Scientists correct the typo behind a genetic liver disease

Every year, thousands of people die because of typos in their genes. There’s a long list of debilitating or fatal genetic diseases that are caused by a single incorrect DNA letter among the three billion in our genome. It’s the equivalent of pulping an entire encyclopaedia on the basis of a single typo. But hope is at hand. We are fast approaching the point when we can proofread these errors out of our genes.

Kosuke Yusa  and Tamir Rashid have taken the latest step towards this goal, by developing a more efficient and less risky way of correcting genetic errors. They took cells from patients with a genetic liver disease, edited the gene responsible, and grew corrected liver cells that successfully treated mice with the same disease.

The disease in question is called alpha 1-antitrypsin deficiency (or alpha-1 for short). It affects 1 in every 2,000 Europeans and is caused by a single typo in the A1AT gene. The error stops people from making enough of the A1AT protein. The little they do make builds up in their liver, overloading it and leading to cirrhosis. At the moment, the only treatment is a liver transplant, and donors are hard to come by.

Yusa and Rashid fixed this problem in three steps: they took skin cells from alpha-1 patients with two bad copies of the A1AT gene; reprogrammed them into stem cells; fixed the error in both copies of the broken gene; and used the corrected stem cells to produce liver cells. This is the first time that anyone has corrected a faulty gene in stem cells derived from a human patient.

The first step relies on methods that were first developed in 2006. In August of that year, Shinya Yamanaka from Kyoto University found a way of reprogramming adult cells so they could create any type of tissue in the body. He could imbue adult cells, which are normally fixed in specific roles, with the limitless potential of stem cells. Since then, research on these “induced pluripotent stem cells” or iPSCs, has raced along at blistering speed. Scientists quickly realised that they could use iPSCs to create an unlimited supply of tissues and organs, tailored to a person’s own genome. They could even fix errors in the reprogrammed cells to create working tissues in people who were suffering from genetic disorders.

A few groups have successfully done this in mice. In 2007, Rudolf Jaenisch used the iPSCs to cure mice of a genetic disorder called sickle cell anaemia, caused by deformed blood cells. Jaenisch made iPSCs from skin cells in the rodents’ tails, corrected the faulty gene that was behind their disease, and injected the cells back into the mice. Just four weeks later, the mice started producing normal blood cells. In 2009, Yupo Ma used the same methods to treat a second genetic disease called haemophilia A, again in mice.

But there are two big problems with these methods. First, they’re not very efficient. If you start off with a large batch of iPSCs with the same faulty gene, you only ever correct a small proportion of them. To single them out, scientists rig the editing process so the corrected cells also gain a marker – say, a gene that makes them resistant to a particular antibiotic. That makes them easy to identify and isolate. Once this is done, the marker can be cut out. That leads to the second problem: the markers tend to leave small bits of DNA behind. In fixing one error, you could introduce several more. At worst, the DNA remnants could disrupt important genes and cause cancers.

Yusa and Rashid solved both of these problems. First, they designed a scissor-like protein called a ‘zinc finger nuclease’ to specifically cut the A1AT gene at its incorrect letter. By precisely targeting the typo, the team could efficiently replace it with the right letter.

Second, they created a marker that can be seamlessly removed. They relied on a jumping gene called piggyBac, which can cut itself out of its surrounding DNA and paste itself back into a different spot. It does so flawlessly; once it jumps out of a piece of DNA, you’d never be able to tell that it was once there. By loading their marker gene into piggyBac, Yusa and Rashid could yank it out once they had identified the corrected cells, without leaving any traces behind or disrupting any genes.

The duo used their corrected iPSCs to grow new liver cells, which produced normal working versions of the A1AT protein. They transplanted these cells into mice with the same faulty gene. Two weeks later, the cells had colonised the rodents’ livers, they were behaving normally, and they hadn’t produced any tumours.

That’s reassuring because even with their new technique, the results weren’t entirely faultless. Yusa and Rashid found that the liver cells had gained 29 new mutations since their days as skin cells. Most of these happened when they were reprogrammed back into stem cells. One was caused by the zinc finger nuclease, and three were due to piggyBac. This isn’t necessarily a problem; cells naturally acquire fresh mutations over time and most are of no consequence. Still, the mutations add a note of caution to an otherwise optimistic study.

The next step will obviously be to test the final transplant stage with human patients. The team want to take things slowly, testing the technique in degrees to make sure that it’s safe for patients. This will probably take several years but they are keen that the hype doesn’t outrun the pace of their work.

For people with alpha 1-antitrypsin deficiency, the technique could solve the shortage of liver transplants. You don’t need a donor when you can just grow a new liver from your own corrected stem cells. Even better, that liver would be genetically identical to the rest of your body, so you wouldn’t have to worry about rejection or immune problems.

The liver is a good place to start when trying to prove that this technique can work, because it regenerates very well naturally. Other organs might be trickier; new neurons, for example, would need to connect with the existing network. Even so, Yusa and Rashid’s study has implications for other genetic diseases. The same techniques could be used to correct other genetic faults – using the zinc finger nuclease to make things more efficient, and piggyBac to avoid disrupting the surrounding genes.

Reference: Yusa, Rashid, Marchand, Varela, Liu, Paschon, Miranda, Ordo, Hannan, Rouhani, Darche, Alexander, Marciniak, Fusaki, Hasegawa, Holmes, di Santo, Lomas, Bradley & Vallier. 2011. Targeted gene correction of a1-antitrypsin deficiency in induced pluripotent stem cells. Nature http://dx.doi.org/10.1038/nature10424

Image by Sirsnapsalot

More on regenerative medicine:

• Gene therapy saves patient from lifetime of blood transfusions
• An entire flatworm regenerated from a single adult cell
• Research into reprogrammed stem cells: an interactive timeline
• Lungs rebuilt in lab and transplanted into rats