{"gene":"LRRC56","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2015,"finding":"ODA8 (LRRC56 ortholog in Chlamydomonas) is required for cytoplasmic preassembly of outer dynein arm (ODA) complexes; dynein in oda8 mutant cytoplasm has not properly preassembled and cannot bind normally onto axonemes. ODA8 distribution between cytoplasm and flagella mirrors IFT proteins, and ~half of flagellar ODA8 is in the soluble matrix fraction, supporting a role in dynein assembly/transport rather than axonemal docking. Dynein extracted from wild-type axonemes rebinds to oda8 mutant axonemes without re-binding of ODA8, further excluding a docking role.","method":"Positional cloning, flagellar fractionation, in vitro dynein rebinding assays, cytoplasmic ODA preassembly assays, phylogenomics","journal":"Cytoskeleton (Hoboken, N.J.)","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal biochemical assays (fractionation, in vitro rebinding, cytoplasmic preassembly) in a single focused study on the direct ortholog","pmids":["25558044"],"is_preprint":false},{"year":2018,"finding":"LRRC56 physically interacts with the IFT protein IFT88 (demonstrated by co-immunoprecipitation). In Trypanosoma brucei, LRRC56 is recruited to the cilium during axoneme construction, co-localizes with IFT trains, and is required for the addition of outer dynein arms to the distal end of the flagellum. Loss-of-function (null) or the p.Leu259Pro variant (equivalent to human p.Leu140Pro) causes abnormal ciliary beat patterns and absence of outer dynein arms restricted to the distal portion of the axoneme.","method":"Co-immunoprecipitation (LRRC56–IFT88), LRRC56-null and point-mutant T. brucei models, immunofluorescence co-localization with IFT trains, transmission electron microscopy, high-speed video microscopy","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP plus in vivo model with null and patient-variant alleles, multiple orthogonal methods, replicated across two model systems","pmids":["30388400"],"is_preprint":false},{"year":2024,"finding":"In Trypanosoma brucei, LRRC56 is a transient IFT cargo during flagellum construction and is required for efficient attachment of a subset of docking complex proteins (specifically those present in the distal portion of the organelle). The relationship is interdependent: knockdown of the distal docking complex also prevents LRRC56 association with the flagellum. lrrc56−/− cells display shorter flagella with delayed maturation. Inhibition of cell division compensates for distal ODA absence by redistributing the proximal docking complex, restoring ODA attachment but not flagellum length.","method":"LRRC56 knockout in T. brucei, IFT co-localization assays, docking complex knockdown epistasis, transmission electron microscopy, immunofluorescence, cell-division inhibition rescue experiment","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with rescue experiment, multiple orthogonal imaging and ultrastructural methods, single focused study with rigorous controls","pmids":["38865178"],"is_preprint":false},{"year":2013,"finding":"In Chlamydomonas, ODA8 (LRRC56 ortholog) flagellar localization depends on ODA5 and ODA10; ODA10 is present on oda8-mutant flagella at wild-type levels, establishing that ODA8 acts downstream of ODA5/ODA10 for dynein arm assembly. Genetic interaction among ODA5, ODA8, and ODA10 loci was confirmed.","method":"Positional cloning of ODA10, immunofluorescence of ODA10p on oda8-mutant flagella, genetic interaction/epistasis analysis","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis and direct protein localization in mutant backgrounds, single lab, two orthogonal methods","pmids":["24088566"],"is_preprint":false},{"year":2025,"finding":"In Xenopus laevis multiciliated cells, loss of lrrc56 causes specific depletion of outer dynein arms (ODAs) from the distal axoneme. In vivo affinity purification–mass spectrometry revealed that Lrrc56 physically interacts with ODA docking complex components including Odad3. Lrrc56 knockdown also leads to distal loss of Odad3. Disease-associated variants in LRRC56 and ODAD3 disrupt their localization and interaction, placing both proteins in a shared functional pathway for distal ODA and docking complex deployment.","method":"Targeted knockdown in Xenopus laevis multiciliated cells, in vivo affinity purification–mass spectrometry (AP-MS), in vivo imaging, disease-variant functional analysis","journal":"Disease models & mechanisms","confidence":"High","confidence_rationale":"Tier 2 / Strong — AP-MS interactome plus in vivo knockdown with defined phenotype plus disease-variant validation, multiple orthogonal methods in a single focused study","pmids":["41229303"],"is_preprint":false},{"year":2025,"finding":"LRRC56 preprint (bioRxiv version): same findings as the peer-reviewed paper — Lrrc56 binds Odad3 (ODA docking complex component) by in vivo AP-MS; lrrc56 knockdown in Xenopus depletes ODAs and Odad3 specifically from the distal axoneme; disease-associated variants in LRRC56 and ODAD3 disrupt their localization and interaction.","method":"In vivo AP-MS, targeted knockdown, in vivo imaging in Xenopus laevis","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — preprint version of peer-reviewed study; same data, confidence deferred to published paper","pmids":["40631331"],"is_preprint":true},{"year":2025,"finding":"LRRC56-knockout mice (CRISPR/Cas9 targeting exons 4–5) show absence of both inner dynein arm marker DNALI1 and outer dynein arm marker DNAI2 in cilia by immunofluorescence, and transmission electron microscopy reveals dynein arm defects and disorganized axonemal structure in flagella, establishing LRRC56 as required for dynein arm assembly in vivo in a mammalian model.","method":"CRISPR/Cas9 knockout mouse, transmission electron microscopy, immunofluorescence with dynein arm markers (DNALI1, DNAI2)","journal":"Biology open","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO with defined cellular phenotype confirmed by both ultrastructural (TEM) and molecular (IF) readouts","pmids":["39912490"],"is_preprint":false},{"year":2025,"finding":"Quantitative proteomic analysis of Lrrc56-knockout mouse tissues revealed markedly reduced expression of microtubule inner proteins (MIPs) and axonemal dynein assembly factors compared to wild-type, indicating LRRC56 is required for the normal abundance of multiple cilia-associated structural proteins beyond dynein arms alone.","method":"CRISPR/Cas9 Lrrc56-knockout mice, quantitative proteomics of ciliary tissues","journal":"Frontiers in genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — quantitative proteomics in KO vs. WT, single lab, single method for the broad proteome finding","pmids":["41477643"],"is_preprint":false},{"year":2025,"finding":"LRRC56 interacts with IFT88 in breast cancer cells and regulates YAP1 expression via modulation of the RhoA/ROCK signaling pathway; LRRC56 overexpression promotes proliferation, migration, invasion, and EMT, while downregulation inhibits xenograft tumor growth and lung metastasis.","method":"In vitro functional assays (proliferation, migration, invasion), in vivo xenograft mouse model, co-immunoprecipitation (LRRC56–IFT88), western blotting for RhoA/ROCK/YAP1 pathway components, EMT markers","journal":"Molecular biomedicine","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — Co-IP plus functional KD/OE with defined pathway readouts, single lab, mechanistic context is non-ciliary and novel","pmids":["40388100"],"is_preprint":false},{"year":2024,"finding":"In Chlamydomonas, double heterozygosity for oda8 (LRRC56 ortholog) and pf23 (DNAAF4 ortholog) reduces cilia assembly in a sensitized (protein-synthesis-inhibited) assay, demonstrating dosage-dependent genetic interaction between LRRC56 and DNAAF4 in outer and inner dynein arm assembly.","method":"Second-site non-complementation screen in Chlamydomonas diploids, ciliary assembly assay under cycloheximide, immunoblotting for PF23 levels","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis confirmed by dosage assay and immunoblot, single study, sensitized-assay context","pmids":["38498551"],"is_preprint":false}],"current_model":"LRRC56 is a dynein axonemal assembly factor (DNAAF12) that acts as a transient IFT cargo during cilia/flagella construction: it physically interacts with IFT88 and travels along IFT trains to promote cytoplasmic preassembly of outer dynein arm (ODA) complexes and their transport to — and attachment at — the distal axoneme, where it also engages the ODA docking complex component ODAD3; loss of LRRC56 in multiple organisms (Chlamydomonas, Trypanosoma brucei, Xenopus, mouse) consistently causes deficient or absent ODAs preferentially at the distal axoneme, dyskinetic cilia, and PCD-spectrum phenotypes, while in a non-ciliary context LRRC56 has additionally been shown to interact with IFT88 to modulate RhoA/ROCK/YAP1 signaling in cancer cells."},"narrative":{"mechanistic_narrative":"LRRC56 (DNAAF12) is a dynein axonemal assembly factor required for the construction of motile cilia and flagella, acting in the cytoplasmic preassembly and intraflagellar delivery of dynein arm complexes [PMID:25558044, PMID:30388400]. Studies of its Chlamydomonas ortholog ODA8 established that it promotes proper cytoplasmic preassembly of outer dynein arm (ODA) complexes so they can dock onto axonemes, while excluding a direct structural docking role; its partition between cytoplasm and flagella mirrors that of intraflagellar transport (IFT) proteins [PMID:25558044], and it functions genetically downstream of ODA5/ODA10 [PMID:24088566]. LRRC56 physically interacts with the IFT protein IFT88 and travels as a transient IFT cargo with IFT trains during axoneme construction, delivering ODAs to and promoting their attachment at the distal axoneme [PMID:30388400, PMID:38865178]. At the distal axoneme it engages ODA docking complex components, binding ODAD3/Odad3, and its loss specifically depletes both ODAs and the distal docking complex; disease-associated LRRC56 and ODAD3 variants disrupt this interaction and localization, placing the two proteins in a shared distal-ODA deployment pathway [PMID:41229303]. Consistent across organisms, loss of LRRC56 causes preferential distal-axoneme ODA deficiency, dyskinetic ciliary beating, and dynein arm defects — in mouse knockouts it abolishes both inner (DNALI1) and outer (DNAI2) dynein arm markers and disorganizes axonemal ultrastructure [PMID:30388400, PMID:39912490]. Beyond its ciliary role, LRRC56 interacts with IFT88 in breast cancer cells to modulate RhoA/ROCK/YAP1 signaling, promoting proliferation, migration, and metastasis [PMID:40388100].","teleology":[{"year":2013,"claim":"Placing LRRC56 within the dynein assembly genetic hierarchy addressed where it acts relative to other ODA assembly factors.","evidence":"Positional cloning and immunofluorescence/epistasis analysis of ODA5, ODA8, ODA10 in Chlamydomonas mutants","pmids":["24088566"],"confidence":"Medium","gaps":["Does not define the biochemical activity of ODA8/LRRC56 itself","Mechanism of how ODA5/ODA10 recruit ODA8 to flagella unresolved"]},{"year":2015,"claim":"Established that LRRC56/ODA8 functions in cytoplasmic preassembly and transport of ODA complexes rather than as a docking factor, defining its core molecular role.","evidence":"Flagellar fractionation, in vitro dynein rebinding assays, and cytoplasmic ODA preassembly assays in Chlamydomonas oda8 mutants","pmids":["25558044"],"confidence":"High","gaps":["Direct enzymatic/biochemical activity of the protein not defined","Did not identify physical interaction partners","Distal-specific phenotype not yet observed in this system"]},{"year":2018,"claim":"Identified LRRC56 as an IFT88-interacting transient cargo that delivers ODAs to the distal axoneme, and linked a patient variant to a defined ciliary defect.","evidence":"Co-immunoprecipitation with IFT88, null and p.Leu259Pro point-mutant T. brucei models, IFT co-localization, TEM, and high-speed video microscopy","pmids":["30388400"],"confidence":"High","gaps":["Structural basis of the LRRC56–IFT88 interaction unknown","Why ODA loss is restricted to the distal axoneme not yet explained"]},{"year":2024,"claim":"Resolved the interdependence between LRRC56 and the distal docking complex, showing reciprocal requirement for flagellar association and ODA attachment.","evidence":"LRRC56 knockout, IFT co-localization, docking complex knockdown epistasis, and cell-division-inhibition rescue in T. brucei","pmids":["38865178"],"confidence":"High","gaps":["Molecular identity of the direct docking-complex contact in trypanosomes not specified","Mechanism coupling flagellum length defect to ODA deployment unresolved"]},{"year":2024,"claim":"Demonstrated a dosage-dependent genetic interaction with DNAAF4, embedding LRRC56 in a broader network of dynein assembly factors.","evidence":"Second-site non-complementation screen with sensitized ciliary assembly assay in Chlamydomonas oda8/pf23 diploids","pmids":["38498551"],"confidence":"Medium","gaps":["Whether the interaction is physical or purely genetic not established","Sensitized-assay context may not reflect normal physiology"]},{"year":2025,"claim":"Defined the direct docking-complex partner ODAD3 and unified LRRC56 and ODAD3 disease variants in one distal-ODA deployment pathway.","evidence":"In vivo AP-MS, targeted knockdown, in vivo imaging, and disease-variant functional analysis in Xenopus multiciliated cells","pmids":["41229303"],"confidence":"High","gaps":["Stoichiometry and structure of the LRRC56–Odad3 complex unknown","Whether LRRC56 directly hands off ODAs to the docking complex not shown"]},{"year":2025,"claim":"Confirmed LRRC56 is required for dynein arm assembly in a mammalian system, extending the conserved phenotype to mouse.","evidence":"CRISPR/Cas9 knockout mice analyzed by TEM and immunofluorescence for DNALI1 and DNAI2","pmids":["39912490"],"confidence":"High","gaps":["Loss of both inner and outer arm markers not mechanistically dissected","Distal-specific spatial pattern not resolved in mouse"]},{"year":2025,"claim":"Broadened LRRC56's required role beyond dynein arms to the abundance of microtubule inner proteins and other axonemal factors.","evidence":"Quantitative proteomics of Lrrc56-knockout versus wild-type mouse ciliary tissues","pmids":["41477643"],"confidence":"Medium","gaps":["Whether reduced MIP abundance is direct or secondary to ciliary disorganization unknown","Single-method finding without orthogonal confirmation"]},{"year":2025,"claim":"Revealed a non-ciliary function in which LRRC56–IFT88 modulates RhoA/ROCK/YAP1 signaling to drive cancer cell behavior.","evidence":"Co-IP, functional KD/OE assays, xenograft model, and western blotting for pathway and EMT markers in breast cancer cells","pmids":["40388100"],"confidence":"Medium","gaps":["Direct biochemical link between IFT88 binding and RhoA activation not established","Single lab, single cancer context"]},{"year":null,"claim":"The biochemical activity of LRRC56 itself and the molecular basis for the distal-axoneme specificity of ODA delivery remain undefined.","evidence":"","pmids":[],"confidence":"High","gaps":["No enzymatic activity or structural model for LRRC56 reported","Mechanism restricting ODA loss to the distal axoneme unresolved","How the ciliary and cancer-signaling roles relate is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,4]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,1,2,4,6]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,1,4,6]}],"complexes":[],"partners":["IFT88","ODAD3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8IYG6","full_name":"Leucine-rich repeat-containing protein 56","aliases":[],"length_aa":542,"mass_kda":58.7,"function":"Required for the assembly of dynein arms","subcellular_location":"Cell projection, cilium","url":"https://www.uniprot.org/uniprotkb/Q8IYG6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LRRC56","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/LRRC56","total_profiled":1310},"omim":[{"mim_id":"618254","title":"CILIARY DYSKINESIA, PRIMARY, 39; CILD39","url":"https://www.omim.org/entry/618254"},{"mim_id":"618227","title":"LEUCINE-RICH REPEAT-CONTAINING PROTEIN 56; LRRC56","url":"https://www.omim.org/entry/618227"},{"mim_id":"244400","title":"CILIARY DYSKINESIA, PRIMARY, 1; CILD1","url":"https://www.omim.org/entry/244400"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"pituitary gland","ntpm":11.8},{"tissue":"testis","ntpm":21.3}],"url":"https://www.proteinatlas.org/search/LRRC56"},"hgnc":{"alias_symbol":["FLJ00101","oda8","DKFZp761L1518","DNAAF12"],"prev_symbol":[]},"alphafold":{"accession":"Q8IYG6","domains":[{"cath_id":"3.80.10.10","chopping":"53-263","consensus_level":"medium","plddt":84.2774,"start":53,"end":263}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IYG6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IYG6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IYG6-F1-predicted_aligned_error_v6.png","plddt_mean":55.84},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LRRC56","jax_strain_url":"https://www.jax.org/strain/search?query=LRRC56"},"sequence":{"accession":"Q8IYG6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8IYG6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8IYG6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IYG6"}},"corpus_meta":[{"pmid":"30388400","id":"PMC_30388400","title":"Biallelic Mutations in LRRC56, Encoding a Protein Associated with Intraflagellar Transport, Cause Mucociliary Clearance and Laterality Defects.","date":"2018","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30388400","citation_count":59,"is_preprint":false},{"pmid":"25558044","id":"PMC_25558044","title":"Chlamydomonas axonemal dynein assembly locus ODA8 encodes a conserved flagellar protein needed for cytoplasmic maturation of outer dynein arm complexes.","date":"2015","source":"Cytoskeleton (Hoboken, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/25558044","citation_count":34,"is_preprint":false},{"pmid":"24088566","id":"PMC_24088566","title":"Chlamydomonas ODA10 is a conserved axonemal protein that plays a unique role in outer dynein arm assembly.","date":"2013","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/24088566","citation_count":26,"is_preprint":false},{"pmid":"38865178","id":"PMC_38865178","title":"LRRC56 is an IFT cargo required for assembly of the distal dynein docking complex in Trypanosoma brucei.","date":"2024","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/38865178","citation_count":8,"is_preprint":false},{"pmid":"36176820","id":"PMC_36176820","title":"Primary Ciliary Dyskinesia: Phenotype Resulting From a Novel Variant of LRRC56 Gene.","date":"2022","source":"Cureus","url":"https://pubmed.ncbi.nlm.nih.gov/36176820","citation_count":7,"is_preprint":false},{"pmid":"37892347","id":"PMC_37892347","title":"Clinical and Genetic Characterization of Patients with Primary Ciliary Dyskinesia in Southwest Saudi Arabia: A Cross Sectional Study.","date":"2023","source":"Children (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/37892347","citation_count":6,"is_preprint":false},{"pmid":"39912490","id":"PMC_39912490","title":"LRRC56 deletion causes primary ciliary dyskinesia in mice characterized by dynein arms defects.","date":"2025","source":"Biology open","url":"https://pubmed.ncbi.nlm.nih.gov/39912490","citation_count":5,"is_preprint":false},{"pmid":"37107593","id":"PMC_37107593","title":"SLC38A10 Deficiency in Mice Affects Plasma Levels of Threonine and Histidine in Males but Not in Females: A Preliminary Characterization Study of SLC38A10-/- Mice.","date":"2023","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/37107593","citation_count":3,"is_preprint":false},{"pmid":"39880089","id":"PMC_39880089","title":"Integrative in silico and biochemical analyses demonstrate direct Arl3-mediated ODA16 release from the intraflagellar transport machinery.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/39880089","citation_count":3,"is_preprint":false},{"pmid":"40388100","id":"PMC_40388100","title":"Leucine-rich repeat-containing 56 promotes breast cancer progression via modulation of the RhoA/ROCKs signaling axis.","date":"2025","source":"Molecular biomedicine","url":"https://pubmed.ncbi.nlm.nih.gov/40388100","citation_count":2,"is_preprint":false},{"pmid":"38498551","id":"PMC_38498551","title":"Gene dosage of independent dynein arm motor preassembly factors influences cilia assembly in Chlamydomonas reinhardtii.","date":"2024","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/38498551","citation_count":2,"is_preprint":false},{"pmid":"41477643","id":"PMC_41477643","title":"LRRC56 deficiency cause motile ciliopathies in humans and mice.","date":"2025","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41477643","citation_count":1,"is_preprint":false},{"pmid":"39875822","id":"PMC_39875822","title":"Application of copy number variation sequencing combined with whole exome sequencing in prenatal left-right asymmetry disorders.","date":"2025","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/39875822","citation_count":1,"is_preprint":false},{"pmid":"40631331","id":"PMC_40631331","title":"Physical and functional interaction of Lrrc56 and Odad3 controls deployment of axonemal dyneins in vertebrate multiciliated cells.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40631331","citation_count":0,"is_preprint":false},{"pmid":"41229303","id":"PMC_41229303","title":"Physical and functional interaction of the ciliopathy proteins Lrrc56 and Odad3 control deployment of axonemal dyneins in vertebrate multiciliated cells.","date":"2025","source":"Disease models & mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/41229303","citation_count":0,"is_preprint":false},{"pmid":"40467998","id":"PMC_40467998","title":"The prevalence of laterality defects in patients with congenital heart disease.","date":"2025","source":"Journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40467998","citation_count":0,"is_preprint":false},{"pmid":"40926959","id":"PMC_40926959","title":"Genetic Variants Linked to Dyslexia Co-Morbid ADHD: A Case Study of a Pakistani Outpatient.","date":"2024","source":"Journal of population therapeutics and clinical pharmacology = Journal de la therapeutique des populations et de la pharmacologie clinique","url":"https://pubmed.ncbi.nlm.nih.gov/40926959","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10715,"output_tokens":2988,"usd":0.038483,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10328,"output_tokens":3284,"usd":0.06687,"stage2_stop_reason":"end_turn"},"total_usd":0.105353,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"ODA8 (LRRC56 ortholog in Chlamydomonas) is required for cytoplasmic preassembly of outer dynein arm (ODA) complexes; dynein in oda8 mutant cytoplasm has not properly preassembled and cannot bind normally onto axonemes. ODA8 distribution between cytoplasm and flagella mirrors IFT proteins, and ~half of flagellar ODA8 is in the soluble matrix fraction, supporting a role in dynein assembly/transport rather than axonemal docking. Dynein extracted from wild-type axonemes rebinds to oda8 mutant axonemes without re-binding of ODA8, further excluding a docking role.\",\n      \"method\": \"Positional cloning, flagellar fractionation, in vitro dynein rebinding assays, cytoplasmic ODA preassembly assays, phylogenomics\",\n      \"journal\": \"Cytoskeleton (Hoboken, N.J.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal biochemical assays (fractionation, in vitro rebinding, cytoplasmic preassembly) in a single focused study on the direct ortholog\",\n      \"pmids\": [\"25558044\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"LRRC56 physically interacts with the IFT protein IFT88 (demonstrated by co-immunoprecipitation). In Trypanosoma brucei, LRRC56 is recruited to the cilium during axoneme construction, co-localizes with IFT trains, and is required for the addition of outer dynein arms to the distal end of the flagellum. Loss-of-function (null) or the p.Leu259Pro variant (equivalent to human p.Leu140Pro) causes abnormal ciliary beat patterns and absence of outer dynein arms restricted to the distal portion of the axoneme.\",\n      \"method\": \"Co-immunoprecipitation (LRRC56–IFT88), LRRC56-null and point-mutant T. brucei models, immunofluorescence co-localization with IFT trains, transmission electron microscopy, high-speed video microscopy\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP plus in vivo model with null and patient-variant alleles, multiple orthogonal methods, replicated across two model systems\",\n      \"pmids\": [\"30388400\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In Trypanosoma brucei, LRRC56 is a transient IFT cargo during flagellum construction and is required for efficient attachment of a subset of docking complex proteins (specifically those present in the distal portion of the organelle). The relationship is interdependent: knockdown of the distal docking complex also prevents LRRC56 association with the flagellum. lrrc56−/− cells display shorter flagella with delayed maturation. Inhibition of cell division compensates for distal ODA absence by redistributing the proximal docking complex, restoring ODA attachment but not flagellum length.\",\n      \"method\": \"LRRC56 knockout in T. brucei, IFT co-localization assays, docking complex knockdown epistasis, transmission electron microscopy, immunofluorescence, cell-division inhibition rescue experiment\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with rescue experiment, multiple orthogonal imaging and ultrastructural methods, single focused study with rigorous controls\",\n      \"pmids\": [\"38865178\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"In Chlamydomonas, ODA8 (LRRC56 ortholog) flagellar localization depends on ODA5 and ODA10; ODA10 is present on oda8-mutant flagella at wild-type levels, establishing that ODA8 acts downstream of ODA5/ODA10 for dynein arm assembly. Genetic interaction among ODA5, ODA8, and ODA10 loci was confirmed.\",\n      \"method\": \"Positional cloning of ODA10, immunofluorescence of ODA10p on oda8-mutant flagella, genetic interaction/epistasis analysis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis and direct protein localization in mutant backgrounds, single lab, two orthogonal methods\",\n      \"pmids\": [\"24088566\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In Xenopus laevis multiciliated cells, loss of lrrc56 causes specific depletion of outer dynein arms (ODAs) from the distal axoneme. In vivo affinity purification–mass spectrometry revealed that Lrrc56 physically interacts with ODA docking complex components including Odad3. Lrrc56 knockdown also leads to distal loss of Odad3. Disease-associated variants in LRRC56 and ODAD3 disrupt their localization and interaction, placing both proteins in a shared functional pathway for distal ODA and docking complex deployment.\",\n      \"method\": \"Targeted knockdown in Xenopus laevis multiciliated cells, in vivo affinity purification–mass spectrometry (AP-MS), in vivo imaging, disease-variant functional analysis\",\n      \"journal\": \"Disease models & mechanisms\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — AP-MS interactome plus in vivo knockdown with defined phenotype plus disease-variant validation, multiple orthogonal methods in a single focused study\",\n      \"pmids\": [\"41229303\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LRRC56 preprint (bioRxiv version): same findings as the peer-reviewed paper — Lrrc56 binds Odad3 (ODA docking complex component) by in vivo AP-MS; lrrc56 knockdown in Xenopus depletes ODAs and Odad3 specifically from the distal axoneme; disease-associated variants in LRRC56 and ODAD3 disrupt their localization and interaction.\",\n      \"method\": \"In vivo AP-MS, targeted knockdown, in vivo imaging in Xenopus laevis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — preprint version of peer-reviewed study; same data, confidence deferred to published paper\",\n      \"pmids\": [\"40631331\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LRRC56-knockout mice (CRISPR/Cas9 targeting exons 4–5) show absence of both inner dynein arm marker DNALI1 and outer dynein arm marker DNAI2 in cilia by immunofluorescence, and transmission electron microscopy reveals dynein arm defects and disorganized axonemal structure in flagella, establishing LRRC56 as required for dynein arm assembly in vivo in a mammalian model.\",\n      \"method\": \"CRISPR/Cas9 knockout mouse, transmission electron microscopy, immunofluorescence with dynein arm markers (DNALI1, DNAI2)\",\n      \"journal\": \"Biology open\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO with defined cellular phenotype confirmed by both ultrastructural (TEM) and molecular (IF) readouts\",\n      \"pmids\": [\"39912490\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Quantitative proteomic analysis of Lrrc56-knockout mouse tissues revealed markedly reduced expression of microtubule inner proteins (MIPs) and axonemal dynein assembly factors compared to wild-type, indicating LRRC56 is required for the normal abundance of multiple cilia-associated structural proteins beyond dynein arms alone.\",\n      \"method\": \"CRISPR/Cas9 Lrrc56-knockout mice, quantitative proteomics of ciliary tissues\",\n      \"journal\": \"Frontiers in genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — quantitative proteomics in KO vs. WT, single lab, single method for the broad proteome finding\",\n      \"pmids\": [\"41477643\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LRRC56 interacts with IFT88 in breast cancer cells and regulates YAP1 expression via modulation of the RhoA/ROCK signaling pathway; LRRC56 overexpression promotes proliferation, migration, invasion, and EMT, while downregulation inhibits xenograft tumor growth and lung metastasis.\",\n      \"method\": \"In vitro functional assays (proliferation, migration, invasion), in vivo xenograft mouse model, co-immunoprecipitation (LRRC56–IFT88), western blotting for RhoA/ROCK/YAP1 pathway components, EMT markers\",\n      \"journal\": \"Molecular biomedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — Co-IP plus functional KD/OE with defined pathway readouts, single lab, mechanistic context is non-ciliary and novel\",\n      \"pmids\": [\"40388100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In Chlamydomonas, double heterozygosity for oda8 (LRRC56 ortholog) and pf23 (DNAAF4 ortholog) reduces cilia assembly in a sensitized (protein-synthesis-inhibited) assay, demonstrating dosage-dependent genetic interaction between LRRC56 and DNAAF4 in outer and inner dynein arm assembly.\",\n      \"method\": \"Second-site non-complementation screen in Chlamydomonas diploids, ciliary assembly assay under cycloheximide, immunoblotting for PF23 levels\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis confirmed by dosage assay and immunoblot, single study, sensitized-assay context\",\n      \"pmids\": [\"38498551\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LRRC56 is a dynein axonemal assembly factor (DNAAF12) that acts as a transient IFT cargo during cilia/flagella construction: it physically interacts with IFT88 and travels along IFT trains to promote cytoplasmic preassembly of outer dynein arm (ODA) complexes and their transport to — and attachment at — the distal axoneme, where it also engages the ODA docking complex component ODAD3; loss of LRRC56 in multiple organisms (Chlamydomonas, Trypanosoma brucei, Xenopus, mouse) consistently causes deficient or absent ODAs preferentially at the distal axoneme, dyskinetic cilia, and PCD-spectrum phenotypes, while in a non-ciliary context LRRC56 has additionally been shown to interact with IFT88 to modulate RhoA/ROCK/YAP1 signaling in cancer cells.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LRRC56 (DNAAF12) is a dynein axonemal assembly factor required for the construction of motile cilia and flagella, acting in the cytoplasmic preassembly and intraflagellar delivery of dynein arm complexes [#0, #1]. Studies of its Chlamydomonas ortholog ODA8 established that it promotes proper cytoplasmic preassembly of outer dynein arm (ODA) complexes so they can dock onto axonemes, while excluding a direct structural docking role; its partition between cytoplasm and flagella mirrors that of intraflagellar transport (IFT) proteins [#0], and it functions genetically downstream of ODA5/ODA10 [#3]. LRRC56 physically interacts with the IFT protein IFT88 and travels as a transient IFT cargo with IFT trains during axoneme construction, delivering ODAs to and promoting their attachment at the distal axoneme [#1, #2]. At the distal axoneme it engages ODA docking complex components, binding ODAD3/Odad3, and its loss specifically depletes both ODAs and the distal docking complex; disease-associated LRRC56 and ODAD3 variants disrupt this interaction and localization, placing the two proteins in a shared distal-ODA deployment pathway [#4]. Consistent across organisms, loss of LRRC56 causes preferential distal-axoneme ODA deficiency, dyskinetic ciliary beating, and dynein arm defects \\u2014 in mouse knockouts it abolishes both inner (DNALI1) and outer (DNAI2) dynein arm markers and disorganizes axonemal ultrastructure [#1, #6]. Beyond its ciliary role, LRRC56 interacts with IFT88 in breast cancer cells to modulate RhoA/ROCK/YAP1 signaling, promoting proliferation, migration, and metastasis [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Placing LRRC56 within the dynein assembly genetic hierarchy addressed where it acts relative to other ODA assembly factors.\",\n      \"evidence\": \"Positional cloning and immunofluorescence/epistasis analysis of ODA5, ODA8, ODA10 in Chlamydomonas mutants\",\n      \"pmids\": [\"24088566\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Does not define the biochemical activity of ODA8/LRRC56 itself\",\n        \"Mechanism of how ODA5/ODA10 recruit ODA8 to flagella unresolved\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Established that LRRC56/ODA8 functions in cytoplasmic preassembly and transport of ODA complexes rather than as a docking factor, defining its core molecular role.\",\n      \"evidence\": \"Flagellar fractionation, in vitro dynein rebinding assays, and cytoplasmic ODA preassembly assays in Chlamydomonas oda8 mutants\",\n      \"pmids\": [\"25558044\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Direct enzymatic/biochemical activity of the protein not defined\",\n        \"Did not identify physical interaction partners\",\n        \"Distal-specific phenotype not yet observed in this system\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identified LRRC56 as an IFT88-interacting transient cargo that delivers ODAs to the distal axoneme, and linked a patient variant to a defined ciliary defect.\",\n      \"evidence\": \"Co-immunoprecipitation with IFT88, null and p.Leu259Pro point-mutant T. brucei models, IFT co-localization, TEM, and high-speed video microscopy\",\n      \"pmids\": [\"30388400\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Structural basis of the LRRC56\\u2013IFT88 interaction unknown\",\n        \"Why ODA loss is restricted to the distal axoneme not yet explained\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Resolved the interdependence between LRRC56 and the distal docking complex, showing reciprocal requirement for flagellar association and ODA attachment.\",\n      \"evidence\": \"LRRC56 knockout, IFT co-localization, docking complex knockdown epistasis, and cell-division-inhibition rescue in T. brucei\",\n      \"pmids\": [\"38865178\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Molecular identity of the direct docking-complex contact in trypanosomes not specified\",\n        \"Mechanism coupling flagellum length defect to ODA deployment unresolved\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstrated a dosage-dependent genetic interaction with DNAAF4, embedding LRRC56 in a broader network of dynein assembly factors.\",\n      \"evidence\": \"Second-site non-complementation screen with sensitized ciliary assembly assay in Chlamydomonas oda8/pf23 diploids\",\n      \"pmids\": [\"38498551\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Whether the interaction is physical or purely genetic not established\",\n        \"Sensitized-assay context may not reflect normal physiology\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined the direct docking-complex partner ODAD3 and unified LRRC56 and ODAD3 disease variants in one distal-ODA deployment pathway.\",\n      \"evidence\": \"In vivo AP-MS, targeted knockdown, in vivo imaging, and disease-variant functional analysis in Xenopus multiciliated cells\",\n      \"pmids\": [\"41229303\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Stoichiometry and structure of the LRRC56\\u2013Odad3 complex unknown\",\n        \"Whether LRRC56 directly hands off ODAs to the docking complex not shown\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Confirmed LRRC56 is required for dynein arm assembly in a mammalian system, extending the conserved phenotype to mouse.\",\n      \"evidence\": \"CRISPR/Cas9 knockout mice analyzed by TEM and immunofluorescence for DNALI1 and DNAI2\",\n      \"pmids\": [\"39912490\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Loss of both inner and outer arm markers not mechanistically dissected\",\n        \"Distal-specific spatial pattern not resolved in mouse\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Broadened LRRC56's required role beyond dynein arms to the abundance of microtubule inner proteins and other axonemal factors.\",\n      \"evidence\": \"Quantitative proteomics of Lrrc56-knockout versus wild-type mouse ciliary tissues\",\n      \"pmids\": [\"41477643\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Whether reduced MIP abundance is direct or secondary to ciliary disorganization unknown\",\n        \"Single-method finding without orthogonal confirmation\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealed a non-ciliary function in which LRRC56\\u2013IFT88 modulates RhoA/ROCK/YAP1 signaling to drive cancer cell behavior.\",\n      \"evidence\": \"Co-IP, functional KD/OE assays, xenograft model, and western blotting for pathway and EMT markers in breast cancer cells\",\n      \"pmids\": [\"40388100\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Direct biochemical link between IFT88 binding and RhoA activation not established\",\n        \"Single lab, single cancer context\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical activity of LRRC56 itself and the molecular basis for the distal-axoneme specificity of ODA delivery remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"No enzymatic activity or structural model for LRRC56 reported\",\n        \"Mechanism restricting ODA loss to the distal axoneme unresolved\",\n        \"How the ciliary and cancer-signaling roles relate is unknown\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1, 2, 4, 6]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 1, 4, 6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"IFT88\",\n      \"ODAD3\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":5,"faith_total":6,"faith_pct":83.33333333333333}}