Age-linked DNA methylation and gene expression patterns in parameningeal head and neck alveolar rhabdomyosarcoma reveal CDK9 as a promising therapeutic target

Background: Alveolar rhabdomyosarcoma (ARMS) primarily affects children in the first decade of life, but it can also occur during adolescence, typically with a more favorable prognosis. This study aimed to explore differences in DNA methylation (DNAm) and gene expression profiles that may account for the worse prognosis in younger patients; and to investigate possible new therapeutic targets. Methods: We conducted whole-genome DNAm and transcriptome analyses on 10 parameningeal head and neck ARMS patients, including 4 patients under 1 year old and 6 over 10 years old. Among the differentially expressed genes, we focused on actionable therapeutic targets and confirmed their protein expression levels by immunohistochemistry. We validated the biological relevance of molecules of interest through functional experiments on rhabdomyosarcoma cell lines. Results: DNAm profiles did not significantly differ across age groups, while gene expression was the primary driver of observed differences. Several enriched pathways characterized younger patients with respect to older ones, including FAS, Integrin, PI3 kinase, and p53 by glucose deprivation. Among actionable molecules, cyclin dependent kinase 9 (CDK9) emerged as a promising therapy target, highly expressed in younger patients. Of note, CDK9 inhibitors specifically inhibit cell growth in bi- and three-dimensional ARMS cellular models, both as a monotherapy and in combination with BRD4 inhibitors. Conclusion: Despite the small sample size, these findings suggest potential age-related molecular mechanisms and highlight candidate genes for further investigation as novel therapeutic targets. Notably, we identified CDK9 as a promising target, warranting further exploration in the context of ARMS treatment.