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Spatial Transcriptomics-correlated Electron Microscopy
© Prof. Dr. Özgün Gökce / University of Bonn

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Spatial Transcriptomics-correlated Electron Microscopy

New approach enables combined mapping of transcriptional and ultrastructural responses to brain injury

In response to injury, cells of the surrounding tissues alter their structures and their gene expression activities. Although tightly intertwined, these two parameters have only been observed separately, due to technical limitations. ImmunoSensation2 member Prof. Dr. Özgün Gökce and colleagues now found a way to monitor transcriptional and ultrastructural responses to injury at once, using Spatial Transcriptomics-correlated Electron Microscopy. The results have recently been published in Nature Communications.

Modern analytical technologies allow for an in-depth analysis of cellular functions and behavior. Nonetheless, such methods mostly shed light only on one, isolated aspect of physiology. This technical limitation makes it hard to identify and connect physiological interrelationships.
Prof. Özgün Gökçe and his team now introduce a new technique to better understand how individual cells modify both their structure and gene activity in response to injury. “We achieved this breakthrough by merging two existing techniques: MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization – editor’s note), which identifies active genes in each cell, and electron microscopy, which gives us a high-resolution view of a cell's structure.” reports Prof. Gökce, who joined ImmunoSensation2 only in early 2023.

“foamy” macrophages in the development of Multiple Sclerosis

Multiple Sclerosis (MS) affects about 700.000 individuals throughout Europe. The disease is caused by immune cells that mistakenly attack and destroy the body's own nerve cells in the spinal cord and brain. Lipid-storing macrophages in the brain, so called “foamy microglia”, are known to propel the inflammatory process, but the knowledge on foamy microglia is very limited. Özgün Gökçe, who is also a member of the Medical Faculty at Bonn University, put his new method to the test on a mouse model of MS. “By integrating electron microscopy, single-cell RNA sequencing, lipid measurements, and MERFISH, we successfully profiled these 'foamy' microglia” Özgün Gökçe explains. “They had accumulated a substantial amount of fat and were found primarily in the region most impacted by the injury.” Further, the scientists identified a small population of T-cells responsible for driving interferon responses in their vicinity. Integrating the datasets revealed correlations between gene expression and ultrastructural features of microglia, offering a new view on the reorganization of cells after brain injury.

Physical attributes and gene expression brought together

The new approach allows a more complete view on the response of cells to various stimuli. “We further segmented hundreds of microglia to digitalize the electron microscopy data, which led to the unprecedented, unbiased clustering of microglia based on their ultrastructure.” Gökçe states. This enabled the integration of ultrastructural and transcriptomic features and allowed the first author Peter Androvic to uncover correlations between the physical attributes of immune cells and their gene activity. “Our research paints a comprehensive picture of how individual cells adapt and behave, in terms of their structure, location, and gene activity, following a type of brain injury. Knowledge of this kind could be instrumental in creating more effective treatments in the future.” Gökçe closes.


Androvic, P., Schifferer, M., Perez Anderson, K. et al. Spatial Transcriptomics-correlated Electron Microscopy maps transcriptional and ultrastructural responses to brain injury. Nat Commun 14, 4115 (2023).


Prof. Dr. Özgün Gökce
Venusberg-Campus 1/99
53127 Bonn

Physicist Richard Feynman once gave advice to biologists, saying: "For rapid progress in biology, we need to improve the electron microscope by a hundredfold." However, he didn't specify what exactly would make the electron microscope a hundred times better. While these microscopes offer high-resolution images, interpreting these images can be challenging. So, we set out to merge the capabilities of the electron microscope with a technology called MERFISH, which can detect thousands of different mRNA molecules, helping us identify various cell types and states. This combination guided us towards specific electron microscopy features that highlight various cellular responses. The results exceeded our expectations, and we were able to link the ultrastructural features of cells to their transcriptional identities. We found that certain transcripts correlate strongly with specific ultrastructural features of a cell, which are closely linked to the cell's function. Although our study focused on the brain, this method could, in theory, be applied to any tissue, opening up opportunities across various fields.

Özgün Gökçe, Bonn July 18th 2023

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