{"gene":"ARL6IP1","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":2014,"finding":"ARL6IP1 harbors reticulon-like short hairpin transmembrane domains that are required for membrane-shaping activity; overexpression induces extensive ER tubular structures, stabilizes ER tubules independent of microtubules, and constricts liposomes into tubules in vitro. ARL6IP1 also binds directly to atlastin, the GTPase mediating tubular ER network formation.","method":"Liposome tubulation assay, overexpression with fluorescence microscopy (ER marker exclusion, microtubule depolymerization), deletion/domain mutagenesis of transmembrane hairpins, co-immunoprecipitation with atlastin","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro liposome constriction assay, domain mutagenesis establishing structure-function, reciprocal binding to atlastin, and multiple orthogonal cell-based assays in a single study","pmids":["24262037"],"is_preprint":false},{"year":2003,"finding":"ARL6IP1 (ARMER) is an ER integral membrane protein with four transmembrane domains and a C-terminal KKXX ER retrieval motif that protects cells from apoptosis by inhibiting caspase-9 activity downstream of cytochrome c release, without blocking cytochrome c release or caspase-9 cleavage itself.","method":"Inducible overexpression system, fluorogenic caspase-9 substrate assay (LEHD-AFC), cytochrome c release assay, siRNA/apoptotic stimuli panel (serum starvation, doxorubicin, UV, TNFα, ER stressors)","journal":"Molecular cancer research : MCR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal apoptosis assays with defined caspase-9 activity readout, single lab, no structural or reconstitution validation","pmids":["12754298"],"is_preprint":false},{"year":2008,"finding":"ARL6IP1 binds directly to addicsin (ARL6IP5) via the hydrophobic region (aa 103–117) of addicsin, forming an ARL6IP1–addicsin heterodimer; this interaction promotes EAAC1-mediated glutamate transport activity in a PKC-dependent manner by increasing EAAC1's glutamate affinity (Km), without affecting maximal velocity (Vmax). An addicsin mutant (Y110A/L112A) that cannot bind ARL6IP1 fails to enhance transport.","method":"Immunoprecipitation, glutamate transport assay with kinetic analysis (Km/Vmax), phorbol ester (PKC activation), site-directed mutagenesis of addicsin binding region","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP, transport kinetics, and mutagenesis in a single study establishing mechanism, single lab","pmids":["18684713"],"is_preprint":false},{"year":2000,"finding":"ARL6IP1 protein is predominantly localized to intracytoplasmic membranes as determined by immunofluorescence microscopy.","method":"Immunofluorescence microscopy","journal":"Genomics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single localization experiment, no functional consequence linked, single lab","pmids":["10995579"],"is_preprint":false},{"year":2013,"finding":"ARL6IP1 is a three-spanning transmembrane protein (topology determined in cells); the CNP (conophylline)-binding domain was mapped by deletion mutation analysis using biotinyl-amino-CNP pulldown.","method":"Topological analysis in cells, deletion mutation analysis, biotinyl-CNP affinity pulldown","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — domain mapping by deletion mutagenesis with chemical probe pulldown, single lab, single study","pmids":["24076029"],"is_preprint":false},{"year":2012,"finding":"In zebrafish, knockdown of arl6ip1 disrupts neural crest migration (crestin+/sox10+ streams) and specification (reduces foxd3, snai1b, sox10 expression) without affecting neural crest induction markers; the migration defect is linked to dampened Shh signaling potentially through defective cilia.","method":"Morpholino knockdown, in situ hybridization for neural crest markers, TUNEL apoptosis assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with multiple marker readouts and epistasis to Shh signaling, single lab in zebrafish model","pmids":["22427906"],"is_preprint":false},{"year":2012,"finding":"In zebrafish, arl6ip1 knockdown causes retinal progenitor cells to remain in an early progenitor state, unable to exit the cell cycle; cyclin D1 remains expressed while p57kip2 and shh are absent, and overexpression of p57kip2 rescues the proliferation defect in morphants.","method":"Morpholino knockdown, FACS DNA content analysis, BrdU labeling, phospho-histone H3 immunostaining, rescue with p57kip2 overexpression plasmid","journal":"Cells, tissues, organs","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with multiple cell-cycle readouts and genetic rescue, single lab in zebrafish model","pmids":["22269635"],"is_preprint":false},{"year":2023,"finding":"ARL6IP1 localizes to mitochondria-associated membranes (MAMs) and maintains ER–mitochondria homeostasis via direct interaction with LC3B and BCL2L13; ARL6IP1 silencing causes mitochondrial dysfunction through dysregulated autophagy and cell death during neuronal differentiation. In a KO mouse model, loss of ARL6IP1 produces demyelination and neuroinflammation in the corticospinal tract.","method":"Subcellular fractionation/MAM isolation, co-immunoprecipitation (ARL6IP1–LC3B and ARL6IP1–BCL2L13), Arl6ip1 knockout mouse generation, in vitro neuronal differentiation with siRNA knockdown, brain histopathology, gene therapy rescue","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP identifying two direct binding partners, KO mouse with defined histopathological phenotype, in vitro mechanistic follow-up, single lab with multiple orthogonal methods","pmids":["37934410"],"is_preprint":false},{"year":2023,"finding":"ARL6IP1 mediates CNP-induced inhibition of BACE1 translation via the 5'UTR; CNP promotes ARL6IP1 interaction with the RNA-binding protein FXR1 and inhibits FXR1 binding to the BACE1 5'UTR, thereby reducing BACE1 protein levels and amyloidogenesis.","method":"RNA pulldown + LC-MS/MS to identify 5'UTR-binding proteins, co-immunoprecipitation (ARL6IP1–FXR1), luciferase 5'UTR reporter assay, in vivo APP/PS1 mouse model with cognitive assessment","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNA pulldown-MS, co-IP, functional reporter assay and in vivo rescue, single lab, multiple orthogonal methods","pmids":["37216506"],"is_preprint":false},{"year":2022,"finding":"ARL6IP1 mRNA is a direct substrate of the RNA-binding protein HuD (ELAVL4); HuD binding stabilizes ARL6IP1 mRNA, sustaining ARL6IP1 protein levels that negatively regulate apoptosis at the ER membrane under stress conditions.","method":"RNA immunoprecipitation/sequencing (RIP-SEQ), synthetic RNA oligonucleotide capture of HuD from cell lysates, recombinant HuD binding assay, RNA transcriptome analysis upon HuD silencing","journal":"Journal of experimental & clinical cancer research : CR","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — RIP-SEQ and recombinant binding assay confirming direct HuD–ARL6IP1 mRNA interaction, single lab, functional consequence inferred rather than directly reconstituted","pmids":["35012594"],"is_preprint":false},{"year":2026,"finding":"ARL6IP1 physically interacts with OLFM4 (validated by Co-IP); OLFM4 overexpression partially rescues the reduction in glycolysis caused by ARL6IP1 knockdown in breast cancer cells, placing ARL6IP1 upstream of OLFM4 in a pathway regulating glycolysis.","method":"Co-immunoprecipitation, extracellular acidification rate (ECAR), glucose consumption, lactate production assays, OLFM4 overexpression rescue","journal":"Combinatorial chemistry & high throughput screening","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP with partial pathway rescue, single lab, no reconstitution or structural validation","pmids":["40444622"],"is_preprint":false}],"current_model":"ARL6IP1 is an ER integral membrane protein with reticulon-like short hairpin transmembrane domains that shapes high-curvature ER tubules by constricting membranes (demonstrated in vitro), binds atlastin to support the tubular ER network, and localizes additionally to mitochondria-associated membranes where it directly interacts with LC3B and BCL2L13 to maintain ER–mitochondria homeostasis and regulate autophagy; it inhibits apoptosis at the level of caspase-9 activity downstream of cytochrome c release, interacts with addicsin (ARL6IP5) to promote EAAC1-mediated glutamate transport in a PKC-dependent manner, and its mRNA is stabilized by the RNA-binding protein HuD, collectively placing ARL6IP1 at the intersection of ER morphology, mitochondrial quality control, apoptosis regulation, and glutamate neurotransmission."},"narrative":{"mechanistic_narrative":"ARL6IP1 is an endoplasmic reticulum integral membrane protein that shapes high-curvature ER tubules through reticulon-like short hairpin transmembrane domains, constricting liposomes into tubules in vitro and binding directly to the ER-network GTPase atlastin to support the tubular ER [PMID:24262037]. Beyond ER morphogenesis, it localizes to mitochondria-associated membranes where it directly binds LC3B and BCL2L13 to maintain ER–mitochondria homeostasis, and its loss drives dysregulated autophagy, mitochondrial dysfunction, and neuronal cell death, with knockout mice developing corticospinal demyelination and neuroinflammation [PMID:37934410]. ARL6IP1 also acts as a negative regulator of apoptosis, inhibiting caspase-9 activity downstream of cytochrome c release without blocking the release or cleavage events themselves [PMID:12754298], and its protein abundance is sustained by HuD (ELAVL4)-mediated stabilization of ARL6IP1 mRNA under stress [PMID:35012594]. Additional functions include promoting EAAC1-mediated glutamate transport through a PKC-dependent heterodimer with addicsin/ARL6IP5 [PMID:18684713] and modulating BACE1 translation by interacting with the RNA-binding protein FXR1 at the BACE1 5'UTR [PMID:37216506].","teleology":[{"year":2000,"claim":"Established the basic subcellular residence of ARL6IP1, framing it as a membrane-associated protein before any function was known.","evidence":"Immunofluorescence microscopy localizing the protein to intracytoplasmic membranes","pmids":["10995579"],"confidence":"Low","gaps":["Single localization experiment with no functional consequence linked","Did not resolve which membrane compartment (ER vs other)"]},{"year":2003,"claim":"Answered whether ARL6IP1 has a role in cell death by showing it is an apoptosis inhibitor acting at a defined point in the caspase cascade.","evidence":"Inducible overexpression with fluorogenic caspase-9 substrate and cytochrome c release assays across multiple apoptotic stimuli","pmids":["12754298"],"confidence":"Medium","gaps":["No direct binding partner identified that mediates caspase-9 inhibition","Single lab, no structural or reconstitution validation","Mechanism by which it blocks caspase-9 activity without affecting cleavage unresolved"]},{"year":2008,"claim":"Identified a discrete protein partner (addicsin/ARL6IP5) and showed the interaction tunes glutamate transporter affinity, linking ARL6IP1 to neurotransmission.","evidence":"Reciprocal co-IP, glutamate transport kinetics (Km/Vmax), PKC activation, and binding-region mutagenesis","pmids":["18684713"],"confidence":"High","gaps":["Physiological context of EAAC1 regulation in vivo not established","How PKC dependence couples to the heterodimer unresolved"]},{"year":2012,"claim":"Probed developmental requirements by loss-of-function in zebrafish, linking arl6ip1 to neural crest migration/specification and to cilia-dependent Shh signaling.","evidence":"Morpholino knockdown with in situ marker analysis and TUNEL apoptosis assays","pmids":["22427906"],"confidence":"Medium","gaps":["Cilia defect inferred rather than directly demonstrated","Molecular link between ER-shaping function and Shh signaling not defined","Morpholino approach without genetic mutant confirmation"]},{"year":2012,"claim":"Extended the developmental role to cell-cycle control, showing arl6ip1 is required for retinal progenitor cell-cycle exit.","evidence":"Morpholino knockdown with FACS DNA content, BrdU, phospho-H3, and p57kip2 rescue","pmids":["22269635"],"confidence":"Medium","gaps":["Mechanistic connection between ARL6IP1 and cyclin D1/p57kip2 regulation unknown","Whether effect is cilia/Shh-mediated not directly tested"]},{"year":2013,"claim":"Resolved membrane topology and mapped a chemical (conophylline) binding domain, providing a structural handle on the protein.","evidence":"Topological analysis in cells with deletion mutagenesis and biotinyl-CNP affinity pulldown","pmids":["24076029"],"confidence":"Medium","gaps":["Functional consequence of CNP binding not established in this study","Three-spanning topology reported alongside other four-TM descriptions"]},{"year":2014,"claim":"Defined the core molecular activity: ARL6IP1 is a membrane-shaping ER protein that generates tubules and partners with atlastin.","evidence":"In vitro liposome constriction, ER tubule induction, microtubule-independence, hairpin domain mutagenesis, and co-IP with atlastin","pmids":["24262037"],"confidence":"High","gaps":["Stoichiometry/structure of the ARL6IP1–atlastin complex not resolved","How membrane-shaping relates to its apoptotic and transport roles unintegrated"]},{"year":2022,"claim":"Connected ARL6IP1 abundance to post-transcriptional control, showing HuD stabilizes its mRNA to sustain anti-apoptotic protein levels.","evidence":"RIP-SEQ, synthetic RNA oligonucleotide capture, and recombinant HuD binding assay","pmids":["35012594"],"confidence":"Medium","gaps":["Functional anti-apoptotic consequence inferred rather than directly reconstituted","Binding site on ARL6IP1 mRNA not mapped"]},{"year":2023,"claim":"Placed ARL6IP1 at mitochondria-associated membranes with two direct partners (LC3B, BCL2L13), linking it to autophagy, mitochondrial homeostasis, and a neurological KO phenotype.","evidence":"MAM fractionation, reciprocal co-IP, KO mouse histopathology, neuronal differentiation siRNA, and gene therapy rescue","pmids":["37934410"],"confidence":"High","gaps":["How ER-shaping activity mechanistically drives the MAM/autophagy function unresolved","Whether LC3B and BCL2L13 binding occur in the same complex unknown"]},{"year":2023,"claim":"Revealed a translational-regulation role, showing ARL6IP1 interacts with FXR1 to suppress BACE1 translation and amyloidogenesis under conophylline treatment.","evidence":"RNA pulldown-MS, co-IP, 5'UTR luciferase reporter, and APP/PS1 in vivo cognitive assessment","pmids":["37216506"],"confidence":"Medium","gaps":["Direct RNA binding by ARL6IP1 vs indirect via FXR1 not fully separated","Single lab; relationship to its ER membrane function unclear"]},{"year":2026,"claim":"Implicated ARL6IP1 in cancer metabolism via OLFM4, placing it upstream of glycolytic regulation in breast cancer cells.","evidence":"Co-IP with OLFM4, ECAR/glucose/lactate assays, and OLFM4 overexpression rescue","pmids":["40444622"],"confidence":"Low","gaps":["Single Co-IP with only partial pathway rescue, no reconstitution or structural validation","Direct vs indirect interaction unresolved","Generality beyond one breast cancer model untested"]},{"year":null,"claim":"How ARL6IP1's ER tubule-shaping activity mechanistically unifies its diverse roles in apoptosis suppression, MAM/autophagy regulation, glutamate transport, and translational control remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No integrated structural model connecting membrane-shaping to its protein/RNA partner functions","Whether distinct activities reflect separate domains or compartment-specific pools is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,2]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[1]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[7]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0]}],"complexes":[],"partners":["ATL1","ARL6IP5","LC3B","BCL2L13","FXR1","ELAVL4","OLFM4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q15041","full_name":"ADP-ribosylation factor-like protein 6-interacting protein 1","aliases":["Apoptotic regulator in the membrane of the endoplasmic reticulum"],"length_aa":203,"mass_kda":23.4,"function":"Positively regulates SLC1A1/EAAC1-mediated glutamate transport by increasing its affinity for glutamate in a PKC activity-dependent manner. Promotes the catalytic efficiency of SLC1A1/EAAC1 probably by reducing its interaction with ARL6IP5, a negative regulator of SLC1A1/EAAC1-mediated glutamate transport (By similarity). Plays a role in the formation and stabilization of endoplasmic reticulum tubules (PubMed:24262037). Negatively regulates apoptosis, possibly by modulating the activity of caspase-9 (CASP9). Inhibits cleavage of CASP9-dependent substrates and downstream markers of apoptosis but not CASP9 itself (PubMed:12754298). May be involved in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation (PubMed:10995579)","subcellular_location":"Endomembrane system; Endoplasmic reticulum membrane; Endoplasmic reticulum","url":"https://www.uniprot.org/uniprotkb/Q15041/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ARL6IP1","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000170540","cell_line_id":"CID000093","localizations":[{"compartment":"er","grade":3}],"interactors":[{"gene":"RABAC1","stoichiometry":10.0},{"gene":"REEP5","stoichiometry":10.0},{"gene":"RAB5C","stoichiometry":4.0},{"gene":"RAB2A","stoichiometry":4.0},{"gene":"ARL6IP5","stoichiometry":0.2},{"gene":"RTN3","stoichiometry":0.2},{"gene":"BCAP31","stoichiometry":0.2},{"gene":"NSF","stoichiometry":0.2},{"gene":"ESYT2","stoichiometry":0.2},{"gene":"CTDNEP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000093","total_profiled":1310},"omim":[{"mim_id":"615685","title":"SPASTIC PARAPLEGIA 61, AUTOSOMAL RECESSIVE; SPG61","url":"https://www.omim.org/entry/615685"},{"mim_id":"607669","title":"ADP-RIBOSYLATION FACTOR-LIKE GTPase 6-INTERACTING PROTEIN 1; ARL6IP1","url":"https://www.omim.org/entry/607669"},{"mim_id":"270800","title":"SPASTIC PARAPLEGIA 5A, AUTOSOMAL RECESSIVE; SPG5A","url":"https://www.omim.org/entry/270800"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Endoplasmic reticulum","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ARL6IP1"},"hgnc":{"alias_symbol":["AIP1","ARMER","KIAA0069","SPG61"],"prev_symbol":["ARL6IP"]},"alphafold":{"accession":"Q15041","domains":[{"cath_id":"-","chopping":"1-203","consensus_level":"medium","plddt":84.833,"start":1,"end":203}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15041","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q15041-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q15041-F1-predicted_aligned_error_v6.png","plddt_mean":84.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ARL6IP1","jax_strain_url":"https://www.jax.org/strain/search?query=ARL6IP1"},"sequence":{"accession":"Q15041","fasta_url":"https://rest.uniprot.org/uniprotkb/Q15041.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q15041/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15041"}},"corpus_meta":[{"pmid":"24262037","id":"PMC_24262037","title":"Arl6IP1 has the ability to shape the mammalian ER membrane in a reticulon-like fashion.","date":"2014","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/24262037","citation_count":49,"is_preprint":false},{"pmid":"12754298","id":"PMC_12754298","title":"ARMER, apoptotic regulator in the membrane of the endoplasmic reticulum, a novel inhibitor of apoptosis.","date":"2003","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/12754298","citation_count":29,"is_preprint":false},{"pmid":"18684713","id":"PMC_18684713","title":"Modulation of the neural glutamate transporter EAAC1 by the addicsin-interacting protein ARL6IP1.","date":"2008","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18684713","citation_count":29,"is_preprint":false},{"pmid":"10995579","id":"PMC_10995579","title":"Characterization, chromosomal localization, and expression during hematopoietic differentiation of the gene encoding Arl6ip, ADP-ribosylation-like factor-6 interacting protein (ARL6).","date":"2000","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/10995579","citation_count":28,"is_preprint":false},{"pmid":"28471035","id":"PMC_28471035","title":"ARL6IP1 mutation causes congenital insensitivity to pain, acromutilation and spastic paraplegia.","date":"2017","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28471035","citation_count":22,"is_preprint":false},{"pmid":"22427906","id":"PMC_22427906","title":"Zebrafish arl6ip1 is required for neural crest development during embryogenesis.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22427906","citation_count":20,"is_preprint":false},{"pmid":"20372863","id":"PMC_20372863","title":"ARL6IP1 mediates cisplatin-induced apoptosis in CaSki cervical cancer cells.","date":"2010","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/20372863","citation_count":16,"is_preprint":false},{"pmid":"35012594","id":"PMC_35012594","title":"RNA binding protein HuD promotes autophagy and tumor stress survival by suppressing mTORC1 activity and augmenting ARL6IP1 levels.","date":"2022","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/35012594","citation_count":15,"is_preprint":false},{"pmid":"24076029","id":"PMC_24076029","title":"Determination of topological structure of ARL6ip1 in cells: identification of the essential binding region of ARL6ip1 for conophylline.","date":"2013","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/24076029","citation_count":15,"is_preprint":false},{"pmid":"31272422","id":"PMC_31272422","title":"Truncating ARL6IP1 variant as the genetic cause of fatal complicated hereditary spastic paraplegia.","date":"2019","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31272422","citation_count":14,"is_preprint":false},{"pmid":"34974280","id":"PMC_34974280","title":"OLFM4 depletion sensitizes gallbladder cancer cells to cisplatin through the ARL6IP1/caspase-3 axis.","date":"2021","source":"Translational oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34974280","citation_count":13,"is_preprint":false},{"pmid":"37216506","id":"PMC_37216506","title":"ARL6IP1 mediates small-molecule-induced alleviation of Alzheimer pathology through FXR1-dependent BACE1 translation initiation.","date":"2023","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/37216506","citation_count":11,"is_preprint":false},{"pmid":"37934410","id":"PMC_37934410","title":"ARL6IP1 gene delivery reduces neuroinflammation and neurodegenerative pathology in hereditary spastic paraplegia model.","date":"2023","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37934410","citation_count":8,"is_preprint":false},{"pmid":"22269635","id":"PMC_22269635","title":"Arl6ip1 plays a role in proliferation during zebrafish retinogenesis.","date":"2012","source":"Cells, tissues, organs","url":"https://pubmed.ncbi.nlm.nih.gov/22269635","citation_count":6,"is_preprint":false},{"pmid":"30708128","id":"PMC_30708128","title":"Proteomic profiling reveals Arl6ip-1 as a candidate target in cancer-induced bone pain rat model after oxycodone treatment.","date":"2019","source":"Neuroscience letters","url":"https://pubmed.ncbi.nlm.nih.gov/30708128","citation_count":4,"is_preprint":false},{"pmid":"40444622","id":"PMC_40444622","title":"ARL6IP1 Inhibits Breast Cancer Tumor Progression by Targeting OLFM4 to Regulate Glycolysis.","date":"2026","source":"Combinatorial chemistry & high throughput screening","url":"https://pubmed.ncbi.nlm.nih.gov/40444622","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10412,"output_tokens":2952,"usd":0.037758,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10333,"output_tokens":3471,"usd":0.06922,"stage2_stop_reason":"end_turn"},"total_usd":0.106978,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"ARL6IP1 harbors reticulon-like short hairpin transmembrane domains that are required for membrane-shaping activity; overexpression induces extensive ER tubular structures, stabilizes ER tubules independent of microtubules, and constricts liposomes into tubules in vitro. ARL6IP1 also binds directly to atlastin, the GTPase mediating tubular ER network formation.\",\n      \"method\": \"Liposome tubulation assay, overexpression with fluorescence microscopy (ER marker exclusion, microtubule depolymerization), deletion/domain mutagenesis of transmembrane hairpins, co-immunoprecipitation with atlastin\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro liposome constriction assay, domain mutagenesis establishing structure-function, reciprocal binding to atlastin, and multiple orthogonal cell-based assays in a single study\",\n      \"pmids\": [\"24262037\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"ARL6IP1 (ARMER) is an ER integral membrane protein with four transmembrane domains and a C-terminal KKXX ER retrieval motif that protects cells from apoptosis by inhibiting caspase-9 activity downstream of cytochrome c release, without blocking cytochrome c release or caspase-9 cleavage itself.\",\n      \"method\": \"Inducible overexpression system, fluorogenic caspase-9 substrate assay (LEHD-AFC), cytochrome c release assay, siRNA/apoptotic stimuli panel (serum starvation, doxorubicin, UV, TNFα, ER stressors)\",\n      \"journal\": \"Molecular cancer research : MCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal apoptosis assays with defined caspase-9 activity readout, single lab, no structural or reconstitution validation\",\n      \"pmids\": [\"12754298\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"ARL6IP1 binds directly to addicsin (ARL6IP5) via the hydrophobic region (aa 103–117) of addicsin, forming an ARL6IP1–addicsin heterodimer; this interaction promotes EAAC1-mediated glutamate transport activity in a PKC-dependent manner by increasing EAAC1's glutamate affinity (Km), without affecting maximal velocity (Vmax). An addicsin mutant (Y110A/L112A) that cannot bind ARL6IP1 fails to enhance transport.\",\n      \"method\": \"Immunoprecipitation, glutamate transport assay with kinetic analysis (Km/Vmax), phorbol ester (PKC activation), site-directed mutagenesis of addicsin binding region\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP, transport kinetics, and mutagenesis in a single study establishing mechanism, single lab\",\n      \"pmids\": [\"18684713\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"ARL6IP1 protein is predominantly localized to intracytoplasmic membranes as determined by immunofluorescence microscopy.\",\n      \"method\": \"Immunofluorescence microscopy\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single localization experiment, no functional consequence linked, single lab\",\n      \"pmids\": [\"10995579\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"ARL6IP1 is a three-spanning transmembrane protein (topology determined in cells); the CNP (conophylline)-binding domain was mapped by deletion mutation analysis using biotinyl-amino-CNP pulldown.\",\n      \"method\": \"Topological analysis in cells, deletion mutation analysis, biotinyl-CNP affinity pulldown\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — domain mapping by deletion mutagenesis with chemical probe pulldown, single lab, single study\",\n      \"pmids\": [\"24076029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"In zebrafish, knockdown of arl6ip1 disrupts neural crest migration (crestin+/sox10+ streams) and specification (reduces foxd3, snai1b, sox10 expression) without affecting neural crest induction markers; the migration defect is linked to dampened Shh signaling potentially through defective cilia.\",\n      \"method\": \"Morpholino knockdown, in situ hybridization for neural crest markers, TUNEL apoptosis assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with multiple marker readouts and epistasis to Shh signaling, single lab in zebrafish model\",\n      \"pmids\": [\"22427906\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"In zebrafish, arl6ip1 knockdown causes retinal progenitor cells to remain in an early progenitor state, unable to exit the cell cycle; cyclin D1 remains expressed while p57kip2 and shh are absent, and overexpression of p57kip2 rescues the proliferation defect in morphants.\",\n      \"method\": \"Morpholino knockdown, FACS DNA content analysis, BrdU labeling, phospho-histone H3 immunostaining, rescue with p57kip2 overexpression plasmid\",\n      \"journal\": \"Cells, tissues, organs\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with multiple cell-cycle readouts and genetic rescue, single lab in zebrafish model\",\n      \"pmids\": [\"22269635\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ARL6IP1 localizes to mitochondria-associated membranes (MAMs) and maintains ER–mitochondria homeostasis via direct interaction with LC3B and BCL2L13; ARL6IP1 silencing causes mitochondrial dysfunction through dysregulated autophagy and cell death during neuronal differentiation. In a KO mouse model, loss of ARL6IP1 produces demyelination and neuroinflammation in the corticospinal tract.\",\n      \"method\": \"Subcellular fractionation/MAM isolation, co-immunoprecipitation (ARL6IP1–LC3B and ARL6IP1–BCL2L13), Arl6ip1 knockout mouse generation, in vitro neuronal differentiation with siRNA knockdown, brain histopathology, gene therapy rescue\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP identifying two direct binding partners, KO mouse with defined histopathological phenotype, in vitro mechanistic follow-up, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"37934410\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ARL6IP1 mediates CNP-induced inhibition of BACE1 translation via the 5'UTR; CNP promotes ARL6IP1 interaction with the RNA-binding protein FXR1 and inhibits FXR1 binding to the BACE1 5'UTR, thereby reducing BACE1 protein levels and amyloidogenesis.\",\n      \"method\": \"RNA pulldown + LC-MS/MS to identify 5'UTR-binding proteins, co-immunoprecipitation (ARL6IP1–FXR1), luciferase 5'UTR reporter assay, in vivo APP/PS1 mouse model with cognitive assessment\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNA pulldown-MS, co-IP, functional reporter assay and in vivo rescue, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"37216506\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ARL6IP1 mRNA is a direct substrate of the RNA-binding protein HuD (ELAVL4); HuD binding stabilizes ARL6IP1 mRNA, sustaining ARL6IP1 protein levels that negatively regulate apoptosis at the ER membrane under stress conditions.\",\n      \"method\": \"RNA immunoprecipitation/sequencing (RIP-SEQ), synthetic RNA oligonucleotide capture of HuD from cell lysates, recombinant HuD binding assay, RNA transcriptome analysis upon HuD silencing\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — RIP-SEQ and recombinant binding assay confirming direct HuD–ARL6IP1 mRNA interaction, single lab, functional consequence inferred rather than directly reconstituted\",\n      \"pmids\": [\"35012594\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ARL6IP1 physically interacts with OLFM4 (validated by Co-IP); OLFM4 overexpression partially rescues the reduction in glycolysis caused by ARL6IP1 knockdown in breast cancer cells, placing ARL6IP1 upstream of OLFM4 in a pathway regulating glycolysis.\",\n      \"method\": \"Co-immunoprecipitation, extracellular acidification rate (ECAR), glucose consumption, lactate production assays, OLFM4 overexpression rescue\",\n      \"journal\": \"Combinatorial chemistry & high throughput screening\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP with partial pathway rescue, single lab, no reconstitution or structural validation\",\n      \"pmids\": [\"40444622\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ARL6IP1 is an ER integral membrane protein with reticulon-like short hairpin transmembrane domains that shapes high-curvature ER tubules by constricting membranes (demonstrated in vitro), binds atlastin to support the tubular ER network, and localizes additionally to mitochondria-associated membranes where it directly interacts with LC3B and BCL2L13 to maintain ER–mitochondria homeostasis and regulate autophagy; it inhibits apoptosis at the level of caspase-9 activity downstream of cytochrome c release, interacts with addicsin (ARL6IP5) to promote EAAC1-mediated glutamate transport in a PKC-dependent manner, and its mRNA is stabilized by the RNA-binding protein HuD, collectively placing ARL6IP1 at the intersection of ER morphology, mitochondrial quality control, apoptosis regulation, and glutamate neurotransmission.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ARL6IP1 is an endoplasmic reticulum integral membrane protein that shapes high-curvature ER tubules through reticulon-like short hairpin transmembrane domains, constricting liposomes into tubules in vitro and binding directly to the ER-network GTPase atlastin to support the tubular ER [#0]. Beyond ER morphogenesis, it localizes to mitochondria-associated membranes where it directly binds LC3B and BCL2L13 to maintain ER\\u2013mitochondria homeostasis, and its loss drives dysregulated autophagy, mitochondrial dysfunction, and neuronal cell death, with knockout mice developing corticospinal demyelination and neuroinflammation [#7]. ARL6IP1 also acts as a negative regulator of apoptosis, inhibiting caspase-9 activity downstream of cytochrome c release without blocking the release or cleavage events themselves [#1], and its protein abundance is sustained by HuD (ELAVL4)-mediated stabilization of ARL6IP1 mRNA under stress [#9]. Additional functions include promoting EAAC1-mediated glutamate transport through a PKC-dependent heterodimer with addicsin/ARL6IP5 [#2] and modulating BACE1 translation by interacting with the RNA-binding protein FXR1 at the BACE1 5'UTR [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established the basic subcellular residence of ARL6IP1, framing it as a membrane-associated protein before any function was known.\",\n      \"evidence\": \"Immunofluorescence microscopy localizing the protein to intracytoplasmic membranes\",\n      \"pmids\": [\"10995579\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single localization experiment with no functional consequence linked\", \"Did not resolve which membrane compartment (ER vs other)\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Answered whether ARL6IP1 has a role in cell death by showing it is an apoptosis inhibitor acting at a defined point in the caspase cascade.\",\n      \"evidence\": \"Inducible overexpression with fluorogenic caspase-9 substrate and cytochrome c release assays across multiple apoptotic stimuli\",\n      \"pmids\": [\"12754298\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct binding partner identified that mediates caspase-9 inhibition\", \"Single lab, no structural or reconstitution validation\", \"Mechanism by which it blocks caspase-9 activity without affecting cleavage unresolved\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Identified a discrete protein partner (addicsin/ARL6IP5) and showed the interaction tunes glutamate transporter affinity, linking ARL6IP1 to neurotransmission.\",\n      \"evidence\": \"Reciprocal co-IP, glutamate transport kinetics (Km/Vmax), PKC activation, and binding-region mutagenesis\",\n      \"pmids\": [\"18684713\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological context of EAAC1 regulation in vivo not established\", \"How PKC dependence couples to the heterodimer unresolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Probed developmental requirements by loss-of-function in zebrafish, linking arl6ip1 to neural crest migration/specification and to cilia-dependent Shh signaling.\",\n      \"evidence\": \"Morpholino knockdown with in situ marker analysis and TUNEL apoptosis assays\",\n      \"pmids\": [\"22427906\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cilia defect inferred rather than directly demonstrated\", \"Molecular link between ER-shaping function and Shh signaling not defined\", \"Morpholino approach without genetic mutant confirmation\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Extended the developmental role to cell-cycle control, showing arl6ip1 is required for retinal progenitor cell-cycle exit.\",\n      \"evidence\": \"Morpholino knockdown with FACS DNA content, BrdU, phospho-H3, and p57kip2 rescue\",\n      \"pmids\": [\"22269635\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic connection between ARL6IP1 and cyclin D1/p57kip2 regulation unknown\", \"Whether effect is cilia/Shh-mediated not directly tested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved membrane topology and mapped a chemical (conophylline) binding domain, providing a structural handle on the protein.\",\n      \"evidence\": \"Topological analysis in cells with deletion mutagenesis and biotinyl-CNP affinity pulldown\",\n      \"pmids\": [\"24076029\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of CNP binding not established in this study\", \"Three-spanning topology reported alongside other four-TM descriptions\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defined the core molecular activity: ARL6IP1 is a membrane-shaping ER protein that generates tubules and partners with atlastin.\",\n      \"evidence\": \"In vitro liposome constriction, ER tubule induction, microtubule-independence, hairpin domain mutagenesis, and co-IP with atlastin\",\n      \"pmids\": [\"24262037\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry/structure of the ARL6IP1\\u2013atlastin complex not resolved\", \"How membrane-shaping relates to its apoptotic and transport roles unintegrated\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Connected ARL6IP1 abundance to post-transcriptional control, showing HuD stabilizes its mRNA to sustain anti-apoptotic protein levels.\",\n      \"evidence\": \"RIP-SEQ, synthetic RNA oligonucleotide capture, and recombinant HuD binding assay\",\n      \"pmids\": [\"35012594\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional anti-apoptotic consequence inferred rather than directly reconstituted\", \"Binding site on ARL6IP1 mRNA not mapped\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Placed ARL6IP1 at mitochondria-associated membranes with two direct partners (LC3B, BCL2L13), linking it to autophagy, mitochondrial homeostasis, and a neurological KO phenotype.\",\n      \"evidence\": \"MAM fractionation, reciprocal co-IP, KO mouse histopathology, neuronal differentiation siRNA, and gene therapy rescue\",\n      \"pmids\": [\"37934410\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How ER-shaping activity mechanistically drives the MAM/autophagy function unresolved\", \"Whether LC3B and BCL2L13 binding occur in the same complex unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed a translational-regulation role, showing ARL6IP1 interacts with FXR1 to suppress BACE1 translation and amyloidogenesis under conophylline treatment.\",\n      \"evidence\": \"RNA pulldown-MS, co-IP, 5'UTR luciferase reporter, and APP/PS1 in vivo cognitive assessment\",\n      \"pmids\": [\"37216506\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct RNA binding by ARL6IP1 vs indirect via FXR1 not fully separated\", \"Single lab; relationship to its ER membrane function unclear\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Implicated ARL6IP1 in cancer metabolism via OLFM4, placing it upstream of glycolytic regulation in breast cancer cells.\",\n      \"evidence\": \"Co-IP with OLFM4, ECAR/glucose/lactate assays, and OLFM4 overexpression rescue\",\n      \"pmids\": [\"40444622\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP with only partial pathway rescue, no reconstitution or structural validation\", \"Direct vs indirect interaction unresolved\", \"Generality beyond one breast cancer model untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ARL6IP1's ER tubule-shaping activity mechanistically unifies its diverse roles in apoptosis suppression, MAM/autophagy regulation, glutamate transport, and translational control remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No integrated structural model connecting membrane-shaping to its protein/RNA partner functions\", \"Whether distinct activities reflect separate domains or compartment-specific pools is unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"ATL1\", \"ARL6IP5\", \"LC3B\", \"BCL2L13\", \"FXR1\", \"ELAVL4\", \"OLFM4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}