Patterned expression of ion channel genes in mouse dorsal raphe nucleus determined with the Allen Mouse Brain Atlas

Abstract

The dorsal raphe nucleus (DR) is the major source of serotonin (5-hydroxytryptamine, 5-HT) in the forebrain and dysfunction of this midbrain structure is implicated in affective disorders. The DR is composed of several types of 5-HT and non-5-HT neurons and their excitable-membrane properties are heterogeneous and overlapping. In order to understand how these properties may be generated, we examined the mRNA expression patterns of voltage- and ligand-gated ion channels in the DR using the Allen Mouse Brain Atlas. Since DR cytoarchitecture is organized with respect to the midline, we sought to identify genes that were expressed in a pattern with respect to the midline, either enriched or depleted, rather than those that were homogenously expressed throughout the DR. Less than 10% of the screened genes for voltage-gated ion channels showed patterned expression within the DR. Identified genes included voltage-gated sodium channel beta subunits, potassium channels, P/Q-, N-type calcium channels, as well as the alpha2/delta-1 calcium channel. Several voltage-gated chloride channels were also identified, although these may function within intracellular compartments. Of the ligand-gated ion channels examined, 20% showed patterned expression. These consisted primarily of glutamate and GABA-A receptor subunits. The identified genes likely contribute to unique excitable properties of different groups of neurons in the DR and may include novel pharmacologic targets for affective disorders.

Fig. 1

Reciprocal midline and paramedial expression of two major cell types in the DR provided the basis for screening for genes expressed in medio-lateral patterns. A1. Expression of tryptophan hydroxylase 2 (Tph2), a marker for 5-HT neurons, is visible at the base of the aqueduct (arrows); Tph2 cells are outlined. The outline from this image is transferred to several other sagittal sections in subsequent figures as a reference for the distribution of 5-HT cells. Coronal sections at rostral (A2.), middle (A3.), and caudal (A4.) levels: note Tph2 expressing cells are enriched on the midline (bracketed area ‘M’), with less expression paramedially. B1–4. GABAergic neurons in the DR defined by the expression of the Vesicular GABA Transporter, Slc32a1 or VGAT. In sagittal section (B1.) note the low density of expression in the circled area where Tph2-expressing cells would lie. In coronal sections at rostral (B2.), middle (B3.), and caudal (B4.) levels, VGAT expressing neurons are more abundant paramedially (bracketed area, ‘PM’) than on the midline.

Fig. 2

Voltage-dependent sodium channel beta subunits Scnb2 (A1. in a sagittal section, not available in coronal series) and Scn3b (B1. sagittal, B2–4. coronal) both appear enriched on the midline.

Fig. 3

Voltage dependent potassium (Kv), inward-rectifying potassium (Kir), and two-pore potassium channels (K_2P) with midline expression patterns. A1. In the sagittal plane Kcna4, (not available in coronal series), appears expressed in a cluster of cells on the midline (arrow). B1–4. Sagittal and coronal sections showing modest enrichment of Kcnq3 on the midline. C1. Kcnk9 is enriched on the midline of the DR. D1–4. Kcnj6 in sagittal and coronal series.

Fig. 4

Calcium channels. A1. Cacna1a and B1. Cacna1b in sagittal sections are enriched in the area of TPH2 expression (circled). Cacna2d1 in sagittal (C1.) and coronal series (C2–4.) series: expressing cells can be seen extending caudal to the DR (arrow). D1–4. In both sagittal and coronal series, Cacng3 appears preferentially expressed in the rostral pole of the DR on the midline (arrows in D1. and D2.). E1–3. Cacng5 appears enriched in ventrally located cells, particularly at rostral levels (arrow in E1.).

Fig. 5

Voltage-dependent chloride channels. A1–4. Ttyh3 expression domain includes rostral and dorsal components of the DR, seen in both sagittal and coronal series (arrows). B1. Clcn3 in sagittal section is visible on the midline. C1–4. Clcn5 appears predominantly expressed in the ventral component of the DR on the midline (arrows). D1. Clcn6 in sagittal section is enriched on the midline.

Fig. 6

Glutamate receptor subunits with notable expression on the midline include A1–3. Gria4 (not available in sagittal series); B1–4. Grik2 and C1–4. Grik5.

Fig. 7

Glutamate receptors showing notable paramedial expression patterns include: A1–3. Gria3 and B1–3. Grik1.

Fig. 8

GABA receptor subunits with expression on the midline. A1. sagittal and A2–A4. cononal series of Gabrb1. B1–B4. Gabrg2 is expressed along the midline. C1–C4. Gabrg3 appears enriched, particularly in the ventral part of the DR, in mid-rostro-caudal location (C3. arrow).

Fig. 9

GABA receptor subunits with paramedial expression patterns. A1–3. Gabra1, B1–3. Gabrb2, and C1–3. Gabrq.