Pan-cancer analysis identified DOK3 as a novel biomarker for predicting prognosis and immunotherapy effectiveness

The DOK3 gene encodes an adaptor protein regulating immune receptor signaling and tumorigenesis, while its pan-cancer significance was poorly characterized. This research aimed to identify DOK3 as a predictive biomarker for predicting prognosis and immunotherapy outcomes in different malignancies. Transcriptomic (TCGA/GTEx), proteomic (CPTAC), and clinical data from 33 cancer types were integrated for comprehensive analysis. The followings were included: (1) evaluation of DOK3 expression in association with patient survival through Kaplan–Meier and Cox regression analyses; (2) assessment of genomic features, including tumor mutation burden (TMB), microsatellite instability (MSI), homologous recombination deficiency (HRD), and copy number variations (CNVs); (3) characterization of the tumor immune microenvironment using CIBERSORT, TIMER2.0, and ESTIMATE; (4) investigation of epigenetic regulation via promoter methylation and RNA modification-related genes; (5) analysis of drug sensitivity through CellMiner data and molecular docking techniques; (6) In addition, functional assays were performed in breast cancer cell lines, including DOK3 knockdown and treatment with epigallocatechin gallate (EGCG). DOK3 expression was upregulated in GBM and KIRC, while downregulated in BRCA and LIHC, exhibiting context-dependent prognostic implications—associated with poor survival in HNSC and SARC (HR > 1.5, p < 0.01), while favorable outcomes in KIRC and GBM. It demonstrated positive correlations with DNA repair genes (e.g., MLH1 and MSH2) and tumor stemness scores, while inversely related to immune infiltration (ESTIMATE, p < 0.001). Promoter hypermethylation of DOK3 was linked to the enhanced cytotoxic T lymphocyte activity (p < 0.05). Notably, DOK3 expression was correlated with M2 macrophage recruitment (R > 0.4, p < 0.001) and immunosuppressive checkpoint markers (CTLA4 and TGFB1). Drug screening prioritized epigallocatechin (binding energy: −9.1 kcal/mol) and homochlorcyclizine (− 8.7 kcal/mol) as potential DOK3 inhibitors. Experimentally, DOK3 silencing reduced tumor cell viability, and EGCG treatment significantly suppressed DOK3 expression, supporting its potential as a therapeutic target. DOK3 drives cancer progression via mechanisms, involving genomic instability and immune evasion, exhibiting dual prognostic roles depending on tumor context. Its immunosuppressive associations and druggable structure highlight DOK3 as a promising target for precision immunotherapy.