Innovations present in the primate interneuron repertoire

An Author Correction to this article was published on 24 November 2020

This article has been updated

Abstract

Primates and rodents, which descended from a common ancestor around 90 million years ago1, exhibit profound differences in behaviour and cognitive capacity; the cellular basis for these differences is unknown. Here we use single-nucleus RNA sequencing to profile RNA expression in 188,776 individual interneurons across homologous brain regions from three primates (human, macaque and marmoset), a rodent (mouse) and a weasel (ferret). Homologous interneuron types—which were readily identified by their RNA-expression patterns—varied in abundance and RNA expression among ferrets, mice and primates, but varied less among primates. Only a modest fraction of the genes identified as ‘markers’ of specific interneuron subtypes in any one species had this property in another species. In the primate neocortex, dozens of genes showed spatial expression gradients among interneurons of the same type, which suggests that regional variation in cortical contexts shapes the RNA expression patterns of adult neocortical interneurons. We found that an interneuron type that was previously associated with the mouse hippocampus—the ‘ivy cell’, which has neurogliaform characteristics—has become abundant across the neocortex of humans, macaques and marmosets but not mice or ferrets. We also found a notable subcortical innovation: an abundant striatal interneuron type in primates that had no molecularly homologous counterpart in mice or ferrets. These interneurons expressed a unique combination of genes that encode transcription factors, receptors and neuropeptides and constituted around 30% of striatal interneurons in marmosets and humans.

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Fig. 1: Analysis of cortical interneurons in ferret, mouse, marmoset, macaque and human.
Fig. 2: Comparing cortical interneurons within regions and across species.
Fig. 3: Cortical LHX6+LAMP5+ interneurons are much more numerous in primates and are molecularly similar to conserved hippocampal interneurons.
Fig. 4: A primate striatal interneuron type not observed in mouse or ferret.

Data availability

Sequencing data included in this manuscript are available at GEO (accession number, GSE151761); sample information is described in Supplementary Table 7. Processed sequencing files—including single-nucleus digital gene expression matrices for each region and cluster assignments for marmoset are available through the NIH’s Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative–Cell Census Network (BICCN) at https://biccn.org/. Processed data from all species can also be queried using an interactive web interface that we created (http://interneuron.mccarrolllab.org).

Code availability

Software and core computational analysis to align and process Drop-seq sequencing reads are freely available: https://github.com/broadinstitute/Drop-seq/releases. Published or publicly available algorithms are cited in the text and in Supplementary Table 8. Source code to reproduce the analysis on http://interneuron.mccarrolllab.org is available on the website. Other custom code is available on reasonable request from the corresponding authors.

Change history

  • 24 November 2020

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Acknowledgements

This work was supported by the Broad Institute’s Stanley Center for Psychiatric Research, by Brain Initiative grant U01MH114819 to G. Feng and S.A.M., by the Dean’s Innovation Award (Harvard Medical School) to G. Fishell and S.A.M., and by the Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, the Poitras Center for Psychiatric Disorders Research at MIT and the McGovern Institute for Brain Research at MIT (G. Feng) and the NINDS RO1NS032457 (C.A.W.). C.A.W. is an Investigator of the Howard Hughes Medical Institute. We thank R. Borges-Monroy for sharing the ferret transcriptome reference; M. W. Baldwin, A. D. Bell, S. Burger, C. Patil and R. L. Buckner for comments on manuscript drafts; C. Mayer for analysis advice; and C. Usher for assistance with manuscript preparation.

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Authors

Contributions

F.M.K., S.A.M., G. Feng and G. Fishell designed the study. F.M.K. prepared and dissected tissue; L.B. and M.G. developed the nucleus Drop-seq protocol. M.G., A.L., C.D.M., N.R., E.B. and L.B. performed Drop-seq and prepared sequencing libraries. M.G. and F.M.K. performed sequencing, alignment and quality-control analyses. F.M.K., A.S., J.N., A.W., D.K., R.d.R. and S.A.M. developed analysis pipelines. F.M.K. analysed the data with input from S.A.M., G. Fishell, M.F., A.L. and A.S. D.K. developed the web resource. D.K., Q.Z., C.W., M.B., V.T., R.S., C.A.W., L.K., S.B. and G. Feng provided tissue for Drop-seq and smFISH experiments. K.L., H.Z., N.R., E.B., M.F.-O., J.D.L., F.M.K. and J.D. performed and analysed smFISH experiments. R.M., B.S. and B.R. contributed fate-mapping experiments. F.M.K. and S.A.M. wrote the paper with input from co-authors.

Corresponding authors

Correspondence to Fenna M. Krienen or Steven A. McCarroll.

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Extended data figures and tables

Extended Data Fig. 1 Interneuron abundances and gene expression in neocortex.

a, Comparison of measured abundances (expressed as the percentage of all Gad1+ cells) of select interneuron populations across three modalities: single-cell Drop-seq (n = 3,859 cells, n = 7 biological replicates), nucleus Drop-seq (8,622 nuclei, n = 11 biological replicates) and stereological counting of smFISH in mouse cortex (n = 3,891 counted cells, n = 3 biological replicates). Cell Drop-seq and smFISH values were obtained from a previous study15. Box plots show median and interquartile range. b, Percentage of interneurons (expressed as a percentage of all neurons) in sensory and association cortex measured with snRNA-seq. Box plots show the median and interquartile range; dots indicate individual brain regions. Ferret, n = 20,285 neurons; mouse, n = 90,159 neurons; marmoset, n = 576,345 neurons; human, n = 303,733 neurons. c, Proportion of MGE and non-MGE interneurons in cortical association regions (PFC, temporal pole and lateral parietal association cortex) and in cortical sensory regions in marmoset (n = 25,946 interneurons across 7 regions from 1 replicate) and human (n = 42,042 interneurons across 4 regions from 2 replicates). Error bars represent binomial confidence intervals.

Extended Data Fig. 2 Marker gene expression across species.

a, Examples of markers that are consistent, or that vary across species, within the four primary interneuron classes. Values are scaled UMI counts per 100,000 transcripts. b, Triple smFISH characterization of IQGAP2, PVALB and VIP in mouse (n = 1 biological replicate) and marmoset (n = 1 biological replicate) cortex. Arrows indicate double-positive cells (either IQGAP2+PVALB+ or IQGAP2+VIP+). Scale bar, 10 μm.

Extended Data Fig. 3 Comparisons of neocortical interneuron types across and within species.

a, Examples of correlation (Pearson’s r) in fold difference of expressed genes between pairs of MGE-derived and of nonMGE-derived interneuron types across pairs of species. Comparing within and then across species corrects for potential species-specific (for example, sequence-related) influences on RNA sampling, as well as for latent technical variables that might distinguish brains of different species. Genes in red have >3-fold expression difference in either cell type in each species pair, showing that the most extreme DEGs (largely consisting of known ‘markers’ of each type) tended to be consistent between species, despite modest correlations overall. Expression values obtained from n = 10,177 mouse and n = 63,096 marmoset cortical interneurons. b, Cortical interneuron t-SNE plots for each species (same data as Fig. 1c), coloured by individual replicate. c, Measure of inter-individual variability in gene expression (mu) in major interneuron types in mouse, marmoset and human. For each cell type, normalized gene expression levels (averaged across individual cells) are compared between pairs of individuals of the same species. Marmosets and mice both exhibited more modest inter-individual differences than humans did, which probably reflects the effects of life histories, environments and age at sampling, which are more uniform in a laboratory setting. Higher values indicate greater variability. Note that while the mice are isogenic, whole-genome sequencing of the marmosets revealed that they exhibited sequence variation comparable to humans. d, mu scores stratified by pLI gene scores. Human haplo-insufficient (high-pLI) genes tended to have lower expression variability than low-pLI genes in humans but not in marmosets or mice.

Extended Data Fig. 4 Regional gene expression variation in neocortex.

a, Schematic of neocortical region locations in marmoset. b, Histogram of the number of rDEGs (>3-fold expression difference) between three representative pairs of regions, in each cell type (cluster) for which there were at least 50 cells per region. c, Histogram of the number of interneuron clusters (cell types) in which a given gene is differentially expressed. At a threshold of >3-fold, most genes are only differentially expressed in a single cell type (cluster). d, Average fold difference of regional enrichment across regions and clusters. Coloured dots represent average fold difference of DEGs in each cluster in marmoset interneurons computed from the region pair depicted. Violin plots represent the distribution of average fold differences in each cluster (cell type) when using rDEGs from other clusters. Three representative region pairs are shown (n = 517 rDEGs genes across clusters for PFC and V1; n = 2,271 genes for A1 and V2; n = 1,622 genes for Par and V2). Horizontal bars on violin plots represent the median differential expression score (when using rDEGs from other clusters). rDEGs identified for any one interneuron type (cluster) tended to also exhibit the same regional bias in the other types (clusters). This suggests that most such differences reflect a common regional signature that is shared by diverse interneurons, rather than being specific to particular interneuron types. e, Fold ratios (log10-transformed) between PFC and V1 for three astrocyte subtypes (n = 32,600 nuclei) in marmosets using rDEGs identified in interneurons in the same brain regions. Box plots show interquartile ranges and medians. Dots show outlier genes. f, As in e but for all seven brain regions. Regions are arranged in anterior–posterior order on the x axis. Box plots show interquartile ranges and medians. Dots show outlier genes.

Extended Data Fig. 5 smFISH validation of graded gene expression in PVALB+ interneurons.

a, Top, sagittal sections of marmoset brain (n = 1 marmoset, at least two tissue sections stained per probe set) stained for PVALB and ASS1 (left) or CRYM (right), two genes that showed quantitatively graded expression in the interneuron snRNA-seq data (see Fig. 2d). Bottom, representative cells from each of the three imaged regions (blue boxes in the top panels). Scale bar, 10 μm. b, Top, spatial distribution of PVALB+ and double-positive interneurons plotted from three imaging windows (blue boxes in a) across the sagittal plane. Bottom, proportion of single-positive (PVALB+ only) and double-positive (PVALB+ASS1+ or PVALB+CRYM+) cells binned along the rostrocaudal axis within imaged regions. c, Mean intensity for each probe within cells identified in b (n = 14,195 double-positive cells in the PVALB+ASS1+ experiments and n = 26,194 double-positive cells in the PVALB+CRYM+ experiments). PVALB itself shows a graded expression (in terms of signal intensity per cell) across the rostrocaudal extent in our snRNA-seq data, with the highest expression (and highest cell numbers) located in the caudal pole (V1). Box plots represent the interquantile range and median values.

Extended Data Fig. 6 Conserved and divergent gene expression across neocortical types.

a, Liger-integrated marmoset (n = 6,739 interneurons) and mouse (n = 6,852 interneurons) datasets. b, Heat map of exemplar genes that had consistent patterns of expression in Liger-integrated marmoset–mouse clusters from a. Each gene (row) is scaled to the scaled maximum (black) expression (values given outside plots) for each species separately. The coloured top bar codes each cluster as one of the major types (as in Fig. 1). Column labels follow labels in a. c, Heat map of exemplar genes that have divergent expression patterns in Liger-integrated marmoset–mouse clusters from a. Each gene (row) is scaled to the scaled maximum (black) expression (values given outside plots) for each species separately. Exemplar genes include those that are widely used as markers for particular interneuron populations but have divergent gene expression across mice and marmosets, such as CALB1 and CALB2.

Extended Data Fig. 7 Integration of marmoset and human interneurons.

a, Liger-integrated marmoset (n = 6,739 interneurons; the same data are used in Extended Data Fig. 6) and human (n = 4,164 interneurons). Human data are from the middle temporal gyrus dataset available from a previously published study11 (SMART-seq v.4). Marmoset data are from temporal lobe interneurons (Drop-seq). b, Heat map of the proportional representation of individual-species clusters (rows) within Liger clusters (columns) labelled as in a. Marmoset clusters were generated from an ICA-based pipeline (see Methods). Human clusters and labels are from a previously publishes study11 (for example, see figure 5d of the previous study11). In both datasets, most clusters contributed predominately to a single Liger cluster, and cells that clustered together in the data for each species (by separate analyses) tended to remain clustered together in the interspecies Liger analysis, suggesting that the integrated analysis preserved the structure present in the individual datasets. Consistent with the finer clustering in the previous study11 (they obtained 45 human interneuron clusters, whereas our marmoset data resolved to 22 clusters), several human clusters often contributed to a Liger cluster, whereas most marmoset clusters singly contributed to a Liger cluster. For example, Liger cluster 22 corresponds to a single marmoset cluster (cluster 1-11) and two distinct (but related) human clusters (Inh L1-2 PAX6 TNFAIP8L3 and Inh L1-2 PAX6 CDH12).

Extended Data Fig. 8 Interneuron distributions in cortex and hippocampus.

a, Left, smFISH for GAD1, LAMP5 and LHX6 in marmoset hippocampal layers (CA1/CA2 subfields; n = 2 biological replicates). Arrowhead indicates triple-positive cells; arrow indicates the LHX6 population. Top row, strata oriens (Str. Or) and strata pyramidale (Str. Py). Bottom row, strata lacunosum moleculare (LMol). Scale bars, 100 μm. Right, quantification of GAD1+LAMP5+LHX6+ (red) and GAD1+LAMP5+LHX6 (cyan) cells as a percentage of all GAD1+ cells in marmoset hippocampus (n = 446 GAD1+ cells counted) (compare to previously published mouse data39). Data are mean ± s.e.m.; dots represent biological replicates. b, smFISH for Gad1, Lamp5 and Lhx6 in mouse hippocampal layers (CA1; n = 2 biological replicates). c, Scatter plots of relative normalized gene expression (log10-transformed) across pairs of marmoset LAMP5 types in neocortex and hippocampus. Data from Fig. 3d; neocortical (n = 5,114 interneurons) and hippocampal (n = 1,589 interneurons). d, Scaled, normalized expression of select gene markers that distinguish the three main LAMP5+ types in marmoset.

Extended Data Fig. 9 Analysis of striatal interneurons.

a, Clustering of an additional dataset of 2,718 marmoset striatal interneurons (acquired using 10X 3′ Chromium v.3 chemistry) confirms the existence of the large TAC3+ population and reveals additional diversity within the main striatal interneuron clusters. The marmoset TAC3+ population comprises two subtypes; markers distinguishing between the two included SULF1, ASB18, ANGPT1 and PLCXD3 (note these are also expressed at varying levels in some of the other striatal interneuron types). This dataset also identified additional markers for the TAC3+ population as a whole relative to other striatal interneurons, such as genes that encode the extracellular matrix protein LTBP2, corticotropin-releasing hormone receptor 2 (CRHR2), the transcriptional repressor PRDM8 and α-1D adrenergic receptor (ADRA1D). b, Scatter plots showing gene expression (log10-transformed) between TAC3+ and PVALB+ or SST+ populations in marmoset striatum. Differentially expressed (>3-fold difference) neuropeptides and transcription factors are labelled. c, The analysis in Fig. 4a was repeated, but additionally included all mouse extra-striatal interneurons from a previous study15. For display, the t-SNE plot shows marmoset striatal interneurons (red), mouse striatal interneurons (blue) and any extra-striatal mouse interneuron that expressed Vip or Tac2 in the previously published dataset15 (grey). Circled cells indicate marmoset TAC3+ population. d, Liger integration of mouse and ferret striatal interneurons. Right, mouse interneurons in a mouse-only ICA-based t-SNE, with cells coloured according to their Liger clusters to confirm that clusters identified by Liger correspond meaningfully to clusters produced by a single-species analysis.

Extended Data Fig. 10 Cross-species patterns of gene expression within striatal interneurons.

a, Individual species-based ICA clustering of ferret (10X 3′ v.3, n = 709 interneurons), mouse (Drop-seq, n = 2,166 interneurons), marmoset (10X 3′ v.3, n = 2,707 interneurons) and human (10X 3′ v.3, n = 1,509 interneurons) striatal datasets. Shades of blue are used to represent the diverse populations of ADARB2+ types (non-MGE+ types, including subpopulations of CCK+ types previously identified in mice42). b, Scaled expression of marker genes among the four most numerous striatal interneuron types that are conserved in all species examined (SST+, CHAT+, TH+ and PVALB+PTHLH+). Bars coloured according to scheme in a. The differential expression of CALB1 across species is one of the most marked examples observed of human-specific expression of a gene in a conserved cell type. c, Gene expression differences in human caudate interneurons between TAC3+ and PVALB+ (left) or TAC3+ and SST+ (right) populations. Neuropeptides (red), transcription factors (purple) and ion channels (yellow) are labelled. d, Data as in c, but instead highlighting genes that were differentially expressed in both marmoset and human (red, with gene symbols) or only in marmoset (blue).

Supplementary information

Reporting Summary

Supplementary Table

Supplementary Table 1. Normalized gene expression levels amongst major cortical interneuron types. The log10 expression levels (normalized to 100,000 transcripts per type) of genes across the major neocortical interneuron types (n = 2,930 cells in ferret; n = 10,177 in mouse; n = 63,096 in marmoset; n = 22,305 in macaque; n = 56,648 in human). The columns are the four major neocortical types: SST+, PVALB+, VIP+, or LAMP5+ described in Figure 1 in the main text.

Supplementary Table

Supplementary Table 2. Inter-individual variability in gene expression. Measure of inter-individual variability in gene expression (mu) in major cortical interneuron types in mouse, marmoset and human. For each interneuron type, normalized (log10) gene expression levels (averaged across individual cells) are compared between pairs of individuals of the same species.

Supplementary Table

Supplementary Table 3. Relationship between inter-individual variability in gene expression and loss of function intolerance. Measure of inter-individual variability in gene expression (mu) values in major cortical interneuron types in mouse, marmoset and human (as in Supplementary Table 2) combined with each gene’s human genomic context and constraint information obtained from1. Genes are filtered to retain those expressed at least 10 per 100,000 transcripts in cortical interneurons in each species. Probability of loss of function intolerance (pLI) scores are stratified as > or < 0.9 for analysis in Extended Data Figure 3.

Supplementary Table

Supplementary Table 4. Normalized expression levels across neocortical regions in marmosets. The log10 expression levels (normalized to 100,000 transcripts per type) of genes across n = 63,096 cortical interneurons in marmosets, with values provided separately for each of n = 7 cortical regions (PFC, A1, S1, Temporal pole, lateral Parietal cortex, V1, V2). Columns are numbered by cluster following clusters shown in Figure 2b in the main text.

Supplementary Table

Supplementary Table 5. Conserved and divergent gene expression across neocortical types in marmoset and mouse. Gene expression levels from Liger integrated marmoset (n=6,739 interneurons) and mouse (n=6,852 interneurons) cortical datasets. Each gene (row) is scaled to the max expression level (within-column values first log10 normalized to 100,000 transcripts per type). Columns (types) with fewer than 50 cells in a species not included.

Supplementary Table

Supplementary Table 6. Cross-species patterns of gene expression within striatal interneurons. The log10 gene expression levels (normalized to 100,000 transcripts per type) of striatal interneuron subtypes in ferret, mouse, marmoset and human. Ferret, marmoset and human data obtained from frozen nuclei by 10X 3’ v.3 chemistry. Mouse data obtained from15. Clusters were obtained for each species separately using ICA dimensionality reduction and Louvain community detection. Subtypes with fewer than 30 cells not included.

Supplementary Table

Supplementary Table 7. Specimen information table. Sample details including number of samples, age and sex, postmortem interval (PMI, when applicable), and brain region.

Supplementary Table

Supplementary Table 8. Reagent and resource table. Reagents and resources used in study.

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Krienen, F.M., Goldman, M., Zhang, Q. et al. Innovations present in the primate interneuron repertoire. Nature 586, 262–269 (2020). https://doi.org/10.1038/s41586-020-2781-z

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