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. 2020 Nov 5;9:e62373. doi: 10.7554/eLife.62373

Figure 7. Examination of Pafah1b haploinsufficiency on PV+INTs using single-nucleus RNA-seq.

(A) Overview of the experimental workflow. (Bi) Uniform Manifold Approximation and Projection (UMAP) dimensional reduction of single-nuclei transcriptomes of hippocampal PV+INTs, highlighting similar enrichments of the clusters between genotypes. (Bii) UMAP visualization of Axo-axonic, Bistratified and Fast-spiking PV+INT subtypes, and table indicating the number of Gad1/Pvalb+ cells recovered in each PV+INT. Cell clusters were color coded and annotated post hoc based on their transcriptional profile identities (Abbreviations: FS, Fast-spiking; DG, Dentate gyrus). (C) Combined heatmap representing the 376 differentially expressed (DE) in hippocampal PV+INTs upon Pafah1b1 haploinsufficiency, at FDR < 0.01 and Fold Change (FC) >10%, as determined by MAST analysis. (D) Ingenuity Pathway Analysis of significantly overrepresented molecular pathways in each PV+INT subtype. (E–H) Heatmap of log2 FC of significant DE genes in each PV+INT subtype, showing a subset of (Ei) uniquely DE cell-adhesion molecules (CAMs), (Eii) commonly DE CAMs, Eiii, DE extracellular matrix modifying genes; (Fi), genes regulating neuronal migration and axon guidance, (Fii), genes that exist in a genetic and biochemical complex with Pafah1b1. (G) regulators of neuronal excitability, and (H) postsynaptic glutamate receptor subunits and associated auxiliary subunits.

Figure 7.

Figure 7—figure supplement 1. Integrated analyses of single-cell/nucleus transcriptomes from PV+INTs from Pafah1b1+/+, Pafah1b1+/-and reference datasets.

Figure 7—figure supplement 1.

(A) UMAP plots of the PV+INTs from Pafah1b1+/+ and Pafah1b1+/- cortical and hippocampal MGE-derived interneurons and pan-GABAergic Allen Institute datasets indicating robust alignments of the PV+INT clusters. UMAP plots representing the expression of (B) Gad1 and (C) Pvalb across all datasets.
Figure 7—figure supplement 2. Annotation of PV+INT subtypes based on discrete marker gene expressions.

Figure 7—figure supplement 2.

(A) Single cell heatmap showing scaled expression values for the top 10 transcriptomic markers in each of the PV+INTs clusters across Pafah1b1+/+, Pafah1b1+/- and reference datasets. (B) UMAP plots depicting the bistratified, axo-axonic and fast-spiking clusters across all datasets. (C) Merged UMAP plots representing the expression of top transcriptomic markers across the PV+INT subtypes across all datasets.