Genetic approaches to elucidating cortical and hippocampal GABAergic interneuron diversity

Abstract

GABAergic interneurons (INs) in the mammalian forebrain represent a diverse population of cells that provide specialized forms of local inhibition to regulate neural circuit activity. Over the last few decades, the development of a palette of genetic tools along with the generation of single-cell transcriptomic data has begun to reveal the molecular basis of IN diversity, thereby providing deep insights into how different IN subtypes function in the forebrain. In this review, we outline the emerging picture of cortical and hippocampal IN speciation as defined by transcriptomics and developmental origin and summarize the genetic strategies that have been utilized to target specific IN subtypes, along with the technical considerations inherent to each approach. Collectively, these methods have greatly facilitated our understanding of how IN subtypes regulate forebrain circuitry via cell type and compartment-specific inhibition and thus have illuminated a path toward potential therapeutic interventions for a variety of neurocognitive disorders.

Keywords: GABAergic interneurons; cortex; hippocampus; intersectional genetics; subtypes; transgenic.

Figure 1

Overview of cortical and hippocampal IN transcriptomic subtypes. (A) Schematic view of the total GABAergic IN scRNAseq data from Yao et al. (2021) [portal.brain-map.org/atlases-and-data/rnaseq; whole cortex and hippocampus—10x genomics (2020) with 10x smart-seq taxonomy (2021)]. Each colored bin represents a subpopulation of cells clustered as described by Yao et al. (2021). Groups of related bins are annotated here based on gene expression and putative cell type assignment, with heatmaps of the primary gene marker mRNA levels represented as trimmed means (counts per million: CPM, with color intensity reflecting log2 scale as indicated) aligned below. These primary markers are as follows(from left to right): Meis2, Id2, Vip, Sst, and Pvalb. The Id2 IN population encompasses neurogliaform cells (NGFCs), α7/canopy cells, Serpinf1, NtnG1, and Sncg subtypes (detailed in Figure 2). The VIP group is represented as one group here, with details elaborated in Figure 3. The Sst group is represented as two main groups: Sst long-range (Sst LR) and other Sst subtypes (detailed in Figure 4). Likewise, the Pvalb group is represented as PV and PV axo-axonic/chandelier (PV AAC/ChC) subtypes (detailed in Figure 5). To complement these primary IN markers, heatmaps for Adarb2 (CGE/POA) and Lhx6 (MGE) are shown, along with Htr3a. (B) Scatterplots of the total IN population from Yao et al. (2021) illustrate the transcriptomic diversity of IN subtypes in reduced dimensional space. The color scheme of the bins in A is maintained in the cell representations shown in the overview, and the general locations of the four main IN groups (Id2, Vip, Sst, and Pvalb) are indicated. Individual scatterplots for Lhx6 (MGE), Adarb2 (CGE/POA), Htr3a, Pvalb, Sst, Id2, and Vip are shown, with the red color intensity reflecting the trimmed mean CPM values (log2 scale) as in (A).

Figure 2

Id2-Lamp5-Sncg transcriptomic subtypes. (A) INs corresponding to MGE-derived NGFC (Lhx6+; bins 5–9), CGE-derived NGFC (non-Lhx6+; bins 10–12), α7 cells (bins 13–14 and Pax6+ bins 19–20), and canopy cells (bins 15–18). Heatmaps for Lhx6, Id2, Lamp5, Ndnf, Npy, Chrna7, Pax6, and Reln transcripts are aligned below (trimmed mean CPM in each bin is represented by red color intensity on a log2 scale, as indicated by the guide located below the heatmaps). (B) INs corresponding to Serpinf1 (bins 21–25), NtnG1 (bins 26–30), and Sncg (bins 31–39) cells. Heatmaps for Id2, Cck, Sncg, NtnG1, Ndnf, Cnr1, Vip, and Reln are aligned below. (C) Individual scatterplots for Id2, Lamp5, Ndnf, Npy, Chrna7, Pax6, Sncg, and Cck are shown, with annotation and arrows highlighting the approximate location of the indicated IN subtypes. HPF, hippocampal formation.

Figure 3

VIP transcriptomic subtypes. (A) Overview of VIP IN transcriptomic diversity, with heatmaps for Vip, Cck, Calb2, Crh, Tac2, Chat, Nos1, and Igfbp6 transcripts shown below (trimmed mean CPM in each bin is represented by red color intensity on a log2 scale, as indicated by the guide located below the heatmaps). Several subgroups of VIP INs are annotated above the colored bins, including Vip/Cck, Vip/Crh, Vip/Calb2, and Calb2 (non-VIP) cells. (B) Individual scatterplots for Vip, Cck, Calb2, and Crh are shown, with annotation and arrows highlighting the approximate location of the indicated IN subtypes. HPF, hippocampal formation.

Figure 4

SST transcriptomic subtypes. (A) Overview of SST IN transcriptomic diversity, with heatmaps for Sst, Npy, Nos1, Pdyn, Crh, Myh8, Etv1, Crhr2, Hpse, Calb2, Tac1, Th, and Pvalb transcripts shown below (trimmed mean CPM in each bin is represented by red color intensity on a log2 scale, as indicated by the guide located below the heatmaps). Different subgroups of SST INs are annotated above the colored bins, including Sst LR (long range), MC (Martinotti), non-MC (non-Martinotti), α2 (Chrna2-expressing OLM and MC cells), hippocampal/entorhinal Sst cells, and Th cells. (B) Individual scatterplots for Sst, Nos1, Pdyn, Calb2, Myh8, Crh, Crhr2, and Th are shown, with annotation and arrows highlighting the approximate location of the indicated IN subtypes.

Figure 5

PV transcriptomic subtypes. (A) Overview of PV (Pvalb) IN transcriptomic diversity, with heatmaps for Pvalb, Sst, Th, Tac1, Unc5b, and Pthlh transcripts shown below (trimmed mean CPM in each bin is represented by red color intensity on a log2 scale, as indicated by the guide located below the heatmaps). The two main groups of PV INs (basket; bins 111–119, and axo-axonic/chandelier; bins 122–123) are annotated above the colored bins. (B) Individual scatterplots for Pvalb, Tac1, Unc5b, and Pthlh are shown, with annotation and arrows highlighting the axo-axonic/chandelier (AAC/ChC) cluster.

Figure 6

Cck mRNA expression levels across INs. Plot of trimmed mean log2 (CPM + 1) Cck mRNA transcript levels for each IN bin using values from Yao et al. (2021). To the right of the plot are illustrative comparisons of the hypothetical degree of cell labeling using CCK immunohistochemistry (IHC) or Cck-Cre; reporter cumulative genetic labeling. Note that the latter method labels a substantial number of Id2/Lamp5 and PV INs (Machold et al., 2023).