Single-cell RNA sequencing reveals new cell types

A new, detailed map of the cerebral cortex, created by researchers at the Karolinska Institutet, has revealed previously unknown cell types and the genes active within them.

Historically, maps of the brain have identified cells by their location, morphology, target specificity, electrophysiological characteristics and molecular markers. These cell properties alone do not contain enough information to identify cell type in all circumstances.

The study, led by Dr Jens Hjerling-Leffler and Dr Sten Linnarsson, used single-cell RNA sequencing (scRNA-seq) to analyse the individual transcriptomes of 3005 cells within the primary somatosensory cortex (S1) and hippocampal CA1 region of mice. The first time this method has been used at this scale on such complex tissue.

By comparing which of the approximately 20,000 genes were active in each cell, they sorted them into nine major classes and 47 molecularly distinct subclasses.

Using the new map, the researchers identified several new cell types. This included an interneuron subclass in the superficial layer of the S1 and six subpopulations of oligodendrocyte.

Oligodendrocytes are responsible for forming the myelin sheath around nerve cells. These findings may help to give a better understanding of myelin related diseases, like multiple sclerosis (MS).

Jens Hjerling-Leffler said:

"Above all, we have created a much more detailed map of the cells of the brain that describes each cell type in detail and shows which genes are active in it. This gives science a new tool for studying these cell types in disease models and helps us to understand better how brain cells respond to disease and injury."

Jens Hjerling-Leffler is a Scientifica customer who currently uses a SliceScope Pro 6000 electrophysiology rig in his lab at the Karolinska Institutet.

Research Paper

Zeisel. A, Muñoz-Manchado A. B., Codeluppi S., Lönnerberg P., La Manno G., Juréus A., Sueli Marques J., Munguba H., Liqun L., Betsholtz C., Rolny C., Castelo-Branco G., Jens Hjerling-Leffler., Linnarsson S. (2015) Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq Science 347;6226 1138-1142 doi: 10.1126/science.aaa1934