{"gene":"NME7","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2014,"finding":"NME7 is a functional component of the γ-tubulin ring complex (γTuRC) that regulates microtubule-nucleating activity. NME7 contains two putative kinase domains (A and B); domain A shows autophosphorylating activity while domain B is catalytically inactive. NME7 interacts with the γTuRC through both domains, with Arg-322 in domain B being crucial for binding. Suppression of NME7 impairs centrosome-based microtubule nucleation without affecting γTuRC assembly or localization. Wild-type NME7 promotes γTuRC-dependent microtubule nucleation, whereas kinase-deficient NME7 does so only poorly, indicating kinase-dependent function.","method":"Co-immunoprecipitation, site-directed mutagenesis (Arg-322, kinase-dead mutants), shRNA knockdown, microtubule nucleation assays, centrosome localization by immunofluorescence","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods including mutagenesis, in vitro nucleation assay, Co-IP, and functional rescue in a single rigorous study","pmids":["24807905"],"is_preprint":false},{"year":2021,"finding":"NME7 protein kinase activity phosphorylates GSK3β at serine 9, thereby promoting β-catenin activation and Wnt/β-catenin signaling. This in turn drives transcription of MTHFD2, a key enzyme in one-carbon metabolism. NME7 overexpression cooperated with c-Myc to drive tumorigenesis in a mouse model, and tumor-derived organoids with NME7 overexpression showed increased sensitivity to MTHFD2 inhibition.","method":"Kinase assay (phosphorylation of GSK3β-S9), co-immunoprecipitation (NME7–GSK3β interaction), knockdown/overexpression in vitro and in vivo, mouse tumorigenesis model, organoid assay, luciferase reporter for β-catenin activity","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct kinase assay and binding demonstrated, multiple cellular and in vivo readouts, single lab","pmids":["34764205"],"is_preprint":false},{"year":2010,"finding":"Nme7 knockout mice develop situs inversus, hydrocephalus, and excessive nasal exudates, phenotypes consistent with defective motile cilia function, supporting a role for NME7 in ciliary motility.","method":"Knockout mouse model (Nme7-/-), gross and histological phenotyping","journal":"Veterinary pathology","confidence":"Medium","confidence_rationale":"Tier 2 / Strong — clean KO with defined multi-organ ciliary phenotype, replicated across multiple labs and organisms","pmids":["20080492"],"is_preprint":false},{"year":2016,"finding":"A homozygous in-frame deletion of 34 amino acids in the second NDK domain of NME7 (the region critical for γTuRC binding) causes situs inversus totalis in humans, confirming that the γTuRC-interacting domain of NME7 is required for normal laterality determination.","method":"Whole-exome sequencing, genotyping, segregation analysis in a consanguineous family","journal":"Human mutation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — human genetics links a specific domain deletion to a ciliary phenotype, consistent with mouse KO data, single family","pmids":["27060491"],"is_preprint":false},{"year":2012,"finding":"Knockdown of Nme7 in mouse embryonic stem cells reduces expression of pluripotency markers (Oct4, Nanog, Klf4, c-Myc, Sox2, ERas, telomerase, Dnmt3B), impairs embryoid body and teratoma formation, and induces morphological differentiation. Overexpression of Nme7 rescues stem cell marker expression and embryoid body formation in the absence of LIF, establishing Nme7 as functionally required for ESC self-renewal.","method":"shRNA functional screen, shRNA knockdown, overexpression rescue, embryoid body formation assay, teratoma assay, qRT-PCR for pluripotency markers","journal":"Stem cells (Dayton, Ohio)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional rescue experiment with multiple readouts in a single lab","pmids":["22899353"],"is_preprint":false},{"year":2021,"finding":"Homozygous Nme7 knockout in rats causes semi-lethal primary ciliary dyskinesia phenotypes including hydrocephalus, situs inversus totalis, postnatal growth retardation, and sterility in both sexes. Thinning of the neocortex was detectable at embryonic day 13.5 and ventricular dilation at birth, indicating NME7 is required for ciliogenesis and ciliary transport in vivo.","method":"CRISPR/Cas9 knockout rat model, histology, transcriptomic profiling (liver and lung)","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR KO with defined multi-organ ciliary phenotype, independent replication of mouse KO findings in rat","pmids":["33916973"],"is_preprint":false},{"year":2025,"finding":"NME7 localizes to centrosomes (including spindle poles during metaphase and basal bodies during ciliogenesis), with a small fraction inside the cilium. NME7 knockdown and knockout impair primary cilium assembly. KO cells show increased sensitivity to nocodazole, indicating a role in ciliary microtubule stability. NME7 deficiency reduces Smoothened (Smo) accumulation within primary cilia, impairing Hedgehog signaling; this role depends on NME7's nucleoside diphosphate kinase activity and γTuRC association.","method":"NME7 knockdown/knockout (siRNA and CRISPR), immunofluorescence localization, nocodazole sensitivity assay, Hedgehog pathway reporter, Smo ciliary trafficking assay","journal":"Life science alliance","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO with multiple specific cellular phenotype readouts, kinase-activity dependence implied but full mutagenesis detail not stated in abstract, single lab","pmids":["39824631"],"is_preprint":false},{"year":2019,"finding":"The NME7AB isoform (an embryonic stem cell growth factor) promotes regression of primed iPSCs to a naïve-like pluripotent state, as evidenced by reactivation of mitochondrial function and increased ATP production in induced naïve-like PSCs compared to primed iPSCs.","method":"iPSC culture with NME7AB in bFGF-depleted medium, mitochondrial respiration assay, ATP measurement","journal":"Biochemistry and biophysics reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single set of functional assays, no mechanistic dissection of how NME7AB acts","pmids":["31467990"],"is_preprint":false}],"current_model":"NME7 is a nucleoside diphosphate kinase family member that functions as a component of the γ-tubulin ring complex (γTuRC), binding through its domain B (Arg-322) and promoting centrosome-based microtubule nucleation in a kinase-dependent manner; it localizes to centrosomes/basal bodies and is required for primary cilium assembly, ciliary microtubule stability, and Hedgehog signaling (via Smo ciliary trafficking); loss of NME7 in mice and rats causes primary ciliary dyskinesia phenotypes (situs inversus, hydrocephalus, infertility), and its kinase activity also phosphorylates GSK3β at Ser9 to activate Wnt/β-catenin signaling and downstream one-carbon metabolism in hepatocellular carcinoma."},"narrative":{"mechanistic_narrative":"NME7 is a nucleoside diphosphate kinase family member that functions in centrosome-based microtubule organization and ciliogenesis [PMID:24807905, PMID:39824631]. It is a functional component of the γ-tubulin ring complex (γTuRC), binding through both of its kinase domains—domain A retains autophosphorylating activity while the catalytically inactive domain B contributes binding via Arg-322—and it promotes γTuRC-dependent microtubule nucleation in a kinase-dependent manner without affecting γTuRC assembly or localization [PMID:24807905]. NME7 localizes to centrosomes, spindle poles, and basal bodies (with a small ciliary fraction) and is required for primary cilium assembly, ciliary microtubule stability, and Smoothened ciliary trafficking that supports Hedgehog signaling, with these roles depending on its NDK activity and γTuRC association [PMID:39824631]. Consistent with a ciliary function, loss of Nme7 in mice and rats produces primary ciliary dyskinesia phenotypes including situs inversus, hydrocephalus, and sterility [PMID:20080492, PMID:33916973], and a homozygous in-frame deletion in the γTuRC-interacting NDK domain causes situs inversus totalis in humans [PMID:27060491]. Independently, NME7 kinase activity phosphorylates GSK3β at Ser9 to activate Wnt/β-catenin signaling and drive MTHFD2-dependent one-carbon metabolism in a hepatocellular carcinoma model [PMID:34764205].","teleology":[{"year":2010,"claim":"Whether NME7 has an in vivo physiological role was unknown; loss-of-function in mice first tied it to motile cilia function through a defined multi-organ phenotype.","evidence":"Nme7 knockout mouse with gross and histological phenotyping","pmids":["20080492"],"confidence":"Medium","gaps":["Does not identify the molecular activity underlying the ciliary defect","No cellular or biochemical mechanism established"]},{"year":2012,"claim":"Beyond cilia, the question of whether NME7 contributes to cell identity was opened by showing it is required for embryonic stem cell self-renewal.","evidence":"shRNA knockdown and overexpression rescue with pluripotency marker, embryoid body, and teratoma assays in mouse ESCs","pmids":["22899353"],"confidence":"Medium","gaps":["Mechanism linking NME7 to pluripotency factor expression not defined","Relationship to its ciliary/centrosomal role unclear"]},{"year":2014,"claim":"The molecular basis of NME7 function was established by showing it is a γTuRC component whose kinase activity and Arg-322 in domain B are required to promote microtubule nucleation.","evidence":"Co-IP, site-directed mutagenesis, shRNA knockdown, and in vitro microtubule nucleation assays","pmids":["24807905"],"confidence":"High","gaps":["Catalytic substrate of domain A within the γTuRC context not identified","Structural basis of γTuRC docking not resolved"]},{"year":2016,"claim":"Whether the γTuRC-binding domain matters for human physiology was answered by linking an in-frame deletion in the second NDK domain to situs inversus totalis.","evidence":"Whole-exome sequencing and segregation analysis in a consanguineous family","pmids":["27060491"],"confidence":"Medium","gaps":["Single family","Functional consequence of the deletion on γTuRC binding not directly assayed in patient cells"]},{"year":2019,"claim":"An extracellular NME7AB isoform was reported to drive primed-to-naïve pluripotency regression with mitochondrial reactivation, raising the possibility of a non-centrosomal mode of action.","evidence":"iPSC culture with NME7AB in bFGF-depleted medium, mitochondrial respiration and ATP assays","pmids":["31467990"],"confidence":"Low","gaps":["No mechanistic dissection of how NME7AB acts; single lab, single assay set","Relationship between secreted NME7AB activity and intracellular γTuRC function unestablished"]},{"year":2021,"claim":"Independent replication in a second species confirmed NME7 as essential for ciliogenesis in vivo via a primary ciliary dyskinesia phenotype.","evidence":"CRISPR/Cas9 knockout rat with histology and transcriptomic profiling","pmids":["33916973"],"confidence":"Medium","gaps":["Does not distinguish motile versus primary cilia contributions at the molecular level"]},{"year":2021,"claim":"A signaling role distinct from centrosomes was defined by showing NME7 phosphorylates GSK3β-Ser9 to activate Wnt/β-catenin and MTHFD2-driven one-carbon metabolism in cancer.","evidence":"Kinase assay, Co-IP, knockdown/overexpression, mouse tumorigenesis model, organoid and β-catenin luciferase reporter assays","pmids":["34764205"],"confidence":"Medium","gaps":["Single lab","How NME7 kinase specificity toward GSK3β is achieved not defined","Connection to its γTuRC/ciliary role unexplored"]},{"year":2025,"claim":"The cellular pathway downstream of NME7's centrosomal localization was resolved by linking it to primary cilium assembly, ciliary microtubule stability, and Hedgehog signaling via Smoothened trafficking.","evidence":"siRNA/CRISPR knockout, immunofluorescence, nocodazole sensitivity, Hedgehog reporter, and Smo ciliary trafficking assays","pmids":["39824631"],"confidence":"Medium","gaps":["Full mutagenesis demonstrating kinase-activity dependence not detailed","Single lab","Mechanism of how NME7 promotes Smo accumulation in cilia not defined"]},{"year":null,"claim":"How NME7's NDK/kinase activity is mechanistically coupled to both γTuRC-based microtubule nucleation and to substrate phosphorylation (e.g., GSK3β) remains unresolved, as does whether these functions operate through a common biochemical activity.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of NME7 within γTuRC","Physiological substrate(s) of the active domain A not catalogued","Relationship between intracellular and secreted-isoform functions unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[0,6]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,6]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[6]}],"complexes":["γTuRC"],"partners":["TUBG1","GSK3B"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y5B8","full_name":"Nucleoside diphosphate kinase 7","aliases":["Putative 3'-5'-DNA exonuclease NDK7","Serine protein kinase NME7","nm23-H7"],"length_aa":376,"mass_kda":42.5,"function":"Possesses an intrinsic kinase activity (PubMed:24807905, PubMed:34764205). Phosphorylates GSK3B at 'Ser-9', leading to the activation of Wnt/beta-catenin signaling (PubMed:34764205). Additionally, exhibits a 3'-5'-DNA exonuclease activity that removes single nucleotides from the 3' terminus of single-stranded DNA substrates and digests overhanging mismatched 3' termini from double-stranded DNA substrates, possibly participating in DNA nucleolytic processing (PubMed:16313181). In vitro, does not seem to have nucleoside diphosphate kinase activity (PubMed:16313181, PubMed:24807905). Functional component of the gamma-tubulin ring complex, implicated in the regulation of its microtubule-nucleating activity in centrosomes, in a kinase activity-dependent manner (PubMed:24807905). May maintain primary cilium assembly and ciliary microtubule stability (PubMed:39824631). Part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, required for motile cilia beating (PubMed:36191189)","subcellular_location":"Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Nucleus; Cytoplasm; Cytoplasm, cytoskeleton, spindle; Cytoplasm, cytoskeleton, cilium axoneme; Cytoplasm, cytoskeleton, flagellum axoneme; Cell projection, cilium; Cytoplasm, cytoskeleton, cilium basal body","url":"https://www.uniprot.org/uniprotkb/Q9Y5B8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NME7","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"MIF","stoichiometry":0.2},{"gene":"TUBG1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/NME7","total_profiled":1310},"omim":[{"mim_id":"613465","title":"NME/NM23 FAMILY, MEMBER 7; NME7","url":"https://www.omim.org/entry/613465"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NME7"},"hgnc":{"alias_symbol":["FLJ37194","NM23-H7","CFAP67"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y5B8","domains":[{"cath_id":"2.30.29.170","chopping":"6-88","consensus_level":"high","plddt":90.6472,"start":6,"end":88},{"cath_id":"3.30.70.141","chopping":"91-220","consensus_level":"high","plddt":95.3803,"start":91,"end":220},{"cath_id":"3.30.70.141","chopping":"238-372","consensus_level":"high","plddt":95.3003,"start":238,"end":372}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y5B8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y5B8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y5B8-F1-predicted_aligned_error_v6.png","plddt_mean":93.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NME7","jax_strain_url":"https://www.jax.org/strain/search?query=NME7"},"sequence":{"accession":"Q9Y5B8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y5B8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y5B8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y5B8"}},"corpus_meta":[{"pmid":"20080492","id":"PMC_20080492","title":"Situs inversus in Dpcd/Poll-/-, Nme7-/- , and Pkd1l1-/- mice.","date":"2010","source":"Veterinary pathology","url":"https://pubmed.ncbi.nlm.nih.gov/20080492","citation_count":73,"is_preprint":false},{"pmid":"24807905","id":"PMC_24807905","title":"NME7 is a functional component of the γ-tubulin ring complex.","date":"2014","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/24807905","citation_count":62,"is_preprint":false},{"pmid":"34764205","id":"PMC_34764205","title":"The Protein Kinase Activity of NME7 Activates Wnt/β-Catenin Signaling to Promote One-Carbon Metabolism in Hepatocellular Carcinoma.","date":"2021","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/34764205","citation_count":31,"is_preprint":false},{"pmid":"27060491","id":"PMC_27060491","title":"A Homozygous Nme7 Mutation Is Associated with Situs Inversus Totalis.","date":"2016","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/27060491","citation_count":29,"is_preprint":false},{"pmid":"22899353","id":"PMC_22899353","title":"A shRNA functional screen reveals Nme6 and Nme7 are crucial for embryonic stem cell renewal.","date":"2012","source":"Stem cells (Dayton, Ohio)","url":"https://pubmed.ncbi.nlm.nih.gov/22899353","citation_count":27,"is_preprint":false},{"pmid":"15726650","id":"PMC_15726650","title":"Expression of the nm23 homologues nm23-H4, nm23-H6, and nm23-H7 in human gastric and colon cancer.","date":"2005","source":"The Journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/15726650","citation_count":25,"is_preprint":false},{"pmid":"33916973","id":"PMC_33916973","title":"Semi-Lethal Primary Ciliary Dyskinesia in Rats Lacking the Nme7 Gene.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33916973","citation_count":17,"is_preprint":false},{"pmid":"34356103","id":"PMC_34356103","title":"Heterozygous Nme7 Mutation Affects Glucose Tolerance in Male Rats.","date":"2021","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/34356103","citation_count":6,"is_preprint":false},{"pmid":"30484681","id":"PMC_30484681","title":"Expression profiling of Nme7 interactome in experimental models of metabolic syndrome.","date":"2018","source":"Physiological research","url":"https://pubmed.ncbi.nlm.nih.gov/30484681","citation_count":6,"is_preprint":false},{"pmid":"31467990","id":"PMC_31467990","title":"The primitive growth factor NME7AB induces mitochondrially active naïve-like pluripotent stem cells.","date":"2019","source":"Biochemistry and biophysics reports","url":"https://pubmed.ncbi.nlm.nih.gov/31467990","citation_count":3,"is_preprint":false},{"pmid":"39824631","id":"PMC_39824631","title":"NME7 maintains primary cilium assembly, ciliary microtubule stability, and Hedgehog signaling.","date":"2025","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/39824631","citation_count":2,"is_preprint":false},{"pmid":"41097086","id":"PMC_41097086","title":"The NME7 Gene Is Involved in the Kinetics of Glucose Processing.","date":"2025","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41097086","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7861,"output_tokens":2290,"usd":0.028966,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9379,"output_tokens":2817,"usd":0.05866,"stage2_stop_reason":"end_turn"},"total_usd":0.087626,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"NME7 is a functional component of the γ-tubulin ring complex (γTuRC) that regulates microtubule-nucleating activity. NME7 contains two putative kinase domains (A and B); domain A shows autophosphorylating activity while domain B is catalytically inactive. NME7 interacts with the γTuRC through both domains, with Arg-322 in domain B being crucial for binding. Suppression of NME7 impairs centrosome-based microtubule nucleation without affecting γTuRC assembly or localization. Wild-type NME7 promotes γTuRC-dependent microtubule nucleation, whereas kinase-deficient NME7 does so only poorly, indicating kinase-dependent function.\",\n      \"method\": \"Co-immunoprecipitation, site-directed mutagenesis (Arg-322, kinase-dead mutants), shRNA knockdown, microtubule nucleation assays, centrosome localization by immunofluorescence\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods including mutagenesis, in vitro nucleation assay, Co-IP, and functional rescue in a single rigorous study\",\n      \"pmids\": [\"24807905\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"NME7 protein kinase activity phosphorylates GSK3β at serine 9, thereby promoting β-catenin activation and Wnt/β-catenin signaling. This in turn drives transcription of MTHFD2, a key enzyme in one-carbon metabolism. NME7 overexpression cooperated with c-Myc to drive tumorigenesis in a mouse model, and tumor-derived organoids with NME7 overexpression showed increased sensitivity to MTHFD2 inhibition.\",\n      \"method\": \"Kinase assay (phosphorylation of GSK3β-S9), co-immunoprecipitation (NME7–GSK3β interaction), knockdown/overexpression in vitro and in vivo, mouse tumorigenesis model, organoid assay, luciferase reporter for β-catenin activity\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct kinase assay and binding demonstrated, multiple cellular and in vivo readouts, single lab\",\n      \"pmids\": [\"34764205\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Nme7 knockout mice develop situs inversus, hydrocephalus, and excessive nasal exudates, phenotypes consistent with defective motile cilia function, supporting a role for NME7 in ciliary motility.\",\n      \"method\": \"Knockout mouse model (Nme7-/-), gross and histological phenotyping\",\n      \"journal\": \"Veterinary pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO with defined multi-organ ciliary phenotype, replicated across multiple labs and organisms\",\n      \"pmids\": [\"20080492\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"A homozygous in-frame deletion of 34 amino acids in the second NDK domain of NME7 (the region critical for γTuRC binding) causes situs inversus totalis in humans, confirming that the γTuRC-interacting domain of NME7 is required for normal laterality determination.\",\n      \"method\": \"Whole-exome sequencing, genotyping, segregation analysis in a consanguineous family\",\n      \"journal\": \"Human mutation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — human genetics links a specific domain deletion to a ciliary phenotype, consistent with mouse KO data, single family\",\n      \"pmids\": [\"27060491\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Knockdown of Nme7 in mouse embryonic stem cells reduces expression of pluripotency markers (Oct4, Nanog, Klf4, c-Myc, Sox2, ERas, telomerase, Dnmt3B), impairs embryoid body and teratoma formation, and induces morphological differentiation. Overexpression of Nme7 rescues stem cell marker expression and embryoid body formation in the absence of LIF, establishing Nme7 as functionally required for ESC self-renewal.\",\n      \"method\": \"shRNA functional screen, shRNA knockdown, overexpression rescue, embryoid body formation assay, teratoma assay, qRT-PCR for pluripotency markers\",\n      \"journal\": \"Stem cells (Dayton, Ohio)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional rescue experiment with multiple readouts in a single lab\",\n      \"pmids\": [\"22899353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Homozygous Nme7 knockout in rats causes semi-lethal primary ciliary dyskinesia phenotypes including hydrocephalus, situs inversus totalis, postnatal growth retardation, and sterility in both sexes. Thinning of the neocortex was detectable at embryonic day 13.5 and ventricular dilation at birth, indicating NME7 is required for ciliogenesis and ciliary transport in vivo.\",\n      \"method\": \"CRISPR/Cas9 knockout rat model, histology, transcriptomic profiling (liver and lung)\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR KO with defined multi-organ ciliary phenotype, independent replication of mouse KO findings in rat\",\n      \"pmids\": [\"33916973\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NME7 localizes to centrosomes (including spindle poles during metaphase and basal bodies during ciliogenesis), with a small fraction inside the cilium. NME7 knockdown and knockout impair primary cilium assembly. KO cells show increased sensitivity to nocodazole, indicating a role in ciliary microtubule stability. NME7 deficiency reduces Smoothened (Smo) accumulation within primary cilia, impairing Hedgehog signaling; this role depends on NME7's nucleoside diphosphate kinase activity and γTuRC association.\",\n      \"method\": \"NME7 knockdown/knockout (siRNA and CRISPR), immunofluorescence localization, nocodazole sensitivity assay, Hedgehog pathway reporter, Smo ciliary trafficking assay\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO with multiple specific cellular phenotype readouts, kinase-activity dependence implied but full mutagenesis detail not stated in abstract, single lab\",\n      \"pmids\": [\"39824631\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The NME7AB isoform (an embryonic stem cell growth factor) promotes regression of primed iPSCs to a naïve-like pluripotent state, as evidenced by reactivation of mitochondrial function and increased ATP production in induced naïve-like PSCs compared to primed iPSCs.\",\n      \"method\": \"iPSC culture with NME7AB in bFGF-depleted medium, mitochondrial respiration assay, ATP measurement\",\n      \"journal\": \"Biochemistry and biophysics reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single set of functional assays, no mechanistic dissection of how NME7AB acts\",\n      \"pmids\": [\"31467990\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NME7 is a nucleoside diphosphate kinase family member that functions as a component of the γ-tubulin ring complex (γTuRC), binding through its domain B (Arg-322) and promoting centrosome-based microtubule nucleation in a kinase-dependent manner; it localizes to centrosomes/basal bodies and is required for primary cilium assembly, ciliary microtubule stability, and Hedgehog signaling (via Smo ciliary trafficking); loss of NME7 in mice and rats causes primary ciliary dyskinesia phenotypes (situs inversus, hydrocephalus, infertility), and its kinase activity also phosphorylates GSK3β at Ser9 to activate Wnt/β-catenin signaling and downstream one-carbon metabolism in hepatocellular carcinoma.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NME7 is a nucleoside diphosphate kinase family member that functions in centrosome-based microtubule organization and ciliogenesis [#0, #6]. It is a functional component of the γ-tubulin ring complex (γTuRC), binding through both of its kinase domains—domain A retains autophosphorylating activity while the catalytically inactive domain B contributes binding via Arg-322—and it promotes γTuRC-dependent microtubule nucleation in a kinase-dependent manner without affecting γTuRC assembly or localization [#0]. NME7 localizes to centrosomes, spindle poles, and basal bodies (with a small ciliary fraction) and is required for primary cilium assembly, ciliary microtubule stability, and Smoothened ciliary trafficking that supports Hedgehog signaling, with these roles depending on its NDK activity and γTuRC association [#6]. Consistent with a ciliary function, loss of Nme7 in mice and rats produces primary ciliary dyskinesia phenotypes including situs inversus, hydrocephalus, and sterility [#2, #5], and a homozygous in-frame deletion in the γTuRC-interacting NDK domain causes situs inversus totalis in humans [#3]. Independently, NME7 kinase activity phosphorylates GSK3β at Ser9 to activate Wnt/β-catenin signaling and drive MTHFD2-dependent one-carbon metabolism in a hepatocellular carcinoma model [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Whether NME7 has an in vivo physiological role was unknown; loss-of-function in mice first tied it to motile cilia function through a defined multi-organ phenotype.\",\n      \"evidence\": \"Nme7 knockout mouse with gross and histological phenotyping\",\n      \"pmids\": [\"20080492\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not identify the molecular activity underlying the ciliary defect\", \"No cellular or biochemical mechanism established\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Beyond cilia, the question of whether NME7 contributes to cell identity was opened by showing it is required for embryonic stem cell self-renewal.\",\n      \"evidence\": \"shRNA knockdown and overexpression rescue with pluripotency marker, embryoid body, and teratoma assays in mouse ESCs\",\n      \"pmids\": [\"22899353\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking NME7 to pluripotency factor expression not defined\", \"Relationship to its ciliary/centrosomal role unclear\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"The molecular basis of NME7 function was established by showing it is a γTuRC component whose kinase activity and Arg-322 in domain B are required to promote microtubule nucleation.\",\n      \"evidence\": \"Co-IP, site-directed mutagenesis, shRNA knockdown, and in vitro microtubule nucleation assays\",\n      \"pmids\": [\"24807905\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Catalytic substrate of domain A within the γTuRC context not identified\", \"Structural basis of γTuRC docking not resolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Whether the γTuRC-binding domain matters for human physiology was answered by linking an in-frame deletion in the second NDK domain to situs inversus totalis.\",\n      \"evidence\": \"Whole-exome sequencing and segregation analysis in a consanguineous family\",\n      \"pmids\": [\"27060491\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single family\", \"Functional consequence of the deletion on γTuRC binding not directly assayed in patient cells\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"An extracellular NME7AB isoform was reported to drive primed-to-naïve pluripotency regression with mitochondrial reactivation, raising the possibility of a non-centrosomal mode of action.\",\n      \"evidence\": \"iPSC culture with NME7AB in bFGF-depleted medium, mitochondrial respiration and ATP assays\",\n      \"pmids\": [\"31467990\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mechanistic dissection of how NME7AB acts; single lab, single assay set\", \"Relationship between secreted NME7AB activity and intracellular γTuRC function unestablished\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Independent replication in a second species confirmed NME7 as essential for ciliogenesis in vivo via a primary ciliary dyskinesia phenotype.\",\n      \"evidence\": \"CRISPR/Cas9 knockout rat with histology and transcriptomic profiling\",\n      \"pmids\": [\"33916973\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not distinguish motile versus primary cilia contributions at the molecular level\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"A signaling role distinct from centrosomes was defined by showing NME7 phosphorylates GSK3β-Ser9 to activate Wnt/β-catenin and MTHFD2-driven one-carbon metabolism in cancer.\",\n      \"evidence\": \"Kinase assay, Co-IP, knockdown/overexpression, mouse tumorigenesis model, organoid and β-catenin luciferase reporter assays\",\n      \"pmids\": [\"34764205\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"How NME7 kinase specificity toward GSK3β is achieved not defined\", \"Connection to its γTuRC/ciliary role unexplored\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The cellular pathway downstream of NME7's centrosomal localization was resolved by linking it to primary cilium assembly, ciliary microtubule stability, and Hedgehog signaling via Smoothened trafficking.\",\n      \"evidence\": \"siRNA/CRISPR knockout, immunofluorescence, nocodazole sensitivity, Hedgehog reporter, and Smo ciliary trafficking assays\",\n      \"pmids\": [\"39824631\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Full mutagenesis demonstrating kinase-activity dependence not detailed\", \"Single lab\", \"Mechanism of how NME7 promotes Smo accumulation in cilia not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NME7's NDK/kinase activity is mechanistically coupled to both γTuRC-based microtubule nucleation and to substrate phosphorylation (e.g., GSK3β) remains unresolved, as does whether these functions operate through a common biochemical activity.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of NME7 within γTuRC\", \"Physiological substrate(s) of the active domain A not catalogued\", \"Relationship between intracellular and secreted-isoform functions unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 6]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\"γTuRC\"],\n    \"partners\": [\"TUBG1\", \"GSK3B\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}