Neurons labeled green in a human brain slice (credit: Allen Institute)
October 12, 2023 03:35 PM EDTUpdated 03:46 PM R&DIn Focus
Most detailed human brain map yet is ‘laying the foundation for finding future cures’
Ryan Cross
Senior Science Correspondent
Scientists have published the most detailed catalog yet of the human brain’s billions of cells and how their genes are used, revealing new clues about what goes wrong in disease and providing new footholds for developing targeted therapies, according to interviews that Endpoints News conducted with more than a dozen people involved in the massive project.
The $250 million cellular parts list is the product of a five-year effort known as the BRAIN Initiative Cell Census Network (BICCN) and was largely funded by the National Institutes of Health.
The project, detailed across 21 studies published on Thursday, has been likened to the Human Genome Project for its scope and ambition. The discovery of more than 3,300 types of brain cells provides a molecular road map that gives scientists new leads in treating disorders such as autism and schizophrenia. It’s also lifting the veil on how human brains develop, and what makes them unique compared to our closest relatives, chimpanzees.
John Ngai
“It doesn’t give us the answer, but it’s a basis for addressing that profound question,” said John Ngai, director of the NIH’s BRAIN Initiative. “And the cell census provides the opportunity to link genetic predispositions with actual disease and point the finger at what cell types are involved. So it is really laying the foundation for finding future cures.”
The cell census — part of the NIH’s Brain Research Through Advancing Innovative Neurotechnologies (BRAIN) initiative launched by former President Barack Obama in 2013 — offers an unprecedented look at how genes are turned on and off throughout the brain.
“Getting this level of resolution has just not been possible until now. And consequently, we haven’t been very successful at coming up with new therapeutics for brain diseases, partly because we just don’t know what we should be targeting,” said Ed Lein, a neuroscientist who is leading several aspects of the projects at the Allen Institute for Brain Science.
Taking a census of the brain
Scientists have long known that the brain contains a remarkable diversity of cell types, thanks to the exquisite ink drawings of Spanish neuroscientist Santiago Ramón y Cajal, who revealed the many arboreal shapes of neurons and their branching connections more than a century ago.
Yet tools that enable scientists to parse fine differences in cells have only recently come into the fore. Single cell sequencing technologies, which can measure many aspects of how cells use their genes, are laying bare the diversity of cells in the brain in stunning detail.
Sten Linnarsson
“Before we had single cell technologies, we were measuring mixtures of cells. It was like having very blurred vision,” said Sten Linnarsson, a molecular biologist at the Karolinska Institute in Sweden. “And single cell technology is like when our iPhone screens became sharp enough that you couldn’t see the pixels anymore. You see all the details.”
But finding the perfect brain is the first step. Researchers in Dirk Keene’s neuropathology lab at the University of Washington are on call day and night in the event that a brain becomes available. Keene has orchestrated a network in Seattle to find people who have recently died and ask their families for permission to anonymously donate the brain to science.
The brain must be unblemished, and needs to be collected and processed within 24 hours, ideally less, because the RNA molecules measured to assess gene expression are notoriously fragile and quickly degrade. A fresh brain has a consistency almost like pudding, Keene said, so his group embeds the organ in dental cement to hold it together.
The resulting block is sliced into 4-millimeter slabs that are carefully frozen in an ultra-cold slurry of a molecule found in natural gas. Genome-containing nuclei dissected from about 100 regions across those brain slices were then analyzed by three teams of researchers to paint a picture of how cells vary across the brain.
Ed Lein
Lein and Linnarsson led a group focused on RNA sequencing, measuring thousands of the messenger molecules — each encoding instructions for making a protein — in more than 3 million nuclei. The resulting data revealed 3,313 kinds of brain cells, many of which were unexpectedly buried deep in the midbrain and hindbrain, evolutionarily ancient brain regions for functions like breathing, eating, and sleeping, rather than in the wrinkled neocortex that’s the seat of higher thinking.
“We’re rarely surprised anymore, but I was surprised by that,” Lein said. “We don’t know what they do yet, but it certainly sets the stage for a lot of discovery that’s probably going to be relevant to behavior and disease.”
Joe Ecker
Joe Ecker, a scientist at the Salk Institute for Biological Studies, led a team that studied DNA methylation — chemical marks that silence genes — throughout the brain. Another group led by Bing Ren from the University of California, San Diego, looked at how chromatin — the condensed form of DNA — is opened or closed in cells across the brain.
Both data-packed studies provide a resource for pinpointing where genetic variants previously uncovered in genome-wide association studies (GWAS) are exerting their positive or negative influences. If a variant is found in DNA that’s unmethylated and unspooled from the rest of the compact chromatin, it’s likely important in that cell.
“Basically it’s providing a tool to interpret all of the GWAS data and bringing it into a cell type-specific context,” Ecker said. “It gives very good clues for where to look in the brain for particular diseases.”
Looking across ages, and species, for clues to disease
Other studies in the BICCN effort compared portions of human brains across development, or compared human brains to those of our closest primate relatives to provide new clues about disorders including autism and schizophrenia, whose roots appear to take hold in cells that appear early in life and disappear from adults.
Arnold Kriegstein
Arnold Kriegstein, a researcher at UCSF, led a study conducting RNA sequencing of brain samples from 106 individuals spanning ages as young as second trimester fetuses, through infants, children, adolescents, and adults.
“Many of the diseases that are the most mysterious and difficult to treat arise during earlier stages of development,” Kriegstein said. “And if we’re going to treat them, or try to prevent them, we really have to have a better understanding of how they emerge.”
In one intriguing observation, his group found that many of the cells expressing the highest number of genes linked to autism were in female brains, even though males are more likely to develop autism, which Kriegstein said suggests that female brains may be “relatively protected” against some of those risk factors.
Such observations may not lead directly to therapies aimed at a developing fetus — an unlikely prospect — but could give biologists and drugmakers a better understanding of how a disease takes shape, “and may help us unravel what the downstream consequences are that we can deal with,” Kriegstein said.
Trygve Bakken
Allen Institute neuroscientist Trygve Bakken led another comparative study between human brains and those of other primates. He found that we share remarkably similar types of brain cells with chimps, but had notable differences in how some genes are expressed at lower or higher levels at the connections between neurons.
Studying these differences is more than a philosophical curiosity. Comparisons across mice, monkeys, and humans can also allow scientists to better understand how similar or different their animal models are to people. Some studies already suggest that several brain diseases could be unique to humans, including some forms of neuropsychiatric conditions and neurodegeneration.
“There are some hypotheses that some of the changes that differentiate us from primates led to higher cognitive abilities, but also put us at greater risk for disease,” Bakken said. Understanding those differences could unlock the mysterious causes of those conditions.
Fueling new medicines
The cell census and comparative brain studies are stepping stones to plotting even more detailed maps of the brain. Those studies are already underway, along with additional NIH-backed efforts to begin designing research tools and genetic medicines that target specific brain cells or circuits, based on data from the census and atlas.
“The goal in the next four to five years is to have a comprehensive atlas and inventory of all cell types in the human brain across the lifespan, and from people with different ancestral backgrounds,” Ngai said.
That effort, known as the BRAIN Initiative Cell Atlas Network (BICAN), will use recently completed mouse brain atlases as a guide. Studies posted on preprint servers, but not yet published in peer-reviewed journals, employed methods known as spatial transcriptomics to precisely reveal how different cell types are arranged cell-by-cell throughout the brain — something that the human cell census only hinted at.
The mouse brain studies reveal about 5,000 cell types, more than have been found in humans so far. “So the final number of cell types in the human brain is probably going to end up well north of 5,000,” Linnarsson said. “It is by far the most complex organ of the body.”
In addition to precisely plotting where all the brain cells are in the BICAN project, the NIH is funding the BRAIN Initiative Connectivity Across Scales project to create a wiring diagram outlining all the connections throughout the human brain.
“If you have the parts list, the atlas, and the wiring diagram, you basically have the ground truth for what the brain looks like,” Ngai said. “That’s not going to tell you how the brain works. But it’s necessary to do so.”
Another NIH effort called the Armamentarium for Precision Brain Cell Access aims to take regulatory elements of DNA used to turn genes on or off in specific cell types and use them to develop viral-based gene therapies or RNA therapies that only work when they are in the right cell. That could help overcome problems with existing gene therapies, which can only be injected into the brain at large, and can’t target particular cells or circuits.
“Ultimately we want to use this as information for developing precision circuit therapies, including gene therapies, in humans,” Ngai said. “And I think we actually have the tools to get us there.”
Even drug developers working with more traditional therapies, such as small molecules, may find the cell census and atlas useful for predicting and minimizing side effects, especially alongside other efforts to develop similar cell atlases for every organ of the body.
“You can take any drug target and see where it’s likely to have an effect anywhere in the body,” Lein said. “And I think that’s going to be golden for therapeutic development.”
Lein and others have compared the potential impact of this brain mapping to the Human Genome Project, which didn’t lead to new therapies immediately, but fundamentally altered how biology was done, and ultimately led to a bounty of new clues about what causes disease.
“In the longer run, this will become just part of how you do science and medicine,” Lein said.
AUTHOR
Ryan Cross
Senior Science Correspondent
[email protected]
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