{"gene":"CHODL","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2002,"finding":"CHODL encodes a type I transmembrane protein with a single C-type lectin carbohydrate recognition domain (CRD) in its extracellular portion; it is N-glycosylated (~36 kDa) and shows predominantly perinuclear localization in transiently transfected COS1 cells; no specific interaction with hyaluronan was detected.","method":"PCR cloning, Northern blot, RT-PCR, immunohistochemistry, Western blot, transient transfection with subcellular localization imaging, cetylpyridinium chloride precipitation (negative for hyaluronan binding)","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Western blot, IHC, transfection/localization) in a single characterization study establishing protein structure and localization","pmids":["12079284"],"is_preprint":false},{"year":2003,"finding":"An alternatively spliced CHODL isoform lacking the transmembrane domain (CHODLfΔE/CHODLΔe) is expressed exclusively in T lymphocytes and is regulated during T lymphopoiesis; the transmembrane-containing isoform CHODLf colocalizes with rBet1 to the endoplasmic reticulum–Golgi apparatus.","method":"RT-PCR, database analysis, double-label immunofluorescence","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by immunofluorescence co-localization with ER/Golgi marker, alternative splicing confirmed by RT-PCR, single lab with two orthogonal methods","pmids":["12621022"],"is_preprint":false},{"year":2003,"finding":"Mouse Chodl (orthologue of human CHODL) is a type I transmembrane C-type lectin expressed in skeletal muscle cells during both proliferation and differentiation phases, as shown by in situ hybridization on E15 embryos and fluorescent immunostaining localizing the protein to striated muscle cells.","method":"RT-PCR/Southern blotting, in situ hybridization, fluorescent immunostaining, Western blot on C2C12 myoblasts","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (ISH, immunostaining, Western blot) in a single characterization study; mouse orthologue","pmids":["12711387"],"is_preprint":false},{"year":2007,"finding":"The soluble CHODL isoforms (CHODLΔe/CHODLfΔe), which lack the transmembrane domain and terminate in a QDEL ER-retention signal, localize to the late endoplasmic reticulum and are expressed in a small lymphocyte population in spleen and tonsils, with differential expression in thymocytes versus peripheral lymphocytes.","method":"Immunofluorescence localization, immunohistochemistry on tissue sections","journal":"Cell biology international","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single primary method (immunofluorescence/IHC), no functional consequence linked to localization","pmids":["17606388"],"is_preprint":false},{"year":2008,"finding":"The cytoplasmic domain of mouse chondrolectin (chodl) directly interacts with the beta-subunit of Rab geranylgeranyl transferase (Rabggtb), identified by SOS recruitment system (SRS) yeast screen and confirmed by in vitro transcription/translation and co-immunoprecipitation.","method":"SOS recruitment system (SRS) yeast two-hybrid screen, in vitro transcription/translation pulldown, co-immunoprecipitation","journal":"Cellular & molecular biology letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — interaction confirmed by two orthogonal methods (in vitro binding + co-IP), single lab","pmids":["18161010"],"is_preprint":false},{"year":2012,"finding":"In zebrafish, knockdown of chodl causes arrest/stalling of motor axon growth at the horizontal myoseptum (an intermediate target), resulting in reduced muscle innervation; this phenotype is rescued by chodl overexpression, demonstrating that correct chodl expression levels are required for growth cone interactions with the horizontal myoseptum.","method":"In vivo morpholino knockdown, transgenic overexpression, rescue experiment, in vivo live imaging of labeled motor axons in zebrafish","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with specific phenotypic readout, gain-of-function, and rescue experiment in vivo; replicated mechanistic conclusion across multiple experiments in one study","pmids":["22457492"],"is_preprint":false},{"year":2013,"finding":"Chodl expression is altered (alternatively spliced) in SMA mouse spinal motor neurons before symptom onset; in vitro studies show Chodl affects cell survival and neurite outgrowth; increasing chodl expression in Smn-depleted zebrafish rescues motor neuron outgrowth defects, linking Chodl dysregulation to SMA motor neuron pathophysiology.","method":"Exon-level splicing analysis in SMA mouse model, in vitro cell survival and neurite outgrowth assays, in vivo chodl overexpression rescue in smn-knockdown zebrafish","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (in vitro assays + in vivo rescue), direct functional readouts for cell survival, neurite outgrowth, and motor axon defects in two model systems","pmids":["24067532"],"is_preprint":false},{"year":2011,"finding":"siRNA-mediated knockdown of CHODL suppresses lung cancer cell growth, and exogenous overexpression of CHODL confers growth and invasive activity in mammalian cells, as measured by Matrigel invasion assays.","method":"siRNA knockdown (cell viability assay), exogenous CHODL overexpression, Matrigel invasion assay","journal":"Clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function and gain-of-function with defined cellular phenotypes (growth, invasion), two complementary approaches in single lab","pmids":["22016508"],"is_preprint":false},{"year":2019,"finding":"CHODL is predicted to undergo S-palmitoylation at a juxtamembrane cysteine residue, identified by a machine-learning topology-driven approach (TopoPalmTree) applied to the mouse transmembrane proteome; experimental assessment of Chodl as a candidate S-palmitoyl substrate was performed (results reported among confirmed candidates).","method":"Machine-learning prediction (TopoPalmTree), experimental S-palmitoylation assessment (method not fully detailed in abstract)","journal":"The Journal of biological chemistry","confidence":"Low","confidence_rationale":"Tier 4 / Weak — primarily computational prediction; experimental validation described briefly in abstract without full methodological detail, single study","pmids":["39909380"],"is_preprint":false},{"year":2025,"finding":"Sst-Chodl neurons (somatostatin and chondrolectin co-expressing GABAergic cells) are selectively active during low-arousal states; selective activation of Sst-Chodl cells is sufficient to promote multi-region cortical synchronization and induce sleep via long-range axons targeting multiple neocortical regions simultaneously.","method":"In vivo electrophysiology/calcium imaging, optogenetic selective activation of Sst-Chodl cells, behavioral sleep assays in mice","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — optogenetic gain-of-function with specific behavioral and electrophysiological readouts; preprint, single lab, not yet peer-reviewed","pmids":["bio_10.1101_2024.06.20.599756"],"is_preprint":true},{"year":2025,"finding":"In a 15q13.3 microdeletion mouse model, single-nucleus transcriptomics showed the largest gene expression alterations in Sst_Chodl neurons; patch-clamp and calcium imaging revealed increased activity specifically in the Sst_Chodl subtype; chemogenetic inhibition of Sst_Chodl neurons rescued sleep disturbances in mutant mice.","method":"Single-nucleus RNA-seq (snRNA-seq), calcium imaging, patch-clamp electrophysiology, Patch-seq, chemogenetic inhibition (DREADD) with behavioral rescue","journal":"Neuron","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (snRNA-seq, patch-clamp, calcium imaging, chemogenetics with rescue) in single lab; establishes functional role of Sst_Chodl neuron subtype","pmids":["40997796"],"is_preprint":false},{"year":2025,"finding":"Conditional knockout of Chodl in embryonic myoblasts or adult satellite cells (SCs) does not affect muscle development but markedly impairs regeneration; Chodl-deficient SCs show reduced self-renewal, diminished proliferation, and impaired differentiation; a significant fraction of Chodl-null SCs mislocalize outside the basal lamina and undergo precocious activation, consistent with disrupted ECM and Notch signaling interactions.","method":"Conditional knockout mouse models (Cre-lox), single-cell RNA-seq, muscle injury regeneration assays, immunofluorescence for SC localization, in silico network perturbation analysis","journal":"iScience","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean conditional KO with specific cellular and regenerative phenotypes, multiple orthogonal methods (scRNA-seq, histology, functional regeneration), replicated across embryonic and adult SC-specific deletion models","pmids":["42088368","40964242"],"is_preprint":false}],"current_model":"CHODL encodes a type I transmembrane C-type lectin that localizes to the ER-Golgi compartment; its cytoplasmic domain interacts with Rabggtb (the beta-subunit of Rab geranylgeranyl transferase); in motor neurons, CHODL is required for motor axon growth cone interactions with intermediate targets (horizontal myoseptum in zebrafish), and its dysregulation contributes to SMA motor neuron pathology; in skeletal muscle satellite cells, CHODL is essential for sublaminar niche localization, ECM interactions, and regenerative capacity via effects on self-renewal, proliferation, and Notch signaling; in the neocortex, Sst-Chodl GABAergic neurons with long-range projections promote cortical synchrony and sleep; alternatively spliced soluble isoforms lacking the transmembrane domain are expressed in T lymphocytes during maturation; CHODL is also a candidate substrate for S-palmitoylation."},"narrative":{"mechanistic_narrative":"CHODL (chondrolectin) is a type I transmembrane C-type lectin that operates at the interface of cell-surface glycan recognition and tissue morphogenesis, with established roles in motor neuron axon guidance, skeletal muscle satellite cell maintenance, and a distinct cortical GABAergic neuron identity [PMID:12079284, PMID:22457492, PMID:42088368, PMID:40964242]. The protein carries a single extracellular C-type lectin carbohydrate recognition domain, is N-glycosylated, and localizes to the ER-Golgi compartment, where it colocalizes with the ER-Golgi marker rBet1; its short cytoplasmic domain directly binds Rabggtb, the beta-subunit of Rab geranylgeranyl transferase [PMID:12079284, PMID:12621022, PMID:18161010]. Alternatively spliced soluble isoforms that lack the transmembrane domain and terminate in a QDEL ER-retention signal are expressed selectively in maturing T lymphocytes and reside in the late endoplasmic reticulum [PMID:12621022, PMID:17606388]. In motor neurons, correct CHODL dosage is required for growth cone interactions with intermediate targets: zebrafish chodl knockdown stalls motor axons at the horizontal myoseptum and reduces muscle innervation, a defect rescued by re-expression, and Chodl is aberrantly spliced in SMA spinal motor neurons where restoring its expression rescues outgrowth in Smn-depleted zebrafish [PMID:22457492, PMID:24067532]. In skeletal muscle, CHODL is dispensable for development but essential for regeneration, maintaining satellite cell self-renewal, proliferation, sublaminar niche localization within the basal lamina, and Notch signaling [PMID:42088368, PMID:40964242]. CHODL also marks a population of long-range somatostatin GABAergic neurons (Sst-Chodl) whose activity drives cortical synchrony and sleep [PMID:bio_10.1101_2024.06.20.599756, PMID:40997796].","teleology":[{"year":2002,"claim":"Established the basic identity of CHODL as a type I transmembrane C-type lectin, defining its domain architecture and subcellular distribution and excluding hyaluronan as a ligand.","evidence":"PCR cloning, Western blot, immunohistochemistry, and transfection/localization imaging in COS1 cells","pmids":["12079284"],"confidence":"Medium","gaps":["No physiological glycan ligand identified for the CRD","Functional consequence of perinuclear localization unresolved"]},{"year":2003,"claim":"Defined the ER-Golgi localization of the transmembrane isoform and discovered a soluble, transmembrane-lacking splice variant expressed selectively in T lymphocytes, indicating isoform-specific deployment.","evidence":"RT-PCR splicing analysis and double-label immunofluorescence with the ER-Golgi marker rBet1; in situ hybridization and immunostaining of mouse muscle","pmids":["12621022","12711387"],"confidence":"Medium","gaps":["Function of the soluble T-cell isoform not determined","Why a secretory-pathway lectin localizes to ER-Golgi rather than the surface is unexplained"]},{"year":2007,"claim":"Refined the soluble isoform's localization to the late ER via a QDEL retention signal and mapped its expression to discrete lymphocyte subpopulations.","evidence":"Immunofluorescence and immunohistochemistry on spleen, tonsil, and thymocyte tissue","pmids":["17606388"],"confidence":"Low","gaps":["Single primary method without functional readout","No link between ER retention and any lymphocyte function"]},{"year":2008,"claim":"Identified the first physical partner of CHODL, showing its cytoplasmic tail binds the beta-subunit of Rab geranylgeranyl transferase, hinting at a link to Rab-dependent membrane trafficking.","evidence":"SOS recruitment yeast screen with in vitro pulldown and co-immunoprecipitation confirmation","pmids":["18161010"],"confidence":"Medium","gaps":["Functional consequence of the Rabggtb interaction not tested","Single lab; reciprocal in vivo validation absent"]},{"year":2012,"claim":"Demonstrated a dosage-sensitive requirement for CHODL in motor axon pathfinding, establishing its role in growth cone interactions with intermediate targets.","evidence":"Morpholino knockdown, overexpression, and rescue with live imaging of motor axons in zebrafish","pmids":["22457492"],"confidence":"High","gaps":["Molecular ligand at the horizontal myoseptum not identified","Whether the CRD mediates the guidance interaction is untested"]},{"year":2013,"claim":"Connected CHODL dysregulation to disease by showing its aberrant splicing in SMA motor neurons and that restoring its expression rescues outgrowth defects in an Smn-deficient model.","evidence":"Exon-level splicing analysis in SMA mice, in vitro neurite/survival assays, and overexpression rescue in smn-knockdown zebrafish","pmids":["24067532"],"confidence":"High","gaps":["Mechanism by which SMN controls Chodl splicing not defined","Whether Chodl correction is therapeutic in mammalian SMA untested"]},{"year":2011,"claim":"Implicated CHODL in cell growth and invasion, suggesting its morphogenetic activity can be co-opted in cancer.","evidence":"siRNA knockdown viability assays, overexpression, and Matrigel invasion assay in lung cancer cells","pmids":["22016508"],"confidence":"Medium","gaps":["Signaling pathway driving invasion not defined","No in vivo tumor model"]},{"year":2019,"claim":"Flagged CHODL as a candidate S-palmitoylation substrate at a juxtamembrane cysteine, a potential layer of post-translational regulation.","evidence":"Machine-learning topology prediction (TopoPalmTree) with brief experimental assessment in the mouse transmembrane proteome","pmids":["39909380"],"confidence":"Low","gaps":["Primarily computational; experimental confirmation reported without full detail","Functional role of palmitoylation unknown"]},{"year":2025,"claim":"Established CHODL as a marker of a functionally distinct cortical neuron class, with Sst-Chodl GABAergic cells driving cortical synchrony and sleep through long-range projections.","evidence":"In vivo electrophysiology/calcium imaging and optogenetic activation with behavioral sleep assays in mice (preprint)","pmids":["bio_10.1101_2024.06.20.599756"],"confidence":"Medium","gaps":["Whether CHODL protein itself contributes to the neuron's function vs. being a marker is untested","Preprint, single lab"]},{"year":2025,"claim":"Linked the Sst_Chodl neuron subtype to sleep disturbance in a 15q13.3 microdeletion disease model, where its hyperactivity is causally responsible and chemogenetic silencing is rescuing.","evidence":"snRNA-seq, patch-clamp, calcium imaging, and chemogenetic inhibition with behavioral rescue in mutant mice","pmids":["40997796"],"confidence":"Medium","gaps":["Role of CHODL gene product in the phenotype not dissected","Mechanism of subtype-selective vulnerability unknown"]},{"year":2025,"claim":"Defined a non-redundant requirement for CHODL in adult muscle regeneration, controlling satellite cell self-renewal, niche localization, and Notch signaling without affecting development.","evidence":"Conditional Cre-lox knockout in embryonic myoblasts and adult satellite cells, scRNA-seq, regeneration assays, and localization immunofluorescence","pmids":["42088368","40964242"],"confidence":"High","gaps":["Direct ECM ligand engaged by the CRD in the niche not identified","How CHODL mechanistically links to Notch signaling unresolved"]},{"year":null,"claim":"The biochemical activity of the CHODL lectin domain remains undefined: no physiological carbohydrate ligand is known, and it is unclear whether its varied tissue roles share a common molecular mechanism.","evidence":"No direct ligand-binding or structure-function study in the available corpus","pmids":[],"confidence":"Low","gaps":["No identified glycan/protein ligand for the CRD","No unifying biochemical mechanism across neurons, muscle, and cancer","Role of the Rabggtb interaction in any tissue phenotype untested"]}],"mechanism_profile":{"molecular_activity":[],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[1,3]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[0,1]}],"pathway":[],"complexes":[],"partners":["RABGGTB","BET1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H9P2","full_name":"Chondrolectin","aliases":["Transmembrane protein MT75"],"length_aa":273,"mass_kda":30.4,"function":"May play a role in the development of the nervous system such as in neurite outgrowth and elongation. May be involved in motor axon growth and guidance","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9H9P2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CHODL","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CHODL","total_profiled":1310},"omim":[{"mim_id":"607247","title":"CHONDROLECTIN; CHODL","url":"https://www.omim.org/entry/607247"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Centrosome","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"lymphoid tissue","ntpm":13.3},{"tissue":"testis","ntpm":29.0}],"url":"https://www.proteinatlas.org/search/CHODL"},"hgnc":{"alias_symbol":["FLJ12627","PRED12","MT75"],"prev_symbol":["C21orf68"]},"alphafold":{"accession":"Q9H9P2","domains":[{"cath_id":"3.10.100.10","chopping":"41-87_95-106_117-179","consensus_level":"high","plddt":95.2978,"start":41,"end":179}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H9P2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H9P2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H9P2-F1-predicted_aligned_error_v6.png","plddt_mean":75.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CHODL","jax_strain_url":"https://www.jax.org/strain/search?query=CHODL"},"sequence":{"accession":"Q9H9P2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H9P2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H9P2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H9P2"}},"corpus_meta":[{"pmid":"26977395","id":"PMC_26977395","title":"Integration 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\"method\": \"PCR cloning, Northern blot, RT-PCR, immunohistochemistry, Western blot, transient transfection with subcellular localization imaging, cetylpyridinium chloride precipitation (negative for hyaluronan binding)\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Western blot, IHC, transfection/localization) in a single characterization study establishing protein structure and localization\",\n      \"pmids\": [\"12079284\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"An alternatively spliced CHODL isoform lacking the transmembrane domain (CHODLfΔE/CHODLΔe) is expressed exclusively in T lymphocytes and is regulated during T lymphopoiesis; the transmembrane-containing isoform CHODLf colocalizes with rBet1 to the endoplasmic reticulum–Golgi apparatus.\",\n      \"method\": \"RT-PCR, database analysis, double-label immunofluorescence\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by immunofluorescence co-localization with ER/Golgi marker, alternative splicing confirmed by RT-PCR, single lab with two orthogonal methods\",\n      \"pmids\": [\"12621022\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Mouse Chodl (orthologue of human CHODL) is a type I transmembrane C-type lectin expressed in skeletal muscle cells during both proliferation and differentiation phases, as shown by in situ hybridization on E15 embryos and fluorescent immunostaining localizing the protein to striated muscle cells.\",\n      \"method\": \"RT-PCR/Southern blotting, in situ hybridization, fluorescent immunostaining, Western blot on C2C12 myoblasts\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (ISH, immunostaining, Western blot) in a single characterization study; mouse orthologue\",\n      \"pmids\": [\"12711387\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"The soluble CHODL isoforms (CHODLΔe/CHODLfΔe), which lack the transmembrane domain and terminate in a QDEL ER-retention signal, localize to the late endoplasmic reticulum and are expressed in a small lymphocyte population in spleen and tonsils, with differential expression in thymocytes versus peripheral lymphocytes.\",\n      \"method\": \"Immunofluorescence localization, immunohistochemistry on tissue sections\",\n      \"journal\": \"Cell biology international\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single primary method (immunofluorescence/IHC), no functional consequence linked to localization\",\n      \"pmids\": [\"17606388\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The cytoplasmic domain of mouse chondrolectin (chodl) directly interacts with the beta-subunit of Rab geranylgeranyl transferase (Rabggtb), identified by SOS recruitment system (SRS) yeast screen and confirmed by in vitro transcription/translation and co-immunoprecipitation.\",\n      \"method\": \"SOS recruitment system (SRS) yeast two-hybrid screen, in vitro transcription/translation pulldown, co-immunoprecipitation\",\n      \"journal\": \"Cellular & molecular biology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — interaction confirmed by two orthogonal methods (in vitro binding + co-IP), single lab\",\n      \"pmids\": [\"18161010\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"In zebrafish, knockdown of chodl causes arrest/stalling of motor axon growth at the horizontal myoseptum (an intermediate target), resulting in reduced muscle innervation; this phenotype is rescued by chodl overexpression, demonstrating that correct chodl expression levels are required for growth cone interactions with the horizontal myoseptum.\",\n      \"method\": \"In vivo morpholino knockdown, transgenic overexpression, rescue experiment, in vivo live imaging of labeled motor axons in zebrafish\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with specific phenotypic readout, gain-of-function, and rescue experiment in vivo; replicated mechanistic conclusion across multiple experiments in one study\",\n      \"pmids\": [\"22457492\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Chodl expression is altered (alternatively spliced) in SMA mouse spinal motor neurons before symptom onset; in vitro studies show Chodl affects cell survival and neurite outgrowth; increasing chodl expression in Smn-depleted zebrafish rescues motor neuron outgrowth defects, linking Chodl dysregulation to SMA motor neuron pathophysiology.\",\n      \"method\": \"Exon-level splicing analysis in SMA mouse model, in vitro cell survival and neurite outgrowth assays, in vivo chodl overexpression rescue in smn-knockdown zebrafish\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (in vitro assays + in vivo rescue), direct functional readouts for cell survival, neurite outgrowth, and motor axon defects in two model systems\",\n      \"pmids\": [\"24067532\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"siRNA-mediated knockdown of CHODL suppresses lung cancer cell growth, and exogenous overexpression of CHODL confers growth and invasive activity in mammalian cells, as measured by Matrigel invasion assays.\",\n      \"method\": \"siRNA knockdown (cell viability assay), exogenous CHODL overexpression, Matrigel invasion assay\",\n      \"journal\": \"Clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function and gain-of-function with defined cellular phenotypes (growth, invasion), two complementary approaches in single lab\",\n      \"pmids\": [\"22016508\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CHODL is predicted to undergo S-palmitoylation at a juxtamembrane cysteine residue, identified by a machine-learning topology-driven approach (TopoPalmTree) applied to the mouse transmembrane proteome; experimental assessment of Chodl as a candidate S-palmitoyl substrate was performed (results reported among confirmed candidates).\",\n      \"method\": \"Machine-learning prediction (TopoPalmTree), experimental S-palmitoylation assessment (method not fully detailed in abstract)\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — primarily computational prediction; experimental validation described briefly in abstract without full methodological detail, single study\",\n      \"pmids\": [\"39909380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Sst-Chodl neurons (somatostatin and chondrolectin co-expressing GABAergic cells) are selectively active during low-arousal states; selective activation of Sst-Chodl cells is sufficient to promote multi-region cortical synchronization and induce sleep via long-range axons targeting multiple neocortical regions simultaneously.\",\n      \"method\": \"In vivo electrophysiology/calcium imaging, optogenetic selective activation of Sst-Chodl cells, behavioral sleep assays in mice\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — optogenetic gain-of-function with specific behavioral and electrophysiological readouts; preprint, single lab, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2024.06.20.599756\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In a 15q13.3 microdeletion mouse model, single-nucleus transcriptomics showed the largest gene expression alterations in Sst_Chodl neurons; patch-clamp and calcium imaging revealed increased activity specifically in the Sst_Chodl subtype; chemogenetic inhibition of Sst_Chodl neurons rescued sleep disturbances in mutant mice.\",\n      \"method\": \"Single-nucleus RNA-seq (snRNA-seq), calcium imaging, patch-clamp electrophysiology, Patch-seq, chemogenetic inhibition (DREADD) with behavioral rescue\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (snRNA-seq, patch-clamp, calcium imaging, chemogenetics with rescue) in single lab; establishes functional role of Sst_Chodl neuron subtype\",\n      \"pmids\": [\"40997796\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Conditional knockout of Chodl in embryonic myoblasts or adult satellite cells (SCs) does not affect muscle development but markedly impairs regeneration; Chodl-deficient SCs show reduced self-renewal, diminished proliferation, and impaired differentiation; a significant fraction of Chodl-null SCs mislocalize outside the basal lamina and undergo precocious activation, consistent with disrupted ECM and Notch signaling interactions.\",\n      \"method\": \"Conditional knockout mouse models (Cre-lox), single-cell RNA-seq, muscle injury regeneration assays, immunofluorescence for SC localization, in silico network perturbation analysis\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean conditional KO with specific cellular and regenerative phenotypes, multiple orthogonal methods (scRNA-seq, histology, functional regeneration), replicated across embryonic and adult SC-specific deletion models\",\n      \"pmids\": [\"42088368\", \"40964242\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CHODL encodes a type I transmembrane C-type lectin that localizes to the ER-Golgi compartment; its cytoplasmic domain interacts with Rabggtb (the beta-subunit of Rab geranylgeranyl transferase); in motor neurons, CHODL is required for motor axon growth cone interactions with intermediate targets (horizontal myoseptum in zebrafish), and its dysregulation contributes to SMA motor neuron pathology; in skeletal muscle satellite cells, CHODL is essential for sublaminar niche localization, ECM interactions, and regenerative capacity via effects on self-renewal, proliferation, and Notch signaling; in the neocortex, Sst-Chodl GABAergic neurons with long-range projections promote cortical synchrony and sleep; alternatively spliced soluble isoforms lacking the transmembrane domain are expressed in T lymphocytes during maturation; CHODL is also a candidate substrate for S-palmitoylation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CHODL (chondrolectin) is a type I transmembrane C-type lectin that operates at the interface of cell-surface glycan recognition and tissue morphogenesis, with established roles in motor neuron axon guidance, skeletal muscle satellite cell maintenance, and a distinct cortical GABAergic neuron identity [#0, #5, #11]. The protein carries a single extracellular C-type lectin carbohydrate recognition domain, is N-glycosylated, and localizes to the ER-Golgi compartment, where it colocalizes with the ER-Golgi marker rBet1; its short cytoplasmic domain directly binds Rabggtb, the beta-subunit of Rab geranylgeranyl transferase [#0, #1, #4]. Alternatively spliced soluble isoforms that lack the transmembrane domain and terminate in a QDEL ER-retention signal are expressed selectively in maturing T lymphocytes and reside in the late endoplasmic reticulum [#1, #3]. In motor neurons, correct CHODL dosage is required for growth cone interactions with intermediate targets: zebrafish chodl knockdown stalls motor axons at the horizontal myoseptum and reduces muscle innervation, a defect rescued by re-expression, and Chodl is aberrantly spliced in SMA spinal motor neurons where restoring its expression rescues outgrowth in Smn-depleted zebrafish [#5, #6]. In skeletal muscle, CHODL is dispensable for development but essential for regeneration, maintaining satellite cell self-renewal, proliferation, sublaminar niche localization within the basal lamina, and Notch signaling [#11]. CHODL also marks a population of long-range somatostatin GABAergic neurons (Sst-Chodl) whose activity drives cortical synchrony and sleep [#9, #10].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Established the basic identity of CHODL as a type I transmembrane C-type lectin, defining its domain architecture and subcellular distribution and excluding hyaluronan as a ligand.\",\n      \"evidence\": \"PCR cloning, Western blot, immunohistochemistry, and transfection/localization imaging in COS1 cells\",\n      \"pmids\": [\"12079284\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No physiological glycan ligand identified for the CRD\", \"Functional consequence of perinuclear localization unresolved\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Defined the ER-Golgi localization of the transmembrane isoform and discovered a soluble, transmembrane-lacking splice variant expressed selectively in T lymphocytes, indicating isoform-specific deployment.\",\n      \"evidence\": \"RT-PCR splicing analysis and double-label immunofluorescence with the ER-Golgi marker rBet1; in situ hybridization and immunostaining of mouse muscle\",\n      \"pmids\": [\"12621022\", \"12711387\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Function of the soluble T-cell isoform not determined\", \"Why a secretory-pathway lectin localizes to ER-Golgi rather than the surface is unexplained\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Refined the soluble isoform's localization to the late ER via a QDEL retention signal and mapped its expression to discrete lymphocyte subpopulations.\",\n      \"evidence\": \"Immunofluorescence and immunohistochemistry on spleen, tonsil, and thymocyte tissue\",\n      \"pmids\": [\"17606388\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single primary method without functional readout\", \"No link between ER retention and any lymphocyte function\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Identified the first physical partner of CHODL, showing its cytoplasmic tail binds the beta-subunit of Rab geranylgeranyl transferase, hinting at a link to Rab-dependent membrane trafficking.\",\n      \"evidence\": \"SOS recruitment yeast screen with in vitro pulldown and co-immunoprecipitation confirmation\",\n      \"pmids\": [\"18161010\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the Rabggtb interaction not tested\", \"Single lab; reciprocal in vivo validation absent\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrated a dosage-sensitive requirement for CHODL in motor axon pathfinding, establishing its role in growth cone interactions with intermediate targets.\",\n      \"evidence\": \"Morpholino knockdown, overexpression, and rescue with live imaging of motor axons in zebrafish\",\n      \"pmids\": [\"22457492\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular ligand at the horizontal myoseptum not identified\", \"Whether the CRD mediates the guidance interaction is untested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Connected CHODL dysregulation to disease by showing its aberrant splicing in SMA motor neurons and that restoring its expression rescues outgrowth defects in an Smn-deficient model.\",\n      \"evidence\": \"Exon-level splicing analysis in SMA mice, in vitro neurite/survival assays, and overexpression rescue in smn-knockdown zebrafish\",\n      \"pmids\": [\"24067532\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which SMN controls Chodl splicing not defined\", \"Whether Chodl correction is therapeutic in mammalian SMA untested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Implicated CHODL in cell growth and invasion, suggesting its morphogenetic activity can be co-opted in cancer.\",\n      \"evidence\": \"siRNA knockdown viability assays, overexpression, and Matrigel invasion assay in lung cancer cells\",\n      \"pmids\": [\"22016508\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signaling pathway driving invasion not defined\", \"No in vivo tumor model\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Flagged CHODL as a candidate S-palmitoylation substrate at a juxtamembrane cysteine, a potential layer of post-translational regulation.\",\n      \"evidence\": \"Machine-learning topology prediction (TopoPalmTree) with brief experimental assessment in the mouse transmembrane proteome\",\n      \"pmids\": [\"39909380\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Primarily computational; experimental confirmation reported without full detail\", \"Functional role of palmitoylation unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established CHODL as a marker of a functionally distinct cortical neuron class, with Sst-Chodl GABAergic cells driving cortical synchrony and sleep through long-range projections.\",\n      \"evidence\": \"In vivo electrophysiology/calcium imaging and optogenetic activation with behavioral sleep assays in mice (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.06.20.599756\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether CHODL protein itself contributes to the neuron's function vs. being a marker is untested\", \"Preprint, single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Linked the Sst_Chodl neuron subtype to sleep disturbance in a 15q13.3 microdeletion disease model, where its hyperactivity is causally responsible and chemogenetic silencing is rescuing.\",\n      \"evidence\": \"snRNA-seq, patch-clamp, calcium imaging, and chemogenetic inhibition with behavioral rescue in mutant mice\",\n      \"pmids\": [\"40997796\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Role of CHODL gene product in the phenotype not dissected\", \"Mechanism of subtype-selective vulnerability unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined a non-redundant requirement for CHODL in adult muscle regeneration, controlling satellite cell self-renewal, niche localization, and Notch signaling without affecting development.\",\n      \"evidence\": \"Conditional Cre-lox knockout in embryonic myoblasts and adult satellite cells, scRNA-seq, regeneration assays, and localization immunofluorescence\",\n      \"pmids\": [\"42088368\", \"40964242\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct ECM ligand engaged by the CRD in the niche not identified\", \"How CHODL mechanistically links to Notch signaling unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical activity of the CHODL lectin domain remains undefined: no physiological carbohydrate ligand is known, and it is unclear whether its varied tissue roles share a common molecular mechanism.\",\n      \"evidence\": \"No direct ligand-binding or structure-function study in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No identified glycan/protein ligand for the CRD\", \"No unifying biochemical mechanism across neurons, muscle, and cancer\", \"Role of the Rabggtb interaction in any tissue phenotype untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [\"RABGGTB\", \"BET1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}