{"gene":"TNFRSF11A","run_date":"2026-04-28T21:42:59","timeline":{"discoveries":[{"year":1998,"finding":"RANK (TNFRSF11A) was identified as the essential signaling receptor for osteoclast differentiation factor (ODF/RANKL) on osteoclast progenitors; soluble RANK and Fab antibody fragments blocked ODF binding to RANK and inhibited osteoclastogenesis, while anti-RANK polyclonal antibody stimulated osteoclastogenesis in the presence of M-CSF.","method":"Molecular cloning, receptor binding assay, antibody blocking, soluble receptor inhibition in osteoclast differentiation assay","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1-2 — direct receptor identification with functional blocking and activation experiments, foundational paper","pmids":["9878548"],"is_preprint":false},{"year":2000,"finding":"Heterozygous insertional duplications (18-bp and 27-bp) in exon 1 of TNFRSF11A affecting the RANK signal peptide cause familial expansile osteolysis; mutant RANK proteins showed perturbed expression levels, lack of normal signal peptide cleavage, and increased RANK-mediated NF-κB signaling in vitro, indicating gain-of-function activating mutations.","method":"Sequencing of patient samples, expression of recombinant mutant RANK proteins, NF-κB reporter assay","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 1-2 — mutation characterization with recombinant protein expression and functional NF-κB signaling assay, strong evidence","pmids":["10615125"],"is_preprint":false},{"year":2002,"finding":"Expansile skeletal hyperphosphatasia (ESH) is caused by a 15-bp tandem duplication in the TNFRSF11A signal peptide, allelic to familial expansile osteolysis, and likely reflects increased NF-κB activity via activated RANK signaling.","method":"Molecular sequencing, genetic analysis","journal":"Journal of bone and mineral research","confidence":"Medium","confidence_rationale":"Tier 2 — genetic identification with mechanistic inference from allelic relationship to functionally characterized FEO mutations","pmids":["11771666"],"is_preprint":false},{"year":2005,"finding":"TRAF6 is an indispensable signaling adaptor for RANK in osteoclastogenesis; however, osteoclast differentiation can occur via a TRANCE-RANK-TRAF6-independent pathway when hematopoietic precursors from RANK-null or TRAF6-null mice are stimulated with TNF-alpha plus TGF-beta in vitro.","method":"Genetic knockout mouse models, in vitro osteoclast differentiation assay with cytokine stimulation","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis using null mice with clear cellular phenotype readout; replicated across TRANCE-, RANK-, and TRAF6-null models","pmids":["16147974"],"is_preprint":false},{"year":2005,"finding":"RANK self-assembles through its cytoplasmic domain at position 534-539 (distinct from TRAF binding domains) ligand-independently, and overexpression of oligomeric RANK induces osteoclastogenesis in a TRAF6-dependent manner without RANKL.","method":"Co-immunoprecipitation with FLAG/HA-tagged RANK constructs, C-terminal deletion mutants, osteoclast differentiation assay, TRAF6 decoy peptide inhibition","journal":"Journal of bone and mineral research","confidence":"Medium","confidence_rationale":"Tier 2-3 — reciprocal co-IP with deletion mapping plus functional osteoclastogenesis assay in single study","pmids":["16234979"],"is_preprint":false},{"year":2007,"finding":"RANK interacts with five members of the TRAF family (TRAF1, 2, 3, 5, 6), of which TRAF6 is indispensable for RANK signaling capability and links RANKL-RANK interaction to downstream NF-κB activation and osteoclastogenic transcriptional programs.","method":"Review of biochemical interaction studies, genetic experiments","journal":"Advances in experimental medicine and biology","confidence":"Medium","confidence_rationale":"Tier 3 — review summarizing established TRAF6-RANK interaction data from multiple labs","pmids":["17633024"],"is_preprint":false},{"year":2008,"finding":"CYLD deubiquitinase negatively regulates RANK signaling by inhibiting TRAF6 ubiquitination, thereby suppressing downstream NF-κB and other signaling events; CYLD is recruited to TRAF6 through physical interaction with the adaptor p62, and CYLD deficiency leads to hyperresponsive RANKL-induced osteoclastogenesis and severe osteoporosis in mice.","method":"CYLD knockout mouse model, in vitro osteoclast differentiation assay, co-immunoprecipitation, ubiquitination assay","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 — clean KO mouse with defined phenotype, co-IP, biochemical ubiquitination assay; multiple orthogonal methods in single study","pmids":["18382763"],"is_preprint":false},{"year":2008,"finding":"Mutations in TNFRSF11A (RANK) cause autosomal recessive osteoclast-poor osteopetrosis with hypogammaglobulinemia; patient monocytes failed to differentiate into osteoclasts upon M-CSF and RANKL stimulation, establishing an osteoclast-intrinsic defect, and immunological analysis showed impairment of immunoglobulin-secreting B cells.","method":"TNFRSF11A sequencing in patients, in vitro osteoclast differentiation assay with patient monocytes, immunological phenotyping","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 — loss-of-function mutations in multiple unrelated families with direct functional validation of osteoclast and B cell defects","pmids":["18606301"],"is_preprint":false},{"year":2008,"finding":"RANKL stimulation of mature osteoclasts via RANK results in translocation of NF-κB to the nucleus and elevation of cytosolic and nuclear calcium levels, demonstrating functional RANK expression in mature (not only precursor) osteoclasts.","method":"Microisolation of pure osteoclast populations, RT-PCR, NF-κB nuclear translocation assay, calcium signaling measurement","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 — direct functional assay in purified primary cells with multiple signaling readouts","pmids":["10606741"],"is_preprint":false},{"year":2009,"finding":"The extracellular domain of RANK binds RANKL as a monomer, while RANKL exists as a trimer; the binding affinity (KD ~1.09 × 10⁻¹⁰ M) was measured by surface plasmon resonance, establishing the high-affinity nature of the RANK-RANKL interaction.","method":"Recombinant protein expression and purification, gel filtration, chemical cross-linking, surface plasmon resonance","journal":"Archives of biochemistry and biophysics","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with quantitative biophysical measurement of binding affinity","pmids":["19416721"],"is_preprint":false},{"year":2010,"finding":"Crystal structures of unliganded RANK and the RANKL-RANK complex revealed that RANK has four full cysteine-rich domains (CRDs), with CRD4 stabilized by a sodium ion and a rigid linkage to CRD3; upon RANKL binding, RANK undergoes a hinge movement between CRD2 and CRD3 to form continuous close contact with RANKL. Mutations reducing RANK-RANKL affinity significantly disrupted osteoclast formation.","method":"X-ray crystallography of RANK alone and in complex with RANKL, site-directed mutagenesis, osteoclast formation assay","journal":"Journal of immunology","confidence":"High","confidence_rationale":"Tier 1 — crystal structures of free and complexed receptor with mutagenesis functional validation","pmids":["20483727"],"is_preprint":false},{"year":2004,"finding":"RANK is expressed by monocytes and RANKL stimulates monocyte chemotaxis via RANK through activation of phosphatidylinositol 3-kinase, phosphodiesterase, and Src kinase pathways; chemotaxis was blocked by osteoprotegerin (decoy receptor for RANKL).","method":"Micropore filter migration assay, signaling enzyme inhibitors, Western blotting, RT-PCR, flow cytometry","journal":"Arthritis and rheumatism","confidence":"Medium","confidence_rationale":"Tier 2 — direct functional assay with pathway inhibitors and receptor expression confirmation","pmids":["15248232"],"is_preprint":false},{"year":2014,"finding":"miR-503 directly targets RANK mRNA (TNFRSF11A) and inhibits RANKL-induced osteoclastogenesis; overexpression of miR-503 reduced RANK protein levels and inhibited osteoclast differentiation in CD14+ PBMCs and in vivo in ovariectomized mice.","method":"miRNA target validation, overexpression/knockdown in primary cells and in vivo (antagomir/agomir), osteoclast differentiation assay, RANK protein quantification","journal":"Journal of bone and mineral research","confidence":"Medium","confidence_rationale":"Tier 2 — direct target validation with in vitro and in vivo functional evidence for RANK as miR-503 target","pmids":["23821519"],"is_preprint":false},{"year":2015,"finding":"RANK signaling in luminal mammary progenitors amplifies WNT responsiveness through upregulation of R-spondin1; loss of RANK prevents proliferation of hormone receptor-negative luminal progenitors and basal cells, suppresses WNT activation, and impairs lobuloalveologenesis. Exogenous R-spondin1 rescues key aspects of RANK deficiency.","method":"Conditional RANK knockout mouse model, human breast tissue analysis, WNT pathway reporter, exogenous R-spondin1 rescue experiment","journal":"Stem cell reports","confidence":"High","confidence_rationale":"Tier 2 — conditional KO with defined phenotype and epistasis rescue experiment; multiple orthogonal methods","pmids":["26095608"],"is_preprint":false},{"year":2013,"finding":"Constitutive RANK signaling in mammary epithelial cells expands luminal and basal mammary compartments including mammary stem and progenitor cell pools, impairs normal luminal cell commitment, accumulates K14+K8+ bipotent cells, and leads to formation of heterogeneous mammary tumors.","method":"Transgenic mouse model with constitutive RANK expression, FACS analysis of mammary cell populations, histology","journal":"Stem cells","confidence":"Medium","confidence_rationale":"Tier 2 — gain-of-function mouse model with defined cellular phenotype readout","pmids":["23766243"],"is_preprint":false},{"year":2016,"finding":"Genetic inactivation of RANK in mammary epithelium markedly delayed onset, reduced incidence, and attenuated progression of Brca1;p53 mutation-driven mammary cancer; RANK/RANKL blockade impaired proliferation and expansion of Brca1;p53 mutant mammary stem cells and progenitors from human BRCA1 mutation carriers.","method":"Conditional RANK knockout in two mouse models, pharmacological RANKL inhibition, in vitro progenitor proliferation assay with human BRCA1-mutant tissue","journal":"Cell research","confidence":"High","confidence_rationale":"Tier 2 — two independent mouse models with conditional KO, human tissue validation, multiple orthogonal approaches","pmids":["27241552"],"is_preprint":false},{"year":2016,"finding":"RANK-independent osteoclastogenesis and bone erosion can occur in inflammatory arthritis via a TNF/IL-6-dependent pathway requiring IL-6R, NFATc1, DNAX-activation protein 12 (DAP12), and cell proliferation but not RANKL or RANK; arthritic mice with inducible RANK deficiency still exhibited bone erosion and synovial osteoclasts.","method":"Conditional RANK knockout mouse model, K/BxN serum-transfer arthritis model, in vitro osteoclast differentiation from RANK-null precursors, micro-CT, histology","journal":"Arthritis & rheumatology","confidence":"High","confidence_rationale":"Tier 2 — conditional KO with in vivo and in vitro validation demonstrating RANK-independent pathway","pmids":["27563728"],"is_preprint":false},{"year":2018,"finding":"STAC2 is a RANKL-inducible protein that physically interacts with RANK and negatively regulates osteoclast formation by inhibiting formation of the RANK signaling complex (containing Gab2 and PLCγ2) and suppressing NF-κB, MAPK activation, and Btk/Tec-mediated PLCγ2 phosphorylation.","method":"Co-immunoprecipitation, overexpression, NF-κB and MAPK reporter assays, osteoclast differentiation assay","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2-3 — co-IP with functional signaling and differentiation assays in single study","pmids":["29348675"],"is_preprint":false},{"year":2015,"finding":"RANKL variants with higher affinity for RANK produce more robust downstream signaling and greater osteoclastogenic potential; the relationship between RANKL-RANK affinity and osteoclastogenesis is biphasic and driven entirely by the kinetic off-rate, indicating that physiological RANKL-RANK interaction is not optimized for maximal signaling.","method":"Yeast surface display, random mutagenesis library screening, surface plasmon resonance binding kinetics, in vitro osteoclast differentiation assay","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 1-2 — in vitro reconstitution with binding kinetics and functional osteoclast assay; single lab but multiple orthogonal methods","pmids":["25864714"],"is_preprint":false},{"year":2022,"finding":"A20 is rapidly recruited to the RANK receptor complex within minutes of RANKL binding and restrains NF-κB activation; this inhibition is independent of A20's deubiquitinating activity but requires its zinc finger (ZnF) 4 and 7 ubiquitin-binding functions. Osteoclast-specific A20 knockout mice develop severe osteoporosis with hyperresponsive RANKL-induced osteoclastogenesis.","method":"Osteoclast-specific conditional A20 knockout mouse, in vitro osteoclast differentiation, co-immunoprecipitation of RANK complex, domain-specific mutants, NF-κB reporter assay","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1-2 — conditional KO with in vivo and in vitro phenotype, biochemical complex recruitment, domain mutagenesis to separate deubiquitinating from ubiquitin-binding functions","pmids":["36194667"],"is_preprint":false},{"year":2012,"finding":"TNFRSF11A (RANK) promoter is epigenetically silenced by CpG methylation in gliomas; demethylation with 5-aza-2'-deoxycytidine restores RANK expression, and RANK overexpression in glioblastoma cells reduces focus formation and increases apoptosis through activation of apoptosis-regulatory signaling pathways.","method":"Pyrosequencing methylation analysis, demethylating agent treatment, RANK overexpression, focus formation assay, flow cytometry for apoptosis, reporter assay","journal":"Neoplasia","confidence":"Medium","confidence_rationale":"Tier 2 — epigenetic silencing demonstrated with functional rescue by demethylation and overexpression with apoptosis readout","pmids":["22787434"],"is_preprint":false},{"year":2014,"finding":"A frameshift mutation (p.Met416Cysfs*110) in TNFRSF11A causes hereditary recurrent fever with increased secretion of inflammatory cytokines (TNFα, IL-18, IL-1Ra, IFN-γ) and altered NF-κB signaling; a chromosomal duplication of TNFRSF11A also causes hereditary recurrent fever, implicating RANK in innate immune regulation and fever.","method":"Array-CGH, sequencing, serum cytokine multiplex measurement (Luminex), NF-κB luciferase reporter assay with wild-type and mutant RANK","journal":"Arthritis & rheumatology","confidence":"Medium","confidence_rationale":"Tier 2 — genetic identification with functional NF-κB assay and cytokine profiling","pmids":["24891336"],"is_preprint":false},{"year":2018,"finding":"A novel splice-site mutation (c.616+3A>G) in TNFRSF11A causing exon 6 skipping and frameshift leads to dysosteosclerosis (autosomal recessive sclerosing bone disease), expanding the phenotypic spectrum of TNFRSF11A loss-of-function mutations.","method":"Whole-exome sequencing, exon trapping assay to demonstrate exon skipping","journal":"Journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 — genetic mutation with direct functional demonstration of splicing effect by exon trapping","pmids":["29568001"],"is_preprint":false},{"year":2012,"finding":"Cell adhesion signaling regulates RANK expression in osteoclast precursors; BMMs under adherent conditions express high RANK and differentiate efficiently into osteoclasts in response to RANKL, while non-adherent conditions reduce RANK expression and impair RANKL-mediated NF-κB signaling. Forced RANK or TRAF6 overexpression rescues osteoclastogenesis under non-adherent conditions.","method":"Adherent vs. non-adherent culture system, RT-PCR, Western blot, RGD-disintegrin inhibition, forced RANK/TRAF6 overexpression, osteoclast differentiation assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 — defined experimental system with rescue experiment establishing RANK expression as downstream of adhesion signaling","pmids":["23139818"],"is_preprint":false},{"year":2001,"finding":"TGF-β1 directly stimulates osteoclast differentiation of pre-osteoclastic RAW 264.7 cells in the presence of M-CSF and RANKL, and dose- and time-dependently increases RANK mRNA and protein expression in these cells.","method":"Osteoclast differentiation assay (TRAP staining), RT-PCR, flow cytometry with fluorescent RANKL probe","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 — direct in vitro functional assay with RANK expression quantification at mRNA and protein levels","pmids":["11573248"],"is_preprint":false},{"year":2002,"finding":"TRANCE (RANKL)-RANK interaction sustains the longevity of interstitial dendritic cells (derived from CD34+ progenitors) that co-express TRANCE and RANK; soluble RANK reduces viability and Bcl-2 expression of these cells, while CD1a+ DCs expressing only RANK are rescued from cell death by exogenous TRANCE or by TRANCE-expressing DCs.","method":"CD34+ progenitor culture, flow cytometry, soluble RANK treatment, viability assay, Bcl-2 expression analysis","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 — direct functional experiment with receptor-ligand blocking and survival readout in primary human cells","pmids":["12393586"],"is_preprint":false}],"current_model":"RANK (TNFRSF11A) is a TNF receptor superfamily member that functions as the essential receptor for RANKL on osteoclast precursors and mature osteoclasts, forming a high-affinity complex (KD ~10⁻¹⁰ M) in which RANK undergoes a CRD2-CRD3 hinge conformational change; RANKL binding recruits TRAF6 (and other TRAFs) to the cytoplasmic domain, activating NF-κB, MAPK, and calcium signaling to drive osteoclast differentiation, activation, and survival, while negative regulators including CYLD (via TRAF6 deubiquitination), A20 (via ubiquitin-binding ZnF domains at the RANK complex), and STAC2 (by disrupting the Gab2/PLCγ2 complex) restrain signaling; RANK also self-assembles via cytoplasmic residues 534-539 to signal ligand-independently, regulates mammary progenitor expansion via R-spondin1/WNT, controls dendritic cell and thymic epithelial cell survival, and loss-of-function mutations cause osteoclast-poor osteopetrosis with immunodeficiency, while gain-of-function signal peptide insertions cause familial expansile osteolysis and related hyperresorptive bone diseases through constitutive NF-κB activation."},"narrative":{"teleology":[{"year":1998,"claim":"Identification of RANK as the essential receptor transducing RANKL signals in osteoclast progenitors resolved how osteoclastogenic cytokine signaling is received at the cell surface, establishing RANK as the central receptor in bone resorption.","evidence":"Molecular cloning, soluble receptor and Fab blocking of ODF binding, and anti-RANK antibody stimulation of osteoclastogenesis in vitro","pmids":["9878548"],"confidence":"High","gaps":["Downstream intracellular signaling adaptors not yet mapped","Role in non-bone tissues unknown"]},{"year":2000,"claim":"Discovery that heterozygous signal-peptide insertions in TNFRSF11A cause familial expansile osteolysis through constitutive NF-κB activation established the first gain-of-function disease mechanism for RANK and linked aberrant receptor processing to ligand-independent signaling.","evidence":"Patient sequencing, recombinant mutant RANK expression, NF-κB reporter assay; allelic ESH mutation identified in 2002","pmids":["10615125","11771666"],"confidence":"High","gaps":["Precise mechanism by which uncleaved signal peptide activates signaling not resolved","Whether mutations promote receptor oligomerization or trafficking defects unclear"]},{"year":2002,"claim":"Demonstration that RANK-RANKL interaction sustains dendritic cell survival via Bcl-2 extended RANK function beyond bone biology to immune cell homeostasis.","evidence":"Soluble RANK blocking and exogenous TRANCE rescue of CD34+-derived dendritic cell viability with Bcl-2 quantification","pmids":["12393586"],"confidence":"Medium","gaps":["Intracellular signaling pathway mediating DC survival through RANK not delineated","In vivo validation in DC-specific RANK KO not performed"]},{"year":2005,"claim":"Genetic epistasis using RANK-null and TRAF6-null mice confirmed TRAF6 as the indispensable cytoplasmic adaptor for RANK-mediated osteoclastogenesis, while revealing a RANK-independent TNF-α/TGF-β backup pathway.","evidence":"In vitro osteoclast differentiation from RANK-null and TRAF6-null hematopoietic precursors with TNF-α/TGF-β stimulation","pmids":["16147974"],"confidence":"High","gaps":["In vivo relevance of the RANK-independent backup pathway unresolved at this point","Other TRAFs' individual contributions not dissected"]},{"year":2005,"claim":"Mapping of a RANK cytoplasmic self-assembly domain (residues 534–539) distinct from TRAF-binding sites showed that RANK can oligomerize and signal ligand-independently, providing a mechanism for how gain-of-function mutations may constitutively activate the receptor.","evidence":"Co-immunoprecipitation of FLAG/HA-tagged RANK deletion mutants, TRAF6 decoy peptide inhibition, osteoclast differentiation assay","pmids":["16234979"],"confidence":"Medium","gaps":["Crystal structure of cytoplasmic domain oligomer not obtained","Self-assembly not validated with biophysical methods beyond co-IP","Physiological stoichiometry on cell surface not determined"]},{"year":2008,"claim":"Identification of CYLD as a negative regulator that deubiquitinates TRAF6 via p62-mediated recruitment to the RANK complex established the first checkpoint mechanism restraining RANK-driven osteoclastogenesis, with CYLD-null mice displaying severe osteoporosis.","evidence":"CYLD knockout mouse, co-IP of CYLD-p62-TRAF6, ubiquitination assays, osteoclast differentiation","pmids":["18382763"],"confidence":"High","gaps":["Whether CYLD acts on other ubiquitin chain types beyond K63 at the RANK complex not fully resolved","Relative contributions of CYLD versus other DUBs not compared"]},{"year":2008,"claim":"Discovery that loss-of-function TNFRSF11A mutations cause autosomal recessive osteopetrosis with hypogammaglobulinemia proved that RANK is non-redundant for both osteoclast formation and B cell terminal differentiation in humans.","evidence":"Patient TNFRSF11A sequencing, failed in vitro osteoclast differentiation from patient monocytes, immunological phenotyping","pmids":["18606301"],"confidence":"High","gaps":["Mechanism of RANK requirement for immunoglobulin-secreting B cells not elucidated","Thymic epithelial cell involvement in patients not assessed"]},{"year":2009,"claim":"Quantitative biophysical measurement of the RANK-RANKL interaction (KD ~1.09 × 10⁻¹⁰ M, monomeric RANK binding trimeric RANKL) provided the affinity benchmark needed to interpret how signaling strength relates to receptor occupancy.","evidence":"Recombinant protein SPR, gel filtration, and chemical cross-linking","pmids":["19416721"],"confidence":"High","gaps":["On-cell binding parameters may differ from solution measurements","Effect of membrane context and pre-assembly not captured"]},{"year":2010,"claim":"Crystal structures of free RANK and the RANKL–RANK complex revealed a four-CRD architecture with a CRD2-CRD3 hinge conformational change upon ligand binding, providing the first atomic-resolution view of how RANKL engages its receptor.","evidence":"X-ray crystallography of unliganded and complexed RANK, site-directed mutagenesis with osteoclast formation assay","pmids":["20483727"],"confidence":"High","gaps":["Full-length receptor structure including transmembrane and cytoplasmic domains unavailable","How extracellular conformational change transmits to cytoplasmic TRAF recruitment not structurally resolved"]},{"year":2013,"claim":"Constitutive RANK signaling in mammary epithelium expanded stem/progenitor populations and disrupted luminal commitment, establishing RANK as a driver of mammary cell fate and tumorigenesis beyond its skeletal role.","evidence":"Transgenic mouse model with constitutive RANK expression, FACS of mammary populations, histology","pmids":["23766243"],"confidence":"Medium","gaps":["Downstream transcriptional program in mammary progenitors not fully mapped","Whether RANK acts cell-autonomously or via paracrine WNT not separated at this stage"]},{"year":2015,"claim":"Conditional RANK knockout in mammary epithelium revealed that RANK amplifies WNT signaling through R-spondin1, and exogenous R-spondin1 rescue demonstrated epistasis, placing RANK upstream of WNT in mammary progenitor expansion.","evidence":"Conditional RANK KO mouse, WNT reporter, R-spondin1 rescue, human breast tissue analysis","pmids":["26095608"],"confidence":"High","gaps":["Direct transcriptional mechanism linking RANK signaling to R-spondin1 gene induction not identified","Whether this axis operates in human breast cancer in vivo unclear"]},{"year":2016,"claim":"Genetic RANK inactivation in mammary epithelium delayed BRCA1/p53-driven breast cancer onset and pharmacological RANKL inhibition suppressed human BRCA1-mutant progenitor expansion, establishing RANK as a therapeutic target in hereditary breast cancer.","evidence":"Two conditional RANK KO mouse models, pharmacological RANKL inhibition, human BRCA1-mutant tissue progenitor assays","pmids":["27241552"],"confidence":"High","gaps":["Long-term efficacy of RANKL inhibition in breast cancer prevention trials not established","Whether RANK-independent compensatory pathways emerge over time not tested"]},{"year":2016,"claim":"Demonstration that RANK-independent osteoclastogenesis occurs in inflammatory arthritis via TNF/IL-6/DAP12 defined the limits of RANK's non-redundancy and explained clinical observations of bone erosion despite RANKL blockade.","evidence":"Conditional RANK KO in K/BxN serum-transfer arthritis model, in vitro differentiation from RANK-null precursors, micro-CT","pmids":["27563728"],"confidence":"High","gaps":["Relative quantitative contribution of RANK-dependent vs RANK-independent osteoclasts in human arthritis not measured","Whether RANK-independent osteoclasts are functionally equivalent not determined"]},{"year":2018,"claim":"Identification of STAC2 as a RANKL-inducible negative feedback inhibitor that disrupts the Gab2/PLCγ2 signaling complex at RANK added a second layer of intrinsic restraint distinct from the CYLD/A20 deubiquitination axis.","evidence":"Co-immunoprecipitation of STAC2-RANK, NF-κB/MAPK reporters, osteoclast differentiation assay","pmids":["29348675"],"confidence":"Medium","gaps":["In vivo validation in STAC2-deficient mice not reported","Structural basis of STAC2 interaction with RANK not determined"]},{"year":2022,"claim":"Discovery that A20 is recruited to the RANK complex within minutes and restrains NF-κB via ubiquitin-binding ZnF4/7 domains (not its deubiquitinase activity) revealed a mechanistically distinct negative regulator and explained severe osteoporosis in osteoclast-specific A20 knockouts.","evidence":"Osteoclast-specific conditional A20 KO mouse, co-IP of RANK complex, ZnF domain mutants, NF-κB reporter","pmids":["36194667"],"confidence":"High","gaps":["Structural basis of A20 recruitment to RANK complex not determined","Whether CYLD and A20 act redundantly or sequentially at the RANK complex not resolved"]},{"year":null,"claim":"How RANK's extracellular conformational change upon RANKL binding is mechanically transmitted through the transmembrane domain to initiate cytoplasmic TRAF6 recruitment remains structurally unresolved, and no full-length RANK structure exists.","evidence":"","pmids":[],"confidence":"High","gaps":["Full-length RANK structure including transmembrane and cytoplasmic domains not solved","Temporal order and cooperativity of TRAF6, CYLD, A20, and STAC2 assembly at the receptor not defined","Whether RANK's mammary WNT-amplifying function uses the same or distinct cytoplasmic signaling complexes as osteoclastogenesis unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[0,8,9,10]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,8,9,10,11]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,5,6,8,17,19]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[7,21,25]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[13,14,15]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[20,25]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[1,2,7,22]}],"complexes":["RANK-RANKL signaling complex","RANK-TRAF6 complex"],"partners":["TNFSF11","TRAF6","CYLD","TNFAIP3","STAC2","GAB2","PLCG2","SQSTM1"],"other_free_text":[]},"mechanistic_narrative":"TNFRSF11A (RANK) is the obligate receptor for RANKL that drives osteoclast differentiation, bone resorption, mammary progenitor expansion, and dendritic cell survival through TRAF6-dependent activation of NF-κB, MAPK, and calcium signaling. The RANK extracellular domain binds trimeric RANKL as a monomer with high affinity (KD ~10⁻¹⁰ M), undergoing a CRD2-CRD3 hinge conformational change that triggers cytoplasmic recruitment of TRAF6 and assembly of a signaling complex containing Gab2 and PLCγ2, which is negatively regulated by the deubiquitinase CYLD (via TRAF6 deubiquitination), A20 (via ubiquitin-binding zinc finger domains recruited directly to the RANK complex), and STAC2 (which disrupts the Gab2/PLCγ2 complex) [PMID:9878548, PMID:20483727, PMID:19416721, PMID:16147974, PMID:18382763, PMID:36194667, PMID:29348675]. In mammary epithelium, RANK signaling amplifies WNT responsiveness through R-spondin1 upregulation, expanding luminal progenitors; genetic RANK inactivation delays BRCA1-mutant mammary tumorigenesis [PMID:26095608, PMID:27241552]. Loss-of-function TNFRSF11A mutations cause autosomal recessive osteoclast-poor osteopetrosis with hypogammaglobulinemia, while gain-of-function signal-peptide insertions cause familial expansile osteolysis and related hyperresorptive bone diseases through constitutive NF-κB activation [PMID:18606301, PMID:10615125, PMID:11771666]."},"prefetch_data":{"uniprot":{"accession":"Q9Y6Q6","full_name":"Tumor necrosis factor receptor superfamily member 11A","aliases":["Osteoclast differentiation factor receptor","ODFR","Receptor activator of NF-KB"],"length_aa":616,"mass_kda":66.0,"function":"Receptor for TNFSF11/RANKL/TRANCE/OPGL; essential for RANKL-mediated osteoclastogenesis (PubMed:9878548). Its interaction with EEIG1 promotes osteoclastogenesis via facilitating the transcription of NFATC1 and activation of PLCG2 (By similarity). Involved in the regulation of interactions between T-cells and dendritic cells (By similarity)","subcellular_location":"Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q9Y6Q6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TNFRSF11A","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TNFRSF11A","total_profiled":1310},"omim":[{"mim_id":"612301","title":"OSTEOPETROSIS, AUTOSOMAL RECESSIVE 7; OPTB7","url":"https://www.omim.org/entry/612301"},{"mim_id":"610900","title":"CHARGED MULTIVESICULAR BODY PROTEIN 5; CHMP5","url":"https://www.omim.org/entry/610900"},{"mim_id":"607507","title":"PSORIATIC ARTHRITIS, SUSCEPTIBILITY TO","url":"https://www.omim.org/entry/607507"},{"mim_id":"607414","title":"FEZ FAMILY ZINC FINGER PROTEIN 2; FEZF2","url":"https://www.omim.org/entry/607414"},{"mim_id":"605018","title":"CYLD LYSINE-63 DEUBIQUITINASE; CYLD","url":"https://www.omim.org/entry/605018"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Plasma membrane","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"intestine","ntpm":28.5},{"tissue":"salivary gland","ntpm":23.7}],"url":"https://www.proteinatlas.org/search/TNFRSF11A"},"hgnc":{"alias_symbol":["RANK","CD265","FEO","ODFR","TRANCE-R"],"prev_symbol":["PDB2","LOH18CR1"]},"alphafold":{"accession":"Q9Y6Q6","domains":[{"cath_id":"2.10.50.10","chopping":"25-94_102-111","consensus_level":"medium","plddt":91.2676,"start":25,"end":111},{"cath_id":"2.10.50.10","chopping":"133-200","consensus_level":"medium","plddt":93.7687,"start":133,"end":200}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y6Q6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y6Q6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y6Q6-F1-predicted_aligned_error_v6.png","plddt_mean":58.91},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TNFRSF11A","jax_strain_url":"https://www.jax.org/strain/search?query=TNFRSF11A"},"sequence":{"accession":"Q9Y6Q6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y6Q6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y6Q6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y6Q6"}},"corpus_meta":[{"pmid":"18395508","id":"PMC_18395508","title":"Functions of RANKL/RANK/OPG in bone modeling and remodeling.","date":"2008","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/18395508","citation_count":1318,"is_preprint":false},{"pmid":"11713196","id":"PMC_11713196","title":"Minireview: the OPG/RANKL/RANK system.","date":"2001","source":"Endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/11713196","citation_count":1046,"is_preprint":false},{"pmid":"16356770","id":"PMC_16356770","title":"RANKL-RANK signaling in osteoclastogenesis and bone disease.","date":"2005","source":"Trends in molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/16356770","citation_count":930,"is_preprint":false},{"pmid":"17634140","id":"PMC_17634140","title":"Biology of RANK, RANKL, and osteoprotegerin.","date":"2007","source":"Arthritis research & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/17634140","citation_count":689,"is_preprint":false},{"pmid":"9878548","id":"PMC_9878548","title":"RANK is the essential signaling receptor for osteoclast differentiation factor in osteoclastogenesis.","date":"1998","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/9878548","citation_count":573,"is_preprint":false},{"pmid":"29047262","id":"PMC_29047262","title":"Current Understanding of RANK Signaling in Osteoclast Differentiation and Maturation.","date":"2017","source":"Molecules and cells","url":"https://pubmed.ncbi.nlm.nih.gov/29047262","citation_count":496,"is_preprint":false},{"pmid":"25368616","id":"PMC_25368616","title":"Biology of the RANKL-RANK-OPG System in Immunity, Bone, and Beyond.","date":"2014","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/25368616","citation_count":487,"is_preprint":false},{"pmid":"10615125","id":"PMC_10615125","title":"Mutations in TNFRSF11A, affecting the signal peptide of RANK, cause familial expansile osteolysis.","date":"2000","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/10615125","citation_count":341,"is_preprint":false},{"pmid":"19076348","id":"PMC_19076348","title":"RANK/RANKL: regulators of immune responses and bone physiology.","date":"2008","source":"Annals of the New York Academy of Sciences","url":"https://pubmed.ncbi.nlm.nih.gov/19076348","citation_count":308,"is_preprint":false},{"pmid":"16147974","id":"PMC_16147974","title":"Osteoclast differentiation independent of the TRANCE-RANK-TRAF6 axis.","date":"2005","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/16147974","citation_count":299,"is_preprint":false},{"pmid":"26684538","id":"PMC_26684538","title":"Bacterial ferrous iron transport: the Feo system.","date":"2015","source":"FEMS microbiology reviews","url":"https://pubmed.ncbi.nlm.nih.gov/26684538","citation_count":285,"is_preprint":false},{"pmid":"17925190","id":"PMC_17925190","title":"The RANKL/RANK/OPG pathway.","date":"2007","source":"Current osteoporosis reports","url":"https://pubmed.ncbi.nlm.nih.gov/17925190","citation_count":256,"is_preprint":false},{"pmid":"18606301","id":"PMC_18606301","title":"Human osteoclast-poor osteopetrosis with hypogammaglobulinemia due to TNFRSF11A (RANK) mutations.","date":"2008","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18606301","citation_count":215,"is_preprint":false},{"pmid":"15883214","id":"PMC_15883214","title":"Dysregulated osteoprotegerin/RANK ligand/RANK axis in clinical and experimental heart failure.","date":"2005","source":"Circulation","url":"https://pubmed.ncbi.nlm.nih.gov/15883214","citation_count":203,"is_preprint":false},{"pmid":"17895323","id":"PMC_17895323","title":"CLINICAL Review #: the role of receptor activator of nuclear factor-kappaB (RANK)/RANK ligand/osteoprotegerin: clinical implications.","date":"2007","source":"The Journal of clinical endocrinology and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/17895323","citation_count":195,"is_preprint":false},{"pmid":"16313338","id":"PMC_16313338","title":"Osteoclast precursors, RANKL/RANK, and immunology.","date":"2005","source":"Immunological reviews","url":"https://pubmed.ncbi.nlm.nih.gov/16313338","citation_count":185,"is_preprint":false},{"pmid":"15615494","id":"PMC_15615494","title":"The OPG/RANKL/RANK system in metabolic bone diseases.","date":"2004","source":"Journal of musculoskeletal & neuronal interactions","url":"https://pubmed.ncbi.nlm.nih.gov/15615494","citation_count":182,"is_preprint":false},{"pmid":"11306358","id":"PMC_11306358","title":"Osteoprotegerin and rank ligand expression in prostate cancer.","date":"2001","source":"Urology","url":"https://pubmed.ncbi.nlm.nih.gov/11306358","citation_count":175,"is_preprint":false},{"pmid":"23821519","id":"PMC_23821519","title":"MiR-503 regulates osteoclastogenesis via targeting RANK.","date":"2014","source":"Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research","url":"https://pubmed.ncbi.nlm.nih.gov/23821519","citation_count":173,"is_preprint":false},{"pmid":"18382763","id":"PMC_18382763","title":"Deubiquitinating enzyme CYLD negatively regulates RANK signaling and osteoclastogenesis in mice.","date":"2008","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/18382763","citation_count":162,"is_preprint":false},{"pmid":"12379618","id":"PMC_12379618","title":"Role of RANKL and RANK in bone loss and arthritis.","date":"2002","source":"Annals of the rheumatic diseases","url":"https://pubmed.ncbi.nlm.nih.gov/12379618","citation_count":160,"is_preprint":false},{"pmid":"33389131","id":"PMC_33389131","title":"Discovery of the RANKL/RANK/OPG system.","date":"2021","source":"Journal of bone and mineral metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/33389131","citation_count":158,"is_preprint":false},{"pmid":"21559440","id":"PMC_21559440","title":"Receptor activator of NF-kB (RANK) expression in primary tumors associates with bone metastasis occurrence in breast cancer patients.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21559440","citation_count":146,"is_preprint":false},{"pmid":"22113597","id":"PMC_22113597","title":"Rank/Rankl/opg: literature review.","date":"2011","source":"Acta reumatologica portuguesa","url":"https://pubmed.ncbi.nlm.nih.gov/22113597","citation_count":141,"is_preprint":false},{"pmid":"25720990","id":"PMC_25720990","title":"The RANKL-RANK Story.","date":"2015","source":"Gerontology","url":"https://pubmed.ncbi.nlm.nih.gov/25720990","citation_count":138,"is_preprint":false},{"pmid":"27241552","id":"PMC_27241552","title":"RANKL/RANK control Brca1 mutation- .","date":"2016","source":"Cell research","url":"https://pubmed.ncbi.nlm.nih.gov/27241552","citation_count":138,"is_preprint":false},{"pmid":"27279652","id":"PMC_27279652","title":"RANK-RANKL signalling in cancer.","date":"2016","source":"Bioscience reports","url":"https://pubmed.ncbi.nlm.nih.gov/27279652","citation_count":133,"is_preprint":false},{"pmid":"11521937","id":"PMC_11521937","title":"The osteoclastogenic molecules RANKL and RANK are associated with periprosthetic osteolysis.","date":"2001","source":"The Journal of bone and joint surgery. British volume","url":"https://pubmed.ncbi.nlm.nih.gov/11521937","citation_count":130,"is_preprint":false},{"pmid":"11771666","id":"PMC_11771666","title":"Expansile skeletal hyperphosphatasia is caused by a 15-base pair tandem duplication in TNFRSF11A encoding RANK and is allelic to familial expansile osteolysis.","date":"2002","source":"Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research","url":"https://pubmed.ncbi.nlm.nih.gov/11771666","citation_count":126,"is_preprint":false},{"pmid":"17530461","id":"PMC_17530461","title":"RANKL, RANK, osteoprotegerin: key partners of osteoimmunology and vascular diseases.","date":"2007","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/17530461","citation_count":125,"is_preprint":false},{"pmid":"27563728","id":"PMC_27563728","title":"RANK-Independent Osteoclast Formation and Bone Erosion in Inflammatory Arthritis.","date":"2016","source":"Arthritis & rheumatology (Hoboken, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/27563728","citation_count":119,"is_preprint":false},{"pmid":"21445556","id":"PMC_21445556","title":"RANKL/RANK-beyond bones.","date":"2011","source":"Journal of molecular medicine (Berlin, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/21445556","citation_count":112,"is_preprint":false},{"pmid":"20483727","id":"PMC_20483727","title":"Structural and functional insights of RANKL-RANK interaction and signaling.","date":"2010","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/20483727","citation_count":103,"is_preprint":false},{"pmid":"14523602","id":"PMC_14523602","title":"Novel aspects on RANK ligand and osteoprotegerin in osteoporosis and vascular disease.","date":"2003","source":"Calcified tissue international","url":"https://pubmed.ncbi.nlm.nih.gov/14523602","citation_count":96,"is_preprint":false},{"pmid":"11573248","id":"PMC_11573248","title":"Regulation of osteoclastogenesis and RANK expression by TGF-beta1.","date":"2001","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11573248","citation_count":94,"is_preprint":false},{"pmid":"30232468","id":"PMC_30232468","title":"Roles of the RANKL-RANK axis in antitumour immunity - implications for therapy.","date":"2018","source":"Nature reviews. Clinical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/30232468","citation_count":91,"is_preprint":false},{"pmid":"19762475","id":"PMC_19762475","title":"Modulation of OPG, RANK and RANKL by human chondrocytes and their implication during osteoarthritis.","date":"2009","source":"Rheumatology (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/19762475","citation_count":89,"is_preprint":false},{"pmid":"29241686","id":"PMC_29241686","title":"RANKL and RANK: From Mammalian Physiology to Cancer Treatment.","date":"2017","source":"Trends in cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/29241686","citation_count":76,"is_preprint":false},{"pmid":"12548579","id":"PMC_12548579","title":"RANK-Fc: a therapeutic antagonist for RANK-L in myeloma.","date":"2003","source":"Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/12548579","citation_count":74,"is_preprint":false},{"pmid":"29953152","id":"PMC_29953152","title":"Toward a mechanistic understanding of Feo-mediated ferrous iron uptake.","date":"2018","source":"Metallomics : integrated biometal science","url":"https://pubmed.ncbi.nlm.nih.gov/29953152","citation_count":72,"is_preprint":false},{"pmid":"12707582","id":"PMC_12707582","title":"RANKL and RANK as novel therapeutic targets for arthritis.","date":"2003","source":"Current opinion in rheumatology","url":"https://pubmed.ncbi.nlm.nih.gov/12707582","citation_count":71,"is_preprint":false},{"pmid":"12393586","id":"PMC_12393586","title":"Long-lived immature dendritic cells mediated by TRANCE-RANK interaction.","date":"2002","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/12393586","citation_count":71,"is_preprint":false},{"pmid":"21225243","id":"PMC_21225243","title":"Zoledronic acid inhibits RANK expression and migration of osteoclast precursors during osteoclastogenesis.","date":"2011","source":"Naunyn-Schmiedeberg's archives of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/21225243","citation_count":68,"is_preprint":false},{"pmid":"17633024","id":"PMC_17633024","title":"TRAFs in RANK signaling.","date":"2007","source":"Advances in experimental medicine and biology","url":"https://pubmed.ncbi.nlm.nih.gov/17633024","citation_count":66,"is_preprint":false},{"pmid":"26095608","id":"PMC_26095608","title":"RANK Signaling Amplifies WNT-Responsive Mammary Progenitors through R-SPONDIN1.","date":"2015","source":"Stem cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/26095608","citation_count":65,"is_preprint":false},{"pmid":"10606741","id":"PMC_10606741","title":"Expression of functional RANK on mature rat and human osteoclasts.","date":"1999","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/10606741","citation_count":65,"is_preprint":false},{"pmid":"30093448","id":"PMC_30093448","title":"Role of the RANK/RANKL Pathway in Multiple Myeloma.","date":"2018","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/30093448","citation_count":63,"is_preprint":false},{"pmid":"14981127","id":"PMC_14981127","title":"Opg, Rank, and Rankl in tooth development: co-ordination of odontogenesis and osteogenesis.","date":"2004","source":"Journal of dental research","url":"https://pubmed.ncbi.nlm.nih.gov/14981127","citation_count":61,"is_preprint":false},{"pmid":"32850393","id":"PMC_32850393","title":"Targeting the RANKL/RANK/OPG Axis for Cancer Therapy.","date":"2020","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/32850393","citation_count":58,"is_preprint":false},{"pmid":"17174136","id":"PMC_17174136","title":"RANK ligand.","date":"2006","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/17174136","citation_count":56,"is_preprint":false},{"pmid":"29146991","id":"PMC_29146991","title":"KLF5 promotes cervical cancer proliferation, migration and invasion in a manner partly dependent on TNFRSF11a expression.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/29146991","citation_count":53,"is_preprint":false},{"pmid":"34214174","id":"PMC_34214174","title":"Rank-in: enabling integrative analysis across microarray and RNA-seq for cancer.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/34214174","citation_count":51,"is_preprint":false},{"pmid":"7737382","id":"PMC_7737382","title":"Oxygen-derived free radical (ODFR) action on hyaluronan (HA), on two HA ester derivatives, and on the metabolism of articular chondrocytes.","date":"1995","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/7737382","citation_count":51,"is_preprint":false},{"pmid":"26562150","id":"PMC_26562150","title":"Genome-Wide Association Study of Late-Onset Myasthenia Gravis: Confirmation of TNFRSF11A and Identification of ZBTB10 and Three Distinct HLA Associations.","date":"2015","source":"Molecular medicine (Cambridge, Mass.)","url":"https://pubmed.ncbi.nlm.nih.gov/26562150","citation_count":51,"is_preprint":false},{"pmid":"34440747","id":"PMC_34440747","title":"The Roadmap of RANKL/RANK Pathway in Cancer.","date":"2021","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/34440747","citation_count":49,"is_preprint":false},{"pmid":"30984193","id":"PMC_30984193","title":"The RANKL-RANK Axis: A Bone to Thymus Round Trip.","date":"2019","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/30984193","citation_count":49,"is_preprint":false},{"pmid":"26921922","id":"PMC_26921922","title":"Role of the RANK/RANKL pathway in breast cancer.","date":"2016","source":"Maturitas","url":"https://pubmed.ncbi.nlm.nih.gov/26921922","citation_count":47,"is_preprint":false},{"pmid":"31462221","id":"PMC_31462221","title":"Measuring rank robustness in scored protein interaction networks.","date":"2019","source":"BMC bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/31462221","citation_count":47,"is_preprint":false},{"pmid":"16234979","id":"PMC_16234979","title":"Self-assembled RANK induces osteoclastogenesis ligand-independently.","date":"2005","source":"Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research","url":"https://pubmed.ncbi.nlm.nih.gov/16234979","citation_count":45,"is_preprint":false},{"pmid":"23766243","id":"PMC_23766243","title":"Constitutive activation of RANK disrupts mammary cell fate leading to tumorigenesis.","date":"2013","source":"Stem cells (Dayton, Ohio)","url":"https://pubmed.ncbi.nlm.nih.gov/23766243","citation_count":43,"is_preprint":false},{"pmid":"35845367","id":"PMC_35845367","title":"Empirical and philosophical problems with the subspecies rank.","date":"2022","source":"Ecology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/35845367","citation_count":41,"is_preprint":false},{"pmid":"15248232","id":"PMC_15248232","title":"Expression and function of RANK in human monocyte chemotaxis.","date":"2004","source":"Arthritis and rheumatism","url":"https://pubmed.ncbi.nlm.nih.gov/15248232","citation_count":40,"is_preprint":false},{"pmid":"24398859","id":"PMC_24398859","title":"RANK-mediated signaling network and cancer metastasis.","date":"2014","source":"Cancer metastasis reviews","url":"https://pubmed.ncbi.nlm.nih.gov/24398859","citation_count":40,"is_preprint":false},{"pmid":"15615493","id":"PMC_15615493","title":"Heritable disorders of the RANKL/OPG/RANK signaling pathway.","date":"2004","source":"Journal of musculoskeletal & neuronal interactions","url":"https://pubmed.ncbi.nlm.nih.gov/15615493","citation_count":35,"is_preprint":false},{"pmid":"33982033","id":"PMC_33982033","title":"RANKL and RANK in extracellular vesicles: surprising new players in bone remodeling.","date":"2021","source":"Extracellular vesicles and circulating nucleic acids","url":"https://pubmed.ncbi.nlm.nih.gov/33982033","citation_count":35,"is_preprint":false},{"pmid":"15615495","id":"PMC_15615495","title":"RANK, RANKL and OPG in inflammatory arthritis and periprosthetic osteolysis.","date":"2004","source":"Journal of musculoskeletal & neuronal interactions","url":"https://pubmed.ncbi.nlm.nih.gov/15615495","citation_count":34,"is_preprint":false},{"pmid":"21087090","id":"PMC_21087090","title":"Physiology and pathophysiology of the RANKL/RANK system.","date":"2010","source":"Biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21087090","citation_count":34,"is_preprint":false},{"pmid":"20564239","id":"PMC_20564239","title":"Genetic variation in the TNFRSF11A gene encoding RANK is associated with susceptibility to Paget's disease of bone.","date":"2010","source":"Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research","url":"https://pubmed.ncbi.nlm.nih.gov/20564239","citation_count":34,"is_preprint":false},{"pmid":"25864714","id":"PMC_25864714","title":"Correlating RANK ligand/RANK binding kinetics with osteoclast formation and function.","date":"2015","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/25864714","citation_count":33,"is_preprint":false},{"pmid":"33552088","id":"PMC_33552088","title":"RANK Signaling in the Differentiation and Regeneration of Thymic Epithelial Cells.","date":"2021","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/33552088","citation_count":32,"is_preprint":false},{"pmid":"12210731","id":"PMC_12210731","title":"Detection and characterization of RANK ligand and osteoprotegerin in the thyroid gland.","date":"2002","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12210731","citation_count":32,"is_preprint":false},{"pmid":"25063546","id":"PMC_25063546","title":"Juvenile Paget's disease with heterozygous duplication within TNFRSF11A encoding RANK.","date":"2014","source":"Bone","url":"https://pubmed.ncbi.nlm.nih.gov/25063546","citation_count":32,"is_preprint":false},{"pmid":"18228207","id":"PMC_18228207","title":"Role of OPG/RANKL/RANK axis on the vasculature.","date":"2008","source":"Histology and histopathology","url":"https://pubmed.ncbi.nlm.nih.gov/18228207","citation_count":31,"is_preprint":false},{"pmid":"19995704","id":"PMC_19995704","title":"OPG/RANK/RANKL signaling system and its significance in nephrology.","date":"2009","source":"Folia histochemica et cytobiologica","url":"https://pubmed.ncbi.nlm.nih.gov/19995704","citation_count":29,"is_preprint":false},{"pmid":"22929916","id":"PMC_22929916","title":"Bone metastasis in breast cancer: the story of RANK-ligand.","date":"2012","source":"Journal of the Egyptian National Cancer Institute","url":"https://pubmed.ncbi.nlm.nih.gov/22929916","citation_count":29,"is_preprint":false},{"pmid":"18843778","id":"PMC_18843778","title":"Circulating osteoprotegerin and soluble RANK ligand in systemic sclerosis.","date":"2008","source":"The Journal of rheumatology","url":"https://pubmed.ncbi.nlm.nih.gov/18843778","citation_count":29,"is_preprint":false},{"pmid":"30737962","id":"PMC_30737962","title":"An osteoclastogenesis system, the RANKL/RANK signalling pathway, contributes to aggravated allergic inflammation.","date":"2019","source":"British journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/30737962","citation_count":28,"is_preprint":false},{"pmid":"19416721","id":"PMC_19416721","title":"The affinity of human RANK binding to its ligand RANKL.","date":"2009","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/19416721","citation_count":28,"is_preprint":false},{"pmid":"28246602","id":"PMC_28246602","title":"NOTCH1 Mutations in Aortic Stenosis: Association with Osteoprotegerin/RANK/RANKL.","date":"2017","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/28246602","citation_count":28,"is_preprint":false},{"pmid":"22787434","id":"PMC_22787434","title":"RANK (TNFRSF11A) is epigenetically inactivated and induces apoptosis in gliomas.","date":"2012","source":"Neoplasia (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/22787434","citation_count":27,"is_preprint":false},{"pmid":"32971123","id":"PMC_32971123","title":"Ellagic acid blocks RANKL-RANK interaction and suppresses RANKL-induced osteoclastogenesis by inhibiting RANK signaling pathways.","date":"2020","source":"Chemico-biological interactions","url":"https://pubmed.ncbi.nlm.nih.gov/32971123","citation_count":27,"is_preprint":false},{"pmid":"21824970","id":"PMC_21824970","title":"Inferring disease and gene set associations with rank coherence in networks.","date":"2011","source":"Bioinformatics (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/21824970","citation_count":27,"is_preprint":false},{"pmid":"29348675","id":"PMC_29348675","title":"STAC2 negatively regulates osteoclast formation by targeting the RANK signaling complex.","date":"2018","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/29348675","citation_count":27,"is_preprint":false},{"pmid":"21987421","id":"PMC_21987421","title":"A nonsynonymous TNFRSF11A variation increases NFκB activity and the severity of Paget's disease.","date":"2012","source":"Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research","url":"https://pubmed.ncbi.nlm.nih.gov/21987421","citation_count":26,"is_preprint":false},{"pmid":"12923331","id":"PMC_12923331","title":"Expression of osteoprotegerin and RANK ligand in breast cancer bone metastasis.","date":"2003","source":"Journal of Korean medical science","url":"https://pubmed.ncbi.nlm.nih.gov/12923331","citation_count":26,"is_preprint":false},{"pmid":"20531232","id":"PMC_20531232","title":"TNFRSF11A and TNFSF11 are associated with age at menarche and natural menopause in white women.","date":"2010","source":"Menopause (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/20531232","citation_count":24,"is_preprint":false},{"pmid":"24147253","id":"PMC_24147253","title":"Role of RANKL/RANK in primary and secondary breast cancer.","date":"2013","source":"World journal of orthopedics","url":"https://pubmed.ncbi.nlm.nih.gov/24147253","citation_count":24,"is_preprint":false},{"pmid":"18928898","id":"PMC_18928898","title":"Expression of bone resorption regulators (RANK, RANKL, and OPG) in odontogenic tumors.","date":"2008","source":"Oral surgery, oral medicine, oral pathology, oral radiology, and endodontics","url":"https://pubmed.ncbi.nlm.nih.gov/18928898","citation_count":24,"is_preprint":false},{"pmid":"32544645","id":"PMC_32544645","title":"TNF-α stimulates the expression of RANK during orthodontic tooth movement.","date":"2020","source":"Archives of oral biology","url":"https://pubmed.ncbi.nlm.nih.gov/32544645","citation_count":24,"is_preprint":false},{"pmid":"17081156","id":"PMC_17081156","title":"Stress, social rank and leukocyte telomere length.","date":"2006","source":"Aging cell","url":"https://pubmed.ncbi.nlm.nih.gov/17081156","citation_count":23,"is_preprint":false},{"pmid":"24891336","id":"PMC_24891336","title":"Brief Report: Involvement of TNFRSF11A molecular defects in autoinflammatory disorders.","date":"2014","source":"Arthritis & rheumatology (Hoboken, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/24891336","citation_count":23,"is_preprint":false},{"pmid":"23139818","id":"PMC_23139818","title":"Cell adhesion signaling regulates RANK expression in osteoclast precursors.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23139818","citation_count":22,"is_preprint":false},{"pmid":"37561047","id":"PMC_37561047","title":"PASSerRank: Prediction of allosteric sites with learning to rank.","date":"2023","source":"Journal of computational chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37561047","citation_count":21,"is_preprint":false},{"pmid":"34545962","id":"PMC_34545962","title":"Uncertainty in denoising of MRSI using low-rank methods.","date":"2021","source":"Magnetic resonance in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34545962","citation_count":21,"is_preprint":false},{"pmid":"12426773","id":"PMC_12426773","title":"Osteoprotegerin, RANK, RANKL.","date":"2001","source":"Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia","url":"https://pubmed.ncbi.nlm.nih.gov/12426773","citation_count":21,"is_preprint":false},{"pmid":"21415639","id":"PMC_21415639","title":"Role of RANK-RANKL-OPG axis in cranial suture homeostasis.","date":"2011","source":"The Journal of craniofacial surgery","url":"https://pubmed.ncbi.nlm.nih.gov/21415639","citation_count":21,"is_preprint":false},{"pmid":"29568001","id":"PMC_29568001","title":"Dysosteosclerosis is also caused by TNFRSF11A mutation.","date":"2018","source":"Journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/29568001","citation_count":20,"is_preprint":false},{"pmid":"35012344","id":"PMC_35012344","title":"Disentangling the Evolutionary History of Feo, the Major Ferrous Iron Transport System in Bacteria.","date":"2022","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/35012344","citation_count":20,"is_preprint":false},{"pmid":"27430581","id":"PMC_27430581","title":"Pioglitazone affects the OPG/RANKL/RANK system and increase osteoclastogenesis.","date":"2016","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/27430581","citation_count":20,"is_preprint":false},{"pmid":"36194667","id":"PMC_36194667","title":"A20 controls RANK-dependent osteoclast formation and bone physiology.","date":"2022","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/36194667","citation_count":19,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":46101,"output_tokens":6195,"usd":0.115614},"stage2":{"model":"claude-opus-4-6","input_tokens":9878,"output_tokens":3864,"usd":0.218985},"total_usd":0.334599,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1998,\n      \"finding\": \"RANK (TNFRSF11A) was identified as the essential signaling receptor for osteoclast differentiation factor (ODF/RANKL) on osteoclast progenitors; soluble RANK and Fab antibody fragments blocked ODF binding to RANK and inhibited osteoclastogenesis, while anti-RANK polyclonal antibody stimulated osteoclastogenesis in the presence of M-CSF.\",\n      \"method\": \"Molecular cloning, receptor binding assay, antibody blocking, soluble receptor inhibition in osteoclast differentiation assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — direct receptor identification with functional blocking and activation experiments, foundational paper\",\n      \"pmids\": [\"9878548\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Heterozygous insertional duplications (18-bp and 27-bp) in exon 1 of TNFRSF11A affecting the RANK signal peptide cause familial expansile osteolysis; mutant RANK proteins showed perturbed expression levels, lack of normal signal peptide cleavage, and increased RANK-mediated NF-κB signaling in vitro, indicating gain-of-function activating mutations.\",\n      \"method\": \"Sequencing of patient samples, expression of recombinant mutant RANK proteins, NF-κB reporter assay\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — mutation characterization with recombinant protein expression and functional NF-κB signaling assay, strong evidence\",\n      \"pmids\": [\"10615125\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Expansile skeletal hyperphosphatasia (ESH) is caused by a 15-bp tandem duplication in the TNFRSF11A signal peptide, allelic to familial expansile osteolysis, and likely reflects increased NF-κB activity via activated RANK signaling.\",\n      \"method\": \"Molecular sequencing, genetic analysis\",\n      \"journal\": \"Journal of bone and mineral research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic identification with mechanistic inference from allelic relationship to functionally characterized FEO mutations\",\n      \"pmids\": [\"11771666\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"TRAF6 is an indispensable signaling adaptor for RANK in osteoclastogenesis; however, osteoclast differentiation can occur via a TRANCE-RANK-TRAF6-independent pathway when hematopoietic precursors from RANK-null or TRAF6-null mice are stimulated with TNF-alpha plus TGF-beta in vitro.\",\n      \"method\": \"Genetic knockout mouse models, in vitro osteoclast differentiation assay with cytokine stimulation\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis using null mice with clear cellular phenotype readout; replicated across TRANCE-, RANK-, and TRAF6-null models\",\n      \"pmids\": [\"16147974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"RANK self-assembles through its cytoplasmic domain at position 534-539 (distinct from TRAF binding domains) ligand-independently, and overexpression of oligomeric RANK induces osteoclastogenesis in a TRAF6-dependent manner without RANKL.\",\n      \"method\": \"Co-immunoprecipitation with FLAG/HA-tagged RANK constructs, C-terminal deletion mutants, osteoclast differentiation assay, TRAF6 decoy peptide inhibition\",\n      \"journal\": \"Journal of bone and mineral research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — reciprocal co-IP with deletion mapping plus functional osteoclastogenesis assay in single study\",\n      \"pmids\": [\"16234979\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"RANK interacts with five members of the TRAF family (TRAF1, 2, 3, 5, 6), of which TRAF6 is indispensable for RANK signaling capability and links RANKL-RANK interaction to downstream NF-κB activation and osteoclastogenic transcriptional programs.\",\n      \"method\": \"Review of biochemical interaction studies, genetic experiments\",\n      \"journal\": \"Advances in experimental medicine and biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — review summarizing established TRAF6-RANK interaction data from multiple labs\",\n      \"pmids\": [\"17633024\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"CYLD deubiquitinase negatively regulates RANK signaling by inhibiting TRAF6 ubiquitination, thereby suppressing downstream NF-κB and other signaling events; CYLD is recruited to TRAF6 through physical interaction with the adaptor p62, and CYLD deficiency leads to hyperresponsive RANKL-induced osteoclastogenesis and severe osteoporosis in mice.\",\n      \"method\": \"CYLD knockout mouse model, in vitro osteoclast differentiation assay, co-immunoprecipitation, ubiquitination assay\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO mouse with defined phenotype, co-IP, biochemical ubiquitination assay; multiple orthogonal methods in single study\",\n      \"pmids\": [\"18382763\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Mutations in TNFRSF11A (RANK) cause autosomal recessive osteoclast-poor osteopetrosis with hypogammaglobulinemia; patient monocytes failed to differentiate into osteoclasts upon M-CSF and RANKL stimulation, establishing an osteoclast-intrinsic defect, and immunological analysis showed impairment of immunoglobulin-secreting B cells.\",\n      \"method\": \"TNFRSF11A sequencing in patients, in vitro osteoclast differentiation assay with patient monocytes, immunological phenotyping\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function mutations in multiple unrelated families with direct functional validation of osteoclast and B cell defects\",\n      \"pmids\": [\"18606301\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"RANKL stimulation of mature osteoclasts via RANK results in translocation of NF-κB to the nucleus and elevation of cytosolic and nuclear calcium levels, demonstrating functional RANK expression in mature (not only precursor) osteoclasts.\",\n      \"method\": \"Microisolation of pure osteoclast populations, RT-PCR, NF-κB nuclear translocation assay, calcium signaling measurement\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct functional assay in purified primary cells with multiple signaling readouts\",\n      \"pmids\": [\"10606741\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The extracellular domain of RANK binds RANKL as a monomer, while RANKL exists as a trimer; the binding affinity (KD ~1.09 × 10⁻¹⁰ M) was measured by surface plasmon resonance, establishing the high-affinity nature of the RANK-RANKL interaction.\",\n      \"method\": \"Recombinant protein expression and purification, gel filtration, chemical cross-linking, surface plasmon resonance\",\n      \"journal\": \"Archives of biochemistry and biophysics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with quantitative biophysical measurement of binding affinity\",\n      \"pmids\": [\"19416721\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Crystal structures of unliganded RANK and the RANKL-RANK complex revealed that RANK has four full cysteine-rich domains (CRDs), with CRD4 stabilized by a sodium ion and a rigid linkage to CRD3; upon RANKL binding, RANK undergoes a hinge movement between CRD2 and CRD3 to form continuous close contact with RANKL. Mutations reducing RANK-RANKL affinity significantly disrupted osteoclast formation.\",\n      \"method\": \"X-ray crystallography of RANK alone and in complex with RANKL, site-directed mutagenesis, osteoclast formation assay\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structures of free and complexed receptor with mutagenesis functional validation\",\n      \"pmids\": [\"20483727\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"RANK is expressed by monocytes and RANKL stimulates monocyte chemotaxis via RANK through activation of phosphatidylinositol 3-kinase, phosphodiesterase, and Src kinase pathways; chemotaxis was blocked by osteoprotegerin (decoy receptor for RANKL).\",\n      \"method\": \"Micropore filter migration assay, signaling enzyme inhibitors, Western blotting, RT-PCR, flow cytometry\",\n      \"journal\": \"Arthritis and rheumatism\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct functional assay with pathway inhibitors and receptor expression confirmation\",\n      \"pmids\": [\"15248232\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"miR-503 directly targets RANK mRNA (TNFRSF11A) and inhibits RANKL-induced osteoclastogenesis; overexpression of miR-503 reduced RANK protein levels and inhibited osteoclast differentiation in CD14+ PBMCs and in vivo in ovariectomized mice.\",\n      \"method\": \"miRNA target validation, overexpression/knockdown in primary cells and in vivo (antagomir/agomir), osteoclast differentiation assay, RANK protein quantification\",\n      \"journal\": \"Journal of bone and mineral research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct target validation with in vitro and in vivo functional evidence for RANK as miR-503 target\",\n      \"pmids\": [\"23821519\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"RANK signaling in luminal mammary progenitors amplifies WNT responsiveness through upregulation of R-spondin1; loss of RANK prevents proliferation of hormone receptor-negative luminal progenitors and basal cells, suppresses WNT activation, and impairs lobuloalveologenesis. Exogenous R-spondin1 rescues key aspects of RANK deficiency.\",\n      \"method\": \"Conditional RANK knockout mouse model, human breast tissue analysis, WNT pathway reporter, exogenous R-spondin1 rescue experiment\",\n      \"journal\": \"Stem cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — conditional KO with defined phenotype and epistasis rescue experiment; multiple orthogonal methods\",\n      \"pmids\": [\"26095608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Constitutive RANK signaling in mammary epithelial cells expands luminal and basal mammary compartments including mammary stem and progenitor cell pools, impairs normal luminal cell commitment, accumulates K14+K8+ bipotent cells, and leads to formation of heterogeneous mammary tumors.\",\n      \"method\": \"Transgenic mouse model with constitutive RANK expression, FACS analysis of mammary cell populations, histology\",\n      \"journal\": \"Stem cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — gain-of-function mouse model with defined cellular phenotype readout\",\n      \"pmids\": [\"23766243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Genetic inactivation of RANK in mammary epithelium markedly delayed onset, reduced incidence, and attenuated progression of Brca1;p53 mutation-driven mammary cancer; RANK/RANKL blockade impaired proliferation and expansion of Brca1;p53 mutant mammary stem cells and progenitors from human BRCA1 mutation carriers.\",\n      \"method\": \"Conditional RANK knockout in two mouse models, pharmacological RANKL inhibition, in vitro progenitor proliferation assay with human BRCA1-mutant tissue\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — two independent mouse models with conditional KO, human tissue validation, multiple orthogonal approaches\",\n      \"pmids\": [\"27241552\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RANK-independent osteoclastogenesis and bone erosion can occur in inflammatory arthritis via a TNF/IL-6-dependent pathway requiring IL-6R, NFATc1, DNAX-activation protein 12 (DAP12), and cell proliferation but not RANKL or RANK; arthritic mice with inducible RANK deficiency still exhibited bone erosion and synovial osteoclasts.\",\n      \"method\": \"Conditional RANK knockout mouse model, K/BxN serum-transfer arthritis model, in vitro osteoclast differentiation from RANK-null precursors, micro-CT, histology\",\n      \"journal\": \"Arthritis & rheumatology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — conditional KO with in vivo and in vitro validation demonstrating RANK-independent pathway\",\n      \"pmids\": [\"27563728\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"STAC2 is a RANKL-inducible protein that physically interacts with RANK and negatively regulates osteoclast formation by inhibiting formation of the RANK signaling complex (containing Gab2 and PLCγ2) and suppressing NF-κB, MAPK activation, and Btk/Tec-mediated PLCγ2 phosphorylation.\",\n      \"method\": \"Co-immunoprecipitation, overexpression, NF-κB and MAPK reporter assays, osteoclast differentiation assay\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — co-IP with functional signaling and differentiation assays in single study\",\n      \"pmids\": [\"29348675\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"RANKL variants with higher affinity for RANK produce more robust downstream signaling and greater osteoclastogenic potential; the relationship between RANKL-RANK affinity and osteoclastogenesis is biphasic and driven entirely by the kinetic off-rate, indicating that physiological RANKL-RANK interaction is not optimized for maximal signaling.\",\n      \"method\": \"Yeast surface display, random mutagenesis library screening, surface plasmon resonance binding kinetics, in vitro osteoclast differentiation assay\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro reconstitution with binding kinetics and functional osteoclast assay; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"25864714\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"A20 is rapidly recruited to the RANK receptor complex within minutes of RANKL binding and restrains NF-κB activation; this inhibition is independent of A20's deubiquitinating activity but requires its zinc finger (ZnF) 4 and 7 ubiquitin-binding functions. Osteoclast-specific A20 knockout mice develop severe osteoporosis with hyperresponsive RANKL-induced osteoclastogenesis.\",\n      \"method\": \"Osteoclast-specific conditional A20 knockout mouse, in vitro osteoclast differentiation, co-immunoprecipitation of RANK complex, domain-specific mutants, NF-κB reporter assay\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — conditional KO with in vivo and in vitro phenotype, biochemical complex recruitment, domain mutagenesis to separate deubiquitinating from ubiquitin-binding functions\",\n      \"pmids\": [\"36194667\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"TNFRSF11A (RANK) promoter is epigenetically silenced by CpG methylation in gliomas; demethylation with 5-aza-2'-deoxycytidine restores RANK expression, and RANK overexpression in glioblastoma cells reduces focus formation and increases apoptosis through activation of apoptosis-regulatory signaling pathways.\",\n      \"method\": \"Pyrosequencing methylation analysis, demethylating agent treatment, RANK overexpression, focus formation assay, flow cytometry for apoptosis, reporter assay\",\n      \"journal\": \"Neoplasia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epigenetic silencing demonstrated with functional rescue by demethylation and overexpression with apoptosis readout\",\n      \"pmids\": [\"22787434\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"A frameshift mutation (p.Met416Cysfs*110) in TNFRSF11A causes hereditary recurrent fever with increased secretion of inflammatory cytokines (TNFα, IL-18, IL-1Ra, IFN-γ) and altered NF-κB signaling; a chromosomal duplication of TNFRSF11A also causes hereditary recurrent fever, implicating RANK in innate immune regulation and fever.\",\n      \"method\": \"Array-CGH, sequencing, serum cytokine multiplex measurement (Luminex), NF-κB luciferase reporter assay with wild-type and mutant RANK\",\n      \"journal\": \"Arthritis & rheumatology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic identification with functional NF-κB assay and cytokine profiling\",\n      \"pmids\": [\"24891336\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"A novel splice-site mutation (c.616+3A>G) in TNFRSF11A causing exon 6 skipping and frameshift leads to dysosteosclerosis (autosomal recessive sclerosing bone disease), expanding the phenotypic spectrum of TNFRSF11A loss-of-function mutations.\",\n      \"method\": \"Whole-exome sequencing, exon trapping assay to demonstrate exon skipping\",\n      \"journal\": \"Journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic mutation with direct functional demonstration of splicing effect by exon trapping\",\n      \"pmids\": [\"29568001\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Cell adhesion signaling regulates RANK expression in osteoclast precursors; BMMs under adherent conditions express high RANK and differentiate efficiently into osteoclasts in response to RANKL, while non-adherent conditions reduce RANK expression and impair RANKL-mediated NF-κB signaling. Forced RANK or TRAF6 overexpression rescues osteoclastogenesis under non-adherent conditions.\",\n      \"method\": \"Adherent vs. non-adherent culture system, RT-PCR, Western blot, RGD-disintegrin inhibition, forced RANK/TRAF6 overexpression, osteoclast differentiation assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — defined experimental system with rescue experiment establishing RANK expression as downstream of adhesion signaling\",\n      \"pmids\": [\"23139818\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"TGF-β1 directly stimulates osteoclast differentiation of pre-osteoclastic RAW 264.7 cells in the presence of M-CSF and RANKL, and dose- and time-dependently increases RANK mRNA and protein expression in these cells.\",\n      \"method\": \"Osteoclast differentiation assay (TRAP staining), RT-PCR, flow cytometry with fluorescent RANKL probe\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct in vitro functional assay with RANK expression quantification at mRNA and protein levels\",\n      \"pmids\": [\"11573248\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"TRANCE (RANKL)-RANK interaction sustains the longevity of interstitial dendritic cells (derived from CD34+ progenitors) that co-express TRANCE and RANK; soluble RANK reduces viability and Bcl-2 expression of these cells, while CD1a+ DCs expressing only RANK are rescued from cell death by exogenous TRANCE or by TRANCE-expressing DCs.\",\n      \"method\": \"CD34+ progenitor culture, flow cytometry, soluble RANK treatment, viability assay, Bcl-2 expression analysis\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct functional experiment with receptor-ligand blocking and survival readout in primary human cells\",\n      \"pmids\": [\"12393586\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RANK (TNFRSF11A) is a TNF receptor superfamily member that functions as the essential receptor for RANKL on osteoclast precursors and mature osteoclasts, forming a high-affinity complex (KD ~10⁻¹⁰ M) in which RANK undergoes a CRD2-CRD3 hinge conformational change; RANKL binding recruits TRAF6 (and other TRAFs) to the cytoplasmic domain, activating NF-κB, MAPK, and calcium signaling to drive osteoclast differentiation, activation, and survival, while negative regulators including CYLD (via TRAF6 deubiquitination), A20 (via ubiquitin-binding ZnF domains at the RANK complex), and STAC2 (by disrupting the Gab2/PLCγ2 complex) restrain signaling; RANK also self-assembles via cytoplasmic residues 534-539 to signal ligand-independently, regulates mammary progenitor expansion via R-spondin1/WNT, controls dendritic cell and thymic epithelial cell survival, and loss-of-function mutations cause osteoclast-poor osteopetrosis with immunodeficiency, while gain-of-function signal peptide insertions cause familial expansile osteolysis and related hyperresorptive bone diseases through constitutive NF-κB activation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TNFRSF11A (RANK) is the obligate receptor for RANKL that drives osteoclast differentiation, bone resorption, mammary progenitor expansion, and dendritic cell survival through TRAF6-dependent activation of NF-κB, MAPK, and calcium signaling. The RANK extracellular domain binds trimeric RANKL as a monomer with high affinity (KD ~10⁻¹⁰ M), undergoing a CRD2-CRD3 hinge conformational change that triggers cytoplasmic recruitment of TRAF6 and assembly of a signaling complex containing Gab2 and PLCγ2, which is negatively regulated by the deubiquitinase CYLD (via TRAF6 deubiquitination), A20 (via ubiquitin-binding zinc finger domains recruited directly to the RANK complex), and STAC2 (which disrupts the Gab2/PLCγ2 complex) [PMID:9878548, PMID:20483727, PMID:19416721, PMID:16147974, PMID:18382763, PMID:36194667, PMID:29348675]. In mammary epithelium, RANK signaling amplifies WNT responsiveness through R-spondin1 upregulation, expanding luminal progenitors; genetic RANK inactivation delays BRCA1-mutant mammary tumorigenesis [PMID:26095608, PMID:27241552]. Loss-of-function TNFRSF11A mutations cause autosomal recessive osteoclast-poor osteopetrosis with hypogammaglobulinemia, while gain-of-function signal-peptide insertions cause familial expansile osteolysis and related hyperresorptive bone diseases through constitutive NF-κB activation [PMID:18606301, PMID:10615125, PMID:11771666].\",\n  \"teleology\": [\n    {\n      \"year\": 1998,\n      \"claim\": \"Identification of RANK as the essential receptor transducing RANKL signals in osteoclast progenitors resolved how osteoclastogenic cytokine signaling is received at the cell surface, establishing RANK as the central receptor in bone resorption.\",\n      \"evidence\": \"Molecular cloning, soluble receptor and Fab blocking of ODF binding, and anti-RANK antibody stimulation of osteoclastogenesis in vitro\",\n      \"pmids\": [\"9878548\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream intracellular signaling adaptors not yet mapped\", \"Role in non-bone tissues unknown\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Discovery that heterozygous signal-peptide insertions in TNFRSF11A cause familial expansile osteolysis through constitutive NF-κB activation established the first gain-of-function disease mechanism for RANK and linked aberrant receptor processing to ligand-independent signaling.\",\n      \"evidence\": \"Patient sequencing, recombinant mutant RANK expression, NF-κB reporter assay; allelic ESH mutation identified in 2002\",\n      \"pmids\": [\"10615125\", \"11771666\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Precise mechanism by which uncleaved signal peptide activates signaling not resolved\", \"Whether mutations promote receptor oligomerization or trafficking defects unclear\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Demonstration that RANK-RANKL interaction sustains dendritic cell survival via Bcl-2 extended RANK function beyond bone biology to immune cell homeostasis.\",\n      \"evidence\": \"Soluble RANK blocking and exogenous TRANCE rescue of CD34+-derived dendritic cell viability with Bcl-2 quantification\",\n      \"pmids\": [\"12393586\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Intracellular signaling pathway mediating DC survival through RANK not delineated\", \"In vivo validation in DC-specific RANK KO not performed\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Genetic epistasis using RANK-null and TRAF6-null mice confirmed TRAF6 as the indispensable cytoplasmic adaptor for RANK-mediated osteoclastogenesis, while revealing a RANK-independent TNF-α/TGF-β backup pathway.\",\n      \"evidence\": \"In vitro osteoclast differentiation from RANK-null and TRAF6-null hematopoietic precursors with TNF-α/TGF-β stimulation\",\n      \"pmids\": [\"16147974\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of the RANK-independent backup pathway unresolved at this point\", \"Other TRAFs' individual contributions not dissected\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Mapping of a RANK cytoplasmic self-assembly domain (residues 534–539) distinct from TRAF-binding sites showed that RANK can oligomerize and signal ligand-independently, providing a mechanism for how gain-of-function mutations may constitutively activate the receptor.\",\n      \"evidence\": \"Co-immunoprecipitation of FLAG/HA-tagged RANK deletion mutants, TRAF6 decoy peptide inhibition, osteoclast differentiation assay\",\n      \"pmids\": [\"16234979\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Crystal structure of cytoplasmic domain oligomer not obtained\", \"Self-assembly not validated with biophysical methods beyond co-IP\", \"Physiological stoichiometry on cell surface not determined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Identification of CYLD as a negative regulator that deubiquitinates TRAF6 via p62-mediated recruitment to the RANK complex established the first checkpoint mechanism restraining RANK-driven osteoclastogenesis, with CYLD-null mice displaying severe osteoporosis.\",\n      \"evidence\": \"CYLD knockout mouse, co-IP of CYLD-p62-TRAF6, ubiquitination assays, osteoclast differentiation\",\n      \"pmids\": [\"18382763\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether CYLD acts on other ubiquitin chain types beyond K63 at the RANK complex not fully resolved\", \"Relative contributions of CYLD versus other DUBs not compared\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Discovery that loss-of-function TNFRSF11A mutations cause autosomal recessive osteopetrosis with hypogammaglobulinemia proved that RANK is non-redundant for both osteoclast formation and B cell terminal differentiation in humans.\",\n      \"evidence\": \"Patient TNFRSF11A sequencing, failed in vitro osteoclast differentiation from patient monocytes, immunological phenotyping\",\n      \"pmids\": [\"18606301\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of RANK requirement for immunoglobulin-secreting B cells not elucidated\", \"Thymic epithelial cell involvement in patients not assessed\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Quantitative biophysical measurement of the RANK-RANKL interaction (KD ~1.09 × 10⁻¹⁰ M, monomeric RANK binding trimeric RANKL) provided the affinity benchmark needed to interpret how signaling strength relates to receptor occupancy.\",\n      \"evidence\": \"Recombinant protein SPR, gel filtration, and chemical cross-linking\",\n      \"pmids\": [\"19416721\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"On-cell binding parameters may differ from solution measurements\", \"Effect of membrane context and pre-assembly not captured\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Crystal structures of free RANK and the RANKL–RANK complex revealed a four-CRD architecture with a CRD2-CRD3 hinge conformational change upon ligand binding, providing the first atomic-resolution view of how RANKL engages its receptor.\",\n      \"evidence\": \"X-ray crystallography of unliganded and complexed RANK, site-directed mutagenesis with osteoclast formation assay\",\n      \"pmids\": [\"20483727\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length receptor structure including transmembrane and cytoplasmic domains unavailable\", \"How extracellular conformational change transmits to cytoplasmic TRAF recruitment not structurally resolved\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Constitutive RANK signaling in mammary epithelium expanded stem/progenitor populations and disrupted luminal commitment, establishing RANK as a driver of mammary cell fate and tumorigenesis beyond its skeletal role.\",\n      \"evidence\": \"Transgenic mouse model with constitutive RANK expression, FACS of mammary populations, histology\",\n      \"pmids\": [\"23766243\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream transcriptional program in mammary progenitors not fully mapped\", \"Whether RANK acts cell-autonomously or via paracrine WNT not separated at this stage\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Conditional RANK knockout in mammary epithelium revealed that RANK amplifies WNT signaling through R-spondin1, and exogenous R-spondin1 rescue demonstrated epistasis, placing RANK upstream of WNT in mammary progenitor expansion.\",\n      \"evidence\": \"Conditional RANK KO mouse, WNT reporter, R-spondin1 rescue, human breast tissue analysis\",\n      \"pmids\": [\"26095608\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct transcriptional mechanism linking RANK signaling to R-spondin1 gene induction not identified\", \"Whether this axis operates in human breast cancer in vivo unclear\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Genetic RANK inactivation in mammary epithelium delayed BRCA1/p53-driven breast cancer onset and pharmacological RANKL inhibition suppressed human BRCA1-mutant progenitor expansion, establishing RANK as a therapeutic target in hereditary breast cancer.\",\n      \"evidence\": \"Two conditional RANK KO mouse models, pharmacological RANKL inhibition, human BRCA1-mutant tissue progenitor assays\",\n      \"pmids\": [\"27241552\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Long-term efficacy of RANKL inhibition in breast cancer prevention trials not established\", \"Whether RANK-independent compensatory pathways emerge over time not tested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Demonstration that RANK-independent osteoclastogenesis occurs in inflammatory arthritis via TNF/IL-6/DAP12 defined the limits of RANK's non-redundancy and explained clinical observations of bone erosion despite RANKL blockade.\",\n      \"evidence\": \"Conditional RANK KO in K/BxN serum-transfer arthritis model, in vitro differentiation from RANK-null precursors, micro-CT\",\n      \"pmids\": [\"27563728\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative quantitative contribution of RANK-dependent vs RANK-independent osteoclasts in human arthritis not measured\", \"Whether RANK-independent osteoclasts are functionally equivalent not determined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identification of STAC2 as a RANKL-inducible negative feedback inhibitor that disrupts the Gab2/PLCγ2 signaling complex at RANK added a second layer of intrinsic restraint distinct from the CYLD/A20 deubiquitination axis.\",\n      \"evidence\": \"Co-immunoprecipitation of STAC2-RANK, NF-κB/MAPK reporters, osteoclast differentiation assay\",\n      \"pmids\": [\"29348675\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo validation in STAC2-deficient mice not reported\", \"Structural basis of STAC2 interaction with RANK not determined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Discovery that A20 is recruited to the RANK complex within minutes and restrains NF-κB via ubiquitin-binding ZnF4/7 domains (not its deubiquitinase activity) revealed a mechanistically distinct negative regulator and explained severe osteoporosis in osteoclast-specific A20 knockouts.\",\n      \"evidence\": \"Osteoclast-specific conditional A20 KO mouse, co-IP of RANK complex, ZnF domain mutants, NF-κB reporter\",\n      \"pmids\": [\"36194667\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of A20 recruitment to RANK complex not determined\", \"Whether CYLD and A20 act redundantly or sequentially at the RANK complex not resolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RANK's extracellular conformational change upon RANKL binding is mechanically transmitted through the transmembrane domain to initiate cytoplasmic TRAF6 recruitment remains structurally unresolved, and no full-length RANK structure exists.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length RANK structure including transmembrane and cytoplasmic domains not solved\", \"Temporal order and cooperativity of TRAF6, CYLD, A20, and STAC2 assembly at the receptor not defined\", \"Whether RANK's mammary WNT-amplifying function uses the same or distinct cytoplasmic signaling complexes as osteoclastogenesis unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [0, 8, 9, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 8, 9, 10, 11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 5, 6, 8, 17, 19]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [7, 21, 25]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [13, 14, 15]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [20, 25]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [1, 2, 7, 22]}\n    ],\n    \"complexes\": [\n      \"RANK-RANKL signaling complex\",\n      \"RANK-TRAF6 complex\"\n    ],\n    \"partners\": [\n      \"TNFSF11\",\n      \"TRAF6\",\n      \"CYLD\",\n      \"TNFAIP3\",\n      \"STAC2\",\n      \"GAB2\",\n      \"PLCG2\",\n      \"SQSTM1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}