Epigenetic survival response suppresses cancer drug toxicity

Research published today in Epigenetics & Chromatin investigated the therapeutic value of bacteria. Here, co-authors Bryan Turner and John Halsall explain more.

The natural world has been a rich source of medicinal drugs for many years, from digoxin (found in foxgloves) used to treat cardiac arrythmia to antibiotics such as penicillin (secreted by moulds). For over 40 years, scientists have been asking if bacteria too might synthesize substances of therapeutic value.


In the 1970s Japanese researchers isolated a group of compounds called Trichostatins from a particular strain of bacteria. Trichostatins, at very low concentrations, slowed the growth of human leukaemia cells in culture and induced them to differentiate, properties that made them potentially useful for treating cancer.

In exploring the mode of action of Trichostatins, Minoru Yoshida and colleagues discovered that they specifically inhibited a group of enzymes with crucial roles in control of gene function in humans and many other organisms, histone deacetylases (HDAC).

DNA in prokaryotes and eukaryotes

Why should bacteria expend precious energy making and secreting complex reagents that inhibit human enzymes? To answer this we need to remember that the living world comprises organisms built from two different types of cell, namely prokaryotic (bacteria and archaea) and eukaryotic (everything else, including us).

The two types of cell have much in common (they evolved from the same ancestor), but differ fundamentally in how they package and regulate their DNA. In eukaryotes alone, DNA is contained within a membrane-bound organelle, the nucleus, and packaged by precisely structured binding to a family of small proteins, the histones.

HDAC inhibitors are used by bacteria to kill microorganisms built from eukaryotic cells, particularly moulds and fungi, that compete for the same resources. They exert their effects by disrupting the epigenetic systems that these organisms (but not bacteria) use to regulate gene expression and thereby control their growth and behavior.

The modification of histones by acetylation of selected lysines is an important component of these regulatory systems and is maintained by the complementary activities of acetylating and deacetylating enzymes. Bacterial deacetylase inhibitors are intended to throw this carefully regulated epigenetic control system into chaos.

Of course, eukaryotes do not take bacterial attacks lying down but fight back with their own toxins, such as penicillin, that disrupt systems unique to bacteria. It is ironic that this arms race in the microbial world has provided compounds of such benefit to humans, whether as medicines or lab reagents .

The promise as anti-cancer drugs

Over recent years, histone deacetylase inhibitors (HDACi) have begun to realize the promise as anti-cancer drugs that first drew them to scientists’ attention. The US Food and Drug Administration (FDA) has approved two for clinical use, SAHA (a synthetic compound based on Trichostatins) and depsipeptide (another bacterial product of different chemical structure).

However, in a series of clinical trials their effectiveness has been patchy, with not many types of cancer being generally susceptible (FDA approval is only for treatment of a specific type of lymphoma), and with wide variation from one patient to another. We need to know more about how cells respond to HDACi.

In this regard, it has been a long-standing puzzle that, despite a mountain of evidence that HDACi cause global histone hyperacetylation and extensive disruption of certain aspects of our epigenetic control systems, human cells survive these potential toxins very well, both in the laboratory and in the real world.

Normal human cells exposed to therapeutic concentrations of two different HDACi, mount a transcription-based survival response.

For example, bacteria in our large intestine produce high levels of short-chain fatty acids (effective HDACi) as metabolic by-products. These bathe the cells lining this organ, without apparent detriment. Why is this? And why are some cancer cells unusually sensitive?

A paper from our laboratory, published in Epigenetics and Chromatin, provides a possible answer by demonstrating, for the first time, that normal human cells exposed to therapeutic concentrations of two different HDACi, mount a transcription-based survival response.

Faced with HDACi, cells reorganize their pattern of gene expression so as to minimize the immediate effects of the inhibitors and to switch the cell to a state of slowed growth that permits survival in face of the epigenetic changes caused by the drug.

What did we find?

The paper identifies families of genes that are crucial components of this survival response. For example, genes encoding components of all the enzyme complexes responsible for protein acetylation are uniformly down-regulated, thereby minimising aberrant acetylation of histones and other proteins when the deacetylating enzymes are blocked.

Growth-promoting cytokines are down-regulated, while there is up-regulation of genes encoding factors needed for resetting patterns of gene expression. In short, the changes allow the cell to put in place a new pattern of gene expression that will allow it to both survive and maintain its identity in the presence of changed environmental circumstances (i.e., the presence of HDACi).

At first sight it is perhaps surprising that human cells should mount such a specific and wide-ranging response to two chemically very different inhibitors. But viewed from an evolutionary perspective, the finding is not unexpected.

Perhaps the response was developed by our earliest, single-celled eukaryotic ancestors to protect themselves against bacterial toxins, in this case HDACi.

Perhaps the response was developed by our earliest, single-celled eukaryotic ancestors to protect themselves against bacterial toxins, in this case HDACi. Like many other epigenetic control mechanisms, it has been passed down, with modification, to us, and is still proving useful. This remains speculative, but experiments to search for a similar response in simpler eukaryotes will throw some light on its evolutionary origins.

The existence of a survival response has clinical implications. Certain cancers may be sensitive to HDACi because their survival response has been disrupted by mutation of one or more of its essential genes. Identification of such mutations will help target cancers susceptible to HDACi therapy and contribute to the further improvement of personalised medicine. Similarly, combining HDACi with drugs that undermine the survival response specifically in cancer cells, may open the way to more successful treatment of currently refractory cancers.

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