Transcriptomics in auditory brain regions

Functional and molecular profiling of cell diversity and identity in the mammalian auditory brainstem

Knowledge about individual cell types is a prerequisite for understanding brain function. Yet in most neural systems, our knowledge of cellular diversity and identity and the impact on function is incomplete. This also holds for the mammalian auditory system composed of a multitude of individual nuclei. The latter are mostly regarded as homogenous cell populations with well-defined structure-function relationships. Our preliminary data challenge this classical view.
Both cell type and cell function are reflected in the transcriptome. Sequencing minute amounts of RNA from single cells, and analyzing the cell-to-cell variability, has become feasible by recent technological advances. Thus, we are now able to molecularly identify cellular heterogeneity. The aim of our package proposal is to decipher the biophysical, anatomical and genetic determinants of neuronal heterogeneity in the mammalian auditory brainstem, and thereby to understand the cellular basis of functional signaling in these circuits. For this purpose, our core experiments will combine whole-cell patch-clamp recordings with single-cell transcriptome analysis. Two thematically closely related projects will be guided individually by Felix Felmy (Hannover) and Eckhard Friauf (Kaiserslautern). Gene sequencing will be done in collaboration with Jörn Walter (Saarbrücken).
Our major goal is to generate a comprehensive cell type atlas with genome-wide expression data for two auditory brainstem nuclei, namely the intermediate nucleus of the lateral lemniscus (INLL) of gerbils and the lateral superior olive (LSO) of mice. The INLL is implicated in cross-frequency processing. As yet, a description of its cellular physiology is missing. The LSO is involved in sound localization. Most LSO neurons receive excitatory and inhibitory inputs that ensure resilience, reliability and temporal precision during ongoing activity. For each nucleus, we present ample evidence for cell type heterogeneity, e.g. different firing patterns across neurons. The origin and extent of this heterogeneity are enigmatic. We hypothesize that the biophysical differences correlate, for example, with the expression of genes encoding ion channels.
By employing Patch-seq profiling of electrophysiologically characterized single neurons, we will identify candidate transcripts that define specific sub-populations, even down to the level of transcription factors. In a meta-analysis, we will finally combine our datasets on INLL and LSO neurons for joint comparison and assessment. We expect to identify common principles between biophysical properties (functional behavior) and related gene products (transcriptome). Collectively, our package proposal will elucidate the cellular basis for the complexity and functional significance and of the INLL and the LSO. It will thus crucially contribute to a more comprehensive understanding of the functional organization of the central auditory system.