Demethylation and transcriptional activation of a TBC1D16 isoform promotes melanoma progression.

  • Major finding: Demethylation and transcriptional activation of a TBC1D16 isoform promotes melanoma progression.

  • Mechanism: The TBC1D16-47KD short isoform regulates EGFR activation by increasing RAB5C GTPase activity.

  • Impact: Epigenetic TBC1D16 reactivation predicts poor outcome and improved response to BRAF/MEK inhibition.

Although metastases account for 90% of cancer-associated deaths, little is known about the role of epigenetic changes in melanoma metastasis. Vizoso and colleagues screened pairs of melanoma, breast cancer, and colon cancer cell lines from matched primary tumor and metastases for genes with differential DNA methylation. This approach identified one gene, TBC1 domain family, member 16 (TBC1D16), which was hypermethylated and downregulated in primary tumor–derived cell lines, but unmethylated and upregulated in matched metastatic cell lines. This demethylation event specifically reactivated the expression of the two short TBC1D16 isoforms, including TBC1D16-47kDa (TBC1D16-47KD). TBC1D16-47KD knockdown in metastatic melanoma cells was associated with reduced proliferation and invasion in vitro, whereas ectopic TBC1D16-47KD expression in primary tumor–derived cells caused increased proliferation. Furthermore, depletion of TBC1D16-47KD in vivo impaired primary melanoma growth and metastasis, whereas overexpression of TBC1D16-47KD in primary tumor cells enhanced melanoma growth and progression. Consistent with its role in regulating RAB GTPases, TBC1D16-47KD directly interacted with RAB5C, a previously unidentified binding partner, and enhanced its GTPase activity, resulting in a reduction in EGFR expression in metastatic cells with epigenetic reactivation of TBC1D16-47KD. TBC1D16-47KD hypomethylation correlated with shorter progression-free survival and decreased overall survival in patients with melanoma. Intriguingly, however, melanoma cells with unmethylated TBC1D16-47KD were more sensitive to BRAF and MEK inhibitors, potentially due to an inability to activate EGFR-driven PI3K–AKT signaling. This increased sensitivity was also observed in clinical samples of metastatic melanoma from patients with unmethylated TBC1D16-47KD, which was associated with complete response to BRAF inhibition; in contrast, TBC1D16-47KD hypermethylation was observed in BRAF inhibitor–resistant samples at relapse. These findings underscore the role of demethylation in metastasis and suggest that epigenetic TBC1D16 reactivation may identify individuals most likely to respond to BRAF and MEK inhibitors.

Vizoso M, Ferreira HJ, Lopez-Serra P, Carmona FJ, Martínez-Cardús A, Girotti MR, et al. Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR. Nat Med 2015 Jun 1 [Epub ahead of print].