Quantitative expression profiling of identified neurons reveals cell-specific constraints on highly variable levels of gene expression

Abstract

The postdevelopmental basis of cellular identity and the unique cellular output of a particular neuron type are of particular interest in the nervous system because a detailed understanding of circuits responsible for complex processes in the brain is impeded by the often ambiguous classification of neurons in these circuits. Neurons have been classified by morphological, electrophysiological, and neurochemical techniques. More recently, molecular approaches, particularly microarray, have been applied to the question of neuronal identity. With the realization that proteins expressed exclusively in only one type of neuron are rare, expression profiles obtained from neuronal subtypes are analyzed to search for diagnostic patterns of gene expression. However, this expression profiling hinges on one critical and implicit assumption: that neurons of the same type in different animals achieve their conserved functional output via conserved levels and quantitative relationships of gene expression. Here we exploit the unambiguously identifiable neurons in the crab stomatogastric ganglion to investigate the precise quantitative expression profiling of neurons at the level of single-cell ion channel expression. By measuring absolute mRNA levels of six different channels in the same individually identified neurons, we demonstrate that not only do individual cell types possess highly variable levels of channel expression but that this variability is constrained by unique patterns of correlated channel expression.

Fig. 1.

Activity patterns of identified neurons in the STG in preparations showing only a pyloric rhythm, and both a gastric mill and pyloric rhythm. (A) Simultaneous intracellular recordings from PD, LP, LPG, and IC neurons during the ongoing pyloric rhythm. (Vertical scale bars: −40 to −60 mV.) (B) Simultaneous intracellular recordings from LPG, IC, LG, and GM cells during the ongoing pyloric and gastric rhythms. (Vertical scale bars: −40 to −60 mV.) Resistor symbols represent electrical synapses, and numbers noted with each cell type represent the number of cells of each type in one ganglion.

Fig. 2.

Distinct patterns of ion channel expression are seen for each cell type. Mean ± SD mRNA copy number for six different ion channels in each of the six cell types are overlaid with the individual data points that generate these means. Letters indicate significant differences (P < 0.05) between cell types as revealed by pairwise post hoc comparisons (Tukey's t test) subsequent to a one-way ANOVA (each panel ANOVA results P < 0.05). LG cells were not found to express measurable levels of shaw, whereas this transcript was not measured in GM cells.

Fig. 3.

Three-dimensional plots for mean ± SEM of shal vs. shab vs. shaw and IH vs. BKKCa vs. para for all six cell types measured reveal no overlap in the expression patterns of unique cell types.

Fig. 4.

Correlated levels of ion channel mRNA in specific STG cell types. (A) Summary of the coordinated expression of ion channels in six different cell types of the STG. Each box represents a possible pairwise correlation between two channels. Within each box, each cell type that was determined to have a significant pairwise correlation for ion channel mRNA levels is listed. *, shaw mRNA was not detected in LG cells, and shaw was not quantified in GM cells. (B–D) Four-way correlations of ion channel expression in GM, LP, and PD cells. (B) Four-way plot of shab vs. shal vs. BKKCa vs. para in GM neurons. mRNA Levels of para are expressed as increasing intensity of color from yellow to red as shown. (C) Four-way plot of shaw vs. shal vs. IH vs. shab in LP cells. (D) Four-way plot of shal vs. IH vs. BKKCa vs. para in PD cells.

Fig. 5.

Cells that share the same pairwise correlation among channels differ in the quantitative relationship between these channels. Each plot shows all of the cell types that share a common pairwise correlation between ion channels. Letters indicate significant differences between the slopes of the regression lines for each shared correlation.