When you clicked to read this story, a band of cells across the top of your
brain sent signals down your spine and out to your hand to tell the muscles in
your index finger to press down with just the right amount of pressure to
activate your mouse or track pad.
A slew of new studies now shows that the area of the brain responsible for
initiating this action -- the primary motor cortex, which controls movement
-- has as many as 116 different types of cells that work together to make
this happen.
The 17 studies, appearing online Oct. 6 in the journal Nature, are the
result of five years of work by a huge consortium of researchers supported
by the National Institutes of Health's Brain Research Through Advancing
Innovative Neurotechnologies (BRAIN) Initiative to identify the myriad of
different cell types in one portion of the brain. It is the first step in a
long-term project to generate an atlas of the entire brain to help
understand how the neural networks in our head control our body and mind and
how they are disrupted in cases of mental and physical problems.
"If you think of the brain as an extremely complex machine, how could we
understand it without first breaking it down and knowing the parts?" asked
cellular neuroscientist Helen Bateup, a University of California, Berkeley,
associate professor of molecular and cell biology and co-author of the
flagship paper that synthesizes the results of the other papers. "The first
page of any manual of how the brain works should read: Here are all the
cellular components, this is how many of them there are, here is where they
are located and who they connect to."
Individual researchers have previously identified dozens of cell types based
on their shape, size, electrical properties and which genes are expressed in
them. The new studies identify about five times more cell types, though many
are subtypes of well-known cell types. For example, cells that release
specific neurotransmitters, like gamma-aminobutyric acid (GABA) or
glutamate, each have more than a dozen subtypes distinguishable from one
another by their gene expression and electrical firing patterns.
While the current papers address only the motor cortex, the BRAIN Initiative
Cell Census Network (BICCN) -- created in 2017 -- endeavors to map all the
different cell types throughout the brain, which consists of more than 160
billion individual cells, both neurons and support cells called glia. The
BRAIN Initiative was launched in 2013 by then-President Barack Obama.
"Once we have all those parts defined, we can then go up a level and start
to understand how those parts work together, how they form a functional
circuit, how that ultimately gives rise to perceptions and behavior and much
more complex things," Bateup said.
Together with former UC Berkeley professor John Ngai, Bateup and UC Berkeley
colleague Dirk Hockemeyer have already used CRISPR-Cas9 to create mice in
which a specific cell type is labeled with a fluorescent marker, allowing
them to track the connections these cells make throughout the brain. For the
flagship journal paper, the Berkeley team created two strains of "knock-in"
reporter mice that provided novel tools for illuminating the connections of
the newly identified cell types, she said.
"One of our many limitations in developing effective therapies for human
brain disorders is that we just don't know enough about which cells and
connections are being affected by a particular disease and therefore can't
pinpoint with precision what and where we need to target," said Ngai, who
led UC Berkeley's Brain Initiative efforts before being tapped last year to
direct the entire national initiative. "Detailed information about the types
of cells that make up the brain and their properties will ultimately enable
the development of new therapies for neurologic and neuropsychiatric
diseases."
Ngai is one of 13 corresponding authors of the flagship paper, which has
more than 250 co-authors in all.
Bateup, Hockemeyer and Ngai collaborated on an earlier study to profile all
the active genes in single dopamine-producing cells in the mouse's midbrain,
which has structures similar to human brains. This same profiling technique,
which involves identifying all the specific messenger RNA molecules and
their levels in each cell, was employed by other BICCN researchers to
profile cells in the motor cortex. This type of analysis, using a technique
called single-cell RNA sequencing, or scRNA-seq, is referred to as
transcriptomics.
The scRNA-seq technique was one of nearly a dozen separate experimental
methods used by the BICCN team to characterize the different cell types in
three different mammals: mice, marmosets and humans. Four of these involved
different ways of identifying gene expression levels and determining the
genome's chromatin architecture and DNA methylation status, which is called
the epigenome. Other techniques included classical electrophysiological
patch clamp recordings to distinguish cells by how they fire action
potentials, categorizing cells by shape, determining their connectivity, and
looking at where the cells are spatially located within the brain. Several
of these used machine learning or artificial intelligence to distinguish
cell types.
"This was the most comprehensive description of these cell types, and with
high resolution and different methodologies," Hockemeyer said. "The
conclusion of the paper is that there's remarkable overlap and consistency
in determining cell types with these different methods."
A team of statisticians combined data from all these experimental methods to
determine how best to classify or cluster cells into different types and,
presumably, different functions based on the observed differences in
expression and epigenetic profiles among these cells. While there are many
statistical algorithms for analyzing such data and identifying clusters, the
challenge was to determine which clusters were truly different from one
another -- truly different cell types -- said Sandrine Dudoit, a UC Berkeley
professor and chair of the Department of Statistics. She and biostatistician
Elizabeth Purdom, UC Berkeley associate professor of statistics, were key
members of the statistical team and co-authors of the flagship paper.
"The idea is not to create yet another new clustering method, but to find
ways of leveraging the strengths of different methods and combining methods
and to assess the stability of the results, the reproducibility of the
clusters you get," Dudoit said. "That's really a key message about all these
studies that look for novel cell types or novel categories of cells: No
matter what algorithm you try, you'll get clusters, so it is key to really
have confidence in your results."
Bateup noted that the number of individual cell types identified in the new
study depended on the technique used and ranged from dozens to 116. One
finding, for example, was that humans have about twice as many different
types of inhibitory neurons as excitatory neurons in this region of the
brain, while mice have five times as many.
"Before, we had something like 10 or 20 different cell types that had been
defined, but we had no idea if the cells we were defining by their patterns
of gene expression were the same ones as those defined based on their
electrophysiological properties, or the same as the neuron types defined by
their morphology," Bateup said.
"The big advance by the BICCN is that we combined many different ways of
defining a cell type and integrated them to come up with a consensus
taxonomy that's not just based on gene expression or on physiology or
morphology, but takes all of those properties into account," Hockemeyer
said. "So, now we can say this particular cell type expresses these genes,
has this morphology, has these physiological properties, and is located in
this particular region of the cortex. So, you have a much deeper, granular
understanding of what that cell type is and its basic properties."
Dudoit cautioned that future studies could show that the number of cell
types identified in the motor cortex is an overestimate, but the current
studies are a good start in assembling a cell atlas of the whole brain.
"Even among biologists, there are vastly different opinions as to how much
resolution you should have for these systems, whether there is this very,
very fine clustering structure or whether you really have higher level cell
types that are more stable," she said. "Nevertheless, these results show the
power of collaboration and pulling together efforts across different groups.
We're starting with a biological question, but a biologist alone could not
have solved that problem. To address a big challenging problem like that,
you want a team of experts in a bunch of different disciplines that are able
to communicate well and work well with each other."
Other members of the UC Berkeley team included postdoctoral scientists
Rebecca Chance and David Stafford, graduate student Daniel Kramer, research
technician Shona Allen of the Department of Molecular and Cell Biology,
doctoral student Hector Roux de Bézieux of the School of Public Health and
postdoctoral fellow Koen Van den Berge of the Department of Statistics.
Bateup is a member of the Helen Wills Neuroscience Institute, Hockemeyer is
a member of the Innovative Genomics Institute, and both are investigators
funded by the Chan Zuckerberg Biohub.
Reference:
BRAIN Initiative Cell Census Network (BICCN). A multimodal cell census and
atlas of the mammalian primary motor cortex. Nature, 2021; 598 (7879): 86
DOI: 10.1038/s41586-021-03950-0
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