In recent years, scientists have discovered how to grow drops of hundreds of thousands of living human neurons that look – and act – like a brain.
These so-called brain organoids have been used to study how brains develop in layers, how they begin to spontaneously produce electrical waves, and even how that development might change into weightlessness. Researchers are now using these pea-sized clusters to explore our evolutionary past.
In a study published Thursday, a team of scientists describes how a gene likely carried by Neanderthals and our other former cousins triggered striking changes in the anatomy and function of brain organoids.
As dramatic as the changes are, scientists say it’s too early to know what these changes mean for the evolution of the modern human brain. “It’s more of a proof of concept,” said Katerina Semendeferi, co-author of the new study and evolutionary anthropologist at the University of California, San Diego.
To build on the findings, she and her co-author, Alysson Muotri, created the UC San Diego Archealization Center, a group of researchers focused on studying organoids and creating new ones with other old genes. “We now have a start and we can start exploring,” said Dr Semendeferi.
Dr Muotri began working with organoids in the brain over ten years ago. To understand how Zika produces birth defects, for example, he and his colleagues infected organoids in the brain with the virus, which prevented the organoids from developing their cortical layers.
In other studies, researchers have looked at how genetic mutations contribute to conditions like autism. They transformed skin samples from volunteers with developmental disabilities and turned the tissue into stem cells. They then transformed these stem cells into brain organoids. The organoids of people with Rett syndrome, a genetic disorder that causes intellectual disability and repetitive hand movements, have developed few connections between neurons.
Dr Semendeferi uses organoids to better understand the evolution of the human brain. In previous work, she and her colleagues found that in monkeys, neurons developing in the cerebral cortex stay close to each other, while in humans, cells can crawl long distances. “It’s a completely different organization,” she said.
But these comparisons span a vast gap in evolutionary time. Our ancestors separated from chimpanzees about seven million years ago. For millions of years after this, our ancestors were bipedal apes, gradually reaching heights and larger brains, and evolving into Neanderthals, Denisovans, and other hominins.
It was difficult to keep up with the evolutionary changes in the brain along the way. Our own lineage separated from that of the Neanderthals and Denisovans about 600,000 years ago. After this split, the fossils show, our brains eventually became more rounded. But what that means for the 80 billion neurons inside is hard to know.
Dr Muotri and Dr Semendeferi have teamed up with evolutionary biologists who study fossilized DNA. These researchers were able to reconstruct the entire genome of Neanderthals by putting together genetic fragments from their bones. Other fossils have produced the genomes of the Denisovans, who separated from the Neanderthals 400,000 years ago and lived for thousands of generations in Asia.
Evolutionary biologists have identified 61 genes that may have played a crucial role in the evolution of modern humans. Each of these genes has a mutation unique to our species, which has appeared over the past 600,000 years, and which has probably had a major impact on the proteins encoded by these genes.
Dr. Muotri and his colleagues wondered what would happen to a brain organoid if they suppressed one of these mutations, changing a gene to the way it was in the genomes of our distant ancestors. The difference between an ancestral organoid and an ordinary organoid could offer clues as to how the mutation influenced our evolution.
However, it took years for scientists to launch the experiment. They struggled to find a way to precisely modify the genes in stem cells before persuading them to turn into organoids.
Once they had found an effective method, they had to choose a gene. Scientists were worried about choosing a gene for their first experiment that would do nothing to the organoid. They thought about how to increase their chances of success.
“Our analysis made us say, ‘Let’s get a gene that changes a lot of other genes,’ Dr Muotri said.
One gene on the list seemed particularly promising in this regard: NOVA1, which makes a protein that then guides the production of proteins from a number of other genes. The fact that it is mainly active only in the developing brain made it more attractive. And humans have a mutation in NOVA1 that isn’t found in other vertebrates, living or extinct.
Dr. Muotri’s colleague, Cleber Trujillo, cultivated a batch of organoids carrying the ancestral version of the NOVA1 gene. After placing one under a microscope next to an ordinary brain organoid, he invited Dr. Muotri to take a look.
The ancestral organoid NOVA1 had a significantly different appearance, with a bumpy popcorn texture instead of a smooth spherical surface. “At that point, things started,” recalls Dr Muotri. “I said, ‘OK, that’s something.'”
The proportion of different types of brain cells was also different in ancestral organoids. And ancestral organoid neurons began to trigger spikes in electrical activity weeks earlier in their development than modern human neurons. But it also took the electric spikes longer to organize themselves into waves.
Other experts were surprised that a single genetic mutation could have such obvious effects on organoids. They had expected subtle changes that might be difficult to observe.
“Looks like the authors found a needle in a haystack based on an extremely elegant study design,” said Philipp Gunz, paleoanthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. , who did not participate in the research.
Simon Fisher, director of the Max Planck Institute for Psycholinguistics in the Netherlands, said the results had to come from a mixture of hard work and luck. “There must have been some degree of serendipity,” he says.
While researchers aren’t sure what changes in organoids mean to our evolutionary history, Dr. Muotri suspects there may be connections to the type of thinking made possible by different types of brains. “The real answer is, I don’t know,” he said. “But everything we see in the very early stages of neurodevelopment could have an implication later in life.”
At the new research center, Dr Semendeferi plans to conduct careful anatomical studies of brain organoids and compare them to human fetal brains. This comparison will help make sense of the changes observed in the ancestral organoid NOVA1.
And Dr. Muotri’s team is working on the list of 60 other genes, to create more organoids that Dr. Semendeferi can examine. Researchers may not be as lucky as they were when they first tried and won’t see much difference with certain genes.
“But others could be similar to NOVA1 and indicate something new – new biology that allows us to rebuild an evolutionary path that has helped us become who we are,” said Dr Muotri.