FHCRC researchers use single-cell RNA-Seq to explore the developmental mechanisms that shape the sense of smell

The sense of smell allows chemicals to be perceived as diverse scents. Researchers at the Fred Hutchinson Cancer Research Center used single neuron RNA-Sequencing (RNA-Seq) to explore developmental mechanisms that shape this ability as nasal olfactory neurons mature in mice. Most mature neurons expressed only one of the roughly 1000 odorant receptor genes (Olfrs) available, and that at high levels. However, many immature neurons expressed low levels of multiple Olfrs. Coexpressed Olfrs localized to overlapping zones of the nasal epithelium, suggesting regional biases, but not to single genomic loci. A single immature neuron could express Olfrs from up to seven different chromosomes. The mature state in which expression of Olfr genes is restricted to one per neuron emerges over a developmental progression that appears independent of neuronal activity requiring sensory transduction molecules.

Olfactory neurons exhibit large-scale shifts in gene expression during development.

(A) Unsupervised analysis of single cell gene expression profiles with Monocle revealed a linear trajectory (black line) along which cells develop in a dimension referred to as “pseudotime”. Coloring of cells based on the expression of developmental markers shows that the trajectory corresponds to a stepwise development from olfactory progenitors to precursors to immature OSNs to mature OSNs. (B) Global analysis of gene expression kinetics along the trajectory identified 3,830 genes that vary significantly over pseudotime development (FDR < 5% by a Tobit-valued generalized linear model likelihood ratio test; see Methods). Hierarchical clustering of these genes via Ward’s method recovered 11 non-redundant groups that covary over the trajectory. Cluster analysis indicates that multiple large shifts in gene expression occur as neurons progress through development. The bar on top shows the locations of individual cells, colored by stage of development, along this developmental trajectory. (C) Kinetic diagrams show the expression of known markers of different developmental stages over the developmental progression. Parentheses indicate the groups in which genes are found in part B. Dots indicate individual cells colored according to developmental stage. Black lines indicate loess smoothing (span = 0.75, degree = 2) of log-transformed FPKM values over developmental pseudotime.