Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior

Abstract

The ventrolateral subdivision of the ventromedial hypothalamus (VMHvl) contains ∼4,000 neurons that project to multiple targets and control innate social behaviors including aggression and mounting. However, the number of cell types in VMHvl and their relationship to connectivity and behavioral function are unknown. We performed single-cell RNA sequencing using two independent platforms-SMART-seq (∼4,500 neurons) and 10x (∼78,000 neurons)-and investigated correspondence between transcriptomic identity and axonal projections or behavioral activation, respectively. Canonical correlation analysis (CCA) identified 17 transcriptomic types (T-types), including several sexually dimorphic clusters, the majority of which were validated by seqFISH. Immediate early gene analysis identified T-types exhibiting preferential responses to intruder males versus females but only rare examples of behavior-specific activation. Unexpectedly, many VMHvl T-types comprise a mixed population of neurons with different projection target preferences. Overall our analysis revealed that, surprisingly, few VMHvl T-types exhibit a clear correspondence with behavior-specific activation and connectivity.

Keywords: VMH; aggression; cell types; estrogen receptor; hypothalamus; mating; metabolism; sexual dimorphism; single-cell RNA sequencing; social behavior.

Figure 1.. VMHvl Transcriptomic Cell Types Revealed by SMART-Seq

(A) Two-dimensional t-distributed stochastic neighbor embedding (t-SNE) plot color-coded by 46 SMART-seq clusters (N = 4,574) from ventral VMH. (B) Expression patterns of major marker genes in VMH (red dashed circle) and surrounding areas by ISH (Allen Mouse Brain Atlas; upper) arranged by anatomical hierarchicy; orange points on t-SNE plots (lower) indicate their expression levels. Anatomic location of clusters is outlined on t-SNE plots (VMH-out: black; VMHvl: green; VMHc or anterior VMH: light blue). (C) Violin plots illustrating expression levels of marker genes by cluster; “max CPM” (right), maximum counts per million reads. Dendrogram and matrix show relatedness between clusters and their spatial locations (see B), respectively. See also Figures S1 and S2.

Figure 2.. Anatomic Distribution of VMH scRNA-Seq Clusters by seqFISH

(A) Schematic of seqFISH procedure in VMH. Light blue solid lines (1) outline ROIs of sequential hybridizations; yellow dashed lines (2) (maximum intensity Z projections) outline VMH and VMHvl. Three major anatomic regions (VMHvl, VMHc, and VMH-out) are color coded (3). Scale bars, 100 μm (inset). (B) Heatmap showing expression level of marker genes (rows) in 27 seqFISH clusters (columns; n = 4,497; VMHvl only). (C) Heatmaps showing correlation between seqFISH and SMART-seq clusters (n = 3,824; VMH only) and their p values (white, p > 0.05 or r < 0.35; see STAR Methods). seqFISH clusters that are the most strongly correlated with each scRNA-seq cluster are marked by red squares. (D) Spatial distribution along A-P axis of seqFISH clusters (color-filled) showing anterior (#3, #5, #10) or posterior (#11, #26) biases, projected onto all segmented VMHvl cells (a–f). Line plot shows quantification for indicated clusters; black dotted line shows chance distribution. Scale bars, 50 μm (inset). See also Figure S3.

Figure 3.. Anterior versus Posterior Projection Biases of Neurons in scRNA-seq Clusters

(A) Schematic of Retro-seq procedure (see STAR Methods) from dPAG, IPAG, or MPOA. (B) Bar plot shows the distributions of cells retrogradely labeled from each target for the major VMH classes. (C and D) Percent of retrogradely labeled cells (C) and their relative frequency compared to non-Retro-seq samples (D) in each VMHvl SMART-seq cluster. Numbers of retro⁺ cells sequenced are listed at the bottom of the graphs. *p < 0.05, **p < 0.01 (Fisher’s exact test).

Figure 4.. VMHvl Transcriptomic Cell Types Revealed by 10x scRNA-seq

(A and B) t-SNE plots showing clusters (A) and their Vglut2 (Slc17a6) expressions (B) for all cells analyzed (N = 149,663). All neuronal clusters (n = 78,476) are outlined in either red (VMH-in) or blue (VMH-out), respectively. (C) t-SNE plot illustrating results of iterative clustering of VMH-in cells (n = 41,385; 29 clusters). (D) Expression levels of four main class-specific marker genes (Esr1, Satb2, Dlk1, and Nr5a1) are color coded (orange) on t-SNE plots; VMH subdivisions are outlined in different colors (VMHvl: light red; VMHc or anterior VMH: light blue). (E) Violin plots show differential expressions of marker genes (VMHvl versus VMHc-enriched; indicated by left brackets) among 29 VMH clusters (C) with their spatial locations (top matrix). See also Figure S4.

Figure 5.. Activation of Neurons in VMHvl Clusters during Different Social Behaviors

(A) Schematic of Act-seq protocol and summary of behavioral assays (see STAR Methods; Figure S4I). (B) Dot plots illustrating Fos induction in 10x VMHvl clusters. Colored and shaded gray dots indicate clusters with a significant (p < 0.05 after multiple comparison corrections across behaviors and clusters; three-way ANOVA and Bonferroni post hoc test), and non-significant induction (p > 0.05) versus control (or clusters from control animals), respectively. Dot size indicates proportion of Fos⁺ cells per cluster after subtraction of control values; color indicates average log₂fold-change (FC) versus control. (C) Expression levels of Fos, Fosl2, and Junb in 6 Esr1 clusters (male only). The clusters showing the highest induction of Fos, Fosl2, or Junb by either M-M (aggression plus M-M CI tests; red points) or M-F (mating plus M-F CI tests; blue points) versus control (black points) are highlighted by red (left; Esr1_5) or blue (right; Esr1_7) shading, respectively (**p < 0.01, ***p < 0.001; three-way ANOVA and Bonferroni post hoc test; data are represented as mean ± SEM). (D) Bar graphs showing the number of different IEGs significantly induced during each social behavior in each cluster (see also Figure S5B) compared with control animals, where average FC > 2 and false discovery rate (FDR) <0.05. See also Figures S5 and S6.

Figure 6.. CCA Clusters and Sexually Dimorphic Cell Types in VMHvl

(A) Dot plots illustrating marker gene expressions in joint CCA clusters for SMART-seq (bottom) and 10x (top) datasets. Dot size and color indicate proportion of expressing cells and average expression level in each cluster, respectively. (B) Bar graph (left) represents the fractions of cells in clusters by sex (orange-red, female; sky blue, male). Far left, log-scaled p values (−log₁₀p) are color coded (Fisher’s exact test; white, p > 0.001). Violin plots show expression of genes specifically enriched in either female-specific (#3) or male-specific (#4, #5, #9) Esr1 clusters. (C) t-SNE plots of VMH cells from males (sky blue) and females (orange-red) illustrating distribution across joint CCA clusters. (D) Heatmap showing average expression in female VMH CCA clusters (n = 8,793) of genes previously identified by bulk RNA-seq (Hashikawa et al., 2017a) as localized to aggression-activated (red) or mating-activated (blue) VMHvl subdivisions in females (VMHpvlm versus VMHpvll). (E) Examples of seqFISH images (left; maximum intensity Z projections) for Pdyn and Rprm, major marker genes differentially expressed between male and female VMHvl. Scale bars, 100 μm (inset). Bar graph (right) showing spatial distribution patterns (along A-P axis) of female Esr1⁺ and Gpc3⁺ or male Esr1⁺ and Gpc3⁺ or Esr1⁺ and Gldn⁺ cells in VMHvl (****p < 0.0001; Fisher’s exact test). (F) Violin plots showing differential expressions of 10 genes (previously identified by scRNA-seq) between female- (Esr1⁺/Gpc3⁺) and male- (Esr1⁺/Gpc3⁺ or Esr1⁺/Gldn⁺) specific cell types in seqFISH. Log-scaled p values (−log₁₀p) are color coded (below; unpaired t test). See also Figure S7.

Figure 7.. Relationship between Behavioral Activation, Projection Specificity, and Transcriptomic Identity in the CCA Framework

(A) Bar graphs, dot plots, and heatmap illustrating Act-seq (top; Figure 5B), Retro-seq (middle; Figures 3C and 3D), and seqFISH (bottom; Figure 2D) data projected onto VMHvl CCA clusters, respectively. Act-seq: bars with colored and gray outlines indicate significant (p < 0.05 after multiple-comparison corrections across behaviors and clusters; three-way ANOVA and Bonferroni post hoc test), and non-significant (p > 0.05) differences in IEG expression versus control, respectively. Filled and open bars indicate significant and non-significant differences in IEG expression versus other clusters within a given behavior or behavioral category, respectively. All M-M and all M-F indicate combined data from all male-male or male-female social behaviors, respectively, for both Fos and Fosl2 expression. Lower bar graphs illustrate data for individual behaviors (Fos only). Retro-seq: dot size indicates the percent of retrogradely labeled VMH cells from dPAG, lPAG, or MPOA (middle); dot colors indicate relative ratio (retrogradely labeled divided by total sequenced populations) of clusters. Shaded gray dots indicate clusters with ratio <1). seqFISH: “Diff (A-P)” indicates percent difference in cell number between anterior versus posterior VMHvl (color scale) for cells in corresponding seqFISH clusters. (B and C) Scatterplots showing correlation between preferential Fos activation during all M-M versus all M-F behaviors (x axis) and projection preference between dPAG versus MPOA (y axis) for major Act-seq clusters (B) and correlation between preferential Fos activation during social fear (using group-housed mice) versus control (x axis) and proportion of cells projecting to lPAG (y axis) for VMHvl CCA clusters (C). (D) Bar graph showing the proportion of double⁺ (Fos⁺ and rHSV⁺) cells among VMHvl^Esr1 neurons between aggression versus control (upper) or M-F social interaction tests (mating + M-F CI tests) versus control (lower) in Esr1-Cre mice injected in dPAG or MPOA with a Cre-dependent retrograde HSV (rHSV). Numbers of mice are listed at the bottom of the graphs. *p < 0.05, one-way ANOVA after multiple-comparison corrections (left) and unpaired t test (right). (E) Venn diagrams (1–3) illustrating joint CCA clusters activated during different behavioral categories (all M-M, all M-F, and social fear) or projecting to dPAG and MPOA versus lPAG, respectively. Venn diagram (4) illustrates clusters distinctively located along A-P axis in male and female VMHvl. (F) Summary hierarchical taxonomy of CCA T-types in VMH; cell classes are labeled at branch points of the dendrogram. Data in (A) and (D) are represented as mean ± SEM. CI, close investigation (see Figure 5).