Bet on drug resistance

Inhibitors of the BET bromodomain proteins are promising cancer therapeutics, but tumour cells are likely to become resistant to these drugs. Anticipated mechanisms of resistance have now been described. See Letter p.413

Many modern cancer drugs target mutationally activated proteins, but this treatment strategy has limitations. Only a relatively small number of mutations are seen recurrently across human tumours1, and drug resistance develops rapidly2. Targeting the epigenome3 — the chemically modified form of DNA, and of associated histones and other proteins that facilitate the packaging of DNA as chromatin, all of which influence gene expression — is one of the alternative approaches being explored. Along with two papers4,5 published in Nature last year, a paper6 on page 413 of this issue provides some insight into the potential of epigenome-targeting drugs called BET inhibitors, and outlines the mechanisms by which tumours might become resistant to these drugs.

It has long been recognized7 that tumour cells have distinct epigenomic features, which can lead to the overproduction of cancer-promoting transcription factors such as MYC. Transcription factors are challenging therapeutic targets, because they lack structures that can be readily targeted with drugs. But developments in our understanding of the epigenome-regulating factors that influence gene expression, many of which seem to be 'druggable', have provided a potential way to sidestep this hurdle.

Among these factors is the bromodomain protein family, which includes the BET subfamily8 (BRD2, 3, 4 and T). BET proteins contain two bromodomains, each with small pockets. These pockets bind to histones that have been tagged with acetyl groups, enabling BET proteins to recruit the cell's transcriptional machinery to specific sites in the genome to regulate gene expression. BET subfamily members such as BRD4, which can regulate MYC gene transcription, have been implicated in various tumours (particularly in cancers of the blood) and are therefore candidate targets for therapy8.

A few years ago, the first of several small-molecule BET inhibitors (JQ1) was discovered, and shown8 to effectively disrupt cancer-cell proliferation. This effect seemed to reflect inhibition of BET-mediated regulation of MYC expression. Early clinical trials of BET inhibitors in leukaemia and lymphoma have been encouraging. Investigators are now seeking other disease contexts in which these inhibitors might work, and predicting the acquired resistance mechanisms that will inevitably arise.

The two 2015 studies4,5 converge on a potential mechanism of resistance to BET inhibition in acute myelogenous leukaemia (AML). In the first, Rathert et al.4 screened mouse AML cells for chromatin-modifying factors that are required for AML-cell survival. They confirmed that AML cells need Brd4, and identified several other factors for which inhibition confers AML-cell resistance to JQ1. In AML cells that were JQ1-resistant, the authors observed changes in specific epigenome features in DNA enhancer regions, which regulate gene expression. These changes meant that MYC gene expression could be activated without Brd4.

Rathert et al. also found that genes associated with the Wnt-signalling pathway, a known driver of tumour development, were upregulated in resistant cells. Wnt activation was sufficient to promote JQ1 resistance, possibly by driving the transcription of MYC at an enhancer generated specifically in the resistant cells (Fig. 1). Finally, the authors found the same mechanism of resistance to JQ1 in some other cancer types and in blood cells taken from people with leukaemia. Together, their data suggest that the usefulness of BET inhibitors could be expanded by combining them with Wnt-pathway inhibitors.

Figure 1: Circumventing BET inhibition.

The BET protein BRD4 can bind to acetyl groups (K) on histone proteins around which DNA is packaged as chromatin. BRD4 recruits the cell's transcriptional machinery, upregulating expression of the cancer-promoting MYC gene. Treatment with BET inhibitors can prevent BRD4–chromatin binding, stilting MYC transcription, but cancer cells rapidly develop drug resistance. Rathert et al.4 and Fong et al.5 report that, in acute myelogenous leukaemia (AML), drug resistance is conferred by activation of the Wnt-signalling pathway, which leads to DNA binding and MYC activation by the protein β-catenin. By contrast, Shu et al.6 find that resistance in triple-negative breast cancer (TNBC) arises owing to activation of the casein kinase 2 (CK2) enzyme. CK2 phosphorylates (P) BRD4, allowing BRD4 to bind to the transcriptional regulator protein MED1 to activate MYC.

Taking a different approach, Fong et al.5 rendered mouse AML cells resistant to BET inhibition by continuously exposing these cells to another BET inhibitor, eventually yielding drug-resistant clonal populations. This experiment also showed that Wnt activation has a role in drug resistance. Furthermore, the resistant cells had features of stem cells, suggesting that the AML cancer-stem-cell population, or a subset thereof, does not respond to BET inhibitors.

The Wnt pathway has previously been shown to be involved in drug resistance in AML cancer stem cells9. Moreover, the drug-resistant nature of cancer stem cells is well established10. However, Rathert and colleagues did not find evidence that the resistant AML cells had stem-cell features — a distinction between the two reports.

In the current study, Shu et al.6 explored BET inhibition in human breast cancer. By profiling a panel of breast-cancer cell lines, they observed that one cancer subtype — 'triple-negative' breast cancer — was sensitive to BET inhibition. Like Fong et al., the authors modelled acquired resistance to BET inhibition by culturing sensitive triple-negative cells in JQ1, and then characterized emergent resistant cells. Resistant cells remained dependent on BRD4, but this dependence did not involve the protein's bromodomains.

A widely active transcriptional regulator protein called MED1 bound more tightly to BRD4 in resistant cells than in sensitive cells. The authors attributed this tighter binding to increased BRD4 phosphorylation mediated by the enzyme casein kinase 2 (CK2). The binding gave rise to bromodomain-independent, BRD4-mediated transcriptional activation of MYC, among other genes (Fig. 1). These data suggest that using a combination of CK2 and BET inhibitors to treat triple-negative breast cancer might prevent drug resistance.

Although many previous studies have demonstrated the efficacy of drugs against triple-negative breast cancer in animal and cell-based models, it is worth noting that these drugs have so far failed to combat tumours in people. As such, optimism should be tempered.

Collectively, these three reports show that BET inhibitors might have a broader potential than had previously been realized. They also highlight the possibility that BET inhibitors could be used in combination with other drugs to overcome both innate and acquired drug resistance. Although the reported resistance mechanisms seem to reflect an adaptation to drug pressure, the root cause of resistance remains unknown. Does a specific mutation cause Wnt or CK2 activation, or are these adaptive changes that drive resistance through reversible epigenetic mechanisms? A complete mechanistic understanding of resistance remains to be defined.

It is important to note that clinical inhibitors of Wnt or CK2 have yet to be developed. Therefore, the hypotheses that emerge from these studies cannot be tested in the clinic. Nonetheless, these three reports provide a good foundation on which to build a better understanding of mechanisms of resistance that should be anticipated in the clinic. Footnote 1


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Correspondence to Jeff Settleman.

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Settleman, J. Bet on drug resistance. Nature 529, 289–290 (2016).

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