Hidden cell layers revealed in the CA1 region of the hippocampus

Hidden cell layers revealed in the CA1 region of the hippocampus

Researchers at the Mark and Mary Stevens Neuroimaging and Informatics Institute (Stevens INI) at the Keck School of Medicine of USC have identified a previously unknown pattern of organization in one of the most important areas of the brain for learning and memory. The study, published innature communication,shows that the CA1 region of the mouse hippocampus, a structure crucial for memory formation, spatial navigation and emotions, has four distinct layers of specialized cell types. This discovery changes our understanding of how information is processed in the brain and could explain why certain cells are more susceptible to diseases such as Alzheimer's and epilepsy.

Researchers have long suspected that different parts of the CA1 region of the hippocampus controlled different aspects of learning and memory, but it was not clear how the underlying cells were arranged.”

Michael S. Bienkowski, PhD, senior author of the study and assistant professor of physiology and neuroscience and of biomedical engineering

"Our study shows that CA1 neurons are organized into four thin, continuous bands, each representing a different type of neuron defined by a unique molecular signature. These layers are not fixed in place, but subtly shift and change thickness along the length of the hippocampus. This pattern of shifts means that each part of CA1 contains its own mix of neuron types, which explains why different regions support different behaviors. This may also clarify why certain CA1 neurons are active in diseases like this Alzheimer's disease and epilepsy: "When a disease targets the cell type of a layer, the effects vary depending on where in CA1 that layer is most pronounced."

Using a powerful RNA labeling method called RNAscope and high-resolution microscopy, the team captured clear snapshots of single molecule gene expression to identify CA1 cell types in mouse brain tissue. In 58,065 CA1 pyramidal cells, they visualized more than 330,000 RNA molecules - the genetic messages that show when and where genes are activated. By tracking these activity patterns, the researchers created a detailed map showing the boundaries between different types of neurons in the CA1 region of the hippocampus.

The results showed that the CA1 region consists of four contiguous layers of neurons, each characterized by a specific set of active genes. In 3D, these layers form sheets that vary slightly in thickness and structure along the length of the hippocampus. This clear, layered pattern helps understand previous studies that viewed the region as a more gradual mixture or mosaic of cell types.

“When we visualized gene RNA patterns at single-cell resolution, we could see clear stripes, like geological layers in rock, each representing a specific type of neuron,” said Maricarmen Pachicano, a doctoral student at the Center for Integrative Connectomics at Stevens INI and co-first author of the paper. "It's like lifting a veil over the brain's internal architecture. These hidden layers could explain differences in the way hippocampal circuits support learning and memory."

The hippocampus is among the first regions affected by Alzheimer's disease and is also involved in epilepsy, depression and other neurological diseases. By revealing the layered structure of CA1, the study provides a roadmap for investigating which specific neuron types are most vulnerable in these diseases.

“Discoveries like these illustrate how modern imaging and data science can transform our view of brain anatomy,” said Arthur W. Toga, PhD, director of the Stevens INI and the Ghada Irani Chair in Neuroscience at the Keck School of Medicine of USC. “This work builds on Stevens INI’s long tradition of imaging the brain at every scale, from molecules to entire networks, and will impact both fundamental neuroscience and translational studies targeting memory and cognition.”

The new CA1 cell type atlas, created using data from the Hippocampus Gene Expression Atlas (HGEA), is freely available to the global research community. The dataset includes interactive 3D visualizations accessible through the augmented reality app Schol-AR created at Stevens INI, allowing scientists to explore hippocampal layers in unprecedented detail.

Because this layering pattern in mice is similar to what has been observed in primate and human brains - including changes in the thickness of the CA1 region - the researchers suspect that it may be a common feature in many mammalian brains. While further studies are needed to confirm this organization in humans, the finding provides a promising foundation for future comparative and translational research on how hippocampal architecture supports memory and cognition.

“Understanding how these layers relate to behavior is the next challenge,” Bienkowski said. “We now have a framework to study how specific layers of neurons contribute to functions as diverse as memory, navigation and emotions, and how their disruption can lead to disease.”

About the study

In addition to Bienkowski and Pachicano, other authors of the study include Shrey Mehta, Angela Hurtado, Tyler Ard, Jim Stanis and Bayla Breningstall.

This work was supported by the National Institutes of Health/National Institute of Aging (K01AG066847, R36AG087310-01, Supplement P30-AG066530-03S1), the National Science Foundation (grant 2121164), and funds from the USC Center for Neural Longevity. Research data reported in this publication was supported by the Office of the Director of the National Institutes of Health under grant number S10OD032285.

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