Modeling the Human Brain | Inside Precision Medicine

No one knows when humans first pondered how knowledge of the brain could be applied to medicine. What we do know is that it happened long ago. As one example, a papyrus from the 17^th century B.C. found in an Egyptian tomb tried to connect head injuries with brain damage. Thousands of years later, though, scientists still face obstacles to learning more about the human brain.

When I ask Stanislav Zakharenko, MD, PhD, director of the division of neural circuits and behavior at St. Jude Children’s Research Hospital in Memphis, TN, about the primary benefits of using models in neurobiological research, he said, “That’s very easy. We don’t have access to the human tissue, and we don’t have easy access to human neurobiology.”

Scientists have examined postmortem brains, recorded electric signals through the skull in living people, and applied various imaging techniques in people performing tasks, but all of these techniques have difficulty answering a key question: how do circuits of neurons work in a human brain?

To explore this question, scientists often studied the brains of model organisms such as mice and rats. Still, scientists wondered how much these models taught us about the human brain. Although rodents and humans are “not that different on the basic level, we are definitely different in many, many, many aspects: our brain is bigger; we’re making more complex calculations and decisions than mice do during the whole day,” Zakharenko said.

Beyond the curiosity about basic brain functions, scientists hope to use this information to better understand brain-related diseases and how to treat them. In some cases, exploring the neurobiology of diseases requires a close look at neurons. So, in addition to studying the brains of rodents, scientists grow cultures of brain cells. This started with 2D cultures, like a single layer of brain cells, and progressed to 3D cultures of cells. In the early 2000s, scientists developed brain organoids, which are 3D cultures of brain cells intended to mimic the human brain. In 2017, Sergiu Pasca, MD, director of the Stanford brain organogenesis program, and his colleagues described simultaneously culturing different types of neural cells to produce assembloids, which are 3D models of more than one brain region, such as two areas of the cortex.Now, scientists face a new question in neuroscience research: how closely do organoids or assembloids replicate the natural structure and function of a brain?

How to make a human brain organoid

Making a human brain organoid starts with pluripotent stem cells, which can make any kind of cell. Although such cells can be obtained from human embryonic tissue, scientists usually start with adult human cells and turn them into induced pluripotent stem cells (iPSCs) through chemical or genetic processes.

Next, 3D culturing methods are used to grow those iPSCs. With the properly timed addition of growth factors and other molecules, the iPSCs develop into specific kinds of brain cells. Instead of growing randomly, these cells self-organize. As a result, the cells build structures, such as specific regions of the human cortex or other brain areas. “The great promise of organoids is the self-organization,” Zakharenko said.

An assembloid is produced by developing and combining organoids that replicate different regions of the brain. With this method, for example, more than one kind of cortical region can be combined to study how the regions interact.

Organoids are usually made through unguided or guided approaches. An unguided protocol “generates different brain regions in a disorganized fashion,” and a guided protocol “generates only one brain region,” explained Alysson Muotri, PhD, professor of pediatrics and cellular and molecular medicine at the University of California San Diego School of Medicine. In addition, Muotri mentioned a third, semi-guided method, which “can be achieved by giving embryonic cues according to human neurodevelopment.”

The basic idea behind organoids and assembloids is that they self-organize in ways that are similar to the normal human brain. “About 50% of biologists believe this is true, and about 50% believe it’s not true,” Zakharenko said. At best, he believes that brain organoids or assembloids make a “very rudimentary model of how these neurons from one brain region connect to the neurons of other brain regions and represent what’s happening in our brain.” Rudimentary or not, he called it “a good first step.”

Synaptic plasticity and schizophrenia

Although Zakharenko did not know it at the time, his first step toward organoids started with his interest in the biology of schizophrenia. For example, he pointed out that the 22q11.2 deletion syndrome, often called DiGeorge syndrome, which arises because a chunk of DNA—25 to 40 genes—is missing on chromosome 22, underlies a high risk of developing schizophrenia. According to Zakharenko, this syndrome creates “a tremendous increase in risk, like 25- or 30-fold” of developing schizophrenia.

The section of DNA deleted in DiGeorge syndrome can also be deleted in mice. In these mouse models of schizophrenia, Zakharenko studied brain circuits, but they seemed normal.

“I was very, very frustrated,” Zakharenko said. “How is it that the deletion of 30 genes can have no consequences whatsoever?”

Eventually, Zakharenko’s team found one consequence. The deletion disrupted circuits between the thalamus, deep in the center of the brain, and the auditory cortex. Moreover, anti-psychotic drugs rescued this disruption. This made sense to Zakharenko, because hallucinations are a common symptom of schizophrenia, and “85% of all of these hallucinations are auditory,” he said.

To look for similar changes in circuits in people with schizophrenia, Zakharenko’s team used a guided protocol to make human thalamic and cortical organoids and then combined them to make human thalamocortical assembloids.

So far, Zakharenko and his colleagues have used these assembloids to study synaptic plasticity, which is the stimulus-based strengthening or weakening between connections that play a role in forming memories. As Zakharenko and his colleagues pointed out: “Aberrant synaptic plasticity is well documented in animal models of autism, schizophrenia, and other psychiatric disorders, but full insight into these disorders requires a human model system.” To use thalamocortical assembloids to study schizophrenia, though, the scientists face a crucial obstacle: schizophrenia-driven hallucinations usually arise in adolescents or young adults, but the assembloids consist of young cells. So, the neurons in these assembloids will not mature enough to allow Zakharenko to study the underlying cause of these hallucinations, “unless we really just wait for 20 years,” he said.

In the meantime, Zakharenko can use the assembloids to study synaptic plasticity. Eventually, similar assembloids might tell scientists more about schizophrenia. “Who knows?” asked Zakharenko. “Maybe people will come up with a model that contains more mature neurons.”

Searching for signals

To help other scientists employ brain organoids, Muotri and his colleagues published a protocol for making semi-guided cortical organoids. As Muotri says, “In my opinion, semi-guided protocols are the future of the organoid technology.”

In semi-guided human cortical organoids, Muotri’s team found various cortical cells, including glial cells and neurons in various stages of development. The performance of a brain, though, is about more than the presence of cells. The neurons form circuits that create patterns of electrical activity across the brain, which can be recorded with electroencephalography.

To find out if such activity developed in Muotri’s organoids, the team grew them on an Axion Biosystems Maestro Pro system, which includes a microelectrode array (MEA). Based on recordings from this platform, Muotri said, “Neural oscillations generated by semi-guided protocols are indistinguishable from the oscillations found in the human brain.” That is, the shapes of the waves look the same, or as Muotri put it: “the ones that can be compared are strikingly similar, confirming the functional advantages of semi-guided organoids.” Nonetheless, Muotri added that “it is important to note that the human brain produces more oscillations than these organoids.”

Other scientists also study the electrophysiology of organoids or assembloids. For instance, Eugenio Martinelli, PhD, professor of electronic engineering at the University of Rome Tor Vergata, used MEAs to explore various features of assembloids. “We monitored the distribution of neuronal spikes over time to study the evolution of network dynamics, including in the presence of specific diseases,” Martinelli said. “By applying targeted external stimuli, we also investigated how neuronal activity patterns responded to perturbations, using novel AI algorithms developed specifically for this application.” This work produced useful information, including “insights into the development of functional connectivity and responsiveness in brain organoids, highlighting their potential as in vitro models for studying neural network behavior and disease modeling,” Martinelli said.

Martinelli plans to dig even deeper into the electrophysiology of brain-related assembloids by using high-density MEAs. With this technology, Martinelli expects his lab to “achieve greater spatial resolution in capturing neuronal signals.” In fact, he plans to combine electrical and optical techniques to study how a neuron’s structure impacts signaling at synapses in these brain assembloids.

“We aim to explore inter-electrode array correlations to gain deeper insights into functional connectivity and information flow within these complex 3D neural models,” Martinelli said. “This research is crucial for advancing our understanding of brain development and for modeling neurological disorders in more physiologically relevant systems.”

Even with unguided protocols, human brain organoids “exhibit spontaneous electrophysiological activity in both stable firing and burst firing patterns,” according to Feng Guo, PhD, associate professor of intelligent systems engineering at Indiana University Bloomington, and his colleagues, but “high variability as well as the heterogeneity of [these] organoids are stumbling blocks for quantitative studies.”

A guided protocol produces more consistent human brain organoids. In these organoids, “periodic oscillatory network activities are observed in 8-month-old organoids,” Guo’s team noted. “Although these neural network activities do not recapitulate the full temporal complexity in adults, synchronous network events exhibit characteristics comparable to those seen in preterm neonatal electroencephalography.”

To make human organoids even better models of the brain, as Guo’s team pointed out, other features, such as a vascular system, need to be added.

Reproducing pathways to pain

Organoids and assembloids can also be used to learn more about one of the most common ailments—pain. In particular, scientists are searching for non-opioid treatments that are effective, but not addictive. Assembloids could provide a crucial model system for testing new treatments for pain. However, pain arises from a complex network of neural pathways. So, model assembloids need to mimic multiple peripheral and central regions of the nervous system.

That’s just what Pasca and his colleagues achieved. These scientists developed a human ascending somatosensory assembloid (hASA) by combining human somatosensory, spinal, thalamic, and cortical organoids. Such an assembloid models pathways from neurons in the spinal cord to ones in the brain, and transmits signals related to pain and other sensory information. As Pasca’s team showed, noxious chemical stimulation produced coordinated neural signaling in hASAs.

In the human peripheral nervous system, specific voltage-gated sodium channels, particularly Na_v1.7 and Na_v1.8, play key roles in processing pain. Pasca’s team used CRISPR-based editing to decrease the levels of Na_v1.7 channels in hASAs. As these scientists reported: “Notably, loss of the sodium channel Na_v1.7, which causes pain insensitivity, disrupted synchrony across hASA.” Increasing the expression of SCN9A, which encodes the proteins that build the Na_v1.7 channels, increased stimulus-induced synchrony of neural activity in the hASAs.

So, this assembloid model of pain could be used in many ways. As Pasca’s team put it: “These experiments demonstrated the ability to functionally assemble the essential components of the human sensory pathway, which could accelerate our understanding of sensory circuits and facilitate therapeutic development.” In particular, the hASAs could be used to screen novel, non-opioid treatments for pain.

Pasca’s team also works on other potential therapies. As one example, Pasca and his colleagues included organoids and assembloids in the development of a model of Timothy syndrome, which they described as “a severe, multisystem disorder characterized by autism, epilepsy … and other neuropsychiatric conditions.” According to Pasca, this work “led to the first potential therapeutic developed exclusively with stem-cell models.” In addition, organoids and assembloids might one day be created from a patient’s disease cells and used to develop a specific treatment for that person.

Most scientists would probably agree that organoids and assembloids reveal much more information about the brain than can be gleaned from a 2D culture of cells. How closely that information correlates with a living human brain, though, remains a matter of debate.

Read more:

1. Birey, F., Andersen, J., Makinson, C.D., et al. Assembly of functionally integrated human forebrain spheroids. Nature 545:54–59. (2017).
2. Patton, M.H., Thomas, K.T., Bayazitov, I.T., et al. Synaptic plasticity in human thalamocortical assembloids. Cell Reports 43, 114503. (2024).
3. Fitzgerald, M.Q., Chu, T., Puppo, F., et al. Generation of ‘semi-guided’ cortical organoids with complex neural oscillations. Nature Protocols 19:2712–2738. (2025).
4. Mencattini, A., Daprati, E., Della-Motre, D., et al. Assembloid learning: opportunities and challenges for personalized approaches to brain functioning in health and disease. Frontiers in Artificial Intelligence 7, 1385871. (2024).
5. Gu, L., Cai, H., Chen, L., et al. Functional neural networks in human brain organoids. BME Frontiers 5, 0065. (2024).
6. Kim, J-i., Imaizumi, K., Jurjut, O., et al. Human assembloid model of the ascending neural sensory pathway. Nature (2025). doi:10.1038/s41586-025-08808-3.
7. Chen, X., Birey, F., Li, M-Y., et al. Antisense oligonucleotide therapeutic approach for Timothy syndrome. Nature 628:818–825. (2024).

Mike May, PhD, is a freelance writer and editor with more than 30 years of experience. He earned an MS in biological engineering from the University of Connecticut and a PhD in neurobiology and behavior from Cornell University. He worked as an associate editor at American Scientist, and he is the author of more than 1,000 articles for clients that include GEN, Nature, Science, Scientific American, and many others. In addition, he served as the editorial director of many publications, including several Nature Outlooks and Scientific American Worldview.