Affinage

WDFY2

WD repeat and FYVE domain-containing protein 2 · UniProt Q96P53

Length
400 aa
Mass
45.2 kDa
Annotated
2026-06-11
21 papers in source corpus 11 papers cited in narrative 11 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

WDFY2 is a PtdIns3P-binding, WD40-repeat endosomal scaffold that defines a distinct subset of early endosomes lying close to the plasma membrane and is required for early endocytic processing of transferrin (PMID:16873553). From this endosomal platform it organizes isoform-specific insulin signaling: WDFY2-positive endosomes selectively recruit Akt2 over Akt1, and WDFY2 binds the insulin receptor through its WD1-4 domain to retain INSR on endosomes and license IRS1/2 phosphorylation and downstream Akt2 activation; Wdfy2 loss in mice produces systemic insulin resistance with impaired hepatic Akt2 signaling (PMID:20189988, PMID:32641353). WDFY2 also operates as a gatekeeper of endosomal recycling by binding the v-SNARE VAMP3 and retaining it on endosomal tubules, thereby restraining VAMP3-dependent surface delivery — its loss redistributes VAMP3 to peripheral vesicles, increasing MT1-MMP (MMP14) secretion, matrix degradation and cell invasion (PMID:31253801), and phosphorylation-triggered release of VAMP3 governs IL-6 vesicle secretion during dendritic cell activation (PMID:40977280). Acting downstream of class III PI3K, WDFY2 regulates LKB1 activity and localization to control epithelial polarity (PMID:29084199). Beyond its endosomal roles, WDFY2 is phosphorylated at Ser84 by the ATM-CHK2 axis upon DNA double-strand breaks, whereupon it is recruited to break sites and bridges the MRE11-RAD50 subcomplex with NBS1 to assemble the MRN complex and promote end resection and homologous recombination repair (PMID:41196680). WDFY2 expression is transcriptionally activated by p63 isoforms through defined promoter response elements (PMID:31789342).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2006 High

    Established WDFY2 as a marker and functional component of a previously undefined subset of early endosomes, answering whether it has a role in endocytic trafficking.

    Evidence RNAi/siLNA loss-of-function with transferrin uptake assays and localization microscopy across C. elegans and mammalian cells

    PMID:16873553

    Open questions at the time
    • Molecular function on these endosomes not defined
    • No binding partners identified at this stage
    • Markers distinguishing this endosome subset beyond transferrin-positive/Rab5-EEA1-negative not fully characterized
  2. 2007 Medium

    Clarified that WDFY2's FYVE domain endosome binding depends on properties beyond PtdIns3P head-group recognition, addressing how FYVE proteins achieve differential membrane targeting.

    Evidence In vitro PtdIns3P binding and cell-based localization assays with FYVE domain mutants

    PMID:17233583

    Open questions at the time
    • WDFY2-specific mutagenesis data not detailed
    • Functional consequence of differential binding for WDFY2 not established
  3. 2010 High

    Defined WDFY2 endosomes as an isoform-selective scaffold for Akt2 in insulin signaling, answering how Akt isoform specificity is achieved spatially.

    Evidence Reciprocal co-localization, siRNA knockdown with insulin stimulation, phospho-substrate immunoblotting, glucose transport and gene expression readouts

    PMID:20189988

    Open questions at the time
    • Direct binding partner linking WDFY2 to Akt2 not yet identified
    • Mechanism of Akt2 protein-level reduction unclear
  4. 2017 High

    Placed WDFY2 in a defined signaling cascade (CIII-PI3K → WDFY2 → LKB1) controlling epithelial polarity, answering which downstream effector links endosomal PI3K to polarity.

    Evidence Genetic epistasis in Drosophila and depletion/rescue in human organoids

    PMID:29084199

    Open questions at the time
    • Direct physical interaction between WDFY2 and LKB1 not established
    • Biochemical mechanism of LKB1 regulation unknown
  5. 2018 Medium

    Showed WDFY2 endosomal levels are set by upstream maturation factors and influence ciliary membrane homeostasis, addressing how WDFY2 endosome abundance is regulated.

    Evidence C. elegans genetics with imaging of endosomal markers and cilia morphology

    PMID:29572244

    Open questions at the time
    • WDFY2 role secondary to the RABS-5/VPS-45 story
    • Direct mechanism linking WDFY2 to polycystin-2 levels not defined
  6. 2019 High

    Identified VAMP3 as a direct WDFY2 partner and established WDFY2 as a gatekeeper restraining MMP recycling and invasion, answering how WDFY2 loss promotes invasive secretion.

    Evidence Co-IP of WDFY2-VAMP3, WDFY2 knockout cells, live-cell imaging, MT1-MMP secretion, ECM degradation and Transwell invasion assays

    PMID:31253801 PMID:31692886

    Open questions at the time
    • Structural basis of WDFY2-VAMP3 interaction not resolved
    • Regulation of the interaction not yet defined
  7. 2019 Medium

    Identified p63 isoforms as direct transcriptional activators of WDFY2, answering how WDFY2 expression is controlled in cancer and developmental contexts.

    Evidence p63 isoform overexpression in TP53-null cells, response element bioinformatics, yeast and mammalian reporter assays

    PMID:31789342

    Open questions at the time
    • Physiological contexts of p63-driven WDFY2 induction not established
    • Single lab
  8. 2020 High

    Resolved the molecular basis of WDFY2's role in insulin signaling by mapping a WD1-4-domain interaction with INSR and demonstrating an in vivo metabolic phenotype, answering how endosomal WDFY2 enables Akt2 activation.

    Evidence Wdfy2 knockout mice, Co-IP with domain mapping, endosomal fractionation, phosphorylation and metabolic assays, AAV rescue in db/db mice

    PMID:32641353

    Open questions at the time
    • Structural details of WD1-4/INSR interface not resolved
    • How endosomal INSR retention is coupled to IRS1/2 recruitment biochemically not fully defined
  9. 2025 Medium

    Extended the WDFY2-VAMP3 axis to immune secretion, showing phosphorylation-dependent release of VAMP3 from WDFY2 controls IL-6 vesicle trafficking, answering how WDFY2-mediated retention is relieved.

    Evidence TIRF microscopy, phosphoproteomics, Co-IP, VAMP3 phosphomimetic/phosphodead mutants, IL-6 secretion assay in LPS-activated dendritic cells

    PMID:40977280

    Open questions at the time
    • Kinase responsible for VAMP3 phosphorylation not identified
    • Single lab extension of prior interaction
  10. 2025 High

    Revealed a non-endosomal nuclear function: ATM-CHK2-driven Ser84 phosphorylation recruits WDFY2 to break sites to scaffold MRN assembly, answering whether WDFY2 acts directly in DNA repair.

    Evidence In vitro kinase assays, S84A mutagenesis, Co-IP with MRE11 and NBS1, laser-induced DSB recruitment, HR reporter and survival assays

    PMID:41196680

    Open questions at the time
    • Structural basis of the MRE11-RAD50/NBS1 bridging not resolved
    • How a PtdIns3P-binding endosomal protein accesses nuclear DSB sites not explained
    • Single lab

Open questions

Synthesis pass · forward-looking unresolved questions
  • How WDFY2 partitions between its endosomal scaffolding roles and nuclear DNA-repair function, and what controls this functional switch, remains unresolved.
  • No model reconciling cytoplasmic endosomal and nuclear DSB localization
  • Determinants of context-specific partner selection (INSR vs VAMP3 vs MRN) unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 4 GO:0008289 lipid binding 2
Localization
GO:0005768 endosome 3 GO:0005634 nucleus 1
Pathway
R-HSA-162582 Signal Transduction 2 R-HSA-5653656 Vesicle-mediated transport 2 R-HSA-73894 DNA Repair 1
Complex memberships
MRN complex

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2006 WDFY2 localizes to a subset of early endosomes residing within 100 nm from the plasma membrane that are positive for transferrin but lack classical markers Rab5 and EEA1; RNAi silencing of WDFY2 in both C. elegans and mammalian cells impairs transferrin endocytosis, establishing a required role in early endocytic processing. RNAi screen in C. elegans, siRNA knockdown in mammalian cells, quantitative fluorescence microscopy, transferrin uptake assay Proceedings of the National Academy of Sciences of the United States of America High 16873553
2007 FYVE domain variation among FYVE domain-containing proteins, including WDFY2, modulates endosomal binding through differences in oligomerization propensity, membrane bilayer insertion, and electrostatic interactions — properties conferred by residues outside the PtdIns3P head-group recognition site. In vitro PtdIns3P binding assays, cell-based endosome localization assays with FYVE domain mutants Biochemical Society symposium Medium 17233583
2010 WDFY2-positive early endosomes specifically co-localize with Akt2 but not Akt1; WDFY2 depletion selectively reduces Akt2 protein levels and impairs insulin-stimulated phosphorylation of Akt substrates, glucose transport, and adipogenic gene expression, establishing WDFY2-enriched endosomes as an isoform-specific scaffold for Akt2 signaling downstream of insulin. Quantitative fluorescence microscopy (co-localization), siRNA knockdown, insulin stimulation assays, phospho-substrate immunoblotting, glucose transport assay, gene expression analysis The Journal of biological chemistry High 20189988
2017 WDFY2 is identified as an LKB1 regulator downstream of class III PI3K (CIII-PI3K) on endosomes; in Drosophila tissues and human organoids, the endosomal (but not autophagic) function of CIII-PI3K controls epithelial polarity through WDFY2-dependent regulation of LKB1 activity and localization. Genetic epistasis in Drosophila, human organoid depletion experiments, in vivo co-depletion rescue assays Nature cell biology High 29084199
2018 In C. elegans, WDFY-2 levels at periciliary endosomes are controlled by the early endosome maturation factors RABS-5 (Rabenosyn-5) and VPS-45, which regulate periciliary vesicle number and ciliary membrane homeostasis including polycystin-2 (PKD-2) levels. C. elegans genetics, fluorescence microscopy of endosomal markers, cilia morphology assays The EMBO journal Medium 29572244
2019 WDFY2 localizes to endosomal tubules via PtdIns3P binding and interacts with the v-SNARE VAMP3; WDFY2 knockout causes redistribution of VAMP3 into small vesicles near the plasma membrane, leading to increased VAMP3-dependent secretion of MT1-MMP (MMP14), enhanced extracellular matrix degradation, and increased cell invasion. Co-immunoprecipitation (WDFY2–VAMP3 interaction), WDFY2 knockout cells, live-cell imaging, MT1-MMP secretion assay, extracellular matrix degradation assay, Transwell invasion assay Nature communications High 31253801
2019 WDFY2 deletion causes increased MMP recycling and secretion from endosomes, leading to elevated matrix degradation and cell invasion, consistent with a gatekeeper role for VAMP3-dependent MMP recycling. WDFY2 knockout, extracellular matrix degradation assay (commentary/summary of PMID:31253801) Molecular & cellular oncology Medium 31692886
2019 p63 transcription factor isoforms (ΔN and TA) transcriptionally activate WDFY2 expression through specific p63 response elements in the WDFY2 promoter, validated in TP53-null cells and yeast-based assays, placing WDFY2 downstream of p63 in cancer regulation and limb development networks. Overexpression of p63 isoforms in TP53-null cells, bioinformatics identification of response elements, yeast-based transcription assay, mammalian reporter assay Bioscience reports Medium 31789342
2020 WDFY2 interacts with the insulin receptor (INSR) via its WD1-4 domain and is required for endosomal localization of INSR after insulin stimulation; this ensures recruitment of IRS1/2 to endosomal INSR, enabling IRS1/2 phosphorylation and downstream Akt2 activation. Wdfy2 knockout mice display systemic insulin resistance with impaired hepatic Akt2 signaling, increased gluconeogenesis, and reduced glycogen accumulation. Wdfy2 knockout mice, co-immunoprecipitation (WDFY2–INSR interaction, domain mapping), endosomal fractionation, phosphorylation assays (Akt2, FoxO1, GSK-3β), glucose/glycogen metabolic assays, adeno-associated virus rescue in db/db mice Diabetes High 32641353
2025 WDFY2 is phosphorylated at serine 84 by the ATM-CHK2 kinase axis in response to DNA double-strand breaks (DSBs); this phosphorylation recruits WDFY2 to DSB sites where it directly interacts with MRE11 and NBS1, bridging the MRE11-RAD50 subcomplex with NBS1 to promote MRN complex formation and DNA end resection required for homologous recombination repair. WDFY2 deficiency or the non-phosphorylatable S84A mutant impairs HR repair and reduces cell survival after DNA damage. In vitro kinase assay (ATM, CHK2), phosphorylation site mutagenesis (S84A), Co-immunoprecipitation (WDFY2–MRE11, WDFY2–NBS1), laser-induced DSB recruitment assay, HR repair reporter assay, cell survival assay Cell reports High 41196680
2025 WDFY2 acts as a chaperone that retains VAMP3 at endosomes; phosphorylation of VAMP3 upon LPS-induced dendritic cell activation releases VAMP3 from WDFY2, enabling trafficking of IL-6-positive VAMP3-positive vesicles to the plasma membrane for IL-6 secretion. Quantitative TIRF microscopy, phosphoproteomic analysis, co-immunoprecipitation (WDFY2–VAMP3), VAMP3 phosphomimetic/phosphodead mutants, IL-6 secretion assay Journal of cell science Medium 40977280

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2006 The WD40 and FYVE domain containing protein 2 defines a class of early endosomes necessary for endocytosis. Proceedings of the National Academy of Sciences of the United States of America 45 16873553
2014 CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma. PLoS genetics 41 24675677
2019 Population-based genome-wide association study of cognitive decline in older adults free of dementia: identification of a novel locus for the attention domain. Neurobiology of aging 36 30954325
2010 Isoform-specific regulation of Akt signaling by the endosomal protein WDFY2. The Journal of biological chemistry 35 20189988
2019 WDFY2 restrains matrix metalloproteinase secretion and cell invasion by controlling VAMP3-dependent recycling. Nature communications 34 31253801
2019 Depletion of MLKL inhibits invasion of radioresistant nasopharyngeal carcinoma cells by suppressing epithelial-mesenchymal transition. Annals of translational medicine 28 32042757
2018 Endosome maturation factors Rabenosyn-5/VPS45 and caveolin-1 regulate ciliary membrane and polycystin-2 homeostasis. The EMBO journal 28 29572244
2007 Evolutionarily conserved structural and functional roles of the FYVE domain. Biochemical Society symposium 27 17233583
2017 Class III phosphatidylinositol-3-OH kinase controls epithelial integrity through endosomal LKB1 regulation. Nature cell biology 25 29084199
2019 Genome-wide DNA methylation investigation of glucocorticoid exposure within buccal samples. Psychiatry and clinical neurosciences 24 30821055
2024 Elucidation of the genetic determination of body weight and size in Chinese local chicken breeds by large-scale genomic analyses. BMC genomics 16 38509464
2017 Overexpression of WDFY2 inhibits prostate cancer cell growth and migration via inactivation of Akt pathway. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 15 28653900
2020 WDFY2 Potentiates Hepatic Insulin Sensitivity and Controls Endosomal Localization of the Insulin Receptor and IRS1/2. Diabetes 11 32641353
2017 A Genome-Wide Association Study and Complex Network Identify Four Core Hub Genes in Bipolar Disorder. International journal of molecular sciences 11 29257106
2019 P63 modulates the expression of the WDFY2 gene which is implicated in cancer regulation and limb development. Bioscience reports 7 31789342
2025 MicroRNA profiling identifies VHL/HIF-2α dependent miR-2355-5p as a key modulator of clear cell Renal cell carcinoma tumor growth. Cancer cell international 6 40016765
2023 Circ_0115118 regulates endometrial functions through the miR-138-1-3p/WDFY2 axis in patients with PCOS†. Biology of reproduction 6 36780172
2023 A pan-cancer analysis of the role of WDFY2 in human tumors. Biotechnology & genetic engineering reviews 4 36971139
2025 Phosphorylation of VAMP3 couples IL-6 exocytosis to dendritic cell activation. Journal of cell science 1 40977280
2025 WDFY2 promotes MRN complex formation required for homologous recombination-mediated DNA repair. Cell reports 1 41196680
2019 Tumor suppression by control of matrix metalloproteinase recycling. Molecular & cellular oncology 1 31692886

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