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Mutations in NONO lead to syndromic intellectual disability and inhibitory synaptic defects

Abstract

The NONO protein has been characterized as an important transcriptional regulator in diverse cellular contexts. Here we show that loss of NONO function is a likely cause of human intellectual disability and that NONO-deficient mice have cognitive and affective deficits. Correspondingly, we find specific defects at inhibitory synapses, where NONO regulates synaptic transcription and gephyrin scaffold structure. Our data identify NONO as a possible neurodevelopmental disease gene and highlight the key role of the DBHS protein family in functional organization of GABAergic synapses.

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Figure 1: NONO mutations and their functional consequences.
Figure 2: Transcriptome analysis in human and mouse cells.
Figure 3: Functional consequences of NONO deficiency in mice.
Figure 4: Effects of NONO deficiency on synaptic biology.
Figure 5: GABA receptor overexpression rescues synaptic structural defects.

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Acknowledgements

We are grateful to the patients and their family members for their participation in our study and to the Functional Genomics Center Zürich (FGCZ) for transcriptomic services. This program has received a state subsidy managed by the National Research Agency under the Investments for the Future program bearing the reference ANR-10-IAHU-01.This study was also supported by the Centre National de la Recherche Scientifique (CNRS), the Fondation pour la Recherche Médicale (DEQ20120323702) and the Ministère de la Recherche et de l'Enseignement Supérieur, as well as by the Swiss National Science Foundation, the Zurich Clinical Research Priority Program “Sleep and Health,” the Zurich Fonds zur Förderung des akademischen Nachwuchses and the Zurich Neurozentrum (ZNZ). D.M., S.A.B. and S.K.T. are affiliates of the ZNZ Life Sciences Zurich graduate program, and S.A.B. is a member of the Zürich Center for Interdisciplinary Sleep Research (ZIS). The DDD study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between the Wellcome Trust and the UK Department of Health, and the Wellcome Trust Sanger Institute (grant number WT098051). The views expressed in this publication are those of the author(s) and not necessarily those of the Wellcome Trust or the Department of Health. The research team acknowledges the support of the UK National Institute for Health Research, through the Comprehensive Clinical Research Network.

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Contributions

L.C., S.A.B., J.-M.F. and S.K.T. designed the study. J.A., M. Rio and K.P. recruited and evaluated the study subjects. N.B. performed and analyzed the human brain imaging, and D.M., P.S., A.S. and M. Rudin performed and analyzed the mouse brain imaging. M.L. analyzed whole-exome sequencing data and performed transcriptional analysis and western blot analysis on patient cells, and L.G. performed circadian analyses on patient cells. S.M. contributed to whole-exome sequencing data analysis. C.B.-F. performed whole-exome sequencing. N.C. and P.N. performed the bioinformatics studies. R.H. and S.J.M. supplied engineered virus for in vivo rescue experiments. D.M. executed and analyzed all experiments on mouse tissues, and D.M. and M.Ž. executed and analyzed experiments in rodent cells. D.M., C.K., F.C., A.-K.F. and D.P.W. performed and analyzed mouse behavioral experiments. A.M. contributed to the clinical evaluation of the patients. K.S.-P. and O.A. contributed to the WES analysis. G.B. prepared cultured neurons for all experiments in this study. All authors contributed to writing and editing the manuscript.

Corresponding authors

Correspondence to Steven A Brown, Shiva K Tyagarajan or Laurence Colleaux.

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The authors declare no competing financial interests.

Additional information

A full list of consortium members appears in the Supplementary Note.

Integrated supplementary information

Supplementary Figure 1 Molecular analyses of patients MCCID1 and MCCID2

(a) Sanger sequencing chromatograms showing the NONO mutations in the probands and their parents. (b) Schematic representation of the NONO transcript showing exon structure. (c) Schematic overview of the NONO protein showing the different functional domains.

Supplementary Figure 2 Photographs of the two patients from the Necker Hospital study, and a third patient from the Deciphering Developmental Disorders cohort

Supplementary Figure 3 Full-length western blot of NONO

Western blot of NONO protein in patients and controls, using a different polyclonal antibody from the one used in Figure 1.

Supplementary Figure 4 Reduced circadian amplitude in patient fibroblasts.

(a) Graph of average circadian oscillations of bioluminescence from Bmal1-luciferase reporter-infected fibroblasts from patients (grey) or siblings (black). Y-axis, background-subtracted bioluminescence in photons per minute; X-axis, time in days. Depicted curve is the average of three independent experiments in technical quadruplicate. (b) Circadian period measured in cells from controls (black bars) and patients (open bars). (c) Circadian amplitude measured in the same cells (arbitrary units). Student t-test, p<0.001. Values for both panels are the average of three independent experiments with fibroblasts from both patients and their siblings in technical quadruplicate.

Source data

Supplementary Figure 5 Brain morphology in Nonogt mice.

(a) Photograph of representative brains from WT (left) and Nonogt (right) mice. (b) Quantification of weight of whole brain, cortex, and cerebellum. N=5-9 mice per genotype. Student t-test. White bars, WT. grey bars, Nonogt. In this and subsequent figures, ***p<0.001, **p<0.01, *p<0.05. Quantification of all brain parameters from different morphological tests is shown in detail in Table S4.

Source data

Supplementary Figure 6 Anxiety-related phenotypes in Nonogt mice.

(a) Percentage of time spent in open arms of elevated plus-maze. N=13-14 mice per genotype. Student t-test, p<0.001 (b) Post-conditioning startle response in prepulse inhibition test. Y-axis, whole-body startle response in volts; X-axis, stimulus in decibels. N=13-14 mice per genotype. Student t-test, p<0.01 or 0.001 as indicated. (c) Open-field exploration. Y-axis, percentage of area surface tiles visited. X-axis, subsequent 5-minute intervals after commencement of test. N=18 mice per genotype, repeated ANOVA, gene p<.0002, time p<.0001, time x gene n.s. (d) Light-dark transition test. Y-axis, percentage of time spent in zones indicated on X-axis. N=18 mice per genotype, repeated ANOVA, gene p<.0001, zone p<.0001, zone x gene p<0.0001. In all panels, Nonogt mice are represented by grey bars/circles, compared to WT littermates (open).

Source data

Supplementary Figure 7 Cell-type- and layer-specific localization of NONO in mouse brain.

(a) Staining of hippocampal cell nuclei by DAPI (blue), anti-NONO (green), and neuron-specific anti-NeuN or astrocyte-specific anti-GFAP (red, left or right column respectively). (b) Identical staining of cortex.

Supplementary Figure 8 Widespread dysregulation of transcription in Nonogt mouse hippocampi.

(a) Volcano plot of deregulated genes. Red dots, p<0.01 and log2>0.5. (b) Reduced GABRA2 mRNA levels in hippocampi of Nonogt mice. White bars, WT. grey bars, Nonogt. Student t-test, N=4. (c) List of most severely deregulated transcripts, showing upregulation of sister DBHS family members Sfpq and Pspc1.

Source data

Supplementary Figure 9 Overexpression of PSPC1 and SFPQ protein in Nonogt mouse hippocampi.

(a) Western blots of hippocampal protein extracts from widtype and Nonogt mice hippocampi, probed with anti-NONO, anti-PSPC1, anti-SFPQ, and anti-β-actin. N=3 mice per genotype. (b) Quantification of (a). White bars, WT. Black bars, Nonogt. Student t-test, p<0.01.

Source data

Supplementary Figure 10 Transcript abundance in different neuronal compartments in Nonogt mice.

(a) Profile of the mouse forebrain synaptic transcriptome. Y-axis, ratio of transcript reads from synaptome RNA sequencing compared to total. Selected transcripts previously characterized to be transported to synapses (Kif5a, Shank3, CamK2A, Arc, Gabra2), present throughout the cell (Map2, Actb), or retained in the nucleus (Neat1) are indicated to demonstrate the quality of synaptosomal transcript enrichment. Blue shading, transcripts more than 1.5x enriched. (b) Quantification of Neat1 compared to Gapdh in whole-cell homogenate, purified nuclei, supernatant, or gradient-purified synaptosomes from WT (white bars) or Nonogt mice (solid bars). (c) Quantification of CamkII compared to Gapdh. (d) Quantification of Gabra2 compared to Gapdh.

Source data

Supplementary Figure 11 Reduction of synaptic GABRA2 in Nonogt mice.

(a) Western blot showing fractionation of mouse forebrain into different neuronal compartments by density gradient centrifugation. Immunohistochemistry using antibodies against NONO, gephyrin, and GABA is pictured. As a control, β-actin and dendrite-enriched PSD-95 are also shown. (b) Quantification of the reduction in GABRA2 levels in each compartment.

Source data

Supplementary Figure 12 Specific reduction of Gabra2 transcript levels in cultured Nonogt neurons.

(a) Single-transcript-resolution RNA in-situ hybridization to detect abundance of collybistin (CB, blue), Gabra1 (blue), Gabra2 (red), and CamKII (red) in WT or Nonogt neurons. Two transcripts were tested in different colors in a single plate of cells, and depicted in a single column. (b) Quantification of collybistin transcript distribution in puncta number per cell for 44-56 cells from 2 experiments. (C) Similar quantification of Gabra2. Solid circles, Nonogt neurons; open circles, WT.

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Supplementary Figures 1–12, Supplementary Tables 1–7 and Supplementary Note (PDF 3997 kb)

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Mircsof, D., Langouët, M., Rio, M. et al. Mutations in NONO lead to syndromic intellectual disability and inhibitory synaptic defects. Nat Neurosci 18, 1731–1736 (2015). https://doi.org/10.1038/nn.4169

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