Surprisingly simple model explains how brain cells organize and connect

ANARCHY IS IN YOUR HEAD

Scientists from UChicago, Harvard, and Yale propose a self-organizing model of connectivity that applies across a wide range of organisms and potentially other types of networks as well.

@ IS SELF ORGANIZATION

UNIVERSITY OF CHICAGO

A new study by physicists and neuroscientists from the University of Chicago, Harvard and Yale describes how connectivity among neurons comes about through general principles of networking and self-organization, rather than the biological features of an individual organism.

The research, published on January 17, 2024 in Nature Physics, accurately describes neuronal connectivity in a variety of model organisms and could apply to non-biological networks like social interactions as well.

“When you’re building simple models to explain biological data, you expect to get a good rough cut that fits some but not all scenarios,” said Stephanie Palmer, PhD, Associate Professor of Physics and Organismal Biology and Anatomy at UChicago and senior author of the paper. “You don’t expect it to work as well when you dig into the minutiae, but when we did that here, it ended up explaining things in a way that was really satisfying.”

Understanding how neurons connect

Neurons form an intricate web of connections between synapses to communicate and interact with each other. While the vast number of connections may seem random, networks of brain cells tend to be dominated by a small number of connections that are much stronger than most.

This “heavy-tailed” distribution of connections (so-called because of the way it looks when plotted on a graph) forms the backbone of circuitry that allows organisms to think, learn, communicate and move. Despite the importance of these strong connections, scientists were unsure if this heavy-tailed pattern arises because of biological processes specific to different organisms, or due to basic principles of network organization.

To answer these questions, Palmer and Christopher Lynn, PhD, Assistant Professor of Physics at Yale University, and Caroline Holmes, PhD, a postdoctoral researcher at Harvard University, analyzed connectomes, or maps of brain cell connections. The connectome data came from several different classic lab animals, including fruit flies, roundworms, marine worms and the mouse retina.

To understand how neurons form connections to one another, they developed a model based on Hebbian dynamics, a term coined by Canadian psychologist Donald Hebb in 1949 that essentially says, “neurons that fire together, wire together.” This means the more two neurons activate together, the stronger their connection becomes.

Across the board, the researchers found these Hebbian dynamics produce “heavy-tailed” connection strengths just like they saw in the different organisms. The results indicate that this kind of organization arises from general principles of networking, rather than something specific to the biology of fruit flies, mice, or worms.

The model also provided an unexpected explanation for another networking phenomenon called clustering, which describes the tendency of cells to link with other cells via connections they share. A good example of clustering occurs in social situations. If one person introduces a friend to a third person, those two people are more likely to become friends with them than if they met separately.

"These are mechanisms that everybody agrees are fundamentally going to happen in neuroscience,” Holmes said. “But we see here that if you treat the data carefully and quantitatively, it can give rise to all of these different effects in clustering and distributions, and then you see those things across all of these different organisms.”

Accounting for randomness

As Palmer pointed out, though, biology doesn’t always fit a neat and tidy explanation, and there is still plenty of randomness and noise involved in brain circuits. Neurons sometimes disconnect and rewire with each other — weak connections are pruned, and stronger connections can be formed elsewhere. This randomness provides a check on the kind of Hebbian organization the researchers found in this data, without which strong connections would grow to dominate the network.

The researchers tweaked their model to account for randomness, which improved its accuracy.

“Without that noise aspect, the model would fail,” Lynn said. “It wouldn’t produce anything that worked, which was surprising to us. It turns out you actually need to balance the Hebbian snowball effect with the randomness to get everything to look like real brains.”

Since these rules arise from general networking principles, the team hopes they can extend this work beyond the brain.

“That’s another cool aspect of this work: the way the science got done,” Palmer said. “The folks on this team have a huge diversity of knowledge, from theoretical physics and big data analysis to biochemical and evolutionary networks. We were focused on the brain here, but now we can talk about other types of networks in future work.”

The study, “Heavy–tailed neuronal connectivity arises from Hebbian self–organization,” was supported by the National Science Foundation, through the Center for the Physics of Biological Function (PHY–1734030) and a Graduate Research Fellowship (C.M.H.); by the James S. McDonnell Foundation through a Postdoctoral Fellowship Award (C.W.L.); and by the National Institutes of Health BRAIN initiative (R01EB026943).

JOURNAL

Nature Physics

DOI

10.1038/s41567-023-02332-9

METHOD OF RESEARCH

Computational simulation/modeling

SUBJECT OF RESEARCH

Cells

ARTICLE TITLE

Heavy–tailed neuronal connectivity arises from Hebbian self–organization

ARTICLE PUBLICATION DATE

17-Jan-2024

Novel tissue-derived brain organoids could revolutionize brain research

Peer-Reviewed Publication

PRINCESS MÁXIMA CENTER FOR PEDIATRIC ONCOLOGY

Brain organoid - full — IMAGE:
AN IMAGE OF A WHOLE HUMAN FETAL BRAIN ORGANOID. STEM CELLS ARE MARKED BY SOX2 (GREY) AND NEURONAL CELLS (TUJ1) ARE COLOR CODED FROM PINK TO YELLOW BASED ON DEPTH.
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CREDIT: PRINCESS MÁXIMA CENTER, HUBRECHT INSTITUTE/B ARTEGIANI, D HENDRIKS, H CLEVERS

Press release – Princess Máxima Center for pediatric oncology

EMBARGO: 8 JANUARY 2024 AT 11:00 AM ET (US)

Scientists have developed 3D mini-organs from human fetal brain tissue that self-organize in vitro. These lab-grown organoids open up a brand-new way of studying how the brain develops. They also offer a valuable means to study the development and treatment of diseases related to brain development, including brain tumors.

Scientists use different ways to model the biology of healthy tissue and disease in the lab. These include cell lines, laboratory animals and, since a few years, 3D mini-organs. These so-called organoids have characteristics and a level of complexity that allows scientists to closely model the functions of an organ in the lab. Organoids can be formed directly from cells of a tissue. Scientists can also ‘guide’ stem cells – found in embryos or in some adult tissues – to develop into the organ they aim to study.

Until now, brain organoids were grown in the lab by coaxing embryonic or pluripotent stem cells to grow into structures representing different areas of the brain. Using a specific cocktail of molecules, they would try to mimic the natural development of the brain – with the ‘recipe’ for each cocktail taking a lot of research to develop.

Now, scientists at the Princess Máxima Center for pediatric oncology and the Hubrecht Institute, both based in Utrecht, the Netherlands, developed brain organoids directly from human fetal brain tissue. The study was published in the prestigious journal Cell today (Monday), and was part-funded by the Dutch Research Council.

The researchers, led by Dr. Delilah Hendriks, Prof. Dr. Hans Clevers and Dr. Benedetta Artegiani, were surprised to find that using small pieces of fetal brain tissue rather than individual cells was vital in growing mini-brains. To grow other mini-organs such as gut, scientists normally break down the original tissue to single cells. Instead working with small pieces of fetal brain tissue, the team found that these pieces could self-organize into organoids.

The brain organoids were roughly the size of a grain of rice. The tissue’s 3D make-up was complex, and it contained a number of different types of brain cells. Importantly, the brain organoids contained many so-called outer radial glia – a cell type found in humans and our evolutionary ancestors. This underlines the organoids’ close similarity to – and use in studying – the human brain.

The whole pieces of brain tissue also produced proteins that make up extracellular matrix – a kind of ‘scaffolding’ around cells. The team believes these proteins could be the reason why the pieces of brain tissue were able to self-organize into 3D brain structures. The presence of extracellular matrix in the organoids will allow further study of the environment of brain cells, and what happens when this goes wrong.

The researchers found that the tissue-derived organoids kept various characteristics of the specific region of the brain from which they were derived. They responded to signaling molecules known to play an important role in brain development. This finding suggests that the tissue-derived organoids could play an important role in untangling the complex network of molecules involved in directing the development of the brain.

Given the ability of the tissue-derived organoids to quickly expand, the team next investigated their potential in modeling brain cancer. The researchers used gene-editing technique CRISPR-Cas9 to introduce faults in the well-known cancer gene TP53 in a small number of cells in the organoids. After three months, the cells with defective TP53 had completely overtaken the healthy cells in the organoid – meaning they had acquired a growth advantage, a typical feature of cancer cells.

They then used CRISPR-Cas9 to switch off three genes linked to the brain tumor, glioblastoma: TP53, PTEN and NF1. The researchers also used these mutant organoids to look at their response to existing cancer drugs. These experiments showed the organoids’ potential for cancer drug research to link certain drugs to specific gene mutations.

The tissue-derived organoids continued to grow in a dish for more than six months. Importantly, the scientists could multiply them, allowing them to grow many similar organoids from one tissue sample. The mini-tumors with the glioblastoma gene changes – were also capable of multiplying, keeping the same mix of mutations. This feature means scientists can carry out repeat experiments with the tissue-derived organoids, increasing the reliability of their findings.

Next, the researchers aim to further explore the potential of their new tissue-derived brain organoids. They also plan to continue their work with bioethicists – who were already involved in shaping this research – to guide the future development and applications of the new brain organoids.

Dr. Benedetta Artegiani, research group leader at the Princess Máxima Center for pediatric oncology who co-led the research, says:

‘Brain organoids from fetal tissue are an invaluable new tool to study human brain development. We can now more easily study how the developing brain expands, and look at the role of different cell types and their environment.

‘Our new, tissue-derived brain model allows us to gain a better understanding of how the developing brain regulates the identity of cells. It could also help understand how mistakes in that process can lead to neurodevelopmental diseases such as microcephaly, as well as other diseases that can stem from derailed development, including childhood brain cancer.’

Dr. Delilah Hendriks, affiliated group leader at the Princess Máxima Center for pediatric oncology, postdoctoral researcher at the Hubrecht Institute and Oncode Investigator, who co-led the research, says:

‘These new fetal tissue-derived organoids can offer novel insights into what shapes the different regions of the brain, and what creates cellular diversity. Our organoids are an important addition to the brain organoid field, that can complement the existing organoids made from pluripotent stem cells. We hope to learn from both models to decode the complexity of the human brain.

‘Being able to keep growing and using the brain organoids from fetal tissue also means that we can learn as much as possible from such precious material. We’re excited to explore the use of these novel tissue organoids for new discoveries about the human brain.’

Prof. dr. Hans Clevers, pioneer in organoid research and former research group leader at the Hubrecht Institute and the Princess Máxima Center for pediatric oncology and Oncode Investigator, co-led the research. He says:

‘With our study, we’re making an important contribution to the organoid and brain research fields. Since we developed the first human gut organoids in 2011, it’s been great to see that the technology has really taken off. Organoids have since been developed for almost all tissues in the human body, both healthy and diseased – including an increasing number of childhood tumors.

‘Until now, we were able to derive organoids from most human organs, but not from the brain – it’s really exciting that we’ve now been able to jump that hurdle as well.’

The study was performed in collaboration with Leiden University Medical Center, Utrecht University, Maastricht University, Erasmus University Rotterdam, and National University of Singapore.

- ENDS -

Notes to editors

The human fetal tissue was derived from healthy abortion material, between gestational weeks 12-15, from fully anonymous donors. The anonymous women donated the tissue voluntarily and upon informed consent. They were informed that the material would be used for research purposes only, and that the research included the understanding of how organs normally develop, including the possibility to grow cells derived from the donated material.

About the Princess Máxima Center for pediatric oncology

When a child is seriously ill from cancer, only one thing matters: a cure.

Every year, 600 children in the Netherlands are diagnosed with cancer. Sadly, one in four of these children dies. That is why in the Princess Máxima Center for pediatric oncology, we work together with passion and without limits every day to improve the survival rate and quality of life of children with cancer. Now, and in the long term. Because children have their whole lives ahead of them.

The Princess Máxima Center is no ordinary hospital, but a research hospital. All children with cancer in the Netherlands are treated here, and it’s where all research into childhood cancer in the country takes place. This makes the Princess Máxima Center the largest pediatric cancer center in Europe. More than 900 healthcare professionals and 450 scientists work closely with Dutch and international hospitals to find better treatments and new perspectives for a cure.

In this way, we offer children today the best possible care, and we take important steps to improve survival for children who cannot not yet be cured.

A zoom-in image of a part of a human fetal brain organoid. Stem cells are marked by SOX2 (cyan) and neuronal cells (TUJ1) are color coded from pink to yellow based on depth.

Four zoom-in images of parts of different human fetal brain organoids. Different neural markers are stained, depicting their cellular heterogeneity and architecture.

CREDIT

Princess Máxima Center, Hubrecht Institute/B Artegiani, D Hendriks, H Clevers