A transcriptomic atlas of mouse cerebellar cortex comprehensively\xa0defines cell types

Velina Kozareva,Naeem Nadaf,Charles Vanderburg,Caroline Martin,Aviv Regev,Wade G Regehr,Tomas Osorno,Evan Macosko,Chong Guo,Stephanie Rudolph

doi:10.1038/s41586-021-03220-z

Velina Kozareva, Naeem Nadaf + Show 8 more

Open Access

https://doi.org/10.1038/s41586-021-03220-z

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Abstract

The cerebellar cortex is a well-studied brain structure with diverse roles in motor learning, coordination, cognition and autonomic regulation. However, a complete inventory of cerebellar cell types is currently lacking. Here, using recent advances in high-throughput transcriptional profiling1–3, we molecularly define cell types across individual lobules of the adult mouse cerebellum. Purkinje neurons showed considerable regional specialization, with the greatest diversity occurring in the posterior lobules. For several types of cerebellar interneuron, the molecular variation within each type was more continuous, rather than discrete. In particular, for the unipolar brush cells—an interneuron population previously subdivided into discrete populations—the continuous variation in gene expression was associated with a graded continuum of electrophysiological properties. Notably, we found that molecular layer interneurons were composed of two molecularly and functionally distinct types. Both types show a continuum of morphological variation through the thickness of the molecular layer, but electrophysiological recordings revealed marked differences between the two types in spontaneous firing, excitability and electrical coupling. Together, these findings provide a comprehensive cellular atlas of the cerebellar cortex, and outline a methodological and conceptual framework for the integration of molecular, morphological and physiological ontologies for defining brain cell types.

Highlights

Achieving a comprehensive survey of cell types in the cerebellum poses some unique challenges
Background text colours correspond to cell types in b. d, Allen Brain Atlas expression staining for selected gene markers of canonical cell populations, indicating cerebellar layer localization
Consistent with the gene expression profile, we observed spikelets in 71% of MLI1s and not in MLI2s (Fig. 4l, m; P < 0.001, Fisher’s exact test). These findings suggest that most MLI1s are coupled to other MLI1s by gap junctions, whereas MLI2s show no electrical coupling to other MLIs. In this Article, we used high-throughput, region-specific transcriptome sampling to build a comprehensive taxonomy of cell types in the mouse cerebellar cortex, and quantify spatial variation across individual regions

Summary

MLI1 4 MLI2

Corresponded to the MLI1 (Sorcs3-positive) and MLI2 (Nxph1-positive, Klhl1-negative) populations, with differentiation of the two types beginning at P4 and largely complete by P16 (Fig. 4d, e, Extended Data Fig. 6a). The expression of Gjd[2], the gene encoding the dominant gap junction protein in MLIs32, was found in MLI1s but not MLI2s, both in our single-nucleus data (Fig. 4i) and by smFISH (Fig. 4j, k), which suggests potential differences in electrical coupling. The two clusters of Golgi cells, another interneuron type known to be electrically coupled[33,34], differentially expressed many of the same markers, including Sorcs[3], Gjd[2] and Nxph[1] in both human and mouse Consistent with the gene expression profile, we observed spikelets in 71% of MLI1s and not in MLI2s (Fig. 4l, m; P < 0.001, Fisher’s exact test) These findings suggest that most MLI1s are coupled to other MLI1s by gap junctions, whereas MLI2s show no electrical coupling to other MLIs

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