Abstract
In response to the dynamic intra‐tumor microenvironment, melanoma cells adopt distinct phenotypic states associated with differential expression of the microphthalmia‐associated transcription factor (MITF). The response to hypoxia is driven by hypoxia‐inducible transcription factors (HIFs) that reprogram metabolism and promote angiogenesis. HIF1α indirectly represses MITF that can activate HIF1α expression. Although HIF and MITF share a highly related DNA‐binding specificity, it is unclear whether they co‐regulate subset of target genes. Moreover, the genomewide impact of hypoxia on melanoma and whether melanoma cell lines representing different phenotypic states exhibit distinct hypoxic responses is unknown. Here we show that three different melanoma cell lines exhibit widely different hypoxia responses with only a core 23 genes regulated in common after 12 hr in hypoxia. Surprisingly, under hypoxia MITF is transiently up‐regulated by HIF1α and co‐regulates a subset of HIF targets including VEGFA. Significantly, we also show that MITF represses itself and also regulates SDHB to control the TCA cycle and suppress pseudo‐hypoxia. Our results reveal a previously unsuspected role for MITF in metabolism and the network of factors underpinning the hypoxic response in melanoma.
Highlights
An increasingly recognized source of therapeutic resistance is pro‐ vided by phenotypic heterogeneity whereby individual cells within tumors are exposed over time to different microenvironmental signals that drive them to adopt specific phenotypic states
Since melanoma cell lines isolated from human tumors tend to fall into either proliferative or invasive, FIGURE 7 microph‐ thalmia‐associated transcription factor (MITF) regulates SDHB to suppress pseudo‐hypoxia. (a) gene set variation analysis (GSVA) analysis showing relative expression of indicated gene sets in the top or bottom 20 CCLE melanoma cell lines ranked by SDHB expression. (b) Analysis of TCGA human melanoma samples ranked by the MITF expression for expression of indicated succinate de‐ hydrogenase (SDH) subunits
The mechanism reported is indirect, with activation of HIF1α leading to up‐regulation of the transcription factor bHLHE40/DEC1, one of the common 23 genes we identify as induced in all three melanoma cell lines examined after 12 hr in hypoxia, and its consequent binding and repression of the MITF pro‐ moter
Summary
An increasingly recognized source of therapeutic resistance is pro‐ vided by phenotypic heterogeneity whereby individual cells within tumors are exposed over time to different microenvironmental signals that drive them to adopt specific phenotypic states. While previous studies have focused on a few selected genes (Widmer et al, 2013), or the hy‐ poxia response in mouse melanocytes (Loftus et al, 2017), the im‐ pact of hypoxia on genomewide gene expression or which genes are direct targets of the HIF family in melanoma remains unknown. Nor is it clear whether melanomas exhibit a melanoma‐specific hypoxia signature compared to hypoxia in other cell types, whether some melanoma cells with distinct phenotypes exhibit a differential re‐ sponse to hypoxia, or whether MITF may contribute to the adaptive response to hypoxia. Neither is it known if a constitutive pseudo‐hy‐ poxia gene expression signature found in some other cancer types under normoxic conditions exists in some melanomas
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