The researchers set out to take a census of all the cells that line our airway, a taxonomy of the tissue made possible by new technology. Perhaps, they thought, they would find different subtypes of cells they already knew existed or would come to better understand the cells’ functions.
As the data came in, though, they pointed to a more intriguing finding: a previously unknown cell, one that was similar to a cell found in the gills of fish and skin of frogs.
Senior researchers were initially dubious. “I thought, ‘It’s great to have graduate students who are so bold,’ but in the back of my head, I was thinking there was no way this was right,” said Dr. Jay Rajagopal, a developmental biologist and pulmonologist at Massachusetts General Hospital.
But in a pair of papers published Wednesday in the journal Nature, two independent research teams reported that they didn’t just unearth this new type of cell, but that the cell appears to play an outsize role in cystic fibrosis.
Taken together, the discoveries could shift the understanding of the basic biology of the devastating lung disease, signal potential targets for new forms of therapies, and one day shake up the market for cystic fibrosis medications.
“They have discovered a previously unknown cell type that could hold the key to understanding the disease cystic fibrosis,” scientists Kyle Travaglini and Mark Krasnow of Stanford University, who were not involved in the research, wrote in an editorial also published Wednesday.
Other outside scientists praised the research but said they had questions about how much influence other types of lung cells still had over cystic fibrosis. The studies in part focused on the trachea, or windpipe, so researchers said they wondered if the same cellular story would hold deep at the ends of the airway, which is where cystic fibrosis first emerges, or if other cell types still had some involvement in the disease.
“That’s predominantly where the CF lesions are,” said Dr. Tien Peng, a CF expert at the University of California, San Francisco, who was not involved with the new studies.
Rajagopal was a co-senior author of one of the papers, along with Aviv Regev, a computational and systems biologist at the Broad Institute. Allon Klein, a systems biologist at Harvard Medical School, and Aron Jaffe, co-leader of respiratory disease research at the Novartis (NVS) Institutes for BioMedical Research, were the senior authors of the other study.
The two Boston-area teams learned of each other’s work as it was ongoing, wound up coordinating their papers’ submission, and together landed on a name for the newly revealed cell: a pulmonary ionocyte.
For patients with cystic fibrosis, goopy mucus builds up in their lungs and can clog their airways. The mucus also acts like fly paper and ensnares bacteria, leading to regular infections and lung damage. About 30,000 people have the disease in the U.S.
Scientists have known that the disease is caused by mutations in the CFTR gene, but the working theory was that the gene was active in cells all over the airway, including ones with tiny hair-like structures called cilia that sweep out mucus and nasty invaders.
The new studies turn that thinking on its head. Instead of humming along in a variety of cells, the gene really only gets going in pulmonary ionocytes, the scientists reported. While ionocytes accounted for at most 2 percent of all cells in the tissue the researchers studied, they were responsible for the vast majority of CFTR activity.
That means when there are disease-causing mutations in the CFTR gene, it is these cells that treatments should target, the studies suggest. If researchers develop a CF gene therapy, for example, they could direct it to ionocytes or the stem cells that produce them.
Still, the research left open the idea that other airway cells are home to some CFTR activity, and outside experts said that future studies should aim to calculate how much CFTR activity throughout the lungs occurs in these ionocytes. Even if there were only a little CFTR expression in other types of cells, they noted, there are enough of them to contribute a sizable amount to the overall activity.
“The challenge now for all of us is to try to fit this information into the whole animal, i.e. the whole lung,” said Dr. Richard Boucher, a CF expert at the University of North Carolina, who was not involved in the studies. “Is [the ionocyte] the only actor in town? I suspect it’s not.”
CFTR encodes an ion channel (also called CFTR) that helps regulate the chemical and acid balance of the epithelium (the layer of tissue that lines the airway). Experts aren’t sure exactly why the cystic fibrosis mutations cause the problems they do — perhaps the channel can no longer control the acid levels of the mucus, which makes it thicker and harder to expel — but “it’s clear that breaking CFTR makes things go really wrong,” said Klein.
As part of their studies, the researchers identified a transcription factor — a molecule that can turn other genes on or off — called FOXI1 that drives CFTR activity. It might be possible then to use FOXI1 to promote the production of healthy pulmonary ionocytes — another potential therapeutic route beyond gene therapy.
“If we knew how to generate the cell, we could try to make more,” Jaffe said. “And by making more, you would hope that would increase the activity of the channel across the epithelium.”
For now, three existing medications — all made by Boston-based Vertex (VRTX) Pharmaceuticals — aim to improve the function of CFTR, but a gene therapy (if one were ever developed) could provide more lasting benefits for patients. Other drugs on the market help patients clear their mucus or stave off infections.
To create their census of airway cell types, the researchers used a technique called single-cell RNA sequencing. First, they broke apart their tissue samples into individual cells, then merged those with a few other key ingredients, leaving each cell ensconced in a tiny droplet of oil.
“Everything has to happen really, really, really quickly,” Regev said. “Otherwise the cells start dying and the RNA that’s in them starts degrading.”
Joining the cells inside their oily nooks is a particle that performs like a pricing gun, labeling each cell’s genetic details with a unique barcode. Thanks to the barcodes, researchers can track which gene came from which cell and can measure the gene expression of each cell.
As the researchers started sorting the data and identifying cell types, there was one pile that stood out as a big unknown. They noticed those cells shared features with cells called ionocytes that are found in fish gills and frog skin and that feature ion channels.
But despite their identification, pulmonary ionocytes still maintain some mystery. The papers’ authors said they’re not sure, for example, why so much CFTR activity appears concentrated in so few cells. As Rajagopal said, “Maybe they’re just super hardworking.”