The Epigenetics Revolution

Thinking back to Chapter 4, imagine a methylated region of DNA. When a cell divides, it separates the two strands of the DNA double helix and copies each one. But the enzymes that copy the DNA can’t themselves copy DNA methylation. As a consequence each new double helix had one methylated strand and one unmethylated one. The DNA methyltransferase called DNMT1 can recognise DNA which has only got DNA methylation on one strand and can replace it on the other strand. This restores the original DNA methylation pattern.

But if dividing cells are treated with 5-azacytidine, this abnormal cytidine base is added into the new strand of DNA as the genome gets copied. Because the abnormal base contains a nitrogen atom instead of a carbon atom, the DNMT1 enzyme can’t replace the missing methyl group. If this continues as the cells keep dividing, the DNA methylation begins to get diluted out.

Something else also happens when dividing cells are treated with 5-azacytidine. We now know that when DNMT1 binds at a region where the DNA contains 5-azacytidine instead of the normal cytidine, the DNMT1 becomes stuck there[172]. This marooned enzyme is then sent to a different part of the cell and is broken down. Because of this, the total levels of DNMT1 enzyme in the cell fall[173][174]. The combination of this decrease in the amount of DNMT1, and the fact that 5-azacytidine can’t be methylated, means that the amount of DNA methylation in the cell keeps dropping. We’ll come back in a little while to why this drop in DNA methylation has an anti-cancer effect.

So, 5-azacytidine is an example of where an anti-cancer agent was unexpectedly shown to work epigenetically. Bizarrely, a rather similar thing happened with our second example of a compound which is now licensed to treat cancer[175].

Another happy accident

In 1971 the scientist Charlotte Friend showed that a very simple compound called DMSO (its full name is dimethyl sulfoxide) had an odd effect on the cancer cells from a mouse model of leukaemia. When these cells were treated with DMSO, they turned red. This was because they had switched on the gene for haemoglobin, the pigment that gives red blood cells their colour[176]. Leukaemia cells normally never switch on this gene and the mechanism behind this effect of DMSO was completely unknown.

Ronald Breslow at Columbia University and Paul Marks and Richard Rifkind at Memorial Sloan-Kettering Cancer Center were intrigued by Charlotte Friend’s research. Ronald Breslow began to design and create a new set of chemicals, using the structure of DMSO as his starting point, and then adding or changing bits, a little like making new combinations of Lego bricks. Paul Marks and Richard Rifkind began to test these chemicals in various cell models. Some of the compounds had a different effect from DMSO. They stopped cells from growing.

After many iterations, learning from each new and more complicated set of structures, the scientists created a molecule called SAHA (suberoylanilide hydroxamic acid). This compound was really effective at stopping growth and/or causing cell death in cancer cell lines[177]. However, it was another two years before the team were able to identify what SAHA was doing in cells. The key moment happened more than 25 years after Charlotte Friend’s breakthrough publication, when Victoria Richon in Paul Marks’ team, read a 1990 paper from a group at the University of Tokyo.

The Japanese group had been working on a compound called Trichostatin A or TSA. TSA was known to be able to stop cells proliferating. The Japanese group showed that treatment with TSA altered the extent to which histone proteins are decorated with the acetyl chemical group in cancer cell lines. Histone acetylation is another epigenetic modification that we first met in Chapter 4. When cells were treated with TSA, the levels of histone acetylation went up. This wasn’t because the compound was activating the enzymes that put the acetyl groups on histones. It was because TSA was inhibiting the enzymes that remove acetyl groups from these chromatin proteins. These proteins are called histone deacetylases, or HDACs for short[178].

Victoria Richon compared the structure of TSA with the structure of SAHA, and the two are shown in Figure 11.2.

^{Figure 11.2 The structures of TSA and SAHA, with the areas of greatest similarity circled. C: carbon; H: hydrogen; N: nitrogen; O: oxygen. For simplicity, some carbon atoms have not been explicitly shown, but are present where there is a junction of two lines.}