x Abu Dhabi, UAEFriday 28 July 2017

Abu Dhabi NYU provost using worm to unlock genetic secrets

A team led by NYU Abu Dhabi's provost is using a roundworm to unlock the secrets of how individual genes interact with each other.

Fabio Piano, provost of New York University Abu Dhabi, says knowing what is required to make a cell divide and being able to control whether that cell is allowed to divide, gives scientists 'a hook into how you attack a protein in a cancer cell to stop it from dividing'.
Fabio Piano, provost of New York University Abu Dhabi, says knowing what is required to make a cell divide and being able to control whether that cell is allowed to divide, gives scientists 'a hook into how you attack a protein in a cancer cell to stop it from dividing'.

A tiny, see-through worm may not seem the most promising place to look for clues about how a single cell turns into a whole organism.

But that is the hope of Dr Fabio Piano, the provost at New York University Abu Dhabi and founding director of NYU's Centre for Genomics and Systems Biology in New York. He, and dozens of other scientists, now have in their possession the world's first genetic "blueprint" of the Caenorhabditis elegans nematode roundworm.

And they believe they are close to uncovering a simple key behind the worm's development: a hidden network of protein "foremen" that move around the worm as it grows, telling its genes when they are needed.

C. elegans has long been a favourite of geneticists, representing, in Prof Piano's words, the "ideal model organism".

Its skin is transparent, making it easy to see and photograph. As the worms ovulate, as their eggs are fertilised, as the cells divide; everything is visible right down to the level of individual cells and their nuclei.

The worms breed and grow quickly. An egg takes just three days to develop into a mature adult - so tests that require many generations of observations can be easily conducted within a practical time-frame. Mutate a gene, and within a week you can see what has changed.

Add to that a more unusual feature of the worm's biology: unlike most animals, C. elegans has an almost entirely consistent cell fate map.

During its development, scientists know exactly which cells will divide to form which other cells. The pattern is the same in every individual, resulting in the same 959 cells, in exactly the same places. When you look at a cell, it is easy to know which one you are looking at, and where it came from.

That is the result of a precisely choreographed development sequence. As the worm grows, each cell must divide at the right time, in the right direction, in the right manner. And that requires precise instructions about how and when to start and stop dividing.

Prof Piano's team studied that division using RNA interference (RNAi) - a technique that can be used to block a single gene, to see what happens (or what does not).

The basic genetics of C. elegans have long been known - its genome was fully sequenced as far back as 1998. More elusive, though, was what all 20,000 of its genes actually did. Which proteins did they code for, and what functions did they carry out in the worms' cells?

In the normal functioning of a cell, each DNA (deoxyribonucleic acid) gene is transcribed into a unique RNA (ribonucleic acid) molecule, each of which then produces a specific protein. It is this second stage - the production of protein by RNA - which is blocked by RNAi.

With the basic genome already described, Prof Piano and his collaborators set about the painstaking task of using RNAi to knock out each of the 20,000 genes in turn.

"We depleted the function of every single gene, one by one, to see what would happen and then wrote a dictionary explaining each function, kind of like parts of a car."

They found that of the 20,000 genes, just half were being expressed in the early developing embryo, while the other half are likely expressed later in development and in the worm's adult life.

They also studied the interactions between the various proteins, and between the genes and proteins.

Putting this together allowed them to draw up a "network" map - essentially a flowchart of each gene, the RNA transcribed from it, the protein produced by that, and the function of each protein. Some proteins act as structural elements; others as signalling enzymes that cause or allow other processes to happen.

"First we try to build the networks, and then we try to understand how they evolve," said Prof Piano. "When we built the first network, in 2005, it was a very exciting moment as it was the first time we had a molecular map of what makes an animal embryo tick."

The nematode remain the only animal for which such detailed genetic information is known.

But after piecing together the network, the scientists realised they were not seeing the full picture. What they had was a description of the top layer of the worm's genetic functioning. They had identified the genes that had crucial functions, but it was clear that other genes were being expressed. But what were all these other genes, with no apparent function, doing?

They found that beneath the basic network "flowchart", there were more complex interactions between different parts of the system. "There are ways in which mutations are buffered by the network and are undetected, or hidden from causing any visible effect," said Prof Piano.

That explains why, in some cases, the same mutation can have different effects on two people - one has symptoms of a disease, and the other not. "We are now trying to reveal the stuff that is underneath, in the buffered genetic systems."

Working out what those elusive genes were up to required a more subtle approach. The scientists first had to upset the network, with a mutation that almost, but not completely, broke its normal functioning.

They then removed a second, previously hidden or buffered gene, to see if that was enough to push the network to complete collapse - or whether it caused the worm to develop strangely.

They did this by using mutations that make a specific gene sensitive to temperature, so they could "dial down" its function by turning up the heat. Using this "dialled down" condition the second gene was depleted by RNAi.

And these double genetic perturbations have indeed started to reveal the "hidden" networks. "Suddenly we started to see other effects with genes we thought had no role."

To get a better picture of these systems at work, they started tracking the proteins by tagging them with a green fluorescent protein extracted from jellyfish. It leaves cellular processes unaffected but glows under ultraviolet light.

Here the worm's transparency was crucial. It let the scientists see exactly where the luminescent marker was at any given time.

By following the fluorescence, they saw that some proteins were moving between the two subnetworks. They would start as part of one network, and then suddenly the connection would break and they would join another. And as they did so, they appeared to be acting almost like a key, switching multi-protein complexes on and off.

"Perhaps we are seeing groups of proteins that could be ready to work, but are not functioning because they are missing the final piece - this key protein," said Prof Piano.

And these - as yet unnamed - protein keys could be crucial to the whole process of the worm's development, moving around the animal to choreograph its growth at every turn.

While some of this research has been published in journals, the most recent findings have yet to be published. According to Prof Piano, it shows "strong evidence" that networks are indeed evolving within a developing embryo.

Better yet, it provides a deeper biological understanding of how evolution could happen, how one species becomes something different - not via the addition or deletion of genes, but by the rewiring of networks.

And it gives clues about why a particular mutation can lead to a devastating disease in one person, and yet leave someone else completely unaffected.

Once the entire genetic network and all these protein connections are mapped, the atlas will provide a foundation for a deeper understanding of how to fight various diseases in, for example, the human body.

"If you know what is required for a cell to divide, and you learn how to break that so it doesn't divide anymore, you have a hook into how you could attack a protein in a cancer cell to stop it from dividing."