Virologists have infected millions of miniature organs with SARS-CoV-2, to learn how the virus wreaks havoc and how to stop it.
Shuibing Chen spent close to two months tending to her mini lungs — some half a million of them. Each one looked like a tiny storm cloud, ensconced in a warm dish and protected by a jelly-like dome. Chen, a stem-cell biologist at Weill Cornell Medicine in New York City, and her team had nurtured them from clumps of human cells, adding nutrients every few days as they grew into 3D air sacs.
These lung organoids matured until they reached the size of a lentil. Then, the team packed them up and transported them just a few blocks away, to a laboratory authorized to work with SARS-CoV-2, the virus responsible for the COVID-19 pandemic. There, the organoids were drowned in virus and each was doused with one of 15,000 drugs. Almost all of the mini lungs died, but a few of the drugs stemmed the infection — representing a handful of possible treatments for COVID-19.
Chen is one of many cell biologists who have been driven by the pandemic to push the boundaries of organoid technology for studying infectious diseases. In the past year, researchers have created mini lungs, guts, livers, brains and more to study how SARS-CoV-2 infects organs. They have learnt which cells the virus targets, the speed of that attack and how the cells retaliate.
“Organoids have found their way into the toolbox of virologists,” says Hans Clevers, a developmental biologist at the Hubrecht Institute in Utrecht, the Netherlands. The technology had previously been used mainly to study basic human biology, development and related disorders, and cancers, with only a few labs using the models to study viruses and other infectious diseases. But the pandemic has brought organoids to centre stage, spurring high-impact papers and demonstrating their value for drug development, says Clevers.
They are a welcome addition, because current methods of studying viruses have several limitations. The typical workhorse of virology is a cancerous cell line from the kidney of an African green monkey (Chlorocebus sabaeus), first extracted almost 60 years ago and dividing ever since. These cells, known as Vero cells, are excellent for growing viruses but don’t reflect the human body’s normal antiviral response. They are “really screwed up”, says Elke Mühlberger, a virologist at Boston University in Massachusetts. Researchers also use some cancerous human cell lines but, similar to the Vero cells, they don’t respond to infections in the way that normal cells would.
Although researchers have now established the potential relevance of organoids for studying new antiviral drugs, their work has not yet led to marketable treatments. “Organoid technology has benefited more from the pandemic than the treatment of COVID-19 has benefited from organoids, yet,” says Clevers.
To realize the technology’s full potential, scientists still need to find ways of growing more complex systems, for example by adding immune cells and blood vessels. Researchers also need to streamline the production process to create thousands, if not millions, of uniform organoids, quickly and cheaply.
“The use of organoids to study viruses is only at its infancy,” says Jie Zhou, a virologist at the University of Hong Kong.
Unculturable viruses
Before she started working with organoids, virologist Mary Estes relied on a much messier way to study the highly contagious vomiting bug norovirus. Nobody could grow the virus in the laboratory. So instead, she would isolate it from the excrement of people who willingly ingested it — and suffered the consequences — for the sake of her research.
In 2011, she saw a paper by Clevers in which he grew mini guts from stem cells scraped off the villi, the tiny tentacles that line people’s intestines1. Clevers had created the first organoids derived from adult stem cells, which grow almost indefinitely under the right conditions, and can build themselves into complex structures that reflect their organ of origin. (Organoids had already been made from embryonic stem cells or induced pluripotent stem (iPS) cells, which can develop into any cell type, but they typically reflect organs early in fetal development.)
“I thought — well, that looks like a system we ought to try,” says Estes, who is at Baylor College of Medicine in Houston, Texas. “Nobody else was using those cultures for virology at the time.”
In 2016 — almost half a century after its identification — Estes became the first person to grow human norovirus in a dish in a way that could be reproduced, in an intestinal organoid2.
Her studies proved that organoids were a good model of disease in people. She discovered, for instance, that norovirus variants did not replicate at all in organoids made from the cells of people who typically don’t get sick from the virus2.
Researchers have since used organoids to study many more viruses, including respiratory syncytial virus (RSV) — a common cause of lung infection in children — in airway organoids, and the rare and mysterious BK virus in kidney organoids.
In 2016, a team infected developing brain organoids with Zika virus and established a link between the infection in pregnant women and microcephaly3, a condition in which a fetus has an atypically small head. Ten days after being infected, the brain organoids were 40% smaller than the uninfected organoids. These neural progenitor cells are “fertile soil for Zika infection”, says Patricia Garcez, a neurobiologist at the Federal University of Rio de Janeiro in Brazil, who led the work.
