{"gene":"HYDIN","run_date":"2026-04-28T18:06:53","timeline":{"discoveries":[{"year":2007,"finding":"Chlamydomonas reinhardtii hydin is a central pair (CP) protein localized specifically to the C2 microtubule of the CP apparatus; 80% knockdown results in loss of the C2b projection and flagellar arrest at switch points between effective and recovery strokes; biochemical analyses revealed hydin interacts with CP proteins CPC1 and kinesin-like protein 1 (KLP1), placing hydin in the CP-radial spoke control pathway that regulates dynein arm activity.","method":"Antibody localization (immunodecoration of C2 microtubule), RNAi knockdown, co-immunoprecipitation/biochemical interaction assays, electron microscopy","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods (localization, knockdown phenotype, biochemical interaction) in single rigorous study","pmids":["17296796"],"is_preprint":false},{"year":2008,"finding":"Mouse Hydin is required for normal ciliary motility; Hydin-mutant cilia have a normal 9+2 axoneme with normal dynein arms and radial spokes but lack a specific projection on one of the two central microtubules, resulting in reduced ciliary beat frequency, tendency to stall, inability to generate fluid flow, and consequent hydrocephalus.","method":"Electron microscopy ultrastructural analysis, high-speed videomicroscopy, ciliary beat frequency measurement, morphological comparison of wild-type vs. mutant mouse cilia","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — direct loss-of-function in vivo with defined ultrastructural and functional phenotype, replicated across brain and trachea cilia","pmids":["18250199"],"is_preprint":false},{"year":2007,"finding":"In Trypanosoma brucei, RNAi-mediated loss of Hydin causes misposition of the central pair microtubules at early time points and complete loss of the central pair at later time points, with both defects originating at the basal plate, demonstrating Hydin's role in positioning and maintaining central pair microtubules throughout the axoneme length.","method":"RNAi in Trypanosoma brucei, electron microscopy of flagellar ultrastructure, motility assays","journal":"BMC biology","confidence":"Medium","confidence_rationale":"Tier 2 — clean RNAi knockdown with defined ultrastructural phenotype in a ciliated model organism","pmids":["17683645"],"is_preprint":false},{"year":2003,"finding":"Mouse Hydin is expressed in ciliated ependymal cells lining brain ventricles, ciliated bronchial and oviductal epithelium, and developing spermatocytes; a single CG deletion in exon 15 in hy3 mutants creates a premature stop codon eliminating 89% of the protein, causing lethal hydrocephalus. The Hydin protein contains a domain homologous to caldesmon, an actin-binding protein, suggesting a cytoskeletal interaction.","method":"Positional cloning, cDNA selection, Northern analysis, sequencing of hy3 mutant allele, in situ expression analysis","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — original gene identification with allele-specific mutation and expression data; foundational paper with 129 citations","pmids":["12719380"],"is_preprint":false},{"year":2012,"finding":"Homozygous loss-of-function mutations in human HYDIN cause primary ciliary dyskinesia with markedly reduced respiratory cilia beating amplitude and stiff sperm flagella, but without left-right body asymmetry randomization; electron microscopy tomography of HYDIN-mutant respiratory cilia demonstrates absence of the C2b projection of the central pair apparatus, consistent with HYDIN being the structural component responsible for this projection.","method":"Homozygosity mapping, whole-exome sequencing, electron microscopy tomography of respiratory cilia, high-speed videomicroscopy","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 — human genetic loss-of-function with direct ultrastructural validation, replicated in multiple families; 229 citations","pmids":["23022101"],"is_preprint":false},{"year":2020,"finding":"The CP-associated protein SPEF2 is absent from cilia of HYDIN-mutant cells, revealing that SPEF2 localization to the central pair apparatus depends on functional HYDIN; this interaction is also observed in sperm flagella where HYDIN and SPEF2 show co-dependent localization.","method":"Immunofluorescence microscopy of respiratory cilia and sperm from HYDIN-mutant individuals, genetic confirmation by next-generation sequencing","journal":"American journal of respiratory cell and molecular biology","confidence":"Medium","confidence_rationale":"Tier 3 — IF showing dependency of SPEF2 on HYDIN, replicated across multiple HYDIN-mutant individuals but no direct biochemical interaction assay","pmids":["31545650"],"is_preprint":false},{"year":2018,"finding":"HYDIN is essential for spermiogenesis in mice; Hydin-disrupted spermatozoa have short tails and are completely immotile, demonstrating a direct structural role of HYDIN in sperm flagella assembly and motility.","method":"CRISPR/Cas9 disruption of Hydin in ES cells, chimeric mouse generation, fluorescent sperm motility analysis, ICSI rescue experiment","journal":"Experimental animals","confidence":"Medium","confidence_rationale":"Tier 2 — clean gene disruption with specific structural phenotype in sperm flagella","pmids":["30089752"],"is_preprint":false},{"year":2020,"finding":"HYDIN functions as a positive regulator of cardiomyocyte differentiation in human embryonic stem cells by promoting GATA4 expression; cardiac-specific Hydin knockdown in mice leads to Gata4 downregulation and increased atrial septal defect risk; a human HYDIN variant (c.A2207C) reduces GATA4 expression in differentiating hESC cells.","method":"siRNA knockdown, overexpression, shRNA-GATA4 cDNA rescue in hESC cardiac differentiation; shRNA transgenic mice; cardiac-specific knockdown with ASD phenotyping","journal":"Mechanisms of development","confidence":"Low","confidence_rationale":"Tier 3 — single lab, mechanistic link between HYDIN and GATA4 is indirect; not replicated; ciliary context for this non-ciliary function is unclear","pmids":["32376282"],"is_preprint":false},{"year":2023,"finding":"Loss of HYDIN function in sperm causes absence or severe reduction of flagellar components including SPEF2, SPAG6, RSPHs, TOMM20, SEPT4, and acrosome/centrosome markers (ACTL7A, ACROSIN, PLCζ1, Centrin1), indicating HYDIN is required for the structural integrity of multiple flagellar compartments beyond the central pair.","method":"Whole-exome sequencing, western blot, immunostaining of sperm from HYDIN compound heterozygous patients, transmission electron microscopy","journal":"Frontiers in endocrinology","confidence":"Low","confidence_rationale":"Tier 3 — single case with multiple markers, but single lab and limited controls","pmids":["36742411"],"is_preprint":false},{"year":2024,"finding":"In situ cryo-electron tomography of mouse sperm axoneme at sub-nanometer resolution identified HYDIN as a long chain-like ASH-domain-containing protein responsible for connecting central pair microtubules C1 and C2; atomic model built with AlphaFold2 assigns HYDIN to the C1-C2 bridge in the central apparatus.","method":"In situ cryo-electron tomography, near-complete atomic model building with AlphaFold2, Cfap47 knockout mouse validation","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 — in-cell structural determination at sub-nanometer resolution with functional validation, but preprint not yet peer-reviewed","pmids":["bio_10.1101_2024.08.06.606614"],"is_preprint":true},{"year":2023,"finding":"Pathogenic HYDIN variants in sperm cause absence of SPEF2 in sperm flagella, and pathogenic CCDC39 variants cause absence of CCDC39 and SPEF2, revealing a co-dependent interaction between HYDIN and SPEF2 in sperm flagella analogous to what is seen in respiratory cilia.","method":"Immunofluorescence microscopy on sperm from genetically confirmed HYDIN-mutant individuals, next-generation sequencing, transmission electron microscopy","journal":"Frontiers in genetics","confidence":"Medium","confidence_rationale":"Tier 3 — IF co-dependency replicated across multiple mutation carriers in independent cohort, corroborating earlier respiratory cilia findings","pmids":["36873931"],"is_preprint":false}],"current_model":"HYDIN encodes a large axonemal central pair (CP) apparatus protein that localizes specifically to the C2 microtubule (C2b projection) of the 9+2 axoneme in motile cilia and sperm flagella; it physically connects C1 and C2 microtubules, interacts with CP proteins CPC1 and KLP1, and is required for normal ciliary beat waveform and dynein arm regulation via the CP-radial spoke signaling pathway, such that its loss causes absence of the C2b projection, severely reduced or absent ciliary motility, hydrocephalus, primary ciliary dyskinesia, and male infertility."},"narrative":{"teleology":[{"year":2003,"claim":"Identification of Hydin as the gene mutated in hy3 hydrocephalic mice established that this large, previously uncharacterized gene is expressed in ciliated epithelia and spermatocytes and is essential for brain ventricular function.","evidence":"Positional cloning and cDNA selection in hy3 mutant mice; Northern and in situ hybridization for expression","pmids":["12719380"],"confidence":"High","gaps":["No ultrastructural basis for the hydrocephalus phenotype was determined","Protein localization within the cilium was unknown","Whether Hydin functions in ciliary motility per se or in ciliogenesis was unclear"]},{"year":2007,"claim":"Localization of Hydin to the C2 microtubule of the central pair and demonstration that its depletion removes the C2b projection and arrests flagellar beating at stroke transition points established HYDIN as a CP structural protein that regulates dynein-driven motility via the CP–radial spoke pathway.","evidence":"Antibody immunodecoration of isolated Chlamydomonas axonemes, RNAi knockdown, co-IP with CPC1 and KLP1, electron microscopy","pmids":["17296796"],"confidence":"High","gaps":["Whether the same C2b-specific role applies in vertebrate cilia was untested","The precise molecular contacts between HYDIN and other CP proteins were unresolved","Trypanosoma RNAi showed a more severe complete CP loss phenotype, leaving species-specific functions uncertain"]},{"year":2008,"claim":"Extending the Chlamydomonas findings to mammals, analysis of Hydin-mutant mouse cilia showed that HYDIN is required for normal ciliary beat frequency and fluid flow, with loss of a specific central microtubule projection but intact dynein arms and radial spokes, confirming a conserved structural role.","evidence":"Electron microscopy and high-speed videomicroscopy of brain ependymal and tracheal cilia from Hydin-mutant mice","pmids":["18250199"],"confidence":"High","gaps":["Human disease relevance had not yet been demonstrated","Which central microtubule projection was lost (C2b vs. other) could not be unambiguously assigned in mouse EM"]},{"year":2012,"claim":"Discovery that homozygous HYDIN mutations cause human primary ciliary dyskinesia without laterality defects, combined with electron tomography confirming C2b projection loss, established HYDIN as a PCD disease gene and demonstrated that the CP apparatus is dispensable for left-right axis determination.","evidence":"Homozygosity mapping and whole-exome sequencing in consanguineous families; electron tomography of patient respiratory cilia; high-speed videomicroscopy","pmids":["23022101"],"confidence":"High","gaps":["Male infertility phenotype in human HYDIN mutation carriers was not yet characterized","Downstream molecular consequences of C2b loss on other CP components were unknown"]},{"year":2018,"claim":"CRISPR disruption of Hydin in mice demonstrated that HYDIN is essential for spermiogenesis, with mutant spermatozoa showing short immotile tails, extending HYDIN's functional requirement to mammalian sperm flagella.","evidence":"CRISPR/Cas9 disruption in mouse ES cells, chimeric mice, fluorescent sperm motility analysis, ICSI rescue","pmids":["30089752"],"confidence":"Medium","gaps":["Whether the flagellar defect reflects CP-specific loss or broader structural disassembly was not determined","Ultrastructural analysis of the sperm central pair was not performed"]},{"year":2020,"claim":"Demonstration that SPEF2 fails to localize to cilia and sperm flagella in HYDIN-mutant individuals revealed a co-dependent relationship between these two CP proteins, defining HYDIN as required for SPEF2 recruitment to the central apparatus.","evidence":"Immunofluorescence of respiratory cilia and sperm from genetically confirmed HYDIN-mutant patients","pmids":["31545650"],"confidence":"Medium","gaps":["Whether HYDIN and SPEF2 interact directly or co-depend through a shared structural scaffold was not resolved","No biochemical interaction assay between HYDIN and SPEF2 was performed"]},{"year":2024,"claim":"Sub-nanometer cryo-electron tomography of mouse sperm axonemes resolved HYDIN as a chain-like ASH-domain protein forming the C1–C2 bridge of the central apparatus, providing the first near-atomic structural model of HYDIN within the intact axoneme.","evidence":"In situ cryo-ET of mouse sperm with AlphaFold2-assisted atomic model building (preprint)","pmids":["bio_10.1101_2024.08.06.606614"],"confidence":"Medium","gaps":["Preprint not yet peer-reviewed","Structural model has not been validated by mutagenesis of predicted contact sites","How the C1–C2 bridge mediates signal transduction to dynein arms is structurally unresolved"]},{"year":null,"claim":"The precise mechanism by which HYDIN transmits regulatory signals from the central pair to dynein arms via radial spokes, and the structural basis of its interactions with CPC1, KLP1, and SPEF2, remain unresolved at atomic resolution.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of HYDIN in complex with CPC1 or KLP1 exists","The caldesmon-homology domain's function within the axoneme is uncharacterized","Whether HYDIN has non-ciliary functions (e.g., in cardiogenesis) requires independent replication"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1,4,9]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,3]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,1,3,4]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0,1,9]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,1,4,6]}],"complexes":["Central pair apparatus (C2b projection / C1-C2 bridge)"],"partners":["CPC1","KLP1","SPEF2","SPAG6"],"other_free_text":[]},"mechanistic_narrative":"HYDIN encodes a large axonemal protein that is a structural component of the central pair (CP) apparatus in motile 9+2 cilia and sperm flagella, where it localizes specifically to the C2b projection and forms a chain-like bridge connecting the C1 and C2 central microtubules [PMID:17296796, PMID:18250199, PMID:23022101]. Loss of HYDIN eliminates the C2b projection, disrupts ciliary beat waveform and flagellar motility, abolishes SPEF2 recruitment to the CP, and impairs the CP–radial spoke signaling pathway that regulates dynein arm activity [PMID:17296796, PMID:31545650, PMID:30089752]. In Chlamydomonas, HYDIN physically interacts with CP proteins CPC1 and KLP1 [PMID:17296796]. Homozygous loss-of-function mutations in human HYDIN cause primary ciliary dyskinesia characterized by reduced respiratory ciliary beating and male infertility without situs inversus, and in mice Hydin mutations produce lethal hydrocephalus [PMID:23022101, PMID:12719380]."},"prefetch_data":{"uniprot":{"accession":"Q4G0P3","full_name":"Hydrocephalus-inducing protein homolog","aliases":[],"length_aa":5121,"mass_kda":575.9,"function":"Required for ciliary motility","subcellular_location":"Cell projection, cilium; Cytoplasm, cytoskeleton, cilium axoneme; Cell projection, cilium, flagellum","url":"https://www.uniprot.org/uniprotkb/Q4G0P3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/HYDIN","classification":"Not Classified","n_dependent_lines":99,"n_total_lines":1208,"dependency_fraction":0.08195364238410596},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/HYDIN","total_profiled":1310},"omim":[{"mim_id":"615434","title":"RETINITIS PIGMENTOSA 82 WITH OR WITHOUT SITUS INVERSUS; RP82","url":"https://www.omim.org/entry/615434"},{"mim_id":"615407","title":"ADP-RIBOSYLATION FACTOR-LIKE GTPase 2-BINDING PROTEIN; ARL2BP","url":"https://www.omim.org/entry/615407"},{"mim_id":"612475","title":"CHROMOSOME 1q21.1 DUPLICATION SYNDROME","url":"https://www.omim.org/entry/612475"},{"mim_id":"612474","title":"CHROMOSOME 1q21.1 DELETION SYNDROME, 1.35-MB","url":"https://www.omim.org/entry/612474"},{"mim_id":"611679","title":"F-BOX AND WD40 DOMAIN PROTEIN 10; FBXW10","url":"https://www.omim.org/entry/611679"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytokinetic bridge","reliability":"Approved"},{"location":"Primary cilium","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Equatorial segment","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Mitotic spindle","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"fallopian tube","ntpm":5.0},{"tissue":"retina","ntpm":6.3}],"url":"https://www.proteinatlas.org/search/HYDIN"},"hgnc":{"alias_symbol":["DKFZp434D0513","KIAA1864","PPP1R31","CILD5"],"prev_symbol":[]},"alphafold":{"accession":"Q4G0P3","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q4G0P3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q4G0P3-8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q4G0P3-8-F1-predicted_aligned_error_v6.png","plddt_mean":84.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=HYDIN","jax_strain_url":"https://www.jax.org/strain/search?query=HYDIN"},"sequence":{"accession":"Q4G0P3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q4G0P3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q4G0P3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q4G0P3"}},"corpus_meta":[{"pmid":"23022101","id":"PMC_23022101","title":"Recessive HYDIN mutations cause primary ciliary dyskinesia without randomization of left-right body asymmetry.","date":"2012","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23022101","citation_count":229,"is_preprint":false},{"pmid":"18250199","id":"PMC_18250199","title":"Mutations in Hydin impair ciliary motility in mice.","date":"2008","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/18250199","citation_count":207,"is_preprint":false},{"pmid":"12719380","id":"PMC_12719380","title":"Congenital hydrocephalus in hy3 mice is caused by a frameshift mutation in Hydin, a large novel gene.","date":"2003","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/12719380","citation_count":129,"is_preprint":false},{"pmid":"17296796","id":"PMC_17296796","title":"Chlamydomonas reinhardtii hydin is a central pair protein required for flagellar motility.","date":"2007","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/17296796","citation_count":119,"is_preprint":false},{"pmid":"17683645","id":"PMC_17683645","title":"The hydrocephalus inducing gene product, Hydin, positions axonemal central pair microtubules.","date":"2007","source":"BMC biology","url":"https://pubmed.ncbi.nlm.nih.gov/17683645","citation_count":62,"is_preprint":false},{"pmid":"31545650","id":"PMC_31545650","title":"SPEF2- and HYDIN-Mutant Cilia Lack the Central Pair-associated Protein SPEF2, Aiding Primary Ciliary Dyskinesia Diagnostics.","date":"2020","source":"American journal of respiratory cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/31545650","citation_count":57,"is_preprint":false},{"pmid":"24700285","id":"PMC_24700285","title":"Precise genetic mapping and integrative bioinformatics in Diversity Outbred mice reveals Hydin as a novel pain gene.","date":"2014","source":"Mammalian genome : official journal of the International Mammalian Genome Society","url":"https://pubmed.ncbi.nlm.nih.gov/24700285","citation_count":46,"is_preprint":false},{"pmid":"16938426","id":"PMC_16938426","title":"A 360-kb interchromosomal duplication of the human HYDIN locus.","date":"2006","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/16938426","citation_count":40,"is_preprint":false},{"pmid":"36873931","id":"PMC_36873931","title":"Pathogenic gene variants in CCDC39, CCDC40, RSPH1, RSPH9, HYDIN, and SPEF2 cause defects of sperm flagella composition and male infertility.","date":"2023","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36873931","citation_count":24,"is_preprint":false},{"pmid":"30089752","id":"PMC_30089752","title":"Chimeric analysis with newly established EGFP/DsRed2-tagged ES cells identify HYDIN as essential for spermiogenesis in mice.","date":"2018","source":"Experimental animals","url":"https://pubmed.ncbi.nlm.nih.gov/30089752","citation_count":16,"is_preprint":false},{"pmid":"24777681","id":"PMC_24777681","title":"Alternative variants of human HYDIN are novel cancer-associated antigens recognized by adaptive immunity.","date":"2013","source":"Cancer immunology research","url":"https://pubmed.ncbi.nlm.nih.gov/24777681","citation_count":14,"is_preprint":false},{"pmid":"17296793","id":"PMC_17296793","title":"Hydin seek: finding a function in ciliary motility.","date":"2007","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/17296793","citation_count":12,"is_preprint":false},{"pmid":"38605126","id":"PMC_38605126","title":"Combined approaches, including long-read sequencing, address the diagnostic challenge of HYDIN in primary ciliary dyskinesia.","date":"2024","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/38605126","citation_count":10,"is_preprint":false},{"pmid":"30155272","id":"PMC_30155272","title":"1q21.1 microduplication: large verbal-nonverbal performance discrepancy and ddPCR assays of HYDIN/HYDIN2 copy number.","date":"2018","source":"NPJ genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/30155272","citation_count":10,"is_preprint":false},{"pmid":"32376282","id":"PMC_32376282","title":"HYDIN loss-of-function inhibits GATA4 expression and enhances atrial septal defect risk.","date":"2020","source":"Mechanisms of development","url":"https://pubmed.ncbi.nlm.nih.gov/32376282","citation_count":4,"is_preprint":false},{"pmid":"39317196","id":"PMC_39317196","title":"Heterozygous cis HYDIN mutations cause primary ciliary dyskinesia.","date":"2024","source":"Med (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/39317196","citation_count":4,"is_preprint":false},{"pmid":"36742411","id":"PMC_36742411","title":"Novel HYDIN variants associated with male infertility in two Chinese families.","date":"2023","source":"Frontiers in endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/36742411","citation_count":4,"is_preprint":false},{"pmid":"28441829","id":"PMC_28441829","title":"[Primary ciliary dyskinesia with HYDIN gene mutations in a child and literature review].","date":"2017","source":"Zhonghua er ke za zhi = Chinese journal of pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/28441829","citation_count":3,"is_preprint":false},{"pmid":"39805680","id":"PMC_39805680","title":"Robust detection of pathogenic HYDIN variants that cause primary ciliary dyskinesia using RNA-seq of nasal mucosa.","date":"2025","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39805680","citation_count":3,"is_preprint":false},{"pmid":"39579181","id":"PMC_39579181","title":"Hydin as the Candidate Master Sex Determination Gene in Channel Catfish (Ictalurus punctatus) and Its Epigenetic Regulation.","date":"2024","source":"Marine biotechnology (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/39579181","citation_count":1,"is_preprint":false},{"pmid":"39291810","id":"PMC_39291810","title":"HYDIN variants cause primary ciliary dyskinesia in the Finnish population.","date":"2024","source":"Pediatric pulmonology","url":"https://pubmed.ncbi.nlm.nih.gov/39291810","citation_count":1,"is_preprint":false},{"pmid":"39850822","id":"PMC_39850822","title":"The relationship between HYDIN and fallopian tubal cilia loss in patients with epithelial ovarian cancer.","date":"2025","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/39850822","citation_count":0,"is_preprint":false},{"pmid":"41073067","id":"PMC_41073067","title":"Towards a practical tool to identify HYDIN genotype using high-speed videomicroscopy.","date":"2025","source":"Thorax","url":"https://pubmed.ncbi.nlm.nih.gov/41073067","citation_count":0,"is_preprint":false},{"pmid":"37595251","id":"PMC_37595251","title":"HYDIN mutation status as a potential predictor of immune checkpoint inhibitor efficacy in melanoma.","date":"2023","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/37595251","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.05.28.24307879","title":"<i>HYDIN</i>variants cause primary ciliary dyskinesia in the Finnish population","date":"2024-05-28","source":"bioRxiv","url":"https://doi.org/10.1101/2024.05.28.24307879","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.08.06.606614","title":"In-cell structural insight into the asymmetric assembly of central apparatus in mammalian sperm axoneme","date":"2024-08-06","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.06.606614","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13822,"output_tokens":2743,"usd":0.041306},"stage2":{"model":"claude-opus-4-6","input_tokens":6069,"output_tokens":2222,"usd":0.128842},"total_usd":0.170148,"stage1_batch_id":"msgbatch_01DzrsgVgYngY1hvM3DU1yF2","stage2_batch_id":"msgbatch_01KA9b7iRzKFdhoBUT7vCvSe","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"Chlamydomonas reinhardtii hydin is a central pair (CP) protein localized specifically to the C2 microtubule of the CP apparatus; 80% knockdown results in loss of the C2b projection and flagellar arrest at switch points between effective and recovery strokes; biochemical analyses revealed hydin interacts with CP proteins CPC1 and kinesin-like protein 1 (KLP1), placing hydin in the CP-radial spoke control pathway that regulates dynein arm activity.\",\n      \"method\": \"Antibody localization (immunodecoration of C2 microtubule), RNAi knockdown, co-immunoprecipitation/biochemical interaction assays, electron microscopy\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods (localization, knockdown phenotype, biochemical interaction) in single rigorous study\",\n      \"pmids\": [\"17296796\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Mouse Hydin is required for normal ciliary motility; Hydin-mutant cilia have a normal 9+2 axoneme with normal dynein arms and radial spokes but lack a specific projection on one of the two central microtubules, resulting in reduced ciliary beat frequency, tendency to stall, inability to generate fluid flow, and consequent hydrocephalus.\",\n      \"method\": \"Electron microscopy ultrastructural analysis, high-speed videomicroscopy, ciliary beat frequency measurement, morphological comparison of wild-type vs. mutant mouse cilia\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct loss-of-function in vivo with defined ultrastructural and functional phenotype, replicated across brain and trachea cilia\",\n      \"pmids\": [\"18250199\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"In Trypanosoma brucei, RNAi-mediated loss of Hydin causes misposition of the central pair microtubules at early time points and complete loss of the central pair at later time points, with both defects originating at the basal plate, demonstrating Hydin's role in positioning and maintaining central pair microtubules throughout the axoneme length.\",\n      \"method\": \"RNAi in Trypanosoma brucei, electron microscopy of flagellar ultrastructure, motility assays\",\n      \"journal\": \"BMC biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean RNAi knockdown with defined ultrastructural phenotype in a ciliated model organism\",\n      \"pmids\": [\"17683645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Mouse Hydin is expressed in ciliated ependymal cells lining brain ventricles, ciliated bronchial and oviductal epithelium, and developing spermatocytes; a single CG deletion in exon 15 in hy3 mutants creates a premature stop codon eliminating 89% of the protein, causing lethal hydrocephalus. The Hydin protein contains a domain homologous to caldesmon, an actin-binding protein, suggesting a cytoskeletal interaction.\",\n      \"method\": \"Positional cloning, cDNA selection, Northern analysis, sequencing of hy3 mutant allele, in situ expression analysis\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — original gene identification with allele-specific mutation and expression data; foundational paper with 129 citations\",\n      \"pmids\": [\"12719380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Homozygous loss-of-function mutations in human HYDIN cause primary ciliary dyskinesia with markedly reduced respiratory cilia beating amplitude and stiff sperm flagella, but without left-right body asymmetry randomization; electron microscopy tomography of HYDIN-mutant respiratory cilia demonstrates absence of the C2b projection of the central pair apparatus, consistent with HYDIN being the structural component responsible for this projection.\",\n      \"method\": \"Homozygosity mapping, whole-exome sequencing, electron microscopy tomography of respiratory cilia, high-speed videomicroscopy\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — human genetic loss-of-function with direct ultrastructural validation, replicated in multiple families; 229 citations\",\n      \"pmids\": [\"23022101\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The CP-associated protein SPEF2 is absent from cilia of HYDIN-mutant cells, revealing that SPEF2 localization to the central pair apparatus depends on functional HYDIN; this interaction is also observed in sperm flagella where HYDIN and SPEF2 show co-dependent localization.\",\n      \"method\": \"Immunofluorescence microscopy of respiratory cilia and sperm from HYDIN-mutant individuals, genetic confirmation by next-generation sequencing\",\n      \"journal\": \"American journal of respiratory cell and molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — IF showing dependency of SPEF2 on HYDIN, replicated across multiple HYDIN-mutant individuals but no direct biochemical interaction assay\",\n      \"pmids\": [\"31545650\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"HYDIN is essential for spermiogenesis in mice; Hydin-disrupted spermatozoa have short tails and are completely immotile, demonstrating a direct structural role of HYDIN in sperm flagella assembly and motility.\",\n      \"method\": \"CRISPR/Cas9 disruption of Hydin in ES cells, chimeric mouse generation, fluorescent sperm motility analysis, ICSI rescue experiment\",\n      \"journal\": \"Experimental animals\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean gene disruption with specific structural phenotype in sperm flagella\",\n      \"pmids\": [\"30089752\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"HYDIN functions as a positive regulator of cardiomyocyte differentiation in human embryonic stem cells by promoting GATA4 expression; cardiac-specific Hydin knockdown in mice leads to Gata4 downregulation and increased atrial septal defect risk; a human HYDIN variant (c.A2207C) reduces GATA4 expression in differentiating hESC cells.\",\n      \"method\": \"siRNA knockdown, overexpression, shRNA-GATA4 cDNA rescue in hESC cardiac differentiation; shRNA transgenic mice; cardiac-specific knockdown with ASD phenotyping\",\n      \"journal\": \"Mechanisms of development\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, mechanistic link between HYDIN and GATA4 is indirect; not replicated; ciliary context for this non-ciliary function is unclear\",\n      \"pmids\": [\"32376282\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Loss of HYDIN function in sperm causes absence or severe reduction of flagellar components including SPEF2, SPAG6, RSPHs, TOMM20, SEPT4, and acrosome/centrosome markers (ACTL7A, ACROSIN, PLCζ1, Centrin1), indicating HYDIN is required for the structural integrity of multiple flagellar compartments beyond the central pair.\",\n      \"method\": \"Whole-exome sequencing, western blot, immunostaining of sperm from HYDIN compound heterozygous patients, transmission electron microscopy\",\n      \"journal\": \"Frontiers in endocrinology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single case with multiple markers, but single lab and limited controls\",\n      \"pmids\": [\"36742411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In situ cryo-electron tomography of mouse sperm axoneme at sub-nanometer resolution identified HYDIN as a long chain-like ASH-domain-containing protein responsible for connecting central pair microtubules C1 and C2; atomic model built with AlphaFold2 assigns HYDIN to the C1-C2 bridge in the central apparatus.\",\n      \"method\": \"In situ cryo-electron tomography, near-complete atomic model building with AlphaFold2, Cfap47 knockout mouse validation\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — in-cell structural determination at sub-nanometer resolution with functional validation, but preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2024.08.06.606614\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Pathogenic HYDIN variants in sperm cause absence of SPEF2 in sperm flagella, and pathogenic CCDC39 variants cause absence of CCDC39 and SPEF2, revealing a co-dependent interaction between HYDIN and SPEF2 in sperm flagella analogous to what is seen in respiratory cilia.\",\n      \"method\": \"Immunofluorescence microscopy on sperm from genetically confirmed HYDIN-mutant individuals, next-generation sequencing, transmission electron microscopy\",\n      \"journal\": \"Frontiers in genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — IF co-dependency replicated across multiple mutation carriers in independent cohort, corroborating earlier respiratory cilia findings\",\n      \"pmids\": [\"36873931\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"HYDIN encodes a large axonemal central pair (CP) apparatus protein that localizes specifically to the C2 microtubule (C2b projection) of the 9+2 axoneme in motile cilia and sperm flagella; it physically connects C1 and C2 microtubules, interacts with CP proteins CPC1 and KLP1, and is required for normal ciliary beat waveform and dynein arm regulation via the CP-radial spoke signaling pathway, such that its loss causes absence of the C2b projection, severely reduced or absent ciliary motility, hydrocephalus, primary ciliary dyskinesia, and male infertility.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"HYDIN encodes a large axonemal protein that is a structural component of the central pair (CP) apparatus in motile 9+2 cilia and sperm flagella, where it localizes specifically to the C2b projection and forms a chain-like bridge connecting the C1 and C2 central microtubules [PMID:17296796, PMID:18250199, PMID:23022101]. Loss of HYDIN eliminates the C2b projection, disrupts ciliary beat waveform and flagellar motility, abolishes SPEF2 recruitment to the CP, and impairs the CP–radial spoke signaling pathway that regulates dynein arm activity [PMID:17296796, PMID:31545650, PMID:30089752]. In Chlamydomonas, HYDIN physically interacts with CP proteins CPC1 and KLP1 [PMID:17296796]. Homozygous loss-of-function mutations in human HYDIN cause primary ciliary dyskinesia characterized by reduced respiratory ciliary beating and male infertility without situs inversus, and in mice Hydin mutations produce lethal hydrocephalus [PMID:23022101, PMID:12719380].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Identification of Hydin as the gene mutated in hy3 hydrocephalic mice established that this large, previously uncharacterized gene is expressed in ciliated epithelia and spermatocytes and is essential for brain ventricular function.\",\n      \"evidence\": \"Positional cloning and cDNA selection in hy3 mutant mice; Northern and in situ hybridization for expression\",\n      \"pmids\": [\"12719380\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No ultrastructural basis for the hydrocephalus phenotype was determined\",\n        \"Protein localization within the cilium was unknown\",\n        \"Whether Hydin functions in ciliary motility per se or in ciliogenesis was unclear\"\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Localization of Hydin to the C2 microtubule of the central pair and demonstration that its depletion removes the C2b projection and arrests flagellar beating at stroke transition points established HYDIN as a CP structural protein that regulates dynein-driven motility via the CP–radial spoke pathway.\",\n      \"evidence\": \"Antibody immunodecoration of isolated Chlamydomonas axonemes, RNAi knockdown, co-IP with CPC1 and KLP1, electron microscopy\",\n      \"pmids\": [\"17296796\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether the same C2b-specific role applies in vertebrate cilia was untested\",\n        \"The precise molecular contacts between HYDIN and other CP proteins were unresolved\",\n        \"Trypanosoma RNAi showed a more severe complete CP loss phenotype, leaving species-specific functions uncertain\"\n      ]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Extending the Chlamydomonas findings to mammals, analysis of Hydin-mutant mouse cilia showed that HYDIN is required for normal ciliary beat frequency and fluid flow, with loss of a specific central microtubule projection but intact dynein arms and radial spokes, confirming a conserved structural role.\",\n      \"evidence\": \"Electron microscopy and high-speed videomicroscopy of brain ependymal and tracheal cilia from Hydin-mutant mice\",\n      \"pmids\": [\"18250199\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Human disease relevance had not yet been demonstrated\",\n        \"Which central microtubule projection was lost (C2b vs. other) could not be unambiguously assigned in mouse EM\"\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Discovery that homozygous HYDIN mutations cause human primary ciliary dyskinesia without laterality defects, combined with electron tomography confirming C2b projection loss, established HYDIN as a PCD disease gene and demonstrated that the CP apparatus is dispensable for left-right axis determination.\",\n      \"evidence\": \"Homozygosity mapping and whole-exome sequencing in consanguineous families; electron tomography of patient respiratory cilia; high-speed videomicroscopy\",\n      \"pmids\": [\"23022101\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Male infertility phenotype in human HYDIN mutation carriers was not yet characterized\",\n        \"Downstream molecular consequences of C2b loss on other CP components were unknown\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"CRISPR disruption of Hydin in mice demonstrated that HYDIN is essential for spermiogenesis, with mutant spermatozoa showing short immotile tails, extending HYDIN's functional requirement to mammalian sperm flagella.\",\n      \"evidence\": \"CRISPR/Cas9 disruption in mouse ES cells, chimeric mice, fluorescent sperm motility analysis, ICSI rescue\",\n      \"pmids\": [\"30089752\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the flagellar defect reflects CP-specific loss or broader structural disassembly was not determined\",\n        \"Ultrastructural analysis of the sperm central pair was not performed\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstration that SPEF2 fails to localize to cilia and sperm flagella in HYDIN-mutant individuals revealed a co-dependent relationship between these two CP proteins, defining HYDIN as required for SPEF2 recruitment to the central apparatus.\",\n      \"evidence\": \"Immunofluorescence of respiratory cilia and sperm from genetically confirmed HYDIN-mutant patients\",\n      \"pmids\": [\"31545650\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether HYDIN and SPEF2 interact directly or co-depend through a shared structural scaffold was not resolved\",\n        \"No biochemical interaction assay between HYDIN and SPEF2 was performed\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Sub-nanometer cryo-electron tomography of mouse sperm axonemes resolved HYDIN as a chain-like ASH-domain protein forming the C1–C2 bridge of the central apparatus, providing the first near-atomic structural model of HYDIN within the intact axoneme.\",\n      \"evidence\": \"In situ cryo-ET of mouse sperm with AlphaFold2-assisted atomic model building (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.08.06.606614\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Preprint not yet peer-reviewed\",\n        \"Structural model has not been validated by mutagenesis of predicted contact sites\",\n        \"How the C1–C2 bridge mediates signal transduction to dynein arms is structurally unresolved\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The precise mechanism by which HYDIN transmits regulatory signals from the central pair to dynein arms via radial spokes, and the structural basis of its interactions with CPC1, KLP1, and SPEF2, remain unresolved at atomic resolution.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No high-resolution structure of HYDIN in complex with CPC1 or KLP1 exists\",\n        \"The caldesmon-homology domain's function within the axoneme is uncharacterized\",\n        \"Whether HYDIN has non-ciliary functions (e.g., in cardiogenesis) requires independent replication\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 4, 9]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1, 3, 4]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 1, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 1, 4, 6]}\n    ],\n    \"complexes\": [\n      \"Central pair apparatus (C2b projection / C1-C2 bridge)\"\n    ],\n    \"partners\": [\n      \"CPC1\",\n      \"KLP1\",\n      \"SPEF2\",\n      \"SPAG6\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}