{"gene":"FNIP2","run_date":"2026-06-09T23:54:44","timeline":{"discoveries":[{"year":2008,"finding":"FNIP2 directly interacts with FLCN (folliculin) and AMPK; C-terminally deleted FLCN mutants (mimicking BHD germline mutations) cannot bind FNIP2, mapping the interaction to the C-terminus of FLCN. FNIP1 and FNIP2 can form homo- or heteromeric multimers with each other.","method":"Co-immunoprecipitation, deletion mutant analysis","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — reciprocal Co-IP with deletion mutants, replicated independently by two labs in the same year","pmids":["18403135","18663353"],"is_preprint":false},{"year":2008,"finding":"FnipL/FNIP2 retains FLCN in the cytoplasm in a reticular pattern through complex formation; C-terminal truncation of FNIP2 abolishes cytoplasmic retention of FLCN, indicating FNIP2 regulates FLCN subcellular localization.","method":"Fluorescence microscopy, siRNA knockdown, C-terminal truncation mutants","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct imaging with functional truncation mutants, single lab but two orthogonal methods","pmids":["18663353"],"is_preprint":false},{"year":2008,"finding":"Knockdown of FNIP2 (FnipL) by siRNA decreases S6K1 phosphorylation, placing FLCN-FNIP2 complex as a positive regulator of mTORC1-S6K1 signaling.","method":"siRNA knockdown, immunoblot for phospho-S6K1","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean KD with defined phosphorylation readout, single lab, single method","pmids":["18663353"],"is_preprint":false},{"year":2009,"finding":"MAPO1 (FNIP2) is required for apoptosis triggered by O6-methylguanine mismatch; siRNA-mediated knockdown suppresses MNU-induced apoptosis, mitochondrial membrane depolarization, and caspase-3 activation. Both mouse and human MAPO1 proteins localize to the cytoplasm.","method":"Retrovirus-mediated gene-trap mutagenesis, siRNA knockdown, flow cytometry (sub-G1), caspase-3 assay, mitochondrial membrane potential assay, immunofluorescence","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gene-trap mutant plus siRNA rescue with multiple orthogonal readouts, single lab","pmids":["19137017"],"is_preprint":false},{"year":2011,"finding":"FNIP2 (MAPO1) functions within the AMPK-MAPO1-FLCN complex in the signaling pathway of apoptosis induced by O6-methylguanine; after MNU exposure, AMPKα phosphorylation is MLH1-dependent and requires MAPO1 and FLCN, as their knockdown abrogates AMPK activation. AICAR-mediated AMPK activation also requires MAPO1 and FLCN and leads to mitochondrial membrane depolarization and cell death.","method":"siRNA knockdown, immunoblot (phospho-AMPKα), AICAR treatment, mitochondrial membrane potential assay","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple siRNA targets with orthogonal readouts, single lab","pmids":["22209521"],"is_preprint":false},{"year":2012,"finding":"FNIP2 (MAPO1) protein is stabilized post-translationally during O6-methylguanine-induced apoptosis via proteasome-mediated regulation: proteasome inhibitor MG132 increases MAPO1 levels; FLCN is required for MAPO1 stability (FLCN knockdown decreases MAPO1 and prevents MNU-induced stabilization); AMPKα keeps MAPO1 destabilized under normal conditions (AMPKα knockdown causes constitutive stabilization); MAPO1 dissociates from AMPK but not FLCN after MNU treatment.","method":"Immunoblotting, proteasome inhibitor (MG132), protein synthesis inhibitor (cycloheximide), siRNA knockdown","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple pharmacological and genetic perturbations with defined biochemical readouts, single lab","pmids":["23201403"],"is_preprint":false},{"year":2014,"finding":"A frameshift mutation in FNIP2 in Weimaraner dogs causes hypomyelination and tract-specific myelin defects in the spinal cord, with failure of maturation of a subpopulation of oligodendrocytes, establishing FNIP2 as required for oligodendrocyte maturation and myelination.","method":"Genome-wide association study, sequencing, histopathology, immunohistochemistry","journal":"Glia","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — naturally occurring loss-of-function mutation with defined cellular phenotype, single study","pmids":["24272703"],"is_preprint":false},{"year":2019,"finding":"Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex reveals: FLCN-FNIP2 adopts an extended conformation with heterodimerized Longin domains contacting both nucleotide-binding domains of the Rag heterodimer, and heterodimerized DENN domains at the distal end. A conserved arginine on FLCN acts as the catalytic arginine finger for GAP activity toward RagC/D, and the structure represents an on-pathway GAP-GTPase intermediate.","method":"Cryo-EM structure determination, biochemical mutagenesis (arginine finger mutant), GTPase activity assay","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution cryo-EM structure with biochemical mutagenesis validation, published in high-impact journal","pmids":["31704029"],"is_preprint":false},{"year":2023,"finding":"Transcription factors MEF2A and MEF2D directly regulate FNIP2 transcription; SRC kinase phosphorylates MEF2D at three conserved tyrosine residues to enhance its transcriptional activity and thus FNIP2 expression, which sustains mTORC1 recruitment to lysosomes and activation in pancreatic cancer.","method":"ChIP, RT-qPCR, luciferase reporter assay, immunoblot, siRNA knockdown, phosphomimetic/unphosphorylatable MEF2D mutants","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and functional mutants with multiple readouts, single lab","pmids":["37772772"],"is_preprint":false},{"year":2026,"finding":"FNIP2 interacts with the SERCA2b calcium channel; inactivation of FNIP2 in Ataxia Telangiectasia (AT) cellular models enhances cytoplasmic calcium availability, stimulates mitochondrial respiration, increases glucose consumption, prevents glycogen accumulation, and improves cell survival, partially rescuing AT metabolic defects.","method":"Co-immunoprecipitation (FNIP2-SERCA2b), metabolomics, flux analysis, bioenergetic measurements, electron tomography, FNIP2 knockdown/knockout in AT cells","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for interaction plus multiple orthogonal functional readouts, single lab","pmids":["41771847"],"is_preprint":false},{"year":2024,"finding":"MITF activates expression of FNIP2 (along with FNIP1 and FLCN), and the resulting FLCN-FNIP2 complex promotes cytoplasmic retention and lysosome-mediated degradation of TFE3 in melanoma, suppressing the mesenchymal/invasive state.","method":"Gene expression analysis, TFE3 deletion, FNIP2/FNIP1/FLCN overexpression, migration and metastasis assays","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, indirect evidence for FNIP2 specifically within a multi-component pathway, single lab","pmids":[],"is_preprint":true}],"current_model":"FNIP2 (also known as FNIPL, KIAA1450, MAPO1) is a scaffold protein that forms heterodimers with FLCN via their C-terminal and Longin/DENN domains; the FLCN-FNIP2 complex acts as a GTPase-activating protein (GAP) for RagC/D GTPases—using a conserved arginine finger on FLCN—to recruit and activate mTORC1 at the lysosomal surface, while also participating in AMPK regulation, DNA damage-induced apoptosis (via stabilization and FLCN/AMPK-dependent signaling in response to O6-methylguanine), regulation of FLCN subcellular localization, oligodendrocyte maturation, and calcium homeostasis through interaction with the SERCA2b channel."},"narrative":{"mechanistic_narrative":"FNIP2 is a cytoplasmic scaffold protein that heterodimerizes with folliculin (FLCN) and, through this complex, acts as a positive regulator of mTORC1 signaling at the lysosomal surface [PMID:18403135, PMID:18663353, PMID:31704029]. The FLCN-FNIP2 heterodimer adopts an extended conformation in which heterodimerized Longin domains engage both nucleotide-binding domains of the Rag GTPase heterodimer and heterodimerized DENN domains lie at the distal end; a conserved arginine on FLCN serves as the catalytic arginine finger driving GAP activity toward RagC/D, captured structurally as an on-pathway GAP-GTPase intermediate [PMID:31704029]. The FLCN-binding interface maps to the C-terminus of both proteins, and FNIP2 can also multimerize with FNIP1; loss of this interaction abolishes FNIP2-mediated cytoplasmic retention of FLCN, defining FNIP2 as a determinant of FLCN subcellular localization [PMID:18403135, PMID:18663353]. Beyond mTORC1, FNIP2 operates within an AMPK-FNIP2-FLCN module required for apoptosis induced by O6-methylguanine mismatch, where MLH1-dependent AMPKα phosphorylation after alkylation damage requires FNIP2 and FLCN, and FNIP2 protein is itself post-translationally stabilized in a FLCN-dependent, AMPK-restrained, proteasome-regulated manner during this response [PMID:19137017, PMID:22209521, PMID:23201403]. FNIP2 transcription is driven by MEF2A/MEF2D, sustaining mTORC1 lysosomal recruitment in pancreatic cancer [PMID:37772772]. A naturally occurring FNIP2 frameshift mutation in Weimaraner dogs causes hypomyelination through failed oligodendrocyte maturation, establishing a developmental requirement for FNIP2 [PMID:24272703]. FNIP2 additionally interacts with the SERCA2b calcium channel and modulates calcium availability and mitochondrial metabolism [PMID:41771847].","teleology":[{"year":2008,"claim":"Established FNIP2 as a direct FLCN- and AMPK-binding partner and mapped the interaction to the FLCN C-terminus, linking FNIP2 to the BHD-associated folliculin pathway.","evidence":"Reciprocal Co-IP with FLCN deletion mutants mimicking BHD germline truncations","pmids":["18403135","18663353"],"confidence":"Medium","gaps":["Did not define the FNIP2 domains mediating FLCN binding","No structural basis for the interaction"]},{"year":2008,"claim":"Showed FNIP2 controls FLCN subcellular localization and that the complex positively regulates mTORC1, placing FNIP2 within a growth-signaling axis.","evidence":"Fluorescence microscopy with FNIP2 C-terminal truncations and siRNA knockdown with phospho-S6K1 readout","pmids":["18663353"],"confidence":"Medium","gaps":["Single-lab, single-method KD for the mTORC1 readout","Mechanism connecting localization to S6K1 phosphorylation not resolved"]},{"year":2009,"claim":"Identified FNIP2/MAPO1 as required for O6-methylguanine-induced apoptosis, assigning it a role in the DNA alkylation damage response distinct from mTORC1 regulation.","evidence":"Gene-trap mutagenesis plus siRNA knockdown with sub-G1, caspase-3, and mitochondrial depolarization readouts","pmids":["19137017"],"confidence":"Medium","gaps":["Did not link the apoptotic role to FLCN at this stage","Molecular trigger for FNIP2 engagement in apoptosis unknown"]},{"year":2011,"claim":"Placed FNIP2 within an AMPK-MAPO1-FLCN module by showing MLH1-dependent AMPKα activation after alkylation damage requires FNIP2 and FLCN.","evidence":"siRNA knockdown with phospho-AMPKα immunoblot and AICAR-induced cell death assays","pmids":["22209521"],"confidence":"Medium","gaps":["Order of events between MLH1, AMPK, and FNIP2 not fully resolved","Whether AMPK directly modifies FNIP2 not addressed"]},{"year":2012,"claim":"Revealed that FNIP2 protein stability is regulated post-translationally during the damage response, with FLCN promoting and AMPK restraining its accumulation.","evidence":"MG132/cycloheximide treatments and siRNA knockdown with immunoblot stability readouts","pmids":["23201403"],"confidence":"Medium","gaps":["E3 ligase mediating FNIP2 proteasomal turnover not identified","Site of regulatory modification unknown"]},{"year":2014,"claim":"Demonstrated an in vivo developmental requirement for FNIP2 in oligodendrocyte maturation and myelination via a natural loss-of-function mutation.","evidence":"GWAS, sequencing, and histopathology of FNIP2-frameshift Weimaraner dogs","pmids":["24272703"],"confidence":"Medium","gaps":["Molecular pathway connecting FNIP2 to oligodendrocyte maturation not defined","Whether the phenotype is FLCN/mTORC1-dependent unaddressed"]},{"year":2019,"claim":"Provided the structural mechanism for FNIP2 function: the FLCN-FNIP2 heterodimer is a RagC/D GAP using a FLCN arginine finger, defining how the complex activates mTORC1.","evidence":"Cryo-EM of FLCN-FNIP2-Rag-Ragulator with arginine-finger mutagenesis and GTPase assays","pmids":["31704029"],"confidence":"High","gaps":["Functional contribution of the distal DENN domains not fully defined","How GAP activity is regulated by upstream signals in cells not addressed"]},{"year":2023,"claim":"Identified transcriptional control of FNIP2 by MEF2A/MEF2D and showed FNIP2 expression sustains lysosomal mTORC1 activation in cancer.","evidence":"ChIP, luciferase reporters, RT-qPCR, and MEF2D phospho-mutants with mTORC1 readouts in pancreatic cancer cells","pmids":["37772772"],"confidence":"Medium","gaps":["Generality of MEF2-driven FNIP2 regulation beyond pancreatic cancer untested","Direct effect of FNIP2 level on RagC/D GAP activity in this context not measured"]},{"year":2026,"claim":"Extended FNIP2 function to calcium and metabolic homeostasis via interaction with SERCA2b, with FNIP2 loss rescuing metabolic defects in Ataxia Telangiectasia models.","evidence":"FNIP2-SERCA2b Co-IP plus metabolomics, flux, bioenergetic, and electron tomography analyses in FNIP2-perturbed AT cells","pmids":["41771847"],"confidence":"Medium","gaps":["Direct vs indirect nature of the SERCA2b interaction not confirmed by reciprocal/structural data","Relationship between this calcium role and the FLCN-mTORC1 axis unclear"]},{"year":null,"claim":"How FNIP2's distinct roles—RagC/D GAP/mTORC1 activation, AMPK-coupled damage-induced apoptosis, oligodendrocyte maturation, and SERCA2b-linked calcium/metabolic control—are integrated or differentially deployed in specific cellular contexts remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model connecting the mTORC1, apoptotic, myelination, and calcium functions","Tissue-specific determinants of which function predominates are unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[7]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,7]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,3]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[7,8]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,7,8]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[3,4]}],"complexes":["FLCN-FNIP2 heterodimer","FLCN-FNIP2-Rag-Ragulator complex","AMPK-MAPO1(FNIP2)-FLCN complex"],"partners":["FLCN","FNIP1","AMPK","RAGC","RAGD","SERCA2B"],"other_free_text":[]}},"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":148,"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":109,"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":"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":13,"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":8523,"output_tokens":2733,"usd":0.033282,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9953,"output_tokens":3426,"usd":0.067708,"stage2_stop_reason":"end_turn"},"total_usd":0.10099,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"FNIP2 directly interacts with FLCN (folliculin) and AMPK; C-terminally deleted FLCN mutants (mimicking BHD germline mutations) cannot bind FNIP2, mapping the interaction to the C-terminus of FLCN. FNIP1 and FNIP2 can form homo- or heteromeric multimers with each other.\",\n      \"method\": \"Co-immunoprecipitation, deletion mutant analysis\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — reciprocal Co-IP with deletion mutants, replicated independently by two labs in the same year\",\n      \"pmids\": [\"18403135\", \"18663353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"FnipL/FNIP2 retains FLCN in the cytoplasm in a reticular pattern through complex formation; C-terminal truncation of FNIP2 abolishes cytoplasmic retention of FLCN, indicating FNIP2 regulates FLCN subcellular localization.\",\n      \"method\": \"Fluorescence microscopy, siRNA knockdown, C-terminal truncation mutants\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct imaging with functional truncation mutants, single lab but two orthogonal methods\",\n      \"pmids\": [\"18663353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Knockdown of FNIP2 (FnipL) by siRNA decreases S6K1 phosphorylation, placing FLCN-FNIP2 complex as a positive regulator of mTORC1-S6K1 signaling.\",\n      \"method\": \"siRNA knockdown, immunoblot for phospho-S6K1\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean KD with defined phosphorylation readout, single lab, single method\",\n      \"pmids\": [\"18663353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"MAPO1 (FNIP2) is required for apoptosis triggered by O6-methylguanine mismatch; siRNA-mediated knockdown suppresses MNU-induced apoptosis, mitochondrial membrane depolarization, and caspase-3 activation. Both mouse and human MAPO1 proteins localize to the cytoplasm.\",\n      \"method\": \"Retrovirus-mediated gene-trap mutagenesis, siRNA knockdown, flow cytometry (sub-G1), caspase-3 assay, mitochondrial membrane potential assay, immunofluorescence\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gene-trap mutant plus siRNA rescue with multiple orthogonal readouts, single lab\",\n      \"pmids\": [\"19137017\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"FNIP2 (MAPO1) functions within the AMPK-MAPO1-FLCN complex in the signaling pathway of apoptosis induced by O6-methylguanine; after MNU exposure, AMPKα phosphorylation is MLH1-dependent and requires MAPO1 and FLCN, as their knockdown abrogates AMPK activation. AICAR-mediated AMPK activation also requires MAPO1 and FLCN and leads to mitochondrial membrane depolarization and cell death.\",\n      \"method\": \"siRNA knockdown, immunoblot (phospho-AMPKα), AICAR treatment, mitochondrial membrane potential assay\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple siRNA targets with orthogonal readouts, single lab\",\n      \"pmids\": [\"22209521\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"FNIP2 (MAPO1) protein is stabilized post-translationally during O6-methylguanine-induced apoptosis via proteasome-mediated regulation: proteasome inhibitor MG132 increases MAPO1 levels; FLCN is required for MAPO1 stability (FLCN knockdown decreases MAPO1 and prevents MNU-induced stabilization); AMPKα keeps MAPO1 destabilized under normal conditions (AMPKα knockdown causes constitutive stabilization); MAPO1 dissociates from AMPK but not FLCN after MNU treatment.\",\n      \"method\": \"Immunoblotting, proteasome inhibitor (MG132), protein synthesis inhibitor (cycloheximide), siRNA knockdown\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple pharmacological and genetic perturbations with defined biochemical readouts, single lab\",\n      \"pmids\": [\"23201403\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"A frameshift mutation in FNIP2 in Weimaraner dogs causes hypomyelination and tract-specific myelin defects in the spinal cord, with failure of maturation of a subpopulation of oligodendrocytes, establishing FNIP2 as required for oligodendrocyte maturation and myelination.\",\n      \"method\": \"Genome-wide association study, sequencing, histopathology, immunohistochemistry\",\n      \"journal\": \"Glia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — naturally occurring loss-of-function mutation with defined cellular phenotype, single study\",\n      \"pmids\": [\"24272703\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex reveals: FLCN-FNIP2 adopts an extended conformation with heterodimerized Longin domains contacting both nucleotide-binding domains of the Rag heterodimer, and heterodimerized DENN domains at the distal end. A conserved arginine on FLCN acts as the catalytic arginine finger for GAP activity toward RagC/D, and the structure represents an on-pathway GAP-GTPase intermediate.\",\n      \"method\": \"Cryo-EM structure determination, biochemical mutagenesis (arginine finger mutant), GTPase activity assay\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution cryo-EM structure with biochemical mutagenesis validation, published in high-impact journal\",\n      \"pmids\": [\"31704029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Transcription factors MEF2A and MEF2D directly regulate FNIP2 transcription; SRC kinase phosphorylates MEF2D at three conserved tyrosine residues to enhance its transcriptional activity and thus FNIP2 expression, which sustains mTORC1 recruitment to lysosomes and activation in pancreatic cancer.\",\n      \"method\": \"ChIP, RT-qPCR, luciferase reporter assay, immunoblot, siRNA knockdown, phosphomimetic/unphosphorylatable MEF2D mutants\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and functional mutants with multiple readouts, single lab\",\n      \"pmids\": [\"37772772\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"FNIP2 interacts with the SERCA2b calcium channel; inactivation of FNIP2 in Ataxia Telangiectasia (AT) cellular models enhances cytoplasmic calcium availability, stimulates mitochondrial respiration, increases glucose consumption, prevents glycogen accumulation, and improves cell survival, partially rescuing AT metabolic defects.\",\n      \"method\": \"Co-immunoprecipitation (FNIP2-SERCA2b), metabolomics, flux analysis, bioenergetic measurements, electron tomography, FNIP2 knockdown/knockout in AT cells\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for interaction plus multiple orthogonal functional readouts, single lab\",\n      \"pmids\": [\"41771847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"MITF activates expression of FNIP2 (along with FNIP1 and FLCN), and the resulting FLCN-FNIP2 complex promotes cytoplasmic retention and lysosome-mediated degradation of TFE3 in melanoma, suppressing the mesenchymal/invasive state.\",\n      \"method\": \"Gene expression analysis, TFE3 deletion, FNIP2/FNIP1/FLCN overexpression, migration and metastasis assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, indirect evidence for FNIP2 specifically within a multi-component pathway, single lab\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"FNIP2 (also known as FNIPL, KIAA1450, MAPO1) is a scaffold protein that forms heterodimers with FLCN via their C-terminal and Longin/DENN domains; the FLCN-FNIP2 complex acts as a GTPase-activating protein (GAP) for RagC/D GTPases—using a conserved arginine finger on FLCN—to recruit and activate mTORC1 at the lysosomal surface, while also participating in AMPK regulation, DNA damage-induced apoptosis (via stabilization and FLCN/AMPK-dependent signaling in response to O6-methylguanine), regulation of FLCN subcellular localization, oligodendrocyte maturation, and calcium homeostasis through interaction with the SERCA2b channel.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FNIP2 is a cytoplasmic scaffold protein that heterodimerizes with folliculin (FLCN) and, through this complex, acts as a positive regulator of mTORC1 signaling at the lysosomal surface [#0, #2, #7]. The FLCN-FNIP2 heterodimer adopts an extended conformation in which heterodimerized Longin domains engage both nucleotide-binding domains of the Rag GTPase heterodimer and heterodimerized DENN domains lie at the distal end; a conserved arginine on FLCN serves as the catalytic arginine finger driving GAP activity toward RagC/D, captured structurally as an on-pathway GAP-GTPase intermediate [#7]. The FLCN-binding interface maps to the C-terminus of both proteins, and FNIP2 can also multimerize with FNIP1; loss of this interaction abolishes FNIP2-mediated cytoplasmic retention of FLCN, defining FNIP2 as a determinant of FLCN subcellular localization [#0, #1]. Beyond mTORC1, FNIP2 operates within an AMPK-FNIP2-FLCN module required for apoptosis induced by O6-methylguanine mismatch, where MLH1-dependent AMPK\\u03b1 phosphorylation after alkylation damage requires FNIP2 and FLCN, and FNIP2 protein is itself post-translationally stabilized in a FLCN-dependent, AMPK-restrained, proteasome-regulated manner during this response [#3, #4, #5]. FNIP2 transcription is driven by MEF2A/MEF2D, sustaining mTORC1 lysosomal recruitment in pancreatic cancer [#8]. A naturally occurring FNIP2 frameshift mutation in Weimaraner dogs causes hypomyelination through failed oligodendrocyte maturation, establishing a developmental requirement for FNIP2 [#6]. FNIP2 additionally interacts with the SERCA2b calcium channel and modulates calcium availability and mitochondrial metabolism [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established FNIP2 as a direct FLCN- and AMPK-binding partner and mapped the interaction to the FLCN C-terminus, linking FNIP2 to the BHD-associated folliculin pathway.\",\n      \"evidence\": \"Reciprocal Co-IP with FLCN deletion mutants mimicking BHD germline truncations\",\n      \"pmids\": [\"18403135\", \"18663353\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define the FNIP2 domains mediating FLCN binding\", \"No structural basis for the interaction\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Showed FNIP2 controls FLCN subcellular localization and that the complex positively regulates mTORC1, placing FNIP2 within a growth-signaling axis.\",\n      \"evidence\": \"Fluorescence microscopy with FNIP2 C-terminal truncations and siRNA knockdown with phospho-S6K1 readout\",\n      \"pmids\": [\"18663353\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab, single-method KD for the mTORC1 readout\", \"Mechanism connecting localization to S6K1 phosphorylation not resolved\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identified FNIP2/MAPO1 as required for O6-methylguanine-induced apoptosis, assigning it a role in the DNA alkylation damage response distinct from mTORC1 regulation.\",\n      \"evidence\": \"Gene-trap mutagenesis plus siRNA knockdown with sub-G1, caspase-3, and mitochondrial depolarization readouts\",\n      \"pmids\": [\"19137017\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not link the apoptotic role to FLCN at this stage\", \"Molecular trigger for FNIP2 engagement in apoptosis unknown\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Placed FNIP2 within an AMPK-MAPO1-FLCN module by showing MLH1-dependent AMPK\\u03b1 activation after alkylation damage requires FNIP2 and FLCN.\",\n      \"evidence\": \"siRNA knockdown with phospho-AMPK\\u03b1 immunoblot and AICAR-induced cell death assays\",\n      \"pmids\": [\"22209521\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Order of events between MLH1, AMPK, and FNIP2 not fully resolved\", \"Whether AMPK directly modifies FNIP2 not addressed\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Revealed that FNIP2 protein stability is regulated post-translationally during the damage response, with FLCN promoting and AMPK restraining its accumulation.\",\n      \"evidence\": \"MG132/cycloheximide treatments and siRNA knockdown with immunoblot stability readouts\",\n      \"pmids\": [\"23201403\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ligase mediating FNIP2 proteasomal turnover not identified\", \"Site of regulatory modification unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrated an in vivo developmental requirement for FNIP2 in oligodendrocyte maturation and myelination via a natural loss-of-function mutation.\",\n      \"evidence\": \"GWAS, sequencing, and histopathology of FNIP2-frameshift Weimaraner dogs\",\n      \"pmids\": [\"24272703\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular pathway connecting FNIP2 to oligodendrocyte maturation not defined\", \"Whether the phenotype is FLCN/mTORC1-dependent unaddressed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Provided the structural mechanism for FNIP2 function: the FLCN-FNIP2 heterodimer is a RagC/D GAP using a FLCN arginine finger, defining how the complex activates mTORC1.\",\n      \"evidence\": \"Cryo-EM of FLCN-FNIP2-Rag-Ragulator with arginine-finger mutagenesis and GTPase assays\",\n      \"pmids\": [\"31704029\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional contribution of the distal DENN domains not fully defined\", \"How GAP activity is regulated by upstream signals in cells not addressed\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified transcriptional control of FNIP2 by MEF2A/MEF2D and showed FNIP2 expression sustains lysosomal mTORC1 activation in cancer.\",\n      \"evidence\": \"ChIP, luciferase reporters, RT-qPCR, and MEF2D phospho-mutants with mTORC1 readouts in pancreatic cancer cells\",\n      \"pmids\": [\"37772772\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Generality of MEF2-driven FNIP2 regulation beyond pancreatic cancer untested\", \"Direct effect of FNIP2 level on RagC/D GAP activity in this context not measured\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Extended FNIP2 function to calcium and metabolic homeostasis via interaction with SERCA2b, with FNIP2 loss rescuing metabolic defects in Ataxia Telangiectasia models.\",\n      \"evidence\": \"FNIP2-SERCA2b Co-IP plus metabolomics, flux, bioenergetic, and electron tomography analyses in FNIP2-perturbed AT cells\",\n      \"pmids\": [\"41771847\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect nature of the SERCA2b interaction not confirmed by reciprocal/structural data\", \"Relationship between this calcium role and the FLCN-mTORC1 axis unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How FNIP2's distinct roles\\u2014RagC/D GAP/mTORC1 activation, AMPK-coupled damage-induced apoptosis, oligodendrocyte maturation, and SERCA2b-linked calcium/metabolic control\\u2014are integrated or differentially deployed in specific cellular contexts remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model connecting the mTORC1, apoptotic, myelination, and calcium functions\", \"Tissue-specific determinants of which function predominates are unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [7, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 7, 8]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"complexes\": [\"FLCN-FNIP2 heterodimer\", \"FLCN-FNIP2-Rag-Ragulator complex\", \"AMPK-MAPO1(FNIP2)-FLCN complex\"],\n    \"partners\": [\"FLCN\", \"FNIP1\", \"AMPK\", \"RagC\", \"RagD\", \"SERCA2b\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}