{"gene":"HORMAD1","run_date":"2026-04-28T18:06:53","timeline":{"discoveries":[{"year":2009,"finding":"HORMAD1 and HORMAD2 preferentially associate with unsynapsed meiotic chromosome axes and are depleted from synapsed axes; TRIP13 AAA-ATPase is required for this depletion, establishing a mutually exclusive relationship between HORMAD-rich domains and synapsed chromatin.","method":"Immunofluorescence on wild-type and mutant mouse spermatocytes; genetic analysis of TRIP13 mutants","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 — multiple mutant backgrounds, direct localization experiments, replicated by multiple labs","pmids":["19851446"],"is_preprint":false},{"year":2009,"finding":"HORMAD1 associates biochemically and cytologically with the meiotic chromosome axis, accumulating during leptotene-to-zygotene and disappearing from synapsed regions at pachytene, then reappearing upon desynapsis at diplotene; establishment of the synaptonemal complex is required for displacement of HORMAD1 from the axis.","method":"Biochemical fractionation, immunofluorescence, analysis of synaptonemal complex mutant strains","journal":"Experimental cell research","confidence":"High","confidence_rationale":"Tier 2 — biochemical and cytological evidence, multiple SC mutant backgrounds","pmids":["19686734"],"is_preprint":false},{"year":2010,"finding":"HORMAD1 is a component of the synaptonemal complex required for double-strand break formation, early recombination events (γH2AX, DMC1, RAD51, RPA foci), homologous chromosome pairing, and meiotic sex chromosome inactivation (MSCI); HORMAD1 co-localizes with γH2AX, ATR, and BRCA1 at the sex body, and its loss abolishes their localization to sex chromosomes.","method":"Hormad1 knockout mouse, immunofluorescence, electron microscopy","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 — clean KO with specific molecular phenotypes, multiple orthogonal readouts","pmids":["21079677"],"is_preprint":false},{"year":2011,"finding":"HORMAD1 ensures sufficient processed DSBs for homology search, promotes synaptonemal complex formation, and is required for efficient recruitment of ATR checkpoint kinase activity to unsynapsed chromatin; SC formation leads to HORMAD1 depletion from chromosome axes, forming a negative feedback loop that coordinates meiotic progression with homologue alignment.","method":"Hormad1 knockout mouse, immunofluorescence, genetic epistasis","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined molecular phenotypes, mechanistic loop established with epistasis","pmids":["21478856"],"is_preprint":false},{"year":2012,"finding":"HORMAD1 is required for the meiotic prophase checkpoint that eliminates asynaptic oocytes; Hormad1 deficiency abrogates massive oocyte loss in Spo11-deficient ovaries (epistasis); HORMAD1 undergoes extensive phosphorylation in Spo11-deficient testes and ovaries through DNA damage-independent signaling.","method":"Hormad1/Spo11 double mutant mice, genetic epistasis, immunofluorescence, phosphorylation analysis","journal":"Genes to cells","confidence":"High","confidence_rationale":"Tier 2 — double KO epistasis with defined checkpoint phenotype","pmids":["22530760"],"is_preprint":false},{"year":2013,"finding":"HORMAD1 deficiency in oocytes promotes DMC1-independent DSB repair, which enables asynaptic oocytes to resist perinatal loss; Hormad1 deficiency rescues Dmc1−/− oocytes, placing HORMAD1 upstream of DMC1-dependent repair pathway choice.","method":"Hormad1/Dmc1 double mutant mice, irradiation of embryonic ovaries, immunofluorescence for γH2AX, RAD51, DMC1","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with double KO, irradiation rescue experiment","pmids":["23759310"],"is_preprint":false},{"year":2015,"finding":"Elevated HORMAD1 expression in triple-negative breast cancer suppresses RAD51-dependent homologous recombination and drives use of alternative DNA repair pathways, generating allelic-imbalanced copy-number aberrations and sensitizing cancer cells to platinum-based chemotherapy and PARP inhibitors.","method":"HORMAD1 knockdown/overexpression in cancer cell lines, HR reporter assays, genomic copy-number profiling","journal":"Cancer discovery","confidence":"High","confidence_rationale":"Tier 2 — functional HR reporter assays plus genomic readout, mechanistic link established","pmids":["25770156"],"is_preprint":false},{"year":2018,"finding":"In lung adenocarcinoma cells, HORMAD1 redistributes to nuclear foci co-localizing with γH2AX after IR; the HORMA domain and C-terminal disordered oligomerization motif are required for IRIF localization; HORMAD1 promotes DSB resection (RPA-ssDNA foci and RAD51 redistribution to DSBs) and HR-mediated repair but not NHEJ; HORMAD1-mediated HR is independent of meiotic partners HORMAD2 and CCDC36.","method":"HORMAD1 depletion, domain mutant analysis, HR and NHEJ reporter assays, immunofluorescence for RPA and RAD51","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1–2 — reporter assays with domain mutagenesis, multiple orthogonal readouts","pmids":["30333500"],"is_preprint":false},{"year":2018,"finding":"HORMAD1 promotes repair of radiation-induced DSBs at the synaptonemal complex axis and influences DNA repair pathway choice in mouse meiocytes; Spo11/Hormad1 double-KO spermatocytes showed fewer remaining DSB repair foci after irradiation compared to Spo11-KO, indicating HORMAD1 slows repair (repair inhibition role).","method":"Spo11/Hormad1 double knockout mouse, irradiation, immunofluorescence for DSB repair foci","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 2 — double-KO epistasis, single study","pmids":["29414051"],"is_preprint":false},{"year":2020,"finding":"Meiotic cohesins REC8 and RAD21L mediate initial chromatin loading of HORMAD1 prior to axial element formation; HORMAD1 physically interacts with meiotic cohesins (REC8, RAD21L) and with AE components SYCP2 and SYCP3; in Sycp2-KO, HORMAD1 still localizes along cohesin axial cores via cohesins; Hormad1/Rec8-dKO but not Hormad1/Rad21L-dKO shows precocious sister chromatid axis separation.","method":"Co-immunoprecipitation, Sycp2 null mice, Hormad1/Rad21L and Hormad1/Rec8 double KO mice, immunofluorescence","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, multiple double-KO genetic epistasis, replicated across genotypes","pmids":["32931493"],"is_preprint":false},{"year":2020,"finding":"Aberrantly expressed HORMAD1 in cancer cells interacts with the MCM8-MCM9 complex and prevents its efficient nuclear localization, causing reduced MLH1 chromatin binding and DNA mismatch repair defects.","method":"Co-immunoprecipitation, nuclear fractionation, MMR assays in HORMAD1-expressing cancer cell lines","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2–3 — Co-IP plus functional MMR assay, single lab","pmids":["32647118"],"is_preprint":false},{"year":2022,"finding":"HORMAD1 loss-of-function in Hormad1−/− spermatocytes alters the lifetime and size of RAD51/DMC1 recombination intermediate configurations and inhibits coil formation in the synaptonemal complex; SPO11 plays a similar but weaker role in coiling and SYCP1 has an opposite effect.","method":"Three-color dSTORM super-resolution microscopy on Hormad1−/− spermatocytes","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 — super-resolution imaging with defined genetic background, single study","pmids":["35857787"],"is_preprint":false},{"year":2023,"finding":"The human HORMAD1 HORMA domain adopts a self-closed conformation with an intra-molecular closure motif interaction; peptide motifs from HORMAD2 and MCM9 bind HORMAD1 in a mode highly similar to the self-closure, sharing a conserved Ser-Glu-Pro sequence; this HORMA-closure motif interaction contributes to DNA mismatch repair and HR repair.","method":"Crystal structure determination, biochemical binding assays, cell-based MMR and HR reporter assays with structure-guided mutants","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 — crystal structure plus biochemical validation plus cell-based functional assays with mutagenesis","pmids":["37794593"],"is_preprint":false},{"year":2023,"finding":"HORMAD1 associates with the replisome and protects stalled DNA replication forks; loss of HORMAD1 leads to nascent DNA strand degradation mediated by the MRE11-DNA2-BLM pathway and reduced RAD51 loading onto stalled forks, resulting in increased DNA breaks and chromosomal defects exacerbated by replication stress.","method":"DNA fiber assay, iPOND (replisome association), RAD51/BRCA2 ChIP/foci analysis, MRE11/DNA2/BLM inhibitor epistasis in HORMAD1-KO cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — DNA fiber assay plus replisome association plus pathway epistasis, multiple orthogonal methods","pmids":["37838177"],"is_preprint":false},{"year":2023,"finding":"A truncating HORMAD1 mutation (p.Gln341*) that removes the nuclear localization signal causes cytoplasmic rather than nuclear localization of the protein, corresponding to spermatogenic arrest at the primary spermatocyte stage in humans.","method":"Whole exome sequencing, cell transfection with GFP-tagged wild-type vs. mutant HORMAD1, immunoblotting, immunofluorescence microscopy","journal":"Human reproduction","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization experiment with functional variant, single family","pmids":["36524333"],"is_preprint":false},{"year":2024,"finding":"Mouse HORMAD1 is differentially phosphorylated at two serine clusters (Ser307 and Ser378) in a substage-specific manner during meiotic prophase I: Ser307 phosphorylation occurs from early leptotene independently of SPO11 (primary, DSB-independent), while Ser378 phosphorylation is abundant on unsynapsed axes after mid-zygotene and is partially SPO11-dependent; Ser307 is phosphorylated on sex chromosome axes but unphosphorylated on desynapsed axes in diplotene.","method":"Phospho-specific antibody generation, immunofluorescence on wild-type and Spo11−/− spermatocytes","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 — phospho-specific antibodies with genetic controls, single lab","pmids":["38897409"],"is_preprint":false},{"year":2026,"finding":"Out-of-context HORMAD1 expression in mitotic cancer cells perturbs mitotic arrest and generates aneuploidy by weakening the spindle assembly checkpoint through a direct HORMAD1/Aurora B interaction that impairs Aurora B/INCENP signalling; these effects are MAD2L1-independent and confer sensitivity to MPS1, Aurora B, and BUB1 inhibitors.","method":"Co-immunoprecipitation of HORMAD1 with Aurora B, live-cell mitotic arrest assays, doxycycline-inducible HORMAD1 TNBC cell lines, aneuploidy quantification, inhibitor sensitivity assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — Co-IP plus functional mitotic phenotype plus genetic independence from MAD2L1, multiple orthogonal methods","pmids":["41813673"],"is_preprint":false},{"year":2026,"finding":"HORMAD1 depletion in TNBC cells induces cellular senescence through accumulation of p27; HORMAD1 promotes ubiquitin-mediated degradation of p27, and ectopic HORMAD1 expression blocks p27-mediated senescence and enhances TNBC cell growth.","method":"Co-immunoprecipitation, flow cytometry for senescence, western blot for p27 ubiquitination, HORMAD1 knockdown/overexpression","journal":"American journal of translational research","confidence":"Medium","confidence_rationale":"Tier 3 — Co-IP plus functional senescence assay, single lab, single study","pmids":["41868954"],"is_preprint":false}],"current_model":"HORMAD1 is a HORMA domain-containing protein that, in meiosis, loads onto unsynapsed chromosome axes via meiotic cohesins (REC8/RAD21L), promotes DSB formation and inter-homologue repair by maintaining ATR checkpoint kinase activity at unsynapsed chromatin, and is depleted from synapsed axes by TRIP13 AAA-ATPase in a synaptonemal-complex-dependent negative feedback loop; in somatic cancer cells where it is aberrantly expressed, HORMAD1 promotes homologous recombination and replication fork protection by facilitating RAD51 loading, interacts with Aurora B/INCENP to weaken the spindle assembly checkpoint, sequesters the MCM8-MCM9 complex in the cytoplasm to impair mismatch repair, and promotes ubiquitin-mediated p27 degradation to prevent senescence."},"narrative":{"teleology":[{"year":2009,"claim":"The discovery that HORMAD1 preferentially marks unsynapsed meiotic axes and is actively removed from synapsed regions by TRIP13 established the principle that HORMA domain proteins serve as sensors of synapsis status on meiotic chromosomes.","evidence":"Immunofluorescence on wild-type and Trip13 mutant mouse spermatocytes; biochemical fractionation and SC-mutant analysis","pmids":["19851446","19686734"],"confidence":"High","gaps":["Mechanism by which TRIP13 catalyzes HORMAD1 removal not defined","Whether HORMAD1 displacement requires a direct TRIP13-HORMAD1 interaction or adaptor proteins"]},{"year":2010,"claim":"Knockout studies revealed that HORMAD1 is required upstream of meiotic DSB formation, early recombination (γH2AX, DMC1, RAD51 foci), homologue pairing, and sex chromosome inactivation—placing it as a master enabler of meiotic recombination and checkpoint activation.","evidence":"Hormad1 knockout mouse with immunofluorescence and electron microscopy for SC, DSB, and MSCI markers","pmids":["21079677"],"confidence":"High","gaps":["How HORMAD1 mechanistically stimulates SPO11-dependent DSB formation remains unknown","Whether HORMAD1 acts catalytically or as a structural scaffold for DSB machinery"]},{"year":2011,"claim":"A negative feedback model was established: HORMAD1 promotes DSBs and ATR checkpoint activity on unsynapsed axes, but SC formation depletes HORMAD1, thereby coupling synapsis completion to checkpoint silencing and meiotic progression.","evidence":"Hormad1 knockout mouse, genetic epistasis for ATR recruitment and SC formation","pmids":["21478856"],"confidence":"High","gaps":["Signal that links SC installation to HORMAD1 removal not molecularly defined","Relative contributions of HORMAD1-dependent DSBs versus checkpoint signaling to meiotic arrest"]},{"year":2012,"claim":"HORMAD1 was shown to operate the meiotic prophase checkpoint in oocytes: Hormad1 deficiency rescued massive oocyte loss in Spo11-null ovaries, demonstrating that HORMAD1 enforces elimination of asynaptic oocytes and undergoes DNA-damage-independent phosphorylation.","evidence":"Hormad1/Spo11 double-KO mice, epistasis for oocyte survival, phosphorylation analysis","pmids":["22530760"],"confidence":"High","gaps":["Kinase(s) responsible for DNA-damage-independent HORMAD1 phosphorylation not identified","Whether phosphorylation is required for checkpoint enforcement"]},{"year":2013,"claim":"Epistasis with Dmc1 revealed that HORMAD1 enforces DMC1-dependent inter-homologue repair pathway choice; its loss permits DMC1-independent repair that allows asynaptic oocytes to survive.","evidence":"Hormad1/Dmc1 double-KO mice, irradiation rescue of embryonic ovaries, repair foci immunofluorescence","pmids":["23759310"],"confidence":"High","gaps":["Molecular mechanism by which HORMAD1 blocks alternative repair pathways not defined","Whether HORMAD1 directly interacts with DMC1 or acts through an intermediary"]},{"year":2015,"claim":"The first cancer-context function was identified: aberrant HORMAD1 expression in triple-negative breast cancer suppresses RAD51-dependent HR and promotes alternative repair, generating genomic instability and creating therapeutic vulnerability to PARP inhibitors and platinum agents.","evidence":"HORMAD1 knockdown/overexpression in TNBC lines, HR reporter assays, genomic copy-number profiling","pmids":["25770156"],"confidence":"High","gaps":["Apparent contradiction with later studies showing HORMAD1 promotes HR in other cancer contexts","Whether HR suppression is dose- or context-dependent not resolved"]},{"year":2018,"claim":"Domain dissection in lung cancer cells showed that the HORMA domain and C-terminal oligomerization motif are both required for HORMAD1 localization to DNA damage foci, where it promotes DSB end resection and RAD51 loading for HR repair independently of meiotic partners HORMAD2 and CCDC36.","evidence":"Domain mutant analysis, HR/NHEJ reporter assays, RPA and RAD51 immunofluorescence in lung adenocarcinoma cells","pmids":["30333500"],"confidence":"High","gaps":["Reconciliation of HR-promoting versus HR-suppressing roles of HORMAD1 across cancer types","How the C-terminal oligomerization motif contributes mechanistically to resection"]},{"year":2020,"claim":"The initial chromatin-loading mechanism for HORMAD1 was defined: meiotic cohesins REC8 and RAD21L physically recruit HORMAD1 to chromatin prior to axial element assembly, with HORMAD1 also binding AE components SYCP2/SYCP3, establishing the hierarchical order of axis assembly.","evidence":"Co-immunoprecipitation, Sycp2-KO, Hormad1/Rec8 and Hormad1/Rad21L double-KO mice","pmids":["32931493"],"confidence":"High","gaps":["Whether REC8 and RAD21L bind HORMAD1 through its HORMA domain closure-motif interface not tested","Stoichiometry and dynamics of the cohesin–HORMAD1 interaction unknown"]},{"year":2020,"claim":"A second oncogenic mechanism was uncovered: HORMAD1 sequesters the MCM8–MCM9 complex away from chromatin, reducing MLH1 loading and causing DNA mismatch repair deficiency in cancer cells.","evidence":"Co-immunoprecipitation, nuclear fractionation, MMR assays in HORMAD1-expressing cancer lines","pmids":["32647118"],"confidence":"Medium","gaps":["Single-lab finding without reciprocal validation of MCM8–MCM9 cytoplasmic sequestration in vivo","Whether HORMAD1-MCM9 interaction uses the same closure-motif interface as meiotic partners not yet determined at that time"]},{"year":2022,"claim":"Super-resolution imaging demonstrated that HORMAD1 loss alters the lifetime, size, and configuration of RAD51/DMC1 recombination intermediates and inhibits SC coiling, revealing a nanoscale structural role in organizing the recombination machinery.","evidence":"Three-color dSTORM on Hormad1−/− spermatocytes","pmids":["35857787"],"confidence":"Medium","gaps":["Whether altered intermediate configurations reflect a direct structural role or indirect consequence of reduced DSBs","Single imaging study awaits independent replication"]},{"year":2023,"claim":"Structural determination of the HORMAD1 HORMA domain revealed a self-closed conformation with an intramolecular closure motif; peptides from HORMAD2 and MCM9 bind this same interface via a conserved Ser-Glu-Pro motif, unifying the meiotic and cancer-context partner interactions through a shared structural mechanism.","evidence":"Crystal structure, biochemical binding assays, structure-guided mutants in MMR and HR reporter assays","pmids":["37794593"],"confidence":"High","gaps":["Full-length HORMAD1 structure with partners not determined","Whether TRIP13-catalyzed conformational change uses the same open/closed transition seen in other HORMA proteins"]},{"year":2023,"claim":"HORMAD1 was found to associate with the replisome and protect stalled replication forks by promoting RAD51 loading; its loss exposes nascent DNA to MRE11–DNA2–BLM-mediated degradation, establishing a replication fork protection function distinct from its DSB repair role.","evidence":"iPOND for replisome association, DNA fiber assays, MRE11/DNA2/BLM inhibitor epistasis in HORMAD1-KO cells","pmids":["37838177"],"confidence":"High","gaps":["Whether fork protection is relevant in meiotic S-phase not tested","Mechanism of HORMAD1 recruitment to the replisome unknown"]},{"year":2023,"claim":"A human truncating HORMAD1 mutation (p.Gln341*) that removes the nuclear localization signal causes cytoplasmic mislocalization and spermatogenic arrest, providing the first direct genetic link between HORMAD1 loss-of-function and human male infertility.","evidence":"Whole-exome sequencing of infertile patient, GFP-tagged WT vs. mutant transfection, immunofluorescence","pmids":["36524333"],"confidence":"Medium","gaps":["Single family; additional independent cases needed","Whether partial nuclear localization persists in patient tissue not examined"]},{"year":2024,"claim":"Substage-specific differential phosphorylation of HORMAD1 at Ser307 (DSB-independent, from leptotene) and Ser378 (partially SPO11-dependent, from mid-zygotene onward) was mapped, suggesting that distinct phospho-forms encode different functional states during meiotic prophase.","evidence":"Phospho-specific antibodies, immunofluorescence on wild-type and Spo11−/− spermatocytes","pmids":["38897409"],"confidence":"Medium","gaps":["Functional consequences of each phosphorylation site not tested by mutagenesis","Kinase identity for each site unknown"]},{"year":2026,"claim":"HORMAD1 was shown to weaken the spindle assembly checkpoint in mitotic cancer cells through direct interaction with Aurora B, impairing Aurora B/INCENP signaling independently of MAD2L1, thereby generating aneuploidy and creating vulnerability to MPS1, Aurora B, and BUB1 inhibitors.","evidence":"Co-IP of HORMAD1 with Aurora B, live-cell mitotic arrest assays, inducible HORMAD1 TNBC lines, aneuploidy quantification, inhibitor sensitivity","pmids":["41813673"],"confidence":"High","gaps":["Whether the HORMAD1–Aurora B interaction uses the HORMA closure-motif interface not tested","In vivo validation of inhibitor sensitivity in HORMAD1-expressing tumors lacking"]},{"year":2026,"claim":"HORMAD1 was found to promote ubiquitin-mediated p27 degradation, preventing cellular senescence in TNBC; its depletion leads to p27 accumulation and senescence, revealing a proliferation-sustaining mechanism in cancer.","evidence":"Co-IP, p27 ubiquitination western blot, senescence flow cytometry, HORMAD1 knockdown/overexpression in TNBC cells","pmids":["41868954"],"confidence":"Medium","gaps":["E3 ubiquitin ligase mediating HORMAD1-dependent p27 degradation not identified","Single lab, single study; independent confirmation needed"]},{"year":null,"claim":"Key unresolved questions include how HORMAD1 mechanistically stimulates SPO11-dependent DSB formation, the identity of kinases phosphorylating HORMAD1 at functionally distinct sites, the structural basis of TRIP13-mediated HORMAD1 removal from synapsed axes, and how HORMAD1's apparently opposing effects on HR (promoting in some cancer contexts, suppressing in others) are reconciled by cellular context or dosage.","evidence":"","pmids":[],"confidence":"Low","gaps":["No reconstituted system for HORMAD1-dependent DSB stimulation","No full-length HORMAD1 structure with TRIP13 or cohesin partners","Context-dependent HR regulation mechanism undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[9,12,10]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,4,16]}],"localization":[{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[0,1,2,9]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[7,13,14]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[2,7,12,13]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[2,3,4,5]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[16]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[6,10,17]}],"complexes":[],"partners":["TRIP13","REC8","RAD21L","SYCP2","MCM9","HORMAD2","AURKB","CDKN1B"],"other_free_text":[]},"mechanistic_narrative":"HORMAD1 is a HORMA domain protein that functions as a central coordinator of meiotic chromosome dynamics and, when aberrantly expressed in somatic cancers, reprograms DNA repair and checkpoint signaling. In meiosis, HORMAD1 is loaded onto unsynapsed chromosome axes via meiotic cohesins REC8 and RAD21L, where it promotes SPO11-dependent double-strand break formation, inter-homologue recombination through DMC1/RAD51, ATR-dependent checkpoint surveillance of unsynapsed chromatin, and meiotic sex chromosome inactivation; synaptonemal complex formation triggers its removal by TRIP13 AAA-ATPase, creating a negative feedback loop that couples synapsis completion to checkpoint silencing [PMID:19851446, PMID:21478856, PMID:32931493]. A truncating HORMAD1 mutation (p.Gln341*) that ablates nuclear localization causes human male infertility with spermatogenic arrest [PMID:36524333]. In cancer cells, HORMAD1 promotes homologous recombination and replication fork protection by facilitating RAD51 loading, sequesters the MCM8–MCM9 complex to impair mismatch repair, weakens the spindle assembly checkpoint through direct interaction with Aurora B/INCENP to generate aneuploidy, and drives p27 degradation to suppress senescence [PMID:30333500, PMID:37838177, PMID:32647118, PMID:41813673, PMID:41868954]."},"prefetch_data":{"uniprot":{"accession":"Q86X24","full_name":"HORMA domain-containing protein 1","aliases":["Cancer/testis antigen 46","CT46","Newborn ovary HORMA protein"],"length_aa":394,"mass_kda":45.2,"function":"Plays a key role in meiotic progression. Regulates 3 different functions during meiosis: ensures that sufficient numbers of processed DNA double-strand breaks (DSBs) are available for successful homology search by increasing the steady-state numbers of single-stranded DSB ends. Promotes synaptonemal-complex formation independently of its role in homology search. Plays a key role in the male mid-pachytene checkpoint and the female meiotic prophase checkpoint: required for efficient build-up of ATR activity on unsynapsed chromosome regions, a process believed to form the basis of meiotic silencing of unsynapsed chromatin (MSUC) and meiotic prophase quality control in both sexes","subcellular_location":"Nucleus; Chromosome","url":"https://www.uniprot.org/uniprotkb/Q86X24/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/HORMAD1","classification":"Not Classified","n_dependent_lines":18,"n_total_lines":1208,"dependency_fraction":0.014900662251655629},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/HORMAD1","total_profiled":1310},"omim":[{"mim_id":"619190","title":"INTERACTOR OF HORMAD1 1; IHO1","url":"https://www.omim.org/entry/619190"},{"mim_id":"618842","title":"HORMA DOMAIN-CONTAINING PROTEIN 2; HORMAD2","url":"https://www.omim.org/entry/618842"},{"mim_id":"618423","title":"ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 31; ANKRD31","url":"https://www.omim.org/entry/618423"},{"mim_id":"618417","title":"MEIOTIC DOUBLE-STRANDED BREAK FORMATION PROTEIN 4; MEI4","url":"https://www.omim.org/entry/618417"},{"mim_id":"609824","title":"HORMA DOMAIN-CONTAINING PROTEIN 1; HORMAD1","url":"https://www.omim.org/entry/609824"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Nucleoli","reliability":"Additional"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"testis","ntpm":110.1}],"url":"https://www.proteinatlas.org/search/HORMAD1"},"hgnc":{"alias_symbol":["DKFZP434A1315","CT46"],"prev_symbol":[]},"alphafold":{"accession":"Q86X24","domains":[{"cath_id":"3.30.900.10","chopping":"10-127_141-257_314-322_386-394","consensus_level":"medium","plddt":84.1411,"start":10,"end":394}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86X24","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86X24-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86X24-F1-predicted_aligned_error_v6.png","plddt_mean":65.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=HORMAD1","jax_strain_url":"https://www.jax.org/strain/search?query=HORMAD1"},"sequence":{"accession":"Q86X24","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86X24.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86X24/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86X24"}},"corpus_meta":[{"pmid":"19851446","id":"PMC_19851446","title":"Mouse HORMAD1 and HORMAD2, two conserved meiotic chromosomal proteins, are depleted from synapsed chromosome axes with the help of TRIP13 AAA-ATPase.","date":"2009","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19851446","citation_count":327,"is_preprint":false},{"pmid":"21478856","id":"PMC_21478856","title":"Meiotic homologue alignment and its quality surveillance are controlled by mouse HORMAD1.","date":"2011","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/21478856","citation_count":194,"is_preprint":false},{"pmid":"21079677","id":"PMC_21079677","title":"Hormad1 mutation disrupts synaptonemal complex formation, recombination, and chromosome segregation in mammalian meiosis.","date":"2010","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/21079677","citation_count":178,"is_preprint":false},{"pmid":"19686734","id":"PMC_19686734","title":"A novel mammalian HORMA domain-containing protein, HORMAD1, preferentially associates with unsynapsed meiotic chromosomes.","date":"2009","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/19686734","citation_count":108,"is_preprint":false},{"pmid":"25770156","id":"PMC_25770156","title":"Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers.","date":"2015","source":"Cancer discovery","url":"https://pubmed.ncbi.nlm.nih.gov/25770156","citation_count":96,"is_preprint":false},{"pmid":"15999985","id":"PMC_15999985","title":"Identification of CT46/HORMAD1, an immunogenic cancer/testis antigen encoding a putative meiosis-related protein.","date":"2005","source":"Cancer immunity","url":"https://pubmed.ncbi.nlm.nih.gov/15999985","citation_count":78,"is_preprint":false},{"pmid":"22530760","id":"PMC_22530760","title":"HORMAD1-dependent checkpoint/surveillance mechanism eliminates asynaptic oocytes.","date":"2012","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/22530760","citation_count":70,"is_preprint":false},{"pmid":"30333500","id":"PMC_30333500","title":"The Cancer/Testes (CT) Antigen HORMAD1 promotes Homologous Recombinational DNA Repair and Radioresistance in Lung adenocarcinoma cells.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/30333500","citation_count":47,"is_preprint":false},{"pmid":"23759310","id":"PMC_23759310","title":"Mouse HORMAD1 is a meiosis i checkpoint protein that modulates DNA double- strand break repair during female meiosis.","date":"2013","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/23759310","citation_count":41,"is_preprint":false},{"pmid":"32931493","id":"PMC_32931493","title":"Meiotic cohesins mediate initial loading of HORMAD1 to the chromosomes and coordinate SC formation during meiotic prophase.","date":"2020","source":"PLoS 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letters","url":"https://pubmed.ncbi.nlm.nih.gov/22776561","citation_count":28,"is_preprint":false},{"pmid":"22893617","id":"PMC_22893617","title":"HORMAD2/CT46.2, a novel cancer/testis gene, is ectopically expressed in lung cancer tissues.","date":"2012","source":"Molecular human reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/22893617","citation_count":28,"is_preprint":false},{"pmid":"30046392","id":"PMC_30046392","title":"Epigenetic activation of HORMAD1 in basal-like breast cancer: role in Rucaparib sensitivity.","date":"2018","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/30046392","citation_count":25,"is_preprint":false},{"pmid":"34036395","id":"PMC_34036395","title":"HORMAD1 promotes docetaxel resistance in triple negative breast cancer by enhancing DNA damage tolerance.","date":"2021","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/34036395","citation_count":23,"is_preprint":false},{"pmid":"35347116","id":"PMC_35347116","title":"The cancer/testis antigen HORMAD1 mediates epithelial-mesenchymal transition to promote tumor growth and metastasis by activating the Wnt/β-catenin signaling pathway in lung cancer.","date":"2022","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/35347116","citation_count":19,"is_preprint":false},{"pmid":"35768547","id":"PMC_35768547","title":"Functional screening reveals HORMAD1-driven gene dependencies associated with translesion synthesis and replication stress tolerance.","date":"2022","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/35768547","citation_count":12,"is_preprint":false},{"pmid":"22407170","id":"PMC_22407170","title":"Single-nucleotide polymorphisms in HORMAD1 may be a risk factor for azoospermia caused by meiotic arrest in Japanese patients.","date":"2012","source":"Asian journal of andrology","url":"https://pubmed.ncbi.nlm.nih.gov/22407170","citation_count":12,"is_preprint":false},{"pmid":"37794593","id":"PMC_37794593","title":"Structural and biochemical insights into the interaction mechanism underlying HORMAD1 and its partner proteins.","date":"2023","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/37794593","citation_count":7,"is_preprint":false},{"pmid":"36524333","id":"PMC_36524333","title":"A biallelic loss of function variant in HORMAD1 within a large consanguineous Turkish family is associated with spermatogenic arrest.","date":"2023","source":"Human reproduction (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/36524333","citation_count":7,"is_preprint":false},{"pmid":"36852691","id":"PMC_36852691","title":"HORMAD1 overexpression predicts response to anthracycline-cyclophosphamide and survival in triple-negative breast cancers.","date":"2023","source":"Molecular oncology","url":"https://pubmed.ncbi.nlm.nih.gov/36852691","citation_count":6,"is_preprint":false},{"pmid":"35857787","id":"PMC_35857787","title":"Multi-color dSTORM microscopy in Hormad1-/- spermatocytes reveals alterations in meiotic recombination intermediates and synaptonemal complex structure.","date":"2022","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35857787","citation_count":5,"is_preprint":false},{"pmid":"37854207","id":"PMC_37854207","title":"The cancer/testis antigen HORMAD1 promotes gastric cancer progression by activating the NF-κB signaling pathway and inducing epithelial-mesenchymal transition.","date":"2023","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/37854207","citation_count":4,"is_preprint":false},{"pmid":"37371097","id":"PMC_37371097","title":"Ectopically Expressed Meiosis-Specific Cancer Testis Antigen HORMAD1 Promotes Genomic Instability in Squamous Cell Carcinomas.","date":"2023","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/37371097","citation_count":3,"is_preprint":false},{"pmid":"37838177","id":"PMC_37838177","title":"The cancer testes antigen, HORMAD1, limits genomic instability in cancer cells by protecting stalled replication forks.","date":"2023","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37838177","citation_count":3,"is_preprint":false},{"pmid":"34296290","id":"PMC_34296290","title":"[Corrigendum] HORMAD1 promotes docetaxel resistance in triple negative breast cancer by enhancing DNA damage tolerance.","date":"2021","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/34296290","citation_count":2,"is_preprint":false},{"pmid":"38897409","id":"PMC_38897409","title":"Differential phosphorylation of two serine clusters in mouse HORMAD1 during meiotic prophase I progression.","date":"2024","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/38897409","citation_count":1,"is_preprint":false},{"pmid":"38185961","id":"PMC_38185961","title":"Expression of HORMAD1 in Chronic Rhinosinusitis and Its Correlation with Inflammatory Factors.","date":"2024","source":"Journal of the College of Physicians and Surgeons--Pakistan : JCPSP","url":"https://pubmed.ncbi.nlm.nih.gov/38185961","citation_count":0,"is_preprint":false},{"pmid":"36778501","id":"PMC_36778501","title":"The Cancer Testes Antigen, HORMAD1, is a Tumor-Specific Replication Fork Protection Factor.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/36778501","citation_count":0,"is_preprint":false},{"pmid":"40875139","id":"PMC_40875139","title":"HORMAD1 Polymorphisms Influence Susceptibility to Esophageal Squamous Cell Carcinoma Through Gene-Smoking Interaction.","date":"2025","source":"Molecular carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/40875139","citation_count":0,"is_preprint":false},{"pmid":"41813673","id":"PMC_41813673","title":"Tumour specific HORMAD1 expression perturbs mitotic arrest and drives sensitivity to mitotic kinase inhibitors.","date":"2026","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41813673","citation_count":0,"is_preprint":false},{"pmid":"41868954","id":"PMC_41868954","title":"HORMAD1 inhibits senescence and promotes proliferation of triple negative breast cancer by facilitating ubiquitination-mediated degradation of p27.","date":"2026","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/41868954","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":17766,"output_tokens":4186,"usd":0.058044},"stage2":{"model":"claude-opus-4-6","input_tokens":7685,"output_tokens":4012,"usd":0.208088},"total_usd":0.266132,"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\": 2009,\n      \"finding\": \"HORMAD1 and HORMAD2 preferentially associate with unsynapsed meiotic chromosome axes and are depleted from synapsed axes; TRIP13 AAA-ATPase is required for this depletion, establishing a mutually exclusive relationship between HORMAD-rich domains and synapsed chromatin.\",\n      \"method\": \"Immunofluorescence on wild-type and mutant mouse spermatocytes; genetic analysis of TRIP13 mutants\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple mutant backgrounds, direct localization experiments, replicated by multiple labs\",\n      \"pmids\": [\"19851446\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"HORMAD1 associates biochemically and cytologically with the meiotic chromosome axis, accumulating during leptotene-to-zygotene and disappearing from synapsed regions at pachytene, then reappearing upon desynapsis at diplotene; establishment of the synaptonemal complex is required for displacement of HORMAD1 from the axis.\",\n      \"method\": \"Biochemical fractionation, immunofluorescence, analysis of synaptonemal complex mutant strains\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — biochemical and cytological evidence, multiple SC mutant backgrounds\",\n      \"pmids\": [\"19686734\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"HORMAD1 is a component of the synaptonemal complex required for double-strand break formation, early recombination events (γH2AX, DMC1, RAD51, RPA foci), homologous chromosome pairing, and meiotic sex chromosome inactivation (MSCI); HORMAD1 co-localizes with γH2AX, ATR, and BRCA1 at the sex body, and its loss abolishes their localization to sex chromosomes.\",\n      \"method\": \"Hormad1 knockout mouse, immunofluorescence, electron microscopy\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with specific molecular phenotypes, multiple orthogonal readouts\",\n      \"pmids\": [\"21079677\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"HORMAD1 ensures sufficient processed DSBs for homology search, promotes synaptonemal complex formation, and is required for efficient recruitment of ATR checkpoint kinase activity to unsynapsed chromatin; SC formation leads to HORMAD1 depletion from chromosome axes, forming a negative feedback loop that coordinates meiotic progression with homologue alignment.\",\n      \"method\": \"Hormad1 knockout mouse, immunofluorescence, genetic epistasis\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined molecular phenotypes, mechanistic loop established with epistasis\",\n      \"pmids\": [\"21478856\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"HORMAD1 is required for the meiotic prophase checkpoint that eliminates asynaptic oocytes; Hormad1 deficiency abrogates massive oocyte loss in Spo11-deficient ovaries (epistasis); HORMAD1 undergoes extensive phosphorylation in Spo11-deficient testes and ovaries through DNA damage-independent signaling.\",\n      \"method\": \"Hormad1/Spo11 double mutant mice, genetic epistasis, immunofluorescence, phosphorylation analysis\",\n      \"journal\": \"Genes to cells\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — double KO epistasis with defined checkpoint phenotype\",\n      \"pmids\": [\"22530760\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"HORMAD1 deficiency in oocytes promotes DMC1-independent DSB repair, which enables asynaptic oocytes to resist perinatal loss; Hormad1 deficiency rescues Dmc1−/− oocytes, placing HORMAD1 upstream of DMC1-dependent repair pathway choice.\",\n      \"method\": \"Hormad1/Dmc1 double mutant mice, irradiation of embryonic ovaries, immunofluorescence for γH2AX, RAD51, DMC1\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with double KO, irradiation rescue experiment\",\n      \"pmids\": [\"23759310\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Elevated HORMAD1 expression in triple-negative breast cancer suppresses RAD51-dependent homologous recombination and drives use of alternative DNA repair pathways, generating allelic-imbalanced copy-number aberrations and sensitizing cancer cells to platinum-based chemotherapy and PARP inhibitors.\",\n      \"method\": \"HORMAD1 knockdown/overexpression in cancer cell lines, HR reporter assays, genomic copy-number profiling\",\n      \"journal\": \"Cancer discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — functional HR reporter assays plus genomic readout, mechanistic link established\",\n      \"pmids\": [\"25770156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In lung adenocarcinoma cells, HORMAD1 redistributes to nuclear foci co-localizing with γH2AX after IR; the HORMA domain and C-terminal disordered oligomerization motif are required for IRIF localization; HORMAD1 promotes DSB resection (RPA-ssDNA foci and RAD51 redistribution to DSBs) and HR-mediated repair but not NHEJ; HORMAD1-mediated HR is independent of meiotic partners HORMAD2 and CCDC36.\",\n      \"method\": \"HORMAD1 depletion, domain mutant analysis, HR and NHEJ reporter assays, immunofluorescence for RPA and RAD51\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — reporter assays with domain mutagenesis, multiple orthogonal readouts\",\n      \"pmids\": [\"30333500\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"HORMAD1 promotes repair of radiation-induced DSBs at the synaptonemal complex axis and influences DNA repair pathway choice in mouse meiocytes; Spo11/Hormad1 double-KO spermatocytes showed fewer remaining DSB repair foci after irradiation compared to Spo11-KO, indicating HORMAD1 slows repair (repair inhibition role).\",\n      \"method\": \"Spo11/Hormad1 double knockout mouse, irradiation, immunofluorescence for DSB repair foci\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — double-KO epistasis, single study\",\n      \"pmids\": [\"29414051\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Meiotic cohesins REC8 and RAD21L mediate initial chromatin loading of HORMAD1 prior to axial element formation; HORMAD1 physically interacts with meiotic cohesins (REC8, RAD21L) and with AE components SYCP2 and SYCP3; in Sycp2-KO, HORMAD1 still localizes along cohesin axial cores via cohesins; Hormad1/Rec8-dKO but not Hormad1/Rad21L-dKO shows precocious sister chromatid axis separation.\",\n      \"method\": \"Co-immunoprecipitation, Sycp2 null mice, Hormad1/Rad21L and Hormad1/Rec8 double KO mice, immunofluorescence\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, multiple double-KO genetic epistasis, replicated across genotypes\",\n      \"pmids\": [\"32931493\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Aberrantly expressed HORMAD1 in cancer cells interacts with the MCM8-MCM9 complex and prevents its efficient nuclear localization, causing reduced MLH1 chromatin binding and DNA mismatch repair defects.\",\n      \"method\": \"Co-immunoprecipitation, nuclear fractionation, MMR assays in HORMAD1-expressing cancer cell lines\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — Co-IP plus functional MMR assay, single lab\",\n      \"pmids\": [\"32647118\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"HORMAD1 loss-of-function in Hormad1−/− spermatocytes alters the lifetime and size of RAD51/DMC1 recombination intermediate configurations and inhibits coil formation in the synaptonemal complex; SPO11 plays a similar but weaker role in coiling and SYCP1 has an opposite effect.\",\n      \"method\": \"Three-color dSTORM super-resolution microscopy on Hormad1−/− spermatocytes\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — super-resolution imaging with defined genetic background, single study\",\n      \"pmids\": [\"35857787\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The human HORMAD1 HORMA domain adopts a self-closed conformation with an intra-molecular closure motif interaction; peptide motifs from HORMAD2 and MCM9 bind HORMAD1 in a mode highly similar to the self-closure, sharing a conserved Ser-Glu-Pro sequence; this HORMA-closure motif interaction contributes to DNA mismatch repair and HR repair.\",\n      \"method\": \"Crystal structure determination, biochemical binding assays, cell-based MMR and HR reporter assays with structure-guided mutants\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure plus biochemical validation plus cell-based functional assays with mutagenesis\",\n      \"pmids\": [\"37794593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"HORMAD1 associates with the replisome and protects stalled DNA replication forks; loss of HORMAD1 leads to nascent DNA strand degradation mediated by the MRE11-DNA2-BLM pathway and reduced RAD51 loading onto stalled forks, resulting in increased DNA breaks and chromosomal defects exacerbated by replication stress.\",\n      \"method\": \"DNA fiber assay, iPOND (replisome association), RAD51/BRCA2 ChIP/foci analysis, MRE11/DNA2/BLM inhibitor epistasis in HORMAD1-KO cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — DNA fiber assay plus replisome association plus pathway epistasis, multiple orthogonal methods\",\n      \"pmids\": [\"37838177\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A truncating HORMAD1 mutation (p.Gln341*) that removes the nuclear localization signal causes cytoplasmic rather than nuclear localization of the protein, corresponding to spermatogenic arrest at the primary spermatocyte stage in humans.\",\n      \"method\": \"Whole exome sequencing, cell transfection with GFP-tagged wild-type vs. mutant HORMAD1, immunoblotting, immunofluorescence microscopy\",\n      \"journal\": \"Human reproduction\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization experiment with functional variant, single family\",\n      \"pmids\": [\"36524333\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Mouse HORMAD1 is differentially phosphorylated at two serine clusters (Ser307 and Ser378) in a substage-specific manner during meiotic prophase I: Ser307 phosphorylation occurs from early leptotene independently of SPO11 (primary, DSB-independent), while Ser378 phosphorylation is abundant on unsynapsed axes after mid-zygotene and is partially SPO11-dependent; Ser307 is phosphorylated on sex chromosome axes but unphosphorylated on desynapsed axes in diplotene.\",\n      \"method\": \"Phospho-specific antibody generation, immunofluorescence on wild-type and Spo11−/− spermatocytes\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — phospho-specific antibodies with genetic controls, single lab\",\n      \"pmids\": [\"38897409\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Out-of-context HORMAD1 expression in mitotic cancer cells perturbs mitotic arrest and generates aneuploidy by weakening the spindle assembly checkpoint through a direct HORMAD1/Aurora B interaction that impairs Aurora B/INCENP signalling; these effects are MAD2L1-independent and confer sensitivity to MPS1, Aurora B, and BUB1 inhibitors.\",\n      \"method\": \"Co-immunoprecipitation of HORMAD1 with Aurora B, live-cell mitotic arrest assays, doxycycline-inducible HORMAD1 TNBC cell lines, aneuploidy quantification, inhibitor sensitivity assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus functional mitotic phenotype plus genetic independence from MAD2L1, multiple orthogonal methods\",\n      \"pmids\": [\"41813673\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"HORMAD1 depletion in TNBC cells induces cellular senescence through accumulation of p27; HORMAD1 promotes ubiquitin-mediated degradation of p27, and ectopic HORMAD1 expression blocks p27-mediated senescence and enhances TNBC cell growth.\",\n      \"method\": \"Co-immunoprecipitation, flow cytometry for senescence, western blot for p27 ubiquitination, HORMAD1 knockdown/overexpression\",\n      \"journal\": \"American journal of translational research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP plus functional senescence assay, single lab, single study\",\n      \"pmids\": [\"41868954\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"HORMAD1 is a HORMA domain-containing protein that, in meiosis, loads onto unsynapsed chromosome axes via meiotic cohesins (REC8/RAD21L), promotes DSB formation and inter-homologue repair by maintaining ATR checkpoint kinase activity at unsynapsed chromatin, and is depleted from synapsed axes by TRIP13 AAA-ATPase in a synaptonemal-complex-dependent negative feedback loop; in somatic cancer cells where it is aberrantly expressed, HORMAD1 promotes homologous recombination and replication fork protection by facilitating RAD51 loading, interacts with Aurora B/INCENP to weaken the spindle assembly checkpoint, sequesters the MCM8-MCM9 complex in the cytoplasm to impair mismatch repair, and promotes ubiquitin-mediated p27 degradation to prevent senescence.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"HORMAD1 is a HORMA domain protein that functions as a central coordinator of meiotic chromosome dynamics and, when aberrantly expressed in somatic cancers, reprograms DNA repair and checkpoint signaling. In meiosis, HORMAD1 is loaded onto unsynapsed chromosome axes via meiotic cohesins REC8 and RAD21L, where it promotes SPO11-dependent double-strand break formation, inter-homologue recombination through DMC1/RAD51, ATR-dependent checkpoint surveillance of unsynapsed chromatin, and meiotic sex chromosome inactivation; synaptonemal complex formation triggers its removal by TRIP13 AAA-ATPase, creating a negative feedback loop that couples synapsis completion to checkpoint silencing [PMID:19851446, PMID:21478856, PMID:32931493]. A truncating HORMAD1 mutation (p.Gln341*) that ablates nuclear localization causes human male infertility with spermatogenic arrest [PMID:36524333]. In cancer cells, HORMAD1 promotes homologous recombination and replication fork protection by facilitating RAD51 loading, sequesters the MCM8–MCM9 complex to impair mismatch repair, weakens the spindle assembly checkpoint through direct interaction with Aurora B/INCENP to generate aneuploidy, and drives p27 degradation to suppress senescence [PMID:30333500, PMID:37838177, PMID:32647118, PMID:41813673, PMID:41868954].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"The discovery that HORMAD1 preferentially marks unsynapsed meiotic axes and is actively removed from synapsed regions by TRIP13 established the principle that HORMA domain proteins serve as sensors of synapsis status on meiotic chromosomes.\",\n      \"evidence\": \"Immunofluorescence on wild-type and Trip13 mutant mouse spermatocytes; biochemical fractionation and SC-mutant analysis\",\n      \"pmids\": [\"19851446\", \"19686734\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which TRIP13 catalyzes HORMAD1 removal not defined\", \"Whether HORMAD1 displacement requires a direct TRIP13-HORMAD1 interaction or adaptor proteins\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Knockout studies revealed that HORMAD1 is required upstream of meiotic DSB formation, early recombination (γH2AX, DMC1, RAD51 foci), homologue pairing, and sex chromosome inactivation—placing it as a master enabler of meiotic recombination and checkpoint activation.\",\n      \"evidence\": \"Hormad1 knockout mouse with immunofluorescence and electron microscopy for SC, DSB, and MSCI markers\",\n      \"pmids\": [\"21079677\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How HORMAD1 mechanistically stimulates SPO11-dependent DSB formation remains unknown\", \"Whether HORMAD1 acts catalytically or as a structural scaffold for DSB machinery\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"A negative feedback model was established: HORMAD1 promotes DSBs and ATR checkpoint activity on unsynapsed axes, but SC formation depletes HORMAD1, thereby coupling synapsis completion to checkpoint silencing and meiotic progression.\",\n      \"evidence\": \"Hormad1 knockout mouse, genetic epistasis for ATR recruitment and SC formation\",\n      \"pmids\": [\"21478856\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signal that links SC installation to HORMAD1 removal not molecularly defined\", \"Relative contributions of HORMAD1-dependent DSBs versus checkpoint signaling to meiotic arrest\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"HORMAD1 was shown to operate the meiotic prophase checkpoint in oocytes: Hormad1 deficiency rescued massive oocyte loss in Spo11-null ovaries, demonstrating that HORMAD1 enforces elimination of asynaptic oocytes and undergoes DNA-damage-independent phosphorylation.\",\n      \"evidence\": \"Hormad1/Spo11 double-KO mice, epistasis for oocyte survival, phosphorylation analysis\",\n      \"pmids\": [\"22530760\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinase(s) responsible for DNA-damage-independent HORMAD1 phosphorylation not identified\", \"Whether phosphorylation is required for checkpoint enforcement\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Epistasis with Dmc1 revealed that HORMAD1 enforces DMC1-dependent inter-homologue repair pathway choice; its loss permits DMC1-independent repair that allows asynaptic oocytes to survive.\",\n      \"evidence\": \"Hormad1/Dmc1 double-KO mice, irradiation rescue of embryonic ovaries, repair foci immunofluorescence\",\n      \"pmids\": [\"23759310\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism by which HORMAD1 blocks alternative repair pathways not defined\", \"Whether HORMAD1 directly interacts with DMC1 or acts through an intermediary\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"The first cancer-context function was identified: aberrant HORMAD1 expression in triple-negative breast cancer suppresses RAD51-dependent HR and promotes alternative repair, generating genomic instability and creating therapeutic vulnerability to PARP inhibitors and platinum agents.\",\n      \"evidence\": \"HORMAD1 knockdown/overexpression in TNBC lines, HR reporter assays, genomic copy-number profiling\",\n      \"pmids\": [\"25770156\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Apparent contradiction with later studies showing HORMAD1 promotes HR in other cancer contexts\", \"Whether HR suppression is dose- or context-dependent not resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Domain dissection in lung cancer cells showed that the HORMA domain and C-terminal oligomerization motif are both required for HORMAD1 localization to DNA damage foci, where it promotes DSB end resection and RAD51 loading for HR repair independently of meiotic partners HORMAD2 and CCDC36.\",\n      \"evidence\": \"Domain mutant analysis, HR/NHEJ reporter assays, RPA and RAD51 immunofluorescence in lung adenocarcinoma cells\",\n      \"pmids\": [\"30333500\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Reconciliation of HR-promoting versus HR-suppressing roles of HORMAD1 across cancer types\", \"How the C-terminal oligomerization motif contributes mechanistically to resection\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"The initial chromatin-loading mechanism for HORMAD1 was defined: meiotic cohesins REC8 and RAD21L physically recruit HORMAD1 to chromatin prior to axial element assembly, with HORMAD1 also binding AE components SYCP2/SYCP3, establishing the hierarchical order of axis assembly.\",\n      \"evidence\": \"Co-immunoprecipitation, Sycp2-KO, Hormad1/Rec8 and Hormad1/Rad21L double-KO mice\",\n      \"pmids\": [\"32931493\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether REC8 and RAD21L bind HORMAD1 through its HORMA domain closure-motif interface not tested\", \"Stoichiometry and dynamics of the cohesin–HORMAD1 interaction unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"A second oncogenic mechanism was uncovered: HORMAD1 sequesters the MCM8–MCM9 complex away from chromatin, reducing MLH1 loading and causing DNA mismatch repair deficiency in cancer cells.\",\n      \"evidence\": \"Co-immunoprecipitation, nuclear fractionation, MMR assays in HORMAD1-expressing cancer lines\",\n      \"pmids\": [\"32647118\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab finding without reciprocal validation of MCM8–MCM9 cytoplasmic sequestration in vivo\", \"Whether HORMAD1-MCM9 interaction uses the same closure-motif interface as meiotic partners not yet determined at that time\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Super-resolution imaging demonstrated that HORMAD1 loss alters the lifetime, size, and configuration of RAD51/DMC1 recombination intermediates and inhibits SC coiling, revealing a nanoscale structural role in organizing the recombination machinery.\",\n      \"evidence\": \"Three-color dSTORM on Hormad1−/− spermatocytes\",\n      \"pmids\": [\"35857787\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether altered intermediate configurations reflect a direct structural role or indirect consequence of reduced DSBs\", \"Single imaging study awaits independent replication\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Structural determination of the HORMAD1 HORMA domain revealed a self-closed conformation with an intramolecular closure motif; peptides from HORMAD2 and MCM9 bind this same interface via a conserved Ser-Glu-Pro motif, unifying the meiotic and cancer-context partner interactions through a shared structural mechanism.\",\n      \"evidence\": \"Crystal structure, biochemical binding assays, structure-guided mutants in MMR and HR reporter assays\",\n      \"pmids\": [\"37794593\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length HORMAD1 structure with partners not determined\", \"Whether TRIP13-catalyzed conformational change uses the same open/closed transition seen in other HORMA proteins\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"HORMAD1 was found to associate with the replisome and protect stalled replication forks by promoting RAD51 loading; its loss exposes nascent DNA to MRE11–DNA2–BLM-mediated degradation, establishing a replication fork protection function distinct from its DSB repair role.\",\n      \"evidence\": \"iPOND for replisome association, DNA fiber assays, MRE11/DNA2/BLM inhibitor epistasis in HORMAD1-KO cells\",\n      \"pmids\": [\"37838177\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether fork protection is relevant in meiotic S-phase not tested\", \"Mechanism of HORMAD1 recruitment to the replisome unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"A human truncating HORMAD1 mutation (p.Gln341*) that removes the nuclear localization signal causes cytoplasmic mislocalization and spermatogenic arrest, providing the first direct genetic link between HORMAD1 loss-of-function and human male infertility.\",\n      \"evidence\": \"Whole-exome sequencing of infertile patient, GFP-tagged WT vs. mutant transfection, immunofluorescence\",\n      \"pmids\": [\"36524333\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single family; additional independent cases needed\", \"Whether partial nuclear localization persists in patient tissue not examined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Substage-specific differential phosphorylation of HORMAD1 at Ser307 (DSB-independent, from leptotene) and Ser378 (partially SPO11-dependent, from mid-zygotene onward) was mapped, suggesting that distinct phospho-forms encode different functional states during meiotic prophase.\",\n      \"evidence\": \"Phospho-specific antibodies, immunofluorescence on wild-type and Spo11−/− spermatocytes\",\n      \"pmids\": [\"38897409\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequences of each phosphorylation site not tested by mutagenesis\", \"Kinase identity for each site unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"HORMAD1 was shown to weaken the spindle assembly checkpoint in mitotic cancer cells through direct interaction with Aurora B, impairing Aurora B/INCENP signaling independently of MAD2L1, thereby generating aneuploidy and creating vulnerability to MPS1, Aurora B, and BUB1 inhibitors.\",\n      \"evidence\": \"Co-IP of HORMAD1 with Aurora B, live-cell mitotic arrest assays, inducible HORMAD1 TNBC lines, aneuploidy quantification, inhibitor sensitivity\",\n      \"pmids\": [\"41813673\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the HORMAD1–Aurora B interaction uses the HORMA closure-motif interface not tested\", \"In vivo validation of inhibitor sensitivity in HORMAD1-expressing tumors lacking\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"HORMAD1 was found to promote ubiquitin-mediated p27 degradation, preventing cellular senescence in TNBC; its depletion leads to p27 accumulation and senescence, revealing a proliferation-sustaining mechanism in cancer.\",\n      \"evidence\": \"Co-IP, p27 ubiquitination western blot, senescence flow cytometry, HORMAD1 knockdown/overexpression in TNBC cells\",\n      \"pmids\": [\"41868954\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ubiquitin ligase mediating HORMAD1-dependent p27 degradation not identified\", \"Single lab, single study; independent confirmation needed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include how HORMAD1 mechanistically stimulates SPO11-dependent DSB formation, the identity of kinases phosphorylating HORMAD1 at functionally distinct sites, the structural basis of TRIP13-mediated HORMAD1 removal from synapsed axes, and how HORMAD1's apparently opposing effects on HR (promoting in some cancer contexts, suppressing in others) are reconciled by cellular context or dosage.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No reconstituted system for HORMAD1-dependent DSB stimulation\", \"No full-length HORMAD1 structure with TRIP13 or cohesin partners\", \"Context-dependent HR regulation mechanism undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [9, 12, 10]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 4, 16]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [0, 1, 2, 9]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [7, 13, 14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [2, 7, 12, 13]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [2, 3, 4, 5]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [16]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [6, 10, 17]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"TRIP13\",\n      \"REC8\",\n      \"RAD21L\",\n      \"SYCP2\",\n      \"MCM9\",\n      \"HORMAD2\",\n      \"AURKB\",\n      \"CDKN1B\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}