Posts Tagged ‘Abby Olena’

Ionocytes (orange) extend through neighboring epithelial cells (nuclei, cyan) to the surface of the respiratory epithelial lining. This newly identified cell type expresses high levels of CFTR, a gene that is associated with cystic fibrosis when mutated.


Two independent research teams have used single-cell RNA sequencing to generate detailed molecular atlases of mouse and human airway cells. The findings, reported in two studies today (August 1) in Nature, reveal the gene-expression patterns of thousands of lung cells, as well as the existence of a previously unknown cell type that expresses high levels of the gene mutated in cystic fibrosis, the cystic fibrosis transmembrane conductance regulator (CFTR).

“These papers are extremely exciting,” says Amy Ryan, a lung biologist at the University of Southern California who was not involved in either study. “They’ve interrogated the cellular composition and the cellular hierarchy of the airways by using a single-cell RNA-sequencing technique. That kind of information is going to have a significant impact on advancing the research that we can do, and hopefully the derivation of new therapeutic approaches for any number of airway diseases.”

Jayaraj Rajagopal, a pulmonary physician at Massachusetts General Hospital and Harvard University and coauthor of one of the studies, had been studying lung regeneration and wanted to use single-cell sequencing to look at differences in the lungs’ stem-cell populations. He and his colleagues teamed up with Aviv Regev, a computational biologist at the Broad Institute of MIT and Harvard University, and together, the two groups characterized the transcriptomes of thousands of epithelial cells from the adult mouse trachea.

Rajagopal, Regev, and colleagues uncovered previously unknown differences in gene expression in several groups of airway cells; identified novel structures in the lung; and found new paths of cellular differentiation. They also described several new cell types, including one that the team has named the pulmonary ionocyte, after salt-regulating cells in fish and amphibian skin. These lung cells express similar genes as fish and amphibian ionocytes, the team found, including a gene coding for the transcription factor Foxi1, which regulates genes that play a role in ion transport.

The team also showed that pulmonary ionocytes highly express CFTR, and are in fact the primary source of its product, CFTR—a membrane protein that helps regulate fluid transport and the consistency of mucus—in both mouse and human lungs, suggesting that the cells might play a role in cystic fibrosis.

“So much that we found rewrites the way we think about lung biology and lung cells,” says Rajagopal. “I think the entire community of pulmonologists and lung biologists will have to take a step back and think about their problems with respect to all these new cell types.”

For the other study, Aron Jaffe, a biologist at Novartis who studies how different airway cell types are made, combined forces with Harvard systems biologist Allon Klein and his team. Klein’s group had previously developed a single-cell RNA-sequencing method that Jaffe describes as “the perfect technology to take a big picture view and really define the full repertoire of epithelial cell types in the airway.”

Jaffe, Klein, and colleagues sequenced RNA from thousands of single human bronchial epithelial and mouse tracheal epithelial cells. The atlas generated by their sequencing analysis revealed pulmonary ionocytes, as well as new gene-expression patterns in familiar cells. The team examined the expression of CFTR in human and mouse ionocytes in order to better understand the possible role for the cells in cystic fibrosis. Consistent with the findings of the other study, the researchers showed that pulmonary ionocytes make the majority of CFTR protein in the airways of humans and mice.

“Finding this new rare cell type that accounts for the majority of CFTR activity in the airway epithelium was really the biggest surprise,” Jaffe tells The Scientist. “CFTR has been studied for a long time, and it was thought that the gene was broadly expressed in many cells in the airway. It turns out that the epithelium is more complicated than previously appreciated.”

These studies are “very exciting work [and] a wonderful example of how new technologies that have come online in the last few years—in this case single-cell RNA sequencing—have made a very dramatic advance in our understanding of aspects of biology,” says Ann Harris, a geneticist at Case Western Reserve University who did not participate in either study.

In terms of future directions, the authors “have shown that transcription factor [Foxi1] is central to the transcriptional program of these ionocytes,” says Harris. One of the next questions is, “does it directly interact with the CFTR gene or is it working through other transcription factors or other proteins that regulate CFTR gene expression?”

According to Jennifer Alexander-Brett, a pulmonary physician and researcher at Washington University School of Medicine in St. Louis who was not involved in the studies, the possibility that a rare cell type could be playing a part in regulating airway physiology is “captivating.”

Apart from investigating the potential role for ionocytes in lung function, Alexander-Brett says that researchers can likely make broad use of the data from the studies—particularly details on the expression of genes coding for transcription factors and cell-surface markers. “One area that we really struggle with in airway biology . . . is [that] we just don’t have good markers” to differentiate cell types, she explains. But these papers are “very comprehensive. There’s a ton of data here.”

D.T. Montoro et al., “A revised airway epithelial hierarchy includes CFTR-expressing ionocytes,” Nature, doi:10.1038/s41586-018-0393-7, 2018.

L.W. Plasschaert et al., “A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte,” Nature, doi:10.1038/s41586-018-0394-6, 2018.


Ultrasound activates auditory pathways in the rodent brain (red arrows) regardless of where in the brain the ultrasound-generating transducer is placed.

By Abby Olena

Activating or suppressing neuronal activity with ultrasound has shown promise both in the lab and the clinic, based on the ability to focus noninvasive, high-frequency sound waves on specific brain areas. But in mice and guinea pigs, it appears that the technique has effects that scientists didn’t expect. In two studies published today (May 24) in Neuron, researchers demonstrate that ultrasound activates the brains of rodents by stimulating an auditory response—not, as researchers had presumed, only the specific neurons where the ultrasound is focused.

“These papers are a very good warning to folks who are trying to use ultrasound as a tool to manipulate brain activity,” says Raag Airan, a neuroradiologist and researcher at Stanford University Medical Center who did not participate in either study, but coauthored an accompanying commentary. “In doing these experiments going forward [the hearing component] is something that every single experimenter is going to have to think about and control,” he adds.

Over the past decade, researchers have used ultrasound to elicit electrical responses from cells in culture and motor and sensory responses from the brains of rodents and primates. Clinicians have also used so-called ultrasonic neuromodulation to treat movement disorders. But the mechanism by which high frequency sound waves work to exert their influence is not well understood.

The University of Minnesota’s Hubert Lim studies ways to restore hearing, but many of the strategies that his group uses are invasive, such as cochlear implants, which require surgery to insert a device inside the ear. He says that he and his colleagues were excited by the prospect of using noninvasive and precise ultrasound to activate the parts of the brain responsible for hearing.

Lim’s team started by stimulating the brains of guinea pigs with audible noise or with pulsed ultrasound directly over the auditory cortex. They were surprised to observe similar neuronal responses to the two different stimuli because ultrasound is outside the spectrum that the guinea pigs—and humans—can hear. The researchers also found that the rodents’ neurons showed comparable electrical activity in the auditory cortex regardless of where in the brain the researchers directed the ultrasound. This raised the question: are the animals’ brains responding directly to the ultrasound or to responses of the auditory system?

When the authors cut the guinea pigs’ auditory nerves or removed their cochlear fluid, the guinea pigs stopped responding to the ultrasound and to audible noise. Lim’s team concluded that what must be happening is ultrasound moves through brain tissue and vibrates the cochlear fluid. This vibration then triggers auditory signaling and indirectly activates the auditory cortex and other brain regions, rather than ultrasound having a direct effect on the activity of the neurons.

“I am actually very hopeful that ultrasound can be a powerful tool that can not only modulate but also treat different neurologic and psychiatric disorders, and that it can achieve a noninvasive yet localized activation,” says Lim. “But what we’re trying to show in this paper is that there are many confounding effects that are actually happening with ultrasound, and we have to remove those effects to really see how it’s activating the brain.”

A coauthor on the companion study, Mikhail Shapiro of Caltech, says that previous work showing that it is possible to apply ultrasound to the brains of mice and rats to elicit electrical activity and movement in their limbs left him and his colleagues curious about how it works. To determine where and when neural activation happens, they applied ultrasonic pulses to the brains of transgenic mice that have neurons that light up when stimulated. As with guinea pigs, ultrasound is inaudible to mice.

“To our surprise, we found that the main activation pattern that we were seeing was not in the region where we were applying the ultrasound directly, but actually in the auditory areas of the brain, those responsible for processing information about sound,” Shapiro tells The Scientist.

Consistent with the findings of Lim and colleagues, Shapiro and his coauthors determined that the mouse brains lit up across the cortex, starting from the auditory cortex. And as in the guinea pigs, the mouse neurons responded similarly to ultrasound and audible sounds. The researchers also showed that both ultrasound and audible noise elicited motor movements that decreased when they used chemicals to deafen the mice.

“We’re not trying to imply that [the effects of ultrasound observed in previous studies are] due to this auditory side effect,” says Shapiro. “We’re very optimistic that now that we know that it’s there, we will be able to design ways to get around it and still be able to use this technology scientifically.”

Shy Shoham, a neuroscientist and biomedical engineer at New York University Langone Medical Center who did not participate in the studies, tells The Scientist that these papers highlight how careful researchers must be in the future when using ultrasound to modify neuronal function. “In the field of neural stimulation in general, we should always be very concerned about off-target effects,” he says. We must “delineate what is real and what isn’t.”

“The big take home point here is that we need to take care of the auditory effects,” says Kim Butts Pauly, who studies ultrasound neuromodulation at Stanford University Medical Center and who coauthored the accompanying commentary with Airan. “There’s been very compelling data from other studies that ultrasound can stimulate the brain and change recordings from the brain that are completely separate from any auditory effects. As we get rid of the auditory effects, then the more subtle effects may become apparent.”

H. Guo et al., “Ultrasound produces extensive brain activation via a cochlear pathway,” Neuron, doi:10.1016/j.neuron.2018.04.036, 2018.

T. Sato et al., “Ultrasonic neuromodulation causes widespread cortical activation via an indirect auditory mechanism,” Neuron, doi:10.1016/j.neuron.2018.05.009, 2018.