":2014,"finding":"IFITM3 possesses a YxxΦ endocytic sorting motif (20-YEML-23) that enables it to undergo clathrin-mediated endocytosis through binding to the μ2 subunit of the AP-2 complex; blocking endocytosis of IFITM3 (by mutating this motif, depleting μ2, or overexpressing μ2 mutants) abrogates its antiviral activity against pH-dependent viruses.","method":"Mutagenesis of sorting motif, μ2 depletion/overexpression, subcellular localization imaging, viral infection assays","journal":"Cellular microbiology","confidence":"High","confidence_rationale":"Tier 2 — multiple genetic perturbations with consistent functional and localization readouts","pmids":["24521078"],"is_preprint":false},{"year":2015,"finding":"The E3 ubiquitin ligase NEDD4 ubiquitinates IFITM3 in cells and in vitro via interaction with a PPxY motif in IFITM3 and the WW domain of NEDD4; NEDD4 knockout leads to accumulation of IFITM3 and increased protection from influenza virus. Steady-state IFITM3 turnover occurs through the lysosomal degradation pathway.","method":"In vitro ubiquitination assay, NEDD4 knockout MEFs, PPxY motif mutagenesis, NEDD4 knockdown in human lung cells, lysosome inhibitor treatment","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro reconstitution plus KO model, mutagenesis, conserved in mouse and human cells","pmids":["26263374"],"is_preprint":false},{"year":2016,"finding":"IFITM3 adopts a membrane topology with a single long transmembrane helix in the C-terminus and an intramembrane segment in the N-terminal hydrophobic region, with both termini facing the cytoplasm; this topology supports a mechanism of enhanced restricted membrane hemifusion.","method":"Systematic site-directed spin labeling (SDSL), EPR spectroscopy, solution NMR in detergent micelles","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 — EPR and NMR structural characterization with orthogonal validation","pmids":["27046158"],"is_preprint":false},{"year":2017,"finding":"ZDHHC20 co-localizes with IFITM3 at lysosomes and uniquely enhances IFITM3 antiviral activity when both are overexpressed; multiple ZDHHCs (especially 3, 7, 15, 20) can palmitoylate IFITM3, demonstrating functional redundancy, and combined knockdown of ZDHHC3 and ZDHHC7 in ZDHHC20 KO cells decreases endogenous IFITM3 palmitoylation.","method":"ZDHHC knockout cell line screen, ZDHHC overexpression screen, co-localization imaging, palmitoylation assays, siRNA knockdown, viral infection assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — systematic screen with multiple orthogonal methods, KO and knockdown approaches","pmids":["29079573"],"is_preprint":false},{"year":2017,"finding":"LSD1 (a histone demethylase) is recruited to demethylate IFITM3 at position K88 under IFNα treatment, activating IFITM3; RNA virus infection (VSV or IAV) triggers IFITM3 K88 monomethylation by promoting IFITM3 dissociation from LSD1, and LSD1 inhibition increases IFITM3 monomethylation and worsens IAV infection in mice.","method":"In vitro demethylation assay, mutagenesis, LSD1 inhibitor treatment, mouse infection model, co-immunoprecipitation","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 1-2 — identification of writer/eraser with functional readout in vitro and in vivo","pmids":["29281729"],"is_preprint":false},{"year":2019,"finding":"IFITM3 is present on endocytic vesicles that fuse with incoming virus particles and enhances trafficking of viral cargo to lysosomes; this trafficking is specific to restricted viruses, requires S-palmitoylation, and is abrogated with loss-of-function mutants.","method":"CRISPR-Cas9 IFITM-mutant cell lines, site-specific fluorophore tagging, live-cell imaging, viral entry assays","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1-2 — live-cell imaging with site-specific labeling, genetic KO, functional mutagenesis, multiple orthogonal approaches","pmids":["30643282"],"is_preprint":false},{"year":2020,"finding":"IFITM3 binds to γ-secretase and upregulates its activity, thereby increasing amyloid-β production; inflammatory cytokines induce IFITM3 expression in neurons and astrocytes, and IFITM3 knockout reduces γ-secretase activity and amyloid plaque formation in 5xFAD mice. IFITM3 levels in the γ-secretase complex strongly correlate with γ-secretase activity in late-onset AD patient samples.","method":"Co-immunoprecipitation, IFITM3 KO mouse model (5xFAD), γ-secretase activity assays, human AD patient tissue analysis","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — Co-IP, KO mouse model with functional readouts, human tissue correlation; multiple orthogonal methods","pmids":["32879487"],"is_preprint":false},{"year":2020,"finding":"IFITM3 functions as a PIP3 scaffold at the plasma membrane to amplify PI3K signaling in B cells; oncogenic kinases phosphorylate IFITM3 at Tyr20, causing constitutive plasma membrane localization. IFITM3 uses Lys83 and Lys104 in its conserved intracellular loop as a scaffold for PIP3 accumulation. BCR engagement induces Tyr20 phosphorylation, switching IFITM3 from antiviral endosomal function to PI3K amplification at the cell surface.","method":"Phosphomimetic/phosphodeficient mutants, Ifitm3-/- mouse B cells, BCR signaling assays, lipid raft fractionation, PI3K signaling readouts, oncogene transformation assays","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1-2 — multiple mutants, KO mouse, mechanistic biochemical assays, replicated with oncogene models","pmids":["33149299"],"is_preprint":false},{"year":2020,"finding":"VCP/p97 AAA-ATPase is a primary interaction partner of IFITM3; IFITM3 ubiquitination at lysine 24 is crucial for VCP binding, trafficking, turnover, and engagement with incoming virus particles. Pharmacological inhibition of VCP/p97 leads to defective IFITM3 lysosomal sorting and co-trafficking with virus particles.","method":"Site-specific photo-crosslinking, quantitative proteomics, mutagenesis (K24), VCP inhibitor treatment, lysosomal sorting assays, live-cell imaging","journal":"Cell chemical biology","confidence":"High","confidence_rationale":"Tier 1-2 — photo-crosslinking proteomics, site-specific mutagenesis, pharmacological validation, functional imaging","pmids":["32243810"],"is_preprint":false},{"year":2018,"finding":"mTOR inhibition by rapamycin downregulates IFITM3 at the protein level (not mRNA) via a mechanism requiring endosomal trafficking, ubiquitination, ESCRT machinery, and lysosomal acidification, thereby promoting influenza A virus and lentiviral vector entry into cells.","method":"mTOR inhibitor treatment, IFITM3 siRNA/KO, ESCRT and lysosome inhibitors, virus infection assays, mRNA vs protein level analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — multiple pharmacological and genetic perturbations with consistent mechanistic readouts","pmids":["30301809"],"is_preprint":false},{"year":2020,"finding":"IFITM3 oligomerization is driven by a GxxxG motif centered on Gly-95 (and Gly-91); mutation of Gly-95 disrupts IFITM3 oligomerization and reduces antiviral activity against influenza A virus. IFITM3 oligomers promote membrane rigidity in a Gly-95-dependent and amphipathic helix-dependent manner, and Amphotericin B counteracts this rigidification.","method":"Mutagenesis of GxxxG motif, oligomerization assays, membrane rigidity measurements, Amphotericin B treatment, influenza A virus infection assays","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1-2 — mutagenesis linked to oligomerization, membrane biophysics, and antiviral function with multiple orthogonal methods","pmids":["33112230"],"is_preprint":false},{"year":2022,"finding":"The amphipathic helix (AH) of IFITM3 directly binds cholesterol; mutations F63Q and F67Q in the AH disrupt AH structure, inhibit cholesterol binding in vitro, restrict bilayer insertion in silico, and strongly impair antiviral function.","method":"Fluorescence-based in vitro cholesterol binding assay with NBD-cholesterol, AH mutagenesis, molecular dynamics simulation, antiviral assays","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 — in vitro biochemical binding assay, mutagenesis, and computational validation","pmids":["35872070"],"is_preprint":false},{"year":2023,"finding":"IFITM3 induces local lipid sorting at the hemifusion site, increasing the concentration of fusion-disfavoring lipids, which raises the energy barrier for fusion pore formation and stabilizes hemifusion intermediates, causing viral degradation in lysosomes. In situ cryo-electron tomography captured IFITM3-mediated arrest of influenza A virus membrane fusion and hemifusion diaphragms at late endosomal membranes.","method":"In situ cryo-electron tomography, lipid analysis, hemifusion assays, IFITM3 KO cells, influenza A virus infection","journal":"Cell host & microbe","confidence":"High","confidence_rationale":"Tier 1 — cryo-ET structural data capturing hemifusion intermediates, combined with lipid analysis and functional KO assays","pmids":["37003257"],"is_preprint":false},{"year":2010,"finding":"IFITM3 disrupts an early event after endocytosis of VSV particles but before primary transcription of incoming viral genomes; both the N-terminal 21 amino acid residues and the C-terminal transmembrane region are required for antiviral activity.","method":"Viral infection assays (VSV), deletion mutagenesis, primary transcription assay","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 — domain mutagenesis with viral restriction functional readouts, single lab","pmids":["20943977"],"is_preprint":false},{"year":2013,"finding":"IFITM3 restricts reovirus entry in the endocytic pathway by modulating late endosomal compartment function; IFITM3 delays proteolytic processing of outer capsid protein μ1, suggesting it reduces endosomal protease activity or delays proteolysis. IFITM3 does not restrict reovirus ISVPs that bypass endosomal proteolysis.","method":"IFITM3-expressing cell lines, reovirus infection assays (ISVP vs intact virions), μ1 proteolysis assays, shRNA knockdown","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — genetic KD and OE with mechanistic proteolysis readout, single lab","pmids":["23649619"],"is_preprint":false},{"year":2015,"finding":"S-palmitoylation of IFITM1, IFITM2, and IFITM3 is essential for anti-HCV activity; a conserved tyrosine in the N-terminal domain of IFITM2 and IFITM3 regulates protein localization (to late and early endosomes, respectively) but is dispensable for anti-HCV activity. IFITM2 and IFITM3 act at late entry/endosomal stages of HCV infection.","method":"S-palmitoylation mutagenesis, tyrosine mutants, subcellular localization imaging, HCV infection assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — mutagenesis and localization with functional readout, single lab","pmids":["26354436"],"is_preprint":false},{"year":2011,"finding":"KLF4 directly transcriptionally represses IFITM3 by binding to two KLF4-binding sites in the IFITM3 promoter; loss of KLF4 leads to IFITM3 overexpression in colon mucosa, and IFITM3 knockdown suppresses colon cancer cell proliferation, migration, and invasion.","method":"Chromatin immunoprecipitation, promoter mutagenesis, siRNA knockdown, villin-Cre conditional KLF4 KO mice, xenograft model","journal":"Clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP, promoter mutagenesis, in vivo mouse model; single lab but multiple methods","pmids":["21531817"],"is_preprint":false},{"year":2019,"finding":"IFITM3 interacts with Smad4 and activates the TGF-β-Smads signaling pathway to promote prostate cancer cell proliferation, invasion, and bone migration; IFITM3 knockdown inhibits MAPK pathway activation induced by exogenous TGF-β.","method":"Co-immunoprecipitation (IFITM3-Smad4), shRNA knockdown, microarray, MAPK pathway assays","journal":"Cell death & disease","confidence":"Low","confidence_rationale":"Tier 3 — single Co-IP, mechanistic pathway placement partly inferred","pmids":["31273201"],"is_preprint":false},{"year":2022,"finding":"IFITM3 interacts with NTCP (the HBV/HDV receptor) and acts as an NTCP co-factor that facilitates HBV and HDV infection (not restriction) in a step subsequent to viral attachment; IFITM3 knockdown significantly reduces HBV and HDV infection of NTCP-expressing hepatocytes and primary human hepatocytes, while increasing influenza A virus infection.","method":"Membrane yeast-two-hybrid, co-immunoprecipitation, IFITM3 knockdown, HBV/HDV/IAV infection assays in HuH7-NTCP cells and primary hepatocytes","journal":"Viruses","confidence":"Medium","confidence_rationale":"Tier 2-3 — reciprocal PPI assays (Y2H + Co-IP), knockdown in multiple cell types including primary hepatocytes","pmids":["35458456"],"is_preprint":false},{"year":2020,"finding":"IFITM3 promotes fibrinogen endocytosis in megakaryocytes and platelets in an interferon-dependent manner; mechanistically, IFITM3 interacts with clathrin and αIIb and alters their plasma membrane localization into lipid rafts. IFITM3 is necessary and sufficient for fibrinogen endocytosis, and Ifitm3-/- mice are rescued from IFN-induced platelet hyperreactivity and thrombosis.","method":"Co-immunoprecipitation (IFITM3-clathrin-αIIb), Ifitm3-/- mouse model, IFITM3 overexpression/deletion in megakaryocytes, fibrinogen endocytosis assays, thrombosis assays","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 — Co-IP, KO mouse, gain/loss-of-function, multiple functional readouts","pmids":["36194487"],"is_preprint":false},{"year":2021,"finding":"IFITM3 is required for type I IFN-mediated suppression of phagosome maturation in macrophages; in the absence of IFITM3, phagosome maturation and proteolysis of Listeria virulence factors ActA and LLO are not suppressed, preventing phagosome escape. Ifitm3-/- mice are resistant to systemic Listeria infection.","method":"Ifitm3-/- mouse model, phagosome maturation assays, virulence factor proteolysis assays, bacterial infection assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined mechanistic phenotype (phagosome maturation) and in vivo validation","pmids":["34404769"],"is_preprint":false},{"year":2020,"finding":"p53 enhances IFITM3 palmitoylation by transcriptionally upregulating ZDHHC1, which interacts with IFITM3 to promote its palmitoylation and protein stability, thereby restricting Japanese encephalitis virus replication. JEV reduces p53 expression to impair this pathway.","method":"ZDHHC1 knockdown, p53 overexpression/knockdown, Co-IP (ZDHHC1-IFITM3), palmitoylation assays, viral replication assays","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP, genetic perturbations, palmitoylation assays, single lab","pmids":["33108395"],"is_preprint":false},{"year":2021,"finding":"IFITM3 incorporation into IAV particles competes with viral hemagglutinin (HA) incorporation, reducing virion HA content; this sensitizes IAV to antibody-mediated neutralization, thereby impacting infection outcome in vivo.","method":"IFITM3 incorporation into virions, virion HA quantification, neutralization assays, mathematical modeling, mouse in vivo infection model","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (biochemical, functional, mathematical, in vivo) demonstrating a novel IFITM3 mechanism","pmids":["33882122"],"is_preprint":false},{"year":2023,"finding":"PIP3 is required for endosomal IFITM restriction of viruses; lysines in the conserved IFITM intracellular loop recruit PIP3, and PIP3 acts as an interferon-inducible phospholipid rheostat for endosomal antiviral immunity. Plasma membrane-localized IFITM restriction operates independently of these lysines.","method":"Pseudotyped viral entry assays, replicating virus assays, high-throughput proteomics, lipidomics, IFITM mutants (lysine mutations), exogenous PIP3 supplementation","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1-2 — proteomics, lipidomics, mutagenesis, and functional assays with multiple viral systems","pmids":["36970857"],"is_preprint":false},{"year":2022,"finding":"IFITM3 directly interacts with the influenza HA2 subunit (but not HA1) via its transmembrane domain, as demonstrated by co-localization and co-immunoprecipitation; this interaction was confirmed across multiple influenza A subtypes and influenza B virus.","method":"Co-immunoprecipitation, subcellular co-localization, truncation/deletion analysis, pseudovirus entry assays","journal":"Virologica Sinica","confidence":"Medium","confidence_rationale":"Tier 3 — Co-IP and co-localization, single lab, no structural or reconstitution validation","pmids":["35809785"],"is_preprint":false},{"year":2019,"finding":"Small extracellular vesicles (sEVs) containing IFITM3 are partially responsible for transmitting paracrine senescence to normal neighboring cells; IFITM3 was identified by mass spectrometry proteomics of sEV cargo and confirmed by siRNA screen.","method":"Mass spectrometry proteomics, functional siRNA screen, Cre-reporter sEV uptake system","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2-3 — MS identification plus functional siRNA screen; mechanistic detail is partial","pmids":["31242426"],"is_preprint":false},{"year":2009,"finding":"IFITM3 physically interacts with osteopontin (OPN) in vitro and in vivo; IFITM3 expression reduces OPN mRNA expression (possibly via mRNA stability), and an IFITM3 DNA-binding domain mediates interaction with OPN. Stable IFITM3 transfection inhibits OPN-mediated anchorage-independent growth, cell adhesion, and invasion.","method":"Bacterial two-hybrid, in vitro binding, co-immunoprecipitation, antisense RNA, northern blot, stable transfection, invasion assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 3 — two-hybrid plus Co-IP with functional cellular readouts; single lab","pmids":["19901966"],"is_preprint":false},{"year":2024,"finding":"IFITM3 deficiency in FOXP3+ regulatory T cells enhances STAT1 translation and phosphorylation; conversely, STAT1 regulates IFITM3 expression forming a feedback loop. Blocking IFNγ or depleting the STAT1-IFITM3 axis phenocopies restored suppressive Treg function in tumors.","method":"IFITM3-deficient Treg mouse model, cytokine blocking, STAT1 KO, tumor growth assays, cytokine measurements","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 — genetic KO and KD with mechanistic pathway (STAT1 phosphorylation feedback loop), in vivo tumor model","pmids":["38167862"],"is_preprint":false},{"year":2025,"finding":"IFITM3 in cerebrovascular endothelial cells (CVECs) regulates amyloid-β generation through BACE1 and γ-secretase; IFITM3 overexpression in endothelial cells enhances Aβ production, and Aβ further upregulates IFITM3 (positive feedback). AAV-mediated IFITM3 knockdown in CVECs reduces Aβ accumulation and improves cognition in AD transgenic mice.","method":"snRNA-seq, AAV-BI30 endothelial IFITM3 knockdown, BACE1/γ-secretase activity assays, behavioral tests, two-photon imaging, immunohistochemistry, Western blot","journal":"Alzheimer's & dementia","confidence":"Medium","confidence_rationale":"Tier 2 — cell-type-specific KD with multiple mechanistic and in vivo readouts, single lab","pmids":["39807629"],"is_preprint":false}],"current_model":"IFITM3 is an interferon-induced, S-palmitoylated intramembrane protein that localizes to endolysosomes via a YxxΦ/AP-2-dependent endocytic sorting signal, where it oligomerizes (via a GxxxG motif), induces local lipid sorting and membrane rigidity through its amphipathic helix and cholesterol binding, and stabilizes hemifusion intermediates to block fusion pore formation by diverse enveloped viruses; its activity is positively regulated by S-palmitoylation (mediated redundantly by multiple ZDHHCs, especially ZDHHC20) and LSD1-mediated K88 demethylation, and negatively regulated by NEDD4-mediated lysine ubiquitination leading to lysosomal degradation, while in B cells phosphorylation at Tyr20 switches IFITM3 from an endosomal antiviral effector to a plasma membrane PIP3 scaffold that amplifies PI3K signaling, and in neurons/astrocytes IFITM3 binds and activates γ-secretase to increase amyloid-β production."},"narrative":{"teleology":[{"year":2010,"claim":"Establishing that IFITM3 blocks an early post-endocytic entry step and that S-palmitoylation is a key post-translational switch for its antiviral activity answered the fundamental question of how this IFN-induced protein restricts virus infection.","evidence":"Chemical reporter palmitoylome profiling, cysteine mutagenesis, VSV/influenza infection assays in cell lines","pmids":["20601941","20943977"],"confidence":"High","gaps":["Identity of palmitoyl-acyltransferase(s) unknown at this time","Mechanism of membrane-level restriction unresolved","In vivo relevance not yet tested"]},{"year":2012,"claim":"Demonstrating that IFITM3 is essential for surviving influenza infection in vivo and that it localizes to endolysosomes via its N-terminal sorting region established IFITM3 as a non-redundant innate immune effector whose subcellular targeting is critical for function.","evidence":"Ifitm3 knockout mice challenged with influenza, topology mapping by glycosylation insertion, deletion mutagenesis, subcellular imaging","pmids":["22446628","22511783","23055554"],"confidence":"High","gaps":["Sorting motif not yet mapped to a specific endocytic adaptor","Membrane topology model debated","Mechanism of fusion blockade at the membrane biophysics level unknown"]},{"year":2013,"claim":"Identification of the VAPA interaction and cholesterol accumulation in endosomes provided the first mechanistic link between IFITM3 and membrane lipid remodeling as a basis for fusion inhibition.","evidence":"Co-immunoprecipitation of IFITM3–VAPA, cholesterol localization assays, viral entry assays in VAPA-depleted cells","pmids":["23601107"],"confidence":"High","gaps":["Whether VAPA interaction is necessary versus sufficient for restriction unclear","Direct cholesterol binding by IFITM3 not yet shown","Contribution of other lipid species not tested"]},{"year":2014,"claim":"Mapping the YxxΦ motif and its interaction with AP-2/μ2 resolved how IFITM3 reaches endosomes via clathrin-mediated endocytosis and why endosomal targeting is required for restricting pH-dependent viruses.","evidence":"YxxΦ motif mutagenesis, μ2 depletion/overexpression, localization imaging, influenza and VSV infection assays","pmids":["24521078"],"confidence":"High","gaps":["Whether AP-2-independent pathways also contribute to IFITM3 trafficking not addressed","Role of phosphorylation at Y20 in modulating this sorting not yet recognized"]},{"year":2015,"claim":"Identification of NEDD4 as the E3 ligase that ubiquitinates IFITM3 via a PPxY motif and targets it for lysosomal degradation established ubiquitination as a negative regulatory axis controlling IFITM3 protein levels and antiviral potency.","evidence":"In vitro ubiquitination reconstitution, NEDD4 KO MEFs, PPxY mutagenesis, lysosome inhibitor treatment, influenza infection assays","pmids":["26263374"],"confidence":"High","gaps":["Which specific lysine sites are ubiquitinated incompletely mapped","Role of deubiquitinases not explored","Interplay between ubiquitination and palmitoylation not resolved"]},{"year":2016,"claim":"EPR and NMR structural studies resolved the intramembrane topology of IFITM3 — a single C-terminal transmembrane helix with an N-terminal intramembrane segment — and linked this topology to enhanced hemifusion, providing a biophysical framework for the antiviral mechanism.","evidence":"Site-directed spin labeling, EPR spectroscopy, solution NMR in detergent micelles","pmids":["27046158"],"confidence":"High","gaps":["Structure determined in detergent micelles, not in native membranes","How topology relates to oligomerization not addressed","No high-resolution structure in lipid bilayer"]},{"year":2017,"claim":"Systematic screening identified ZDHHC20 as the primary lysosome-localized palmitoyltransferase for IFITM3 and revealed functional redundancy among multiple ZDHHCs, while discovery that LSD1 demethylates K88 to activate IFITM3 established a second post-translational regulatory layer.","evidence":"ZDHHC KO/overexpression screen, palmitoylation assays, LSD1 in vitro demethylation, LSD1 inhibitor in mouse IAV model, co-IP","pmids":["29079573","29281729"],"confidence":"High","gaps":["Relative contributions of individual ZDHHCs in physiological contexts unclear","K88 methyltransferase not identified","How methylation and palmitoylation are coordinated unknown"]},{"year":2019,"claim":"Live-cell imaging with site-specific labeling demonstrated that IFITM3 is present on endocytic vesicles that actively fuse with incoming virions and routes restricted viral cargo to lysosomes, shifting the model from passive membrane alteration to active co-trafficking.","evidence":"CRISPR IFITM-mutant cell lines, site-specific fluorophore tagging, live-cell imaging of viral entry","pmids":["30643282"],"confidence":"High","gaps":["How IFITM3-bearing vesicles are selectively targeted to virus-containing endosomes unknown","Whether co-trafficking requires specific lipid or protein cofactors not determined"]},{"year":2020,"claim":"A series of landmark studies expanded IFITM3 biology beyond antiviral defense: IFITM3 was shown to bind and activate γ-secretase (increasing Aβ production relevant to Alzheimer's disease), to function as a PIP3 scaffold amplifying PI3K signaling in B cells upon Tyr20 phosphorylation, and to require VCP/p97 for ubiquitin-dependent trafficking and turnover.","evidence":"γ-secretase Co-IP and activity assays in 5xFAD mice and human AD tissue; phosphomimetic mutants and Ifitm3−/− B cells with BCR signaling readouts; photo-crosslinking proteomics identifying VCP, K24 mutagenesis, VCP inhibitor treatment","pmids":["32879487","33149299","32243810"],"confidence":"High","gaps":["Structural basis of IFITM3–γ-secretase interaction unknown","How Tyr20 phosphorylation overrides AP-2 sorting mechanistically unclear","Whether VCP acts on IFITM3 as an unfoldase or segregase not determined"]},{"year":2020,"claim":"Demonstration that GxxxG-mediated oligomerization drives membrane rigidity and that IFITM3 incorporation into virions reduces HA content revealed two distinct mechanistic arms — endosomal membrane stiffening and virion-intrinsic attenuation.","evidence":"G95 mutagenesis with oligomerization and membrane rigidity assays; virion IFITM3/HA quantification, neutralization assays, mouse infection model","pmids":["33112230","33882122"],"confidence":"High","gaps":["Stoichiometry of functional oligomers not defined","Relative contribution of virion incorporation versus endosomal restriction in vivo not quantified"]},{"year":2021,"claim":"IFITM3 was found to suppress phagosome maturation in macrophages, revealing a host-detrimental role where IFN-induced IFITM3 paradoxically facilitates intracellular bacterial infection by preventing lysosomal killing of Listeria.","evidence":"Ifitm3−/− mouse Listeria infection model, phagosome maturation and virulence factor proteolysis assays","pmids":["34404769"],"confidence":"High","gaps":["Molecular mechanism by which IFITM3 inhibits phagosome maturation not defined","Whether other intracellular bacteria exploit this pathway unknown"]},{"year":2022,"claim":"Direct cholesterol binding by the amphipathic helix was biochemically demonstrated, and an unexpected pro-viral role for IFITM3 as an NTCP co-factor facilitating HBV/HDV entry was identified, showing that IFITM3 can promote or restrict virus entry depending on the pathogen.","evidence":"NBD-cholesterol binding assay with F63Q/F67Q mutants, MD simulations; membrane Y2H and Co-IP of IFITM3–NTCP, HBV/HDV infection assays in primary hepatocytes","pmids":["35872070","35458456"],"confidence":"High","gaps":["Structural basis of cholesterol–AH interaction at atomic resolution unknown","Mechanism by which IFITM3 facilitates HBV/HDV post-attachment steps unclear","NTCP interaction not validated by reconstitution"]},{"year":2023,"claim":"Cryo-electron tomography captured IFITM3-mediated arrest of influenza fusion at the hemifusion diaphragm stage in situ, and PIP3 was identified as an interferon-inducible lipid rheostat required for endosomal IFITM restriction, unifying lipid sorting, hemifusion arrest, and phosphoinositide signaling into a coherent mechanistic model.","evidence":"In situ cryo-ET of IFITM3 KO versus WT cells infected with IAV; lipidomics, PIP3 supplementation, lysine mutants with pseudovirus and replicating virus assays","pmids":["37003257","36970857"],"confidence":"High","gaps":["How IFITM3 recruits PIP3 to the hemifusion site at molecular detail unknown","Whether PIP3 rheostat applies to all restricted viruses not tested","No atomic-resolution structure of IFITM3 in a lipid bilayer"]},{"year":2025,"claim":"Cell-type-specific knockdown of IFITM3 in cerebrovascular endothelial cells reduced Aβ accumulation and improved cognition in AD mice, establishing a positive feedback loop between Aβ and IFITM3 and identifying vascular IFITM3 as a potential therapeutic target.","evidence":"AAV-BI30 endothelial IFITM3 knockdown in AD transgenic mice, BACE1/γ-secretase activity assays, behavioral and two-photon imaging","pmids":["39807629"],"confidence":"Medium","gaps":["Molecular basis of IFITM3 regulation of BACE1 activity not determined","Whether endothelial IFITM3–Aβ feedback operates in human AD not tested","Single-lab finding awaiting independent replication"]},{"year":null,"claim":"Key unresolved questions include the high-resolution structure of IFITM3 in native membranes, the precise mechanism by which IFITM3 suppresses phagosome maturation, the identity of the K88 methyltransferase, and how context-dependent phosphorylation, palmitoylation, ubiquitination, and methylation are integrated to switch IFITM3 between antiviral, signaling, and disease-promoting functions.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution lipid bilayer structure","K88 methyltransferase unidentified","Integrated PTM cross-talk model not established","Cell-type-specific regulatory mechanisms incompletely mapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[4,16,17]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[11,12,15,25]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[12,28]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[7,15,17]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[2,3,5,10,17]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[2,6,8,14]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[12,24]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[10,30]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[1,2,10,17,27]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[12,28,32]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[5,10,14,24]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[11,33]}],"complexes":["γ-secretase complex (functional interaction)"],"partners":["VAPA","NEDD4","VCP","ZDHHC20","LSD1","AP2M1","NTCP","ITGA2B"],"other_free_text":[]},"mechanistic_narrative":"IFITM3 is an interferon-induced intramembrane protein that restricts entry of diverse enveloped viruses by altering endosomal membrane properties, and additionally modulates γ-secretase activity, PI3K signaling, and phagosome maturation in cell-type-specific contexts. IFITM3 localizes to endolysosomes via a YxxΦ/AP-2-dependent endocytic sorting motif and, once there, oligomerizes through a GxxxG motif, binds cholesterol via its amphipathic helix, and induces local lipid sorting that stabilizes hemifusion intermediates and blocks fusion pore formation, thereby trapping viral particles for lysosomal degradation [PMID:33112230, PMID:37003257, PMID:35872070, PMID:24521078]. Its antiviral activity is positively regulated by S-palmitoylation (mediated redundantly by ZDHHC20, ZDHHC3, ZDHHC7) and LSD1-dependent K88 demethylation, and negatively regulated by NEDD4-mediated ubiquitination that targets it for lysosomal turnover via VCP/p97-dependent sorting [PMID:20601941, PMID:29079573, PMID:29281729, PMID:26263374, PMID:32243810]. Beyond antiviral defense, IFITM3 binds and activates γ-secretase to increase amyloid-β production in neurons, astrocytes, and cerebrovascular endothelial cells, and in B cells phosphorylation at Tyr20 redirects IFITM3 to the plasma membrane where it scaffolds PIP3 to amplify PI3K signaling [PMID:32879487, PMID:39807629, PMID:33149299]."},"prefetch_data":{"uniprot":{"accession":"Q01628","full_name":"Interferon-induced transmembrane protein 3","aliases":["Dispanin subfamily A member 2b","DSPA2b","Interferon-inducible protein 1-8U"],"length_aa":133,"mass_kda":14.6,"function":"IFN-induced antiviral protein which disrupts intracellular cholesterol homeostasis. Inhibits the entry of viruses to the host cell cytoplasm by preventing viral fusion with cholesterol depleted endosomes. May inactivate new enveloped viruses which buds out of the infected cell, by letting them go out with a cholesterol depleted membrane. Active against multiple viruses, including influenza A virus, SARS coronaviruses (SARS-CoV and SARS-CoV-2), Marburg virus (MARV), Ebola virus (EBOV), Dengue virus (DNV), West Nile virus (WNV), human immunodeficiency virus type 1 (HIV-1), hepatitis C virus (HCV) and vesicular stomatitis virus (VSV) (PubMed:26354436, PubMed:33239446, PubMed:33270927). Can inhibit: influenza virus hemagglutinin protein-mediated viral entry, MARV and EBOV GP1,2-mediated viral entry, SARS-CoV and SARS-CoV-2 S protein-mediated viral entry and VSV G protein-mediated viral entry (PubMed:33270927). Plays a critical role in the structural stability and function of vacuolar ATPase (v-ATPase). Establishes physical contact with the v-ATPase of endosomes which is critical for proper clathrin localization and is also required for the function of the v-ATPase to lower the pH in phagocytic endosomes thus establishing an antiviral state. In hepatocytes, IFITM proteins act in a coordinated manner to restrict HCV infection by targeting the endocytosed HCV virion for lysosomal degradation (PubMed:26354436). IFITM2 and IFITM3 display anti-HCV activity that may complement the anti-HCV activity of IFITM1 by inhibiting the late stages of HCV entry, possibly in a coordinated manner by trapping the virion in the endosomal pathway and targeting it for degradation at the lysosome (PubMed:26354436). Exerts opposing activities on SARS-CoV-2, including amphipathicity-dependent restriction of virus at endosomes and amphipathicity-independent enhancement of infection at the plasma membrane (PubMed:33270927)","subcellular_location":"Cell membrane; Late endosome membrane; Early endosome membrane; Lysosome membrane; Cytoplasm, perinuclear region","url":"https://www.uniprot.org/uniprotkb/Q01628/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/IFITM3","classification":"Common Essential","n_dependent_lines":1045,"n_total_lines":1090,"dependency_fraction":0.9587155963302753},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/IFITM3","total_profiled":1310},"omim":[{"mim_id":"616207","title":"NEGATIVE REGULATOR OF ANTIVIRAL RESPONSE, NONCODING; NRAV","url":"https://www.omim.org/entry/616207"},{"mim_id":"614757","title":"INTERFERON-INDUCED TRANSMEMBRANE PROTEIN 5; IFITM5","url":"https://www.omim.org/entry/614757"},{"mim_id":"614680","title":"INFLUENZA, SEVERE, SUSCEPTIBILITY TO","url":"https://www.omim.org/entry/614680"},{"mim_id":"606480","title":"ZINC METALLOPROTEINASE STE24; ZMPSTE24","url":"https://www.omim.org/entry/606480"},{"mim_id":"605579","title":"INTERFERON-INDUCED TRANSMEMBRANE PROTEIN 3; IFITM3","url":"https://www.omim.org/entry/605579"}],"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/IFITM3"},"hgnc":{"alias_symbol":["1-8U","DSPA2b"],"prev_symbol":[]},"alphafold":{"accession":"Q01628","domains":[{"cath_id":"1.20.58","chopping":"62-133","consensus_level":"medium","plddt":70.9264,"start":62,"end":133}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q01628","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q01628-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q01628-F1-predicted_aligned_error_v6.png","plddt_mean":59.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=IFITM3","jax_strain_url":"https://www.jax.org/strain/search?query=IFITM3"},"sequence":{"accession":"Q01628","fasta_url":"https://rest.uniprot.org/uniprotkb/Q01628.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q01628/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q01628"}},"corpus_meta":[{"pmid":"22446628","id":"PMC_22446628","title":"IFITM3 restricts the morbidity and mortality associated with influenza.","date":"2012","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/22446628","citation_count":622,"is_preprint":false},{"pmid":"20601941","id":"PMC_20601941","title":"Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3.","date":"2010","source":"Nature chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/20601941","citation_count":312,"is_preprint":false},{"pmid":"23601107","id":"PMC_23601107","title":"The antiviral effector IFITM3 disrupts intracellular cholesterol homeostasis to block viral entry.","date":"2013","source":"Cell host & microbe","url":"https://pubmed.ncbi.nlm.nih.gov/23601107","citation_count":296,"is_preprint":false},{"pmid":"32879487","id":"PMC_32879487","title":"The innate immunity protein IFITM3 modulates γ-secretase in Alzheimer's disease.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/32879487","citation_count":285,"is_preprint":false},{"pmid":"20943977","id":"PMC_20943977","title":"Interferon-induced cell membrane proteins, IFITM3 and tetherin, inhibit vesicular stomatitis virus infection via distinct mechanisms.","date":"2010","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/20943977","citation_count":261,"is_preprint":false},{"pmid":"31242426","id":"PMC_31242426","title":"Small Extracellular Vesicles Are Key Regulators of Non-cell Autonomous Intercellular Communication in Senescence via the Interferon Protein IFITM3.","date":"2019","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/31242426","citation_count":221,"is_preprint":false},{"pmid":"30643282","id":"PMC_30643282","title":"IFITM3 directly engages and shuttles incoming virus particles to lysosomes.","date":"2019","source":"Nature chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/30643282","citation_count":192,"is_preprint":false},{"pmid":"23354485","id":"PMC_23354485","title":"Enhanced survival of lung tissue-resident memory CD8⁺ T cells during infection with influenza virus due to selective expression of IFITM3.","date":"2013","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/23354485","citation_count":191,"is_preprint":false},{"pmid":"22511783","id":"PMC_22511783","title":"S-palmitoylation and ubiquitination differentially regulate interferon-induced transmembrane protein 3 (IFITM3)-mediated resistance to influenza virus.","date":"2012","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22511783","citation_count":175,"is_preprint":false},{"pmid":"23055554","id":"PMC_23055554","title":"The N-terminal region of IFITM3 modulates its antiviral activity by regulating IFITM3 cellular localization.","date":"2012","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/23055554","citation_count":156,"is_preprint":false},{"pmid":"30723081","id":"PMC_30723081","title":"Human megakaryocytes possess intrinsic antiviral immunity through regulated induction of IFITM3.","date":"2019","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/30723081","citation_count":148,"is_preprint":false},{"pmid":"26354436","id":"PMC_26354436","title":"The Interferon-induced Transmembrane Proteins, IFITM1, IFITM2, and IFITM3 Inhibit Hepatitis C Virus Entry.","date":"2015","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26354436","citation_count":148,"is_preprint":false},{"pmid":"24521078","id":"PMC_24521078","title":"Identification of an endocytic signal essential for the antiviral action of IFITM3.","date":"2014","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/24521078","citation_count":119,"is_preprint":false},{"pmid":"23720721","id":"PMC_23720721","title":"IFITM-2 and IFITM-3 but not IFITM-1 restrict Rift Valley fever virus.","date":"2013","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/23720721","citation_count":109,"is_preprint":false},{"pmid":"21531817","id":"PMC_21531817","title":"KLF4-mediated negative regulation of IFITM3 expression plays a critical role in colon cancer pathogenesis.","date":"2011","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/21531817","citation_count":105,"is_preprint":false},{"pmid":"26263374","id":"PMC_26263374","title":"E3 Ubiquitin Ligase NEDD4 Promotes Influenza Virus Infection by Decreasing Levels of the Antiviral Protein IFITM3.","date":"2015","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/26263374","citation_count":102,"is_preprint":false},{"pmid":"23649619","id":"PMC_23649619","title":"Interferon-inducible transmembrane protein 3 (IFITM3) restricts reovirus cell entry.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23649619","citation_count":101,"is_preprint":false},{"pmid":"27601221","id":"PMC_27601221","title":"Natural mutations in IFITM3 modulate post-translational regulation and toggle antiviral specificity.","date":"2016","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/27601221","citation_count":93,"is_preprint":false},{"pmid":"29079573","id":"PMC_29079573","title":"The palmitoyltransferase ZDHHC20 enhances interferon-induced transmembrane protein 3 (IFITM3) palmitoylation and antiviral activity.","date":"2017","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29079573","citation_count":88,"is_preprint":false},{"pmid":"33149299","id":"PMC_33149299","title":"IFITM3 functions as a PIP3 scaffold to amplify PI3K signalling in B cells.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/33149299","citation_count":87,"is_preprint":false},{"pmid":"27384652","id":"PMC_27384652","title":"The Interferon-Stimulated Gene Ifitm3 Restricts West Nile Virus Infection and Pathogenesis.","date":"2016","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/27384652","citation_count":83,"is_preprint":false},{"pmid":"30301809","id":"PMC_30301809","title":"mTOR inhibitors lower an intrinsic barrier to virus infection mediated by IFITM3.","date":"2018","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/30301809","citation_count":74,"is_preprint":false},{"pmid":"30662816","id":"PMC_30662816","title":"Antiviral Protection by IFITM3 In Vivo.","date":"2018","source":"Current clinical microbiology reports","url":"https://pubmed.ncbi.nlm.nih.gov/30662816","citation_count":71,"is_preprint":false},{"pmid":"33113474","id":"PMC_33113474","title":"The Interferon-induced transmembrane protein 3 gene (IFITM3) rs12252 C variant is associated with COVID-19.","date":"2020","source":"Cytokine","url":"https://pubmed.ncbi.nlm.nih.gov/33113474","citation_count":67,"is_preprint":false},{"pmid":"37003257","id":"PMC_37003257","title":"IFITM3 blocks influenza virus entry by sorting lipids and stabilizing hemifusion.","date":"2023","source":"Cell host & microbe","url":"https://pubmed.ncbi.nlm.nih.gov/37003257","citation_count":65,"is_preprint":false},{"pmid":"25405885","id":"PMC_25405885","title":"Regulation of the trafficking and antiviral activity of IFITM3 by post-translational modifications.","date":"2014","source":"Future microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/25405885","citation_count":65,"is_preprint":false},{"pmid":"33112230","id":"PMC_33112230","title":"Homology-guided identification of a conserved motif linking the antiviral functions of IFITM3 to its oligomeric state.","date":"2020","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/33112230","citation_count":63,"is_preprint":false},{"pmid":"24278312","id":"PMC_24278312","title":"Defining the range of pathogens susceptible to Ifitm3 restriction using a knockout mouse model.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24278312","citation_count":62,"is_preprint":false},{"pmid":"32595654","id":"PMC_32595654","title":"Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells.","date":"2020","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/32595654","citation_count":55,"is_preprint":false},{"pmid":"28531322","id":"PMC_28531322","title":"Evaluation of IFITM3 rs12252 Association With Severe Pediatric Influenza Infection.","date":"2017","source":"The Journal of infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/28531322","citation_count":54,"is_preprint":false},{"pmid":"31273201","id":"PMC_31273201","title":"IFITM3 promotes bone metastasis of prostate cancer cells by mediating activation of the TGF-β signaling pathway.","date":"2019","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/31273201","citation_count":54,"is_preprint":false},{"pmid":"10606237","id":"PMC_10606237","title":"Interferon-inducible gene family 1-8U expression in colitis-associated colon cancer and severely inflamed mucosa in ulcerative colitis.","date":"1999","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/10606237","citation_count":50,"is_preprint":false},{"pmid":"27046158","id":"PMC_27046158","title":"Combined approaches of EPR and NMR illustrate only one transmembrane helix in the human IFITM3.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27046158","citation_count":49,"is_preprint":false},{"pmid":"28100616","id":"PMC_28100616","title":"The V3 Loop of HIV-1 Env Determines Viral Susceptibility to IFITM3 Impairment of Viral Infectivity.","date":"2017","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/28100616","citation_count":48,"is_preprint":false},{"pmid":"33711707","id":"PMC_33711707","title":"The influence of IFITM3 polymorphisms on susceptibility to SARS-CoV-2 infection and severity of COVID-19.","date":"2021","source":"Cytokine","url":"https://pubmed.ncbi.nlm.nih.gov/33711707","citation_count":46,"is_preprint":false},{"pmid":"38167862","id":"PMC_38167862","title":"FOXP3+ regulatory T cell perturbation mediated by the IFNγ-STAT1-IFITM3 feedback loop is essential for anti-tumor immunity.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38167862","citation_count":45,"is_preprint":false},{"pmid":"32602823","id":"PMC_32602823","title":"Bat SARS-Like WIV1 coronavirus uses the ACE2 of multiple animal species as receptor and evades IFITM3 restriction via TMPRSS2 activation of membrane fusion.","date":"2020","source":"Emerging microbes & infections","url":"https://pubmed.ncbi.nlm.nih.gov/32602823","citation_count":45,"is_preprint":false},{"pmid":"27707929","id":"PMC_27707929","title":"Constitutively Expressed IFITM3 Protein in Human Endothelial Cells Poses an Early Infection Block to Human Influenza Viruses.","date":"2016","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/27707929","citation_count":44,"is_preprint":false},{"pmid":"33364194","id":"PMC_33364194","title":"Malignancy and IFITM3: Friend or Foe?","date":"2020","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/33364194","citation_count":41,"is_preprint":false},{"pmid":"30087833","id":"PMC_30087833","title":"IFITM3 promotes hepatocellular carcinoma invasion and metastasis by regulating MMP9 through p38/MAPK signaling.","date":"2018","source":"FEBS open bio","url":"https://pubmed.ncbi.nlm.nih.gov/30087833","citation_count":41,"is_preprint":false},{"pmid":"29202190","id":"PMC_29202190","title":"Lack of Truncated IFITM3 Transcripts in Cells Homozygous for the rs12252-C Variant That is Associated With Severe Influenza Infection.","date":"2018","source":"The Journal of infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/29202190","citation_count":38,"is_preprint":false},{"pmid":"30987701","id":"PMC_30987701","title":"IFITM3: How genetics influence influenza infection demographically.","date":"2019","source":"Biomedical journal","url":"https://pubmed.ncbi.nlm.nih.gov/30987701","citation_count":38,"is_preprint":false},{"pmid":"24370119","id":"PMC_24370119","title":"The role of IFITM3 in the growth and migration of human glioma cells.","date":"2013","source":"BMC neurology","url":"https://pubmed.ncbi.nlm.nih.gov/24370119","citation_count":37,"is_preprint":false},{"pmid":"29917090","id":"PMC_29917090","title":"IFITM3 Restricts Human Metapneumovirus Infection.","date":"2018","source":"The Journal of infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/29917090","citation_count":37,"is_preprint":false},{"pmid":"31964738","id":"PMC_31964738","title":"IFITM3 Reduces Retroviral Envelope Abundance and Function and Is Counteracted by glycoGag.","date":"2020","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/31964738","citation_count":36,"is_preprint":false},{"pmid":"25270246","id":"PMC_25270246","title":"Mechanism and biological significance of the overexpression of IFITM3 in gastric cancer.","date":"2014","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/25270246","citation_count":36,"is_preprint":false},{"pmid":"12861389","id":"PMC_12861389","title":"Inhibition of proliferation by 1-8U in interferon-alpha-responsive and non-responsive cell lines.","date":"2003","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/12861389","citation_count":36,"is_preprint":false},{"pmid":"36880581","id":"PMC_36880581","title":"Interferon-induced transmembrane protein 3 (IFITM3) limits lethality of SARS-CoV-2 in mice.","date":"2023","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/36880581","citation_count":35,"is_preprint":false},{"pmid":"36194487","id":"PMC_36194487","title":"IFITM3 regulates fibrinogen endocytosis and platelet reactivity in nonviral sepsis.","date":"2022","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/36194487","citation_count":35,"is_preprint":false},{"pmid":"31826928","id":"PMC_31826928","title":"Bat IFITM3 restriction depends on S-palmitoylation and a polymorphic site within the CD225 domain.","date":"2019","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/31826928","citation_count":35,"is_preprint":false},{"pmid":"33002418","id":"PMC_33002418","title":"EVs Containing Host Restriction Factor IFITM3 Inhibited ZIKV Infection of Fetuses in Pregnant Mice through Trans-placenta Delivery.","date":"2020","source":"Molecular therapy : the journal of the American Society of Gene Therapy","url":"https://pubmed.ncbi.nlm.nih.gov/33002418","citation_count":35,"is_preprint":false},{"pmid":"29940276","id":"PMC_29940276","title":"Association between IFITM3 rs12252 polymorphism and influenza susceptibility and severity: A meta-analysis.","date":"2018","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/29940276","citation_count":33,"is_preprint":false},{"pmid":"37210413","id":"PMC_37210413","title":"Aβ Induces Neuroinflammation and Microglial M1 Polarization via cGAS-STING-IFITM3 Signaling Pathway in BV-2 Cells.","date":"2023","source":"Neurochemical research","url":"https://pubmed.ncbi.nlm.nih.gov/37210413","citation_count":33,"is_preprint":false},{"pmid":"30949979","id":"PMC_30949979","title":"IFITM3 knockdown reduces the expression of CCND1 and CDK4 and suppresses the growth of oral squamous cell carcinoma cells.","date":"2019","source":"Cellular oncology (Dordrecht, Netherlands)","url":"https://pubmed.ncbi.nlm.nih.gov/30949979","citation_count":33,"is_preprint":false},{"pmid":"29281729","id":"PMC_29281729","title":"Histone demethylase LSD1 restricts influenza A virus infection by erasing IFITM3-K88 monomethylation.","date":"2017","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/29281729","citation_count":32,"is_preprint":false},{"pmid":"32243810","id":"PMC_32243810","title":"Site-Specific Photo-Crosslinking Proteomics Reveal Regulation of IFITM3 Trafficking and Turnover by VCP/p97 ATPase.","date":"2020","source":"Cell chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/32243810","citation_count":31,"is_preprint":false},{"pmid":"26600246","id":"PMC_26600246","title":"Respiratory DC Use IFITM3 to Avoid Direct Viral Infection and Safeguard Virus-Specific CD8+ T Cell Priming.","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/26600246","citation_count":31,"is_preprint":false},{"pmid":"36423162","id":"PMC_36423162","title":"IFITM3 Inhibits SARS-CoV-2 Infection and Is Associated with COVID-19 Susceptibility.","date":"2022","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/36423162","citation_count":30,"is_preprint":false},{"pmid":"35872070","id":"PMC_35872070","title":"Cholesterol Binds the Amphipathic Helix of IFITM3 and Regulates Antiviral Activity.","date":"2022","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/35872070","citation_count":30,"is_preprint":false},{"pmid":"30650117","id":"PMC_30650117","title":"Rapid interferon independent expression of IFITM3 following T cell activation protects cells from influenza virus infection.","date":"2019","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/30650117","citation_count":30,"is_preprint":false},{"pmid":"30272306","id":"PMC_30272306","title":"miR‑29a suppresses the growth and metastasis of hepatocellular carcinoma through IFITM3.","date":"2018","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/30272306","citation_count":30,"is_preprint":false},{"pmid":"33240681","id":"PMC_33240681","title":"The frequency of combined IFITM3 haplotype involving the reference alleles of both rs12252 and rs34481144 is in line with COVID-19 standardized mortality ratio of ethnic groups in England.","date":"2020","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/33240681","citation_count":29,"is_preprint":false},{"pmid":"19946179","id":"PMC_19946179","title":"Identification of the polymorphisms in IFITM3 gene and their association in a Korean population with ulcerative colitis.","date":"2010","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/19946179","citation_count":28,"is_preprint":false},{"pmid":"21914072","id":"PMC_21914072","title":"Identification of the IFITM3 gene as an inhibitor of hepatitis C viral translation in a stable STAT1 cell line.","date":"2011","source":"Journal of viral hepatitis","url":"https://pubmed.ncbi.nlm.nih.gov/21914072","citation_count":28,"is_preprint":false},{"pmid":"31212878","id":"PMC_31212878","title":"IFITM3 Clusters on Virus Containing Endosomes and Lysosomes Early in the Influenza A Infection of Human Airway Epithelial Cells.","date":"2019","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/31212878","citation_count":26,"is_preprint":false},{"pmid":"31637620","id":"PMC_31637620","title":"IFITM3/STAT3 axis promotes glioma cells invasion and is modulated by TGF-β.","date":"2019","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/31637620","citation_count":25,"is_preprint":false},{"pmid":"35941699","id":"PMC_35941699","title":"IFITM3 promotes malignant progression, cancer stemness and chemoresistance of gastric cancer by targeting MET/AKT/FOXO3/c-MYC axis.","date":"2022","source":"Cell & bioscience","url":"https://pubmed.ncbi.nlm.nih.gov/35941699","citation_count":25,"is_preprint":false},{"pmid":"33491750","id":"PMC_33491750","title":"Exosomes released by imatinib‑resistant K562 cells contain specific membrane markers, IFITM3, CD146 and CD36 and increase the survival of imatinib‑sensitive cells in the presence of imatinib.","date":"2020","source":"International journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/33491750","citation_count":25,"is_preprint":false},{"pmid":"36012150","id":"PMC_36012150","title":"Increased Expression of Interferon-Induced Transmembrane 3 (IFITM3) in Stroke and Other Inflammatory Conditions in the Brain.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36012150","citation_count":23,"is_preprint":false},{"pmid":"34404769","id":"PMC_34404769","title":"Listeria exploits IFITM3 to suppress antibacterial activity in phagocytes.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34404769","citation_count":22,"is_preprint":false},{"pmid":"31852866","id":"PMC_31852866","title":"IFITM3 upregulates c-myc expression to promote hepatocellular carcinoma proliferation via the ERK1/2 signalling pathway.","date":"2019","source":"Bioscience trends","url":"https://pubmed.ncbi.nlm.nih.gov/31852866","citation_count":22,"is_preprint":false},{"pmid":"28834009","id":"PMC_28834009","title":"Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane-Associated Protein IFITM3 and Modified Variants.","date":"2017","source":"Angewandte Chemie (International ed. in English)","url":"https://pubmed.ncbi.nlm.nih.gov/28834009","citation_count":22,"is_preprint":false},{"pmid":"36403064","id":"PMC_36403064","title":"Increased risk of COVID-19 mortality rate in IFITM3 rs6598045 G allele carriers infected by SARS-CoV-2 delta variant.","date":"2022","source":"Human genomics","url":"https://pubmed.ncbi.nlm.nih.gov/36403064","citation_count":22,"is_preprint":false},{"pmid":"35458456","id":"PMC_35458456","title":"IFITM3 Interacts with the HBV/HDV Receptor NTCP and Modulates Virus Entry and Infection.","date":"2022","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/35458456","citation_count":22,"is_preprint":false},{"pmid":"23874452","id":"PMC_23874452","title":"A functional promoter polymorphism of IFITM3 is associated with susceptibility to pediatric tuberculosis in Han Chinese population.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23874452","citation_count":22,"is_preprint":false},{"pmid":"33882122","id":"PMC_33882122","title":"IFITM3 incorporation sensitizes influenza A virus to antibody-mediated neutralization.","date":"2021","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/33882122","citation_count":21,"is_preprint":false},{"pmid":"36970857","id":"PMC_36970857","title":"Interferon-inducible phospholipids govern IFITM3-dependent endosomal antiviral immunity.","date":"2023","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/36970857","citation_count":20,"is_preprint":false},{"pmid":"28842783","id":"PMC_28842783","title":"Population genetics of IFITM3 in Portugal and Central Africa reveals a potential modifier of influenza severity.","date":"2017","source":"Immunogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/28842783","citation_count":20,"is_preprint":false},{"pmid":"36306674","id":"PMC_36306674","title":"Interferon-induced transmembrane protein 3 (IFITM3) and its antiviral activity.","date":"2022","source":"Current opinion in structural biology","url":"https://pubmed.ncbi.nlm.nih.gov/36306674","citation_count":19,"is_preprint":false},{"pmid":"34078739","id":"PMC_34078739","title":"Human IFITM3 restricts chikungunya virus and Mayaro virus infection and is susceptible to virus-mediated counteraction.","date":"2021","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/34078739","citation_count":19,"is_preprint":false},{"pmid":"38218875","id":"PMC_38218875","title":"IFITM3 promotes glioblastoma stem cell-mediated angiogenesis via regulating JAK/STAT3/bFGF signaling pathway.","date":"2024","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/38218875","citation_count":18,"is_preprint":false},{"pmid":"33108395","id":"PMC_33108395","title":"p53 promotes ZDHHC1-mediated IFITM3 palmitoylation to inhibit Japanese encephalitis virus replication.","date":"2020","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/33108395","citation_count":18,"is_preprint":false},{"pmid":"35949487","id":"PMC_35949487","title":"The association of ACE1, ACE2, TMPRSS2, IFITM3 and VDR polymorphisms with COVID-19 severity: A systematic review and meta-analysis.","date":"2022","source":"EXCLI journal","url":"https://pubmed.ncbi.nlm.nih.gov/35949487","citation_count":18,"is_preprint":false},{"pmid":"32370187","id":"PMC_32370187","title":"The Robust Restriction of Zika Virus by Type-I Interferon in A549 Cells Varies by Viral Lineage and Is Not Determined by IFITM3.","date":"2020","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/32370187","citation_count":18,"is_preprint":false},{"pmid":"31597765","id":"PMC_31597765","title":"HA-Dependent Tropism of H5N1 and H7N9 Influenza Viruses to Human Endothelial Cells Is Determined by Reduced Stability of the HA, Which Allows the Virus To Cope with Inefficient Endosomal Acidification and Constitutively Expressed IFITM3.","date":"2019","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/31597765","citation_count":17,"is_preprint":false},{"pmid":"23639725","id":"PMC_23639725","title":"Widespread but tissue-specific patterns of interferon-induced transmembrane protein 3 (IFITM3, FRAGILIS, MIL-1) in the mouse gastrula.","date":"2013","source":"Gene expression patterns : GEP","url":"https://pubmed.ncbi.nlm.nih.gov/23639725","citation_count":17,"is_preprint":false},{"pmid":"33174121","id":"PMC_33174121","title":"Ethnic variation in risk genotypes based on single nucleotide polymorphisms (SNPs) of the interferon-inducible transmembrane 3 (IFITM3) gene, a susceptibility factor for pandemic 2009 H1N1 influenza A virus.","date":"2020","source":"Immunogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/33174121","citation_count":17,"is_preprint":false},{"pmid":"34659578","id":"PMC_34659578","title":"TUG1 promotes the expression of IFITM3 in hepatocellular carcinoma by competitively binding to miR-29a.","date":"2021","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/34659578","citation_count":16,"is_preprint":false},{"pmid":"32952601","id":"PMC_32952601","title":"miR-152-3p Affects the Progression of Colon Cancer via the KLF4/IFITM3 Axis.","date":"2020","source":"Computational and mathematical methods in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32952601","citation_count":16,"is_preprint":false},{"pmid":"19901966","id":"PMC_19901966","title":"Interferon-induced transmembrane 3 binds osteopontin in vitro: expressed in vivo IFITM3 reduced OPN expression.","date":"2009","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/19901966","citation_count":16,"is_preprint":false},{"pmid":"39807629","id":"PMC_39807629","title":"Inhibition of IFITM3 in cerebrovascular endothelium alleviates Alzheimer's-related phenotypes.","date":"2025","source":"Alzheimer's & dementia : the journal of the Alzheimer's Association","url":"https://pubmed.ncbi.nlm.nih.gov/39807629","citation_count":14,"is_preprint":false},{"pmid":"39477971","id":"PMC_39477971","title":"Innate immune control of influenza virus interspecies adaptation via IFITM3.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39477971","citation_count":14,"is_preprint":false},{"pmid":"33465303","id":"PMC_33465303","title":"HCMV infection and IFITM3 rs12252 are associated with Rasmussen's encephalitis disease progression.","date":"2021","source":"Annals of clinical and translational neurology","url":"https://pubmed.ncbi.nlm.nih.gov/33465303","citation_count":14,"is_preprint":false},{"pmid":"35802304","id":"PMC_35802304","title":"MiR-487b suppressed inflammation and neuronal apoptosis in spinal cord injury by targeted Ifitm3.","date":"2022","source":"Metabolic brain disease","url":"https://pubmed.ncbi.nlm.nih.gov/35802304","citation_count":14,"is_preprint":false},{"pmid":"33061814","id":"PMC_33061814","title":"Comprehensive analysis of two potential novel SARS-CoV-2 entries, TMPRSS2 and IFITM3, in healthy individuals and cancer patients.","date":"2020","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33061814","citation_count":14,"is_preprint":false},{"pmid":"33817671","id":"PMC_33817671","title":"Outside-in induction of the IFITM3 trafficking system by infections, including SARS-CoV-2, in the pathobiology of Alzheimer's disease.","date":"2021","source":"Brain, behavior, & immunity - health","url":"https://pubmed.ncbi.nlm.nih.gov/33817671","citation_count":14,"is_preprint":false},{"pmid":"33298540","id":"PMC_33298540","title":"Escape of HIV-1 envelope glycoprotein from the restriction of infection by IFITM3.","date":"2020","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/33298540","citation_count":13,"is_preprint":false},{"pmid":"38973391","id":"PMC_38973391","title":"LPS-induced senescence of macrophages aggravates calcification and senescence of vascular smooth muscle cells via IFITM3.","date":"2024","source":"Renal failure","url":"https://pubmed.ncbi.nlm.nih.gov/38973391","citation_count":13,"is_preprint":false},{"pmid":"35809785","id":"PMC_35809785","title":"Transmembrane domain of IFITM3 is responsible for its interaction with influenza virus HA2 subunit.","date":"2022","source":"Virologica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/35809785","citation_count":12,"is_preprint":false},{"pmid":"29121968","id":"PMC_29121968","title":"Association of IFITM3 rs12252 polymorphisms, BMI, diabetes, and hypercholesterolemia with mild flu in an Iranian population.","date":"2017","source":"Virology journal","url":"https://pubmed.ncbi.nlm.nih.gov/29121968","citation_count":12,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":50785,"output_tokens":8134,"usd":0.137183},"stage2":{"model":"claude-opus-4-6","input_tokens":11966,"output_tokens":4167,"usd":0.246007},"total_usd":0.38319,"stage1_batch_id":"msgbatch_01DzrsgVgYngY1hvM3DU1yF2","stage2_batch_id":"msgbatch_01KA9b7iRzKFdhoBUT7vCvSe","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"IFITM3 antiviral activity is post-translationally regulated by S-palmitoylation on membrane-proximal cysteines, which controls its clustering in membrane compartments and its antiviral activity against influenza virus.\",\n      \"method\": \"Chemical reporter-based palmitoylome profiling, site-directed mutagenesis of cysteine residues, influenza virus infection assays\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods (chemical proteomics, mutagenesis, functional antiviral assays) in a single study\",\n      \"pmids\": [\"20601941\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"IFITM3 is essential for defending the host against influenza A virus in vivo; knockout mice develop fulminant viral pneumonia with a normally low-pathogenicity virus, and protection is rescued by re-introduction of Ifitm3.\",\n      \"method\": \"Knockout mouse model, viral challenge, in vitro complementation\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined phenotype, rescue experiment, replicated in vitro and in vivo\",\n      \"pmids\": [\"22446628\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"IFITM3 localizes to endolysosomes and prevents endocytosed virus particles from accessing the host cytoplasm; S-palmitoylation enhances membrane affinity and antiviral activity, while lysine ubiquitination decreases endolysosomal localization and antiviral activity. IFITM3 is proposed to adopt an intramembrane topology with both N and C termini facing the cytoplasm.\",\n      \"method\": \"Fluorescence imaging, cellular fractionation, N-linked glycosylation site insertion, protein lipidation mapping, mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods (imaging, fractionation, topology mapping, mutagenesis) with functional readouts\",\n      \"pmids\": [\"22511783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The N-terminal 21-amino-acid region of IFITM3 is required for its endosomal localization and antiviral activity against pH-dependent viruses (influenza A); deletion of this region relocates IFITM3 to the cell periphery, abolishing restriction of pH-dependent viruses but not HIV-1.\",\n      \"method\": \"Deletion mutagenesis, subcellular localization imaging, viral infection assays\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — mutagenesis linked to localization and function with multiple viral systems\",\n      \"pmids\": [\"23055554\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"IFITM3 interacts with VAPA and prevents its association with OSBP, thereby disrupting intracellular cholesterol homeostasis; this induces cholesterol accumulation in multivesicular bodies and late endosomes, inhibiting fusion of virion-containing intraluminal vesicles with endosomal membranes and blocking virus release into the cytosol.\",\n      \"method\": \"Co-immunoprecipitation, ectopic expression/depletion of VAPA, cholesterol localization assays, viral entry assays\",\n      \"journal\": \"Cell host & microbe\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, genetic manipulation (depletion/overexpression), mechanistic functional readouts\",\n      \"pmids\": [\"23601107\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"IFITM3 possesses a YxxΦ endocytic sorting motif (20-YEML-23) that enables it to undergo clathrin-mediated endocytosis through binding to the μ2 subunit of the AP-2 complex; blocking endocytosis of IFITM3 (by mutating this motif, depleting μ2, or overexpressing μ2 mutants) abrogates its antiviral activity against pH-dependent viruses.\",\n      \"method\": \"Mutagenesis of sorting motif, μ2 depletion/overexpression, subcellular localization imaging, viral infection assays\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple genetic perturbations with consistent functional and localization readouts\",\n      \"pmids\": [\"24521078\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The E3 ubiquitin ligase NEDD4 ubiquitinates IFITM3 in cells and in vitro via interaction with a PPxY motif in IFITM3 and the WW domain of NEDD4; NEDD4 knockout leads to accumulation of IFITM3 and increased protection from influenza virus. Steady-state IFITM3 turnover occurs through the lysosomal degradation pathway.\",\n      \"method\": \"In vitro ubiquitination assay, NEDD4 knockout MEFs, PPxY motif mutagenesis, NEDD4 knockdown in human lung cells, lysosome inhibitor treatment\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro reconstitution plus KO model, mutagenesis, conserved in mouse and human cells\",\n      \"pmids\": [\"26263374\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"IFITM3 adopts a membrane topology with a single long transmembrane helix in the C-terminus and an intramembrane segment in the N-terminal hydrophobic region, with both termini facing the cytoplasm; this topology supports a mechanism of enhanced restricted membrane hemifusion.\",\n      \"method\": \"Systematic site-directed spin labeling (SDSL), EPR spectroscopy, solution NMR in detergent micelles\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — EPR and NMR structural characterization with orthogonal validation\",\n      \"pmids\": [\"27046158\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ZDHHC20 co-localizes with IFITM3 at lysosomes and uniquely enhances IFITM3 antiviral activity when both are overexpressed; multiple ZDHHCs (especially 3, 7, 15, 20) can palmitoylate IFITM3, demonstrating functional redundancy, and combined knockdown of ZDHHC3 and ZDHHC7 in ZDHHC20 KO cells decreases endogenous IFITM3 palmitoylation.\",\n      \"method\": \"ZDHHC knockout cell line screen, ZDHHC overexpression screen, co-localization imaging, palmitoylation assays, siRNA knockdown, viral infection assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — systematic screen with multiple orthogonal methods, KO and knockdown approaches\",\n      \"pmids\": [\"29079573\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"LSD1 (a histone demethylase) is recruited to demethylate IFITM3 at position K88 under IFNα treatment, activating IFITM3; RNA virus infection (VSV or IAV) triggers IFITM3 K88 monomethylation by promoting IFITM3 dissociation from LSD1, and LSD1 inhibition increases IFITM3 monomethylation and worsens IAV infection in mice.\",\n      \"method\": \"In vitro demethylation assay, mutagenesis, LSD1 inhibitor treatment, mouse infection model, co-immunoprecipitation\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — identification of writer/eraser with functional readout in vitro and in vivo\",\n      \"pmids\": [\"29281729\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"IFITM3 is present on endocytic vesicles that fuse with incoming virus particles and enhances trafficking of viral cargo to lysosomes; this trafficking is specific to restricted viruses, requires S-palmitoylation, and is abrogated with loss-of-function mutants.\",\n      \"method\": \"CRISPR-Cas9 IFITM-mutant cell lines, site-specific fluorophore tagging, live-cell imaging, viral entry assays\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — live-cell imaging with site-specific labeling, genetic KO, functional mutagenesis, multiple orthogonal approaches\",\n      \"pmids\": [\"30643282\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"IFITM3 binds to γ-secretase and upregulates its activity, thereby increasing amyloid-β production; inflammatory cytokines induce IFITM3 expression in neurons and astrocytes, and IFITM3 knockout reduces γ-secretase activity and amyloid plaque formation in 5xFAD mice. IFITM3 levels in the γ-secretase complex strongly correlate with γ-secretase activity in late-onset AD patient samples.\",\n      \"method\": \"Co-immunoprecipitation, IFITM3 KO mouse model (5xFAD), γ-secretase activity assays, human AD patient tissue analysis\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, KO mouse model with functional readouts, human tissue correlation; multiple orthogonal methods\",\n      \"pmids\": [\"32879487\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"IFITM3 functions as a PIP3 scaffold at the plasma membrane to amplify PI3K signaling in B cells; oncogenic kinases phosphorylate IFITM3 at Tyr20, causing constitutive plasma membrane localization. IFITM3 uses Lys83 and Lys104 in its conserved intracellular loop as a scaffold for PIP3 accumulation. BCR engagement induces Tyr20 phosphorylation, switching IFITM3 from antiviral endosomal function to PI3K amplification at the cell surface.\",\n      \"method\": \"Phosphomimetic/phosphodeficient mutants, Ifitm3-/- mouse B cells, BCR signaling assays, lipid raft fractionation, PI3K signaling readouts, oncogene transformation assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple mutants, KO mouse, mechanistic biochemical assays, replicated with oncogene models\",\n      \"pmids\": [\"33149299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"VCP/p97 AAA-ATPase is a primary interaction partner of IFITM3; IFITM3 ubiquitination at lysine 24 is crucial for VCP binding, trafficking, turnover, and engagement with incoming virus particles. Pharmacological inhibition of VCP/p97 leads to defective IFITM3 lysosomal sorting and co-trafficking with virus particles.\",\n      \"method\": \"Site-specific photo-crosslinking, quantitative proteomics, mutagenesis (K24), VCP inhibitor treatment, lysosomal sorting assays, live-cell imaging\",\n      \"journal\": \"Cell chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — photo-crosslinking proteomics, site-specific mutagenesis, pharmacological validation, functional imaging\",\n      \"pmids\": [\"32243810\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"mTOR inhibition by rapamycin downregulates IFITM3 at the protein level (not mRNA) via a mechanism requiring endosomal trafficking, ubiquitination, ESCRT machinery, and lysosomal acidification, thereby promoting influenza A virus and lentiviral vector entry into cells.\",\n      \"method\": \"mTOR inhibitor treatment, IFITM3 siRNA/KO, ESCRT and lysosome inhibitors, virus infection assays, mRNA vs protein level analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple pharmacological and genetic perturbations with consistent mechanistic readouts\",\n      \"pmids\": [\"30301809\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"IFITM3 oligomerization is driven by a GxxxG motif centered on Gly-95 (and Gly-91); mutation of Gly-95 disrupts IFITM3 oligomerization and reduces antiviral activity against influenza A virus. IFITM3 oligomers promote membrane rigidity in a Gly-95-dependent and amphipathic helix-dependent manner, and Amphotericin B counteracts this rigidification.\",\n      \"method\": \"Mutagenesis of GxxxG motif, oligomerization assays, membrane rigidity measurements, Amphotericin B treatment, influenza A virus infection assays\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — mutagenesis linked to oligomerization, membrane biophysics, and antiviral function with multiple orthogonal methods\",\n      \"pmids\": [\"33112230\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The amphipathic helix (AH) of IFITM3 directly binds cholesterol; mutations F63Q and F67Q in the AH disrupt AH structure, inhibit cholesterol binding in vitro, restrict bilayer insertion in silico, and strongly impair antiviral function.\",\n      \"method\": \"Fluorescence-based in vitro cholesterol binding assay with NBD-cholesterol, AH mutagenesis, molecular dynamics simulation, antiviral assays\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro biochemical binding assay, mutagenesis, and computational validation\",\n      \"pmids\": [\"35872070\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"IFITM3 induces local lipid sorting at the hemifusion site, increasing the concentration of fusion-disfavoring lipids, which raises the energy barrier for fusion pore formation and stabilizes hemifusion intermediates, causing viral degradation in lysosomes. In situ cryo-electron tomography captured IFITM3-mediated arrest of influenza A virus membrane fusion and hemifusion diaphragms at late endosomal membranes.\",\n      \"method\": \"In situ cryo-electron tomography, lipid analysis, hemifusion assays, IFITM3 KO cells, influenza A virus infection\",\n      \"journal\": \"Cell host & microbe\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-ET structural data capturing hemifusion intermediates, combined with lipid analysis and functional KO assays\",\n      \"pmids\": [\"37003257\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"IFITM3 disrupts an early event after endocytosis of VSV particles but before primary transcription of incoming viral genomes; both the N-terminal 21 amino acid residues and the C-terminal transmembrane region are required for antiviral activity.\",\n      \"method\": \"Viral infection assays (VSV), deletion mutagenesis, primary transcription assay\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — domain mutagenesis with viral restriction functional readouts, single lab\",\n      \"pmids\": [\"20943977\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"IFITM3 restricts reovirus entry in the endocytic pathway by modulating late endosomal compartment function; IFITM3 delays proteolytic processing of outer capsid protein μ1, suggesting it reduces endosomal protease activity or delays proteolysis. IFITM3 does not restrict reovirus ISVPs that bypass endosomal proteolysis.\",\n      \"method\": \"IFITM3-expressing cell lines, reovirus infection assays (ISVP vs intact virions), μ1 proteolysis assays, shRNA knockdown\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic KD and OE with mechanistic proteolysis readout, single lab\",\n      \"pmids\": [\"23649619\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"S-palmitoylation of IFITM1, IFITM2, and IFITM3 is essential for anti-HCV activity; a conserved tyrosine in the N-terminal domain of IFITM2 and IFITM3 regulates protein localization (to late and early endosomes, respectively) but is dispensable for anti-HCV activity. IFITM2 and IFITM3 act at late entry/endosomal stages of HCV infection.\",\n      \"method\": \"S-palmitoylation mutagenesis, tyrosine mutants, subcellular localization imaging, HCV infection assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mutagenesis and localization with functional readout, single lab\",\n      \"pmids\": [\"26354436\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"KLF4 directly transcriptionally represses IFITM3 by binding to two KLF4-binding sites in the IFITM3 promoter; loss of KLF4 leads to IFITM3 overexpression in colon mucosa, and IFITM3 knockdown suppresses colon cancer cell proliferation, migration, and invasion.\",\n      \"method\": \"Chromatin immunoprecipitation, promoter mutagenesis, siRNA knockdown, villin-Cre conditional KLF4 KO mice, xenograft model\",\n      \"journal\": \"Clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP, promoter mutagenesis, in vivo mouse model; single lab but multiple methods\",\n      \"pmids\": [\"21531817\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"IFITM3 interacts with Smad4 and activates the TGF-β-Smads signaling pathway to promote prostate cancer cell proliferation, invasion, and bone migration; IFITM3 knockdown inhibits MAPK pathway activation induced by exogenous TGF-β.\",\n      \"method\": \"Co-immunoprecipitation (IFITM3-Smad4), shRNA knockdown, microarray, MAPK pathway assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single Co-IP, mechanistic pathway placement partly inferred\",\n      \"pmids\": [\"31273201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"IFITM3 interacts with NTCP (the HBV/HDV receptor) and acts as an NTCP co-factor that facilitates HBV and HDV infection (not restriction) in a step subsequent to viral attachment; IFITM3 knockdown significantly reduces HBV and HDV infection of NTCP-expressing hepatocytes and primary human hepatocytes, while increasing influenza A virus infection.\",\n      \"method\": \"Membrane yeast-two-hybrid, co-immunoprecipitation, IFITM3 knockdown, HBV/HDV/IAV infection assays in HuH7-NTCP cells and primary hepatocytes\",\n      \"journal\": \"Viruses\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — reciprocal PPI assays (Y2H + Co-IP), knockdown in multiple cell types including primary hepatocytes\",\n      \"pmids\": [\"35458456\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"IFITM3 promotes fibrinogen endocytosis in megakaryocytes and platelets in an interferon-dependent manner; mechanistically, IFITM3 interacts with clathrin and αIIb and alters their plasma membrane localization into lipid rafts. IFITM3 is necessary and sufficient for fibrinogen endocytosis, and Ifitm3-/- mice are rescued from IFN-induced platelet hyperreactivity and thrombosis.\",\n      \"method\": \"Co-immunoprecipitation (IFITM3-clathrin-αIIb), Ifitm3-/- mouse model, IFITM3 overexpression/deletion in megakaryocytes, fibrinogen endocytosis assays, thrombosis assays\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP, KO mouse, gain/loss-of-function, multiple functional readouts\",\n      \"pmids\": [\"36194487\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"IFITM3 is required for type I IFN-mediated suppression of phagosome maturation in macrophages; in the absence of IFITM3, phagosome maturation and proteolysis of Listeria virulence factors ActA and LLO are not suppressed, preventing phagosome escape. Ifitm3-/- mice are resistant to systemic Listeria infection.\",\n      \"method\": \"Ifitm3-/- mouse model, phagosome maturation assays, virulence factor proteolysis assays, bacterial infection assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined mechanistic phenotype (phagosome maturation) and in vivo validation\",\n      \"pmids\": [\"34404769\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"p53 enhances IFITM3 palmitoylation by transcriptionally upregulating ZDHHC1, which interacts with IFITM3 to promote its palmitoylation and protein stability, thereby restricting Japanese encephalitis virus replication. JEV reduces p53 expression to impair this pathway.\",\n      \"method\": \"ZDHHC1 knockdown, p53 overexpression/knockdown, Co-IP (ZDHHC1-IFITM3), palmitoylation assays, viral replication assays\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP, genetic perturbations, palmitoylation assays, single lab\",\n      \"pmids\": [\"33108395\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"IFITM3 incorporation into IAV particles competes with viral hemagglutinin (HA) incorporation, reducing virion HA content; this sensitizes IAV to antibody-mediated neutralization, thereby impacting infection outcome in vivo.\",\n      \"method\": \"IFITM3 incorporation into virions, virion HA quantification, neutralization assays, mathematical modeling, mouse in vivo infection model\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (biochemical, functional, mathematical, in vivo) demonstrating a novel IFITM3 mechanism\",\n      \"pmids\": [\"33882122\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PIP3 is required for endosomal IFITM restriction of viruses; lysines in the conserved IFITM intracellular loop recruit PIP3, and PIP3 acts as an interferon-inducible phospholipid rheostat for endosomal antiviral immunity. Plasma membrane-localized IFITM restriction operates independently of these lysines.\",\n      \"method\": \"Pseudotyped viral entry assays, replicating virus assays, high-throughput proteomics, lipidomics, IFITM mutants (lysine mutations), exogenous PIP3 supplementation\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — proteomics, lipidomics, mutagenesis, and functional assays with multiple viral systems\",\n      \"pmids\": [\"36970857\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"IFITM3 directly interacts with the influenza HA2 subunit (but not HA1) via its transmembrane domain, as demonstrated by co-localization and co-immunoprecipitation; this interaction was confirmed across multiple influenza A subtypes and influenza B virus.\",\n      \"method\": \"Co-immunoprecipitation, subcellular co-localization, truncation/deletion analysis, pseudovirus entry assays\",\n      \"journal\": \"Virologica Sinica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP and co-localization, single lab, no structural or reconstitution validation\",\n      \"pmids\": [\"35809785\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Small extracellular vesicles (sEVs) containing IFITM3 are partially responsible for transmitting paracrine senescence to normal neighboring cells; IFITM3 was identified by mass spectrometry proteomics of sEV cargo and confirmed by siRNA screen.\",\n      \"method\": \"Mass spectrometry proteomics, functional siRNA screen, Cre-reporter sEV uptake system\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — MS identification plus functional siRNA screen; mechanistic detail is partial\",\n      \"pmids\": [\"31242426\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"IFITM3 physically interacts with osteopontin (OPN) in vitro and in vivo; IFITM3 expression reduces OPN mRNA expression (possibly via mRNA stability), and an IFITM3 DNA-binding domain mediates interaction with OPN. Stable IFITM3 transfection inhibits OPN-mediated anchorage-independent growth, cell adhesion, and invasion.\",\n      \"method\": \"Bacterial two-hybrid, in vitro binding, co-immunoprecipitation, antisense RNA, northern blot, stable transfection, invasion assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — two-hybrid plus Co-IP with functional cellular readouts; single lab\",\n      \"pmids\": [\"19901966\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"IFITM3 deficiency in FOXP3+ regulatory T cells enhances STAT1 translation and phosphorylation; conversely, STAT1 regulates IFITM3 expression forming a feedback loop. Blocking IFNγ or depleting the STAT1-IFITM3 axis phenocopies restored suppressive Treg function in tumors.\",\n      \"method\": \"IFITM3-deficient Treg mouse model, cytokine blocking, STAT1 KO, tumor growth assays, cytokine measurements\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO and KD with mechanistic pathway (STAT1 phosphorylation feedback loop), in vivo tumor model\",\n      \"pmids\": [\"38167862\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"IFITM3 in cerebrovascular endothelial cells (CVECs) regulates amyloid-β generation through BACE1 and γ-secretase; IFITM3 overexpression in endothelial cells enhances Aβ production, and Aβ further upregulates IFITM3 (positive feedback). AAV-mediated IFITM3 knockdown in CVECs reduces Aβ accumulation and improves cognition in AD transgenic mice.\",\n      \"method\": \"snRNA-seq, AAV-BI30 endothelial IFITM3 knockdown, BACE1/γ-secretase activity assays, behavioral tests, two-photon imaging, immunohistochemistry, Western blot\",\n      \"journal\": \"Alzheimer's & dementia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — cell-type-specific KD with multiple mechanistic and in vivo readouts, single lab\",\n      \"pmids\": [\"39807629\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"IFITM3 is an interferon-induced, S-palmitoylated intramembrane protein that localizes to endolysosomes via a YxxΦ/AP-2-dependent endocytic sorting signal, where it oligomerizes (via a GxxxG motif), induces local lipid sorting and membrane rigidity through its amphipathic helix and cholesterol binding, and stabilizes hemifusion intermediates to block fusion pore formation by diverse enveloped viruses; its activity is positively regulated by S-palmitoylation (mediated redundantly by multiple ZDHHCs, especially ZDHHC20) and LSD1-mediated K88 demethylation, and negatively regulated by NEDD4-mediated lysine ubiquitination leading to lysosomal degradation, while in B cells phosphorylation at Tyr20 switches IFITM3 from an endosomal antiviral effector to a plasma membrane PIP3 scaffold that amplifies PI3K signaling, and in neurons/astrocytes IFITM3 binds and activates γ-secretase to increase amyloid-β production.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"IFITM3 is an interferon-induced intramembrane protein that restricts entry of diverse enveloped viruses by altering endosomal membrane properties, and additionally modulates γ-secretase activity, PI3K signaling, and phagosome maturation in cell-type-specific contexts. IFITM3 localizes to endolysosomes via a YxxΦ/AP-2-dependent endocytic sorting motif and, once there, oligomerizes through a GxxxG motif, binds cholesterol via its amphipathic helix, and induces local lipid sorting that stabilizes hemifusion intermediates and blocks fusion pore formation, thereby trapping viral particles for lysosomal degradation [PMID:33112230, PMID:37003257, PMID:35872070, PMID:24521078]. Its antiviral activity is positively regulated by S-palmitoylation (mediated redundantly by ZDHHC20, ZDHHC3, ZDHHC7) and LSD1-dependent K88 demethylation, and negatively regulated by NEDD4-mediated ubiquitination that targets it for lysosomal turnover via VCP/p97-dependent sorting [PMID:20601941, PMID:29079573, PMID:29281729, PMID:26263374, PMID:32243810]. Beyond antiviral defense, IFITM3 binds and activates γ-secretase to increase amyloid-β production in neurons, astrocytes, and cerebrovascular endothelial cells, and in B cells phosphorylation at Tyr20 redirects IFITM3 to the plasma membrane where it scaffolds PIP3 to amplify PI3K signaling [PMID:32879487, PMID:39807629, PMID:33149299].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Establishing that IFITM3 blocks an early post-endocytic entry step and that S-palmitoylation is a key post-translational switch for its antiviral activity answered the fundamental question of how this IFN-induced protein restricts virus infection.\",\n      \"evidence\": \"Chemical reporter palmitoylome profiling, cysteine mutagenesis, VSV/influenza infection assays in cell lines\",\n      \"pmids\": [\"20601941\", \"20943977\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of palmitoyl-acyltransferase(s) unknown at this time\", \"Mechanism of membrane-level restriction unresolved\", \"In vivo relevance not yet tested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrating that IFITM3 is essential for surviving influenza infection in vivo and that it localizes to endolysosomes via its N-terminal sorting region established IFITM3 as a non-redundant innate immune effector whose subcellular targeting is critical for function.\",\n      \"evidence\": \"Ifitm3 knockout mice challenged with influenza, topology mapping by glycosylation insertion, deletion mutagenesis, subcellular imaging\",\n      \"pmids\": [\"22446628\", \"22511783\", \"23055554\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Sorting motif not yet mapped to a specific endocytic adaptor\", \"Membrane topology model debated\", \"Mechanism of fusion blockade at the membrane biophysics level unknown\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identification of the VAPA interaction and cholesterol accumulation in endosomes provided the first mechanistic link between IFITM3 and membrane lipid remodeling as a basis for fusion inhibition.\",\n      \"evidence\": \"Co-immunoprecipitation of IFITM3–VAPA, cholesterol localization assays, viral entry assays in VAPA-depleted cells\",\n      \"pmids\": [\"23601107\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether VAPA interaction is necessary versus sufficient for restriction unclear\", \"Direct cholesterol binding by IFITM3 not yet shown\", \"Contribution of other lipid species not tested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Mapping the YxxΦ motif and its interaction with AP-2/μ2 resolved how IFITM3 reaches endosomes via clathrin-mediated endocytosis and why endosomal targeting is required for restricting pH-dependent viruses.\",\n      \"evidence\": \"YxxΦ motif mutagenesis, μ2 depletion/overexpression, localization imaging, influenza and VSV infection assays\",\n      \"pmids\": [\"24521078\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether AP-2-independent pathways also contribute to IFITM3 trafficking not addressed\", \"Role of phosphorylation at Y20 in modulating this sorting not yet recognized\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identification of NEDD4 as the E3 ligase that ubiquitinates IFITM3 via a PPxY motif and targets it for lysosomal degradation established ubiquitination as a negative regulatory axis controlling IFITM3 protein levels and antiviral potency.\",\n      \"evidence\": \"In vitro ubiquitination reconstitution, NEDD4 KO MEFs, PPxY mutagenesis, lysosome inhibitor treatment, influenza infection assays\",\n      \"pmids\": [\"26263374\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which specific lysine sites are ubiquitinated incompletely mapped\", \"Role of deubiquitinases not explored\", \"Interplay between ubiquitination and palmitoylation not resolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"EPR and NMR structural studies resolved the intramembrane topology of IFITM3 — a single C-terminal transmembrane helix with an N-terminal intramembrane segment — and linked this topology to enhanced hemifusion, providing a biophysical framework for the antiviral mechanism.\",\n      \"evidence\": \"Site-directed spin labeling, EPR spectroscopy, solution NMR in detergent micelles\",\n      \"pmids\": [\"27046158\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure determined in detergent micelles, not in native membranes\", \"How topology relates to oligomerization not addressed\", \"No high-resolution structure in lipid bilayer\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Systematic screening identified ZDHHC20 as the primary lysosome-localized palmitoyltransferase for IFITM3 and revealed functional redundancy among multiple ZDHHCs, while discovery that LSD1 demethylates K88 to activate IFITM3 established a second post-translational regulatory layer.\",\n      \"evidence\": \"ZDHHC KO/overexpression screen, palmitoylation assays, LSD1 in vitro demethylation, LSD1 inhibitor in mouse IAV model, co-IP\",\n      \"pmids\": [\"29079573\", \"29281729\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contributions of individual ZDHHCs in physiological contexts unclear\", \"K88 methyltransferase not identified\", \"How methylation and palmitoylation are coordinated unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Live-cell imaging with site-specific labeling demonstrated that IFITM3 is present on endocytic vesicles that actively fuse with incoming virions and routes restricted viral cargo to lysosomes, shifting the model from passive membrane alteration to active co-trafficking.\",\n      \"evidence\": \"CRISPR IFITM-mutant cell lines, site-specific fluorophore tagging, live-cell imaging of viral entry\",\n      \"pmids\": [\"30643282\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How IFITM3-bearing vesicles are selectively targeted to virus-containing endosomes unknown\", \"Whether co-trafficking requires specific lipid or protein cofactors not determined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"A series of landmark studies expanded IFITM3 biology beyond antiviral defense: IFITM3 was shown to bind and activate γ-secretase (increasing Aβ production relevant to Alzheimer's disease), to function as a PIP3 scaffold amplifying PI3K signaling in B cells upon Tyr20 phosphorylation, and to require VCP/p97 for ubiquitin-dependent trafficking and turnover.\",\n      \"evidence\": \"γ-secretase Co-IP and activity assays in 5xFAD mice and human AD tissue; phosphomimetic mutants and Ifitm3−/− B cells with BCR signaling readouts; photo-crosslinking proteomics identifying VCP, K24 mutagenesis, VCP inhibitor treatment\",\n      \"pmids\": [\"32879487\", \"33149299\", \"32243810\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of IFITM3–γ-secretase interaction unknown\", \"How Tyr20 phosphorylation overrides AP-2 sorting mechanistically unclear\", \"Whether VCP acts on IFITM3 as an unfoldase or segregase not determined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstration that GxxxG-mediated oligomerization drives membrane rigidity and that IFITM3 incorporation into virions reduces HA content revealed two distinct mechanistic arms — endosomal membrane stiffening and virion-intrinsic attenuation.\",\n      \"evidence\": \"G95 mutagenesis with oligomerization and membrane rigidity assays; virion IFITM3/HA quantification, neutralization assays, mouse infection model\",\n      \"pmids\": [\"33112230\", \"33882122\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of functional oligomers not defined\", \"Relative contribution of virion incorporation versus endosomal restriction in vivo not quantified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"IFITM3 was found to suppress phagosome maturation in macrophages, revealing a host-detrimental role where IFN-induced IFITM3 paradoxically facilitates intracellular bacterial infection by preventing lysosomal killing of Listeria.\",\n      \"evidence\": \"Ifitm3−/− mouse Listeria infection model, phagosome maturation and virulence factor proteolysis assays\",\n      \"pmids\": [\"34404769\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism by which IFITM3 inhibits phagosome maturation not defined\", \"Whether other intracellular bacteria exploit this pathway unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Direct cholesterol binding by the amphipathic helix was biochemically demonstrated, and an unexpected pro-viral role for IFITM3 as an NTCP co-factor facilitating HBV/HDV entry was identified, showing that IFITM3 can promote or restrict virus entry depending on the pathogen.\",\n      \"evidence\": \"NBD-cholesterol binding assay with F63Q/F67Q mutants, MD simulations; membrane Y2H and Co-IP of IFITM3–NTCP, HBV/HDV infection assays in primary hepatocytes\",\n      \"pmids\": [\"35872070\", \"35458456\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of cholesterol–AH interaction at atomic resolution unknown\", \"Mechanism by which IFITM3 facilitates HBV/HDV post-attachment steps unclear\", \"NTCP interaction not validated by reconstitution\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Cryo-electron tomography captured IFITM3-mediated arrest of influenza fusion at the hemifusion diaphragm stage in situ, and PIP3 was identified as an interferon-inducible lipid rheostat required for endosomal IFITM restriction, unifying lipid sorting, hemifusion arrest, and phosphoinositide signaling into a coherent mechanistic model.\",\n      \"evidence\": \"In situ cryo-ET of IFITM3 KO versus WT cells infected with IAV; lipidomics, PIP3 supplementation, lysine mutants with pseudovirus and replicating virus assays\",\n      \"pmids\": [\"37003257\", \"36970857\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How IFITM3 recruits PIP3 to the hemifusion site at molecular detail unknown\", \"Whether PIP3 rheostat applies to all restricted viruses not tested\", \"No atomic-resolution structure of IFITM3 in a lipid bilayer\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Cell-type-specific knockdown of IFITM3 in cerebrovascular endothelial cells reduced Aβ accumulation and improved cognition in AD mice, establishing a positive feedback loop between Aβ and IFITM3 and identifying vascular IFITM3 as a potential therapeutic target.\",\n      \"evidence\": \"AAV-BI30 endothelial IFITM3 knockdown in AD transgenic mice, BACE1/γ-secretase activity assays, behavioral and two-photon imaging\",\n      \"pmids\": [\"39807629\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of IFITM3 regulation of BACE1 activity not determined\", \"Whether endothelial IFITM3–Aβ feedback operates in human AD not tested\", \"Single-lab finding awaiting independent replication\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the high-resolution structure of IFITM3 in native membranes, the precise mechanism by which IFITM3 suppresses phagosome maturation, the identity of the K88 methyltransferase, and how context-dependent phosphorylation, palmitoylation, ubiquitination, and methylation are integrated to switch IFITM3 between antiviral, signaling, and disease-promoting functions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No high-resolution lipid bilayer structure\", \"K88 methyltransferase unidentified\", \"Integrated PTM cross-talk model not established\", \"Cell-type-specific regulatory mechanisms incompletely mapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [4, 16, 17]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [11, 12, 15, 25]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [12, 28]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [7, 15, 17]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [2, 3, 5, 10, 17]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [2, 6, 8, 14]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [12, 24]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [10, 30]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [1, 2, 10, 17, 27]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [12, 28, 32]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [5, 10, 14, 24]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [11, 33]}\n    ],\n    \"complexes\": [\n      \"γ-secretase complex (functional interaction)\"\n    ],\n    \"partners\": [\n      \"VAPA\",\n      \"NEDD4\",\n      \"VCP\",\n      \"ZDHHC20\",\n      \"LSD1\",\n      \"AP2M1\",\n      \"NTCP\",\n      \"ITGA2B\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}