Most research on Neanderthal brains should be done by looking at the size and shape of the petrified skulls.Credit: Natural History Museum, London / Science Photo Library
Researchers have created small, brain-like ‘organoids’ that contain a gene variant housed by two extinct family members, Neanderthals and Denisovans. The tissues produced by the development of human stem cells are not a true version of the brain of these species, but they do show distinct differences from human organoids, including size, shape, and texture. The findings, published1 in Science on February 11, scientists can help understand the genetic pathways that have made the brains of humans possible.
“This is an extraordinary article with extraordinary claims,” said Gray Camp, a developmental biologist at the University of Basel in Switzerland, whose laboratory reported last year.2 growing brain organs that contain a gene that is common to Neanderthals and humans. The latest work takes research further by looking at gene variants that humans lost during evolution. But Camp remains skeptical about the implications of the results, saying the work opens up more questions that need to be explored.
Humans are more closely related to Neanderthals and Denisovans than to any living primate, and about 40% of the Neanderthal genome can still be found distributed in living humans. But researchers have limited resources to study the brains of these ancient species – soft tissue is not well preserved, and most studies depend on inspecting the size and shape of fossilized skulls. Knowing how the species ‘genes differ from humans’ is important because it helps researchers understand what makes humans unique – especially in our brains.
Brain organoids containing an archaic gene variant (below) were smaller and more textured than human organoids (above).Credit: CA Trujillo et al./Science
The researchers, led by Alysson Muotri, a neuroscientist at the University of California, San Diego, used the genomic editing technique CRISPR – Cas9 to introduce the Neanderthal and Denisovan form of a gene. NOVA1 in human pluripotent stem cells, which can develop into any cell type. They cultured it to form organoids, clumps of brain-like tissue, up to 5 millimeters wide, along with normal human brain organoids for comparison.
It was immediately clear that the organoids were the archaic variant of NOVA1 was different. “Once we saw the shape of organoids, we knew we wanted to do something,” says Muotri. Human brain organoids are usually smooth and spherical, while the organs of antiquity had no rough, complex surfaces and were smaller. This is probably due to differences in how the cells grow and multiply, the authors say.
Genome Comparison
To determine which archaic gene to express in the organoids, the researchers compared a library of human genome sequences with almost complete genomes of two Neanderthals and one Denisovan. They found 61 genes for which the human version is consistently different from the ancient species. Of these, NOVA1 is involved in the formation of the synapse of the brain, or nerve connections, and is associated with neurological disorders when its activity is altered.
The human NOVA1 no difference from the archaic variant – which still occurs in other living primates – by a single base that the researchers in CRISPR – Cas9 processed in the stem cells. The difference exchanges a single amino acid in the NOVA1 protein produced by the archaic organoids. ‘The fact that all people, or almost all people, now have this version and not the old version, means that it has given us a huge advantage at certain points during evolution. So the question we have now is: what are these benefits? ‘says Muotri.
The differences between the resulting organoids continued at the molecular level. The team found 277 genes that had different activities between the ancient gene and human organoids; of these genes are known to affect neuronal development and connectivity. As a result, the archaic organoids contain different levels of synapse proteins and their neurons fire in less orderly patterns than those in the control tissues. There is also evidence that they have aged faster.
Big difference
‘The most important finding is that you return [the gene] to an ancestral condition, and you see an effect in the organoid, ‘says Wolfgang Enard, an evolutionary geneticist at the Ludwig Maximilian University of Munich in Germany. He is surprised that such a small genetic difference causes such obvious changes, but he is skeptical that the strange appearance of the organoids tells us much about the Neanderthal brain.
Camp also warns that these antiogenic organoids are unlikely to fully represent true Neanderthal tissue. Instead, the observed properties may be due to the alteration of an important protein that occurs in humans due to composite effects of many mutations that are stacked on top of each other over time. “It’s like Jenga,” he says, “you don’t take out the amino acid and the brain.”
Yet the edited-organoid approach may be useful in studying brain evolution among primates, says Suzana Herculano-Houzel, an evolutionary neuroscientist at Vanderbilt University in Nashville, Tennessee. Muotri’s team plans to have organoids edited to contain other inverted genes that can provide insights into the human brain. If researchers can understand the evolutionary path that humans have brought to our current state, he can improve the understanding of diseases specifically for the human brain.