{"gene":"DCLK1","run_date":"2026-04-28T17:46:02","timeline":{"discoveries":[{"year":2000,"finding":"DCLK1 (DCAMKL1) protein associates with microtubules, stimulates polymerization of purified tubulin, and induces formation of aster-like microtubule structures and microtubule bundling in cell lines; its kinase domain is functional (phosphorylates myelin basic protein and itself), but kinase activity is dispensable for microtubule polymerization activity.","method":"In vitro microtubule polymerization assay with purified DCAMKL1; transfection/overexpression with time-lapse imaging; in vitro kinase assay; kinase-dead mutagenesis","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 1 — reconstituted in vitro with purified protein, mutagenesis, and live imaging; single rigorous paper with multiple orthogonal methods","pmids":["11124993"],"is_preprint":false},{"year":2004,"finding":"Two short splice variants of DCLK (DCLK-short-A and -B) both phosphorylate autocamtide and syntide (CaMK-specific substrates); removal of the distinct C-terminal ends causes a ~10-fold increase in kinase activity, indicating the C-termini function as autoinhibitory domains.","method":"In vitro kinase assay with CaMK substrates; truncation mutagenesis of C-terminal domains","journal":"Brain research. Molecular brain research","confidence":"High","confidence_rationale":"Tier 1 — in vitro kinase assay with mutagenesis demonstrating autoinhibitory mechanism","pmids":["14741399"],"is_preprint":false},{"year":2009,"finding":"siRNA-mediated knockdown of DCAMKL-1 in colorectal cancer cells and xenografts results in tumor growth arrest, upregulation of pri-let-7a miRNA, decreased luciferase activity from a let-7a reporter, and decreased c-Myc expression, establishing DCAMKL-1 as a negative regulator of let-7a miRNA biogenesis.","method":"siRNA knockdown in HCT116/SW480 cells; xenograft model; luciferase reporter assay for let-7a; FACS-sorted DCAMKL-1+ cells analyzed for pri-let-7a","journal":"Gastroenterology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (KD, xenograft, reporter assay, FACS) in a single study; foundational mechanism paper","pmids":["19445940"],"is_preprint":false},{"year":2011,"finding":"siRNA knockdown of DCAMKL-1 in human pancreatic cancer cells induces miR-200a (an EMT inhibitor), downregulates ZEB1, ZEB2, Snail, Slug, Twist, and reduces c-Myc and KRAS through a let-7a-dependent mechanism, and reduces Notch-1 through a miR-144-dependent mechanism.","method":"siRNA knockdown; miRNA qRT-PCR; immunoblot; colocalization IHC in mouse model","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods, in vitro and in vivo; replicated across labs","pmids":["21285251"],"is_preprint":false},{"year":2013,"finding":"DCAMKL1 represses osteoblast differentiation by antagonizing Runx2 (the master osteoblast transcription factor); Dcamkl1-null mice display elevated bone mass secondary to increased bone formation, and the cleidocranial dysplasia phenotype of Runx2+/- mice is reversed by introduction of a Dcamkl1-null allele.","method":"shRNA forward genetic screen; targeted disruption of Dcamkl1 (knockout mouse); epistasis with Runx2+/- mice; molecular experiments","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis in vivo combined with KO phenotype and molecular validation","pmids":["23918955"],"is_preprint":false},{"year":2013,"finding":"DCLK1 knockdown in pancreatic cancer xenografts upregulates miR-145, leading to decreased OCT4, SOX2, NANOG, KLF4, KRAS, and RREB1; increases let-7a, decreasing LIN28B; and increases miR-200, decreasing VEGFR1, VEGFR2, and EMT transcription factors ZEB1, ZEB2, SNAIL, SLUG. Luciferase reporter assays confirmed post-transcriptional regulation.","method":"PLGA-nanoparticle siRNA knockdown in xenografts; miRNA/mRNA qRT-PCR; luciferase reporter assay","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 — in vivo xenograft plus luciferase reporter confirmation; multiple independent targets validated","pmids":["24040120"],"is_preprint":false},{"year":2016,"finding":"DCLK1 labels a subset of dendritic microtubules and is required for KIF1 (kinesin-3)-dependent dense-core vesicle trafficking into dendrites and for dendrite development in hippocampal neurons; systematic kinesin screen identified DCLK1-labeled microtubules as a dendritic transport cue.","method":"Systematic screen of 45 kinesin family members; live-cell imaging; KD/KO in hippocampal neurons; DCV trafficking assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — systematic screen plus loss-of-function with defined trafficking phenotype; replicated across conditions","pmids":["26758546"],"is_preprint":false},{"year":2016,"finding":"DCLK1 phosphorylates MAP7D1 at Serine 315 to promote axon elongation in cortical neurons; knockdown of MAP7D1 impairs callosal axon elongation but not radial migration, and a phosphomimetic MAP7D1 S315E mutant rescues axon elongation defects in Dclk1 knockdown neurons.","method":"Proteomic identification of substrate; in vitro kinase assay; shRNA knockdown in cortical neurons; rescue with phosphomimetic mutant (S315E)","journal":"Developmental neurobiology","confidence":"High","confidence_rationale":"Tier 1 — kinase substrate identified by proteomics, validated by in vitro assay and phosphomimetic rescue","pmids":["27503845"],"is_preprint":false},{"year":2018,"finding":"DCLK1 induces NF-κBp65 expression through the PI3K/Akt/Sp1 axis and activates NF-κBp65 through PI3K/Akt/IκBα during EMT in colorectal cancer cells; silencing DCLK1 inhibits CRC invasion and metastasis in vivo.","method":"siRNA knockdown; immunoblot; pathway inhibitor experiments; in vivo metastasis model","journal":"International journal of cancer","confidence":"Medium","confidence_rationale":"Tier 2 — multiple pathway methods but single lab","pmids":["29277893"],"is_preprint":false},{"year":2018,"finding":"Dclk1 expression in intestinal tuft cells is required for inflammation-induced Cox2 expression and prostaglandin E2 (PGE2) production; PGE2 rescues proliferative defects in Dclk1-deficient colonic organoids, linking Dclk1 to epithelial repair via a PGE2-dependent paracrine mechanism.","method":"Villin-Cre;Dclk1flox/flox (intestinal epithelial knockout mice); colonic organoid culture; PGE2 rescue experiments; qPCR and immunostaining","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 2 — genetic KO with defined molecular mechanism and organoid rescue; multiple orthogonal methods","pmids":["30478383"],"is_preprint":false},{"year":2019,"finding":"KDM3A (histone demethylase that removes H3K9me1/2) binds to the DCLK1 promoter and positively regulates DCLK1 expression in pancreatic cancer; knockdown of KDM3A reduces DCLK1 levels and impairs invasion, migration, and spheroid formation.","method":"ChIP assay for KDM3A binding at DCLK1 promoter; KDM3A shRNA knockdown; KDM3A overexpression; RNA-seq; orthotopic tumor model","journal":"Gastroenterology","confidence":"High","confidence_rationale":"Tier 1-2 — ChIP demonstrates direct promoter binding; multiple orthogonal methods in vitro and in vivo","pmids":["31442435"],"is_preprint":false},{"year":2016,"finding":"Dclk1 interaction with ATM is critical for ATM activation and DNA damage response following radiation injury; Dclk1 deletion reduces ATM-mediated pro-survival signaling and impairs intestinal crypt restitution.","method":"VillinCre;Dclk1flox/flox mice; total body irradiation; co-immunoprecipitation (DCLK1–ATM interaction); analysis of ATM phosphorylation and COX2 activation","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2-3 — genetic KO with Co-IP, but limited biochemical follow-up on mechanism; single lab","pmids":["27876863"],"is_preprint":false},{"year":2021,"finding":"The DCLK1 C-terminal autoinhibitory domain (AID) blocks the ATP-binding site competitively; neuronal calcium sensor HPCAL1 binds directly to the AID in a Ca2+-dependent manner, releasing autoinhibition and activating kinase activity; cancer-associated mutations in the AID disrupt autoinhibition to upregulate kinase activity.","method":"Crystal structure of DCLK1 kinase in autoinhibited state; direct binding assay (HPCAL1–AID); Ca2+-dependence assays; biochemical analysis of AID mutations","journal":"Innovation","confidence":"High","confidence_rationale":"Tier 1 — crystal structure plus biochemical reconstitution of autoinhibition/activation mechanism; mutagenesis of cancer-associated variants","pmids":["34977835"],"is_preprint":false},{"year":2021,"finding":"Crystal structures of DCLK1 kinase domain in complex with inhibitor DCLK1-IN-1 reveal that the compound induces a drastic conformational change of the ATP binding site; DCLK1-IN-1 binds DCLK1 long isoforms but does not prevent DCLK1's MAP (microtubule-associated protein) function, separating kinase and MAP activities.","method":"X-ray crystallography of DCLK1 kinase domain–inhibitor complex; structure-activity relationship analysis; MAP function assay","journal":"Communications biology","confidence":"High","confidence_rationale":"Tier 1 — multiple crystal structures plus functional separation of kinase vs. MAP activity","pmids":["34545159"],"is_preprint":false},{"year":2020,"finding":"DCLK1 kinase activity is required for DCLK1-dependent cancer cell migration and growth; chemical toolkit (DCLK1-IN-1, resistance mutation G532A, kinase-dead D511N/D533N) established DCLK1 kinase activity regulates RNA processing pathways; CDK11 was identified as a potential DCLK1 substrate by phosphoproteomics.","method":"Selective kinase inhibitor (DCLK1-IN-1); resistance mutation G532A; kinase-dead mutants (D511N, D533N); phosphoproteomics; engineered DCLK1-dependent cancer cell line","journal":"Cell chemical biology","confidence":"High","confidence_rationale":"Tier 1-2 — chemical-genetic toolkit with phosphoproteomics; multiple orthogonal approaches in single paper","pmids":["32755567"],"is_preprint":false},{"year":2022,"finding":"DCLK1 binds and phosphorylates XRCC5 (Ku80); phosphorylated XRCC5 transcriptionally activates COX-2, enhancing prostaglandin E2 production and generating a pro-inflammatory tumor microenvironment that drives aggressive colorectal cancer behavior.","method":"Comprehensive proteomics/genomics to identify DCLK1 binding partners; Co-IP (DCLK1–XRCC5); in vitro kinase assay (DCLK1 phosphorylates XRCC5); COX-2 transcriptional reporter; CRC mouse models","journal":"Theranostics","confidence":"High","confidence_rationale":"Tier 1-2 — Co-IP, in vitro kinase assay, and downstream transcriptional/functional validation in vitro and in vivo","pmids":["35910805"],"is_preprint":false},{"year":2023,"finding":"Macrophage DCLK1 directly binds IKKβ and phosphorylates IKKβ at S177/181, facilitating NF-κB activation and inflammatory gene expression; macrophage-specific DCLK1 deletion attenuates atherosclerosis and reduces inflammation in ApoE-/- mice.","method":"Co-immunoprecipitation; LC-MS/MS identification of IKKβ as DCLK1 binding partner; in vitro phosphorylation assay (DCLK1 phosphorylates IKKβ S177/181); macrophage-specific knockout; RNA-seq; pharmacological inhibition","journal":"EMBO molecular medicine","confidence":"High","confidence_rationale":"Tier 1-2 — Co-IP/MS discovery of IKKβ, in vitro phosphorylation assay, and specific KO with in vivo phenotype; multiple orthogonal methods","pmids":["36896602"],"is_preprint":false},{"year":2023,"finding":"Macrophage DCLK1 mediates RIP2/TAK1 phosphorylation upon high-fat diet/palmitate challenge, leading to inflammatory cytokine release that promotes cardiac hypertrophy and fibrosis; macrophage-specific (not cardiomyocyte-specific) DCLK1 knockout prevents obesity-induced cardiomyopathy.","method":"Macrophage-specific and cardiomyocyte-specific DCLK1 KO mice; high-fat diet model; RNA sequencing; immunoblot for RIP2/TAK1 phosphorylation; pharmacological inhibition","journal":"Cell death & disease","confidence":"High","confidence_rationale":"Tier 2 — cell-type-specific KO with mechanistic pathway (RIP2/TAK1) and RNA-seq; multiple methods","pmids":["37443105"],"is_preprint":false},{"year":2019,"finding":"Overexpression of DCLK1-AL (isoform 2/alpha-long) in pancreatic cancer cells increases KRAS activation (demonstrated by RAS pull-down assay) and co-immunoprecipitation confirms DCLK1–KRAS interaction; DCLK1-AL overexpression drives increased invasion and drug resistance downstream of KRAS/PI3K/AKT/mTOR.","method":"Lentiviral stable overexpression; RAS pull-down assay; co-immunoprecipitation; Matrigel invasion assay; drug resistance assays; KPC mouse model","journal":"Journal of oncology","confidence":"Medium","confidence_rationale":"Tier 2-3 — RAS pull-down and Co-IP with functional follow-up; single lab","pmids":["31467540"],"is_preprint":false},{"year":2019,"finding":"DCLK1 interacts with CCAR1 through its C-terminal domain and phosphorylates CCAR1 at Ser343, stabilizing CCAR1; DCLK1-mediated CCAR1 stabilization positively regulates β-catenin signaling, maintaining cancer stemness and 5-FU resistance in colorectal cancer.","method":"Co-IP (DCLK1–CCAR1); in vitro phosphorylation assay (Ser343 site identified); domain mapping; β-catenin pathway inhibitor rescue; in vitro and in vivo CRC models","journal":"Clinical and translational medicine","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP and phosphorylation site identification with functional validation; single lab","pmids":["35522902"],"is_preprint":false},{"year":2015,"finding":"Human colorectal cancers predominantly express a short DCLK1 isoform (DCLK1-S) from an alternate β-promoter in intron V, while normal colons express DCLK1-L from the 5′(α)-promoter; activated NF-κBp65 drives the β-promoter, whereas β-catenin/TCF4/LEF activates the α-promoter in cancer cells.","method":"In silico analysis; molecular biology (promoter cloning, luciferase reporter assay for promoter activity); qRT-PCR in patient cohort","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2-3 — promoter reporter assays establish transcription factor binding; single lab","pmids":["26447334"],"is_preprint":false},{"year":2021,"finding":"DCLK1 influences small extracellular vesicle (sEV/exosome) biogenesis in a kinase-dependent manner; DCLK1 overexpression promotes sEV-mediated cell migration, and DCLK1-IN-1 (kinase inhibitor) reverses increases in sEV size/concentration and alters cargo selection of proteins involved in EV biogenesis (KTN1, CHMP1A, MYO1G) and migration/adhesion.","method":"DCLK1 overexpression in GC cells; sEV isolation; quantitative proteome analysis; DCLK1-IN-1 kinase inhibitor; migration assay","journal":"Proteomics","confidence":"Medium","confidence_rationale":"Tier 2 — quantitative proteomics and pharmacological inhibitor demonstrate kinase-dependent sEV cargo regulation; single lab","pmids":["33991177"],"is_preprint":false},{"year":2021,"finding":"miR-195 directly interacts with the 3′-UTR of Dclk1 mRNA to inhibit DCLK1 translation; RNA-binding protein HuR competes with miR-195 for Dclk1 mRNA binding and increases DCLK1 expression; transgenic miR-195 overexpression reduces intestinal tuft cell numbers via DCLK1 suppression.","method":"miR-195 transgenic mice; intestinal organoids; RNA pulldown/RIP; luciferase 3′-UTR reporter; competition assay between HuR and miR-195","journal":"American journal of physiology. Cell physiology","confidence":"High","confidence_rationale":"Tier 2 — direct 3′-UTR reporter assay, RIP, in vivo transgenic mouse; multiple orthogonal methods","pmids":["33788631"],"is_preprint":false},{"year":2022,"finding":"DCLK1 promotes CRC immune evasion by upregulating CXCL1, which recruits MDSCs via CXCR2; DCLK1-knockout tumors fail to establish in immune-competent mice due to increased CD8+ T cell infiltration and reduced MDSCs; CXCL1 overexpression rescues DCLK1-/- tumor growth.","method":"CRISPR-Cas9 DCLK1 knockout tumor cells; subcutaneous and orthotopic transplantation models; flow cytometry of tumor-infiltrating immune cells; MDSC–T cell co-culture; CXCL1 rescue overexpression; RNA sequencing","journal":"Cellular and molecular gastroenterology and hepatology","confidence":"High","confidence_rationale":"Tier 2 — CRISPR KO with in vivo rescue and mechanistic pathway validation; multiple orthogonal methods","pmids":["36309200"],"is_preprint":false},{"year":2021,"finding":"DCLK1-isoform2 overexpression in pancreatic cancer cells drives polarization of macrophages from M1 toward immunosuppressive M2 phenotype via secreted chemokines/cytokines; M2-macrophages educated by DCLK1-isoform2 enhance PDAC cell migration, invasion, and self-renewal; DCLK1-isoform2-educated M2 macrophages inhibit CD8+ T-cell proliferation and granzyme-B activation.","method":"Stable DCLK1-isoform2 overexpression; macrophage co-culture/polarization assays; organoid-immune cell co-culture; CD8+ T cell activation assays; autochthonous KPCY mouse model","journal":"Molecular cancer therapeutics","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro and in vivo co-culture assays; single lab","pmids":["32371580"],"is_preprint":false},{"year":2021,"finding":"DCLK1-S short splice variant promotes ESCC progression via MAPK/ERK signaling leading to MMP2 upregulation and EMT activation; ERK1/2 inhibitor SCH772984 attenuates the proliferative and migratory phenotype induced by DCLK1-S.","method":"CRISPR/Cas9 DCLK1 total KO with DCLK1-S rescue; RNA-sequencing; KEGG pathway analysis; in vitro migration/invasion assays; in vivo tumor and metastasis models; ERK inhibitor rescue","journal":"Molecular cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — CRISPR KO with isoform-specific rescue and pathway inhibitor; single lab","pmids":["34610960"],"is_preprint":false}],"current_model":"DCLK1 is a bifunctional protein with an N-terminal doublecortin-like microtubule-binding domain (which promotes tubulin polymerization and dendritic cargo transport via KIF1 kinesins) and a C-terminal serine/threonine kinase domain that is held in autoinhibition by its AID until released by Ca²⁺-bound HPCAL1; its kinase activity phosphorylates substrates including MAP7D1 (promoting axon elongation), IKKβ S177/181 (activating NF-κB inflammatory signaling), XRCC5/Ku80 (activating COX-2/PGE2), and CCAR1 S343 (stabilizing β-catenin signaling), while it also functions as a negative regulator of tumor-suppressor miRNAs (let-7a, miR-200a, miR-145) to sustain EMT and cancer stemness, and is epigenetically regulated by KDM3A-mediated H3K9 demethylation and by alternative promoter usage generating distinct long (neuronal/normal epithelial) and short (cancer-associated) isoforms."},"narrative":{"teleology":[{"year":2000,"claim":"Establishing DCLK1 as a bifunctional protein resolved whether the doublecortin-like domain and kinase domain operate independently: the microtubule polymerization/bundling activity was shown to be kinase-independent, defining DCLK1 as both a MAP and a kinase.","evidence":"In vitro tubulin polymerization with purified DCAMKL1, kinase-dead mutagenesis, and live-cell imaging in cell lines","pmids":["11124993"],"confidence":"High","gaps":["Identity of physiological kinase substrates unknown","Regulation of kinase activation not addressed","In vivo function not tested"]},{"year":2004,"claim":"Discovery that the C-terminal domain functions as an autoinhibitory element (removal causing ~10-fold kinase activation) established a regulatory paradigm for DCLK1 kinase control, but the structural basis and activating signal remained unknown.","evidence":"In vitro kinase assay with CaMK substrates and truncation mutagenesis of short DCLK splice variants","pmids":["14741399"],"confidence":"High","gaps":["Structural mechanism of autoinhibition unresolved","Physiological signal that relieves autoinhibition unknown","Whether autoinhibition operates in vivo not demonstrated"]},{"year":2009,"claim":"Linking DCLK1 to tumor-suppressor miRNA regulation answered how a kinase/MAP protein controls cancer stemness: DCLK1 negatively regulates let-7a biogenesis, and its knockdown induces let-7a and suppresses c-Myc, establishing a non-canonical oncogenic function.","evidence":"siRNA knockdown in CRC cell lines and xenografts; let-7a luciferase reporter; FACS sorting of DCLK1⁺ cells","pmids":["19445940"],"confidence":"High","gaps":["Mechanism by which DCLK1 represses let-7a biogenesis (direct or indirect) unresolved","Whether kinase activity is required for miRNA regulation unknown"]},{"year":2011,"claim":"Extension to miR-200a, miR-144, and EMT transcription factor networks broadened DCLK1's oncogenic role beyond let-7a, demonstrating that DCLK1 controls multiple miRNA axes converging on EMT, KRAS, and Notch signaling in pancreatic cancer.","evidence":"siRNA knockdown in pancreatic cancer cells; miRNA qRT-PCR; immunoblot; IHC in mouse model","pmids":["21285251","24040120"],"confidence":"High","gaps":["Direct versus indirect mechanism of miRNA repression still unclear","No kinase-dead rescue to test kinase dependence"]},{"year":2013,"claim":"Genetic epistasis in mice revealed an unexpected skeletal function: Dclk1 represses osteoblast differentiation by antagonizing Runx2, and Dclk1 loss rescues cleidocranial dysplasia in Runx2⁺/⁻ mice, establishing DCLK1 as a physiological brake on bone formation.","evidence":"Dclk1 knockout mice; genetic epistasis with Runx2⁺/⁻; shRNA screen; bone formation analysis","pmids":["23918955"],"confidence":"High","gaps":["Molecular mechanism linking DCLK1 to Runx2 inhibition (direct phosphorylation vs. intermediate) not identified","Cell-type specificity of effect in bone not resolved"]},{"year":2015,"claim":"Identification of alternative promoter usage (α-promoter for long isoform in normal epithelium; β-promoter for short isoform in cancer driven by NF-κBp65) resolved the paradox of DCLK1 as both a normal cell marker and cancer protein, attributing oncogenic functions to the short isoform.","evidence":"Promoter cloning and luciferase reporter assays; qRT-PCR across patient cohort","pmids":["26447334"],"confidence":"Medium","gaps":["Functional differences between long and short isoforms not fully dissected biochemically","Promoter switch mechanism in tumorigenesis not defined","Single-lab finding"]},{"year":2016,"claim":"A systematic kinesin screen established that DCLK1-decorated microtubules serve as a dendritic transport code recognized by KIF1 motors, explaining how DCLK1 directs dense-core vesicle trafficking into dendrites and supports dendrite morphogenesis.","evidence":"Screen of 45 kinesins; live-cell DCV trafficking assay; KD/KO in hippocampal neurons","pmids":["26758546"],"confidence":"High","gaps":["How DCLK1 labeling is restricted to dendritic microtubules unknown","Whether kinase activity modulates the MAP-based trafficking role not tested"]},{"year":2016,"claim":"Identification of MAP7D1 as a direct DCLK1 kinase substrate (phosphorylated at S315) provided the first defined neuronal substrate linking DCLK1 kinase activity specifically to axon elongation rather than radial migration.","evidence":"Phosphoproteomic substrate identification; in vitro kinase assay; phosphomimetic S315E rescue of Dclk1 KD axon defect in cortical neurons","pmids":["27503845"],"confidence":"High","gaps":["Additional neuronal substrates likely exist but are unidentified","Whether MAP7D1 phosphorylation affects microtubule dynamics directly not tested"]},{"year":2018,"claim":"Intestinal epithelial Dclk1 knockout revealed that tuft-cell DCLK1 is required for injury-induced COX-2 expression and PGE₂ production, establishing a paracrine epithelial repair mechanism where PGE₂ rescues proliferative defects in Dclk1-deficient organoids.","evidence":"Villin-Cre;Dclk1-flox intestinal KO mice; colonic organoid culture with PGE₂ rescue","pmids":["30478383"],"confidence":"High","gaps":["Whether DCLK1 kinase activity is required for COX-2 induction or whether the MAP domain contributes not distinguished","Upstream signal activating DCLK1 in tuft cells upon injury unknown"]},{"year":2019,"claim":"Epigenetic control of DCLK1 was established when KDM3A was shown to bind the DCLK1 promoter and demethylate H3K9me1/2, directly activating DCLK1 transcription in pancreatic cancer and linking chromatin remodeling to DCLK1-driven stemness and invasion.","evidence":"ChIP for KDM3A at DCLK1 promoter; KDM3A shRNA/overexpression; RNA-seq; orthotopic tumor model","pmids":["31442435"],"confidence":"High","gaps":["Whether other histone marks or chromatin remodelers regulate DCLK1 not explored","Relationship between KDM3A regulation and isoform-specific promoter usage not addressed"]},{"year":2020,"claim":"Development of DCLK1-IN-1 and a chemical-genetic toolkit (resistance mutation G532A, kinase-dead mutants) formally demonstrated that kinase activity drives cancer cell migration and growth, and phosphoproteomics revealed regulation of RNA processing pathways and CDK11 as a candidate substrate.","evidence":"Selective inhibitor DCLK1-IN-1; engineered DCLK1-dependent cells; resistance mutations; phosphoproteomics","pmids":["32755567"],"confidence":"High","gaps":["CDK11 as substrate not validated by in vitro phosphorylation","RNA processing pathway mechanism downstream of DCLK1 kinase not elucidated"]},{"year":2021,"claim":"Crystal structure of the autoinhibited DCLK1 kinase domain revealed that the AID competitively blocks the ATP-binding site; Ca²⁺-dependent HPCAL1 binding to the AID releases autoinhibition, finally identifying the physiological activation signal for DCLK1 kinase and explaining how cancer-associated AID mutations constitutively activate kinase activity.","evidence":"X-ray crystallography of autoinhibited kinase; HPCAL1–AID direct binding assay; Ca²⁺ dependence; cancer mutation analysis","pmids":["34977835"],"confidence":"High","gaps":["Whether HPCAL1 is the sole activator in all tissue contexts unknown","Structural basis of HPCAL1–AID interaction not resolved at atomic level"]},{"year":2021,"claim":"Co-crystal structures of DCLK1 with DCLK1-IN-1 showed the inhibitor induces a drastic ATP-site conformational change without disrupting MAP function, formally separating kinase and MAP activities at the structural level.","evidence":"X-ray crystallography of DCLK1–inhibitor complexes; MAP function assay under inhibitor treatment","pmids":["34545159"],"confidence":"High","gaps":["Whether kinase-independent MAP functions contribute to cancer phenotypes not resolved","Selectivity profile of DCLK1-IN-1 across the kinome not fully established"]},{"year":2022,"claim":"Identification of XRCC5/Ku80 as a direct DCLK1 phosphorylation target that transcriptionally activates COX-2 provided a molecular mechanism linking DCLK1 kinase activity to PGE₂-driven pro-inflammatory tumor microenvironment remodeling in CRC.","evidence":"Proteomics-based partner identification; Co-IP; in vitro kinase assay; COX-2 reporter; CRC mouse models","pmids":["35910805"],"confidence":"High","gaps":["Specific phosphorylation site(s) on XRCC5 not mapped","Relationship to XRCC5's known DNA repair function not explored"]},{"year":2022,"claim":"DCLK1 was shown to drive immune evasion by upregulating CXCL1, which recruits MDSCs via CXCR2 and suppresses CD8⁺ T cell infiltration; CXCL1 overexpression rescued tumor growth in DCLK1-KO cells, establishing a specific immune-evasion axis.","evidence":"CRISPR KO tumor transplantation in immune-competent mice; flow cytometry; MDSC–T cell co-culture; CXCL1 rescue","pmids":["36309200"],"confidence":"High","gaps":["Mechanism by which DCLK1 upregulates CXCL1 (kinase-dependent or not) undefined","Whether DCLK1-mediated immune evasion operates in non-CRC cancers not tested"]},{"year":2023,"claim":"Direct phosphorylation of IKKβ at S177/181 by DCLK1 in macrophages established DCLK1 as a bona fide upstream activator of canonical NF-κB signaling; macrophage-specific DCLK1 deletion attenuated atherosclerosis, defining a cell-type-specific inflammatory kinase function outside epithelial tissues.","evidence":"Co-IP/LC-MS/MS; in vitro phosphorylation; macrophage-specific KO in ApoE⁻/⁻ mice; RNA-seq","pmids":["36896602"],"confidence":"High","gaps":["Whether DCLK1 phosphorylates IKKβ in epithelial cells not tested","Upstream signal activating DCLK1 in macrophages not identified"]},{"year":2023,"claim":"Extension to obesity-induced cardiomyopathy showed macrophage DCLK1 mediates RIP2/TAK1 phosphorylation upon palmitate challenge, linking DCLK1 to metabolic inflammation beyond atherosclerosis and demonstrating that cardiomyocyte DCLK1 is dispensable for this phenotype.","evidence":"Macrophage-specific and cardiomyocyte-specific DCLK1 KO mice on HFD; immunoblot for RIP2/TAK1 phosphorylation; RNA-seq","pmids":["37443105"],"confidence":"High","gaps":["Whether DCLK1 directly phosphorylates RIP2 and/or TAK1 not demonstrated by in vitro kinase assay","Generalizability to other metabolic inflammatory conditions unknown"]},{"year":null,"claim":"How DCLK1's kinase versus MAP activities are coordinately regulated in vivo, and whether Ca²⁺/HPCAL1 activation operates in non-neuronal tissues (e.g., tuft cells, macrophages), remain central unresolved questions.","evidence":"","pmids":[],"confidence":"Low","gaps":["No in vivo demonstration of HPCAL1-dependent DCLK1 activation in any tissue","Full substrate repertoire undefined—most substrates identified in single studies","How isoform-specific expression (DCLK1-L vs. DCLK1-S) differentially engages MAP and kinase functions in normal versus cancer contexts is mechanistically unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,7,12,14,15,16,19]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,6,13]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0,6]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[14,16]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[4,6,7]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[8,16,17,18,19]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[16,17,23,24]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[2,3,5,8,15,23,25]}],"complexes":[],"partners":["MAP7D1","XRCC5","IKBKB","CCAR1","HPCAL1","ATM","KRAS","KIF1A"],"other_free_text":[]},"mechanistic_narrative":"DCLK1 is a bifunctional protein that couples microtubule regulation with serine/threonine kinase signaling across neuronal development, epithelial homeostasis, and inflammatory responses. Its N-terminal doublecortin-like domain directly polymerizes and bundles microtubules independently of kinase activity, labels dendritic microtubules to guide KIF1-dependent vesicle trafficking, and is required for dendrite development [PMID:11124993, PMID:26758546]. The C-terminal kinase domain is held in autoinhibition by an autoinhibitory domain that competitively blocks the ATP-binding site until Ca²⁺-bound HPCAL1 releases it; once active, DCLK1 phosphorylates MAP7D1 (promoting axon elongation), IKKβ S177/181 (activating NF-κB-driven inflammation and atherosclerosis), XRCC5/Ku80 (activating COX-2/PGE₂), and CCAR1 S343 (stabilizing β-catenin signaling and cancer stemness) [PMID:34977835, PMID:27503845, PMID:36896602, PMID:35910805, PMID:35522902]. In cancer, DCLK1 sustains EMT and immune evasion by repressing tumor-suppressor miRNAs (let-7a, miR-200, miR-145), upregulating CXCL1-mediated MDSC recruitment, and is driven by a cancer-specific short isoform transcribed from an alternative β-promoter activated by NF-κBp65 [PMID:19445940, PMID:24040120, PMID:36309200, PMID:26447334]."},"prefetch_data":{"uniprot":{"accession":"O15075","full_name":"Serine/threonine-protein kinase DCLK1","aliases":["Doublecortin domain-containing protein 3A","Doublecortin-like and CAM kinase-like 1","Doublecortin-like kinase 1"],"length_aa":740,"mass_kda":82.2,"function":"Probable kinase that may be involved in a calcium-signaling pathway controlling neuronal migration in the developing brain. 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in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34336664","citation_count":20,"is_preprint":false},{"pmid":"34610960","id":"PMC_34610960","title":"DCLK1-Short Splice Variant Promotes Esophageal Squamous Cell Carcinoma Progression via the MAPK/ERK/MMP2 Pathway.","date":"2021","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/34610960","citation_count":19,"is_preprint":false},{"pmid":"32530623","id":"PMC_32530623","title":"Synthesis and Structure-Activity Relationships of DCLK1 Kinase Inhibitors Based on a 5,11-Dihydro-6H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6-one Scaffold.","date":"2020","source":"Journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32530623","citation_count":19,"is_preprint":false},{"pmid":"27900578","id":"PMC_27900578","title":"Potential Mechanism of Neurite Outgrowth Enhanced by Electrical Stimulation: Involvement of MicroRNA-363-5p Targeting DCLK1 Expression in Rat.","date":"2016","source":"Neurochemical 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Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/35404759","citation_count":18,"is_preprint":false},{"pmid":"36309200","id":"PMC_36309200","title":"DCLK1 Suppresses Tumor-Specific Cytotoxic T Lymphocyte Function Through Recruitment of MDSCs via the CXCL1-CXCR2 Axis.","date":"2022","source":"Cellular and molecular gastroenterology and hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/36309200","citation_count":18,"is_preprint":false},{"pmid":"32755567","id":"PMC_32755567","title":"Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing.","date":"2020","source":"Cell chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/32755567","citation_count":17,"is_preprint":false},{"pmid":"34733368","id":"PMC_34733368","title":"DCLK1 and its interaction partners: An effective therapeutic target for colorectal cancer.","date":"2021","source":"Oncology 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microtubule polymerization assay with purified DCAMKL1; transfection/overexpression with time-lapse imaging; in vitro kinase assay; kinase-dead mutagenesis\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted in vitro with purified protein, mutagenesis, and live imaging; single rigorous paper with multiple orthogonal methods\",\n      \"pmids\": [\"11124993\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Two short splice variants of DCLK (DCLK-short-A and -B) both phosphorylate autocamtide and syntide (CaMK-specific substrates); removal of the distinct C-terminal ends causes a ~10-fold increase in kinase activity, indicating the C-termini function as autoinhibitory domains.\",\n      \"method\": \"In vitro kinase assay with CaMK substrates; truncation mutagenesis of C-terminal domains\",\n      \"journal\": \"Brain research. Molecular brain research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro kinase assay with mutagenesis demonstrating autoinhibitory mechanism\",\n      \"pmids\": [\"14741399\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"siRNA-mediated knockdown of DCAMKL-1 in colorectal cancer cells and xenografts results in tumor growth arrest, upregulation of pri-let-7a miRNA, decreased luciferase activity from a let-7a reporter, and decreased c-Myc expression, establishing DCAMKL-1 as a negative regulator of let-7a miRNA biogenesis.\",\n      \"method\": \"siRNA knockdown in HCT116/SW480 cells; xenograft model; luciferase reporter assay for let-7a; FACS-sorted DCAMKL-1+ cells analyzed for pri-let-7a\",\n      \"journal\": \"Gastroenterology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (KD, xenograft, reporter assay, FACS) in a single study; foundational mechanism paper\",\n      \"pmids\": [\"19445940\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"siRNA knockdown of DCAMKL-1 in human pancreatic cancer cells induces miR-200a (an EMT inhibitor), downregulates ZEB1, ZEB2, Snail, Slug, Twist, and reduces c-Myc and KRAS through a let-7a-dependent mechanism, and reduces Notch-1 through a miR-144-dependent mechanism.\",\n      \"method\": \"siRNA knockdown; miRNA qRT-PCR; immunoblot; colocalization IHC in mouse model\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods, in vitro and in vivo; replicated across labs\",\n      \"pmids\": [\"21285251\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DCAMKL1 represses osteoblast differentiation by antagonizing Runx2 (the master osteoblast transcription factor); Dcamkl1-null mice display elevated bone mass secondary to increased bone formation, and the cleidocranial dysplasia phenotype of Runx2+/- mice is reversed by introduction of a Dcamkl1-null allele.\",\n      \"method\": \"shRNA forward genetic screen; targeted disruption of Dcamkl1 (knockout mouse); epistasis with Runx2+/- mice; molecular experiments\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis in vivo combined with KO phenotype and molecular validation\",\n      \"pmids\": [\"23918955\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DCLK1 knockdown in pancreatic cancer xenografts upregulates miR-145, leading to decreased OCT4, SOX2, NANOG, KLF4, KRAS, and RREB1; increases let-7a, decreasing LIN28B; and increases miR-200, decreasing VEGFR1, VEGFR2, and EMT transcription factors ZEB1, ZEB2, SNAIL, SLUG. Luciferase reporter assays confirmed post-transcriptional regulation.\",\n      \"method\": \"PLGA-nanoparticle siRNA knockdown in xenografts; miRNA/mRNA qRT-PCR; luciferase reporter assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo xenograft plus luciferase reporter confirmation; multiple independent targets validated\",\n      \"pmids\": [\"24040120\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"DCLK1 labels a subset of dendritic microtubules and is required for KIF1 (kinesin-3)-dependent dense-core vesicle trafficking into dendrites and for dendrite development in hippocampal neurons; systematic kinesin screen identified DCLK1-labeled microtubules as a dendritic transport cue.\",\n      \"method\": \"Systematic screen of 45 kinesin family members; live-cell imaging; KD/KO in hippocampal neurons; DCV trafficking assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — systematic screen plus loss-of-function with defined trafficking phenotype; replicated across conditions\",\n      \"pmids\": [\"26758546\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"DCLK1 phosphorylates MAP7D1 at Serine 315 to promote axon elongation in cortical neurons; knockdown of MAP7D1 impairs callosal axon elongation but not radial migration, and a phosphomimetic MAP7D1 S315E mutant rescues axon elongation defects in Dclk1 knockdown neurons.\",\n      \"method\": \"Proteomic identification of substrate; in vitro kinase assay; shRNA knockdown in cortical neurons; rescue with phosphomimetic mutant (S315E)\",\n      \"journal\": \"Developmental neurobiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — kinase substrate identified by proteomics, validated by in vitro assay and phosphomimetic rescue\",\n      \"pmids\": [\"27503845\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"DCLK1 induces NF-κBp65 expression through the PI3K/Akt/Sp1 axis and activates NF-κBp65 through PI3K/Akt/IκBα during EMT in colorectal cancer cells; silencing DCLK1 inhibits CRC invasion and metastasis in vivo.\",\n      \"method\": \"siRNA knockdown; immunoblot; pathway inhibitor experiments; in vivo metastasis model\",\n      \"journal\": \"International journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple pathway methods but single lab\",\n      \"pmids\": [\"29277893\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Dclk1 expression in intestinal tuft cells is required for inflammation-induced Cox2 expression and prostaglandin E2 (PGE2) production; PGE2 rescues proliferative defects in Dclk1-deficient colonic organoids, linking Dclk1 to epithelial repair via a PGE2-dependent paracrine mechanism.\",\n      \"method\": \"Villin-Cre;Dclk1flox/flox (intestinal epithelial knockout mice); colonic organoid culture; PGE2 rescue experiments; qPCR and immunostaining\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO with defined molecular mechanism and organoid rescue; multiple orthogonal methods\",\n      \"pmids\": [\"30478383\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"KDM3A (histone demethylase that removes H3K9me1/2) binds to the DCLK1 promoter and positively regulates DCLK1 expression in pancreatic cancer; knockdown of KDM3A reduces DCLK1 levels and impairs invasion, migration, and spheroid formation.\",\n      \"method\": \"ChIP assay for KDM3A binding at DCLK1 promoter; KDM3A shRNA knockdown; KDM3A overexpression; RNA-seq; orthotopic tumor model\",\n      \"journal\": \"Gastroenterology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — ChIP demonstrates direct promoter binding; multiple orthogonal methods in vitro and in vivo\",\n      \"pmids\": [\"31442435\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Dclk1 interaction with ATM is critical for ATM activation and DNA damage response following radiation injury; Dclk1 deletion reduces ATM-mediated pro-survival signaling and impairs intestinal crypt restitution.\",\n      \"method\": \"VillinCre;Dclk1flox/flox mice; total body irradiation; co-immunoprecipitation (DCLK1–ATM interaction); analysis of ATM phosphorylation and COX2 activation\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — genetic KO with Co-IP, but limited biochemical follow-up on mechanism; single lab\",\n      \"pmids\": [\"27876863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The DCLK1 C-terminal autoinhibitory domain (AID) blocks the ATP-binding site competitively; neuronal calcium sensor HPCAL1 binds directly to the AID in a Ca2+-dependent manner, releasing autoinhibition and activating kinase activity; cancer-associated mutations in the AID disrupt autoinhibition to upregulate kinase activity.\",\n      \"method\": \"Crystal structure of DCLK1 kinase in autoinhibited state; direct binding assay (HPCAL1–AID); Ca2+-dependence assays; biochemical analysis of AID mutations\",\n      \"journal\": \"Innovation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure plus biochemical reconstitution of autoinhibition/activation mechanism; mutagenesis of cancer-associated variants\",\n      \"pmids\": [\"34977835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Crystal structures of DCLK1 kinase domain in complex with inhibitor DCLK1-IN-1 reveal that the compound induces a drastic conformational change of the ATP binding site; DCLK1-IN-1 binds DCLK1 long isoforms but does not prevent DCLK1's MAP (microtubule-associated protein) function, separating kinase and MAP activities.\",\n      \"method\": \"X-ray crystallography of DCLK1 kinase domain–inhibitor complex; structure-activity relationship analysis; MAP function assay\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple crystal structures plus functional separation of kinase vs. MAP activity\",\n      \"pmids\": [\"34545159\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"DCLK1 kinase activity is required for DCLK1-dependent cancer cell migration and growth; chemical toolkit (DCLK1-IN-1, resistance mutation G532A, kinase-dead D511N/D533N) established DCLK1 kinase activity regulates RNA processing pathways; CDK11 was identified as a potential DCLK1 substrate by phosphoproteomics.\",\n      \"method\": \"Selective kinase inhibitor (DCLK1-IN-1); resistance mutation G532A; kinase-dead mutants (D511N, D533N); phosphoproteomics; engineered DCLK1-dependent cancer cell line\",\n      \"journal\": \"Cell chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — chemical-genetic toolkit with phosphoproteomics; multiple orthogonal approaches in single paper\",\n      \"pmids\": [\"32755567\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DCLK1 binds and phosphorylates XRCC5 (Ku80); phosphorylated XRCC5 transcriptionally activates COX-2, enhancing prostaglandin E2 production and generating a pro-inflammatory tumor microenvironment that drives aggressive colorectal cancer behavior.\",\n      \"method\": \"Comprehensive proteomics/genomics to identify DCLK1 binding partners; Co-IP (DCLK1–XRCC5); in vitro kinase assay (DCLK1 phosphorylates XRCC5); COX-2 transcriptional reporter; CRC mouse models\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — Co-IP, in vitro kinase assay, and downstream transcriptional/functional validation in vitro and in vivo\",\n      \"pmids\": [\"35910805\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Macrophage DCLK1 directly binds IKKβ and phosphorylates IKKβ at S177/181, facilitating NF-κB activation and inflammatory gene expression; macrophage-specific DCLK1 deletion attenuates atherosclerosis and reduces inflammation in ApoE-/- mice.\",\n      \"method\": \"Co-immunoprecipitation; LC-MS/MS identification of IKKβ as DCLK1 binding partner; in vitro phosphorylation assay (DCLK1 phosphorylates IKKβ S177/181); macrophage-specific knockout; RNA-seq; pharmacological inhibition\",\n      \"journal\": \"EMBO molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — Co-IP/MS discovery of IKKβ, in vitro phosphorylation assay, and specific KO with in vivo phenotype; multiple orthogonal methods\",\n      \"pmids\": [\"36896602\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Macrophage DCLK1 mediates RIP2/TAK1 phosphorylation upon high-fat diet/palmitate challenge, leading to inflammatory cytokine release that promotes cardiac hypertrophy and fibrosis; macrophage-specific (not cardiomyocyte-specific) DCLK1 knockout prevents obesity-induced cardiomyopathy.\",\n      \"method\": \"Macrophage-specific and cardiomyocyte-specific DCLK1 KO mice; high-fat diet model; RNA sequencing; immunoblot for RIP2/TAK1 phosphorylation; pharmacological inhibition\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — cell-type-specific KO with mechanistic pathway (RIP2/TAK1) and RNA-seq; multiple methods\",\n      \"pmids\": [\"37443105\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Overexpression of DCLK1-AL (isoform 2/alpha-long) in pancreatic cancer cells increases KRAS activation (demonstrated by RAS pull-down assay) and co-immunoprecipitation confirms DCLK1–KRAS interaction; DCLK1-AL overexpression drives increased invasion and drug resistance downstream of KRAS/PI3K/AKT/mTOR.\",\n      \"method\": \"Lentiviral stable overexpression; RAS pull-down assay; co-immunoprecipitation; Matrigel invasion assay; drug resistance assays; KPC mouse model\",\n      \"journal\": \"Journal of oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — RAS pull-down and Co-IP with functional follow-up; single lab\",\n      \"pmids\": [\"31467540\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"DCLK1 interacts with CCAR1 through its C-terminal domain and phosphorylates CCAR1 at Ser343, stabilizing CCAR1; DCLK1-mediated CCAR1 stabilization positively regulates β-catenin signaling, maintaining cancer stemness and 5-FU resistance in colorectal cancer.\",\n      \"method\": \"Co-IP (DCLK1–CCAR1); in vitro phosphorylation assay (Ser343 site identified); domain mapping; β-catenin pathway inhibitor rescue; in vitro and in vivo CRC models\",\n      \"journal\": \"Clinical and translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP and phosphorylation site identification with functional validation; single lab\",\n      \"pmids\": [\"35522902\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Human colorectal cancers predominantly express a short DCLK1 isoform (DCLK1-S) from an alternate β-promoter in intron V, while normal colons express DCLK1-L from the 5′(α)-promoter; activated NF-κBp65 drives the β-promoter, whereas β-catenin/TCF4/LEF activates the α-promoter in cancer cells.\",\n      \"method\": \"In silico analysis; molecular biology (promoter cloning, luciferase reporter assay for promoter activity); qRT-PCR in patient cohort\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — promoter reporter assays establish transcription factor binding; single lab\",\n      \"pmids\": [\"26447334\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DCLK1 influences small extracellular vesicle (sEV/exosome) biogenesis in a kinase-dependent manner; DCLK1 overexpression promotes sEV-mediated cell migration, and DCLK1-IN-1 (kinase inhibitor) reverses increases in sEV size/concentration and alters cargo selection of proteins involved in EV biogenesis (KTN1, CHMP1A, MYO1G) and migration/adhesion.\",\n      \"method\": \"DCLK1 overexpression in GC cells; sEV isolation; quantitative proteome analysis; DCLK1-IN-1 kinase inhibitor; migration assay\",\n      \"journal\": \"Proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — quantitative proteomics and pharmacological inhibitor demonstrate kinase-dependent sEV cargo regulation; single lab\",\n      \"pmids\": [\"33991177\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"miR-195 directly interacts with the 3′-UTR of Dclk1 mRNA to inhibit DCLK1 translation; RNA-binding protein HuR competes with miR-195 for Dclk1 mRNA binding and increases DCLK1 expression; transgenic miR-195 overexpression reduces intestinal tuft cell numbers via DCLK1 suppression.\",\n      \"method\": \"miR-195 transgenic mice; intestinal organoids; RNA pulldown/RIP; luciferase 3′-UTR reporter; competition assay between HuR and miR-195\",\n      \"journal\": \"American journal of physiology. Cell physiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct 3′-UTR reporter assay, RIP, in vivo transgenic mouse; multiple orthogonal methods\",\n      \"pmids\": [\"33788631\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DCLK1 promotes CRC immune evasion by upregulating CXCL1, which recruits MDSCs via CXCR2; DCLK1-knockout tumors fail to establish in immune-competent mice due to increased CD8+ T cell infiltration and reduced MDSCs; CXCL1 overexpression rescues DCLK1-/- tumor growth.\",\n      \"method\": \"CRISPR-Cas9 DCLK1 knockout tumor cells; subcutaneous and orthotopic transplantation models; flow cytometry of tumor-infiltrating immune cells; MDSC–T cell co-culture; CXCL1 rescue overexpression; RNA sequencing\",\n      \"journal\": \"Cellular and molecular gastroenterology and hepatology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — CRISPR KO with in vivo rescue and mechanistic pathway validation; multiple orthogonal methods\",\n      \"pmids\": [\"36309200\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DCLK1-isoform2 overexpression in pancreatic cancer cells drives polarization of macrophages from M1 toward immunosuppressive M2 phenotype via secreted chemokines/cytokines; M2-macrophages educated by DCLK1-isoform2 enhance PDAC cell migration, invasion, and self-renewal; DCLK1-isoform2-educated M2 macrophages inhibit CD8+ T-cell proliferation and granzyme-B activation.\",\n      \"method\": \"Stable DCLK1-isoform2 overexpression; macrophage co-culture/polarization assays; organoid-immune cell co-culture; CD8+ T cell activation assays; autochthonous KPCY mouse model\",\n      \"journal\": \"Molecular cancer therapeutics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro and in vivo co-culture assays; single lab\",\n      \"pmids\": [\"32371580\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DCLK1-S short splice variant promotes ESCC progression via MAPK/ERK signaling leading to MMP2 upregulation and EMT activation; ERK1/2 inhibitor SCH772984 attenuates the proliferative and migratory phenotype induced by DCLK1-S.\",\n      \"method\": \"CRISPR/Cas9 DCLK1 total KO with DCLK1-S rescue; RNA-sequencing; KEGG pathway analysis; in vitro migration/invasion assays; in vivo tumor and metastasis models; ERK inhibitor rescue\",\n      \"journal\": \"Molecular cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — CRISPR KO with isoform-specific rescue and pathway inhibitor; single lab\",\n      \"pmids\": [\"34610960\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DCLK1 is a bifunctional protein with an N-terminal doublecortin-like microtubule-binding domain (which promotes tubulin polymerization and dendritic cargo transport via KIF1 kinesins) and a C-terminal serine/threonine kinase domain that is held in autoinhibition by its AID until released by Ca²⁺-bound HPCAL1; its kinase activity phosphorylates substrates including MAP7D1 (promoting axon elongation), IKKβ S177/181 (activating NF-κB inflammatory signaling), XRCC5/Ku80 (activating COX-2/PGE2), and CCAR1 S343 (stabilizing β-catenin signaling), while it also functions as a negative regulator of tumor-suppressor miRNAs (let-7a, miR-200a, miR-145) to sustain EMT and cancer stemness, and is epigenetically regulated by KDM3A-mediated H3K9 demethylation and by alternative promoter usage generating distinct long (neuronal/normal epithelial) and short (cancer-associated) isoforms.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"DCLK1 is a bifunctional protein that couples microtubule regulation with serine/threonine kinase signaling across neuronal development, epithelial homeostasis, and inflammatory responses. Its N-terminal doublecortin-like domain directly polymerizes and bundles microtubules independently of kinase activity, labels dendritic microtubules to guide KIF1-dependent vesicle trafficking, and is required for dendrite development [PMID:11124993, PMID:26758546]. The C-terminal kinase domain is held in autoinhibition by an autoinhibitory domain that competitively blocks the ATP-binding site until Ca²⁺-bound HPCAL1 releases it; once active, DCLK1 phosphorylates MAP7D1 (promoting axon elongation), IKKβ S177/181 (activating NF-κB-driven inflammation and atherosclerosis), XRCC5/Ku80 (activating COX-2/PGE₂), and CCAR1 S343 (stabilizing β-catenin signaling and cancer stemness) [PMID:34977835, PMID:27503845, PMID:36896602, PMID:35910805, PMID:35522902]. In cancer, DCLK1 sustains EMT and immune evasion by repressing tumor-suppressor miRNAs (let-7a, miR-200, miR-145), upregulating CXCL1-mediated MDSC recruitment, and is driven by a cancer-specific short isoform transcribed from an alternative β-promoter activated by NF-κBp65 [PMID:19445940, PMID:24040120, PMID:36309200, PMID:26447334].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Establishing DCLK1 as a bifunctional protein resolved whether the doublecortin-like domain and kinase domain operate independently: the microtubule polymerization/bundling activity was shown to be kinase-independent, defining DCLK1 as both a MAP and a kinase.\",\n      \"evidence\": \"In vitro tubulin polymerization with purified DCAMKL1, kinase-dead mutagenesis, and live-cell imaging in cell lines\",\n      \"pmids\": [\"11124993\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of physiological kinase substrates unknown\", \"Regulation of kinase activation not addressed\", \"In vivo function not tested\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Discovery that the C-terminal domain functions as an autoinhibitory element (removal causing ~10-fold kinase activation) established a regulatory paradigm for DCLK1 kinase control, but the structural basis and activating signal remained unknown.\",\n      \"evidence\": \"In vitro kinase assay with CaMK substrates and truncation mutagenesis of short DCLK splice variants\",\n      \"pmids\": [\"14741399\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural mechanism of autoinhibition unresolved\", \"Physiological signal that relieves autoinhibition unknown\", \"Whether autoinhibition operates in vivo not demonstrated\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Linking DCLK1 to tumor-suppressor miRNA regulation answered how a kinase/MAP protein controls cancer stemness: DCLK1 negatively regulates let-7a biogenesis, and its knockdown induces let-7a and suppresses c-Myc, establishing a non-canonical oncogenic function.\",\n      \"evidence\": \"siRNA knockdown in CRC cell lines and xenografts; let-7a luciferase reporter; FACS sorting of DCLK1⁺ cells\",\n      \"pmids\": [\"19445940\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which DCLK1 represses let-7a biogenesis (direct or indirect) unresolved\", \"Whether kinase activity is required for miRNA regulation unknown\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Extension to miR-200a, miR-144, and EMT transcription factor networks broadened DCLK1's oncogenic role beyond let-7a, demonstrating that DCLK1 controls multiple miRNA axes converging on EMT, KRAS, and Notch signaling in pancreatic cancer.\",\n      \"evidence\": \"siRNA knockdown in pancreatic cancer cells; miRNA qRT-PCR; immunoblot; IHC in mouse model\",\n      \"pmids\": [\"21285251\", \"24040120\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct versus indirect mechanism of miRNA repression still unclear\", \"No kinase-dead rescue to test kinase dependence\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Genetic epistasis in mice revealed an unexpected skeletal function: Dclk1 represses osteoblast differentiation by antagonizing Runx2, and Dclk1 loss rescues cleidocranial dysplasia in Runx2⁺/⁻ mice, establishing DCLK1 as a physiological brake on bone formation.\",\n      \"evidence\": \"Dclk1 knockout mice; genetic epistasis with Runx2⁺/⁻; shRNA screen; bone formation analysis\",\n      \"pmids\": [\"23918955\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism linking DCLK1 to Runx2 inhibition (direct phosphorylation vs. intermediate) not identified\", \"Cell-type specificity of effect in bone not resolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identification of alternative promoter usage (α-promoter for long isoform in normal epithelium; β-promoter for short isoform in cancer driven by NF-κBp65) resolved the paradox of DCLK1 as both a normal cell marker and cancer protein, attributing oncogenic functions to the short isoform.\",\n      \"evidence\": \"Promoter cloning and luciferase reporter assays; qRT-PCR across patient cohort\",\n      \"pmids\": [\"26447334\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional differences between long and short isoforms not fully dissected biochemically\", \"Promoter switch mechanism in tumorigenesis not defined\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"A systematic kinesin screen established that DCLK1-decorated microtubules serve as a dendritic transport code recognized by KIF1 motors, explaining how DCLK1 directs dense-core vesicle trafficking into dendrites and supports dendrite morphogenesis.\",\n      \"evidence\": \"Screen of 45 kinesins; live-cell DCV trafficking assay; KD/KO in hippocampal neurons\",\n      \"pmids\": [\"26758546\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How DCLK1 labeling is restricted to dendritic microtubules unknown\", \"Whether kinase activity modulates the MAP-based trafficking role not tested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identification of MAP7D1 as a direct DCLK1 kinase substrate (phosphorylated at S315) provided the first defined neuronal substrate linking DCLK1 kinase activity specifically to axon elongation rather than radial migration.\",\n      \"evidence\": \"Phosphoproteomic substrate identification; in vitro kinase assay; phosphomimetic S315E rescue of Dclk1 KD axon defect in cortical neurons\",\n      \"pmids\": [\"27503845\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Additional neuronal substrates likely exist but are unidentified\", \"Whether MAP7D1 phosphorylation affects microtubule dynamics directly not tested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Intestinal epithelial Dclk1 knockout revealed that tuft-cell DCLK1 is required for injury-induced COX-2 expression and PGE₂ production, establishing a paracrine epithelial repair mechanism where PGE₂ rescues proliferative defects in Dclk1-deficient organoids.\",\n      \"evidence\": \"Villin-Cre;Dclk1-flox intestinal KO mice; colonic organoid culture with PGE₂ rescue\",\n      \"pmids\": [\"30478383\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether DCLK1 kinase activity is required for COX-2 induction or whether the MAP domain contributes not distinguished\", \"Upstream signal activating DCLK1 in tuft cells upon injury unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Epigenetic control of DCLK1 was established when KDM3A was shown to bind the DCLK1 promoter and demethylate H3K9me1/2, directly activating DCLK1 transcription in pancreatic cancer and linking chromatin remodeling to DCLK1-driven stemness and invasion.\",\n      \"evidence\": \"ChIP for KDM3A at DCLK1 promoter; KDM3A shRNA/overexpression; RNA-seq; orthotopic tumor model\",\n      \"pmids\": [\"31442435\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other histone marks or chromatin remodelers regulate DCLK1 not explored\", \"Relationship between KDM3A regulation and isoform-specific promoter usage not addressed\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Development of DCLK1-IN-1 and a chemical-genetic toolkit (resistance mutation G532A, kinase-dead mutants) formally demonstrated that kinase activity drives cancer cell migration and growth, and phosphoproteomics revealed regulation of RNA processing pathways and CDK11 as a candidate substrate.\",\n      \"evidence\": \"Selective inhibitor DCLK1-IN-1; engineered DCLK1-dependent cells; resistance mutations; phosphoproteomics\",\n      \"pmids\": [\"32755567\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"CDK11 as substrate not validated by in vitro phosphorylation\", \"RNA processing pathway mechanism downstream of DCLK1 kinase not elucidated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Crystal structure of the autoinhibited DCLK1 kinase domain revealed that the AID competitively blocks the ATP-binding site; Ca²⁺-dependent HPCAL1 binding to the AID releases autoinhibition, finally identifying the physiological activation signal for DCLK1 kinase and explaining how cancer-associated AID mutations constitutively activate kinase activity.\",\n      \"evidence\": \"X-ray crystallography of autoinhibited kinase; HPCAL1–AID direct binding assay; Ca²⁺ dependence; cancer mutation analysis\",\n      \"pmids\": [\"34977835\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether HPCAL1 is the sole activator in all tissue contexts unknown\", \"Structural basis of HPCAL1–AID interaction not resolved at atomic level\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Co-crystal structures of DCLK1 with DCLK1-IN-1 showed the inhibitor induces a drastic ATP-site conformational change without disrupting MAP function, formally separating kinase and MAP activities at the structural level.\",\n      \"evidence\": \"X-ray crystallography of DCLK1–inhibitor complexes; MAP function assay under inhibitor treatment\",\n      \"pmids\": [\"34545159\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether kinase-independent MAP functions contribute to cancer phenotypes not resolved\", \"Selectivity profile of DCLK1-IN-1 across the kinome not fully established\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identification of XRCC5/Ku80 as a direct DCLK1 phosphorylation target that transcriptionally activates COX-2 provided a molecular mechanism linking DCLK1 kinase activity to PGE₂-driven pro-inflammatory tumor microenvironment remodeling in CRC.\",\n      \"evidence\": \"Proteomics-based partner identification; Co-IP; in vitro kinase assay; COX-2 reporter; CRC mouse models\",\n      \"pmids\": [\"35910805\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific phosphorylation site(s) on XRCC5 not mapped\", \"Relationship to XRCC5's known DNA repair function not explored\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"DCLK1 was shown to drive immune evasion by upregulating CXCL1, which recruits MDSCs via CXCR2 and suppresses CD8⁺ T cell infiltration; CXCL1 overexpression rescued tumor growth in DCLK1-KO cells, establishing a specific immune-evasion axis.\",\n      \"evidence\": \"CRISPR KO tumor transplantation in immune-competent mice; flow cytometry; MDSC–T cell co-culture; CXCL1 rescue\",\n      \"pmids\": [\"36309200\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which DCLK1 upregulates CXCL1 (kinase-dependent or not) undefined\", \"Whether DCLK1-mediated immune evasion operates in non-CRC cancers not tested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Direct phosphorylation of IKKβ at S177/181 by DCLK1 in macrophages established DCLK1 as a bona fide upstream activator of canonical NF-κB signaling; macrophage-specific DCLK1 deletion attenuated atherosclerosis, defining a cell-type-specific inflammatory kinase function outside epithelial tissues.\",\n      \"evidence\": \"Co-IP/LC-MS/MS; in vitro phosphorylation; macrophage-specific KO in ApoE⁻/⁻ mice; RNA-seq\",\n      \"pmids\": [\"36896602\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether DCLK1 phosphorylates IKKβ in epithelial cells not tested\", \"Upstream signal activating DCLK1 in macrophages not identified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Extension to obesity-induced cardiomyopathy showed macrophage DCLK1 mediates RIP2/TAK1 phosphorylation upon palmitate challenge, linking DCLK1 to metabolic inflammation beyond atherosclerosis and demonstrating that cardiomyocyte DCLK1 is dispensable for this phenotype.\",\n      \"evidence\": \"Macrophage-specific and cardiomyocyte-specific DCLK1 KO mice on HFD; immunoblot for RIP2/TAK1 phosphorylation; RNA-seq\",\n      \"pmids\": [\"37443105\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether DCLK1 directly phosphorylates RIP2 and/or TAK1 not demonstrated by in vitro kinase assay\", \"Generalizability to other metabolic inflammatory conditions unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DCLK1's kinase versus MAP activities are coordinately regulated in vivo, and whether Ca²⁺/HPCAL1 activation operates in non-neuronal tissues (e.g., tuft cells, macrophages), remain central unresolved questions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No in vivo demonstration of HPCAL1-dependent DCLK1 activation in any tissue\", \"Full substrate repertoire undefined—most substrates identified in single studies\", \"How isoform-specific expression (DCLK1-L vs. DCLK1-S) differentially engages MAP and kinase functions in normal versus cancer contexts is mechanistically unresolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 7, 12, 14, 15, 16, 19]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 6, 13]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [14, 16]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [4, 6, 7]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [8, 16, 17, 18, 19]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [16, 17, 23, 24]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [2, 3, 5, 8, 15, 23, 25]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"MAP7D1\",\n      \"XRCC5\",\n      \"IKBKB\",\n      \"CCAR1\",\n      \"HPCAL1\",\n      \"ATM\",\n      \"KRAS\",\n      \"KIF1A\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}