Stanford-led study finds the human brain is built from two separate organs, not one

The human brain, long described as a single organ that grew more complex over the course of evolution, is in fact assembled from two separate lineages of cells that arise independently in the earliest days of embryonic development and never mix, according to a study published this month in Nature Neuroscience. Researchers led by Stanford Medicine found that the forebrain and midbrain — the tissue responsible for language, abstract reasoning and conscious thought — descend from a wholly different population of progenitor cells than the hindbrain, the older structure that keeps the heart beating, the lungs breathing and the throat swallowing.

The finding, based on experiments in mouse embryos and human stem cells and cross-checked against five other species spanning more than half a billion years of evolution, upends a developmental model that has stood largely unchallenged since the nineteenth century, when anatomists first described the vertebrate brain as a single tube that bulges into three connected chambers. The new work indicates that the "tube" is better understood as two separate organs pushed together early in development and wired to cooperate, rather than one structure that differentiates from a common source.

What the researchers found

The Stanford-led team, working with collaborators at the Loh Laboratory at Stanford's Institute for Stem Cell Biology and Regenerative Medicine along with scientists at Caltech and UC San Francisco, traced brain development back to gastrulation, the earliest stage at which an embryo organizes into distinct layers of tissue. At that point, they identified two populations of progenitor cells that are already committed to different fates and that never overlap. One population switches on a gene called Otx2 and goes on to build the forebrain and midbrain. The other switches on a gene called Gbx2 and builds only the hindbrain, also known as the brainstem.

Using single-cell sequencing, the researchers showed that the two progenitor populations carry different chromatin configurations — the molecular packaging that determines which genes a cell can and cannot turn on — effectively locking each group onto its own developmental track before the rest of the nervous system has even formed. The team then confirmed the same forebrain-versus-hindbrain split in chickens, zebrafish and acorn worms, and pointed to jellyfish, which possess two separate nerve nets at opposite ends of their bodies, as a living example of what the ancestral, unfused arrangement may have looked like. Altogether the comparison spans roughly 550 million years of animal evolution, according to the Stanford Medicine announcement of the findings.

Kyle Loh, an associate professor of developmental biology at Stanford and the study's senior author, said the divide was more fundamental than anything the field had previously described in the brain's early architecture. "We've shown for the first time that the front of the brain arises from a totally different progenitor cell than the back of the brain," Loh said, according to the university. "Our discovery means that we can now grow neurons from the back of the brain, the hindbrain, in a petri dish and study their functions."

How the field got here

Textbooks have for more than a century depicted the vertebrate central nervous system as arising from a single neural tube that folds shut along the embryo's back and then balloons into three primary vesicles — the prosencephalon, mesencephalon and rhombencephalon, which mature into the forebrain, midbrain and hindbrain. That model treated the three regions as sequential subdivisions of one continuous structure, the way a single piece of dough might be pinched into three connected sections. Because the boundaries were visible anatomically but the underlying cell lineages had never been mapped with modern single-cell tools, researchers had assumed, without testing directly, that all three vesicles traced back to a shared pool of neural progenitor cells.

Rayyan Jokhai, a graduate student in Loh's lab and one of the study's co-first authors along with fellow graduate student Carolyn Dundes, said the result ran against that assumption from the outset. "I was surprised at our findings because the word 'brain' implies a contiguous organ that likely has a singular origin," Jokhai said. The lab's earlier attempts to coax stem cells into hindbrain neurons had produced disappointing yields, Jokhai added, and the new lineage map explained why: those experiments had been starting from forebrain-destined progenitor cells that were never capable of making the switch. "Previous attempts to make hindbrain neurons likely tried to coax forebrain and midbrain progenitors into hindbrain cells, which our study shows is not possible," Jokhai said.

"Our research suggests that evolution took two existing neural systems and pushed them together spatially. Having the brain as one organ would probably be more efficient, but we rely on this primordial way to make the brain as two separate pieces." — Kyle Loh, associate professor of developmental biology, Stanford Medicine

Who stands to benefit

The practical payoff is a new way to grow hindbrain and brainstem tissue in the laboratory. Using the lineage map, the team generated functional human hindbrain motor neurons from pluripotent stem cells, cells that had been largely inaccessible to researchers because standard stem-cell protocols default toward forebrain fates. That matters most directly for patients with diseases that begin in the brainstem and spinal cord, including amyotrophic lateral sclerosis and spinal muscular atrophy, both of which destroy the motor neurons that the new protocol can now produce on demand. Jokhai said the lab intends to use the resulting cells as a disease model. "Now we have a model to better understand these devastating diseases, and work toward regenerative therapies for them," Jokhai said.

The hindbrain also governs breathing, heart rate, blood pressure and hunger signaling, so the same cell-culture approach could eventually give researchers a more direct way to study conditions tied to those functions, including some forms of obesity linked to disrupted hindbrain appetite circuits, and congenital breathing disorders in infants. Loh's team reported that the work was supported by the National Institutes of Health, the National Science Foundation, the California Institute for Regenerative Medicine, the Spinal Muscular Atrophy Foundation, the Howard Hughes Medical Institute and several private foundations, according to Stanford.

Reaction and what comes next

The study has drawn attention from developmental biologists outside the Stanford group for the scale of the evolutionary comparison as much as for the mechanism itself. Coverage in ScienceDaily's summary of the paper and in a write-up from Neuroscience News both framed the result as a rare case of a discovery that changes how a basic organ is defined rather than simply adding detail to an existing picture; a separate account from Medical Xpress noted that the split origin had gone undetected for so long in part because the forebrain-to-hindbrain boundary looks seamless once the neural tube has closed, masking the fact that the cells on either side of it were never interchangeable.

Dundes, the study's other co-first author, said she hoped the finding would draw more young scientists into basic developmental biology rather than only translational work. "I hope our study inspires future scientists to study developmental biology," Dundes said. "I can't think of anything more rewarding than unraveling a little mystery of our brain's origins."

The Stanford group's next step is to determine what keeps the two progenitor populations from mixing once they are established, and whether nudging the boundary between them in either direction is possible without disrupting development elsewhere. The lab is also working to scale up production of the lab-grown hindbrain motor neurons for use in drug-screening experiments aimed at ALS and spinal muscular atrophy, according to Stanford, with the goal of testing candidate therapies against human cells rather than animal models alone. Loh said the underlying question, of why vertebrates never fully merged the two systems into one, remains open. Having the brain as one organ would probably be more efficient, he said, but evolution instead preserved it as two.