Abstract
Sensory stimuli drive the maturation and function of the mammalian nervous system in part through the activation of gene expression networks that regulate synapse development and plasticity. These networks have primarily been studied in mice, and it is not known whether there are species- or clade-specific activity-regulated genes that control features of brain development and function. Here we use transcriptional profiling of human fetal brain cultures to identify an activity-dependent secreted factor, Osteocrin (OSTN), that is induced by membrane depolarization of human but not mouse neurons. We find that OSTN has been repurposed in primates through the evolutionary acquisition of DNA regulatory elements that bind the activity-regulated transcription factor MEF2. In addition, we demonstrate that OSTN is expressed in primate neocortex and restricts activity-dependent dendritic growth in human neurons. These findings suggest that, in response to sensory input, OSTN regulates features of neuronal structure and function that are unique to primates.
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Acknowledgements
We thank E. Curran, T. Hartmann, P. Schade, P. Zhang, J. M. Gray, M. Hemberg, X. Adiconis, J. Z. Levin, J. Zieg, D. R. Hochbaum, T. J. Cherry and M. M. Andzelm for their technical assistance or advice. This work was supported by grants from the NIH: P50MH106933 and 1RC2MH089952 (M.E.G.), 5F32NS086270 (G.L.B.), EY16187 (M.S.L.), EY12196 (V.K.B.), and T32GM007753 (A.N.M. and E.D.). B.A. is supported by The Ellen R. and Melvin J. Gordon Center for the Cure and Treatment of Paralysis.
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B.A., G.L.B., and M.E.G. performed or directed all experiments and wrote the manuscript with E.C.G. B.A., D.A.H. and M.G.Y. performed or analysed gene expression experiments. G.L.B. performed iPSC differentiation and luciferase reporter assays with assistance from M.G.Y., K.M. and M.B.-S. V.K.B., G.L.B. and M.S.L. performed monocular inactivation experiments. B.A., M.G.Y. and G.L.B. performed FISH. B.A. and M.G.Y. performed dendritic growth assays. E.-L.Y. and N.Sh. contributed to overexpression studies. A.N.M. and A.A.R. cloned initial reporter constructs. I.S. provided RiboTag-Seq data and mouse brain sections. L.S.H. generated the OSTN antibody. M.P. and N.Se. provided human brain sections. M.C., J.N.P. and C.A.W. provided human tissue for initial culture experiments. M.A., B.A., M.G.Y., and E.D. performed ChIP experiments. C.R.S. assisted with RNA-seq experiments.
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Reviewer Information Nature thanks M. Oldham, F. Polleux and the other anonymous reviewer(s) for their contribution to the peer review of this work.
Extended data figures and tables
Extended Data Figure 1 hFBCs are mixed neuronal cultures that show high reproducibility.
a, Gestational week and sex of hFBC samples used in profiling of activity-dependent gene expression. b, Representative images of DIV6 hFBC neurons immunostained with the neuronal marker MAP2 alone or together with the glial marker GFAP and DAPI nuclear dye. Scale bar, 75 μm. c, Quantification of MAP2- and GFAP-positive cells in hFBCs. Mean ± s.d. from three independent cultures shown. d, Representative image of hFBC neurons immunostained with MAP2 (green), SATB2 (red) and CTIP2 (blue). Scale bar, 57 μm. e, Quantification of the SATB2- and CTIP-immunoreactive subpopulations of MAP2-positive hFBC neurons. Mean ± s.d. from three independent cultures shown. f, Heatmap showing the Spearman correlation rS of coding gene expression profiles among five biological hFBC replicates (H1–H5) (unstimulated neurons). g, Dendrogram of correlations among the gene expression profiles of hFBC replicates (H1–H5) and 10 human tissues, including whole brain37, based on hierarchical clustering with distance measure 1 − rS.
Extended Data Figure 2 hFBCs are mixed neuronal cultures with a substantial representation of cortical neuronal subtypes.
a, Quantile distribution constructed from combined log-gene expression levels of five unstimulated hFBC samples, with associated colour scale (see Methods). b–e, Expression of selected marker genes classified by neuronal subtype (b), glial cell type (c), brain region (d), neural progenitor cell type (e), and non-neural cell type (f).
Extended Data Figure 3 RNA-seq profiling of activity-dependent gene expression in human neuronal cultures.
a, b, RNA-seq analysis of membrane depolarization-induced hFBC gene expression changes after 1 h (a) or 6 h (b). Scatterplots depict the geometric mean of genes’ non-zero expression values ± s.e.m. from five independent hFBC cultures. Fold change is proportional to distance from the diagonal. Genes passing filters for expression and significant activity-dependent changes are highlighted in red (BH-corrected P values controlled for FDR ≤ 0.15 based on a negative binomial model38, magnitude of change (ratio ≥ 2.0 or ≤ 0.5), and above-background expression (RPKM > 0.57) on either axis, total reads ≥ 3 per time point). Selected genes exhibiting activity-regulated expression in human neurons but not in mouse neurons are indicated in blue. c, d, Pie charts showing the predicted subcellular localization of hFBC activity-responsive gene products induced following 1 h (c) or 6 h (d) KCl treatment. Analysis was performed using Ingenuity and GeneCards databases.
Extended Data Figure 4 Ostn is neither expressed nor activity-regulated in mouse cortical neurons in vitro and in vivo.
a, UCSC genome browser tracks for RNA-seq data from DIV7 cultured mouse cortical neurons depolarized for 0, 1 or 6 h with 55 mM KCl. The Ostn locus (grey) shows neither basal expression nor activity-dependent induction. The known activity-regulated gene Npas4 shows clear activity-dependent induction at 1 and 6 h. Finally, the cortex-enriched transcription factor Mef2C and the layer IV marker RorB show no significant expression changes in response to depolarization. b, UCSC genome browser tracks for RNA-seq data from visual cortices of dark-adapted (P42–P56) mice that were exposed to light for 0, 1, and 7.5 h. RNAs from excitatory and inhibitory neurons were isolated through the expression of a RiboTag transgene using Emx and Gad2 Cre-lines, respectively34. The Ostn (grey), Npas4, Mef2C and RorB loci show similar responses as in a. All genome browser tracks y-axis min = 0 and max = 10. c, FISH images of radial sections from primary visual cortex of dark-adapted (P42–P56) mice exposed to light for 0 and 7.5 h. Upper panels, grey-scale images of Npas4 (left) and Ostn (right) probes. Lower panels, green-coloured images from upper panels, with nuclei marked with DAPI (magenta). Scale bar, 110 μm; cortical layers I–VI are indicated.
Extended Data Figure 5 Differentiation and characterization of human iPSC-derived cortical neurons.
a, Schematic of the iPSC cortical neuron differentiation protocol44 (see Methods). b, Immunostaining of DIV82 iPSC-derived neurons shows expression of cortical layer markers TBR1 (layer VI), CTIP2 (layer V), and SATB2 (layers II–IV). c, Quantitative RT–PCR analysis of known activity-dependent genes from DIV82 iPSC-derived neurons 0, 1, and 6 h after membrane depolarization with 55 mM KCl. Data shown as mean ± s.e.m. from two independent iPSC lines. Scale bar, 100 μm.
Extended Data Figure 6 OSTN is primarily expressed in the neocortex of human brain.
BrainSpan (http://www.brainspan.org) RNA-seq data showing expression levels of OSTN (red) and BDNF (grey) in 6 human brain regions (a–f; neocortex, hippocampus (HIP), amygdala (AMY), striatum (STR), mediodorsal nucleus of the thalamus (MD), and cerebellar cortex (CBC)) and OSTN in subregions of the human cortex from 8 pcw through 40 years old (g). Loess-fit curves depict mean expression with bands showing one s.e.m. h, FISH images showing OSTN expression in a radial section of human fetal brain (pcw16) illustrating selective enrichment of OSTN in the developing cortical plate of the paracentral lobule. Isolated OSTN signal also appears to be localized to migrating neurons (arrowheads) of the subplate. Scale bar, 200 μm. MZ, marginal zone; CP, cortical plate; SP, subplate; IZ, intermediate zone; SVZ, subventricular zone; VZ, ventricular zone.
Extended Data Figure 7 Luciferase and ChIP assays in human and mouse neurons.
Direct comparison of the ability of the human and mouse −2kb regulatory sequences to drive reporter expression in mouse (a; n = 8) and human (b; n = 3) neuronal cultures in response to KCl depolarization. n = number of biological replicates. Mean normalized firefly luciferase activity (Fluc/Ren) ± s.e.m., Student’s t-test, NS, not significant, *P < 0.05, **P < 0.01, ***P < 0.001. c, Luciferase assays performed in mouse neurons in the presence of calcineurin inhibitors (CsA and FK506, red) or vehicle (DMSO, black), Student’s t-test, *P < 0.05. d, ChIP–seq using a pan-MEF2 antibody (purple), an MEF2C-specific antibody (fuschia), and an antibody specific for H3K27ac (green) in hFBCs (left) and mouse cortical neuron cultures (right) shows enrichment for MEF2 binding at the known MEF2-regulated gene Nr4a1 (also known as Nur77). Y-axis scales here and in Fig. 2e were adjusted for each experiment to normalize for variability in ChIP efficiency between these two different culture systems. We chose scales by setting MEF2 and H3K27ac enrichment to approximately equal levels at this positive-control locus, yielding all human tracks at max 10, mouse pan-Mef2, Mef2c, and input tracks at max 20, and mouse active chromatin (H3K27ac) at max 50. e, UCSC genome browser tracks for RNA-seq, ChIP–seq and vertebrate evolutionary conservation at the mouse Ostn locus, shaded yellow. RNA-seq tracks show no Ostn expression or induction in DIV7 mouse cortical neuron cultures following KCl depolarization (0, 1 and 6 h). ChIP–seq tracks45 show H3K27ac peaks that mark active cis-regulatory regions at two time points: 0 h and 2 h after KCl depolarization. The nearby genes Uts2b and Ccdc50 are also shown for comparison. No active cis-regulatory sites were found surrounding the Ostn locus. H3K27ac tracks are shown with max 5 and RNA-seq tracks with max 10.
Extended Data Figure 8 Luciferase reporter constructs and the complete set of assays.
a, Detailed summary of all luciferase assay reporter construct variants of the human genomic sequence −2 kb upstream of the OSTN transcription start site. b, Summary of all luciferase assays performed in mouse cortical cultures. Categories of construct modifications are indicated and grouped by colour. Biological replicate numbers are indicated on the graph. Significant differences tested for by one-way ANOVA DF = (33, 266) and P < 1.0 × 10−13. Pair-wise comparisons were made using Holm–Sidak test for multiple comparisons using an overall error rate of 0.05, ***P < 1.22 × 10−5. All values are mean ± s.e.m.
Extended Data Figure 9 FISH for OSTN mRNA in macaque brain.
Layer IVC of active ocular dominance columns in primary visual cortex (V1) shows expression of OSTN after monocular inactivation of monkey#1 (a) and monkey#2 (b). Scale bar, 1,000 μm. c, Expanded panel shows detail of partially tangential portion of tissue section in which OSTN is expressed in layer IVC ocular dominance column stripes. Scale bar, 1,000 μm. d, OSTN expression is also enriched in layer IV of the multimodal parietal cortex. Scale bar, 250 μm. e–h, Representative FISH images of layer IVC neurons from the active columns, showing co-expression of OSTN with various cell-type markers, including VGLUT1 (glutamatergic neurons, e; 94.2 ± 2.8% of OSTN+ cells were VGLUT1+, n = 170), RORB (layer IV, f; 93.3 ± 6.1% of OSTN+ cells were RORB+, n = 92), MEF2C (g; 100% ± 0 of OSTN+ cells were MEF2C+, n = 148), and MEF2A (h; 100% ± 0 of OSTN+ cells were MEF2A+, n = 148). Data are represented as mean ± s.d. Nuclei are visualized with DAPI. Scale bar (e–h), 2 μm.
Extended Data Figure 10 Biochemical detection and immunolocalization of endogenous OSTN protein in human neurons.
a, ELISA quantification of secreted OSTN in the culture medium of hFBCs under CAP conditions in two biological replicates (Rep#1 and #2). Rat monoclonal anti-OSTN antibody and rat monoclonal anti-CD31 (control antibody) were used as the detection antibodies. n = number of biological replicates. Mean ± s.e.m., Student’s t-test ***P < 0.001. b, Quantitative RT–PCR analysis of OSTN induction in hFBC neurons treated with scrambled siRNA (n = 5) or two independent siRNAs against the OSTN transcript (#1; n = 5 and #2; n = 4) for three days in the presence and absence of CAP. OSTN expression is normalized to GAPDH. c, d, Immunofluorescence images of DIV28 hFBC neurons transfected with −2kbhOSTN:GFP and left untreated (c) or maintained under CAP conditions (d). e–g, Immunofluorescence images of DIV28 hFBC neurons transfected with −2kbhOSTN:GFP (arrows) and treated with CAP for 3 days with (f) or without (e) treatment with siRNA targeting OSTN. Endogenous OSTN is predominantly localized in the soma and primary dendrites. Scale bar, 15 μm. (g) Higher magnification of OSTN immunostaining after 3 day CAP treatment reveals punctate structures (arrowheads) in the dendrites. Scale bars, 48 μm (c, d), 23 μm (e, f), 15 μm (g).
Supplementary information
Supplementary Table 1
Complete list of genes that are upregulated or downregulated in response to 1 hr or 6 hr KCl depolarization in hFBCs. (XLSX 31 kb)
Supplementary Table 2
Complete list of genes that are upregulated or downregulated in response to 1 hr or 6 hr KCl depolarization in cultured mouse cortical neurons. (XLSX 157 kb)
Supplementary Table 3
Complete list of genes that are upregulated or downregulated in response to 1 hr or 6 hr KCl depolarization in cultured rat cortical neurons. (XLSX 134 kb)
Supplementary Table 4
Comparison of activity-induced genes in hFBCs following 1 or 6 hrs of KCl-induced depolarization with genes induced under similar conditions in mouse and rat cultures. (XLSX 44 kb)
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Ataman, B., Boulting, G., Harmin, D. et al. Evolution of Osteocrin as an activity-regulated factor in the primate brain. Nature 539, 242–247 (2016). https://doi.org/10.1038/nature20111
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DOI: https://doi.org/10.1038/nature20111
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