{"gene":"ALMS1","run_date":"2026-06-09T22:02:43","timeline":{"discoveries":[{"year":2005,"finding":"ALMS1 protein localizes to centrosomes and to the base of cilia (basal bodies) in multiple cell types; fibroblasts with disrupted ALMS1 assemble morphologically normal primary cilia and microtubule cytoskeletons, suggesting the Alström syndrome phenotype results from impaired ciliary function rather than defective ciliogenesis.","method":"Immunofluorescence microscopy of human fibroblasts and multiple tissues; analysis of ALMS1-disrupted fibroblasts","journal":"Diabetes","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct subcellular localization by immunofluorescence replicated across multiple labs and cell types, with functional consequence (impaired function not assembly)","pmids":["15855349"],"is_preprint":false},{"year":2005,"finding":"Loss of Alms1 in mice causes mislocalization of rhodopsin to the outer nuclear layer and accumulation of intracellular vesicles in photoreceptor inner segments, implicating ALMS1 in intracellular trafficking.","method":"Immunohistochemistry and electron microscopy of Alms1-/- (gene-trap) mouse retinas","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — two independent orthogonal methods (IHC + EM) in a clean KO mouse model with defined cellular phenotype","pmids":["16000322"],"is_preprint":false},{"year":2006,"finding":"Knockdown of Alms1 in mouse kidney epithelial cells causes stunted primary cilia and prevents calcium influx in response to mechanical stimuli; this stunted-cilia phenotype is rescued by a 5′ fragment of Alms1 cDNA, placing ALMS1 upstream of mechanosensory calcium signaling in kidney cilia.","method":"siRNA knockdown in vitro; calcium imaging; rescue with Alms1 cDNA fragment","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with specific cellular phenotype (stunted cilia, loss of calcium response), rescued by re-expression; multiple orthogonal methods","pmids":["17206865"],"is_preprint":false},{"year":2010,"finding":"ALMS1 localizes specifically to the proximal ends of centrioles and basal bodies, colocalizing with the centrosome cohesion protein C-Nap1. RNAi depletion of ALMS1 causes markedly diminished centrosomal levels of C-Nap1 and compromised cohesion of parental centrioles.","method":"Super-resolution/structured immunofluorescence; RNAi knockdown; co-localization analysis in human cells","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Moderate — precise localization mapped by immunofluorescence, functional consequence (centriole cohesion loss) demonstrated by RNAi; single lab but two orthogonal methods","pmids":["20844083"],"is_preprint":false},{"year":2010,"finding":"ALMS1 protein localizes to basal bodies of cochlear hair cells and supporting cells; Alms1-disrupted mice display stereociliary bundle shape and orientation defects (planar cell polarity defects) and accelerated outer hair cell loss, implying ALMS1 functions in planar cell polarity signaling in the cochlea.","method":"Immunofluorescence in neonatal rat organ of Corti; histological analysis of Alms1-disrupted mouse cochleae; DPOAE measurements","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct localization experiment plus KO mouse phenotypic analysis with multiple orthogonal methods (histology, electrophysiology)","pmids":["21071598"],"is_preprint":false},{"year":2012,"finding":"The carboxy-terminal region of murine ALMS1 interacts with α-actinin isoforms (α-actinin 1, α-actinin 4) and with components of the endosome recycling pathway (myosin Vb, Rad50-interacting protein 1, huntingtin-associated protein 1A); human fibroblasts with disrupted ALMS1 show reduced transferrin uptake and impaired transferrin clearance, indicating a role for ALMS1 in endocytic recycling.","method":"Yeast two-hybrid screen in mouse tissue libraries; transferrin uptake/clearance assay in human ALMS1-deficient fibroblasts; immunofluorescence of MDCK cells with N- and C-terminal ALMS1 antibodies","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Moderate — Y2H binding with multiple partners confirmed, functional assay in patient fibroblasts, and differential localization of isoforms; single lab, multiple orthogonal methods","pmids":["22693585"],"is_preprint":false},{"year":2010,"finding":"ALMS1 transcription is regulated by the ubiquitous factor Sp1 and by RFX (Regulatory Factor X) proteins, which bind an evolutionarily conserved X-box in the proximal ALMS1 promoter and drive ALMS1 expression during growth arrest (low-serum conditions).","method":"Luciferase reporter assay; EMSA; chromatin immunoprecipitation (ChIP); RNA interference; 5′ RACE","journal":"Gene","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — multiple orthogonal methods (reporter assay, EMSA, ChIP, RNAi) in a single lab establishing transcriptional regulatory mechanism","pmids":["20381594"],"is_preprint":false},{"year":2011,"finding":"ALMS1-deficient human dermal fibroblasts display cytoskeletal abnormalities (actin disorganization), impaired cell migration, up-regulated collagen production, increased cell cycle length, and resistance to apoptosis, constitutively resembling an activated myofibroblast phenotype, supporting a role for ALMS1 in cytoskeletal organization, cell cycle control, and apoptosis.","method":"Genome-wide gene expression analysis; ultrastructural characterization (EM); functional assays (migration, apoptosis, collagen production) in 4 patient-derived dermal fibroblast cultures","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple functional assays and genome-wide profiling in patient fibroblasts, single lab","pmids":["21541333"],"is_preprint":false},{"year":2012,"finding":"A truncating mutation in Alms1 (foz allele) causes a ~70% postnatal reduction in hypothalamic neurons displaying AC3-marked cilia, correlating with loss of appetite-regulating receptors (Mchr1, Sstr3) from cilia, indicating ALMS1 maintains the stability/maintenance of neuronal cilia involved in satiety regulation.","method":"Immunofluorescence and cilia marker analysis in foz/foz mouse hypothalami; in vivo localization of Alms1 at ciliary bases of hypothalamic neurons","journal":"Developmental neurobiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo localization combined with quantitative ciliary marker analysis in KO mouse, single lab","pmids":["22581473"],"is_preprint":false},{"year":2010,"finding":"Knockdown of Alms1 in 3T3-L1 preadipocytes impairs lipid accumulation and reduces adipocyte gene expression following hormonal induction of adipogenesis by at least 2-fold, establishing a cell-autonomous role for ALMS1 in adipogenesis; proximal insulin signaling in mature adipocytes is unaffected.","method":"Stable shRNA knockdown (>80%) in 3T3-L1 cells; adipogenesis induction assay; insulin-stimulated glucose uptake assay; gene expression analysis","journal":"International journal of obesity","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD with specific phenotypic readout; single lab; negative result on insulin signaling is methodologically informative","pmids":["20514046"],"is_preprint":false},{"year":2021,"finding":"ALMS1 depletion (siRNA knockdown in hTERT-RPE1 cells) results in the formation of longer cilia with altered morphology (twisting and bending of the axoneme) and reduces TGF-β1-mediated activation of SMAD2/3, placing ALMS1 upstream of TGF-β/BMP signaling through the primary cilium.","method":"siRNA knockdown; immunofluorescence of cilia morphology; western blot of phospho-SMAD2/3 after TGF-β1 stimulation in ALMS1-depleted hTERT-RPE1 cells","journal":"Frontiers in cell and developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with defined morphological and signaling phenotypes, two orthogonal readouts, single lab","pmids":["33598462"],"is_preprint":false},{"year":2022,"finding":"Depletion of ALMS1 (CRISPR KO in HeLa and hTERT-BJ-5ta cells) causes apoptosis resistance, G2/M cell cycle arrest, reduced SMAD3 phosphorylation (but not SMAD2), and impaired cell migration; proteomic profiling links ALMS1 loss to altered focal adhesion and cell-substrate adherens junction pathways.","method":"CRISPR/Cas9 KO; flow cytometry (cell cycle, apoptosis); western blot (SMAD2/3 phosphorylation); migration assay; proteomic profiling with TGF-β stimulation","journal":"Frontiers in molecular biosciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR KO with multiple functional readouts; single lab, two cell line models","pmids":["36325276"],"is_preprint":false},{"year":2023,"finding":"Endogenously tagged ALMS1 (CRISPR/Cas9) co-purifies with centrosomal and microtubule-associated proteins; the centrosomal protein CEP70 is a novel ALMS1 interactor identified by affinity-based complex analysis; CEP70 reduction decreases ALMS1 at the ciliary basal body, and domain analysis maps the interaction to the TPR-containing C-terminal fragment of CEP70.","method":"Endogenous tagging by CRISPR/Cas9 followed by affinity-based protein complex analysis (co-IP/MS); immunofluorescence in ALMS1-deficient hTERT-RPE1 cells; domain-deletion analysis of CEP70","journal":"Molecular & cellular proteomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — endogenous-tag co-IP/MS plus functional validation by KD; single lab, multiple orthogonal methods","pmids":["38122899"],"is_preprint":false},{"year":2024,"finding":"ALMS1 depletion in hTERT-BJ-5ta fibroblasts (CRISPR KO) disrupts TGF-β pathway cross-signaling with PI3K/AKT, EGFR1, and p53 pathways; integrated RNA-seq and proteomics identify altered collagen fibril organization, β-oxidation of fatty acids, and eicosanoid metabolism; ALMS1 loss leads to over-activation of AKT, associated with decreased PTEN expression.","method":"CRISPR/Cas9 KO; RNA-seq; proteomics; western blot (AKT phosphorylation, PTEN); pathway enrichment analysis","journal":"Biology direct","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — integrated multi-omics in CRISPR KO model with biochemical validation; single lab","pmids":["38062477"],"is_preprint":false},{"year":2024,"finding":"ALMS1 knockout iPSC-derived cardiomyocytes show increased contractility, altered calcium extrusion and impaired calcium handling dynamics, increased glycolytic and mitochondrial respiration, and increased senescence, establishing ALMS1 as a regulator of cardiomyocyte calcium handling, metabolism, and senescence.","method":"CRISPR KO in iPSC-CMs; MuscleMotion analysis; calcium optical mapping; Seahorse metabolic assay; senescence-associated β-galactosidase staining","journal":"Molecular genetics and metabolism","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — iPSC-CM KO model with multiple orthogonal functional assays; single lab","pmids":["39243575"],"is_preprint":false},{"year":2019,"finding":"Loss of alms1 in zebrafish causes gene expression changes in β-cells consistent with insulin hypersecretion and glucose sensing failure, and defects in peripheral glucose uptake, supporting hyperinsulinemia as a primary causative defect in ALMS1-associated T2DM; these findings were corroborated in cultured murine β-cells lacking Alms1.","method":"CRISPR/Cas9 alms1 knockout zebrafish; β-cell isolation and gene expression profiling; glucose tolerance testing; murine β-cell Alms1 KD as corroboration","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined KO model with cell-type-specific expression profiling and functional metabolic readouts; corroborated in two model organisms","pmids":["31220269"],"is_preprint":false},{"year":2024,"finding":"Mesenchymal/preadipocyte-specific Alms1 knockout (Pdgfrα-Cre) in mice recapitulates insulin resistance, fatty liver, and dyslipidemia seen in global Alms1 KO, establishing that loss of Alms1 specifically in the mesenchymal/adipose lineage is sufficient to cause systemic metabolic dysfunction.","method":"Conditional KO using Pdgfrα-Cre × floxed Alms1 mice; metabolic phenotyping (glucose tolerance, insulin resistance, body composition, food intake); histological analysis of liver and adipose tissue","journal":"Molecular metabolism","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional KO with cell-type specificity, global vs. conditional comparison, multiple metabolic readouts; replicated in both sexes","pmids":["38583571"],"is_preprint":false},{"year":2025,"finding":"ALMS1 (an intrinsically disordered protein) acts as an external mediator of centriole biogenesis by facilitating assembly and disassembly of a 'cartwheel seed' (CS) composed of CEP152, CEP63, and PCNT. ALMS1 interacts with CEP152, CEP63, and PCNT; these proteins form aggregates without ALMS1 that seed cartwheel assembly. Disease-linked ALMS1 mutations cause cartwheel expansion and shedding leading to ectopic centriole formation; ALMS1 depletion abolishes CS assembly and centriole biogenesis, while reintroduction generates de novo centrioles.","method":"CRISPR/Cas9 mutagenesis; Ultrastructure Expansion Microscopy; co-immunoprecipitation identifying CEP152, CEP63, PCNT as interactors; centriole counting; rescue by ALMS1 re-expression","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1-2 / Moderate — preprint with structural imaging and mutagenesis plus binding partner identification; awaits peer review","pmids":["40667363"],"is_preprint":true},{"year":2025,"finding":"In Drosophila, the two ALMS1 orthologs (Alms1a and Alms1b) are required for centriole duplication: Alms1a is a PCM protein loaded proximally at onset of procentriole formation, while Alms1b caps the base of mature centrioles. Acute loss (RNAi) completely disrupts procentriole formation prior to Sas-6 cartwheel assembly by preventing amplification of the Plk4-Ana2 pool at the duplication site and subsequent Sas-6 recruitment; chronic loss affects PCM maturation.","method":"Ultrastructure Expansion Microscopy; RNAi knockdown; RNA null alleles; immunofluorescence for Sas-6, Plk4, Ana2 in Drosophila","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Drosophila ortholog study with high-resolution imaging and genetic tools establishing epistatic placement of Alms1 upstream of Plk4-Ana2-Sas-6 axis; single lab","pmids":["40021845"],"is_preprint":false},{"year":2021,"finding":"Treatment of ALMS1S1645*/S1645* patient fibroblasts with translational readthrough-inducing drugs (PTC124/ataluren or amlexanox) restores full-length ALMS1 protein expression, improves ciliogenesis, recovers IFT88 expression, and corrects SSTR3 mis-localization, demonstrating that restored ALMS1 protein is sufficient to rescue ciliary function defects.","method":"Drug treatment of patient fibroblasts; western blot for ALMS1 protein; immunofluorescence of cilia number/length; IFT88 and SSTR3 localization","journal":"EBioMedicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional protein restoration with multiple ciliary readouts in patient cells; single lab","pmids":["34365092"],"is_preprint":false},{"year":2025,"finding":"Phosphoproteomic analysis of ALMS1 CRISPR KO cells identifies CDC42 as a central protein in the interactome regulating the TGF-β pathway; ALMS1 loss deregulates TGF-β signaling and related processes including endocytosis, as revealed by network diffusion analysis of differentially phosphorylated proteins.","method":"CRISPR/Cas9 KO; phosphoproteomics; protein-protein interaction network analysis; kinase-substrate interaction analysis","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — phosphoproteomic screen with computational network analysis; candidate proteins not biochemically validated in this study","pmids":["41193622"],"is_preprint":false}],"current_model":"ALMS1 encodes a large (~460 kDa), intrinsically disordered centrosomal/basal body protein that localizes specifically to the proximal ends of centrioles and basal bodies, where it (1) mediates centriole biogenesis by facilitating assembly and disassembly of CEP152/CEP63/PCNT-containing cartwheel seeds upstream of the Plk4-Ana2-Sas-6 axis, (2) maintains centriole cohesion by supporting centrosomal C-Nap1 levels, (3) is required for normal ciliary maintenance and mechanosensory calcium signaling in kidney epithelial cells and for planar cell polarity in cochlear hair cells, (4) interacts with α-actinin isoforms and endosome recycling components (myosin Vb) and regulates transferrin recycling, (5) modulates TGF-β/SMAD signaling and adipogenesis, and (6) plays essential roles in cardiomyocyte calcium handling, metabolism, and cell cycle arrest; its transcription is driven by Sp1 and ciliary-gene regulator RFX proteins, and its loss in the mesenchymal/adipose lineage is sufficient to cause the insulin resistance, dyslipidemia, and fatty liver characteristic of Alström syndrome."},"narrative":{"mechanistic_narrative":"ALMS1 is a large intrinsically disordered protein that localizes to the proximal ends of centrioles and to the base of cilia, where it governs centriole biogenesis, centrosome cohesion, and ciliary maintenance across multiple tissues [PMID:15855349, PMID:20844083, PMID:40667363]. At the centriole, ALMS1 acts as an external mediator of cartwheel assembly: it binds CEP152, CEP63, and PCNT and controls the ordered assembly and disassembly of a cartwheel seed upstream of the Plk4–Ana2–Sas-6 axis, such that its depletion abolishes centriole formation and disease-linked mutations cause cartwheel expansion and ectopic centrioles, a role conserved in the Drosophila Alms1 orthologs [PMID:40667363, PMID:40021845]. It additionally supports centrosomal C-Nap1 levels to maintain cohesion of parental centrioles and depends on the TPR-containing region of CEP70 for its retention at the basal body [PMID:20844083, PMID:38122899]. ALMS1 is required for normal ciliary structure and function rather than for de novo ciliogenesis: its loss yields stunted or abnormally elongated cilia, abolishes mechanosensory calcium influx in kidney epithelia, perturbs planar cell polarity in cochlear hair cells, and destabilizes signaling-receptor-bearing neuronal cilia involved in satiety [PMID:15855349, PMID:17206865, PMID:21071598, PMID:22581473, PMID:33598462]. Through its disordered C-terminus ALMS1 binds α-actinin isoforms and endosome-recycling components including myosin Vb, and its loss impairs transferrin uptake and recycling, linking it to endocytic trafficking; in photoreceptors its loss causes rhodopsin mislocalization and vesicle accumulation [PMID:16000322, PMID:22693585]. ALMS1 modulates ciliary TGF-β/SMAD signaling—reducing SMAD2/3 (notably SMAD3) phosphorylation—and its loss reorganizes focal adhesion, cytoskeletal, cell-cycle, apoptotic, and metabolic programs, producing G2/M arrest, apoptosis resistance, AKT over-activation with reduced PTEN, and altered fatty-acid oxidation [PMID:21541333, PMID:33598462, PMID:36325276, PMID:38062477]. Functionally it is required for adipogenesis, cardiomyocyte calcium handling and metabolism, and β-cell glucose sensing, and its transcription is driven by Sp1 and the ciliary regulator RFX during growth arrest [PMID:20381594, PMID:20514046, PMID:39243575, PMID:31220269]. Loss of Alms1 specifically in the mesenchymal/adipose lineage is sufficient to reproduce the insulin resistance, dyslipidemia, and fatty liver of Alström syndrome, and translational readthrough that restores full-length ALMS1 in patient fibroblasts rescues ciliary defects [PMID:38583571, PMID:34365092].","teleology":[{"year":2005,"claim":"Established where ALMS1 acts and whether its phenotype reflects failed ciliogenesis or impaired ciliary function, resolving the cellular basis of Alström syndrome.","evidence":"Immunofluorescence across human tissues and analysis of ALMS1-disrupted fibroblasts; KO mouse retina by IHC and EM","pmids":["15855349","16000322"],"confidence":"High","gaps":["Did not define molecular partners at the centrosome/basal body","Mechanism linking localization to trafficking defects unresolved"]},{"year":2006,"claim":"Placed ALMS1 upstream of mechanosensory calcium signaling in cilia by showing depletion stunts cilia and blocks flow-induced calcium influx, rescuable by re-expression.","evidence":"siRNA knockdown, calcium imaging, and cDNA-fragment rescue in mouse kidney epithelial cells","pmids":["17206865"],"confidence":"High","gaps":["Mechanism connecting ALMS1 to the calcium channel machinery not identified","Which ALMS1 domain mediates the rescue not mapped"]},{"year":2010,"claim":"Mapped ALMS1 to proximal centriole ends and assigned a centrosome-cohesion role via support of C-Nap1, and defined a planar-cell-polarity function in the cochlea.","evidence":"Structured/super-resolution IF and RNAi in human cells; basal-body IF plus KO mouse cochlear histology and DPOAE","pmids":["20844083","21071598"],"confidence":"High","gaps":["Whether ALMS1 directly binds C-Nap1 not shown","PCP signaling components linked to ALMS1 not identified"]},{"year":2010,"claim":"Defined the transcriptional control of ALMS1, linking its expression to ciliary gene programs (RFX) and to growth arrest.","evidence":"Luciferase reporters, EMSA, ChIP, RNAi, and 5' RACE on the ALMS1 promoter","pmids":["20381594"],"confidence":"High","gaps":["Physiological signals controlling Sp1/RFX-driven ALMS1 induction not defined"]},{"year":2012,"claim":"Identified ALMS1 C-terminal physical partners and demonstrated a role in endocytic recycling, connecting the centrosomal protein to membrane trafficking.","evidence":"Yeast two-hybrid screen, transferrin uptake/clearance in patient fibroblasts, and isoform-specific IF in MDCK cells","pmids":["22693585"],"confidence":"High","gaps":["Y2H interactions not validated by reciprocal co-IP in human cells","How recycling defects relate to ciliary phenotypes unresolved"]},{"year":2011,"claim":"Showed ALMS1 loss reprograms fibroblasts toward an activated myofibroblast state, implicating it in cytoskeletal organization, cell-cycle control, and apoptosis.","evidence":"Genome-wide expression, EM, and migration/apoptosis/collagen assays in patient dermal fibroblasts","pmids":["21541333"],"confidence":"Medium","gaps":["Causal molecular driver of the myofibroblast phenotype not isolated","Limited to patient-derived cells without isogenic controls"]},{"year":2012,"claim":"Demonstrated ALMS1 is required to maintain signaling-receptor-bearing neuronal cilia, linking ciliary stability to satiety regulation.","evidence":"Ciliary marker quantification and in vivo basal-body localization in foz/foz mouse hypothalamus","pmids":["22581473"],"confidence":"Medium","gaps":["Mechanism of receptor retention in cilia not defined","Single allele model"]},{"year":2019,"claim":"Established a cell-autonomous metabolic role for ALMS1 in adipogenesis and in β-cell glucose sensing, supporting hyperinsulinemia as a primary defect.","evidence":"shRNA knockdown adipogenesis assays in 3T3-L1; CRISPR KO zebrafish β-cell profiling and glucose tolerance, corroborated in murine β-cells","pmids":["20514046","31220269"],"confidence":"Medium","gaps":["Molecular link between centrosomal/ciliary ALMS1 and metabolic transcription unresolved","β-cell defect mechanism not pinned to a pathway"]},{"year":2021,"claim":"Placed ALMS1 upstream of ciliary TGF-β/SMAD signaling and showed restoring full-length protein rescues ciliary defects, providing proof-of-concept that ALMS1 protein is the relevant deficiency.","evidence":"siRNA and phospho-SMAD2/3 western in RPE1 cells; readthrough drug treatment of patient fibroblasts with ciliary readouts","pmids":["33598462","34365092"],"confidence":"Medium","gaps":["How ALMS1 controls SMAD activation mechanistically not defined","Drug effects shown only in cultured fibroblasts"]},{"year":2024,"claim":"Integrated multi-omics in CRISPR KO cells extended ALMS1 function to cross-talk with PI3K/AKT, EGFR, p53, and metabolic pathways, and to cardiomyocyte calcium handling, metabolism, and senescence.","evidence":"CRISPR KO with flow cytometry, SMAD/AKT/PTEN western, RNA-seq/proteomics; iPSC-cardiomyocyte contractility, calcium mapping, Seahorse, and senescence assays","pmids":["36325276","38062477","39243575"],"confidence":"Medium","gaps":["Direct effectors connecting ALMS1 to AKT/PTEN regulation not identified","Network associations partly correlative"]},{"year":2024,"claim":"Showed mesenchymal/adipose-lineage loss of Alms1 is sufficient to cause systemic Alström-like metabolic disease, localizing the disease origin to a specific lineage.","evidence":"Pdgfrα-Cre conditional Alms1 KO mice with metabolic phenotyping versus global KO","pmids":["38583571"],"confidence":"High","gaps":["Cell-intrinsic molecular mechanism in adipose progenitors not resolved"]},{"year":2025,"claim":"Defined ALMS1's core molecular activity as an external mediator of cartwheel-seed assembly during centriole biogenesis, acting upstream of the Plk4-Ana2-Sas-6 axis, conserved from flies to humans.","evidence":"Ultrastructure expansion microscopy, CRISPR mutagenesis, co-IP of CEP152/CEP63/PCNT, and rescue in human cells (preprint); UExM and RNAi of Drosophila Alms1a/b","pmids":["40667363","40021845"],"confidence":"Medium","gaps":["Human cartwheel-seed mechanism in a preprint awaiting peer review","Structural basis of ALMS1 binding to CEP152/CEP63/PCNT not solved"]},{"year":2025,"claim":"Implicated CDC42 as a hub in the ALMS1 phospho-interactome regulating TGF-β signaling and endocytosis.","evidence":"Phosphoproteomics and network diffusion analysis in CRISPR KO cells","pmids":["41193622"],"confidence":"Low","gaps":["Candidate hub CDC42 not biochemically validated in this study","Network inference is computational and correlative"]},{"year":null,"claim":"It remains unresolved how ALMS1's centriolar/ciliary scaffolding activity mechanistically connects to its metabolic, trafficking, and signaling functions across tissues.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying mechanism links centriole biogenesis to insulin resistance/adipogenesis","No high-resolution structure of ALMS1 or its complexes","Direct enzymatic or scaffolding activity not biochemically defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[5]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[3,17]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[17,18]}],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[0,3,12]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,2,10]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[3,17,18]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,10,11]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,5]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[9,14,15,16]}],"complexes":["cartwheel seed (CEP152/CEP63/PCNT)"],"partners":["CEP152","CEP63","PCNT","CEP70","ACTN1","ACTN4","MYO5B","C-NAP1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8TCU4","full_name":"Centrosome-associated protein ALMS1","aliases":["Alstrom syndrome protein 1"],"length_aa":4168,"mass_kda":461.1,"function":"Involved in PCM1-dependent intracellular transport. Required, directly or indirectly, for the localization of NCAPD2 to the proximal ends of centrioles. Required for proper formation and/or maintenance of primary cilia (PC), microtubule-based structures that protrude from the surface of epithelial cells","subcellular_location":"Cytoplasm; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Cytoplasm, cytoskeleton, cilium basal body; Cytoplasm, cytoskeleton, spindle pole","url":"https://www.uniprot.org/uniprotkb/Q8TCU4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ALMS1","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"HSPA4","stoichiometry":0.2},{"gene":"TUBB4B","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/ALMS1","total_profiled":1310},"omim":[{"mim_id":"617735","title":"CHROMOSOME 10 OPEN READING FRAME 90; C10ORF90","url":"https://www.omim.org/entry/617735"},{"mim_id":"617728","title":"CENTROSOMAL PROTEIN, 295-KD; CEP295","url":"https://www.omim.org/entry/617728"},{"mim_id":"613553","title":"X-PROLYL AMINOPEPTIDASE 3; XPNPEP3","url":"https://www.omim.org/entry/613553"},{"mim_id":"609254","title":"SENIOR-LOKEN SYNDROME 5; SLSN5","url":"https://www.omim.org/entry/609254"},{"mim_id":"606844","title":"ALMS1 CENTROSOME AND BASAL BODY ASSOCIATED PROTEIN; ALMS1","url":"https://www.omim.org/entry/606844"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Centrosome","reliability":"Supported"},{"location":"Basal body","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"},{"location":"Flagellar centriole","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Microtubules","reliability":"Additional"},{"location":"Mid piece","reliability":"Additional"},{"location":"End piece","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"testis","ntpm":20.7}],"url":"https://www.proteinatlas.org/search/ALMS1"},"hgnc":{"alias_symbol":["KIAA0328"],"prev_symbol":[]},"alphafold":{"accession":"Q8TCU4","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TCU4","model_url":"","pae_url":"","plddt_mean":null},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ALMS1","jax_strain_url":"https://www.jax.org/strain/search?query=ALMS1"},"sequence":{"accession":"Q8TCU4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8TCU4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8TCU4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TCU4"}},"corpus_meta":[{"pmid":"11941369","id":"PMC_11941369","title":"Mutations in ALMS1 cause obesity, type 2 diabetes and neurosensory degeneration in Alström syndrome.","date":"2002","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/11941369","citation_count":293,"is_preprint":false},{"pmid":"11941370","id":"PMC_11941370","title":"Mutation of ALMS1, a large gene with a tandem repeat encoding 47 amino acids, causes Alström syndrome.","date":"2002","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/11941370","citation_count":224,"is_preprint":false},{"pmid":"15855349","id":"PMC_15855349","title":"Subcellular localization of ALMS1 supports involvement of centrosome and basal body dysfunction in the pathogenesis of obesity, insulin resistance, and type 2 diabetes.","date":"2005","source":"Diabetes","url":"https://pubmed.ncbi.nlm.nih.gov/15855349","citation_count":182,"is_preprint":false},{"pmid":"16000322","id":"PMC_16000322","title":"Alms1-disrupted mice recapitulate human Alström syndrome.","date":"2005","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/16000322","citation_count":147,"is_preprint":false},{"pmid":"17206865","id":"PMC_17206865","title":"A role for Alström syndrome protein, alms1, in kidney ciliogenesis and cellular quiescence.","date":"2006","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/17206865","citation_count":145,"is_preprint":false},{"pmid":"16513793","id":"PMC_16513793","title":"Fat aussie--a new Alström syndrome mouse showing a critical role for ALMS1 in obesity, diabetes, and spermatogenesis.","date":"2006","source":"Molecular endocrinology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/16513793","citation_count":138,"is_preprint":false},{"pmid":"17594715","id":"PMC_17594715","title":"Spectrum of ALMS1 variants and evaluation of genotype-phenotype correlations in Alström syndrome.","date":"2007","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/17594715","citation_count":128,"is_preprint":false},{"pmid":"25846608","id":"PMC_25846608","title":"Alström Syndrome: Mutation Spectrum of ALMS1.","date":"2015","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/25846608","citation_count":125,"is_preprint":false},{"pmid":"16516152","id":"PMC_16516152","title":"Adaptive failure to high-fat diet characterizes steatohepatitis in Alms1 mutant mice.","date":"2006","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/16516152","citation_count":95,"is_preprint":false},{"pmid":"20844083","id":"PMC_20844083","title":"Centriolar association of ALMS1 and likely centrosomal functions of the ALMS motif-containing proteins C10orf90 and KIAA1731.","date":"2010","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/20844083","citation_count":89,"is_preprint":false},{"pmid":"30421101","id":"PMC_30421101","title":"ALMS1 and Alström syndrome: a recessive form of metabolic, neurosensory and cardiac deficits.","date":"2018","source":"Journal of molecular medicine (Berlin, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/30421101","citation_count":84,"is_preprint":false},{"pmid":"21071598","id":"PMC_21071598","title":"Alström Syndrome protein ALMS1 localizes to basal bodies of cochlear hair cells and regulates cilium-dependent planar cell polarity.","date":"2010","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/21071598","citation_count":79,"is_preprint":false},{"pmid":"22693585","id":"PMC_22693585","title":"The Alström syndrome protein, ALMS1, interacts with α-actinin and components of the endosome recycling pathway.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22693585","citation_count":68,"is_preprint":false},{"pmid":"16720663","id":"PMC_16720663","title":"Syndromic obesity and diabetes: changes in body composition with age and mutation analysis of ALMS1 in 12 United Kingdom kindreds with Alstrom syndrome.","date":"2006","source":"The Journal of clinical endocrinology and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/16720663","citation_count":65,"is_preprint":false},{"pmid":"22581473","id":"PMC_22581473","title":"A truncating mutation of Alms1 reduces the number of hypothalamic neuronal cilia in obese mice.","date":"2012","source":"Developmental neurobiology","url":"https://pubmed.ncbi.nlm.nih.gov/22581473","citation_count":60,"is_preprint":false},{"pmid":"21541333","id":"PMC_21541333","title":"ALMS1-deficient fibroblasts over-express extra-cellular matrix components, display cell cycle delay and are resistant to apoptosis.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21541333","citation_count":57,"is_preprint":false},{"pmid":"21901789","id":"PMC_21901789","title":"Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosis.","date":"2011","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/21901789","citation_count":53,"is_preprint":false},{"pmid":"24319333","id":"PMC_24319333","title":"Whole-exome sequencing identifies a novel ALMS1 mutation (p.Q2051X) in two Japanese brothers with Alström syndrome.","date":"2013","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/24319333","citation_count":32,"is_preprint":false},{"pmid":"29193673","id":"PMC_29193673","title":"Ophthalmic features of cone-rod dystrophy caused by pathogenic variants in the ALMS1 gene.","date":"2017","source":"Acta ophthalmologica","url":"https://pubmed.ncbi.nlm.nih.gov/29193673","citation_count":30,"is_preprint":false},{"pmid":"20381594","id":"PMC_20381594","title":"Transcriptional regulation of the Alström syndrome gene ALMS1 by members of the RFX family and Sp1.","date":"2010","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/20381594","citation_count":28,"is_preprint":false},{"pmid":"33639992","id":"PMC_33639992","title":"A deleterious mutation in the ALMS1 gene in a naturally occurring model of hypertrophic cardiomyopathy in the Sphynx cat.","date":"2021","source":"Orphanet journal of rare diseases","url":"https://pubmed.ncbi.nlm.nih.gov/33639992","citation_count":27,"is_preprint":false},{"pmid":"20514046","id":"PMC_20514046","title":"Knockdown of the Alström syndrome-associated gene Alms1 in 3T3-L1 preadipocytes impairs adipogenesis but has no effect on cell-autonomous insulin action.","date":"2010","source":"International journal of obesity (2005)","url":"https://pubmed.ncbi.nlm.nih.gov/20514046","citation_count":26,"is_preprint":false},{"pmid":"33598462","id":"PMC_33598462","title":"ALMS1 Regulates TGF-β Signaling and Morphology of Primary Cilia.","date":"2021","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/33598462","citation_count":25,"is_preprint":false},{"pmid":"24972238","id":"PMC_24972238","title":"Homozygous loss-of-function mutation in ALMS1 causes the lethal disorder mitogenic cardiomyopathy in two siblings.","date":"2014","source":"European journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24972238","citation_count":25,"is_preprint":false},{"pmid":"19279085","id":"PMC_19279085","title":"Population genomic analysis of ALMS1 in humans reveals a surprisingly complex evolutionary history.","date":"2009","source":"Molecular biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/19279085","citation_count":24,"is_preprint":false},{"pmid":"26010121","id":"PMC_26010121","title":"ALMS1 null mutations: a common cause of Leber congenital amaurosis and early-onset severe cone-rod dystrophy.","date":"2015","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/26010121","citation_count":24,"is_preprint":false},{"pmid":"33683834","id":"PMC_33683834","title":"The lncRNA ALMS1-IT1 may promote malignant progression of lung adenocarcinoma via AVL9-mediated activation of the cyclin-dependent kinase pathway.","date":"2021","source":"FEBS open bio","url":"https://pubmed.ncbi.nlm.nih.gov/33683834","citation_count":19,"is_preprint":false},{"pmid":"34365092","id":"PMC_34365092","title":"Translational readthrough of ciliopathy genes BBS2 and ALMS1 restores protein, ciliogenesis and function in patient fibroblasts.","date":"2021","source":"EBioMedicine","url":"https://pubmed.ncbi.nlm.nih.gov/34365092","citation_count":19,"is_preprint":false},{"pmid":"23652376","id":"PMC_23652376","title":"A novel ALMS1 splice mutation in a non-obese juvenile-onset insulin-dependent syndromic diabetic patient.","date":"2013","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/23652376","citation_count":18,"is_preprint":false},{"pmid":"24503146","id":"PMC_24503146","title":"Atypical Alstrom syndrome with novel ALMS1 mutations precluded by current diagnostic criteria.","date":"2014","source":"European journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24503146","citation_count":18,"is_preprint":false},{"pmid":"16601972","id":"PMC_16601972","title":"Common variations in the ALMS1 gene do not contribute to susceptibility to type 2 diabetes in a large white UK population.","date":"2006","source":"Diabetologia","url":"https://pubmed.ncbi.nlm.nih.gov/16601972","citation_count":17,"is_preprint":false},{"pmid":"31220269","id":"PMC_31220269","title":"Genomic knockout of alms1 in zebrafish recapitulates Alström syndrome and provides insight into metabolic phenotypes.","date":"2019","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31220269","citation_count":16,"is_preprint":false},{"pmid":"26077327","id":"PMC_26077327","title":"Nonsyndromic Early-Onset Cone-Rod Dystrophy and Limb-Girdle Muscular Dystrophy in a Consanguineous Israeli Family are Caused by Two Independent yet Linked Mutations in ALMS1 and DYSF.","date":"2015","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/26077327","citation_count":16,"is_preprint":false},{"pmid":"24122612","id":"PMC_24122612","title":"Identification of a glutamic acid repeat polymorphism of ALMS1 as a novel genetic risk marker for early-onset myocardial infarction by genome-wide linkage analysis.","date":"2013","source":"Circulation. Cardiovascular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24122612","citation_count":16,"is_preprint":false},{"pmid":"24049434","id":"PMC_24049434","title":"Novel ALMS1 mutations in Chinese patients with Alström syndrome.","date":"2013","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/24049434","citation_count":14,"is_preprint":false},{"pmid":"27665122","id":"PMC_27665122","title":"Whole exome sequencing identifies a homozygous nonsense variation in ALMS1 gene in a patient with syndromic obesity.","date":"2016","source":"Obesity research & clinical practice","url":"https://pubmed.ncbi.nlm.nih.gov/27665122","citation_count":13,"is_preprint":false},{"pmid":"31889847","id":"PMC_31889847","title":"Whole exome sequencing identifies rare biallelic ALMS1 missense and stop gain mutations in familial Alström syndrome patients.","date":"2019","source":"Saudi journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/31889847","citation_count":10,"is_preprint":false},{"pmid":"29720996","id":"PMC_29720996","title":"Rare Compound Heterozygous Frameshift Mutations in ALMS1 Gene Identified Through Exome Sequencing in a Taiwanese Patient With Alström Syndrome.","date":"2018","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/29720996","citation_count":10,"is_preprint":false},{"pmid":"34147365","id":"PMC_34147365","title":"LHCGR and ALMS1 defects likely cooperate in the development of polycystic ovary syndrome indicated by double-mutant mice.","date":"2021","source":"Journal of genetics and genomics = Yi chuan xue bao","url":"https://pubmed.ncbi.nlm.nih.gov/34147365","citation_count":9,"is_preprint":false},{"pmid":"37071642","id":"PMC_37071642","title":"Presence of known feline ALMS1 and MYBPC3 variants in a diverse cohort of cats with hypertrophic cardiomyopathy in Japan.","date":"2023","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/37071642","citation_count":9,"is_preprint":false},{"pmid":"36325276","id":"PMC_36325276","title":"Depletion of ALMS1 affects TGF-β signalling pathway and downstream processes such as cell migration and adhesion capacity.","date":"2022","source":"Frontiers in molecular biosciences","url":"https://pubmed.ncbi.nlm.nih.gov/36325276","citation_count":8,"is_preprint":false},{"pmid":"33981653","id":"PMC_33981653","title":"Identification of a Rare Exon 19 Skipping Mutation in ALMS1 Gene in Alström Syndrome Patients From Two Unrelated Saudi Families.","date":"2021","source":"Frontiers in pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/33981653","citation_count":8,"is_preprint":false},{"pmid":"18654604","id":"PMC_18654604","title":"Identification of a novel ALMS1 mutation in a Chinese family with Alström syndrome.","date":"2008","source":"Eye (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/18654604","citation_count":8,"is_preprint":false},{"pmid":"28724398","id":"PMC_28724398","title":"Whole genome sequencing identifies a novel ALMS1 gene mutation in two Chinese siblings with Alström syndrome.","date":"2017","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28724398","citation_count":8,"is_preprint":false},{"pmid":"38583571","id":"PMC_38583571","title":"Mesenchymal-specific Alms1 knockout in mice recapitulates metabolic features of Alström syndrome.","date":"2024","source":"Molecular metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/38583571","citation_count":7,"is_preprint":false},{"pmid":"28135309","id":"PMC_28135309","title":"Characterization of Alstrom Syndrome 1 (ALMS1) Transcript Variants in Hodgkin Lymphoma Cells.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28135309","citation_count":7,"is_preprint":false},{"pmid":"29715191","id":"PMC_29715191","title":"Five novel ALMS1 gene mutations in six patients with Alström syndrome.","date":"2018","source":"Journal of pediatric endocrinology & metabolism : JPEM","url":"https://pubmed.ncbi.nlm.nih.gov/29715191","citation_count":7,"is_preprint":false},{"pmid":"33264725","id":"PMC_33264725","title":"Generation of an induced pluripotent stem cell line from an Alström Syndrome patient with ALMS1 mutation (c.3902C > A, c.6436C > T) and a gene correction isogenic iPSC line.","date":"2020","source":"Stem cell research","url":"https://pubmed.ncbi.nlm.nih.gov/33264725","citation_count":7,"is_preprint":false},{"pmid":"32973878","id":"PMC_32973878","title":"Atypical Retinal Phenotype in a Patient With Alström Syndrome and Biallelic Novel Pathogenic Variants in ALMS1, Including a de novo Variation.","date":"2020","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32973878","citation_count":7,"is_preprint":false},{"pmid":"38062477","id":"PMC_38062477","title":"Loss of the centrosomal protein ALMS1 alters lipid metabolism and the regulation of extracellular matrix-related processes.","date":"2023","source":"Biology direct","url":"https://pubmed.ncbi.nlm.nih.gov/38062477","citation_count":6,"is_preprint":false},{"pmid":"39334527","id":"PMC_39334527","title":"LncRNA ALMS1-IT1 modulates ferroptosis and immune evasion in colorectal cancer through activating STAT3.","date":"2024","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39334527","citation_count":6,"is_preprint":false},{"pmid":"35912300","id":"PMC_35912300","title":"Novel Mutations in the MKKS, BBS7, and ALMS1 Genes in Iranian Children with Clinically Suspected Bardet-Biedl Syndrome.","date":"2022","source":"Case reports in ophthalmological medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35912300","citation_count":6,"is_preprint":false},{"pmid":"31669637","id":"PMC_31669637","title":"Whole exome sequencing identified two homozygous ALMS1 mutations in an Iranian family with Alström syndrome.","date":"2019","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/31669637","citation_count":6,"is_preprint":false},{"pmid":"38122899","id":"PMC_38122899","title":"Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters.","date":"2023","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/38122899","citation_count":6,"is_preprint":false},{"pmid":"34455967","id":"PMC_34455967","title":"Upregulated Long Non-coding RNA ALMS1-IT1 Promotes Neuroinflammation by Activating NF-κB Signaling in Ischemic Cerebral Injury.","date":"2021","source":"Current pharmaceutical design","url":"https://pubmed.ncbi.nlm.nih.gov/34455967","citation_count":5,"is_preprint":false},{"pmid":"39243575","id":"PMC_39243575","title":"Characterisation of infantile cardiomyopathy in Alström syndrome using ALMS1 knockout induced pluripotent stem cell derived cardiomyocyte model.","date":"2024","source":"Molecular genetics and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/39243575","citation_count":5,"is_preprint":false},{"pmid":"28402684","id":"PMC_28402684","title":"A Nonsense ALMS1 Mutation Underlies Alström Syndrome in an Extended Mennonite Kindred Settled in North Mexico.","date":"2017","source":"Genetic testing and molecular biomarkers","url":"https://pubmed.ncbi.nlm.nih.gov/28402684","citation_count":5,"is_preprint":false},{"pmid":"32945434","id":"PMC_32945434","title":"A novel variant in ALMS1 in a patient with Alström syndrome and prenatal diagnosis for the fetus in the family: A case report and literature review.","date":"2020","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/32945434","citation_count":4,"is_preprint":false},{"pmid":"38546151","id":"PMC_38546151","title":"Overburden of rare ALMS1 deleterious variants in Chinese early-onset type 2 diabetes with severe insulin resistance.","date":"2024","source":"Diabetes/metabolism research and reviews","url":"https://pubmed.ncbi.nlm.nih.gov/38546151","citation_count":4,"is_preprint":false},{"pmid":"37345275","id":"PMC_37345275","title":"HCM-associated ALMS1 variant: Allele drop-out and frequency in Italian Sphynx cats.","date":"2023","source":"Animal genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37345275","citation_count":4,"is_preprint":false},{"pmid":"33669459","id":"PMC_33669459","title":"Prevalent ALMS1 Pathogenic Variants in Spanish Alström Patients.","date":"2021","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/33669459","citation_count":4,"is_preprint":false},{"pmid":"38155680","id":"PMC_38155680","title":"Unique phenotypic-genotypic correlation in Saudi patients with ALMS1 mutations.","date":"2023","source":"Saudi journal of ophthalmology : official journal of the Saudi Ophthalmological Society","url":"https://pubmed.ncbi.nlm.nih.gov/38155680","citation_count":4,"is_preprint":false},{"pmid":"34148947","id":"PMC_34148947","title":"Novel Mutations of the ALMS1 Gene in Patients with Alström Syndrome.","date":"2021","source":"Internal medicine (Tokyo, Japan)","url":"https://pubmed.ncbi.nlm.nih.gov/34148947","citation_count":4,"is_preprint":false},{"pmid":"35292292","id":"PMC_35292292","title":"Whole-Genome Sequencing Identifies Novel Heterozygous Mutation in ALMS1 in Three Men With Both Peyronie's and Dupuytren's Disease.","date":"2022","source":"Urology","url":"https://pubmed.ncbi.nlm.nih.gov/35292292","citation_count":4,"is_preprint":false},{"pmid":"33782391","id":"PMC_33782391","title":"Whole-exome sequencing identifies two novel ALMS1 mutations in Indian patients with Leber congenital amaurosis.","date":"2021","source":"Human genome variation","url":"https://pubmed.ncbi.nlm.nih.gov/33782391","citation_count":4,"is_preprint":false},{"pmid":"31810438","id":"PMC_31810438","title":"A case report of two siblings with Alstrom syndrome without hearing loss associated with two new ALMS1 variants.","date":"2019","source":"BMC ophthalmology","url":"https://pubmed.ncbi.nlm.nih.gov/31810438","citation_count":4,"is_preprint":false},{"pmid":"40021845","id":"PMC_40021845","title":"Drosophila Alms1 proteins regulate centriolar cartwheel assembly by enabling Plk4-Ana2 amplification loop.","date":"2025","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/40021845","citation_count":3,"is_preprint":false},{"pmid":"33793549","id":"PMC_33793549","title":"alms1 mutant zebrafish do not show hair cell phenotypes seen in other cilia mutants.","date":"2021","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/33793549","citation_count":3,"is_preprint":false},{"pmid":"39095761","id":"PMC_39095761","title":"Whole-exome sequencing revealed a novel mutation of the ALMS1 gene in a Chinese family with Alström syndrome: a case report.","date":"2024","source":"BMC pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/39095761","citation_count":3,"is_preprint":false},{"pmid":"36685911","id":"PMC_36685911","title":"A novel missense ALMS1 variant causes aberrant splicing identified in a cohort of patients with Alström syndrome.","date":"2023","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36685911","citation_count":3,"is_preprint":false},{"pmid":"39386593","id":"PMC_39386593","title":"ALMS1 KO rat: a new model of metabolic syndrome with spontaneous hypertension.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39386593","citation_count":2,"is_preprint":false},{"pmid":"36162988","id":"PMC_36162988","title":"New pathogenic variants of ALMS1 gene in two Chinese families with Alström Syndrome.","date":"2022","source":"BMC ophthalmology","url":"https://pubmed.ncbi.nlm.nih.gov/36162988","citation_count":2,"is_preprint":false},{"pmid":"39335220","id":"PMC_39335220","title":"Prevalence of Hypertrophic Cardiomyopathy and ALMS1 Variant in Sphynx Cats in New Zealand.","date":"2024","source":"Animals : an open access journal from MDPI","url":"https://pubmed.ncbi.nlm.nih.gov/39335220","citation_count":2,"is_preprint":false},{"pmid":"33565060","id":"PMC_33565060","title":"[Analysis of ALMS1 gene variants in seven patients with Alström syndrome].","date":"2021","source":"Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33565060","citation_count":2,"is_preprint":false},{"pmid":"33969109","id":"PMC_33969109","title":"Alström syndrome with a novel mutation of ALMS1 and Graves' hyperthyroidism: A case report and review of the literature.","date":"2021","source":"World journal of clinical cases","url":"https://pubmed.ncbi.nlm.nih.gov/33969109","citation_count":2,"is_preprint":false},{"pmid":"26910739","id":"PMC_26910739","title":"A novel ALMS1 homozygous mutation in two Turkish brothers with Alström syndrome.","date":"2016","source":"Journal of pediatric endocrinology & metabolism : JPEM","url":"https://pubmed.ncbi.nlm.nih.gov/26910739","citation_count":2,"is_preprint":false},{"pmid":"37937857","id":"PMC_37937857","title":"Unraveling Alström syndrome: Homozygous mutation c.2729C>G in ALMS1 gene across an extended family.","date":"2023","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37937857","citation_count":1,"is_preprint":false},{"pmid":"38428329","id":"PMC_38428329","title":"New variants of ALMS1 gene and familial Alström syndrome case series.","date":"2024","source":"Brazilian journal of otorhinolaryngology","url":"https://pubmed.ncbi.nlm.nih.gov/38428329","citation_count":1,"is_preprint":false},{"pmid":"41691606","id":"PMC_41691606","title":"Alms1 KO Rat: A New Model of Cardiometabolic Syndrome With Spontaneous Hypertension.","date":"2026","source":"Acta physiologica (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/41691606","citation_count":1,"is_preprint":false},{"pmid":"39122231","id":"PMC_39122231","title":"Identification of novel compound heterozygous variants of the ALMS1 gene in a child with Alström syndrome by whole genome sequencing.","date":"2024","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/39122231","citation_count":1,"is_preprint":false},{"pmid":"37873427","id":"PMC_37873427","title":"Mesenchymal-specific Alms1 knockout in mice recapitulates key metabolic features of Alström Syndrome.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37873427","citation_count":0,"is_preprint":false},{"pmid":"41193622","id":"PMC_41193622","title":"Phosphoproteomic profiling highlights CDC42 and CDK2 as key players in the regulation of the TGF-β pathway in ALMS1 and BBS1 knockout models.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/41193622","citation_count":0,"is_preprint":false},{"pmid":"41044667","id":"PMC_41044667","title":"Endocrine metabolism characteristics of Alström syndrome in 25 Chinese patients and identification of a new splice site in the ALMS1 gene.","date":"2025","source":"Diabetology & metabolic syndrome","url":"https://pubmed.ncbi.nlm.nih.gov/41044667","citation_count":0,"is_preprint":false},{"pmid":"40667363","id":"PMC_40667363","title":"Centriole biogenesis is seeded by CEP152-CEP63-PCNT aggregates propagating outside the centriole through the Alström syndrome protein ALMS1.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40667363","citation_count":0,"is_preprint":false},{"pmid":"41751610","id":"PMC_41751610","title":"Characterisation of a Missense Variant of the Alström Syndrome Centrosome and Basal Body Associated Protein (ALMS1) Gene Associated with Cardiomyopathy Using Induced Pluripotent Stem Cells.","date":"2026","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/41751610","citation_count":0,"is_preprint":false},{"pmid":"36927560","id":"PMC_36927560","title":"Diagnosis, treatment and genetic analysis of a case of Alstrom syndrome caused by compoud heterozygous mutation of ALMS1.","date":"2022","source":"Yi chuan = Hereditas","url":"https://pubmed.ncbi.nlm.nih.gov/36927560","citation_count":0,"is_preprint":false},{"pmid":"40686969","id":"PMC_40686969","title":"Integrating Multiomics and Machine Learning: Senescence-Regulated ALMS1-IT1/miR-7c-5p/HMGA2 Axis as a Novel Therapeutic Target for Head and Neck Squamous Cell Carcinoma.","date":"2025","source":"ACS omega","url":"https://pubmed.ncbi.nlm.nih.gov/40686969","citation_count":0,"is_preprint":false},{"pmid":"36537469","id":"PMC_36537469","title":"Identification of a novel mutation in ALMS1 in a Chinese patient with monogenic diabetic syndrome by whole-exome sequencing.","date":"2022","source":"Nigerian journal of clinical practice","url":"https://pubmed.ncbi.nlm.nih.gov/36537469","citation_count":0,"is_preprint":false},{"pmid":"41549937","id":"PMC_41549937","title":"Clinical Presentation of a Child With a Novel ALMS1 Variant Associated With Alström Syndrome and Favorable Response to GLP-1 Receptor Agonist Therapy.","date":"2026","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/41549937","citation_count":0,"is_preprint":false},{"pmid":"38569205","id":"PMC_38569205","title":"A CASE OF ALSTRÖM SYNDROME WITH A NOVEL VARIANT IN ALMS1 GENE PRESENTING WITH CONE ROD DYSTROPHY AS FIRST FINDING.","date":"2025","source":"Retinal cases & brief reports","url":"https://pubmed.ncbi.nlm.nih.gov/38569205","citation_count":0,"is_preprint":false},{"pmid":"42035521","id":"PMC_42035521","title":"Generation of an induced pluripotent stem cell line from an Alström syndrome patient with biallelic ALMS1 pathogenic variants.","date":"2026","source":"Stem cell research","url":"https://pubmed.ncbi.nlm.nih.gov/42035521","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.06.26.661604","title":"Adaptable centriole biogenesis via the intrinsically disordered protein ALMS1","date":"2025-06-27","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.26.661604","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.04.19.639742","title":"<i>alms1</i>  regulates the immune response and brain ageing in zebrafish","date":"2025-04-21","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.19.639742","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.09.22.614364","title":"<i>ALMS1</i>  KO rat: a new model of metabolic syndrome with spontaneous hypertension","date":"2024-09-24","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.22.614364","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":46807,"output_tokens":5615,"usd":0.112323,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":14206,"output_tokens":4656,"usd":0.093715,"stage2_stop_reason":"end_turn"},"total_usd":0.206038,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2005,\n      \"finding\": \"ALMS1 protein localizes to centrosomes and to the base of cilia (basal bodies) in multiple cell types; fibroblasts with disrupted ALMS1 assemble morphologically normal primary cilia and microtubule cytoskeletons, suggesting the Alström syndrome phenotype results from impaired ciliary function rather than defective ciliogenesis.\",\n      \"method\": \"Immunofluorescence microscopy of human fibroblasts and multiple tissues; analysis of ALMS1-disrupted fibroblasts\",\n      \"journal\": \"Diabetes\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct subcellular localization by immunofluorescence replicated across multiple labs and cell types, with functional consequence (impaired function not assembly)\",\n      \"pmids\": [\"15855349\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Loss of Alms1 in mice causes mislocalization of rhodopsin to the outer nuclear layer and accumulation of intracellular vesicles in photoreceptor inner segments, implicating ALMS1 in intracellular trafficking.\",\n      \"method\": \"Immunohistochemistry and electron microscopy of Alms1-/- (gene-trap) mouse retinas\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — two independent orthogonal methods (IHC + EM) in a clean KO mouse model with defined cellular phenotype\",\n      \"pmids\": [\"16000322\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Knockdown of Alms1 in mouse kidney epithelial cells causes stunted primary cilia and prevents calcium influx in response to mechanical stimuli; this stunted-cilia phenotype is rescued by a 5′ fragment of Alms1 cDNA, placing ALMS1 upstream of mechanosensory calcium signaling in kidney cilia.\",\n      \"method\": \"siRNA knockdown in vitro; calcium imaging; rescue with Alms1 cDNA fragment\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with specific cellular phenotype (stunted cilia, loss of calcium response), rescued by re-expression; multiple orthogonal methods\",\n      \"pmids\": [\"17206865\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"ALMS1 localizes specifically to the proximal ends of centrioles and basal bodies, colocalizing with the centrosome cohesion protein C-Nap1. RNAi depletion of ALMS1 causes markedly diminished centrosomal levels of C-Nap1 and compromised cohesion of parental centrioles.\",\n      \"method\": \"Super-resolution/structured immunofluorescence; RNAi knockdown; co-localization analysis in human cells\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — precise localization mapped by immunofluorescence, functional consequence (centriole cohesion loss) demonstrated by RNAi; single lab but two orthogonal methods\",\n      \"pmids\": [\"20844083\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"ALMS1 protein localizes to basal bodies of cochlear hair cells and supporting cells; Alms1-disrupted mice display stereociliary bundle shape and orientation defects (planar cell polarity defects) and accelerated outer hair cell loss, implying ALMS1 functions in planar cell polarity signaling in the cochlea.\",\n      \"method\": \"Immunofluorescence in neonatal rat organ of Corti; histological analysis of Alms1-disrupted mouse cochleae; DPOAE measurements\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct localization experiment plus KO mouse phenotypic analysis with multiple orthogonal methods (histology, electrophysiology)\",\n      \"pmids\": [\"21071598\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The carboxy-terminal region of murine ALMS1 interacts with α-actinin isoforms (α-actinin 1, α-actinin 4) and with components of the endosome recycling pathway (myosin Vb, Rad50-interacting protein 1, huntingtin-associated protein 1A); human fibroblasts with disrupted ALMS1 show reduced transferrin uptake and impaired transferrin clearance, indicating a role for ALMS1 in endocytic recycling.\",\n      \"method\": \"Yeast two-hybrid screen in mouse tissue libraries; transferrin uptake/clearance assay in human ALMS1-deficient fibroblasts; immunofluorescence of MDCK cells with N- and C-terminal ALMS1 antibodies\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Y2H binding with multiple partners confirmed, functional assay in patient fibroblasts, and differential localization of isoforms; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"22693585\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"ALMS1 transcription is regulated by the ubiquitous factor Sp1 and by RFX (Regulatory Factor X) proteins, which bind an evolutionarily conserved X-box in the proximal ALMS1 promoter and drive ALMS1 expression during growth arrest (low-serum conditions).\",\n      \"method\": \"Luciferase reporter assay; EMSA; chromatin immunoprecipitation (ChIP); RNA interference; 5′ RACE\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — multiple orthogonal methods (reporter assay, EMSA, ChIP, RNAi) in a single lab establishing transcriptional regulatory mechanism\",\n      \"pmids\": [\"20381594\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"ALMS1-deficient human dermal fibroblasts display cytoskeletal abnormalities (actin disorganization), impaired cell migration, up-regulated collagen production, increased cell cycle length, and resistance to apoptosis, constitutively resembling an activated myofibroblast phenotype, supporting a role for ALMS1 in cytoskeletal organization, cell cycle control, and apoptosis.\",\n      \"method\": \"Genome-wide gene expression analysis; ultrastructural characterization (EM); functional assays (migration, apoptosis, collagen production) in 4 patient-derived dermal fibroblast cultures\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple functional assays and genome-wide profiling in patient fibroblasts, single lab\",\n      \"pmids\": [\"21541333\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"A truncating mutation in Alms1 (foz allele) causes a ~70% postnatal reduction in hypothalamic neurons displaying AC3-marked cilia, correlating with loss of appetite-regulating receptors (Mchr1, Sstr3) from cilia, indicating ALMS1 maintains the stability/maintenance of neuronal cilia involved in satiety regulation.\",\n      \"method\": \"Immunofluorescence and cilia marker analysis in foz/foz mouse hypothalami; in vivo localization of Alms1 at ciliary bases of hypothalamic neurons\",\n      \"journal\": \"Developmental neurobiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo localization combined with quantitative ciliary marker analysis in KO mouse, single lab\",\n      \"pmids\": [\"22581473\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Knockdown of Alms1 in 3T3-L1 preadipocytes impairs lipid accumulation and reduces adipocyte gene expression following hormonal induction of adipogenesis by at least 2-fold, establishing a cell-autonomous role for ALMS1 in adipogenesis; proximal insulin signaling in mature adipocytes is unaffected.\",\n      \"method\": \"Stable shRNA knockdown (>80%) in 3T3-L1 cells; adipogenesis induction assay; insulin-stimulated glucose uptake assay; gene expression analysis\",\n      \"journal\": \"International journal of obesity\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with specific phenotypic readout; single lab; negative result on insulin signaling is methodologically informative\",\n      \"pmids\": [\"20514046\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ALMS1 depletion (siRNA knockdown in hTERT-RPE1 cells) results in the formation of longer cilia with altered morphology (twisting and bending of the axoneme) and reduces TGF-β1-mediated activation of SMAD2/3, placing ALMS1 upstream of TGF-β/BMP signaling through the primary cilium.\",\n      \"method\": \"siRNA knockdown; immunofluorescence of cilia morphology; western blot of phospho-SMAD2/3 after TGF-β1 stimulation in ALMS1-depleted hTERT-RPE1 cells\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with defined morphological and signaling phenotypes, two orthogonal readouts, single lab\",\n      \"pmids\": [\"33598462\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Depletion of ALMS1 (CRISPR KO in HeLa and hTERT-BJ-5ta cells) causes apoptosis resistance, G2/M cell cycle arrest, reduced SMAD3 phosphorylation (but not SMAD2), and impaired cell migration; proteomic profiling links ALMS1 loss to altered focal adhesion and cell-substrate adherens junction pathways.\",\n      \"method\": \"CRISPR/Cas9 KO; flow cytometry (cell cycle, apoptosis); western blot (SMAD2/3 phosphorylation); migration assay; proteomic profiling with TGF-β stimulation\",\n      \"journal\": \"Frontiers in molecular biosciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR KO with multiple functional readouts; single lab, two cell line models\",\n      \"pmids\": [\"36325276\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Endogenously tagged ALMS1 (CRISPR/Cas9) co-purifies with centrosomal and microtubule-associated proteins; the centrosomal protein CEP70 is a novel ALMS1 interactor identified by affinity-based complex analysis; CEP70 reduction decreases ALMS1 at the ciliary basal body, and domain analysis maps the interaction to the TPR-containing C-terminal fragment of CEP70.\",\n      \"method\": \"Endogenous tagging by CRISPR/Cas9 followed by affinity-based protein complex analysis (co-IP/MS); immunofluorescence in ALMS1-deficient hTERT-RPE1 cells; domain-deletion analysis of CEP70\",\n      \"journal\": \"Molecular & cellular proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — endogenous-tag co-IP/MS plus functional validation by KD; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"38122899\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ALMS1 depletion in hTERT-BJ-5ta fibroblasts (CRISPR KO) disrupts TGF-β pathway cross-signaling with PI3K/AKT, EGFR1, and p53 pathways; integrated RNA-seq and proteomics identify altered collagen fibril organization, β-oxidation of fatty acids, and eicosanoid metabolism; ALMS1 loss leads to over-activation of AKT, associated with decreased PTEN expression.\",\n      \"method\": \"CRISPR/Cas9 KO; RNA-seq; proteomics; western blot (AKT phosphorylation, PTEN); pathway enrichment analysis\",\n      \"journal\": \"Biology direct\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — integrated multi-omics in CRISPR KO model with biochemical validation; single lab\",\n      \"pmids\": [\"38062477\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ALMS1 knockout iPSC-derived cardiomyocytes show increased contractility, altered calcium extrusion and impaired calcium handling dynamics, increased glycolytic and mitochondrial respiration, and increased senescence, establishing ALMS1 as a regulator of cardiomyocyte calcium handling, metabolism, and senescence.\",\n      \"method\": \"CRISPR KO in iPSC-CMs; MuscleMotion analysis; calcium optical mapping; Seahorse metabolic assay; senescence-associated β-galactosidase staining\",\n      \"journal\": \"Molecular genetics and metabolism\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — iPSC-CM KO model with multiple orthogonal functional assays; single lab\",\n      \"pmids\": [\"39243575\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Loss of alms1 in zebrafish causes gene expression changes in β-cells consistent with insulin hypersecretion and glucose sensing failure, and defects in peripheral glucose uptake, supporting hyperinsulinemia as a primary causative defect in ALMS1-associated T2DM; these findings were corroborated in cultured murine β-cells lacking Alms1.\",\n      \"method\": \"CRISPR/Cas9 alms1 knockout zebrafish; β-cell isolation and gene expression profiling; glucose tolerance testing; murine β-cell Alms1 KD as corroboration\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined KO model with cell-type-specific expression profiling and functional metabolic readouts; corroborated in two model organisms\",\n      \"pmids\": [\"31220269\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Mesenchymal/preadipocyte-specific Alms1 knockout (Pdgfrα-Cre) in mice recapitulates insulin resistance, fatty liver, and dyslipidemia seen in global Alms1 KO, establishing that loss of Alms1 specifically in the mesenchymal/adipose lineage is sufficient to cause systemic metabolic dysfunction.\",\n      \"method\": \"Conditional KO using Pdgfrα-Cre × floxed Alms1 mice; metabolic phenotyping (glucose tolerance, insulin resistance, body composition, food intake); histological analysis of liver and adipose tissue\",\n      \"journal\": \"Molecular metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional KO with cell-type specificity, global vs. conditional comparison, multiple metabolic readouts; replicated in both sexes\",\n      \"pmids\": [\"38583571\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ALMS1 (an intrinsically disordered protein) acts as an external mediator of centriole biogenesis by facilitating assembly and disassembly of a 'cartwheel seed' (CS) composed of CEP152, CEP63, and PCNT. ALMS1 interacts with CEP152, CEP63, and PCNT; these proteins form aggregates without ALMS1 that seed cartwheel assembly. Disease-linked ALMS1 mutations cause cartwheel expansion and shedding leading to ectopic centriole formation; ALMS1 depletion abolishes CS assembly and centriole biogenesis, while reintroduction generates de novo centrioles.\",\n      \"method\": \"CRISPR/Cas9 mutagenesis; Ultrastructure Expansion Microscopy; co-immunoprecipitation identifying CEP152, CEP63, PCNT as interactors; centriole counting; rescue by ALMS1 re-expression\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — preprint with structural imaging and mutagenesis plus binding partner identification; awaits peer review\",\n      \"pmids\": [\"40667363\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In Drosophila, the two ALMS1 orthologs (Alms1a and Alms1b) are required for centriole duplication: Alms1a is a PCM protein loaded proximally at onset of procentriole formation, while Alms1b caps the base of mature centrioles. Acute loss (RNAi) completely disrupts procentriole formation prior to Sas-6 cartwheel assembly by preventing amplification of the Plk4-Ana2 pool at the duplication site and subsequent Sas-6 recruitment; chronic loss affects PCM maturation.\",\n      \"method\": \"Ultrastructure Expansion Microscopy; RNAi knockdown; RNA null alleles; immunofluorescence for Sas-6, Plk4, Ana2 in Drosophila\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Drosophila ortholog study with high-resolution imaging and genetic tools establishing epistatic placement of Alms1 upstream of Plk4-Ana2-Sas-6 axis; single lab\",\n      \"pmids\": [\"40021845\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Treatment of ALMS1S1645*/S1645* patient fibroblasts with translational readthrough-inducing drugs (PTC124/ataluren or amlexanox) restores full-length ALMS1 protein expression, improves ciliogenesis, recovers IFT88 expression, and corrects SSTR3 mis-localization, demonstrating that restored ALMS1 protein is sufficient to rescue ciliary function defects.\",\n      \"method\": \"Drug treatment of patient fibroblasts; western blot for ALMS1 protein; immunofluorescence of cilia number/length; IFT88 and SSTR3 localization\",\n      \"journal\": \"EBioMedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional protein restoration with multiple ciliary readouts in patient cells; single lab\",\n      \"pmids\": [\"34365092\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Phosphoproteomic analysis of ALMS1 CRISPR KO cells identifies CDC42 as a central protein in the interactome regulating the TGF-β pathway; ALMS1 loss deregulates TGF-β signaling and related processes including endocytosis, as revealed by network diffusion analysis of differentially phosphorylated proteins.\",\n      \"method\": \"CRISPR/Cas9 KO; phosphoproteomics; protein-protein interaction network analysis; kinase-substrate interaction analysis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — phosphoproteomic screen with computational network analysis; candidate proteins not biochemically validated in this study\",\n      \"pmids\": [\"41193622\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ALMS1 encodes a large (~460 kDa), intrinsically disordered centrosomal/basal body protein that localizes specifically to the proximal ends of centrioles and basal bodies, where it (1) mediates centriole biogenesis by facilitating assembly and disassembly of CEP152/CEP63/PCNT-containing cartwheel seeds upstream of the Plk4-Ana2-Sas-6 axis, (2) maintains centriole cohesion by supporting centrosomal C-Nap1 levels, (3) is required for normal ciliary maintenance and mechanosensory calcium signaling in kidney epithelial cells and for planar cell polarity in cochlear hair cells, (4) interacts with α-actinin isoforms and endosome recycling components (myosin Vb) and regulates transferrin recycling, (5) modulates TGF-β/SMAD signaling and adipogenesis, and (6) plays essential roles in cardiomyocyte calcium handling, metabolism, and cell cycle arrest; its transcription is driven by Sp1 and ciliary-gene regulator RFX proteins, and its loss in the mesenchymal/adipose lineage is sufficient to cause the insulin resistance, dyslipidemia, and fatty liver characteristic of Alström syndrome.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ALMS1 is a large intrinsically disordered protein that localizes to the proximal ends of centrioles and to the base of cilia, where it governs centriole biogenesis, centrosome cohesion, and ciliary maintenance across multiple tissues [#0, #3, #17]. At the centriole, ALMS1 acts as an external mediator of cartwheel assembly: it binds CEP152, CEP63, and PCNT and controls the ordered assembly and disassembly of a cartwheel seed upstream of the Plk4–Ana2–Sas-6 axis, such that its depletion abolishes centriole formation and disease-linked mutations cause cartwheel expansion and ectopic centrioles, a role conserved in the Drosophila Alms1 orthologs [#17, #18]. It additionally supports centrosomal C-Nap1 levels to maintain cohesion of parental centrioles and depends on the TPR-containing region of CEP70 for its retention at the basal body [#3, #12]. ALMS1 is required for normal ciliary structure and function rather than for de novo ciliogenesis: its loss yields stunted or abnormally elongated cilia, abolishes mechanosensory calcium influx in kidney epithelia, perturbs planar cell polarity in cochlear hair cells, and destabilizes signaling-receptor-bearing neuronal cilia involved in satiety [#0, #2, #4, #8, #10]. Through its disordered C-terminus ALMS1 binds α-actinin isoforms and endosome-recycling components including myosin Vb, and its loss impairs transferrin uptake and recycling, linking it to endocytic trafficking; in photoreceptors its loss causes rhodopsin mislocalization and vesicle accumulation [#1, #5]. ALMS1 modulates ciliary TGF-β/SMAD signaling—reducing SMAD2/3 (notably SMAD3) phosphorylation—and its loss reorganizes focal adhesion, cytoskeletal, cell-cycle, apoptotic, and metabolic programs, producing G2/M arrest, apoptosis resistance, AKT over-activation with reduced PTEN, and altered fatty-acid oxidation [#7, #10, #11, #13]. Functionally it is required for adipogenesis, cardiomyocyte calcium handling and metabolism, and β-cell glucose sensing, and its transcription is driven by Sp1 and the ciliary regulator RFX during growth arrest [#6, #9, #14, #15]. Loss of Alms1 specifically in the mesenchymal/adipose lineage is sufficient to reproduce the insulin resistance, dyslipidemia, and fatty liver of Alström syndrome, and translational readthrough that restores full-length ALMS1 in patient fibroblasts rescues ciliary defects [#16, #19].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established where ALMS1 acts and whether its phenotype reflects failed ciliogenesis or impaired ciliary function, resolving the cellular basis of Alström syndrome.\",\n      \"evidence\": \"Immunofluorescence across human tissues and analysis of ALMS1-disrupted fibroblasts; KO mouse retina by IHC and EM\",\n      \"pmids\": [\"15855349\", \"16000322\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define molecular partners at the centrosome/basal body\", \"Mechanism linking localization to trafficking defects unresolved\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Placed ALMS1 upstream of mechanosensory calcium signaling in cilia by showing depletion stunts cilia and blocks flow-induced calcium influx, rescuable by re-expression.\",\n      \"evidence\": \"siRNA knockdown, calcium imaging, and cDNA-fragment rescue in mouse kidney epithelial cells\",\n      \"pmids\": [\"17206865\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism connecting ALMS1 to the calcium channel machinery not identified\", \"Which ALMS1 domain mediates the rescue not mapped\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Mapped ALMS1 to proximal centriole ends and assigned a centrosome-cohesion role via support of C-Nap1, and defined a planar-cell-polarity function in the cochlea.\",\n      \"evidence\": \"Structured/super-resolution IF and RNAi in human cells; basal-body IF plus KO mouse cochlear histology and DPOAE\",\n      \"pmids\": [\"20844083\", \"21071598\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ALMS1 directly binds C-Nap1 not shown\", \"PCP signaling components linked to ALMS1 not identified\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined the transcriptional control of ALMS1, linking its expression to ciliary gene programs (RFX) and to growth arrest.\",\n      \"evidence\": \"Luciferase reporters, EMSA, ChIP, RNAi, and 5' RACE on the ALMS1 promoter\",\n      \"pmids\": [\"20381594\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological signals controlling Sp1/RFX-driven ALMS1 induction not defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identified ALMS1 C-terminal physical partners and demonstrated a role in endocytic recycling, connecting the centrosomal protein to membrane trafficking.\",\n      \"evidence\": \"Yeast two-hybrid screen, transferrin uptake/clearance in patient fibroblasts, and isoform-specific IF in MDCK cells\",\n      \"pmids\": [\"22693585\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Y2H interactions not validated by reciprocal co-IP in human cells\", \"How recycling defects relate to ciliary phenotypes unresolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Showed ALMS1 loss reprograms fibroblasts toward an activated myofibroblast state, implicating it in cytoskeletal organization, cell-cycle control, and apoptosis.\",\n      \"evidence\": \"Genome-wide expression, EM, and migration/apoptosis/collagen assays in patient dermal fibroblasts\",\n      \"pmids\": [\"21541333\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal molecular driver of the myofibroblast phenotype not isolated\", \"Limited to patient-derived cells without isogenic controls\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrated ALMS1 is required to maintain signaling-receptor-bearing neuronal cilia, linking ciliary stability to satiety regulation.\",\n      \"evidence\": \"Ciliary marker quantification and in vivo basal-body localization in foz/foz mouse hypothalamus\",\n      \"pmids\": [\"22581473\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of receptor retention in cilia not defined\", \"Single allele model\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Established a cell-autonomous metabolic role for ALMS1 in adipogenesis and in β-cell glucose sensing, supporting hyperinsulinemia as a primary defect.\",\n      \"evidence\": \"shRNA knockdown adipogenesis assays in 3T3-L1; CRISPR KO zebrafish β-cell profiling and glucose tolerance, corroborated in murine β-cells\",\n      \"pmids\": [\"20514046\", \"31220269\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular link between centrosomal/ciliary ALMS1 and metabolic transcription unresolved\", \"β-cell defect mechanism not pinned to a pathway\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Placed ALMS1 upstream of ciliary TGF-β/SMAD signaling and showed restoring full-length protein rescues ciliary defects, providing proof-of-concept that ALMS1 protein is the relevant deficiency.\",\n      \"evidence\": \"siRNA and phospho-SMAD2/3 western in RPE1 cells; readthrough drug treatment of patient fibroblasts with ciliary readouts\",\n      \"pmids\": [\"33598462\", \"34365092\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How ALMS1 controls SMAD activation mechanistically not defined\", \"Drug effects shown only in cultured fibroblasts\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Integrated multi-omics in CRISPR KO cells extended ALMS1 function to cross-talk with PI3K/AKT, EGFR, p53, and metabolic pathways, and to cardiomyocyte calcium handling, metabolism, and senescence.\",\n      \"evidence\": \"CRISPR KO with flow cytometry, SMAD/AKT/PTEN western, RNA-seq/proteomics; iPSC-cardiomyocyte contractility, calcium mapping, Seahorse, and senescence assays\",\n      \"pmids\": [\"36325276\", \"38062477\", \"39243575\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct effectors connecting ALMS1 to AKT/PTEN regulation not identified\", \"Network associations partly correlative\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed mesenchymal/adipose-lineage loss of Alms1 is sufficient to cause systemic Alström-like metabolic disease, localizing the disease origin to a specific lineage.\",\n      \"evidence\": \"Pdgfrα-Cre conditional Alms1 KO mice with metabolic phenotyping versus global KO\",\n      \"pmids\": [\"38583571\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cell-intrinsic molecular mechanism in adipose progenitors not resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined ALMS1's core molecular activity as an external mediator of cartwheel-seed assembly during centriole biogenesis, acting upstream of the Plk4-Ana2-Sas-6 axis, conserved from flies to humans.\",\n      \"evidence\": \"Ultrastructure expansion microscopy, CRISPR mutagenesis, co-IP of CEP152/CEP63/PCNT, and rescue in human cells (preprint); UExM and RNAi of Drosophila Alms1a/b\",\n      \"pmids\": [\"40667363\", \"40021845\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Human cartwheel-seed mechanism in a preprint awaiting peer review\", \"Structural basis of ALMS1 binding to CEP152/CEP63/PCNT not solved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Implicated CDC42 as a hub in the ALMS1 phospho-interactome regulating TGF-β signaling and endocytosis.\",\n      \"evidence\": \"Phosphoproteomics and network diffusion analysis in CRISPR KO cells\",\n      \"pmids\": [\"41193622\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Candidate hub CDC42 not biochemically validated in this study\", \"Network inference is computational and correlative\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how ALMS1's centriolar/ciliary scaffolding activity mechanistically connects to its metabolic, trafficking, and signaling functions across tissues.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying mechanism links centriole biogenesis to insulin resistance/adipogenesis\", \"No high-resolution structure of ALMS1 or its complexes\", \"Direct enzymatic or scaffolding activity not biochemically defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3, 17]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [17, 18]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [0, 3, 12]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 2, 10]},\n      {\"term_id\": \"GO:0005813\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [3, 17, 18]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 10, 11]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [9, 14, 15, 16]}\n    ],\n    \"complexes\": [\"cartwheel seed (CEP152/CEP63/PCNT)\"],\n    \"partners\": [\"CEP152\", \"CEP63\", \"PCNT\", \"CEP70\", \"ACTN1\", \"ACTN4\", \"MYO5B\", \"C-Nap1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}