Branched evolution and genomic intratumor heterogeneity in the pathogenesis of cutaneous T-cell lymphoma

Abstract

Mycosis fungoides (MF) is a slowly progressive cutaneous T-cell lymphoma (CTCL) for which there is no cure. In the early plaque stage the disease is indolent, but development of tumors heralds an increased risk of metastasis and death. Previous research into the genomic landscape of CTCL revealed a complex pattern of >50 driver mutations implicated in more than a dozen of signaling pathways. However, the genomic mechanisms governing disease progression and treatment resistance remain unknown. Building on our previous discovery of the clonotypic heterogeneity of MF, we hypothesized that this lymphoma does not progress in a linear fashion as currently thought, but comprises heterogeneous mutational subclones. We sequenced exomes of 49 cases of MF and identified 28 previously unreported putative driver genes. MF exhibited extensive intratumoral heterogeneity (ITH) of a median of six subclones showing branched pattern of phylogenetic relationships. Stage progression was correlated with an increase in ITH and redistribution of mutations from the stem to the clades. The pattern of clonal driver mutations was highly variable with no consistent mutations between patients. A similar intratumoral heterogeneity was detected in leukemic CTCL (Sézary syndrome). Based on these findings we propose a model of the pathogenesis of MF comprising neutral, divergent evolution of cancer subclones and discuss how ITH impacts the efficacy of targeted drug therapies and immunotherapies of CTCL.

Independent evolution of cutaneous lymphoma subclones in different microenvironments of the skin

“…To further examine the phylogenetic relationships between the subclones in the epidermal and dermal compartments we adopted the previously described bioinformatic approach based on the analysis of the mutational pattern between cancer cells (17). We found evidence of subclonal heterogeneity in all samples confirming previous findings of ITH in MF (17).…”

“…Currently, data are too limited to be able to investigate the prognostic role of ITH in MF. Some indirect evidence, such as the correlation between the presence of Pautrier microabscesses with the risk of progression (35) and higher ITH in MF tumors as compared to early plaques (17) suggest that this indeed may be the case. One of the indications that ecological heterogeneity in MF may have functional significance is the non-overlapping pattern of driver mutations in epidermal and dermal neoplastic cells, which potentially would limit the efficacy of targeted therapies.…”

“…Solid lines symbolize the phylogenetic relationship between the generations of malignant cells and illustrate divergent, neutral evolution of the subclones. Based on data in this paper and our previous work (15)(16)(17)36 ).…”

“…The substantial clonotypic discordance between the epidermal and dermal compartments prompted a question regarding differences and similarities in their mutational evolution. In our previous work, we characterized 75 putative driver mutations involved in the pathogenesis and progression of MF (17). Similarities in the patterns of driver mutations between the epidermal and the dermal infiltrate would suggest parallel evolution in both compartments whereas lack of substantial overlap would indicate a neutral evolution.…”

“…To further examine the phylogenetic relationships between the subclones in the epidermal and dermal compartments we adopted the previously described bioinformatic approach based on the analysis of the mutational pattern between cancer cells (17). We found evidence of subclonal heterogeneity in all samples confirming previous findings of ITH in MF (17). A slightly higher number of subclones were found in epidermal (5-8 subclones) versus the dermal layers (4-5 subclones) ( Fig 3A ) reflecting the differences in clonotypic richness between those compartments ( Fig 3B ).…”