Toward an integrated classification of neuronal cell types: morphoelectric and transcriptomic characterization of individual GABAergic cortical neurons

Abstract

Neurons are frequently classified into distinct groups or cell types on the basis of structural, physiological, or genetic attributes. To better constrain the definition of neuronal cell types, we characterized the transcriptomes and intrinsic physiological properties of over 3,700 GABAergic mouse visual cortical neurons and reconstructed the local morphologies of 350 of those neurons. We found that most transcriptomic types (t-types) occupy specific laminar positions within mouse visual cortex, and many of those t-types exhibit consistent electrophysiological and morphological features. We observed that these properties could vary continuously between ttypes, which limited the ability to predict specific t-types from other data modalities. Despite that, the data support the presence of at least 20 interneuron met-types that have congruent morphological, electrophysiological, and transcriptomic properties.

Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons

“…3a, right). Relatively few genes (177 genome-wide) showed enriched expression in dissociated nuclei relative to Patch-seq cells, suggesting that high quality transcriptomes collected in this data set do not show the increased dropout rate reported in our previous study 32 . This is likely because we are comparing our human Patch-seq cells to a reference of dissociated human nuclei, rather than dissociated mouse cells.…”

“…The subset of neurons (109) with sufficient biocytin labeling and intact apical dendrites were imaged at high resolution, then subsequently manually reconstructed based on the image. L2/3 pyramidal neurons from mouse visual cortex were analyzed using the same Patch-seq platform 32 , resulting in 120 neurons with high-quality electrophysiology and transcriptome data mapping to the three L2/3 glutamatergic t-types, and 60 neurons with data in all three modalities.…”

“…c ) Joint UMAP of dissociated mouse cells from Fig. 1e and 133 glutamatergic Patch-seq neurons from supragranular cortex in VISp, which were classified as described for mouse GABAergic neurons 32 . Panels and labels as in b .…”

“…We performed all steps of RNA-processing and sequencing as described for mouse Patch-seq cells 32 . We used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, 634894) to reverse transcribe poly(A) RNA and amplify full-length cDNA according to the manufacturer’s instructions.…”

Light microscopy based approach for mapping connectivity with molecular specificity

“…morphology, physiology, or molecular expression) to using a combination of these properties in a multimodal fashion 41 . Recent studies have demonstrated the power of this multimodal approach to curate and refine definitions of inhibitory and excitatory neuronal cell types in visual cortex 42,43 . Similarly, our multimodal strategy for measuring morphology, molecular markers, and connectivity can be also applied towards refining cell type definitions across the brain.…”