Seeing a New World

May I wish readers a Happy New Year – and indeed extend my felicitations to non-readers with the hope that they too will become followers! What a good idea! Not least because I suspect many are viewing the new year with a mixture of anxiety and despair. But I can promise there’s nothing like the sanity of science to restore you after a few minutes contemplating how we’re doing on the economic and political fronts.

Your starter for 2017

By happy chance a few weeks ago I tried to explain how it’s now possible to ‘re-write the manual of life’ – that is, to engineer our DNA, to fix broken genes if you like. This means that, in theory, it’s possible to correct errors in our genetic code that cause genetic diseases. As there are over 6,000 of these and they include Down syndrome, cystic fibrosis and Alzheimer’s disease, there’s no need to say it’s important. There are several ways of going about this but the one I described is called CRISPR and it’s had a lot of media coverage.

Right on cue

Well done then Keiichiro Suzuki, Juan Carlos Belmonte and friends from the Salk Institute in California together with colleagues from other centres in Spain, Saudi Arabia and China for their December paper describing a new CRISPR twist. They used a rat model of retinitis pigmentosa, a genetic disease that is a major cause of inherited blindness, afflicting about one and a half million people worldwide (one in 4,000 in the UK).

The CRISPR-Cas9 system is great but it works best in dividing cells (e.g., in skin and gut that are renewing all the time) and it’s particularly useful for knocking out genes rather than inserting new DNA. The latest modification allows a new gene to be inserted into a specific site in the DNA of cells that are not dividing (e.g., those of the eye or brain).

The bits of CRISPR-Cas9, which insert DNA at very precise locations within the genome, are delivered to target cells as part of an inert virus. However, the package also includes DNA that encourages the cells to use a repair process that can be turned on even in non-dividing cells. So CRISPR-Cas9 cuts the cell’s DNA at an exact sequence and the cell then repairs the double-strand breaks (by a process called non-homologous end joining (NHEJ) that glues the broken ends directly together). Give the cell a new bit of DNA (e.g., your favorite gene) and that will get patched in – bear in mind that the cell doesn’t ‘know’ what it’s doing: it just tries to fix damaged DNA with whatever’s at hand.

And the target?

Retinitis pigmentosa occurs when a chunk of a gene called Mertk is lost. After quite a lot of experiments to show that their method worked, Suzuki, Belmonte & Co made a viral carrier that included a normal Mertk gene and injected it under the retina of rats with the disease. After about 5 weeks the rats were making Mertk RNA as a result of the gene being correctly ‘knocked-in’ to eye cells. The light-detecting region of the eye, greatly reduced by the disease, was significantly restored, with associated appearance of MERTK protein.

      Diseased    Normal     Treated                         Diseased         Normal         Treated

pic

Left trio: Sections of the light-detecting layers of the eye in diseased (left), normal (centre) and diseased post-treatment rats (right). Right trio: corresponding fluorescence images showing MERTK expression (red: highlighted by white arrows); Cells labeled blue. (Suzuki et al. Nature 1–6 (2016) doi:10.1038/nature20565)

How did the rats see it?

Well, after treatment they were able to detect light and had significantly recovered their visual functions, albeit not to completely normal levels.

The usual caveats apply: the method isn’t hyper-efficient and a human treatment is still a long way off. Nevertheless, it’s a significant step.

The same group has also shown, using a way of re-programming the expression of just four genes, that it’s possible to arrest the signs of ageing. In other words, in mice this time, tinkering with these genes can increase lifespan – and yes, we have versions of these genes and in us they also control cell renewal.

So the New Year message is clear to see. If we can avoid turning the planet into a desert or blowing ourselves to smithereens the future is really rosy – and maybe even infinite!

References

Suzuki, K. et al. (2016). In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540, 144-149.

Ocampo, A. et al. (2016). In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming. Cell 167, 1719–1733.

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Pig’s ’ere – and far from a bore

First love

When I was a lad I quite often worked on my Uncle’s farm in Cumberland and it was there that I first fell in love. It was reciprocated too, in a sort of way – I think largely contingent on presenting myself regularly bearing armfuls of potato peelings and summoning the courage to lean over the wall and do a bit of ear tickling. To this day pigs remain a love of my life and, given my enthusiasm for the wonders of DNA sequencing, readers will be unsurprised that the convergence of the two is irresistible.

Sequencing Sus scrofa

The genome sequence of a female domestic pig (with the less than alluring name of T. J. Tabasco), together with those of some of her relatives, have just been published. Before we get on to why you less love-struck unfortunates should give a grunt, we should make clear that no animals were harmed in unveiling this sequence. Rather, a small piece of an ear or a few teaspoons of blood were enough to grow cells from which DNA was distributed to the research groups involved.

1.11807_Pig1_cutout

Almost like a pig

So what did the members of the Swine Genome Sequencing Consortium gives us as the result of their labours? Well some things you would have guessed anyway: pigs have about as much DNA in their cells as we do (about 3,000 million base pairs). Of course they do: they’d have to be pretty similar for folk to go round falling in love with them. And within that sequence they have more genes encoding smell receptors than any other animal (over 1300) – which obviously helps if you have to rootle around for a bite to eat and not become reliant on admirers bringing gifts, though you can sense a downside to being so olfactorily endowed.

Them and us

But what about the differences? Well, close though I feel to them, pigs and humans last had a common ancestor about 90 million years ago and a domesticated pig first trotted out of South East Asia about 4 million years ago. Separate strains of the domestic pig then evolved in western Europe and East Asia that diverged from the various strains of wild boar – though the separation is somewhat murky due to pigs being prone to roam – a habit that led to what is delicately called ‘genetic mixing.’ So Hampshires and Large Whites turn out to be more closely related to European wild boars than they are to Chinese pigs such as the Meishan.

Model humans

One of the things that happened as pigs went their separate evolutionary way is that their DNA became unusually prone to being broken. Although damaged DNA is usually repaired two consequences tend to arise. Sometimes a gene just gets lost and this has happened with quite a few that we originally shared with pigs that enable us to taste things like salt: by losing that sensitivity pigs have acquired the ability to eat things we can’t. The other result is that pigs are quite good at shuffling bits of DNA to make novel genes (and hence proteins) – something called alternative splicing. But perhaps the most important outcome is that pig DNA has acquired about 100 changes (mutations) that in humans are linked to increased risk of things like Alzheimer’s disease and diabetes.

Pigs have a long and noble history as good models for human disease and we use their heart valves in replacement surgery (how’s that for reciprocated love?). Having a peek at their DNA has revealed that they also offer a natural model to find out what happens in some of our worst afflictions.

Pigs: giving us their hearts, sorting out our frailties – and making more roast dinners than you can shake a stick at. Everyone should love ‘em!

Reference

Groenen, M.A.M. et al., (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491, 393-398.