Targeted Deep Sequencing of Mycosis Fungoides Reveals Intracellular Signaling Pathways Associated with Aggressiveness and Large Cell Transformation

SIMPLE SUMMARY: In order to decipher the molecular mechanisms of large cell transformation (LCT) in mycosis fungoides (MF), we screened 51 longitudinally obtained skin samples of mycosis fungoides patients (n = 27) with versus without large-cell transformation by the means of targeted deep sequencing in close clinicopathological correlation. The analysis of longitudinally obtained tissue revealed a dynamic mutational profile in the context of an evolutionary selection processes with the example of PLCG1 alterations. In patients with an aggressive clinical course, we detected high mutational heterogeneity revealing the highest frequency of mutations in patients with LCT. The affected genes included members of the JAK/STAT signaling pathway and epigenetic modifiers. The key findings of our analysis included recurrent activating RAS mutations (KRAS and NRAS) being exclusively present in LCT MF; what is of note is that these molecular aberrations were already present in early stages; thus, RAS mutations in MF exhibit a prognostic marker for a higher risk of relapse and progression and restricted prognosis. As RAS mutated tumors are currently in the focus of novel targeted treatment options in several clinical trials, such personalized treatment modalities might offer novel therapeutic options for RAS mutated MF patients. ABSTRACT: Introduction: Large-cell transformation (LCT) of mycosis fungoides (MF) has been associated with a higher risk of relapse and progression and, consequently, restricted prognosis. Its molecular pathogenesis has not been elucidated yet. Materials and Methods: In order to address molecular mechanisms of LCT, we performed hybrid capture panel-based sequencing of skin biopsies from 10 patients suffering from MF with LCT versus 17 patients without LCT including follow-up biopsies during clinical course, respectively (51 samples in total). The analyzed patients were attributed to three different groups based on the presence of LCT and clinical behavior. Results: While indolent MF cases without LCT did not show pathogenic driver mutations, a high rate of oncogenic alterations was detected in patients with LCT and aggressive clinical courses. Various genes of different oncogenic signaling pathways, including the MAPK and JAK-STAT signaling pathways, as well as epigenetic modifiers were affected. A high inter-individual and distinctive intra-individual mutation diversity was observed. Oncogenic RAS mutations were exclusively detected in patients with LCT. Conclusion: Our data demonstrate that LCT transition of MF is associated with increased frequency of somatic mutations in cancer-associated genes. In particular, the activation of RAS signaling—together with epigenetic dysregulation—may crucially contribute to the molecular pathogenesis of the LCT phenotype, thus conveying its adverse clinical behavior.