The Epigenetics Revolution

So, by the early years of the 21st century scientists had found a way of maintaining pluripotent ES cells in culture dishes and they knew quite a lot about their biology. They had also worked out how to change the culture conditions so that the ES cells would differentiate into various cell types including liver cells, heart cells, neurons etc. But how does this help with the dream we laid out earlier? Could the labs use this information to create new ways of driving cells backwards, to the top of Waddington’s landscape? Would it be possible to take a fully differentiated cell and treat it in a lab so that it would become just like an ES cell, with all the potential that implies? Whilst scientists had good reason to believe this would be theoretically possible, that’s a long way from actually being able to do it. But it was a wonderfully tantalising prospect for scientists interested in using stem cells to treat human diseases.

By the middle of the first decade of this century, over twenty genes had been identified that seemed to be critical to ES cells. It wasn’t necessarily clear how they worked together and there was every reason to think that there was still plenty we didn’t understand about the biology of ES cells. It was assumed that it would be almost inconceivably difficult to take a mature cell and essentially recreate the vastly complex intracellular conditions that are found in an ES cell.

The triumph of optimism

Sometimes the greatest scientific breakthroughs happen because someone ignores the prevailing pessimism. In this case, the optimist who decided to test what everyone else had assumed was impossible was the aforementioned Shinya Yamanaka, with his postdoctoral research associate Kazutoshi Takahashi.

Professor Yamanaka is one of the youngest luminaries in the stem cell and pluripotency field. He was born in Osaka in the early 1960s and rather unusually he has held successful academic positions in high profile institutions in both Japan and the USA. He originally trained as a clinician and became an orthopaedic surgeon. Specialists in this discipline are sometimes dismissed by other surgeons as ‘the hammer and chisel brigade’. This is unfair, but it is true that orthopaedic surgical practice is about as far away from elegant molecular biology and stem cell science as it’s possible to get.

Perhaps more than any of the other researchers working in the stem cell field, Professor Yamanaka had been driven by a desire to find a way of creating pluripotent cells from differentiated cells in a lab. He started this stage of his work with a list of 24 genes which were vitally important in ES cells. These were all genes called ‘pluripotency genes’ – they have to be switched on if ES cells are to remain pluripotent. If you use various experimental techniques to switch these genes off, the ES cells start to differentiate, just like those beating heart cells in the culture dish, and they never revert to being ES cells again. Indeed, that is partly what happens quite naturally during mammalian development, when cells differentiate and become specialised – they switch off these pluripotency genes.

Shinya Yamanaka decided to test if combinations of these genes would drive differentiated cells backwards to a more primitive developmental stage. It seemed a long shot and there was always the worry that if the results were negative – i.e. if none of the cells went ‘backwards’ – he wouldn’t know if it was because it just wasn’t possible or if he just hadn’t got the experimental conditions right. This was a risk for an established scientist like Yamanaka, but it was an even bigger gamble for a relatively junior associate like Takahashi, because of the way that the scientific career ladder works.

When faced with the exposure of damaging personal love letters, the Duke of Wellington famously responded, ‘Publish and be damned!’ The mantra for scientists is almost the same but differs in one critical respect. For us, it’s ‘publish or be damned’ – if you don’t publish papers, you can’t get research funding and you can’t get jobs in universities. And it is rare indeed to get a paper into a good journal if the message of your years of effort boils down to, ‘I tried and I tried but it didn’t work.’ So to take on a project with relatively little likelihood of positive results is a huge leap of faith and we have to admire Takahashi’s courage, in particular.

Yamanaka and Takahashi chose their 24 genes and decided to test them in a cell type known as MEFs – mouse embryonic fibroblasts. Fibroblasts are the main cells in connective tissue and are found in all sorts of organs including skin. They’re really easy to extract and they grow very easily in culture, so are a great source of cells for experiments. Because the ones known as MEFs are from embryos the hope was that they would still retain a bit of capacity to revert to very early cell types under the right conditions.