Nav: Home

Discovery gives cystic fibrosis researchers new direction

August 01, 2018

When scientists discovered the gene that causes cystic fibrosis in 1989, they were optimistic that a cure was on the horizon. As the years rolled by, hundreds of mutations were identified in the gene, but new treatments were slow to emerge and a cure has yet to materialize. One major reason for the delay is that scientists have had trouble figuring out precisely where the gene is active. Now they know.

A multi-disciplinary team of researchers at the Novartis Institutes for BioMedical Research (NIBR) and Harvard Medical School (HMS) started out trying to catalogue all the different cells in the airway and the paths they take to become those cells. In the process, they discovered a completely new type of cell, which they name a pulmonary ionocyte. When the cystic fibrosis gene from 1989, dubbed CFTR, is active, it is usually in the pulmonary ionocyte, which makes up just one-to-two percent of the airway. The team reported this discovery online in Nature on August 1. A similar finding was reported by scientists at the Broad Institute and Massachusetts General Hospital in the same journal on the same day.

"We can use this information to be a bit more clever when we devise therapeutic approaches to cystic fibrosis," says Aron Jaffe, co-corresponding author and a co-leader of respiratory disease research at NIBR.

"As people work toward cures, knowing you are looking at one percent of the cell population seems essential for any type of trouble shooting to improve a therapy or develop new therapies," adds Allon Klein, co-corresponding author and assistant professor of systems biology at HMS.

Noting that many of the CFTR mutations only stop part of the gene's function, Jaffe suggests, for example, for those mutations you might try increasing the amount of pulmonary ionocytes to increase the amount of CFTR activity. The discovery also could make the task of teams trying to use gene therapy to correct the CFTR mutations a lot easier.

"I was surprised to spot potential paths to new therapies so quickly after doing the initial experiments," says Lindsey Plasschaert, co-first author and postdoctoral researcher at NIBR.

This type of research on the fundamental nature of different types of cells rarely yields insights with direct implications for drug discovery.

Technology painted the path

Finding the new cell was no easy task. The team used a new technology called single-cell RNA sequencing to determine which genes were active in each individual cell in samples of airway tissue. Since gene activity defines a cell's function¬--and thus its identity--they could use the technology to sort and catalogue the many cells that allow us to make use of the air we breathe.

The secret--and the hard part--is being able to look at the gene activity of just one cell at a time. The NIBR scientists began working with the HMS scientists in 2015, about the time the HMS scientists published a seminal paper on their single-cell RNA sequencing platform, which is called InDrops. Up to that point researchers had been able to perform single-cell analysis of genetic activity on a few cells at a time, not the thousands of cells needed for a catalogue like the one Jaffe envisioned for the airway.

InDrops allows scientists to capture individual cells in water droplets and then wrap those in oil so that the contents of the cells don't mix. In order to look at only active genes, it starts with the cell's messenger RNA. Messenger RNA delivers information encoded in the DNA to the machinery that produces proteins, and it is only made when a gene is active.

Ideally, scientists would sequence the messenger RNA to identify the source genes. But with no good method for sequencing RNA, it must be converted back into DNA. Doing this on many thousands of isolated cells would be a time consuming and expensive task, so Klein's lab figured out how to rapidly label the contents of the cell with tiny pieces of DNA that act as bar codes by isolating each cell in a tiny water droplet in oil.

"We are introducing the DNA into the droplets using squishy gels," says Klein. "Each has about a billion little tags on it, which are then used to decorate all the material from the cell, and then we can break the droplets open and the contents of each cell are now tagged with a different bar code. And we can read out the bar codes later and figure out which genetic material came from which cell."

InDrops is now commercially available, but the Novartis researchers were able to access the technology for the airway project when it had just been invented. And Klein's lab is on the cutting edge of analyzing the data that it produces. Graduate student Rapolas Zilionis, co-first author on the paper, handled this for the team along with Virginia Savova from the Klein lab.

"They analyzed the data and then fed it into an interactive viewer that allowed me to go through and look for differences in gene activity between the different cell types," Plasschaert explains.

New cell pops out

Looking at that activity was essential to the catalogue of cell types envisioned at the start of the project. The analysis revealed a couple clusters of cells that did not appear to be like anything in the scientific literature, which sent Plasschaert down a laborious journey to further characterize those cells.

In essence, she was looking at a bowl of jelly beans, and she could tell some were colors not seen before, but she had no idea what flavor they were, or for her cells, their function. The experiments she designed showed that one set resembled the ionocytes--or cells that transport ions--found in some other tissues, most commonly in fish and frogs.

In fish, ionocytes transport ions in order to maintain an equilibrium with the water that surrounds them. In a bit of an evolutionary parallel, the cells discovered by the Novartis-Harvard team--which the researchers call pulmonary ionocytes--move ions at the interface between our tissues and the air around us. After considering various ways the ionocytes could do this, Plasschaert settled on CFTR activity.

The CFTR protein was known to transport ions. And Plasschaert conducted several experiments to show that the newly discovered pulmonary ionocytes have much more of the CFTR activity than another type of cell, ciliated cells, previously thought to be the main site of CFTR activity in the airway.

"The key finding turned out to be the high level of CFTR activity in the ionocytes and not in the ciliated cells people expected," Plasschaert says. "This will help us target the functionally relevant cells for cystic fibrosis therapies going forward."

Graduate student Zilionis says that from the beginning he was excited by the project's main goal of cataloguing the types of cells that make up our airway and was surprised that it produced a result with therapeutic potential so quickly.

"We can now design ways to isolate pulmonary ionocytes," he says. "We can get those cells in a dish and start doing things with them, looking for how they impact disease."
The co-first author on the paper, Rapolas Zilionis, is a visiting graduate student to the Klein lab from Vilnius University.

Novartis Institutes for BioMedical Research

Related Cystic Fibrosis Articles:

Rare mutations drive cystic fibrosis in Caribbean
Cystic Fibrosis (CF) in the Caribbean is dominated by unusual gene mutations not often observed in previously studied CF populations, according to comprehensive genome sequencing led by physician-scientists at UC San Francisco and Centro de Neumología Pediátrica in San Juan.
Cystic fibrosis carriers at increased risk of digestive symptoms
Researchers have found that carriers of the most common genetic variant that causes cystic fibrosis experience some symptoms similar to those of people with cystic fibrosis.
In cystic fibrosis, lungs feed deadly bacteria
A steady supply of its favorite food helps a deadly bacterium thrive in the lungs of people with cystic fibrosis, according to a new study by Columbia researchers.
Cibio knocks out cystic fibrosis
The fight against cystic fibrosis continues, targeting in particular some of the mutations that cause it.
Hypertonic saline may help babies with cystic fibrosis breathe better
Babies with cystic fibrosis may breathe better by inhaling hypertonic saline, according to a randomized controlled trial conducted in Germany and published in the American Thoracic Society's American Journal of Respiratory and Critical Care Medicine.
Understanding antibiotic resistance in patients with cystic fibrosis
Patients with cystic fibrosis who carried antibiotic-resistant bacteria in their lungs had significantly lower microbial diversity and more aggressive disease, according to a small study published in Heliyon.
Research shows that cystic fibrosis impacts growth in the womb
New research, published in Thorax, funded by the Cystic Fibrosis Trust has shown that babies with cystic fibrosis (CF) are born weighing less than babies without the condition, even allowing that they are more likely to be born prematurely.
Discovery gives cystic fibrosis researchers new direction
A multi-disciplinary team of researchers at the Novartis Institutes for BioMedical Research (NIBR) and Harvard Medical School (HMS) started out trying to catalogue all the different cells in the airway and the paths they take to become those cells.
Supplemental antioxidants may reduce exacerbations in cystic fibrosis
An antioxidant-enriched vitamin may decrease respiratory exacerbations in people with cystic fibrosis (CF), according to new research published online in April in the American Journal of Respiratory and Critical Care Medicine.
Protein structure could unlock new treatments for cystic fibrosis
Biochemists at the University of Zurich have used cryo-electron microscopy to determine the detailed architecture of the chloride channel TMEM16A.
More Cystic Fibrosis News and Cystic Fibrosis Current Events

Top Science Podcasts

We have hand picked the top science podcasts of 2019.
Now Playing: TED Radio Hour

In & Out Of Love
We think of love as a mysterious, unknowable force. Something that happens to us. But what if we could control it? This hour, TED speakers on whether we can decide to fall in — and out of — love. Guests include writer Mandy Len Catron, biological anthropologist Helen Fisher, musician Dessa, One Love CEO Katie Hood, and psychologist Guy Winch.
Now Playing: Science for the People

#543 Give a Nerd a Gift
Yup, you guessed it... it's Science for the People's annual holiday episode that helps you figure out what sciency books and gifts to get that special nerd on your list. Or maybe you're looking to build up your reading list for the holiday break and a geeky Christmas sweater to wear to an upcoming party. Returning are pop-science power-readers John Dupuis and Joanne Manaster to dish on the best science books they read this past year. And Rachelle Saunders and Bethany Brookshire squee in delight over some truly delightful science-themed non-book objects for those whose bookshelves are already full. Since...
Now Playing: Radiolab

An Announcement from Radiolab