A pan-cancer analysis of TLK1 and TLK2: genomic instability, immunomodulation, and therapeutic implications

Abstract Tousled-like kinases TLK1 and TLK2 are evolutionarily conserved serine/threonine kinases involved in the DNA damage response and cell cycle regulation; however, their pan-cancer molecular profiles and clinical relevance remain largely unexplored. By integrating multi-omics data from TCGA and GTEx across 33 cancer types, we demonstrate that TLK1 and TLK2 exhibit distinct expression patterns and are associated with patient prognosis in a cancer type-specific manner. Genetic alterations in TLK1 and TLK2 were frequently observed and significantly correlated with multiple markers of genomic instability, including tumor mutation burden, microsatellite instability, and homologous recombination deficiency. Functional experiments showed that knockdown of TLK1 or TLK2 in cancer cell lines markedly increased DNA damage, impaired cellular proliferation, and induced apoptosis, with TLK2 exhibiting a more prominent role in DNA repair processes. Furthermore, both kinases were negatively correlated with immune and stromal scores, and their expression levels were linked to specific immune cell subsets—positively with resting CD4 + T cells and macrophages, but negatively with CD8 + T cells and activated NK cells. Additional functional immune analyses revealed that TLK1/TLK2 expression correlated positively with immune exclusion signatures and MDSC infiltration, rather than with classical T-cell exhaustion markers. Multiplex immunohistochemistry in colorectal cancer tissues further resolved these associations into divergent phenotypes: TLK1-high tumors exhibited reduced T cell infiltration consistent with immune exclusion, whereas TLK2-high tumors showed Treg enrichment and CD39 upregulation indicative of an immunosuppressive microenvironment. Notably, TLK1 and TLK2 expression demonstrated predictive utility for responses to chemotherapy and immunotherapy across several malignancies. Our findings underscore the multifaceted roles of TLK1 and TLK2 in tumorigenesis and tumor immune modulation, supporting their potential as prognostic biomarkers and promising therapeutic targets in precision oncology.