Age-related sperm DNA methylation changes are transmitted to offspring and associated with abnormal behavior and dysregulated gene expression

Abstract

Advanced paternal age (APA) has been shown to be a significant risk factor in the offspring for neurodevelopmental psychiatric disorders, such as schizophrenia and autism spectrum disorders. During aging, de novo mutations accumulate in the male germline and are frequently transmitted to the offspring with deleterious effects. In addition, DNA methylation during spermatogenesis is an active process, which is susceptible to errors that can be propagated to subsequent generations. Here we test the hypothesis that the integrity of germline DNA methylation is compromised during the aging process. A genome-wide DNA methylation screen comparing sperm from young and old mice revealed a significant loss of methylation in the older mice in regions associated with transcriptional regulation. The offspring of older fathers had reduced exploratory and startle behaviors and exhibited similar brain DNA methylation abnormalities as observed in the paternal sperm. Offspring from old fathers also had transcriptional dysregulation of developmental genes implicated in autism and schizophrenia. Our findings demonstrate that DNA methylation abnormalities arising in the sperm of old fathers are a plausible mechanism to explain some of the risks that APA poses to resulting offspring.

Introduction

Advanced paternal age (APA) is a risk factor for a wide range of health conditions in the offspring. Previously, APA was associated with sporadic cases of rare single gene disorders,1 such as achondroplastic dwarfism, Apert syndrome and Pfeiffer syndrome (reviewed in ref. 2) More recently, numerous studies show that APA is a risk factor for relatively common, polygenic disorders, including neurodevelopmental psychiatric disorders, such as schizophrenia (SCZ),3 autism spectrum disorders (ASD),4,5 bipolar disease6 and attention deficit/hyperactivity disorder.7 However, the mechanism by which APA contributes to these complex disorders remains unresolved.

Male fertility requires ongoing cell division of spermatogonia in the testes throughout life. With each cell division, both genetic and epigenetic information must be preserved in the newly synthesized DNA to maintain stability of the germline. Failure to maintain the fidelity of information contained within the genome of spermatogonia can have a substantial impact on offspring health and has been proposed as a general mechanism of the APA effect.8,9 Recent evidence indicate that de novo single nucleotide variations10, 11, 12, 13 and copy number variations,14, 15 contribute to psychiatric disease and that APA is associated with an increased rate of these types of mutations.16,17

Likewise, aging is also associated with altered DNA methylation in both mammalian somatic and germ cells,18 and has been hypothesized to underlie the paternal age effect.8 Furthermore, DNA methylation abnormalities have been associated with SCZ, ASD and bipolar disease.19,20 Hence, we reasoned that aging effects on sperm DNA methylation might be a factor influencing offspring susceptibility to relatively common, complex neurodevelopmental disorders associated with APA.

Subjects and methods

Paternal age breeding

Old and young father offsprings (OFO and YFO) were generated by breeding 12–14-month and 3-month-old male 129SvEv/Tac mice from Taconic (Hudson, NY, USA), respectively, with 3-month-old female 129SvEv/Tac mice. To control for maternal and litter effects on the offspring, each male was placed with two females to generate litters from different mothers. After 2 weeks, the male mouse was removed to prevent any paternal contact with the offspring and the females were separated into individual cages. Newborn litters were monitored for pup number and survival (Supplementary Table S1). The offspring were left in the cage with the mother until weaning at 21 days. Throughout the breeding all mice were individually marked to determine the paternal and maternal origin of the offspring. Mice were kept on a 7:00 to 19:00 h light cycle.

Behavioral testing

At 12 weeks of age all male offspring were weighed (Supplementary Table S1) and underwent behavioral testing. Mice received 1 week of rest between each behavioral task. All testing was performed during the light cycle and during the same time of day for each behavior.

Open field (OF)

The mice were placed in the center of a large square (17 × 17 × 12 inches) plexiglas chamber under bright ambient light conditions (800 lux). Activity was monitored in 5 min bins for 30 min using infrared beams. The measures recorded included total ambulatory distance and time, vertical activity and center activity.

Startle activity

Mice were placed in acoustically isolated startle chambers (MED Associates, St Albans, VA, USA). The test started with a 5 min acclimation followed by three consecutive sessions of trials. The background noise was 70 dB throughout the acclimation and trial periods. Sessions 1 and 3 included 10 trials of startle stimuli (120 dB; 40 ms). Session 2 consisted of 56 trials in which startle response magnitude, peak latency and onset latency to each stimulus were recorded for trials, in which the startle stimulus was presented alone or preceded by 100 ms with a 15 ms prepulse. The prepulse amplitude was 2, 4 or 8 dB above background. Startle responses were measured by the downward force (N) applied to a forcemeter between 30 and 70 ms after the onset of the startle stimulus. Prepulse inhibition (PPI) was calculated as 1−ppr[x]/sr, where ppr[x] is the average startle response across trials presenting a prepulse of amplitude x, and sr is the average startle response across trials in which the startle stimulus was presented alone.

Statistical analysis of behavioral data

All behavioral data was analyzed using a two-tailed student t-tests and one- or two-way analysis of variance (ANOVA).

Methyl-MAPS

Procedure

Genomic DNA was isolated from one brain hemisphere of four OFO and four young father offspring (YFO) mice. This preparation included midbrain and forebrain structures, but not the hindbrain or cerebellum. Sperm DNA was isolated from epididymal sperm of the old and young fathers of the above offspring. Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) libraries were constructed, sequenced and then mapped onto the mouse genome as previously described.21,22 Individual mate-pair libraries were created for each offspring, while sperm DNA was pooled to generate old and young father libraries. Briefly, 7 μg DNA was digested with methylation-dependent (McrBC) and methylation-sensitive (restriction enzyme) enzymes in parallel. McrBC endonuclease generates the unmethylated compartment and is able to interrogate the methylation state of >80% of the CG sites in the genome. The methylated compartment is generated by digestion with a panel of all known methylation-sensitive tetranucleotide restriction enzymes, collectively termed RE (HpaII, HhaI, AciI, BstUI and HpyCH4IV), each of which cuts at a specific 4 bp sequence only if the CG in the recognition site is unmethylated. Libraries of fragments >800 bp in size were constructed utilizing EcoP15’s unique digestion properties. Deep sequencing of digested sequence fragments was performed on the SOLiD sequencing platform from Life Technologies by Beckman Coulter Genomics (Danvers, MA, USA). Mapping of paired-end sequenced fragments were performed with the SOLiD software analysis package (Life Technologies, Grand Island, NY, USA).

Model gene analysis

Methyl-MAPS data analysis pipeline along with estimation of CpG methylation frequencies were previously described.23 Pair-wise comparison between YFO and OFO individual samples did not show significant differences, thus we pooled the YFO and OFO samples to increase coverage as well as to be consistent with the young father sperm (YFS) and old father sperm libraries (OFS), which were pooled DNA from four mice per group. Reads were summed up for YFO and OFO and the combined counts were processed with the Methyl-MAPS data analysis pipeline. For the gene model analyses, genomic feature annotations were downloaded from the UCSC Bioinformatics website (http://genome.ucsc.edu/), including CpG islands (CGIs) and RefSeq gene annotations. All annotations and methylation data were indexed by individual CpG sites and stored in a MySQL database for use in subsequent analyses. CpG dinucleotides were overlapped with the following mutually exclusive genomic features: promoters, first exons, first introns, internal exons, internal introns and last exon. RefSeq gene annotations were based on the Mouse Genome NCBI Build 37. Only genes with complete start and end coding sequences were used in our analysis. The promoter regions were defined as 1 kb upstream of the transcription start site (TSS). We used the definitions of Maunakea et al.24 for CGI promoters and intragenic CGIs.

The gene model was built based on the following gene feature criteria that included: 4000 bp upstream of TSS; 300 bp of the first exon; 10 000 bp of the first intron; 200 bp of the internal exon; 4000 bp of the internal intron; 1000 bp of the last exon; and 2000 bp of the region after poly(A) signal. A total number of 20 496 RefSeq genes that satisfy (1) annotation of complete coding region start and end sites and (2)3 exons were included in the gene model generation. The 5′- and 3′-ends of exons were anchors of the model, where each RefSeq gene was aligned. The methylation level of each position was the average of methylation of corresponding CpGs from Refseq genes. To avoid stochastic variation, we applied a 50-bp non-overlapping smoothing window.

Determination of DNA methylation differences

For each gene and associated genomic features, methylation levels were averaged within each group. These average values were used to compute methylation differences (mDiffs), which were then summed across all genes and corresponding gene features in the gene model. As noted above, 100-bp sliding windows were used to determine mDiffs within genomic regions for each gene feature. We used Wilcox rank sum test to identify regions with statistically significant DNA mDiff between groups and adjusted for multiple testing with the Benjamini–Hochberg method.

RNA-seq

Both library construction and sequencing were performed by the Columbia Genome Center. Briefly, poly-A containing messenger RNA was purified using poly-T oligo-attached magnetic beads (200 ng–1 μg per sample, RNA Integrity Number>8 required) and libraries were prepared using the Illumina TruSeq RNA prep kit (Illumina, San Diego, CA, USA). Libraries were then sequenced using an Illumina HiSeq2000 (Illumina) at the Columbia Genome Center. We multiplexed samples in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane.

Off-Line Basecaller (OLB-1.9.4) was used for base calling and the pass filter reads were mapped to the mouse genome (NCBI37/mm9) using Tophat (version 2.0.4; ref. 25) with 2 mismatches (read-mismatches=2) and 10 maximum multiple hits (max-multihits=10). To tackle the mapping issue of reads that are from exon–exon junctions, Tophat infers novel exon–exon junctions ab initio, and combine them with junctions from known messenger RNA sequences (refgenes) as the reference annotation. We estimated the relative abundance (aka expression level) of genes and splice isoforms using cufflinks (version 2.0.2; ref. 26) with default settings. We tested for differentially expressed genes under various conditions using cuffdiff, a program included in the cufflinks package. The variance of the expression level was estimated based on a negative binomial distribution that models the number reads from high-throughput sequencing experiments.

The Ingenuity Pathways Knowledge Base (IPA) was used to identify enriched functional gene networks and canonical pathways among the differentially expressed genes between OFO vs YFO. The full 17-gene list that resulted from the differential gene expression analysis was used for the analysis. The P-values were calculated by IPA by using a right-tailed Fisher's exact test. A cutoff of P<0.05 was used for significance, as suggested by the software.

Results

To determine the effect of aging on sperm DNA methylation, we performed genome-wide methylation profiling of epididymal sperm DNA pooled from young father sperm (YFS; 3-month-old; n=4) or old father sperm (OFS; 12–14 mo; n=4) using the Methyl-MAPS approach21,22 to query 18 779 892 (88%) CpG sites ≥8 × coverage. We organized the resulting OFS and YFS DNA methylation data by aligning CpGs by their genomic position in relation to the TSS, first, internal and last exons across 20 496 RefSeq genes. We compared DNA methylation changes and we calculated the mDiff by subtracting YFS methylation values from OFS values at each qualifying CpG site (Figure 1a). In the proximal promoter region (±1 kb of TSS), DNA methylation levels were similar between the two groups, with only a small region of significant hypomethylation in OFO 300–550 bp upstream of the TSS. However, further up and downstream of the TSS, we observed a profound loss of CpG methylation in OFS compared with YFS. The difference in methylation between OFS and YFS (Figure 1b) was significant at 300–550 bp, 850–3250 bp upstream of the TSS and 750–3000 bp, 3100–3200 bp downstream of the 3′ position of the first exon (P<0.05–0.01). These regions correspond to CGI shore regions that are known to contain variability in DNA methylation that is associated with changes in gene expression.27

Figure 1
figure1

The effect of aging on sperm DNA methylation. (a) Old father sperm (OFS) and YFS methylation patterns in a model gene. (b) DNA methylation differences between OFS and YFS (OFS−YFS) from 4 kb upstream of the TSS, across splice sites and 2 kb downstream of the poly (a) region. Red (P<0.001) and yellow (P<0.005) stars highlight 50 bp regions with statistically significant methylation differences. (c) CpG density (#CpGs/100 bp) for 20 496 RefSeq genes.

PowerPoint slide

In addition to the methylation changes near the TSS, we also observed a significant loss of methylation in OFS at intron/exon splice junctions. Specifically, there was a significant mDiff 50–800 bp upstream and downstream of internal exons, 450–700 bp upstream and 450–1500 bp, 1700–1750 bp and 1850–1950 bp downstream of the last exon (P<0.05–0.01). Despite these local changes we found no evidence of global changes28 in methylation or hydroxymethylation of mouse sperm DNA (Supplementary Figure S1).

We next sought to determine whether the alterations in sperm DNA methylation observed in OFS would affect brain DNA methylation patterns and behavioral performance of the offspring. Thus, before harvesting the sperm from the old and young fathers, they were mated with 3-month-old females to obtain OFO and YFO. As described in the Methods, each male was mated with two females to determine potential maternal and litter effects. There were no differences between the two groups in litter size and viability at birth, and only a small difference in body weight at the time of behavioral testing (Supplementary Table S1).

OFO and YFO were tested for exploratory and acoustic startle behaviors. OFO displayed significantly decreased exploratory activity (P<0.05; YFO=100, OFO n=87) in the OF compared with YFO (Figure 2a). The effect of APA on exploratory activity is robust and has been observed in several independent cohorts (Supplementary Figure S2). Although the OFO had a slight weight difference compared with YFO, a one-way ANOVA using weight as a covariate found no significant effect of it on exploratory activity. This effect did not appear to be the result of increased anxiety as there was no significant difference between groups in the time spent in the center of the OF (Supplementary Figure S3) or on other anxiety measures (Supplementary Figure S4).

Figure 2
figure2

The effect of advanced paternal age (APA) on offspring behavior. (a) The effect of APA on offspring exploratory behavior in the old father (OF) as measured by total ambulatory distance (cm). Young father offspring (YFO; n=100); old father offspring (OFO; n=88); mean±s.e.m., student t-test *P<0.05. (b) The effect of APA on offspring startle amplitude (N) to a 120 dB startle stimulus. Mean±s.e.m., student t-test *P<0.05. (c) The effect of APA on prepulse inhibition (%) to a 72, 76 and 78 dB prepulse, followed by a 120 dB startle stimulus. Mean±s.e.m., two-way analysis of variance, ***P<0.001.

PowerPoint slide

Abnormal prepulse inhibition is observed in both SCZ (reviewed in ref. 29) and ASD.30 We found that the acoustic startle response was significantly reduced in OFO (n=87) compared with YFO (Figure 2b, n=100; P<0.05) and that 72, 76 or 78 db prepulse stimuli (P<0.001) were less effective in reducing startle in OFO (Figure 2c). No significant difference was observed between OFO and YFO in their latency to startle, and weight was not a contributing factor to the effect.

To test for maternal effects contributing to the behavioral deficits in OFO, we performed a two-way ANOVA using maternal identity as an independent variable but found no effect on exploratory activity and prepulse inhibition.

In different cohorts, we expanded the behavioral battery to assess additional endophenotypes of SCZ and ASD, including social interaction, anxiety and learning and memory, but found no effect of APA on these domains (Supplementary Figures S4d–f).

Based on our behavioral findings in OFO and YFO mice, we reasoned that if transmitted patterns of sperm DNA methylation were responsible for these behavioral differences, evidence of altered DNA methylation should be detectable in the brains of these two groups. To test this hypothesis, we performed Methyl-MAPS on DNA from individual brains of OFO and YFO and mapped genic methylation patterns in the same way as performed for the sperm DNA methylation analysis (Figure 3a). Similar to the sperm data, for the brain DNA methylation data we analyzed only high coverage CpG sites (8 × coverage), across all samples comprising 6 283 961 CpG sites equivalent to ~29% of all CpGs in the genome. Statistical analysis of the mDiff between YFO and OFO confirmed that, similar to OFS, OFO have significantly reduced methylation 900–950 bp, 1050–1200 bp upstream of the TSS and 800–1600 bp downstream of the first exon (P<0.05–0.01, Figure 3b). A previous study found global hypermethylation of cerebellar DNA from offspring of aged fathers,31 however, we found no evidence of this in the brains of OFO (Supplementary Figure S1c).

Figure 3
figure3

The effect of advanced paternal age (APA) on offspring brain DNA methylation. (a) Old and young father offsprings (OFO and YFO) methylation patterns in a model gene. (b) The DNA methylation difference between OFO and YFO (OFO−YFO). Red (P<0.001) and Yellow (P<0.005) stars highlight 50 bp regions with statistically significant methylation differences. (c) CpG density (#CpGs/100 bp) for 20 496 RefSeq genes.

PowerPoint slide

The main effect of APA on both paternal sperm and offspring brain DNA methylation is a loss of methylation at the regions flanking the TSS. These regions, which are about 1 kb upstream and downstream of the TSS, overlap with CGI shores where alterations in DNA methylation is known to be associated with changes in gene expression.27 To determine if the observed changes in DNA methylation in OFS and OFO are specific to CGI promoters and corresponds to CGI shores, we compared the mDiff of both sperm and offspring brain samples at CGI and non-CGI promoters. As shown in Figures 4a and b, there is a significant loss of methylation at the regions flanking both CGI and non-CGI promoters in OFS compared with YFS. However, the mDiff is greater at CGI promoters and the regions corresponding to CGI shores. In the offspring, there is a significant loss of methylation in OFO only in the regions flanking CGI promoters and not in non-CGI promoters. A similar pattern was observed at intragenic CGI shores, with OFS showing significant loss of methylation, however, this was not significantly different in their offspring (Supplementary Figure S5).

Figure 4
figure4

The effect of advanced paternal age (APA) on CpG island (CGI) methylation. DNA methylation difference at CGI (black line) and non-CGI (blue line) promoters between: (a) Old and young father samples (OFS and YFS), and (b) old and young father offsprings (OFO and YFO). Slate (P<0.001 for CGI), orange brown (P<0.005 for CGI), purple (P<0.001 for non-CGI) and magenta (P<0.005 for non-CGI) stars highlight 100 bp regions with statistically significant methylation differences. (c) CpG density (#CpGs/100 bp) for 20 496 RefSeq genes.

PowerPoint slide

Because DNA methylation at CGI shores is associated with alterations in gene expression,27 we performed RNA-seq on the remaining hemisphere of the same offspring, which was used to determine whole-genome methylation patterns. We identified 17 genes as differentially expressed between the two groups (Supplementary Table S2). These genes have mainly neuronal functions and an IPA revealed that 9 out of 17 genes form a network involved in ‘cellular development’, ‘nervous system development and function’, and ‘embryonic development’ (Supplementary Figure S6). The ‘physiological system development and function’ analysis similarly revealed a significant association with ‘nervous system development and function’, which is driven by a significant number of genes which have been previously associated with cerebellar granule cell innervation and morphology (Cbln1, Cbln3, En2 and NeuroD1). The ‘disease and disorder’ analysis revealed a significant association with ‘neurological disease’ (seven genes) and ‘developmental disorders’ (four genes), which appears to be driven by disorders affecting the cerebellum, such as cerebellar ataxia (CA8, Cbln1, Cbln3 and NeuroD1), as well as autism (En2) and mental retardation (CA8). These genes have an important role in the functioning of the nervous system, although to date most associated with cerebellar function and dysfunction. The differentially expressed genes in OFO brains (En2, Cbln1 and NeuroD1) are also associated with regulation of cortical, hippocampal and striatal function, during development.

To determine the relationship between DNA methylation and gene expression in OFO compared with YFO, we performed a correlation analysis of the mDiff values from the Methyl-MAPS data set, with the differential gene expression log2 scores (Supplementary Figure 7). We specifically focused on the mDiff of CpG sites in the distal and proximal promotor region (−1 to −4000 kb from the TSS). Pearson correlation co-efficient revealed a negative correlation (r=−0.01098) that was not quite significant (P=0.2059). This suggests that within our data set, overall, DNA methylation follows the traditional observation of having an inhibitory effect on gene expression, however, there are other influencing factors as well. These are likely to include developmentally regulated expression changes and microRNA expression changes.

Discussion

This study demonstrates that aging is associated with a loss of sperm DNA methylation at CGI shores, that these abnormalities are also present in the ensuing offspring with effects on both behavior and gene expression. The main effect of APA on offspring behavior, is reduced exploratory activity and PPI, the latter of which is commonly affected in patients with SCZ or ASD (reviewed in refs. 32, 33).

The effects of APA on behavior in mice, has been reported by other groups in past (reviewed by Foldi et al.34), however, the results have been quite variable between different labs. While one group reports a similar decrease in exploratory activity as we observe,35 others report an increase36 or no effect.37 This variability is not simply due to strain differences, but is likely to result from slight variations in the paternal age at breeding, handling of the mice and procedural differences. In our hands, the effect of APA on locomotor activity is relatively small, but consistent between cohorts. Maternal influences on offspring behavior are difficult to exclude. To minimize sire influences on maternal behavior some studies have used either cross-fostering or in vitro fertilization experiments. However, both strategies have been shown to induce epigenetic changes in the offspring38,39 and would likely produce their own confounds.

Paternal transmission of DNA methylation patterns has been reported as a consequence of dietary conditions,40 exposure to environmental toxins41 and odor memory formation.42 However, it is widely held that DNA methylation differences occurring during spermatogenesis are not transmitted to offspring due to the reprogramming of methylation patterns that occurs in the embryo after fertilization. Generally, reprogramming in the preimplantation embryo results in demethylation of the paternal genome43 and subsequent remethylation according to the maternal genome. Nevertheless, some genomic regions, including intracisternal A-particle elements44 and imprinted genes,45 are known to escape reprogramming and the paternal methylation pattern is inherited by the offspring. Interestingly, in mice, evidence suggests that DNA methylation of imprinted genes is altered in the offspring brains of older fathers, however, the methylation state of these genes in the paternal sperm was not explored.31 Our results indicate that some of the DNA methylation abnormalities in OFS are transferred to the offspring, and that reprogramming resets some but not all of these alterations.

It is striking that CGI shores in sperm DNA are particularly sensitive to demethylation with advancing age. At the end of mammalian spermatogenesis, chromatin is extensively remodeled and all but a small percent of nucleosomes are replaced by protamines, allowing the DNA to be packaged more densely. These residual nucleosomes are retained specifically at unmethylated CpG-dense regions, such as CGI promoters,46,47 suggesting a mechanism by which CGI shores are more susceptible to methylation abnormalities in the sperm. Intriguingly, nucleosome retention in sperm is associated with the establishment of DNA methylation-free regions in the early embryo46 and has been proposed as a mechanism of transgenerational inheritance.46,47 Whether this mechanism is involved in the process of how paternal age-associated DNA methylation abnormalities are transferred to the offspring remains to be explored.

Our finding that both CGI shores and splice junctions are abnormally methylated in OFO, suggests that APA can have broad effects on gene expression and cell signaling in the offspring. The RNA-seq results from offspring brain RNA, suggest that most of the genes that are abnormally expressed in the OFO are involved in early stages of neurodevelopment, including brain patterning and synaptogenesis. These are processes that are implicated in the pathology of both SCZ and autism. Some of the genes, such as En2 and CA8, have previously been associated with ASD and mental retardation and the majority of the genes act in signaling networks associated with neurodevelopmental psychiatric disorders, suggesting that these could be novel candidate genes for further exploration.

The exact relationship between APA-associated DNA methylation alterations and previously reported de novo mutations16,17 remains unclear. APA-associated alterations in DNA methylation may be: (1) independent of single nucleotide variations,48 (2) a consequence of mutational events,49 or (3) may influence the mutation rate of certain regions.50 While our current experiments do not address these possibilities, our findings nonetheless demonstrate that age-related DNA methylation abnormalities of paternal origin are a viable candidate mechanism underlying de novo cases of neurodevelopmental disorders such as autism and SCZ.

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Acknowledgements

We thank Dr Timothy Bestor for invaluable help with experimental design and helpful discussions; Jackie Tinsley, Prashant Donthamsetti, Heather El-Amamy and Matthew Gingrich for experimental help; Caitlin McOmish for helpful discussions. This research was supported by grants from the Simons Foundation and the National Institute of Mental Health (5R21MH073794) to JAG, the G Harold & Leila Y Mathers Foundation to DM and JAG; a NARSAD Young Investigator Award and Sackler Award to MHM.

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Correspondence to M H Milekic.

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Milekic, M., Xin, Y., O’Donnell, A. et al. Age-related sperm DNA methylation changes are transmitted to offspring and associated with abnormal behavior and dysregulated gene expression. Mol Psychiatry 20, 995–1001 (2015). https://doi.org/10.1038/mp.2014.84

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