A research team led by Dr. Àlex Bayés, Head of the Molecular Physiology of the Synapse Group at the Institut de Recerca Sant Pau (IR Sant Pau), has achieved what for decades had been an elusive goal: obtaining a precise, differentiated molecular portrait of individual synaptic types in the hippocampus, the brain structure that serves as the core of learning and memory.
The study, published in Nature Communications and conducted almost entirely at IR Sant Pau, details with unprecedented resolution which proteins are present in each type of synapse and in what quantities. This reveals patterns that help explain how connections that appear similar can perform different functions and display specific characteristics. Understanding how these connections are altered is critical because synaptic dysfunction is implicated in most neurological and psychiatric diseases, from Alzheimer’s and Parkinson’s to epilepsy and schizophrenia.
Synapses, the contact points between neurons, are extremely numerous and diverse: the human brain is estimated to contain between 100 and 1,000 trillion of them. Each one transmits information with slight variations in structure and function, allowing neural circuits to process signals flexibly and precisely. However, until now it was unknown how this diversity was reflected at the molecular level. “For years, scientists have known that each type of synapse has unique electrical properties, but they had not been able to map their protein composition accurately due to technical limitations,” explains Dr. Bayés. “Available methods required analyzing large tissue fragments that mixed different classes of connections, producing an average profile that blurred subtle yet critical differences for their function.”
Studying synapses individually has been an almost impossible challenge for decades. They are tiny structures—barely one micron—distributed densely and interwoven throughout the brain, making physical isolation difficult. Moreover, their number is so colossal that, if each synapse were a grain of sand, there would be enough to fill half a stadium like Camp Nou, an image that illustrates the magnitude of the challenge facing neuroscience.
The IR Sant Pau team has overcome this obstacle through a combination of tools that take synaptic analysis to a new level. Laser-capture microdissection makes it possible to precisely isolate microscopic hippocampal layers, selecting only those regions containing the synapse type of interest. Then, an optimized protocol for extracting synaptic proteins preserves the integrity of these molecules and prevents losses, which is crucial when working with minuscule amounts of material.
Thanks to this approach, the researchers were able to characterize individually the proteome of the three synapse types that make up the trisynaptic hippocampal circuit, perhaps the most extensively studied circuit in the brain. It is a characteristic network that transmits information in three steps: first from the entorhinal cortex to the dentate gyrus, then from the dentate gyrus to the CA3 region, and finally from CA3 to CA1. This circuit is essential for memory processing and the integration of sensory and contextual information.
The importance of this achievement is not only technical. “Because we can examine specific synapses without requiring genetic manipulation, the methodology can also be applied to human samples, opening a range of possibilities for precisely studying how these connections are altered in neurological diseases,” notes Dr. Bayés.
The study revealed a surprising pattern: the three synapses analyzed share the vast majority of their proteins but vary significantly in the relative quantities of each. The comparison can be understood as if all of them used the same basic ingredients for cooking but modified the proportions to create different recipes with their nuances in flavor, texture, and properties.
In this “synaptic menu,” there is one ingredient always present that defines the character of the dish: glutamate receptors and the proteins that regulate them. Glutamate is the main excitatory neurotransmitter in the brain, and its receptors are essential for signal transmission and synaptic plasticity—the mechanism that allows connections to strengthen or weaken depending on experience.
“We observed that the functional identity of each synapse is not built on an exclusive set of proteins, but rather on how it adjusts the proportion of shared components to meet its needs,” says Dr. Àlex Bayés, “and what is most surprising is that, in all cases, glutamate receptors and their regulators form the core of that specialization.”
Quantitative differences in protein composition translate into specialized functional profiles. CA3–CA1 synapses display very precise control of a specific AMPA receptor subtype (GluA2), a high capacity to remodel their structure, and elevated energy consumption, all of which are associated with their role in memory consolidation and long-term plasticity.
DG–CA3 synapses stand out for their high abundance of metabotropic glutamate receptors (mGluR1) and for possessing especially active machinery for local protein synthesis in their presynaptic terminals. This feature allows them to adapt rapidly to changes in neuronal activity.
Meanwhile, EC–DG synapses present a distinct extracellular matrix, rich in proteoglycans, which may influence the mobility and stability of receptors, as well as specialized metabolic pathways to obtain energy from specific amino acids. These traits may relate to their role in the first stage of processing the information reaching the hippocampus.
The study also identified a genetic component in this specialization: each neuron type activates or silences specific synaptic genes to adjust the molecular composition of its connections. This differential regulation was observed especially in genes related to glutamate receptors and the proteins that modulate their function, confirming that their central role in synaptic specialization is also encoded in the neuron’s genetic program.
“This is the first time we can link the molecular specialization of a synapse so directly to gene expression programs unique to each neuron. This brings us closer to understanding how synaptic diversity translates into unique functions for each brain circuit,” adds Dr. Bayés.
The ability to analyze the molecular identity of specific synapses with such precision not only in animal models but also in human tissue opens a range of applications in biomedical research. The hippocampus is one of the first structures affected in neurodegenerative diseases such as Alzheimer’s, so understanding how these “molecular recipes” are altered could help identify early biomarkers and develop more specific therapeutic strategies.
Reig-Viader R, Del Castillo-Berges D, Burgas-Pau A, Arco-Alonso D, Zerpa-Rios O, Ramos-Vicente D, Picañol J, Castellanos A, Soto D, Roher N, Sindreu C, Bayés À. Synaptic proteome diversity is shaped by the levels of glutamate receptors and their regulatory proteins. Nat Commun 2025;16:10487. https://doi.org/10.1038/s41467-025-65490-9
