The Dendrite Nanomap

Our brain consists of billions of neurons, communicating with each other through synapses. The signal-receiving side is often located on a special compartment, called a dendritic spine. Due to their tiny nature, these dendritic spines are very difficult to analyze, as they are too small for conventional microscopy and cannot be isolated to study them with biochemical methods. During my PhD I tackled this problem in an elegant combination of state-of-the-art super-resolution microscopy and quantitative biochemistry, to create the most detailed model of any cellular compartment to date. This revealed that all spines are very similar in their composition, refuting a long standing hypothesis that it is the protein composition that separates mature from immature spines.

Dendritic spines

The neurons in our brain need to communicate constantly with each other to retrieve memories, store new information and perform tasks. They do so at synapses, defined points of contact with a very defined structure. The efficacy of this communication, the so-called synaptic strength, is thought to be one the major mechanisms to store information. Each neuron can therefore modulate the strength of each synapse, with the main effects happening on the postsynaptic side, that means every neuron tweaks how strong it reacts to given inputs. These modulations happen by changing the protein composition and the structure of these dendritic spines. For a long time, mushroom shapes spines have been associated with information storage and learning, whereas stubby spines have been thought of as immature spines.

Protein localization is similar between classes

We imaged over 100 different proteins, using latest state-of-the art microscopy. This enabled us to localize each one of them with nanometer precision. Surprisingly, we found very limited differences between the different spine classes. Even when we manually annotated over 40.000 spine images, we could not detect distinct localizations. Compare the images on the left, showing the average localization of the same protein, PSD95, in both mushroom and stubby spines.

Protein composition is identical between classes

Our microscopy analysis could only show us where proteins are, but not in what quantities. We therefore reasoned that maybe the proteins are present in different numbers. To verify this hypothesis we performed quantitative mass-spectrometry to count the proteins. Surprisingly, there is virtually now different between the two classes. This highlights that any functional differences between these spines can solely be found in their structure, not in their protein composition.

A quantitative 3D model

By combining all information, we could create a realistic model of dendritic spines. It depicts over 100 different proteins each at their precise position at the nanometer level and in the correct numbers. Isn’t this an unprecedented view into the inner workings of a cell?