{"gene":"KCND1","run_date":"2026-04-28T18:06:54","timeline":{"discoveries":[{"year":2001,"finding":"KChIP1 (K+ channel-interacting protein 1) directly modulates Kv4.1 channel properties: it accelerates Kv4.1 inactivation kinetics, shifts activation in a depolarizing direction, increases current amplitude, and accelerates recovery from inactivation. The Kv4.1 N-terminus is involved in mediating the differential effects of KChIP1 on Kv4.1 versus Kv4.2, as demonstrated using chimeric constructs.","method":"Heterologous expression with whole-cell electrophysiology; chimeric Kv4.1/Kv4.2 constructs to map N-terminus involvement","journal":"FEBS letters","confidence":"High","confidence_rationale":"Tier 1 — in vitro functional reconstitution with chimeric mutagenesis across two channel members","pmids":["11423117"],"is_preprint":false},{"year":1998,"finding":"Kv4.1 (together with Kv4.2) is a major subunit of the somatodendritic A-type potassium current in neostriatal cholinergic interneurons. The A-current governs slow, repetitive firing of these interneurons. Coexpression of Kv4.1 and Kv4.2 was established by single-cell RT-PCR, and the biophysical properties (inactivation recovery kinetics) matched those of Kv4.1/Kv4.2 but not Kv1.4.","method":"Whole-cell voltage-clamp, single-cell RT-PCR, immunocytochemistry, pharmacological dissection (4-AP, TEA, Cd2+)","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (electrophysiology, molecular profiling, immunocytochemistry) in a single study with >100 citations","pmids":["9547221"],"is_preprint":false},{"year":2020,"finding":"Kv4.1 is preferentially expressed in mature dentate granule cells (DGCs) and is the key ion channel regulating low-frequency firing. Intracellular perfusion of Kv4.1 antibody increased firing rates selectively in low-frequency GCs. Kv4.1 knockdown in the dentate gyrus increased firing frequency and impaired contextual pattern separation, placing Kv4.1 as a critical determinant of sparse coding.","method":"Immunofluorescence, Western blot, intracellular antibody perfusion during patch clamp, in vivo viral knockdown of Kv4.1 in DG, behavioral testing (contextual discrimination)","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods including loss-of-function with defined cellular and behavioral phenotypes","pmids":["32047055"],"is_preprint":false},{"year":2021,"finding":"Calbindin regulates Kv4.1 surface trafficking and neuronal excitability via CaMKII-dependent phosphorylation at serine 555. In calbindin knockout (CBKO) mice, reduced Ca2+ buffering leads to increased CaMKII activation, decreased surface expression of Kv4.1, reduced K+ current, and hyperexcitability of dentate GCs. This mechanism was confirmed by manipulating calbindin expression in HT22 cells.","method":"Calbindin KO mouse model, patch clamp electrophysiology, surface biotinylation, CaMKII phosphorylation assay at S555, cell-line overexpression/knockdown, behavioral testing","journal":"Experimental & molecular medicine","confidence":"High","confidence_rationale":"Tier 2 — identified specific phosphorylation site with multiple orthogonal methods and in vivo/in vitro concordance","pmids":["34234278"],"is_preprint":false},{"year":2021,"finding":"Kv4.1 downregulation in dentate granule cells (DGCs) of Tg2576 Alzheimer's model mice reduces 4-AP-sensitive K+ currents, causing hyperexcitability and impaired pattern separation. Antioxidant treatment restores Kv4.1 protein expression and normalizes hyperexcitability and pattern separation, linking oxidative stress to Kv4.1 downregulation.","method":"Whole-cell patch clamp, RT-PCR, Western blot, antioxidant treatment rescue, behavioral pattern separation task in Tg2576 mice","journal":"Molecular brain","confidence":"High","confidence_rationale":"Tier 2 — loss-of-function phenotype with rescue by antioxidant; multiple methods in vivo and ex vivo","pmids":["33785038"],"is_preprint":false},{"year":2019,"finding":"Kv4.1 underlies the A-type potassium current (IA) in myelinated primary afferent neurons. Spinal nerve ligation reduces Kv4.1 mRNA and IA current density in injured A-fiber neurons, and spinal GDNF infusion reverses both the reduction in Kv4.1 expression and IA, thereby reducing neuronal hyperexcitability. Among five IA-related Kv subunits examined, only Kv4.1 expression changes paralleled IA changes.","method":"In vitro patch clamp, in situ hybridization histochemistry, spinal GDNF infusion, L5 spinal nerve ligation model in rats","journal":"Molecular pain","confidence":"Medium","confidence_rationale":"Tier 2 — parallel expression and functional changes across treatment conditions; single lab, correlative mechanistic inference","pmids":["30868936"],"is_preprint":false},{"year":2009,"finding":"Kv4.1 channel activity is required for cell proliferation in tumorigenic human mammary epithelial cells. siRNA-mediated knockdown of Kv4.1 suppresses proliferation, establishing a functional role for this channel in tumor cell growth.","method":"siRNA knockdown, cell proliferation assay, Western blot, mRNA analysis in cancer cell lines and human breast cancer tissues","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 — siRNA knockdown with proliferation phenotype; single lab, single method for mechanism","pmids":["19401188"],"is_preprint":false},{"year":2010,"finding":"Kv4.1 is required for G1-S cell cycle progression in human gastric cancer cells. siRNA-mediated knockdown of Kv4.1 inhibits proliferation and induces a G1-S transition block, as shown by flow cytometry.","method":"siRNA knockdown, flow cytometric cell cycle analysis, Western blot, cell proliferation assay","journal":"Biological & pharmaceutical bulletin","confidence":"Medium","confidence_rationale":"Tier 3 — siRNA knockdown with specific cell cycle phenotype; single lab, two methods","pmids":["20930388"],"is_preprint":false},{"year":2022,"finding":"Kv4.1 is co-expressed with auxiliary subunits KChIP2 and DPP10 in NK1R+ secondary nociceptive neurons and excitatory interneurons of spinal lamina I. Intrathecal knockdown of Kv4.1 via antisense oligodeoxynucleotide induces mechanical hypersensitivity in naive rats, demonstrating a direct role for Kv4.1 in pain regulation.","method":"Immunohistochemistry (antibody localization), antisense oligodeoxynucleotide knockdown, behavioral testing (mechanical/thermal hypersensitivity)","journal":"European journal of pain","confidence":"Medium","confidence_rationale":"Tier 2–3 — in vivo knockdown with behavioral phenotype; single lab, defines Kv4.1/KChIP2/DPP10 complex in pain neurons","pmids":["36097791"],"is_preprint":false},{"year":2024,"finding":"Hemizygous KCND1 variants (missense and protein-truncating) in the cytoplasmic N- or C-terminus or transmembrane segments S1/S4 of Kv4.1 cause variant-specific alterations in biophysical channel properties. Functional characterization in heterologous expression systems with and without auxiliary β-subunits showed diverse changes in channel function, establishing that Kv4.1 dysfunction underlies an X-linked neurodevelopmental disorder.","method":"Trio whole-exome sequencing, heterologous expression, whole-cell electrophysiology with and without auxiliary subunits, gene matching cohort","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 1–2 — functional variant characterization in heterologous system with multiple variants; domain-specific mutagenesis context","pmids":["38772379"],"is_preprint":false},{"year":2024,"finding":"SsTx-P2, a 53-amino acid peptide from centipede venom, potently inhibits Kv4.1 channel current with 95% inhibition at 1.0 μmol/L. The peptide shares a conserved helical structure identified by structure prediction.","method":"Ion-exchange and HPLC purification, whole-cell patch clamp in HEK293 cells transfected with Kv4.1, MALDI-TOF mass spectrometry, Edman sequencing, structural modeling","journal":"Journal of Zhejiang University Medical Sciences","confidence":"Medium","confidence_rationale":"Tier 1 — direct pharmacological inhibition assay in heterologous system; single study, no mutagenesis of binding site","pmids":["38268403"],"is_preprint":false}],"current_model":"KCND1/Kv4.1 encodes a voltage-gated A-type potassium channel α-subunit that is modulated by auxiliary subunits (KChIP1, KChIP2, DPP10) and by CaMKII-dependent phosphorylation at serine 555 downstream of calbindin-mediated Ca2+ buffering; it controls neuronal excitability in dentate granule cells, nociceptors, and cholinergic interneurons, and loss-of-function variants in its cytoplasmic and transmembrane domains cause an X-linked neurodevelopmental disorder."},"narrative":{"teleology":[{"year":1998,"claim":"Establishing that Kv4.1 (with Kv4.2) forms the molecular basis of the somatodendritic A-type K+ current in neostriatal cholinergic interneurons resolved the identity of the channel subunits governing slow repetitive firing in these neurons.","evidence":"Whole-cell voltage-clamp, single-cell RT-PCR, immunocytochemistry, and pharmacological dissection in neostriatal cholinergic interneurons","pmids":["9547221"],"confidence":"High","gaps":["Relative contribution of Kv4.1 versus Kv4.2 to the native current was not resolved","No knockout or knockdown confirmation","Mechanism of subunit heteromerization not addressed"]},{"year":2001,"claim":"Demonstrating that KChIP1 directly modulates Kv4.1 gating — accelerating inactivation, shifting activation, increasing amplitude, and speeding recovery — established the principle that auxiliary subunits tune Kv4.1 channel properties, with the N-terminus mediating subunit-specific effects.","evidence":"Heterologous coexpression of KChIP1 with Kv4.1 and Kv4.1/Kv4.2 chimeras, whole-cell electrophysiology","pmids":["11423117"],"confidence":"High","gaps":["Only KChIP1 tested; modulation by other KChIPs or DPPs not examined","Structural basis of N-terminus interaction not determined","Native neuronal reconstitution not performed"]},{"year":2009,"claim":"Discovery that Kv4.1 knockdown suppresses proliferation in mammary and gastric cancer cells revealed a non-neuronal role for the channel in cell cycle progression at the G1-S boundary.","evidence":"siRNA knockdown with proliferation assays and flow cytometry in human cancer cell lines","pmids":["19401188","20930388"],"confidence":"Medium","gaps":["Mechanism linking K+ conductance to cell cycle not identified","No rescue experiment with channel re-expression","Single-lab findings for each cancer type"]},{"year":2019,"claim":"Showing that Kv4.1 uniquely underlies IA in myelinated primary afferent neurons and that its expression is reduced by nerve injury (restored by GDNF) connected Kv4.1 to neuropathic pain mechanisms.","evidence":"Patch clamp, in situ hybridization, L5 spinal nerve ligation and GDNF infusion in rats","pmids":["30868936"],"confidence":"Medium","gaps":["Correlative — no selective Kv4.1 knockdown in afferents","Molecular pathway from GDNF signaling to Kv4.1 transcription not mapped","Single lab"]},{"year":2020,"claim":"Demonstrating that Kv4.1 determines the low-frequency firing mode of mature dentate granule cells and is required for contextual pattern separation established a causal link between this channel and hippocampal sparse coding.","evidence":"Intracellular antibody block, viral knockdown of Kv4.1 in mouse dentate gyrus, behavioral pattern separation task","pmids":["32047055"],"confidence":"High","gaps":["How Kv4.1 is preferentially enriched in mature versus immature GCs is unknown","Contribution of auxiliary subunits in DGCs not addressed","Circuit-level mechanism of pattern separation impairment not resolved"]},{"year":2021,"claim":"Identification of CaMKII phosphorylation at serine 555 as the mechanism by which calbindin loss reduces Kv4.1 surface expression, causing GC hyperexcitability, provided the first post-translational regulatory mechanism for Kv4.1 trafficking.","evidence":"Calbindin KO mice, surface biotinylation, phospho-specific assays at S555, HT22 cell manipulation, patch clamp","pmids":["34234278"],"confidence":"High","gaps":["Whether other kinases also phosphorylate S555 is unknown","Structural consequence of S555 phosphorylation on channel trafficking not determined","Phosphatase counter-regulation not identified"]},{"year":2021,"claim":"Linking Kv4.1 downregulation to oxidative stress in Tg2576 Alzheimer's mice, with antioxidant rescue of both channel expression and pattern separation, positioned Kv4.1 as a convergence point for Alzheimer's-associated hippocampal dysfunction.","evidence":"Patch clamp, Western blot, RT-PCR, antioxidant rescue, behavioral testing in Tg2576 mice","pmids":["33785038"],"confidence":"High","gaps":["Direct transcriptional or post-transcriptional mechanism of oxidative-stress-mediated Kv4.1 reduction not identified","Applicability to human AD not tested","Specificity of antioxidant rescue for Kv4.1 versus other channels unclear"]},{"year":2022,"claim":"Defining the Kv4.1/KChIP2/DPP10 complex in spinal lamina I nociceptive neurons and showing that intrathecal Kv4.1 knockdown causes mechanical hypersensitivity extended the pain role of Kv4.1 from primary afferents to the spinal cord.","evidence":"Immunohistochemistry, antisense oligodeoxynucleotide knockdown, behavioral testing in rats","pmids":["36097791"],"confidence":"Medium","gaps":["Antisense knockdown lacks subunit selectivity confirmation","Electrophysiological characterization in spinal neurons not performed","Role of KChIP2/DPP10 in pain modulation via Kv4.1 not functionally tested"]},{"year":2024,"claim":"Functional characterization of hemizygous KCND1 variants from patients with X-linked neurodevelopmental disorder established causative genotype–phenotype relationships, showing domain-specific biophysical alterations with and without auxiliary subunits.","evidence":"Trio whole-exome sequencing, heterologous expression with whole-cell electrophysiology ± auxiliary subunits, multi-family cohort","pmids":["38772379"],"confidence":"High","gaps":["No patient-derived neuronal models tested","In vivo validation with knock-in animal models absent","Therapeutic rescue strategies not explored"]},{"year":null,"claim":"Key unresolved questions include the structural basis of auxiliary subunit modulation specific to Kv4.1, the transcriptional regulation underlying neuron-type-specific Kv4.1 expression, and whether Kv4.1-targeted interventions can rescue neurodevelopmental or neurodegenerative phenotypes in vivo.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of Kv4.1 alone or with auxiliary subunits","Transcriptional and epigenetic regulation of KCND1 expression uncharacterized","No therapeutic or gene-replacement rescue in animal models of KCND1 disease"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[0,1,2,9]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[3,9]}],"pathway":[{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[1,2,5]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3]}],"complexes":["Kv4.1/KChIP1 complex","Kv4.1/KChIP2/DPP10 complex"],"partners":["KCNIP1","KCNIP2","DPP10","KCND2","CAMK2A","CALB1"],"other_free_text":[]},"mechanistic_narrative":"KCND1 encodes the Kv4.1 voltage-gated potassium channel α-subunit, which conducts the somatodendritic A-type potassium current (IA) that controls neuronal excitability, firing frequency, and sparse coding across multiple neuron types including dentate granule cells, neostriatal cholinergic interneurons, and spinal nociceptive neurons. Kv4.1 channel properties are modulated by auxiliary subunits KChIP1, KChIP2, and DPP10, which alter inactivation kinetics, activation voltage, current amplitude, and recovery from inactivation [PMID:11423117, PMID:36097791]; surface trafficking of Kv4.1 is regulated by CaMKII-dependent phosphorylation at serine 555, a pathway controlled by calbindin-mediated calcium buffering [PMID:34234278]. In dentate granule cells, Kv4.1 is essential for low-frequency firing and contextual pattern separation, and its downregulation by oxidative stress contributes to hippocampal hyperexcitability in Alzheimer's disease models [PMID:32047055, PMID:33785038]. Hemizygous loss-of-function and missense variants in KCND1 cause an X-linked neurodevelopmental disorder with variant-specific biophysical defects across the channel's cytoplasmic and transmembrane domains [PMID:38772379]."},"prefetch_data":{"uniprot":{"accession":"Q9NSA2","full_name":"A-type voltage-gated potassium channel KCND1","aliases":["Potassium voltage-gated channel subfamily D member 1","Shal-type potassium channel KCND1","Voltage-gated potassium channel subunit Kv4.1"],"length_aa":647,"mass_kda":71.3,"function":"A-type voltage-gated potassium channel that mediates transmembrane potassium transport in excitable membranes in the brain (PubMed:15454437). Mediates A-type current I(SA) in suprachiasmatic nucleus (SCN) neurons. Exhibits a low-threshold A-type current with a hyperpolarized steady-state inactivation midpoint and the recovery process was steeply voltage-dependent, with recovery being markedly faster at more negative potentials. May regulates repetitive firing rates in the suprachiasmatic nucleus (SCN) neurons and circadian rhythms in neuronal excitability and behavior. Contributes to the regulation of the circadian rhythm of action potential firing in suprachiasmatic nucleus neurons, which regulates the circadian rhythm of locomotor activity. The regulatory subunit KCNIP1 modulates the kinetics of channel inactivation, increases the current amplitudes and accelerates recovery from inactivation, shifts activation in a depolarizing direction (By similarity). The regulatory subunit DPP10 decreases the voltage sensitivity of the inactivation channel gating (PubMed:15454437)","subcellular_location":"Cell membrane","url":"https://www.uniprot.org/uniprotkb/Q9NSA2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/KCND1","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/KCND1","total_profiled":1310},"omim":[{"mim_id":"608182","title":"POTASSIUM CHANNEL-INTERACTING PROTEIN 4","url":"https://www.omim.org/entry/608182"},{"mim_id":"605411","title":"POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 3; KCND3","url":"https://www.omim.org/entry/605411"},{"mim_id":"605410","title":"POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 2; KCND2","url":"https://www.omim.org/entry/605410"},{"mim_id":"604662","title":"POTASSIUM CHANNEL-INTERACTING PROTEIN 3; KCNIP3","url":"https://www.omim.org/entry/604662"},{"mim_id":"604660","title":"POTASSIUM CHANNEL-INTERACTING PROTEIN 1; KCNIP1","url":"https://www.omim.org/entry/604660"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Uncertain","locations":[{"location":"Nucleoplasm","reliability":"Uncertain"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":11.7}],"url":"https://www.proteinatlas.org/search/KCND1"},"hgnc":{"alias_symbol":["Kv4.1"],"prev_symbol":[]},"alphafold":{"accession":"Q9NSA2","domains":[{"cath_id":"3.30.710.10","chopping":"40-156","consensus_level":"high","plddt":88.6334,"start":40,"end":156},{"cath_id":"1.20.120.350","chopping":"179-212_219-308","consensus_level":"high","plddt":86.5149,"start":179,"end":308},{"cath_id":"1.10.287.70","chopping":"315-426","consensus_level":"high","plddt":91.0519,"start":315,"end":426}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NSA2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NSA2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NSA2-F1-predicted_aligned_error_v6.png","plddt_mean":69.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=KCND1","jax_strain_url":"https://www.jax.org/strain/search?query=KCND1"},"sequence":{"accession":"Q9NSA2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NSA2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NSA2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NSA2"}},"corpus_meta":[{"pmid":"9547221","id":"PMC_9547221","title":"Somatodendritic depolarization-activated potassium currents in rat neostriatal cholinergic interneurons are predominantly of the A type and attributable to coexpression of Kv4.2 and Kv4.1 subunits.","date":"1998","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/9547221","citation_count":187,"is_preprint":false},{"pmid":"11423117","id":"PMC_11423117","title":"Different effects of the Ca(2+)-binding protein, KChIP1, on two Kv4 subfamily members, Kv4.1 and Kv4.2.","date":"2001","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/11423117","citation_count":34,"is_preprint":false},{"pmid":"33785038","id":"PMC_33785038","title":"Impaired pattern separation in Tg2576 mice is associated with hyperexcitable dentate gyrus caused by Kv4.1 downregulation.","date":"2021","source":"Molecular brain","url":"https://pubmed.ncbi.nlm.nih.gov/33785038","citation_count":27,"is_preprint":false},{"pmid":"37253771","id":"PMC_37253771","title":"Long non-coding RNA KCND1 protects hearts from hypertrophy by targeting YBX1.","date":"2023","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/37253771","citation_count":20,"is_preprint":false},{"pmid":"19401188","id":"PMC_19401188","title":"Silencing of Kv4.1 potassium channels inhibits cell proliferation of tumorigenic human mammary epithelial cells.","date":"2009","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/19401188","citation_count":20,"is_preprint":false},{"pmid":"20930388","id":"PMC_20930388","title":"Involvement of Kv4.1 K(+) channels in gastric cancer cell proliferation.","date":"2010","source":"Biological & pharmaceutical bulletin","url":"https://pubmed.ncbi.nlm.nih.gov/20930388","citation_count":20,"is_preprint":false},{"pmid":"32047055","id":"PMC_32047055","title":"Kv4.1, a Key Ion Channel For Low Frequency Firing of Dentate Granule Cells, Is Crucial for Pattern Separation.","date":"2020","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/32047055","citation_count":20,"is_preprint":false},{"pmid":"30868936","id":"PMC_30868936","title":"Spinal glial cell line-derived neurotrophic factor infusion reverses reduction of Kv4.1-mediated A-type potassium currents of injured myelinated primary afferent neurons in a neuropathic pain model.","date":"2019","source":"Molecular pain","url":"https://pubmed.ncbi.nlm.nih.gov/30868936","citation_count":18,"is_preprint":false},{"pmid":"34234278","id":"PMC_34234278","title":"Calbindin regulates Kv4.1 trafficking and excitability in dentate granule cells via CaMKII-dependent phosphorylation.","date":"2021","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34234278","citation_count":10,"is_preprint":false},{"pmid":"36097791","id":"PMC_36097791","title":"K+ channel Kv4.1 is expressed in the nociceptors/secondary nociceptive neurons and participates in pain regulation.","date":"2022","source":"European journal of pain (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/36097791","citation_count":3,"is_preprint":false},{"pmid":"38772379","id":"PMC_38772379","title":"Etiological involvement of KCND1 variants in an X-linked neurodevelopmental disorder with variable expressivity.","date":"2024","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/38772379","citation_count":2,"is_preprint":false},{"pmid":"38268403","id":"PMC_38268403","title":"Isolation and structural identification of a potassium ion channel Kv4.1 inhibitor SsTx-P2 from centipede venom.","date":"2024","source":"Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38268403","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7770,"output_tokens":2881,"usd":0.033263},"stage2":{"model":"claude-opus-4-6","input_tokens":6222,"output_tokens":2595,"usd":0.143978},"total_usd":0.177241,"stage1_batch_id":"msgbatch_01DzrsgVgYngY1hvM3DU1yF2","stage2_batch_id":"msgbatch_01KA9b7iRzKFdhoBUT7vCvSe","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"KChIP1 (K+ channel-interacting protein 1) directly modulates Kv4.1 channel properties: it accelerates Kv4.1 inactivation kinetics, shifts activation in a depolarizing direction, increases current amplitude, and accelerates recovery from inactivation. The Kv4.1 N-terminus is involved in mediating the differential effects of KChIP1 on Kv4.1 versus Kv4.2, as demonstrated using chimeric constructs.\",\n      \"method\": \"Heterologous expression with whole-cell electrophysiology; chimeric Kv4.1/Kv4.2 constructs to map N-terminus involvement\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro functional reconstitution with chimeric mutagenesis across two channel members\",\n      \"pmids\": [\"11423117\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Kv4.1 (together with Kv4.2) is a major subunit of the somatodendritic A-type potassium current in neostriatal cholinergic interneurons. The A-current governs slow, repetitive firing of these interneurons. Coexpression of Kv4.1 and Kv4.2 was established by single-cell RT-PCR, and the biophysical properties (inactivation recovery kinetics) matched those of Kv4.1/Kv4.2 but not Kv1.4.\",\n      \"method\": \"Whole-cell voltage-clamp, single-cell RT-PCR, immunocytochemistry, pharmacological dissection (4-AP, TEA, Cd2+)\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (electrophysiology, molecular profiling, immunocytochemistry) in a single study with >100 citations\",\n      \"pmids\": [\"9547221\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Kv4.1 is preferentially expressed in mature dentate granule cells (DGCs) and is the key ion channel regulating low-frequency firing. Intracellular perfusion of Kv4.1 antibody increased firing rates selectively in low-frequency GCs. Kv4.1 knockdown in the dentate gyrus increased firing frequency and impaired contextual pattern separation, placing Kv4.1 as a critical determinant of sparse coding.\",\n      \"method\": \"Immunofluorescence, Western blot, intracellular antibody perfusion during patch clamp, in vivo viral knockdown of Kv4.1 in DG, behavioral testing (contextual discrimination)\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including loss-of-function with defined cellular and behavioral phenotypes\",\n      \"pmids\": [\"32047055\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Calbindin regulates Kv4.1 surface trafficking and neuronal excitability via CaMKII-dependent phosphorylation at serine 555. In calbindin knockout (CBKO) mice, reduced Ca2+ buffering leads to increased CaMKII activation, decreased surface expression of Kv4.1, reduced K+ current, and hyperexcitability of dentate GCs. This mechanism was confirmed by manipulating calbindin expression in HT22 cells.\",\n      \"method\": \"Calbindin KO mouse model, patch clamp electrophysiology, surface biotinylation, CaMKII phosphorylation assay at S555, cell-line overexpression/knockdown, behavioral testing\",\n      \"journal\": \"Experimental & molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — identified specific phosphorylation site with multiple orthogonal methods and in vivo/in vitro concordance\",\n      \"pmids\": [\"34234278\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Kv4.1 downregulation in dentate granule cells (DGCs) of Tg2576 Alzheimer's model mice reduces 4-AP-sensitive K+ currents, causing hyperexcitability and impaired pattern separation. Antioxidant treatment restores Kv4.1 protein expression and normalizes hyperexcitability and pattern separation, linking oxidative stress to Kv4.1 downregulation.\",\n      \"method\": \"Whole-cell patch clamp, RT-PCR, Western blot, antioxidant treatment rescue, behavioral pattern separation task in Tg2576 mice\",\n      \"journal\": \"Molecular brain\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function phenotype with rescue by antioxidant; multiple methods in vivo and ex vivo\",\n      \"pmids\": [\"33785038\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Kv4.1 underlies the A-type potassium current (IA) in myelinated primary afferent neurons. Spinal nerve ligation reduces Kv4.1 mRNA and IA current density in injured A-fiber neurons, and spinal GDNF infusion reverses both the reduction in Kv4.1 expression and IA, thereby reducing neuronal hyperexcitability. Among five IA-related Kv subunits examined, only Kv4.1 expression changes paralleled IA changes.\",\n      \"method\": \"In vitro patch clamp, in situ hybridization histochemistry, spinal GDNF infusion, L5 spinal nerve ligation model in rats\",\n      \"journal\": \"Molecular pain\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — parallel expression and functional changes across treatment conditions; single lab, correlative mechanistic inference\",\n      \"pmids\": [\"30868936\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Kv4.1 channel activity is required for cell proliferation in tumorigenic human mammary epithelial cells. siRNA-mediated knockdown of Kv4.1 suppresses proliferation, establishing a functional role for this channel in tumor cell growth.\",\n      \"method\": \"siRNA knockdown, cell proliferation assay, Western blot, mRNA analysis in cancer cell lines and human breast cancer tissues\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — siRNA knockdown with proliferation phenotype; single lab, single method for mechanism\",\n      \"pmids\": [\"19401188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Kv4.1 is required for G1-S cell cycle progression in human gastric cancer cells. siRNA-mediated knockdown of Kv4.1 inhibits proliferation and induces a G1-S transition block, as shown by flow cytometry.\",\n      \"method\": \"siRNA knockdown, flow cytometric cell cycle analysis, Western blot, cell proliferation assay\",\n      \"journal\": \"Biological & pharmaceutical bulletin\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — siRNA knockdown with specific cell cycle phenotype; single lab, two methods\",\n      \"pmids\": [\"20930388\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Kv4.1 is co-expressed with auxiliary subunits KChIP2 and DPP10 in NK1R+ secondary nociceptive neurons and excitatory interneurons of spinal lamina I. Intrathecal knockdown of Kv4.1 via antisense oligodeoxynucleotide induces mechanical hypersensitivity in naive rats, demonstrating a direct role for Kv4.1 in pain regulation.\",\n      \"method\": \"Immunohistochemistry (antibody localization), antisense oligodeoxynucleotide knockdown, behavioral testing (mechanical/thermal hypersensitivity)\",\n      \"journal\": \"European journal of pain\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — in vivo knockdown with behavioral phenotype; single lab, defines Kv4.1/KChIP2/DPP10 complex in pain neurons\",\n      \"pmids\": [\"36097791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Hemizygous KCND1 variants (missense and protein-truncating) in the cytoplasmic N- or C-terminus or transmembrane segments S1/S4 of Kv4.1 cause variant-specific alterations in biophysical channel properties. Functional characterization in heterologous expression systems with and without auxiliary β-subunits showed diverse changes in channel function, establishing that Kv4.1 dysfunction underlies an X-linked neurodevelopmental disorder.\",\n      \"method\": \"Trio whole-exome sequencing, heterologous expression, whole-cell electrophysiology with and without auxiliary subunits, gene matching cohort\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — functional variant characterization in heterologous system with multiple variants; domain-specific mutagenesis context\",\n      \"pmids\": [\"38772379\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SsTx-P2, a 53-amino acid peptide from centipede venom, potently inhibits Kv4.1 channel current with 95% inhibition at 1.0 μmol/L. The peptide shares a conserved helical structure identified by structure prediction.\",\n      \"method\": \"Ion-exchange and HPLC purification, whole-cell patch clamp in HEK293 cells transfected with Kv4.1, MALDI-TOF mass spectrometry, Edman sequencing, structural modeling\",\n      \"journal\": \"Journal of Zhejiang University Medical Sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — direct pharmacological inhibition assay in heterologous system; single study, no mutagenesis of binding site\",\n      \"pmids\": [\"38268403\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"KCND1/Kv4.1 encodes a voltage-gated A-type potassium channel α-subunit that is modulated by auxiliary subunits (KChIP1, KChIP2, DPP10) and by CaMKII-dependent phosphorylation at serine 555 downstream of calbindin-mediated Ca2+ buffering; it controls neuronal excitability in dentate granule cells, nociceptors, and cholinergic interneurons, and loss-of-function variants in its cytoplasmic and transmembrane domains cause an X-linked neurodevelopmental disorder.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"KCND1 encodes the Kv4.1 voltage-gated potassium channel α-subunit, which conducts the somatodendritic A-type potassium current (IA) that controls neuronal excitability, firing frequency, and sparse coding across multiple neuron types including dentate granule cells, neostriatal cholinergic interneurons, and spinal nociceptive neurons. Kv4.1 channel properties are modulated by auxiliary subunits KChIP1, KChIP2, and DPP10, which alter inactivation kinetics, activation voltage, current amplitude, and recovery from inactivation [PMID:11423117, PMID:36097791]; surface trafficking of Kv4.1 is regulated by CaMKII-dependent phosphorylation at serine 555, a pathway controlled by calbindin-mediated calcium buffering [PMID:34234278]. In dentate granule cells, Kv4.1 is essential for low-frequency firing and contextual pattern separation, and its downregulation by oxidative stress contributes to hippocampal hyperexcitability in Alzheimer's disease models [PMID:32047055, PMID:33785038]. Hemizygous loss-of-function and missense variants in KCND1 cause an X-linked neurodevelopmental disorder with variant-specific biophysical defects across the channel's cytoplasmic and transmembrane domains [PMID:38772379].\",\n  \"teleology\": [\n    {\n      \"year\": 1998,\n      \"claim\": \"Establishing that Kv4.1 (with Kv4.2) forms the molecular basis of the somatodendritic A-type K+ current in neostriatal cholinergic interneurons resolved the identity of the channel subunits governing slow repetitive firing in these neurons.\",\n      \"evidence\": \"Whole-cell voltage-clamp, single-cell RT-PCR, immunocytochemistry, and pharmacological dissection in neostriatal cholinergic interneurons\",\n      \"pmids\": [\"9547221\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contribution of Kv4.1 versus Kv4.2 to the native current was not resolved\", \"No knockout or knockdown confirmation\", \"Mechanism of subunit heteromerization not addressed\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Demonstrating that KChIP1 directly modulates Kv4.1 gating — accelerating inactivation, shifting activation, increasing amplitude, and speeding recovery — established the principle that auxiliary subunits tune Kv4.1 channel properties, with the N-terminus mediating subunit-specific effects.\",\n      \"evidence\": \"Heterologous coexpression of KChIP1 with Kv4.1 and Kv4.1/Kv4.2 chimeras, whole-cell electrophysiology\",\n      \"pmids\": [\"11423117\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Only KChIP1 tested; modulation by other KChIPs or DPPs not examined\", \"Structural basis of N-terminus interaction not determined\", \"Native neuronal reconstitution not performed\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Discovery that Kv4.1 knockdown suppresses proliferation in mammary and gastric cancer cells revealed a non-neuronal role for the channel in cell cycle progression at the G1-S boundary.\",\n      \"evidence\": \"siRNA knockdown with proliferation assays and flow cytometry in human cancer cell lines\",\n      \"pmids\": [\"19401188\", \"20930388\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking K+ conductance to cell cycle not identified\", \"No rescue experiment with channel re-expression\", \"Single-lab findings for each cancer type\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showing that Kv4.1 uniquely underlies IA in myelinated primary afferent neurons and that its expression is reduced by nerve injury (restored by GDNF) connected Kv4.1 to neuropathic pain mechanisms.\",\n      \"evidence\": \"Patch clamp, in situ hybridization, L5 spinal nerve ligation and GDNF infusion in rats\",\n      \"pmids\": [\"30868936\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Correlative — no selective Kv4.1 knockdown in afferents\", \"Molecular pathway from GDNF signaling to Kv4.1 transcription not mapped\", \"Single lab\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstrating that Kv4.1 determines the low-frequency firing mode of mature dentate granule cells and is required for contextual pattern separation established a causal link between this channel and hippocampal sparse coding.\",\n      \"evidence\": \"Intracellular antibody block, viral knockdown of Kv4.1 in mouse dentate gyrus, behavioral pattern separation task\",\n      \"pmids\": [\"32047055\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How Kv4.1 is preferentially enriched in mature versus immature GCs is unknown\", \"Contribution of auxiliary subunits in DGCs not addressed\", \"Circuit-level mechanism of pattern separation impairment not resolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identification of CaMKII phosphorylation at serine 555 as the mechanism by which calbindin loss reduces Kv4.1 surface expression, causing GC hyperexcitability, provided the first post-translational regulatory mechanism for Kv4.1 trafficking.\",\n      \"evidence\": \"Calbindin KO mice, surface biotinylation, phospho-specific assays at S555, HT22 cell manipulation, patch clamp\",\n      \"pmids\": [\"34234278\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other kinases also phosphorylate S555 is unknown\", \"Structural consequence of S555 phosphorylation on channel trafficking not determined\", \"Phosphatase counter-regulation not identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linking Kv4.1 downregulation to oxidative stress in Tg2576 Alzheimer's mice, with antioxidant rescue of both channel expression and pattern separation, positioned Kv4.1 as a convergence point for Alzheimer's-associated hippocampal dysfunction.\",\n      \"evidence\": \"Patch clamp, Western blot, RT-PCR, antioxidant rescue, behavioral testing in Tg2576 mice\",\n      \"pmids\": [\"33785038\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct transcriptional or post-transcriptional mechanism of oxidative-stress-mediated Kv4.1 reduction not identified\", \"Applicability to human AD not tested\", \"Specificity of antioxidant rescue for Kv4.1 versus other channels unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defining the Kv4.1/KChIP2/DPP10 complex in spinal lamina I nociceptive neurons and showing that intrathecal Kv4.1 knockdown causes mechanical hypersensitivity extended the pain role of Kv4.1 from primary afferents to the spinal cord.\",\n      \"evidence\": \"Immunohistochemistry, antisense oligodeoxynucleotide knockdown, behavioral testing in rats\",\n      \"pmids\": [\"36097791\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Antisense knockdown lacks subunit selectivity confirmation\", \"Electrophysiological characterization in spinal neurons not performed\", \"Role of KChIP2/DPP10 in pain modulation via Kv4.1 not functionally tested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Functional characterization of hemizygous KCND1 variants from patients with X-linked neurodevelopmental disorder established causative genotype–phenotype relationships, showing domain-specific biophysical alterations with and without auxiliary subunits.\",\n      \"evidence\": \"Trio whole-exome sequencing, heterologous expression with whole-cell electrophysiology ± auxiliary subunits, multi-family cohort\",\n      \"pmids\": [\"38772379\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No patient-derived neuronal models tested\", \"In vivo validation with knock-in animal models absent\", \"Therapeutic rescue strategies not explored\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis of auxiliary subunit modulation specific to Kv4.1, the transcriptional regulation underlying neuron-type-specific Kv4.1 expression, and whether Kv4.1-targeted interventions can rescue neurodevelopmental or neurodegenerative phenotypes in vivo.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structure of Kv4.1 alone or with auxiliary subunits\", \"Transcriptional and epigenetic regulation of KCND1 expression uncharacterized\", \"No therapeutic or gene-replacement rescue in animal models of KCND1 disease\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [0, 1, 2, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [3, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [1, 2, 5]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\n      \"Kv4.1/KChIP1 complex\",\n      \"Kv4.1/KChIP2/DPP10 complex\"\n    ],\n    \"partners\": [\n      \"KCNIP1\",\n      \"KCNIP2\",\n      \"DPP10\",\n      \"KCND2\",\n      \"CAMK2A\",\n      \"CALB1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}