Transcriptome analysis for the development of cell-type specific labeling to study olfactory circuits

Abstract

In each sensory system of the brain, mechanisms exist to extract distinct features from stimuli to generate a variety of behavioural repertoires. These often correspond to different cell types at some stage in sensory processing. In the mammalian olfactory system, complex information processing starts in the olfactory bulb, whose output is conveyed by mitral and tufted cells (MCs and TCs). Despite many differences between them, and despite the crucial position they occupy in the information hierarchy, little is known how these two types of projection neurons differ at the mRNA level. Here, we sought to identify genes that are differentially expressed between MCs and TCs, with an ultimate goal to generate a cell-type specific Cre-driver line, starting from a transcriptome analysis using a large and publicly available single-cell RNA-seq dataset (Zeisel et al., 2018). Despite many genes showing differential expressions, we identified only a few that were abundantly and consistently expressed only in MCs. After further validating these putative markers using in-situ hybridization, two genes, namely Pkib and Lbdh2, remained as promising candidates. Using CRISPR/Cas9-mediated gene editing, we generated Cre-driver lines and analysed the resulting recombination patterns. This analysis indicated that our new inducible Cre-driver line, Lbhd2-CreERT2, can be used to genetically label MCs in a tamoxifen dose-dependent manner, as assessed by soma locations, projection patterns and sensory-evoked responses. Hence this line is a promising tool for future investigations of cell-type specific contributions to olfactory processing and demonstrates the power of publicly accessible data in accelerating science.

Molecular characterization of projection neuron subtypes in the mouse olfactory bulb

“…CCK distinguishes a subset of TCs (superficial TCs, (Liu and Shipley, 1994; Seroogy et al, 1985; Short and Wachowiak, 2019; Sun et al, 2020). Vasopressin expressing cells might constitute a further subset of superficial TCs (Lukas et al, 2019), and recently the Lbhd2 gene has been used to obtain more specific genetic access to MCs (Koldaeva et al, 2020). Heterogeneous expression of both the GABAa receptor as well as voltage-gated potassium channel subunits have been observed (Padmanabhan and Urban, 2010; Panzanelli et al, 2005), albeit not linked to specific cell types.…”