New technique reveals genes underlying human evolution

One of the best ways to study human evolution is to compare ourselves to non-human species that are closely related to us from an evolutionary point of view. That closeness can help scientists pinpoint exactly what makes us human, but that scope is so narrow that it can also be extremely difficult to define. To address this complication, Stanford University researchers have developed a new technique to compare genetic differences.

Through two separate series of experiments with this technique, the researchers discovered new genetic differences between humans and chimpanzees. They found significant disparities in the expression of the gene SSTR2 – which modulates the activity of neurons in the cerebral cortex and has been associated in humans with certain neuropsychiatric diseases such as Alzheimer’s disease and schizophrenia – and the gene EVC2, which is related. to face shape. The results were published on March 17 in Nature and Nature Genetics, respectively.

“It’s important to study human evolution, not only to understand where we come from, but also why humans get so many diseases that don’t occur in other species,” said Rachel Agoglia, a recent graduate student of genetics at Stanford and lead author of the Nature paper.

The Nature paper describes the new technique, which involves joining human and chimpanzee skin cells modified to act as stem cells – highly malleable cells that can be stimulated to transform into a variety of other cell types (albeit not a complete organism).

“These cells serve a very important specific purpose in this type of research by enabling us to accurately compare the genes of humans and chimpanzees and their activities side by side,” said Hunter Fraser, associate professor of biology at Stanford’s School of Humanities and Sciences. Fraser is the senior author of the Nature Genetics paper and co-senior author of the Nature paper with Sergiu Pașca, associate professor of psychiatry and behavioral sciences at Stanford School of Medicine.

Close equations

The Fraser lab is particularly interested in how the genetics of humans and other primates relate at the level of cis regulatory elements, which influence the expression of nearby genes (located on the same DNA molecule or chromosome). The alternative – called transregulatory factors – can remotely regulate expression of genes on other chromosomes elsewhere in the genome. Due to their broad effects, trans-regulatory factors (such as proteins) are less likely to differ between closely related species than are cis-regulatory elements.

But even if scientists have access to similar human and chimpanzee cells, there is a risk of confounding factors. For example, differences in the timing of development between species are a major hurdle in studying brain development, Pașca explained. This is because the brains of humans and chimpanzees develop at very different rates and there is no exact way to compare them directly. By housing the DNA of humans and chimpanzees in the same cell nucleus, scientists can rule out most confounding factors.

For the first experiments using these cells, Agoglia coaxed the cells to form so-called cortical spheroids or organoids – a bundle of brain cells that closely mimics a developing mammalian cerebral cortex. The Pașca lab is at the forefront of developing brain organoids and assembloids with the aim of investigating how the human brain is assembled and how this process fails in diseases.

“The human brain is essentially inaccessible at the molecular and cellular levels for most of its development, so we introduced cortical spheroids to help us access these important processes,” said Pașca, who is also Bonnie Uytengsu and family director. from Stanford Brain. Organogenesis.

As the 3D clusters of brain cells develop and mature in a shell, their genetic activity mimics what happens in the early neurological development in each species. Because human and chimpanzee DNA are linked in the same cellular environment, they are exposed to the same conditions and mature in parallel. Therefore, any observed differences in the genetic activity of the two can be reasonably attributed to actual genetic differences between our two species.

By studying brain organoids derived from the fused cells cultured for 200 days, the researchers found thousands of genes that showed cis-regulatory differences between species. They decided to further investigate one of these genes – SSTR2 – which was more strongly expressed in human neurons and functions as a receptor for a neurotransmitter called somatostatin. In subsequent comparisons between human cells and chimpanzee cells, the researchers confirmed this increased protein expression of SSTR2 in human cortical cells. When the researchers exposed the chimpanzee cells and human cells to a small molecule of drug that binds to SSTR2, they found that human neurons responded to the drug much more than the chimpanzee cells.

This suggests a way in which the activity of human neurons in cortical circuits can be altered by neurotransmitters. Interestingly, this neuromodulating activity may also be related to the disease as SSTR2 has been shown to be involved in brain diseases.

“The evolution of the primate brain may have to do with adding advanced neuromodulatory features to neural circuits, which under certain circumstances can be disrupted and increase susceptibility to neuropsychiatric disorders,” said Pașca.

Fraser said these results are essentially “a proof of concept that the activity we see in these fused cells is actually relevant to cellular physiology.”

Exploring extreme differences

For the experiments published in Nature Genetics, the team converted their fused cells into cranial neural crest cells, which cause bones and cartilage in the skull and face and determine the appearance of the face.

“We were interested in these types of cells because facial differences are considered some of the most extreme anatomical differences between humans and chimpanzees – and these differences actually affect other aspects of our behavior and evolution, such as nutrition, our senses, brain expansion and speech,” said David Gokhman, a postdoctoral researcher in the Fraser laboratory and lead author of the Nature Genetics paper. “Also, the most common congenital diseases in humans are related to facial structure.”

In the fused cells, the researchers identified a gene expression pathway that is much more active in the cells’ chimpanzee genes than in the human genes – with one specific gene, called EVC2, which appears to be six times more active in chimpanzees. Existing research has shown that people with inactive EVC2 genes have flatter faces than others, suggesting that this gene could explain why humans have flatter faces than other primates.

In addition, the researchers found that 25 observable facial features associated with inactive EVC2 differ noticeably between humans and chimpanzees – and 23 of them differ in the direction the researchers would have predicted, given the lower EVC2 activity in humans. In follow-up experiments, in which the researchers reduced the activity of EVC2 in mice, the rodents also had flatter faces.

Another resource in the toolbox

This new experimental platform is not intended to replace existing cell comparison studies, but the researchers hope it will support many new findings about human evolution and evolution in general.

“Human development and the human genome have been very well studied,” said Fraser. “My lab is very interested in human evolution, but because we can build on such a wealth of knowledge, this work can also reveal new insights into the broader evolution process.”

Looking ahead, the Fraser lab is working to differentiate the fused cells into other cell types, such as muscle cells, other types of neurons, skin cells, and cartilage, to expand their research into unique human traits. The Pașca Laboratory, meanwhile, is interested in investigating genetic inequalities associated with astrocytes – large, multifunctional cells in the central nervous system that scientists often overlook in favor of the flashy neurons.

“While humans often think about how neurons evolved, we should not underestimate how astrocytes have changed during evolution. Only the size difference between human astrocytes and astrocytes in other primates is huge,” Pașca said. “My mentor, the late Ben Barres, called astrocytes ‘the foundation of humanity’ and we absolutely think he was up to something.”