Every cell in the human brain contains the same sequence of DNA, but in different cell types, different genes are copied onto strands of RNA that serve as blueprints for proteins. The resulting changes in which proteins are present in which cells, and at what levels, give rise to enormous diversity in the types of brain cells and the complexity of the brain. Understanding which cells rely on which DNA sequences to function is critical not only to understanding how the brain works, but also to understanding how DNA mutations lead to brain diseases and how to treat them.
Abstract representation of cellular diversity in the brain. Individual nuclei are colored in the bright hues of t-SNE plots used in epigenomic analyses, to distinguish individual brain cell types. The background color layer represents the local environmental factors affecting cell function in each brain region. Source: Michael Nunn
Margarita Behrens, a research professor in the Salk Computational Neurobiology Laboratory, is a co-principal investigator of the new work. In 2020, Eck and Behrens led the Salk team to analyze 161 types of cells in the mouse brain based on methyl chemical marks on DNA, which indicate when genes are turned on or off. This DNA regulation is called methylation and is a layer of cellular identity.
In the new paper, the researchers used the same tool to determine DNA methylation patterns in more than 500,000 brain cells in 46 regions in the brains of three healthy adult male organ donors. Mouse brains are essentially the same across animals, containing about 80 million neurons, while human brains vary even more, containing about 80 billion neurons.
"Going from mice to humans was a big jump and presented some technical challenges that we had to overcome," Behrens said. "But we were able to adapt what we figured out in mice and still get very high-quality results in the human brain."
At the same time, the researchers also used a second technique, analyzing the three-dimensional structure of DNA molecules in each cell, to gain more information about which DNA sequences are actively used. Exposed DNA regions are more easily accessible to cells than tightly folded DNA.
"This is the first time we've looked at these dynamic genomic structures at a whole new level of brain cell type granularity, and how they might regulate which genes are active in which cell types," said Jingtian Zhou, co-first author of the new paper and a postdoctoral researcher in Ecker's lab.
Other research groups, whose work is also published in this special issue of Science, used cells from the same three human brains to test their cell profiling techniques, including a group led by Bing Ren at the University of California, San Diego, who also co-authored the Eck and Behrens study. Ren's research group has uncovered links between specific brain cell types and neuropsychiatric disorders, including schizophrenia, bipolar disorder, Alzheimer's disease and major depressive disorder. Additionally, the team developed artificial intelligence deep learning models that can predict the risk of these diseases.
Other groups in the global collaboration focus on measuring RNA levels to classify cells into subtypes. Based on DNA studies conducted by Eck and Behrens' teams, the teams found a high degree of correspondence between which genes are activated and which genes are transcribed into RNA in each brain region.
Because the new Salk study was intended as a pilot study to test the effectiveness of these techniques in the human brain, the researchers said they cannot yet draw conclusions about how many cell types might be found in the human brain or how those types differ between mice and humans.
"The possibility of discovering unique cell types in humans that we don't see in mice is really exciting," said Wei Tian, co-first author of the new paper and a scientist in Ecker's lab. "We've made amazing progress, but there are more questions to ask."
In 2022, the National Institutes of Health Brain Initiative (NIHBrain Initiative) launched a new Brain Initiative Cell Atlas Network (BRAIN Initiative Cell Atlas Network, BICAN), which will be a follow-up to the work of BICCN. At Salk, a new BICAN-funded Center for Multiomic Human Brain Cell Atlas aims to study cells from more than a dozen human brains and ask questions about how the brain changes during development, across the lifespan and in disease. Eck said studying more brains in more detail will pave the way to a better understanding of how certain brain cell types go awry in brain disorders and diseases: "We want to gain a comprehensive understanding of the brain across a person's life so that we can pinpoint exactly when, how and which cell types go awry in response to disease and potentially prevent or reverse these harmful changes."