{"gene":"FNIP2","run_date":"2026-04-28T17:46:04","timeline":{"discoveries":[{"year":2008,"finding":"FNIP2 interacts with folliculin (FLCN) and AMPK, forming a trimeric complex; C-terminally deleted FLCN mutants (mimicking BHD germline mutations) cannot bind FNIP2, indicating the interaction requires the FLCN C-terminus. FNIP1 and FNIP2 can form homo- or heteromeric multimers with each other.","method":"Co-immunoprecipitation, yeast two-hybrid, deletion mutant analysis","journal":"Gene","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP replicated across two independent labs (PMID:18403135 and PMID:18663353)","pmids":["18403135","18663353"],"is_preprint":false},{"year":2008,"finding":"FNIP2 retains FLCN in the cytoplasm in a reticular pattern through their complex formation; C-terminal truncation of FNIP2 abolishes this cytoplasmic retention, causing FLCN to relocalize to the nucleus.","method":"Fluorescence microscopy, co-localization, C-terminal truncation mutants","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization experiment with functional consequence, single lab","pmids":["18663353"],"is_preprint":false},{"year":2008,"finding":"Knockdown of FNIP1 and FNIP2 (via siRNA) reduces S6K1 phosphorylation, indicating that FLCN-FNIP2 and FLCN-FNIP1 complexes positively regulate mTORC1-dependent S6K1 phosphorylation.","method":"siRNA knockdown, western blot for S6K1 phosphorylation","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — KD with defined signaling phenotype, single lab","pmids":["18663353"],"is_preprint":false},{"year":2019,"finding":"Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex reveals that FLCN-FNIP2 functions as a GTPase-activating protein (GAP) for RagC/D GTPases; FLCN and FNIP2 heterodimerize through their Longin domains (which contact both nucleotide-binding domains of the Rag heterodimer) and their DENN domains (which interact distally); a conserved arginine on FLCN acts as the catalytic arginine finger for GAP activity.","method":"Cryo-EM structure determination, biochemical GAP assays, arginine finger mutagenesis","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structure with biochemical validation and active-site mutagenesis in a single high-impact study","pmids":["31704029"],"is_preprint":false},{"year":2009,"finding":"FNIP2 (MAPO1) is required for apoptosis triggered by O6-methylguanine DNA damage; FNIP2-deficient cells show suppressed MNU-induced apoptosis, with loss of mitochondrial membrane depolarization and caspase-3 activation, while p53, CHK1, and H2AX phosphorylation remain intact, placing FNIP2 downstream of DNA damage signaling but upstream of mitochondrial apoptosis.","method":"Retroviral gene-trap mutagenesis, siRNA knockdown, mitochondrial membrane potential assay, caspase-3 activation assay","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis by loss-of-function with defined pathway placement and multiple orthogonal phenotypic readouts, single lab","pmids":["19137017"],"is_preprint":false},{"year":2011,"finding":"FNIP2 (MAPO1) forms a complex with AMPK and FLCN that is required for AMPK activation in response to O6-methylguanine damage; knockdown of FNIP2 or FLCN prevents AMPKα phosphorylation after MNU treatment; AMPK activation in this context is MLH1-dependent and leads to mitochondrial membrane depolarization and cell death.","method":"siRNA knockdown, western blot for AMPKα phosphorylation, mitochondrial membrane depolarization assay, AICAR stimulation","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 2 — KD with defined signaling phenotype and pathway epistasis, single lab replicated across two papers","pmids":["22209521"],"is_preprint":false},{"year":2012,"finding":"FNIP2 (MAPO1) protein stability is regulated by FLCN and AMPK: FLCN binding stabilizes FNIP2 (FLCN knockdown reduces FNIP2 levels and prevents its MNU-induced stabilization), whereas AMPK binding promotes FNIP2 degradation (AMPKα knockdown stabilizes FNIP2 basally); after MNU treatment FNIP2 dissociates from AMPK but maintains FLCN binding, and FNIP2 is subject to proteasome-mediated degradation.","method":"Immunoblotting, siRNA knockdown, proteasome inhibitor (MG132) and protein synthesis inhibitor (cycloheximide) treatment, co-immunoprecipitation","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal biochemical approaches, single lab","pmids":["23201403"],"is_preprint":false},{"year":2014,"finding":"A frameshift mutation in canine FNIP2 results in hypomyelination of the brain and a tract-specific myelin defect in the spinal cord, with loss of mature oligodendrocytes in peripheral spinal cord tracts, establishing a role for FNIP2 in oligodendrocyte maturation and CNS myelination.","method":"Genome-wide association study, gene sequencing, histopathology of CNS tissue from affected dogs","journal":"Glia","confidence":"Medium","confidence_rationale":"Tier 2 — natural loss-of-function mutation with defined cellular phenotype (oligodendrocyte maturation), single study","pmids":["24272703"],"is_preprint":false},{"year":2023,"finding":"Transcription factors MEF2A and MEF2D directly regulate FNIP2 transcription, and SRC phosphorylates MEF2D at three conserved tyrosines to enhance this transcriptional activity; increased FNIP2 (as part of FLCN-FNIP2 complex acting as RRAGC/D GAP) promotes MTORC1 lysosomal recruitment and activation in pancreatic cancer cells.","method":"ChIP, siRNA/shRNA knockdown, phospho-mutagenesis, lysosomal fractionation, mTORC1 activity assays","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods in single lab establishing transcriptional regulation and downstream signaling","pmids":["37772772"],"is_preprint":false},{"year":2026,"finding":"FNIP2 interacts with the SERCA2b calcium channel; inactivation of FNIP2 enhances cytoplasmic calcium availability, stimulating mitochondrial respiration and increasing glucose consumption, thereby preventing glycogen accumulation and improving survival in Ataxia Telangiectasia cells.","method":"Co-immunoprecipitation (FNIP2-SERCA2b), FNIP2 knockdown/knockout, metabolomics, flux analysis, bioenergetic measurements, electron tomography","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 — novel binding partner identified by Co-IP with multiple functional readouts, single lab","pmids":["41771847"],"is_preprint":false},{"year":2024,"finding":"In melanoma cells, MITF directly or indirectly activates transcription of FNIP2 (together with FNIP1 and FLCN); elevated FNIP2/FNIP1/FLCN promotes cytoplasmic retention and lysosome-mediated degradation of TFE3, suppressing the mesenchymal/invasive melanoma state.","method":"Genetic deletion of TFE3, FNIP2 expression analysis, lysosomal degradation assay, migration/metastasis assays","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 — preprint, FNIP2-specific mechanistic detail is inferred within a broader pathway study","pmids":["bio_10.1101_2024.07.11.603140"],"is_preprint":true}],"current_model":"FNIP2 functions as an obligate heterodimer partner of folliculin (FLCN), forming an extended complex in which Longin and DENN domain pairs heterodimerize; together FLCN-FNIP2 acts as a GTPase-activating protein (GAP) for RagC/D GTPases (using a conserved FLCN arginine finger), thereby promoting lysosomal recruitment and activation of mTORC1 in response to nutrients; additionally, FNIP2 participates in AMPK-dependent apoptosis signaling triggered by O6-methylguanine DNA damage, interacts with the SERCA2b calcium channel to regulate mitochondrial respiration, and is required for normal oligodendrocyte maturation and CNS myelination."},"narrative":{"teleology":[{"year":2008,"claim":"Identifying FNIP2 as a direct FLCN- and AMPK-binding partner established that a second folliculin-interacting protein exists and that BHD-associated FLCN truncations disrupt this interaction, framing FNIP2 within the tumor-suppressor pathway.","evidence":"Reciprocal co-immunoprecipitation and yeast two-hybrid in two independent labs with deletion mutant mapping","pmids":["18403135","18663353"],"confidence":"High","gaps":["Stoichiometry and competitive versus cooperative binding between FNIP1 and FNIP2 on FLCN not resolved","Whether FNIP2 has FLCN-independent functions was untested"]},{"year":2008,"claim":"Demonstrating that FNIP2 retains FLCN in the cytoplasm and that knockdown of FNIP1/FNIP2 reduces S6K1 phosphorylation placed the FLCN–FNIP2 complex upstream of mTORC1 signaling.","evidence":"Fluorescence microscopy with truncation mutants and siRNA knockdown with pS6K1 western blot","pmids":["18663353"],"confidence":"Medium","gaps":["Whether FNIP2-dependent cytoplasmic retention is the mechanism of mTORC1 regulation or an independent function was unclear","Single-lab observation without independent replication at the time"]},{"year":2009,"claim":"Showing that FNIP2 loss suppresses O6-methylguanine-induced apoptosis without affecting upstream DNA damage checkpoints positioned FNIP2 as a dedicated mediator between mismatch-repair signaling and mitochondrial cell death.","evidence":"Gene-trap mutagenesis and siRNA in MNU-treated cells with mitochondrial membrane potential and caspase-3 readouts","pmids":["19137017"],"confidence":"Medium","gaps":["Direct target of FNIP2 in the apoptotic cascade was unidentified","Relevance outside alkylating-agent context not tested"]},{"year":2011,"claim":"Linking FNIP2 and FLCN to MLH1-dependent AMPKα phosphorylation after O6-methylguanine damage identified AMPK activation as the specific step requiring FNIP2 in the apoptotic pathway.","evidence":"siRNA knockdown of FNIP2 and FLCN with pAMPKα western blot and AICAR stimulation","pmids":["22209521"],"confidence":"Medium","gaps":["Mechanism by which FNIP2 facilitates AMPK phosphorylation (scaffold vs. conformational) was unknown","Whether this AMPK-dependent function is separable from mTORC1 regulation was not addressed"]},{"year":2012,"claim":"Establishing that FLCN stabilizes FNIP2 while AMPK binding promotes its proteasomal degradation revealed a reciprocal regulatory loop controlling FNIP2 protein levels during stress.","evidence":"Cycloheximide chase, MG132 treatment, and co-IP after siRNA knockdown of FLCN or AMPKα","pmids":["23201403"],"confidence":"Medium","gaps":["Ubiquitin ligase responsible for FNIP2 degradation was not identified","Post-translational modification sites on FNIP2 mediating stability changes were unmapped"]},{"year":2014,"claim":"A natural canine FNIP2 frameshift mutation causing CNS hypomyelination demonstrated an in vivo requirement for FNIP2 in oligodendrocyte maturation, extending its biological roles beyond cancer signaling.","evidence":"GWAS, gene sequencing, and CNS histopathology in affected dogs","pmids":["24272703"],"confidence":"Medium","gaps":["Molecular mechanism linking FNIP2 to oligodendrocyte differentiation was not determined","Whether mTORC1 or AMPK dysregulation underlies the myelination defect was untested"]},{"year":2019,"claim":"The cryo-EM structure of the FLCN–FNIP2–Rag–Ragulator complex resolved the molecular basis of nutrient-dependent mTORC1 activation: FLCN and FNIP2 heterodimerize via Longin and DENN domain pairs, and FLCN contributes a catalytic arginine finger for RagC/D GAP activity.","evidence":"Cryo-EM structure determination with biochemical GAP assays and arginine-finger mutagenesis","pmids":["31704029"],"confidence":"High","gaps":["Conformational transitions that release FLCN–FNIP2 from the lysosome upon nutrient withdrawal were not captured","Whether FNIP2 contributes catalytic residues beyond the scaffold role was not addressed"]},{"year":2023,"claim":"Identifying MEF2A/D-driven and SRC-enhanced transcriptional control of FNIP2 revealed how oncogenic signaling in pancreatic cancer amplifies FLCN–FNIP2 GAP activity to hyperactivate mTORC1.","evidence":"ChIP, siRNA/shRNA, phospho-mutagenesis, lysosomal fractionation, and mTORC1 activity assays in pancreatic cancer cells","pmids":["37772772"],"confidence":"Medium","gaps":["Whether MEF2-SRC regulation of FNIP2 operates in non-cancer contexts was unknown","Relative contribution of FNIP2 versus FNIP1 in this transcriptional program was not dissected"]},{"year":2026,"claim":"Discovery of a direct FNIP2–SERCA2b interaction showed that FNIP2 restrains cytoplasmic calcium availability; its loss boosts mitochondrial respiration and glucose consumption, linking FNIP2 to calcium-dependent metabolic control.","evidence":"Co-IP of FNIP2–SERCA2b, FNIP2 knockout, metabolomics, flux analysis, and electron tomography in Ataxia Telangiectasia cells","pmids":["41771847"],"confidence":"Medium","gaps":["Whether FNIP2 modulates SERCA2b enzymatic activity or simply sequesters it is unresolved","Generalizability beyond ATM-deficient cells not demonstrated","Relationship between SERCA2b binding and FLCN–FNIP2 complex formation is undefined"]},{"year":null,"claim":"Key unresolved questions include whether FNIP2 has catalytic contributions to GAP activity beyond scaffolding, the identity of the E3 ligase controlling FNIP2 turnover, the molecular pathway through which FNIP2 loss impairs oligodendrocyte maturation, and whether FNIP2's calcium-regulatory and mTORC1 functions are mechanistically coupled.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural data on FNIP2-specific catalytic residues in GAP reaction","E3 ubiquitin ligase for FNIP2 degradation unknown","Mechanism linking FNIP2 to oligodendrocyte differentiation undefined","Whether SERCA2b and Rag–Ragulator interactions are mutually exclusive or concurrent is untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,8]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,5]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,3]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[3,8]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,3,8]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[4,5]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[3,8]}],"complexes":["FLCN-FNIP2","FLCN-FNIP2-Rag-Ragulator"],"partners":["FLCN","PRKAA1","RRAGC","RRAGD","ATP2A2","FNIP1"],"other_free_text":[]},"mechanistic_narrative":"FNIP2 is a cytoplasmic scaffolding protein that heterodimerizes with folliculin (FLCN) through paired Longin and DENN domains and connects nutrient sensing to mTORC1 activation and AMPK-dependent stress signaling. The FLCN–FNIP2 heterodimer functions as a GTPase-activating protein (GAP) for RagC/D GTPases—using a conserved FLCN arginine finger—to promote lysosomal recruitment and activation of mTORC1 in response to amino acids [PMID:31704029, PMID:37772772]. FNIP2 also participates in an FLCN–AMPK complex that mediates O6-methylguanine-triggered, MLH1-dependent AMPK activation and mitochondrial apoptosis, and it interacts with the SERCA2b calcium channel to modulate cytoplasmic calcium availability and mitochondrial respiration [PMID:22209521, PMID:41771847]. Loss-of-function mutation of FNIP2 in dogs causes CNS hypomyelination due to defective oligodendrocyte maturation, establishing an in vivo requirement for this gene in myelination [PMID:24272703]."},"prefetch_data":{"uniprot":{"accession":"Q9P278","full_name":"Folliculin-interacting protein 2","aliases":["FNIP1-like protein","O6-methylguanine-induced apoptosis 1 protein"],"length_aa":1114,"mass_kda":122.1,"function":"Binding partner of the GTPase-activating protein FLCN: involved in the cellular response to amino acid availability by regulating the non-canonical mTORC1 signaling cascade controlling the MiT/TFE factors TFEB and TFE3 (PubMed:18663353, PubMed:31672913, PubMed:36103527). Required to promote FLCN recruitment to lysosomes and interaction with Rag GTPases, leading to activation of the non-canonical mTORC1 signaling (By similarity). In low-amino acid conditions, component of the lysosomal folliculin complex (LFC) on the membrane of lysosomes, which inhibits the GTPase-activating activity of FLCN, thereby inactivating mTORC1 and promoting nuclear translocation of TFEB and TFE3 (PubMed:31672913, PubMed:36103527). Upon amino acid restimulation, disassembly of the LFC complex liberates the GTPase-activating activity of FLCN, leading to activation of mTORC1 and subsequent inactivation of TFEB and TFE3 (PubMed:31672913). Together with FLCN, regulates autophagy: following phosphorylation by ULK1, interacts with GABARAP and promotes autophagy (PubMed:25126726). In addition to its role in mTORC1 signaling, also acts as a co-chaperone of HSP90AA1/Hsp90: inhibits the ATPase activity of HSP90AA1/Hsp90, leading to activate both kinase and non-kinase client proteins of HSP90AA1/Hsp90 (PubMed:18403135). Acts as a scaffold to load client protein FLCN onto HSP90AA1/Hsp90 (PubMed:18403135). Competes with the activating co-chaperone AHSA1 for binding to HSP90AA1, thereby providing a reciprocal regulatory mechanism for chaperoning of client proteins (PubMed:18403135). May play a role in the signal transduction pathway of apoptosis induced by O6-methylguanine-mispaired lesions (By similarity)","subcellular_location":"Lysosome membrane; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9P278/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FNIP2","classification":"Not Classified","n_dependent_lines":7,"n_total_lines":1208,"dependency_fraction":0.005794701986754967},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FNIP2","total_profiled":1310},"omim":[{"mim_id":"612768","title":"FOLLICULIN-INTERACTING PROTEIN 2; FNIP2","url":"https://www.omim.org/entry/612768"},{"mim_id":"610594","title":"FOLLICULIN-INTERACTING PROTEIN 1; FNIP1","url":"https://www.omim.org/entry/610594"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Centriolar satellite","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/FNIP2"},"hgnc":{"alias_symbol":["KIAA1450","FNIPL","MAPO1"],"prev_symbol":[]},"alphafold":{"accession":"Q9P278","domains":[{"cath_id":"3.30.450,3.30.450","chopping":"40-70_125-175_307-392","consensus_level":"medium","plddt":83.9274,"start":40,"end":392},{"cath_id":"-","chopping":"394-455_480-538_933-1062","consensus_level":"high","plddt":87.8163,"start":394,"end":1062}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9P278","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9P278-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9P278-F1-predicted_aligned_error_v6.png","plddt_mean":57.16},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FNIP2","jax_strain_url":"https://www.jax.org/strain/search?query=FNIP2"},"sequence":{"accession":"Q9P278","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9P278.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9P278/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9P278"}},"corpus_meta":[{"pmid":"18403135","id":"PMC_18403135","title":"Identification and characterization of a novel folliculin-interacting protein FNIP2.","date":"2008","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/18403135","citation_count":147,"is_preprint":false},{"pmid":"18663353","id":"PMC_18663353","title":"Interaction of folliculin (Birt-Hogg-Dubé gene product) with a novel Fnip1-like (FnipL/Fnip2) protein.","date":"2008","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/18663353","citation_count":107,"is_preprint":false},{"pmid":"31704029","id":"PMC_31704029","title":"Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex.","date":"2019","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/31704029","citation_count":105,"is_preprint":false},{"pmid":"34249911","id":"PMC_34249911","title":"Whole Transcriptome Analysis Reveals a Potential Regulatory Mechanism of LncRNA-FNIP2/miR-24-3p/FNIP2 Axis in Chicken Adipogenesis.","date":"2021","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/34249911","citation_count":22,"is_preprint":false},{"pmid":"22209521","id":"PMC_22209521","title":"Activation of AMP-activated protein kinase by MAPO1 and FLCN induces apoptosis triggered by alkylated base mismatch in DNA.","date":"2011","source":"DNA repair","url":"https://pubmed.ncbi.nlm.nih.gov/22209521","citation_count":18,"is_preprint":false},{"pmid":"37772772","id":"PMC_37772772","title":"Direct regulation of FNIP1 and FNIP2 by MEF2 sustains MTORC1 activation and tumor progression in pancreatic cancer.","date":"2023","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/37772772","citation_count":11,"is_preprint":false},{"pmid":"19137017","id":"PMC_19137017","title":"A novel protein, MAPO1, that functions in apoptosis triggered by O6-methylguanine mispair in DNA.","date":"2009","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/19137017","citation_count":9,"is_preprint":false},{"pmid":"24272703","id":"PMC_24272703","title":"A mutation in the canine gene encoding folliculin-interacting protein 2 (FNIP2) associated with a unique disruption in spinal cord myelination.","date":"2014","source":"Glia","url":"https://pubmed.ncbi.nlm.nih.gov/24272703","citation_count":9,"is_preprint":false},{"pmid":"36316722","id":"PMC_36316722","title":"Folliculin-interacting protein FNIP2 impacts on overweight and obesity through a polymorphism in a conserved 3' untranslated region.","date":"2022","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/36316722","citation_count":5,"is_preprint":false},{"pmid":"23201403","id":"PMC_23201403","title":"Stabilization of MAPO1 by specific binding with folliculin and AMP-activated protein kinase in O⁶-methylguanine-induced apoptosis.","date":"2012","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/23201403","citation_count":4,"is_preprint":false},{"pmid":"41771847","id":"PMC_41771847","title":"Targeting the FNIP2-SERCA2b axis improves metabolic and mitochondrial defects in Ataxia Telangiectasia.","date":"2026","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/41771847","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.07.11.603140","title":"Antagonistic Roles for MITF and TFE3 in Melanoma Plasticity","date":"2024-07-12","source":"bioRxiv","url":"https://doi.org/10.1101/2024.07.11.603140","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7751,"output_tokens":2707,"usd":0.031929},"stage2":{"model":"claude-opus-4-6","input_tokens":6049,"output_tokens":2736,"usd":0.147968},"total_usd":0.179897,"stage1_batch_id":"msgbatch_0118RScg3WGaGkaZRtWZbtce","stage2_batch_id":"msgbatch_01Cpfzvtbj42aqp5oYZ5Te2s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"FNIP2 interacts with folliculin (FLCN) and AMPK, forming a trimeric complex; C-terminally deleted FLCN mutants (mimicking BHD germline mutations) cannot bind FNIP2, indicating the interaction requires the FLCN C-terminus. FNIP1 and FNIP2 can form homo- or heteromeric multimers with each other.\",\n      \"method\": \"Co-immunoprecipitation, yeast two-hybrid, deletion mutant analysis\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP replicated across two independent labs (PMID:18403135 and PMID:18663353)\",\n      \"pmids\": [\"18403135\", \"18663353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"FNIP2 retains FLCN in the cytoplasm in a reticular pattern through their complex formation; C-terminal truncation of FNIP2 abolishes this cytoplasmic retention, causing FLCN to relocalize to the nucleus.\",\n      \"method\": \"Fluorescence microscopy, co-localization, C-terminal truncation mutants\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization experiment with functional consequence, single lab\",\n      \"pmids\": [\"18663353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Knockdown of FNIP1 and FNIP2 (via siRNA) reduces S6K1 phosphorylation, indicating that FLCN-FNIP2 and FLCN-FNIP1 complexes positively regulate mTORC1-dependent S6K1 phosphorylation.\",\n      \"method\": \"siRNA knockdown, western blot for S6K1 phosphorylation\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KD with defined signaling phenotype, single lab\",\n      \"pmids\": [\"18663353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex reveals that FLCN-FNIP2 functions as a GTPase-activating protein (GAP) for RagC/D GTPases; FLCN and FNIP2 heterodimerize through their Longin domains (which contact both nucleotide-binding domains of the Rag heterodimer) and their DENN domains (which interact distally); a conserved arginine on FLCN acts as the catalytic arginine finger for GAP activity.\",\n      \"method\": \"Cryo-EM structure determination, biochemical GAP assays, arginine finger mutagenesis\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure with biochemical validation and active-site mutagenesis in a single high-impact study\",\n      \"pmids\": [\"31704029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"FNIP2 (MAPO1) is required for apoptosis triggered by O6-methylguanine DNA damage; FNIP2-deficient cells show suppressed MNU-induced apoptosis, with loss of mitochondrial membrane depolarization and caspase-3 activation, while p53, CHK1, and H2AX phosphorylation remain intact, placing FNIP2 downstream of DNA damage signaling but upstream of mitochondrial apoptosis.\",\n      \"method\": \"Retroviral gene-trap mutagenesis, siRNA knockdown, mitochondrial membrane potential assay, caspase-3 activation assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis by loss-of-function with defined pathway placement and multiple orthogonal phenotypic readouts, single lab\",\n      \"pmids\": [\"19137017\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"FNIP2 (MAPO1) forms a complex with AMPK and FLCN that is required for AMPK activation in response to O6-methylguanine damage; knockdown of FNIP2 or FLCN prevents AMPKα phosphorylation after MNU treatment; AMPK activation in this context is MLH1-dependent and leads to mitochondrial membrane depolarization and cell death.\",\n      \"method\": \"siRNA knockdown, western blot for AMPKα phosphorylation, mitochondrial membrane depolarization assay, AICAR stimulation\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KD with defined signaling phenotype and pathway epistasis, single lab replicated across two papers\",\n      \"pmids\": [\"22209521\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"FNIP2 (MAPO1) protein stability is regulated by FLCN and AMPK: FLCN binding stabilizes FNIP2 (FLCN knockdown reduces FNIP2 levels and prevents its MNU-induced stabilization), whereas AMPK binding promotes FNIP2 degradation (AMPKα knockdown stabilizes FNIP2 basally); after MNU treatment FNIP2 dissociates from AMPK but maintains FLCN binding, and FNIP2 is subject to proteasome-mediated degradation.\",\n      \"method\": \"Immunoblotting, siRNA knockdown, proteasome inhibitor (MG132) and protein synthesis inhibitor (cycloheximide) treatment, co-immunoprecipitation\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal biochemical approaches, single lab\",\n      \"pmids\": [\"23201403\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"A frameshift mutation in canine FNIP2 results in hypomyelination of the brain and a tract-specific myelin defect in the spinal cord, with loss of mature oligodendrocytes in peripheral spinal cord tracts, establishing a role for FNIP2 in oligodendrocyte maturation and CNS myelination.\",\n      \"method\": \"Genome-wide association study, gene sequencing, histopathology of CNS tissue from affected dogs\",\n      \"journal\": \"Glia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — natural loss-of-function mutation with defined cellular phenotype (oligodendrocyte maturation), single study\",\n      \"pmids\": [\"24272703\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Transcription factors MEF2A and MEF2D directly regulate FNIP2 transcription, and SRC phosphorylates MEF2D at three conserved tyrosines to enhance this transcriptional activity; increased FNIP2 (as part of FLCN-FNIP2 complex acting as RRAGC/D GAP) promotes MTORC1 lysosomal recruitment and activation in pancreatic cancer cells.\",\n      \"method\": \"ChIP, siRNA/shRNA knockdown, phospho-mutagenesis, lysosomal fractionation, mTORC1 activity assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods in single lab establishing transcriptional regulation and downstream signaling\",\n      \"pmids\": [\"37772772\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"FNIP2 interacts with the SERCA2b calcium channel; inactivation of FNIP2 enhances cytoplasmic calcium availability, stimulating mitochondrial respiration and increasing glucose consumption, thereby preventing glycogen accumulation and improving survival in Ataxia Telangiectasia cells.\",\n      \"method\": \"Co-immunoprecipitation (FNIP2-SERCA2b), FNIP2 knockdown/knockout, metabolomics, flux analysis, bioenergetic measurements, electron tomography\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — novel binding partner identified by Co-IP with multiple functional readouts, single lab\",\n      \"pmids\": [\"41771847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In melanoma cells, MITF directly or indirectly activates transcription of FNIP2 (together with FNIP1 and FLCN); elevated FNIP2/FNIP1/FLCN promotes cytoplasmic retention and lysosome-mediated degradation of TFE3, suppressing the mesenchymal/invasive melanoma state.\",\n      \"method\": \"Genetic deletion of TFE3, FNIP2 expression analysis, lysosomal degradation assay, migration/metastasis assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — preprint, FNIP2-specific mechanistic detail is inferred within a broader pathway study\",\n      \"pmids\": [\"bio_10.1101_2024.07.11.603140\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"FNIP2 functions as an obligate heterodimer partner of folliculin (FLCN), forming an extended complex in which Longin and DENN domain pairs heterodimerize; together FLCN-FNIP2 acts as a GTPase-activating protein (GAP) for RagC/D GTPases (using a conserved FLCN arginine finger), thereby promoting lysosomal recruitment and activation of mTORC1 in response to nutrients; additionally, FNIP2 participates in AMPK-dependent apoptosis signaling triggered by O6-methylguanine DNA damage, interacts with the SERCA2b calcium channel to regulate mitochondrial respiration, and is required for normal oligodendrocyte maturation and CNS myelination.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"FNIP2 is a cytoplasmic scaffolding protein that heterodimerizes with folliculin (FLCN) through paired Longin and DENN domains and connects nutrient sensing to mTORC1 activation and AMPK-dependent stress signaling. The FLCN–FNIP2 heterodimer functions as a GTPase-activating protein (GAP) for RagC/D GTPases—using a conserved FLCN arginine finger—to promote lysosomal recruitment and activation of mTORC1 in response to amino acids [PMID:31704029, PMID:37772772]. FNIP2 also participates in an FLCN–AMPK complex that mediates O6-methylguanine-triggered, MLH1-dependent AMPK activation and mitochondrial apoptosis, and it interacts with the SERCA2b calcium channel to modulate cytoplasmic calcium availability and mitochondrial respiration [PMID:22209521, PMID:41771847]. Loss-of-function mutation of FNIP2 in dogs causes CNS hypomyelination due to defective oligodendrocyte maturation, establishing an in vivo requirement for this gene in myelination [PMID:24272703].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Identifying FNIP2 as a direct FLCN- and AMPK-binding partner established that a second folliculin-interacting protein exists and that BHD-associated FLCN truncations disrupt this interaction, framing FNIP2 within the tumor-suppressor pathway.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation and yeast two-hybrid in two independent labs with deletion mutant mapping\",\n      \"pmids\": [\"18403135\", \"18663353\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Stoichiometry and competitive versus cooperative binding between FNIP1 and FNIP2 on FLCN not resolved\",\n        \"Whether FNIP2 has FLCN-independent functions was untested\"\n      ]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Demonstrating that FNIP2 retains FLCN in the cytoplasm and that knockdown of FNIP1/FNIP2 reduces S6K1 phosphorylation placed the FLCN–FNIP2 complex upstream of mTORC1 signaling.\",\n      \"evidence\": \"Fluorescence microscopy with truncation mutants and siRNA knockdown with pS6K1 western blot\",\n      \"pmids\": [\"18663353\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether FNIP2-dependent cytoplasmic retention is the mechanism of mTORC1 regulation or an independent function was unclear\",\n        \"Single-lab observation without independent replication at the time\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Showing that FNIP2 loss suppresses O6-methylguanine-induced apoptosis without affecting upstream DNA damage checkpoints positioned FNIP2 as a dedicated mediator between mismatch-repair signaling and mitochondrial cell death.\",\n      \"evidence\": \"Gene-trap mutagenesis and siRNA in MNU-treated cells with mitochondrial membrane potential and caspase-3 readouts\",\n      \"pmids\": [\"19137017\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct target of FNIP2 in the apoptotic cascade was unidentified\",\n        \"Relevance outside alkylating-agent context not tested\"\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Linking FNIP2 and FLCN to MLH1-dependent AMPKα phosphorylation after O6-methylguanine damage identified AMPK activation as the specific step requiring FNIP2 in the apoptotic pathway.\",\n      \"evidence\": \"siRNA knockdown of FNIP2 and FLCN with pAMPKα western blot and AICAR stimulation\",\n      \"pmids\": [\"22209521\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which FNIP2 facilitates AMPK phosphorylation (scaffold vs. conformational) was unknown\",\n        \"Whether this AMPK-dependent function is separable from mTORC1 regulation was not addressed\"\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Establishing that FLCN stabilizes FNIP2 while AMPK binding promotes its proteasomal degradation revealed a reciprocal regulatory loop controlling FNIP2 protein levels during stress.\",\n      \"evidence\": \"Cycloheximide chase, MG132 treatment, and co-IP after siRNA knockdown of FLCN or AMPKα\",\n      \"pmids\": [\"23201403\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Ubiquitin ligase responsible for FNIP2 degradation was not identified\",\n        \"Post-translational modification sites on FNIP2 mediating stability changes were unmapped\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"A natural canine FNIP2 frameshift mutation causing CNS hypomyelination demonstrated an in vivo requirement for FNIP2 in oligodendrocyte maturation, extending its biological roles beyond cancer signaling.\",\n      \"evidence\": \"GWAS, gene sequencing, and CNS histopathology in affected dogs\",\n      \"pmids\": [\"24272703\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Molecular mechanism linking FNIP2 to oligodendrocyte differentiation was not determined\",\n        \"Whether mTORC1 or AMPK dysregulation underlies the myelination defect was untested\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"The cryo-EM structure of the FLCN–FNIP2–Rag–Ragulator complex resolved the molecular basis of nutrient-dependent mTORC1 activation: FLCN and FNIP2 heterodimerize via Longin and DENN domain pairs, and FLCN contributes a catalytic arginine finger for RagC/D GAP activity.\",\n      \"evidence\": \"Cryo-EM structure determination with biochemical GAP assays and arginine-finger mutagenesis\",\n      \"pmids\": [\"31704029\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Conformational transitions that release FLCN–FNIP2 from the lysosome upon nutrient withdrawal were not captured\",\n        \"Whether FNIP2 contributes catalytic residues beyond the scaffold role was not addressed\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identifying MEF2A/D-driven and SRC-enhanced transcriptional control of FNIP2 revealed how oncogenic signaling in pancreatic cancer amplifies FLCN–FNIP2 GAP activity to hyperactivate mTORC1.\",\n      \"evidence\": \"ChIP, siRNA/shRNA, phospho-mutagenesis, lysosomal fractionation, and mTORC1 activity assays in pancreatic cancer cells\",\n      \"pmids\": [\"37772772\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether MEF2-SRC regulation of FNIP2 operates in non-cancer contexts was unknown\",\n        \"Relative contribution of FNIP2 versus FNIP1 in this transcriptional program was not dissected\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Discovery of a direct FNIP2–SERCA2b interaction showed that FNIP2 restrains cytoplasmic calcium availability; its loss boosts mitochondrial respiration and glucose consumption, linking FNIP2 to calcium-dependent metabolic control.\",\n      \"evidence\": \"Co-IP of FNIP2–SERCA2b, FNIP2 knockout, metabolomics, flux analysis, and electron tomography in Ataxia Telangiectasia cells\",\n      \"pmids\": [\"41771847\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether FNIP2 modulates SERCA2b enzymatic activity or simply sequesters it is unresolved\",\n        \"Generalizability beyond ATM-deficient cells not demonstrated\",\n        \"Relationship between SERCA2b binding and FLCN–FNIP2 complex formation is undefined\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include whether FNIP2 has catalytic contributions to GAP activity beyond scaffolding, the identity of the E3 ligase controlling FNIP2 turnover, the molecular pathway through which FNIP2 loss impairs oligodendrocyte maturation, and whether FNIP2's calcium-regulatory and mTORC1 functions are mechanistically coupled.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural data on FNIP2-specific catalytic residues in GAP reaction\",\n        \"E3 ubiquitin ligase for FNIP2 degradation unknown\",\n        \"Mechanism linking FNIP2 to oligodendrocyte differentiation undefined\",\n        \"Whether SERCA2b and Rag–Ragulator interactions are mutually exclusive or concurrent is untested\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 8]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [3, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 3, 8]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [3, 8]}\n    ],\n    \"complexes\": [\n      \"FLCN-FNIP2\",\n      \"FLCN-FNIP2-Rag-Ragulator\"\n    ],\n    \"partners\": [\n      \"FLCN\",\n      \"PRKAA1\",\n      \"RRAGC\",\n      \"RRAGD\",\n      \"ATP2A2\",\n      \"FNIP1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}