As a professor of pediatrics and cellular and molecular medicine at the University of California San Diego School of Medicine, Alysson R. Muotri, PhD, has long studied how the brain develops and what goes wrong in neurological disorders. For about the same time, you've also been curious about the evolution of the human brain: what change that makes us so different from previous Neanderthals and Denisovans, our closest evolutionary relatives, now extinct?
Evolutionary studies rely heavily on two tools, genetics and fossil analysis, to explore how a species changes over time. But neither approach can reveal much about brain development and function because brains don't fossilize, Muotri said. There is no physical record to study.
So Muotri decided to test stem cells, a tool not often applied in evolutionary reconstructions. Stem cells, self-renewing precursors to other cell types, can be used to build brain organoids, "mini brains" in a laboratory dish. Muotri and his colleagues have pioneered the use of stem cells to compare humans with other primates, such as chimpanzees and bonobos, but until now a comparison with extinct species was not believed possible.
In a study published February 11, 2021, in Science, Muotri's team cataloged the differences between the genomes of various modern human populations and Neanderthals and Denisovans, who lived during the Pleistocene epoch, approximately 2.6 million to 11,700 ago. years.Mimicking an alteration they found in a gene, the researchers used stem cells to engineer "Neanderthal" brain organoids.
"It's fascinating to see that a single base pair alteration in human DNA can change the way the brain is wired," said Muotri, lead author of the study and director of the UC San Diego Stem Cell Program and member of the Sanford Consortium for Regenerative Medicine. "We don't know exactly how and when in our evolutionary history that change occurred. But it appears to be significant and could help explain some of our modern capacities in social behavior, language, adaptation, creativity, and use of technology."
The team initially found 61 genes that differed between modern humans and our extinct relatives. One of these altered genes, NOVA1, caught Muotri's attention because it is a master genetic regulator that influences many other genes during early brain development. The researchers used CRISPR gene editing to engineer modern human stem cells with the Neanderthal-like mutation in NOVA1. They then persuaded the stem cells to form brain cells and, ultimately, Neanderthal brain organoids.
Brain organoids are small clumps of brain cells made up of stem cells, but they're not exactly brains (for one, they lack connections to other organ systems, such as blood vessels). However, organoids are useful models for studying genetics, disease development, and responses to infections and therapeutic drugs. Muotri's team has even optimized the process of building brain organoids to achieve organized electrical oscillatory waves similar to those produced by the human brain.
Neanderthal brain organoids looked very different from modern human brain organoids, even to the naked eye. They were clearly different in shape.Looking deeper, the team discovered that modern and Neanderthal brain organoids also differ in the way their cells proliferate and in how their synapses, the connections between neurons, are formed. Even the proteins involved in the synapses differed. And the electrical impulses showed greater activity in earlier stages, but were not synchronized in networks in Neanderthalized brain organoids. "We look forward to this new combination of stem cell biology, neuroscience, and palaeogenomics. The ability to apply the comparative approach of modern humans to other extinct hominins, such as Neanderthals and Denisovans, using brain organoids that carry ancestral genetic variants is completely new field of study ".
According to Muotri, the changes in the neural network in Neanderthal brain organoids parallel the way that newborn non-human primates acquire new abilities more rapidly than human newborns.
"This study focused on a single gene that differed between modern humans and our extinct relatives. Next, we want to take a look at the other 60 genes and what happens when each one, or a combination of two or more, is altered." , Muotri said.
To continue this work, Muotri has partnered with Katerina Semendeferi, professor of anthropology at UC San Diego and co-author of the study, to co-lead the new UC San Diego Center for Archealization, or ArchC.
"We will merge and integrate this incredible stem cell work with anatomical comparisons of various species and neurological conditions to create further hypotheses about the brain function of our extinct relatives," said Semendeferi. "This neuroarchealization approach will complement efforts to understand the minds of our ancestors and close relatives, such as Neanderthals."
Study co-authors include: Cleber A. Trujillo, Isaac A. Chaim, Emily C. Wheeler, Assael A. Madrigal, Justin Buchanan, Sebastian Preissl, Allen Wang, Priscilla D. Negraes, and Ryan Szeto, UC San Diego; Edward S. Rice, Nathan K. Schaefer, Ashley Byrne, Maximillian Marin, Christopher Vollmers, Angela N. Brooks, Richard E. Green, UC Santa Cruz; Roberto H. Herai, Pontifícia Universidade Católica do Paraná; Alik Huseynov, Imperial College London; Mariana SA Ferraz, Fernando da S. Borges, Alexandre H. Kihara, Universidade Federal do ABC; Jonathan D. Lautz, Stephen EP Smith, Seattle Children's Research Institute and University of Washington; Beth Shapiro, UC Santa Cruz and the Howard Hughes Medical Institute;and Gene W. Yeo, UC San Diego, Science, Technology and Research Agency (Singapore) and National University of Singapore.
Funding for this research came, in part, from the Neanderthal Brain Foundation, National Institutes of Health (grants U19MH1073671, K12GM068524, K01AA026911), Brain and Behavior Research Foundation (NARSAD Independent Investigator Grant), National Science Foundation (grant 1754451), Gordon and Betty Moore Foundation (grant GBMF3804), Co Ordenção de Aperfeiçoamento de Pessoal de Nível Superior (Capes, Brazil), FAPESP (São Paulo Research Foundation, grant 2017 / 26439-0), CNPq (National Council for Scientific and Technological Development of Brazil, grants 431000 / 2016-6, 312047 / 2017-7) and Fundación Loulou.
Disclosure: Alysson R. Muotri is a co-founder and a stakeholder in TISMOO, a brain organoid modeling and genetic analysis company that focuses on personalized therapeutic applications for autism spectrum disorder and other genetically based neurological disorders. The terms of this agreement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies.