{"gene":"DCLK2","run_date":"2026-06-09T23:54:41","timeline":{"discoveries":[{"year":2004,"finding":"DCLK2 (DCK2) has microtubule (MT) binding activity associated with its doublecortin-like (DC) domain, and protein kinase activity mediated by a separate kinase domain, with the two domains functioning independently. Overexpression of DCK2 stabilizes the MT cytoskeleton against cold-induced depolymerization. Autophosphorylation of DCK2 strongly reduces its affinity for MTs, suggesting a phosphorylation-dependent switch for reversible control of MT dynamics. In sympathetic neurons, DCK2 localizes to the cell body and terminal segments of axons and dendrites.","method":"Biochemical domain analysis, MT binding assays, cold-induced depolymerization assay, autophosphorylation assay, immunofluorescence localization in sympathetic neurons","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro biochemical assays (MT binding, kinase activity, autophosphorylation) with domain mutagenesis logic, supported by cell-based localization, single lab but multiple orthogonal methods","pmids":["15611072"],"is_preprint":false},{"year":2006,"finding":"DCLK2 (CLICK-II/DCAMKL2) is a CaM kinase I/IV-related kinase highly expressed in neurons. Unlike CaMKI/CaMKIV and CaMKII which activate CREB-dependent transcription, DCLK2 is unable to significantly phosphorylate CREB Ser-133 and instead inhibits CRE-dependent gene expression by a dominant mechanism bypassing CREB, mediated by phosphorylated TORC2.","method":"CRE-reporter assay, CREB phosphorylation assay, overexpression in cells, comparison with CaMKI/CaMKIV/CaMKII","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-based reporter and phosphorylation assays, multiple comparisons, single lab","pmids":["16684769"],"is_preprint":false},{"year":2009,"finding":"Dcx and Dclk2 are coexpressed in the developing hippocampus, and double-null (Dcx;Dclk2) mice display spontaneous seizures originating in the hippocampus, dosage-dependent disrupted hippocampal lamination, cell-autonomous simplification of pyramidal dendritic arborizations, and reduced inhibitory synaptic tone. Loss of somatostatin-positive interneurons and elevated c-fos were identified, indicating that hippocampal dysmaturation and insufficient inhibitory input underlie epilepsy in this model.","method":"Genetic double-knockout mouse model, EEG, immunohistochemistry, electrophysiology, in situ hybridization","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — double KO mouse with multiple orthogonal readouts (electrophysiology, histology, immunostaining), clear genetic epistasis","pmids":["19342486"],"is_preprint":false},{"year":2014,"finding":"The kinase fragment of zebrafish DCLK2 (zDCLK2) translocates from the cytoplasm into the nucleus under hyperosmotic stress (NaCl or mannitol). The kinase domain interacts with the transcription factor JDP2, identified by two-hybrid screening, and phosphorylates JDP2 efficiently only in the presence of histone.","method":"Two-hybrid screening, subcellular fractionation/localization under hyperosmotic conditions, in vitro kinase assay with JDP2 and histone","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — yeast two-hybrid plus in vitro kinase assay, single lab, zebrafish ortholog","pmids":["24582561"],"is_preprint":false},{"year":2024,"finding":"DCLK2 directly binds to and phosphorylates TBK1 on Ser172, activating TBK1 signaling in clear cell renal cell carcinoma (ccRCC). A short isoform, DCLK2203, predominates in ccRCC and promotes cell growth and tumorigenesis via TBK1 phosphorylation and activation. Depletion of DCLK2 inhibits anchorage-independent colony growth and kidney tumorigenesis in orthotopic xenograft models.","method":"Kinome-wide siRNA screen, Co-immunoprecipitation, in vitro kinase assay, site-specific phosphorylation (Ser172), overexpression/knockdown cell lines, orthotopic xenograft mouse models","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — kinome siRNA screen followed by direct kinase assay, Co-IP, site-specific phosphorylation identification, and in vivo xenograft validation, single lab but multiple orthogonal methods","pmids":["38211588"],"is_preprint":false},{"year":2025,"finding":"BBOX1 suppresses ccRCC tumorigenesis by disrupting TBK1 activation through preventing TBK1's interaction with its upstream activator DCLK2, establishing a BBOX1-DCLK2-TBK1 axis in ccRCC metabolic dysregulation.","method":"Co-immunoprecipitation (interaction disruption), xenograft tumor growth assay, transcriptomic analysis","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP interaction disruption and in vivo models, single lab, corroborates prior DCLK2-TBK1 findings","pmids":["39934163"],"is_preprint":false},{"year":2024,"finding":"Cpeb4 upregulates Dclk2 expression by increasing Dclk2 mRNA stability. Dclk2 then phosphorylates the transcription factor Ehf, causing p-Ehf to exit the nucleus, which reduces Ehf's repression of Caspase1 and Caspase3 promoters and thereby promotes neuronal pyroptosis in chronic cerebral ischemia models.","method":"mRNA stability assays, knockdown experiments in HT22 cells and CCI mouse model, subcellular fractionation of Ehf, promoter activity assays for Caspase1/Caspase3, kinase assay (Dclk2 phosphorylating Ehf)","journal":"Journal of cerebral blood flow and metabolism","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple functional assays (mRNA stability, promoter activity, subcellular redistribution, kinase assay), single lab","pmids":["38513137"],"is_preprint":false},{"year":2022,"finding":"DCLK2 promotes breast cancer cell invasion and metastasis. Silencing DCLK2 does not affect proliferation but significantly suppresses migration, invasion, and lung metastasis. Overexpression of DCLK2 enhances migratory and invasive abilities of normal breast epithelial cells. DCLK2 knockdown blocks the epithelial-mesenchymal transition (EMT) process. TCF4/β-catenin inhibitor LF3 downregulates DCLK2 expression.","method":"Lentiviral overexpression and knockdown, scratch/Transwell migration and invasion assays, tail vein metastasis in vivo model, Western blot for EMT markers","journal":"Clinical & translational oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss- and gain-of-function with in vivo metastasis model and EMT marker analysis, single lab","pmids":["36477947"],"is_preprint":false},{"year":2023,"finding":"DCLK2 was identified as a BAF (SWI/SNF) complex-interacting kinase in neurons; inhibition of DCLK2 attenuates activity-dependent BAF complex phosphorylation selectively, placing DCLK2 as a kinase that mediates synaptic activity-induced phosphorylation of BAF complexes.","method":"Chemical perturbation (kinase inhibition), mass spectrometry of BAF complex composition and phosphorylation in depolarized primary cortical neurons","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single inhibitor experiment, indirect evidence of BAF interaction, no direct binding or mutagenesis shown","pmids":["37873481"],"is_preprint":true}],"current_model":"DCLK2 is a dual-domain protein with an N-terminal doublecortin-like microtubule-binding domain and a C-terminal serine/threonine kinase domain that function independently; autophosphorylation reduces its MT affinity, suggesting a phosphorylation-dependent switch for MT dynamics in neurons; in the nucleus it phosphorylates substrates including JDP2 (under hyperosmotic stress) and the transcription factor Ehf (promoting neuronal pyroptosis); in cancer it directly phosphorylates TBK1 on Ser172 to drive oncogenic signaling in ccRCC (opposed by BBOX1), promotes EMT-driven breast cancer invasion, and interacts with the BAF chromatin-remodeling complex in neurons; genetically, Dclk2 cooperates with Dcx to regulate hippocampal lamination and inhibitory circuit maturation, with double-null mice displaying spontaneous seizures."},"narrative":{"mechanistic_narrative":"DCLK2 is a dual-function neuronal protein combining microtubule-regulatory and serine/threonine kinase activities, with roles spanning cytoskeletal dynamics, neuronal development, transcriptional control, and oncogenic signaling [PMID:15611072, PMID:19342486]. Its N-terminal doublecortin-like domain binds and stabilizes microtubules against depolymerization, while a separable kinase domain functions independently; autophosphorylation lowers microtubule affinity, providing a phosphorylation-dependent switch for microtubule dynamics [PMID:15611072]. Genetically, Dclk2 acts redundantly with Dcx to control hippocampal lamination, pyramidal dendritic arborization, and inhibitory circuit maturation, and double-null mice develop spontaneous hippocampal seizures with loss of somatostatin-positive interneurons [PMID:19342486]. As a kinase, DCLK2 phosphorylates substrates to control gene expression: it phosphorylates the transcription factor Ehf, driving its nuclear exit, derepressing Caspase1/Caspase3, and promoting neuronal pyroptosis in cerebral ischemia [PMID:38513137], and it relocates to the nucleus under hyperosmotic stress to phosphorylate JDP2 in a histone-dependent manner [PMID:24582561]. In cancer, DCLK2 directly binds and phosphorylates TBK1 on Ser172 to activate oncogenic signaling in clear cell renal cell carcinoma, an axis antagonized by BBOX1 [PMID:38211588, PMID:39934163], and it drives epithelial-mesenchymal transition and metastasis in breast cancer [PMID:36477947].","teleology":[{"year":2004,"claim":"Established the bipartite architecture of DCLK2, showing that microtubule binding and kinase activity reside in independent domains and that autophosphorylation provides a reversible switch governing microtubule affinity.","evidence":"Biochemical domain analysis, MT binding and cold-depolymerization assays, autophosphorylation assay, and neuronal immunolocalization","pmids":["15611072"],"confidence":"High","gaps":["Physiological trigger for autophosphorylation in vivo not identified","No structural model of the DC-kinase interplay","Endogenous kinase substrates not defined here"]},{"year":2006,"claim":"Distinguished DCLK2 from related CaM kinases by showing it does not activate CREB but instead represses CRE-dependent transcription, implicating it in transcriptional control beyond cytoskeletal regulation.","evidence":"CRE-reporter and CREB phosphorylation assays with overexpression, compared against CaMKI/IV/II","pmids":["16684769"],"confidence":"Medium","gaps":["Direct substrate mediating TORC2 phosphorylation not established","Overexpression-based; endogenous relevance unconfirmed","Single lab"]},{"year":2009,"claim":"Defined the developmental role of Dclk2, showing genetic redundancy with Dcx in hippocampal lamination and inhibitory circuit maturation and a causal link to epilepsy.","evidence":"Dcx;Dclk2 double-knockout mice with EEG, histology, electrophysiology, and in situ hybridization","pmids":["19342486"],"confidence":"High","gaps":["Molecular substrates underlying lamination defects unknown","Single-knockout Dclk2 phenotype minimal, obscuring its independent contribution","Mechanism linking cytoskeletal/kinase activity to interneuron loss unresolved"]},{"year":2014,"claim":"Showed stress-regulated nuclear translocation of the DCLK2 kinase fragment and identified JDP2 as a histone-dependent substrate, linking the kinase to stress-responsive transcriptional regulation.","evidence":"Yeast two-hybrid, subcellular fractionation under hyperosmotic stress, and in vitro kinase assay (zebrafish ortholog)","pmids":["24582561"],"confidence":"Medium","gaps":["Functional consequence of JDP2 phosphorylation not determined","Zebrafish ortholog; human conservation untested","Requirement for histone mechanistically unexplained"]},{"year":2022,"claim":"Identified a pro-metastatic role for DCLK2 in breast cancer, distinguishing its invasion-promoting function from proliferation and linking it to EMT and Wnt signaling.","evidence":"Lentiviral gain/loss-of-function, migration/invasion assays, tail-vein metastasis model, EMT marker Western blots, LF3 inhibitor treatment","pmids":["36477947"],"confidence":"Medium","gaps":["Direct kinase substrate driving EMT not identified","Whether DCLK2 is a TCF4/β-catenin target or upstream regulator unclear","Single lab"]},{"year":2023,"claim":"Placed DCLK2 as a kinase coupling synaptic activity to chromatin remodeling by mediating activity-dependent BAF complex phosphorylation.","evidence":"Kinase inhibition with mass spectrometry of BAF composition and phosphorylation in depolarized cortical neurons (preprint)","pmids":["37873481"],"confidence":"Low","gaps":["Preprint; no direct binding or mutagenesis shown","BAF interaction inferred indirectly from inhibitor effect","Phosphosites on BAF subunits not mapped"]},{"year":2024,"claim":"Defined DCLK2 as a direct upstream activating kinase of TBK1 in renal cancer, establishing a druggable oncogenic kinase relationship and identifying a tumor-predominant short isoform.","evidence":"Kinome-wide siRNA screen, Co-IP, in vitro kinase assay with Ser172 site mapping, knockdown/overexpression, and orthotopic xenografts","pmids":["38211588"],"confidence":"High","gaps":["Determinants of DCLK2203 isoform predominance unknown","Whether DC domain contributes to TBK1 regulation untested","Generalizability beyond ccRCC unaddressed"]},{"year":2024,"claim":"Connected upstream Cpeb4-mediated Dclk2 induction to a pyroptotic transcriptional program via Ehf phosphorylation, defining a mechanism for neuronal death in cerebral ischemia.","evidence":"mRNA stability assays, knockdown in HT22 cells and CCI mouse model, Ehf subcellular fractionation, Caspase1/3 promoter assays, and kinase assay","pmids":["38513137"],"confidence":"Medium","gaps":["Ehf phosphosite not mapped","Whether nuclear export is direct consequence of phosphorylation unproven","Single lab"]},{"year":2025,"claim":"Corroborated and contextualized the DCLK2-TBK1 axis by identifying BBOX1 as an antagonist that blocks the DCLK2-TBK1 interaction in ccRCC.","evidence":"Co-IP interaction-disruption, xenograft tumor growth, and transcriptomic analysis","pmids":["39934163"],"confidence":"Medium","gaps":["Mechanism by which BBOX1 disrupts the interaction unresolved","Whether BBOX1 acts catalytically or by competition unknown","Single lab"]},{"year":null,"claim":"How DCLK2's microtubule-binding and kinase activities are coordinated across its distinct neuronal-developmental, transcriptional, and oncogenic contexts, and what governs substrate and isoform selection, remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified model linking the DC domain to kinase substrate choice","Structural basis of substrate recognition (TBK1, Ehf, JDP2) undefined","Regulation of subcellular partitioning between cytoplasm and nucleus poorly understood"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[4,6,3]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,4]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[4,7]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[2]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[6]}],"complexes":[],"partners":["TBK1","JDP2","EHF","BBOX1","DCX"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8N568","full_name":"Serine/threonine-protein kinase DCLK2","aliases":["CaMK-like CREB regulatory kinase 2","CL2","CLICK-II","CLICK2","Doublecortin domain-containing protein 3B","Doublecortin-like and CAM kinase-like 2","Doublecortin-like kinase 2"],"length_aa":766,"mass_kda":83.6,"function":"Protein kinase with a significantly reduced C(a2+)/CAM affinity and dependence compared to other members of the CaMK family. May play a role in the down-regulation of CRE-dependent gene activation probably by phosphorylation of the CREB coactivator CRTC2/TORC2 and the resulting retention of TORC2 in the cytoplasm (By similarity)","subcellular_location":"Cytoplasm, cytoskeleton","url":"https://www.uniprot.org/uniprotkb/Q8N568/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DCLK2","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/DCLK2","total_profiled":1310},"omim":[{"mim_id":"614994","title":"CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE IG; CAMK1G","url":"https://www.omim.org/entry/614994"},{"mim_id":"613167","title":"DOUBLECORTIN-LIKE KINASE 3; DCLK3","url":"https://www.omim.org/entry/613167"},{"mim_id":"613166","title":"DOUBLECORTIN-LIKE KINASE 2; DCLK2","url":"https://www.omim.org/entry/613166"},{"mim_id":"300121","title":"DOUBLECORTIN; DCX","url":"https://www.omim.org/entry/300121"},{"mim_id":"300067","title":"LISSENCEPHALY, X-LINKED, 1; LISX1","url":"https://www.omim.org/entry/300067"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":45.8},{"tissue":"retina","ntpm":17.1}],"url":"https://www.proteinatlas.org/search/DCLK2"},"hgnc":{"alias_symbol":["MGC45428","DCDC3","DCDC3B","DCK2"],"prev_symbol":["DCAMKL2"]},"alphafold":{"accession":"Q8N568","domains":[{"cath_id":"3.10.20.230","chopping":"73-148","consensus_level":"high","plddt":85.8478,"start":73,"end":148},{"cath_id":"3.10.20.230","chopping":"198-284","consensus_level":"high","plddt":75.2311,"start":198,"end":284},{"cath_id":"3.30.200.20","chopping":"393-471","consensus_level":"medium","plddt":91.4608,"start":393,"end":471},{"cath_id":"1.10.510.10","chopping":"476-701","consensus_level":"high","plddt":88.5465,"start":476,"end":701}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N568","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N568-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N568-F1-predicted_aligned_error_v6.png","plddt_mean":69.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DCLK2","jax_strain_url":"https://www.jax.org/strain/search?query=DCLK2"},"sequence":{"accession":"Q8N568","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N568.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N568/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N568"}},"corpus_meta":[{"pmid":"21832240","id":"PMC_21832240","title":"Rare copy number variation discovery and cross-disorder comparisons identify risk genes for ADHD.","date":"2011","source":"Science translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/21832240","citation_count":284,"is_preprint":false},{"pmid":"29572931","id":"PMC_29572931","title":"Genetic predisposition in anti-LGI1 and anti-NMDA receptor encephalitis.","date":"2018","source":"Annals of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/29572931","citation_count":116,"is_preprint":false},{"pmid":"7282953","id":"PMC_7282953","title":"Cardiac output during cardiopulmonary resuscitation at various compression rates and durations.","date":"1981","source":"The American journal of physiology","url":"https://pubmed.ncbi.nlm.nih.gov/7282953","citation_count":99,"is_preprint":false},{"pmid":"8810266","id":"PMC_8810266","title":"Altered regulation of G1 cyclins in oxidant-induced growth arrest of lung alveolar epithelial cells. Accumulation of inactive cyclin E-DCK2 complexes.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8810266","citation_count":71,"is_preprint":false},{"pmid":"31583809","id":"PMC_31583809","title":"Genetics of resilience: Implications from genome-wide association studies and candidate genes of the stress response system in posttraumatic stress disorder and depression.","date":"2019","source":"American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31583809","citation_count":71,"is_preprint":false},{"pmid":"19342486","id":"PMC_19342486","title":"Mice lacking doublecortin and doublecortin-like kinase 2 display altered hippocampal neuronal maturation and spontaneous seizures.","date":"2009","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/19342486","citation_count":64,"is_preprint":false},{"pmid":"23726375","id":"PMC_23726375","title":"Epilepsy associated with autism and attention deficit hyperactivity disorder: is there a genetic link?","date":"2013","source":"Brain & development","url":"https://pubmed.ncbi.nlm.nih.gov/23726375","citation_count":59,"is_preprint":false},{"pmid":"31081985","id":"PMC_31081985","title":"Genome-wide analyses of psychological resilience in U.S. Army soldiers.","date":"2019","source":"American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31081985","citation_count":45,"is_preprint":false},{"pmid":"24239623","id":"PMC_24239623","title":"Structural determinants for ERK5 (MAPK7) and leucine rich repeat kinase 2 activities of benzo[e]pyrimido-[5,4-b]diazepine-6(11H)-ones.","date":"2013","source":"European journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24239623","citation_count":40,"is_preprint":false},{"pmid":"16684769","id":"PMC_16684769","title":"Molecular identification and characterization of a family of kinases with homology to Ca2+/calmodulin-dependent protein kinases I/IV.","date":"2006","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16684769","citation_count":32,"is_preprint":false},{"pmid":"16223721","id":"PMC_16223721","title":"dMi-2 chromatin binding and remodeling activities are regulated by dCK2 phosphorylation.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16223721","citation_count":30,"is_preprint":false},{"pmid":"15611072","id":"PMC_15611072","title":"Doublecortin kinase-2, a novel doublecortin-related protein kinase associated with terminal segments of axons and dendrites.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15611072","citation_count":29,"is_preprint":false},{"pmid":"29095916","id":"PMC_29095916","title":"Transcriptomic difference in bovine blastocysts following vitrification and slow freezing at morula stage.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/29095916","citation_count":28,"is_preprint":false},{"pmid":"18075264","id":"PMC_18075264","title":"Alternative transcripts of Dclk1 and Dclk2 and their expression in doublecortin knockout mice.","date":"2008","source":"Developmental neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/18075264","citation_count":18,"is_preprint":false},{"pmid":"31919093","id":"PMC_31919093","title":"Analysis of retrotransposon subfamily DNA methylation reveals novel early epigenetic changes in chronic lymphocytic leukemia.","date":"2021","source":"Haematologica","url":"https://pubmed.ncbi.nlm.nih.gov/31919093","citation_count":17,"is_preprint":false},{"pmid":"24582561","id":"PMC_24582561","title":"Nuclear translocation of doublecortin-like protein kinase and phosphorylation of a transcription factor JDP2.","date":"2014","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/24582561","citation_count":11,"is_preprint":false},{"pmid":"38211588","id":"PMC_38211588","title":"Kinome-wide siRNA screen identifies a DCLK2-TBK1 oncogenic signaling axis in clear cell renal cell carcinoma.","date":"2024","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/38211588","citation_count":10,"is_preprint":false},{"pmid":"31578829","id":"PMC_31578829","title":"Exome sequencing study of partial agenesis of the corpus callosum in men with developmental delay, epilepsy, and microcephaly.","date":"2019","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/31578829","citation_count":10,"is_preprint":false},{"pmid":"32109663","id":"PMC_32109663","title":"Gene discovery for high-density lipoprotein cholesterol level change over time in prospective family studies.","date":"2020","source":"Atherosclerosis","url":"https://pubmed.ncbi.nlm.nih.gov/32109663","citation_count":9,"is_preprint":false},{"pmid":"39934163","id":"PMC_39934163","title":"BBOX1 restrains TBK1-mTORC1 oncogenic signaling in clear cell renal cell carcinoma.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39934163","citation_count":7,"is_preprint":false},{"pmid":"25784603","id":"PMC_25784603","title":"Hippocampal transcriptional and neurogenic changes evoked by combination yohimbine and imipramine treatment.","date":"2015","source":"Progress in neuro-psychopharmacology & biological psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/25784603","citation_count":7,"is_preprint":false},{"pmid":"36477947","id":"PMC_36477947","title":"Doublecortin-like kinase 2 promotes breast cancer cell invasion and metastasis.","date":"2022","source":"Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico","url":"https://pubmed.ncbi.nlm.nih.gov/36477947","citation_count":5,"is_preprint":false},{"pmid":"38513137","id":"PMC_38513137","title":"Cpeb4-mediated Dclk2 promotes neuronal pyroptosis induced by chronic cerebral ischemia through phosphorylation of Ehf.","date":"2024","source":"Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/38513137","citation_count":4,"is_preprint":false},{"pmid":"37873481","id":"PMC_37873481","title":"Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37873481","citation_count":4,"is_preprint":false},{"pmid":"39728450","id":"PMC_39728450","title":"Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos.","date":"2024","source":"Metabolites","url":"https://pubmed.ncbi.nlm.nih.gov/39728450","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15169,"output_tokens":2655,"usd":0.042666,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9872,"output_tokens":3394,"usd":0.067105,"stage2_stop_reason":"end_turn"},"total_usd":0.109771,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"DCLK2 (DCK2) has microtubule (MT) binding activity associated with its doublecortin-like (DC) domain, and protein kinase activity mediated by a separate kinase domain, with the two domains functioning independently. Overexpression of DCK2 stabilizes the MT cytoskeleton against cold-induced depolymerization. Autophosphorylation of DCK2 strongly reduces its affinity for MTs, suggesting a phosphorylation-dependent switch for reversible control of MT dynamics. In sympathetic neurons, DCK2 localizes to the cell body and terminal segments of axons and dendrites.\",\n      \"method\": \"Biochemical domain analysis, MT binding assays, cold-induced depolymerization assay, autophosphorylation assay, immunofluorescence localization in sympathetic neurons\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemical assays (MT binding, kinase activity, autophosphorylation) with domain mutagenesis logic, supported by cell-based localization, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"15611072\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"DCLK2 (CLICK-II/DCAMKL2) is a CaM kinase I/IV-related kinase highly expressed in neurons. Unlike CaMKI/CaMKIV and CaMKII which activate CREB-dependent transcription, DCLK2 is unable to significantly phosphorylate CREB Ser-133 and instead inhibits CRE-dependent gene expression by a dominant mechanism bypassing CREB, mediated by phosphorylated TORC2.\",\n      \"method\": \"CRE-reporter assay, CREB phosphorylation assay, overexpression in cells, comparison with CaMKI/CaMKIV/CaMKII\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-based reporter and phosphorylation assays, multiple comparisons, single lab\",\n      \"pmids\": [\"16684769\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Dcx and Dclk2 are coexpressed in the developing hippocampus, and double-null (Dcx;Dclk2) mice display spontaneous seizures originating in the hippocampus, dosage-dependent disrupted hippocampal lamination, cell-autonomous simplification of pyramidal dendritic arborizations, and reduced inhibitory synaptic tone. Loss of somatostatin-positive interneurons and elevated c-fos were identified, indicating that hippocampal dysmaturation and insufficient inhibitory input underlie epilepsy in this model.\",\n      \"method\": \"Genetic double-knockout mouse model, EEG, immunohistochemistry, electrophysiology, in situ hybridization\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — double KO mouse with multiple orthogonal readouts (electrophysiology, histology, immunostaining), clear genetic epistasis\",\n      \"pmids\": [\"19342486\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The kinase fragment of zebrafish DCLK2 (zDCLK2) translocates from the cytoplasm into the nucleus under hyperosmotic stress (NaCl or mannitol). The kinase domain interacts with the transcription factor JDP2, identified by two-hybrid screening, and phosphorylates JDP2 efficiently only in the presence of histone.\",\n      \"method\": \"Two-hybrid screening, subcellular fractionation/localization under hyperosmotic conditions, in vitro kinase assay with JDP2 and histone\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — yeast two-hybrid plus in vitro kinase assay, single lab, zebrafish ortholog\",\n      \"pmids\": [\"24582561\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DCLK2 directly binds to and phosphorylates TBK1 on Ser172, activating TBK1 signaling in clear cell renal cell carcinoma (ccRCC). A short isoform, DCLK2203, predominates in ccRCC and promotes cell growth and tumorigenesis via TBK1 phosphorylation and activation. Depletion of DCLK2 inhibits anchorage-independent colony growth and kidney tumorigenesis in orthotopic xenograft models.\",\n      \"method\": \"Kinome-wide siRNA screen, Co-immunoprecipitation, in vitro kinase assay, site-specific phosphorylation (Ser172), overexpression/knockdown cell lines, orthotopic xenograft mouse models\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — kinome siRNA screen followed by direct kinase assay, Co-IP, site-specific phosphorylation identification, and in vivo xenograft validation, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"38211588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"BBOX1 suppresses ccRCC tumorigenesis by disrupting TBK1 activation through preventing TBK1's interaction with its upstream activator DCLK2, establishing a BBOX1-DCLK2-TBK1 axis in ccRCC metabolic dysregulation.\",\n      \"method\": \"Co-immunoprecipitation (interaction disruption), xenograft tumor growth assay, transcriptomic analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP interaction disruption and in vivo models, single lab, corroborates prior DCLK2-TBK1 findings\",\n      \"pmids\": [\"39934163\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cpeb4 upregulates Dclk2 expression by increasing Dclk2 mRNA stability. Dclk2 then phosphorylates the transcription factor Ehf, causing p-Ehf to exit the nucleus, which reduces Ehf's repression of Caspase1 and Caspase3 promoters and thereby promotes neuronal pyroptosis in chronic cerebral ischemia models.\",\n      \"method\": \"mRNA stability assays, knockdown experiments in HT22 cells and CCI mouse model, subcellular fractionation of Ehf, promoter activity assays for Caspase1/Caspase3, kinase assay (Dclk2 phosphorylating Ehf)\",\n      \"journal\": \"Journal of cerebral blood flow and metabolism\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple functional assays (mRNA stability, promoter activity, subcellular redistribution, kinase assay), single lab\",\n      \"pmids\": [\"38513137\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DCLK2 promotes breast cancer cell invasion and metastasis. Silencing DCLK2 does not affect proliferation but significantly suppresses migration, invasion, and lung metastasis. Overexpression of DCLK2 enhances migratory and invasive abilities of normal breast epithelial cells. DCLK2 knockdown blocks the epithelial-mesenchymal transition (EMT) process. TCF4/β-catenin inhibitor LF3 downregulates DCLK2 expression.\",\n      \"method\": \"Lentiviral overexpression and knockdown, scratch/Transwell migration and invasion assays, tail vein metastasis in vivo model, Western blot for EMT markers\",\n      \"journal\": \"Clinical & translational oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss- and gain-of-function with in vivo metastasis model and EMT marker analysis, single lab\",\n      \"pmids\": [\"36477947\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DCLK2 was identified as a BAF (SWI/SNF) complex-interacting kinase in neurons; inhibition of DCLK2 attenuates activity-dependent BAF complex phosphorylation selectively, placing DCLK2 as a kinase that mediates synaptic activity-induced phosphorylation of BAF complexes.\",\n      \"method\": \"Chemical perturbation (kinase inhibition), mass spectrometry of BAF complex composition and phosphorylation in depolarized primary cortical neurons\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single inhibitor experiment, indirect evidence of BAF interaction, no direct binding or mutagenesis shown\",\n      \"pmids\": [\"37873481\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"DCLK2 is a dual-domain protein with an N-terminal doublecortin-like microtubule-binding domain and a C-terminal serine/threonine kinase domain that function independently; autophosphorylation reduces its MT affinity, suggesting a phosphorylation-dependent switch for MT dynamics in neurons; in the nucleus it phosphorylates substrates including JDP2 (under hyperosmotic stress) and the transcription factor Ehf (promoting neuronal pyroptosis); in cancer it directly phosphorylates TBK1 on Ser172 to drive oncogenic signaling in ccRCC (opposed by BBOX1), promotes EMT-driven breast cancer invasion, and interacts with the BAF chromatin-remodeling complex in neurons; genetically, Dclk2 cooperates with Dcx to regulate hippocampal lamination and inhibitory circuit maturation, with double-null mice displaying spontaneous seizures.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DCLK2 is a dual-function neuronal protein combining microtubule-regulatory and serine/threonine kinase activities, with roles spanning cytoskeletal dynamics, neuronal development, transcriptional control, and oncogenic signaling [#0, #2]. Its N-terminal doublecortin-like domain binds and stabilizes microtubules against depolymerization, while a separable kinase domain functions independently; autophosphorylation lowers microtubule affinity, providing a phosphorylation-dependent switch for microtubule dynamics [#0]. Genetically, Dclk2 acts redundantly with Dcx to control hippocampal lamination, pyramidal dendritic arborization, and inhibitory circuit maturation, and double-null mice develop spontaneous hippocampal seizures with loss of somatostatin-positive interneurons [#2]. As a kinase, DCLK2 phosphorylates substrates to control gene expression: it phosphorylates the transcription factor Ehf, driving its nuclear exit, derepressing Caspase1/Caspase3, and promoting neuronal pyroptosis in cerebral ischemia [#6], and it relocates to the nucleus under hyperosmotic stress to phosphorylate JDP2 in a histone-dependent manner [#3]. In cancer, DCLK2 directly binds and phosphorylates TBK1 on Ser172 to activate oncogenic signaling in clear cell renal cell carcinoma, an axis antagonized by BBOX1 [#4, #5], and it drives epithelial-mesenchymal transition and metastasis in breast cancer [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established the bipartite architecture of DCLK2, showing that microtubule binding and kinase activity reside in independent domains and that autophosphorylation provides a reversible switch governing microtubule affinity.\",\n      \"evidence\": \"Biochemical domain analysis, MT binding and cold-depolymerization assays, autophosphorylation assay, and neuronal immunolocalization\",\n      \"pmids\": [\"15611072\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological trigger for autophosphorylation in vivo not identified\", \"No structural model of the DC-kinase interplay\", \"Endogenous kinase substrates not defined here\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Distinguished DCLK2 from related CaM kinases by showing it does not activate CREB but instead represses CRE-dependent transcription, implicating it in transcriptional control beyond cytoskeletal regulation.\",\n      \"evidence\": \"CRE-reporter and CREB phosphorylation assays with overexpression, compared against CaMKI/IV/II\",\n      \"pmids\": [\"16684769\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct substrate mediating TORC2 phosphorylation not established\", \"Overexpression-based; endogenous relevance unconfirmed\", \"Single lab\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defined the developmental role of Dclk2, showing genetic redundancy with Dcx in hippocampal lamination and inhibitory circuit maturation and a causal link to epilepsy.\",\n      \"evidence\": \"Dcx;Dclk2 double-knockout mice with EEG, histology, electrophysiology, and in situ hybridization\",\n      \"pmids\": [\"19342486\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular substrates underlying lamination defects unknown\", \"Single-knockout Dclk2 phenotype minimal, obscuring its independent contribution\", \"Mechanism linking cytoskeletal/kinase activity to interneuron loss unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showed stress-regulated nuclear translocation of the DCLK2 kinase fragment and identified JDP2 as a histone-dependent substrate, linking the kinase to stress-responsive transcriptional regulation.\",\n      \"evidence\": \"Yeast two-hybrid, subcellular fractionation under hyperosmotic stress, and in vitro kinase assay (zebrafish ortholog)\",\n      \"pmids\": [\"24582561\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of JDP2 phosphorylation not determined\", \"Zebrafish ortholog; human conservation untested\", \"Requirement for histone mechanistically unexplained\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified a pro-metastatic role for DCLK2 in breast cancer, distinguishing its invasion-promoting function from proliferation and linking it to EMT and Wnt signaling.\",\n      \"evidence\": \"Lentiviral gain/loss-of-function, migration/invasion assays, tail-vein metastasis model, EMT marker Western blots, LF3 inhibitor treatment\",\n      \"pmids\": [\"36477947\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct kinase substrate driving EMT not identified\", \"Whether DCLK2 is a TCF4/β-catenin target or upstream regulator unclear\", \"Single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Placed DCLK2 as a kinase coupling synaptic activity to chromatin remodeling by mediating activity-dependent BAF complex phosphorylation.\",\n      \"evidence\": \"Kinase inhibition with mass spectrometry of BAF composition and phosphorylation in depolarized cortical neurons (preprint)\",\n      \"pmids\": [\"37873481\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Preprint; no direct binding or mutagenesis shown\", \"BAF interaction inferred indirectly from inhibitor effect\", \"Phosphosites on BAF subunits not mapped\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined DCLK2 as a direct upstream activating kinase of TBK1 in renal cancer, establishing a druggable oncogenic kinase relationship and identifying a tumor-predominant short isoform.\",\n      \"evidence\": \"Kinome-wide siRNA screen, Co-IP, in vitro kinase assay with Ser172 site mapping, knockdown/overexpression, and orthotopic xenografts\",\n      \"pmids\": [\"38211588\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Determinants of DCLK2203 isoform predominance unknown\", \"Whether DC domain contributes to TBK1 regulation untested\", \"Generalizability beyond ccRCC unaddressed\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected upstream Cpeb4-mediated Dclk2 induction to a pyroptotic transcriptional program via Ehf phosphorylation, defining a mechanism for neuronal death in cerebral ischemia.\",\n      \"evidence\": \"mRNA stability assays, knockdown in HT22 cells and CCI mouse model, Ehf subcellular fractionation, Caspase1/3 promoter assays, and kinase assay\",\n      \"pmids\": [\"38513137\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ehf phosphosite not mapped\", \"Whether nuclear export is direct consequence of phosphorylation unproven\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Corroborated and contextualized the DCLK2-TBK1 axis by identifying BBOX1 as an antagonist that blocks the DCLK2-TBK1 interaction in ccRCC.\",\n      \"evidence\": \"Co-IP interaction-disruption, xenograft tumor growth, and transcriptomic analysis\",\n      \"pmids\": [\"39934163\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which BBOX1 disrupts the interaction unresolved\", \"Whether BBOX1 acts catalytically or by competition unknown\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DCLK2's microtubule-binding and kinase activities are coordinated across its distinct neuronal-developmental, transcriptional, and oncogenic contexts, and what governs substrate and isoform selection, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified model linking the DC domain to kinase substrate choice\", \"Structural basis of substrate recognition (TBK1, Ehf, JDP2) undefined\", \"Regulation of subcellular partitioning between cytoplasm and nucleus poorly understood\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [4, 6, 3]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [4, 7]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TBK1\", \"JDP2\", \"Ehf\", \"BBOX1\", \"DCX\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}