Autism-associated SHANK3 haploinsufficiency causes Ih channelopathy in human neurons

Abstract

Heterozygous SHANK3 mutations are associated with idiopathic autism and Phelan-McDermid syndrome. SHANK3 is a ubiquitously expressed scaffolding protein that is enriched in postsynaptic excitatory synapses. Here, we used engineered conditional mutations in human neurons and found that heterozygous and homozygous SHANK3 mutations severely and specifically impaired hyperpolarization-activated cation (Ih) channels. SHANK3 mutations caused alterations in neuronal morphology and synaptic connectivity; chronic pharmacological blockage of Ih channels reproduced these phenotypes, suggesting that they may be secondary to Ih-channel impairment. Moreover, mouse Shank3-deficient neurons also exhibited severe decreases in Ih currents. SHANK3 protein interacted with hyperpolarization-activated cyclic nucleotide-gated channel proteins (HCN proteins) that form Ih channels, indicating that SHANK3 functions to organize HCN channels. Our data suggest that SHANK3 mutations predispose to autism, at least partially, by inducing an Ih channelopathy that may be amenable to pharmacological intervention.

Figure 1. SHANK3 haploinsufficiency impairs dendritic development of human neurons

A) Diagram of the SHANK3 gene and of the three major SHANK3 transcripts that are blocked by conditional deletion of exon 13 (yellow). B & C) SHANK3 targeting strategy in human ES cells. Homologous recombination was mediated using recombinant adeno-associated virus (AAV) (B) and confirmed by PCR (Fig. S1B). The PGK-puromycin resistance cassette (brown box) was excised by Flp-recombinase to generate the conditional KO (cKO) allele (SHANK3^+/cKO; panel C). SHANK3^+/cKO ES cells were converted into human SHANK3^+/+ or SHANK3^+/− neurons by co-expression of Ngn2 with either mutant inactive Cre-recombinase (ΔCre) or active Cre-recombinase (Cre). D) Reduction of SHANK3 protein levels in human SHANK3^+/− neurons derived from two independent SHANK3^+/cKO ES cell clones. E) Representative images of SHANK3^+/+ and SHANK3^+/− neurons (day 21) labeled by double immunofluorescence for MAP2 (red) and synapsin (green). F) Representative dendritic arborization analyses by MetaMorph software of SHANK3^+/+ and SHANK3^+/− neurons (sparsely transfected with EGFP). G) SHANK3 haploinsufficiency impairs dendritic arborization (summary graphs of indicated parameters measured in matching SHANK3^+/+ and SHANK3^+/− neurons derived from independent SHANK3^+/cKO ES cell clones; normalized to SHANK3^+/+ controls). H) Representative images of SHANK3^+/+ and SHANK3^+/− dendrites stained for MAP2 (red) and synapsin (green) for analysis of synaptic puncta by MetaMorph software. I) Summary graphs of dendritic synaptic puncta density and size in SHANK3^+/+ and SHANK3^+/− neurons derived from two independent SHANK3^+/cKO ES cell clones. Data in G and I are means ± SEM. Numbers of cells/independent cultures analyzed are shown in the bars. Statistical significance was evaluated by Student’s t-test, (*, p<0.05; **, p<0.01). For additional data, see Figs. S1, S2.

Figure 2. SHANK3 haploinsufficiency increases electrical input resistance of human neurons and decreases overall synaptic strength

A) Input resistance (R_in) but not capacitance (C_m) is increased in SHANK3^+/− neurons (summary graphs from matching human SHANK3^+/+ and SHANK3^+/− neurons derived from two independent SHANK3^+/cKO ES cell clones). B) Evoked synaptic transmission is decreased in SHANK3^+/− human neurons (representative EPSC traces (left) and EPSC amplitude summary graphs (right) for independent sets of neurons). C) Amplitudes but not frequencies of spontaneous mEPSCs (monitored in 1 μM tetrodotoxin) are impaired in SHANK3^+/− neurons (top, representative traces; bottom, cumulative plots and summary graphs of the mEPSC frequency (left) and amplitude (right)). Data are means ± SEM. Numbers of cells/cultures analyzed are shown in bars. Statistical significance was evaluated by either Student’s t-test (bar graphs) or Kolmogorov-Smirnov-test (cumulative probability plots), (**, p<0.01; ***, p<0.001).

Figure 3. Homozygous SHANK3 deletion aggravates SHANK3 haploinsufficiency phenotype

A) Diagram of homozygous SHANK3^cKO/cKO alleles (see Supplemental Information for details). B) SHANK3^−/− neurons lack major SHANK3 proteins. Images depict immunoblots of matching SHANK3^+/+ and SHANK3^−/− neurons derived from two independent SHANK3^cKO/cKO ES cell clones. C) Representative images of matching SHANK3^+/+ and SHANK3^−/− neurons (day 21) stained by double immunofluorescence for MAP2 (red) and synapsin (green). D) Homozygous SHANK3 deletion severely impairs dendritic arborization (summary graphs of indicated parameter [normalized to SHANK3^+/+ controls] measured in matching SHANK3^+/+ and SHANK3^−/− neurons derived from two independent SHANK3^cKO/cKO ES cell clones). E) Representative images of dendrites stained for MAP2 (red) and synapsin (green) for analysis of synaptic puncta in SHANK3^+/+ and SHANK3^−/− neurons. F) Homozygous SHANK3 deletion reduces synapse density (summary graphs of synaptic puncta density and size on proximal dendrites of isogenic SHANK3^+/+ and SHANK3^−/− neurons from two independent SHANK3^cKO/cKO ES cell clones). G) Homozygous SHANK3 deletion increases neuronal input resistance (R_in, top) and decreases capacitance (C_m, bottom). H) Homozygous SHANK3 deletion reduces evoked EPSC amplitudes (left, representative traces; right, summary graphs of EPSC amplitudes). I) Homozygous SHANK3 deletion decreases the frequency and amplitude of mEPSCs (top, representative traces; bottom, cumulative plots and summary graphs of mEPSC interevent intervals and frequency (bottom left) or mEPSC amplitudes (bottom right)). Data in bar diagrams are means ± SEM. Numbers of cells/cultures analyzed are shown in bars. Statistical significance was evaluated by Student’s t-test (bar graphs) or Kolmogorov-Smirnov-test (cumulative probability plots), (*, p<0.05; **, p<0.01; ***, p<0.001). For additional data, see Fig. S3-S5.

Figure 4. SHANK3 deletions impair I_h-currents in human neurons, and SHANK3 proteins interact with HCN channels

A) Neuronal silencing by blocking glutamate receptors with CNQX (20 μM) and AP5 (50 μM) does not alter neuronal input resistance (R_in). B) Blocking I_h-currents with ZD7288 (100 μM) increases the input resistance (R_in) of wild-type neurons, abolishing the difference between wild-type and mutant neurons. C) SHANK3^+/− and SHANK3^−/− neurons exhibit a more negative resting potential (V_rest) than SHANK3^+/+ neurons; inhibition of I_h-currents in SHANK3^+/+ neurons with ZD7288 (5 μM) abolishes the difference. D & E) SHANK3^+/− (D) and SHANK3^−/− neurons (E) exhibit decreased I_h-current amplitudes compared to matching SHANK3^+/+ neurons (left, experimental protocol and sample traces; right, current/voltage relation of I_h-currents, which are validated by inhibition with ZD7288). F) Kinetics of I_h-current activation is impaired in SHANK3^+/− and SHANK3^−/− neurons (left, representative capacity- and leak current-subtracted I_h-current recordings fitted with a double-exponential function [yellow line superimposed on traces]; center and right, summary graphs of time constants and amplitudes of fast and slow components of I_h-current activation at a test potential of −120 mV). G) SHANK3 protein binds to HCN-channels mediating I_h-currents. Representative immunoblots document co-immunoprecipitation of Myc-tagged SHANK3 with HA-tagged HCN1, HCN2, and HCN3 proteins co-expressed in transfected HEK293T cells; cells expressing only one or the other protein serve as negative controls. H) Levels of endogenous HCN3 and HCN4 proteins are decreased in SHANK3^−/− neurons as determined by quantitative immunoblotting (for representative blots, see Fig. S10). Data are means ± SEM. Numbers of cells/cultures analyzed are shown in bars or brackets. Statistical significance was evaluated by Student’s t-test (bar graphs in F, H), or two-way ANOVA (bar graphs in A-C) and two-way repeated measure ANOVA (I-V plots in D, E) followed by Bonferroni’s post hoc test, (*, p<0.05; **, p<0.01; ***, p<0.001).

Figure 5. SHANK3 mutations render neurons hyperexcitable by impairing I_h-currents

A) SHANK3^+/− mutant neurons reach action potential (AP) firing threshold earlier than matching SHANK3^+/+ human neurons and exhibit a steeper input-output relationship as assessed by the number of APs elicited by increasing current injections (from −10 pA to +50 pA, 1 s, 5 pA increments) during current-clamp recordings. I_h-channel channel inhibition with ZD7288 abolishes the difference (left, experimental protocol and representative traces; right, plots of the mean action potential number vs. injected current). B) Summary graphs of active electrical properties of matching SHANK3^+/+ and SHANK3^+/− neurons (measured without or with ZD7288 application). From left to right: AP firing threshold, AP amplitude, and AP after-hyperpolarization amplitude (AHP). C) Same as A, but for matching SHANK3^−/− and SHANK3^+/+ neurons. D) Same as B, but for matching SHANK3^−/− and SHANK3^+/+ neurons. Data are means ± SEM. Numbers of cells/cultures analyzed are shown in bars or brackets. Statistical significance was evaluated by two-way ANOVA (bar graphs), or two-way repeated measure ANOVA followed by Bonferroni’s post hoc test (input-output plots), (n.s., not significant; *, p<0.05; **, p<0.01; ***, p<0.001).

Figure 6. Developing hippocampal neurons from Shank3 knockout mice reproduce phenotype of human SHANK3-mutant neurons

A & B) Dendritic arborization (A) and synapse formation (B) are impaired in developing Shank3-deficient mouse neurons (top, representative images of hippocampal neurons (A) and dendritic segments (B); bottom, summary graphs of the indicated dendritic, cellular and synaptic parameters). Neurons cultured from littermate Shank3^+/+, Shank3^+/− or Shank3^−/− mice were stained at 8 days in vitro (DIV8) for MAP2 (red) and synapsin (green). C) Hetero- and homozygous Shank3 deletions increase neuronal input resistance (top), decrease cell capacitance (center), and enhance the resting membrane potential (bottom) in hippocampal neurons cultured from littermate Shank3^+/+, Shank3^+/−, and Shank3^−/− mice and analyzed at DIV8-9. D) Hetero- and homozygous Shank3 deletions impair neuronal I_h-currents in hippocampal neurons at DIV8-9 (left, experimental protocol and sample traces; right, summary graph of the current/voltage relation). E) Hetero- and homozygous Shank3 deletions decelerate I_h-current activation (left top, experimental protocol; left bottom, capacitance- and leak current-subtracted representative traces fitted with the sum of two exponential functions shown superimposed on the traces in yellow; right, summary graphs of activation time constants (τ) and component amplitudes obtained at a test potential of −120 mV). F) Hetero- and homozygous Shank3 deletions render hippocampal neurons hyperexcitable (left, experimental protocol and representative traces of stepwise depolarizing current injections; right, summary plots of the action potential number vs. injected current during current-clamp recordings of neurons analyzed at DIV8-9). Data are means ± SEM. Numbers of cells/cultures analyzed are shown in bars or brackets. Statistical significance was evaluated by one-way ANOVA followed by Tukey’s post hoc test (bar graphs), or two-way repeated measure ANOVA followed by Bonferroni’s post hoc test (I-V plot), (*, p<0.05; **, p<0.01; ***, p<0.001). For additional data, see Fig. S12-S13.

Figure 7. Chronic inhibition of I_h-currents in human neurons mimics SHANK3 haploinsufficiency phenotype

A) Chronic partial inhibition of I_h-currents in wild-type SHANK3^+/+ neurons causes dendritic arborization defects similar to SHANK3^+/− haploinsufficiency. Matching SHANK3^+/+ and SHANK3^+/− neurons were differentiated from SHANK3^+/cKO ES cells; SHANK3^+/+ neurons were treated with low-dose ZD7288 (1 μM or 5 μM) from day 3-21 of neural induction (top, representative images of neurons double-labeled for MAP2 and synapsin; bottom, summary graphs of indicated parameters normalized to the untreated SHANK3^+/+ control). B) Chronic inhibition of I_h-currents in SHANK3^+/+ neurons decreases synapse numbers. Experiments were performed as described for panel A (left, representative images of dendritic segments double labeled for MAP2 and synapsin; right, summary graphs of density and size of synaptic puncta). C) Chronic inhibition of I_h-currents in SHANK3^+/+ neurons significantly increases input resistance (R_in, top) and decreases cell capacitance (C_m, bottom). Experiments were performed as described for panel A; recordings were performed after washout of ZD7288. D) Chronic inhibition of I_h-currents in SHANK3^+/+ neurons with ZD7288 (1 μM) reduces the frequency and amplitude of spontaneous mEPSCs (top, representative traces; bottom left, summary plots of the interevent interval and summary graph of the mEPSC frequency; bottom right, same for the mEPSC amplitude). Experiments were performed as described for panel A; recordings were performed after washout of ZD7288. Data are means ± SEM. Numbers of cells/cultures analyzed are shown in the bars. Statistical significance was evaluated by Student’s t-test (bar graphs in C and D), one-way ANOVA followed by Tukey’s post hoc test (bar graphs in B), or two-way ANOVA followed by Bonferroni’s post hoc test (bar graphs in A) or Kolmogorov-Smirnov-test (cumulative probability plots in D), (*, p<0.05; **, p<0.01; ***, p<0.001).