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GRIN3B missense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders

Published online by Cambridge University Press:  30 January 2017

TOBIAS HORNIG ,
BJÖRN GRÜNING ,
KOUSIK KUNDU ,
TORSTEN HOUWAART ,
ROLF BACKOFEN ,
KNUT BIBER  and
CLAUS NORMANN
TOBIAS HORNIG*
Affiliation:
Department of Psychiatry and Psychotherapy, University Medical Center, Albert–Ludwigs University, Hauptstr. 5, 79104 Freiburg, Germany
BJÖRN GRÜNING
Affiliation:
Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges–Koehler–Allee 106, Freiburg 79110, Germany
KOUSIK KUNDU
Affiliation:
Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges–Koehler–Allee 106, Freiburg 79110, Germany
TORSTEN HOUWAART
Affiliation:
Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges–Koehler–Allee 106, Freiburg 79110, Germany
ROLF BACKOFEN
Affiliation:
Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges–Koehler–Allee 106, Freiburg 79110, Germany
KNUT BIBER
Affiliation:
Department of Psychiatry and Psychotherapy, University Medical Center, Albert–Ludwigs University, Hauptstr. 5, 79104 Freiburg, Germany
CLAUS NORMANN
Affiliation:
Department of Psychiatry and Psychotherapy, University Medical Center, Albert–Ludwigs University, Hauptstr. 5, 79104 Freiburg, Germany
*
*Corresponding author: Tobias Hornig, Department of Psychiatry, University Medical Center, Albert–Ludwigs University, Hauptstr. 5, 79104 Freiburg, Germany. Tel: +49 761 270 69310. Fax: +49 761 270 67060. E-mail: [email protected]
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Summary

Glutamate is the most important excitatory neurotransmitter in the brain. The N-methyl-D-aspartate (NMDA) receptor is a glutamate-gated ionotropic cation channel that is composed of several subunits and modulated by a glycine binding site. Many forms of synaptic plasticity depend on the influx of calcium ions through NMDA receptors, and NMDA receptor dysfunction has been linked to a number of neuropsychiatric disorders, including schizophrenia. Whole-exome sequencing was performed in a family with a strong history of psychotic disorders over three generations. We used an iterative strategy to obtain condense and meaningful variants. In this highly affected family, we found a frameshift mutation (rs10666583) in the GRIN3B gene, which codes for the GluN3B subunit of the NMDA receptor in all family members with a psychotic disorder, but not in the healthy relatives. Matsuno et al., also reported this null variant as a risk factor for schizophrenia in 2015. In a broader sample of 22 patients with psychosis, the allele frequency of the rs10666583 mutation variant was increased compared to those of healthy population samples and unaffected relatives. Compared to the 1000 Genomes Project population, we found a significant increase of this variant with a large effect size among patients. The amino acid shift degrades the S1/S2 glycine binding domain of the dominant modulatory GluN3B subunit of the NMDA receptor, which subsequently affects the permeability of the channel pore to calcium ions. A decreased glycine affinity for the GluN3B subunit might cause impaired functional capability of the NMDA receptor and could be an important risk factor for the pathogenesis of psychotic disorders.

Type
Research Papers
Information
Genetics Research , Volume 99 , 2017 , e1
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright
Copyright © Cambridge University Press 2017

1. Introduction

The glutamatergic transmission system is the most important excitatory network in the human central nervous system. The ionotropic postsynaptic N-methyl-D-aspartate (NMDA) receptor belongs to the superfamily of glutamate-gated ion channels (Johnson & Ascher, Reference Johnson and Ascher1987; Dalkara et al., Reference Dalkara, Erdemli, Barun and Onur1992). Three subfamilies (GluN1–3) with seven subunits are currently known (Table 1) (Low & Wee, Reference Low and Wee2010; Siegel & Brady, Reference Siegel and Brady2011; Paoletti et al., Reference Paoletti, Bellone and Zhou2013). These subunits build heterodimeric or heterotrimeric complexes and form NMDA receptor subtypes and they include different glutamate (GluN2A, B, C and D) and glycine binding domains (GluN1 and GluN3A/B). The glycine binding sites modulate the permeability of the NMDA receptor. As summarized in Table 1, the subunits show differential mRNA expression in the central nervous system (Wee et al., Reference Wee, Zhang, Khanna and Low2008; Low & Wee, Reference Low and Wee2010; Paoletti et al., Reference Paoletti, Bellone and Zhou2013).

Table 1. N-methyl-D-aspartate receptor subunits, their main transmitter affinity and localization.

FB: forebrain; CB: cerebellum; MB: midbrain; HB: hindbrain; PC: pyramidal cells; OB: olfactory bulb; Hip: hippocampus; NC: neocortex; SC: spinal cord; Str: striatum.

NMDA receptors are ligand-gated cation channels that are blocked by magnesium ions (Mg2+) in the resting state and have functional relevance in learning and memory, synaptogenesis and inducing synaptic plasticity (Harris et al., Reference Harris, Ganong and Cotman1984; Teyler, Reference Teyler1987; Normann et al., Reference Normann, Peckys, Schulze, Walden, Jonas and Bischofberger2000; Vargas-Caballero & Robinson, Reference Vargas-Caballero and Robinson2004; Normann & Clark, Reference Normann and Clark2005; Fan et al., Reference Fan, Jin and Wang2014). Disturbances in NMDA receptor function have been linked to memory and learning deficits and neuropsychiatric disorders such as schizophrenia, major depression and bipolar affective disorders (Zarate et al., Reference Zarate, Singh and Manji2006; Bitanihirwe et al., Reference Bitanihirwe, Lim, Kelley, Kaneko and Woo2009; Li et al., Reference Li, Liu, Dwyer, Banasr, Lee and Son2011; Zhou & Sheng, Reference Zhou and Sheng2013).

The glutamate hypothesis of schizophrenia was established in the early 1980s by Kim and Kornhuber (Kim et al., Reference Kim, Kornhuber, Schmid-Burgk and Holzmüller1980; Kornhuber et al., Reference Kornhuber, Kornhuber, Kim and Kornhuber1984). In experimental animals, acute blockade of glutamatergic transmission affects the dopaminergic system and induces hyper-dopaminergic conditions in distinct regions of the cerebral cortex (Moghaddam & Adams, Reference Moghaddam and Adams1998; López-Gil et al., Reference López-Gil, Babot, Amargós-Bosch, Suñol, Artigas and Adell2007). Gene expression and gene polymorphism studies have indicated altered Neuregulin 1 and Dysbindin genes in patients with schizophrenia as causing functional disturbances in glutamatergic synaptic plasticity (Mátyás, Reference Mátyás2006; Giegling et al., Reference Giegling, Genius, Benninghoff and Rujescu2010; Balu & Coyle, Reference Balu and Coyle2011; Geddes et al., Reference Geddes, Huang and Newell2011). Moreover, there are indications of abnormal expression of postsynaptic second messenger components of the NMDA receptor, such as the postsynaptic density protein 95 (PSD-95) or glutamate transporters 1 and 2 (Kristiansen et al., Reference Kristiansen, Huerta, Beneyto and Meador-Woodruff2007; Bauer et al., Reference Bauer, Gupta, Harotunian, Meador-Woodruff and McCullumsmith2008; de Bartolomeis et al., Reference de Bartolomeis, Latte, Tomasetti and Iasevoli2014). Psychopharmacological studies have demonstrated propsychotic effects for glutamate agonists and antipsychotic effects for glutamate antagonists (Javitt, Reference Javitt2009; Blot et al., Reference Blot, Bai and Otani2013; Cioffi, Reference Cioffi2013; Laruelle, Reference Laruelle2014). Unlike the GluN2 subunits that have binding sites for glutamate, the GluN1 and GluN3 subunits have binding sites for glycine. There are suggestions of genetic variations and drug–gene interactions with the GRIN3B gene, which encodes GluN3B (Lipsky & Goldman, Reference Lipsky and Goldman2003; Putnam et al., Reference Putnam, Sun and Zhao2011; Tarabeux et al., Reference Tarabeux, Kebir, Gauthier, Hamdan, Xiong and Piton2011; Lin et al., Reference Lin, Hsieh, Liu, Hwang, Chien, Hwu and Liu2014). Recently, Matsuno and co-workers found a genetic variation of GluN3B within its coding region (insCGTT) that was significantly overrepresented in patients with schizophrenia, and this was proved to be functionally null (Matsuno et al., Reference Matsuno, Ohi, Hashimoto, Yamamori, Yasuda and Fujimoto2015).

In 2001, Andersson and colleagues characterized the GRIN3A and GRIN3B genes (Andersson et al., Reference Andersson, Stenqvist, Attersand and von Euler2001). The GRIN3B gene is localized on chromosome 9q13·3 and consists of eight coding exons. The GluN3B protein, consisting of 1043 amino acids, shows the highest homology with GluN3A and GluN1, and it seems to be a dominant modulatory subunit of the NMDA receptor family (Low & Wee, Reference Low and Wee2010). The N-terminal extracellular subunit is composed of two lysine/arginine/ornithine-binding protein-like domains (Stern-Bach et al., Reference Stern-Bach, Bettler, Hartley, Sheppard, O'Hara and Heinemann1994; Armstrong et al., Reference Armstrong, Sun, Chen and Gouaux1998; Dingledine et al., Reference Dingledine, Borges, Bowie and Traynelis1999; Matsuda et al., Reference Matsuda, Kamiya, Matsuda and Yuzaki2002): S1 (exon 3, amino acid sequence position 422–540) and S2 (exon 4, amino acid sequence position 696–779). These domains have high affinity for glycine (Yao & Mayer, Reference Yao and Mayer2006). Interestingly, GRIN3B-knockout mice showed deficits in coordination, motor learning and activity, as well as altered social behaviour (Niemann et al., Reference Niemann, Kanki, Fukui, Takao, Fukaya and Hynynen2007)

Here, we report a family with a strong history of psychotic disorders in which we analysed the exome sequences from eight family members over three generations. We found a missense frameshift mutation in the GRIN3B gene in all of the affected family members, but not in any unaffected family member. This mutation variant, which is known as rs10666583, was previously described by Matsuno et al. in 2015 as a null variant. Moreover, we show an overrepresentation of the rs10666583 variant in a sample of schizophrenic patients compared to the 1000 Genomes Project database.

2. Methods

(i) Participants

ReelinSys is a systems biology project funded by the German Federal Ministry of Education and Research. In this project, we performed triplet-based exome sequencing in 35 families containing patients with schizophrenia (n = 22) and depression (n = 19) in order to detect de novo mutations. In these 35 families, we performed sequencing for both patients and their unaffected parents and siblings. All subjects were of Caucasian ethnicity. Approval was obtained from the ethics committee of Albert–Ludwigs University Freiburg (No. 94/13) before initiation of the study.

During the inclusion process of one of the 22 schizophrenic patients, we registered a history of psychotic disorders in five of their family members over three generations, and only three of their family members had no such history (Fig. 1). We than carried out whole-exome sequencing analysis of all eight of these family members in order to detect all of the mutations that were present only in the affected members. The clinical diagnosis of schizophrenia was made by experienced senior consultant psychiatrists based on a structured interview according to Diagnostic and Statistical Manual of Mental Disorders-5 criteria, and their ability to consent was based on the psychopathological interview according to the Arbeitsgemeinschaft für Methodik und Dokumentation in der Psychiatrie system and refers to the common principles of decision-making. After giving informed written consent to participate on a voluntary basis, the patients were included in this study. We did not include patients who were judicially housed or were situated in legal care.

Fig. 1. Pedigree of the family, with affected members coloured black. Schizophrenic patients: 1–5; healthy family members: a–c.

Patients and their relatives over the age of 18 years were included in this study and all individuals provided written informed consent to participate on a voluntary basis. Because of ethical considerations, one infant sibling was excluded from the study. A medical history was obtained for all patients, and all participants received full neurological and medical examinations, electroencephalogram examinations and routine blood tests in order to exclude individuals with other medical or neurological disorders. The clinical state of psychotic symptoms was assessed using the Positive and Negative Syndrome Scale (Kay et al., Reference Kay, Fiszbein and Opler1987), followed by an assessment of formal thought and language disorder (Kircher et al., Reference Kircher, Krug, Stratmann, Ghazi, Schales and Frauenheim2014). The family medical histories and life charts of all family members were documented in electronic case report form. For more details regarding these procedures, refer to the German Clinical Trials Register (DRKS-ID: DRKS00004761). The relevant demographic and clinical data are presented in Table 2.

Table 2. Demographic and clinical data of all family members.

PANSS: Positive and Negative Syndrome Scale.

(ii) DNA preparation

Blood samples (10 ml) were collected from every subject in ethylenediaminetetraacetic acid tubes. For DNA extraction from peripheral blood leukocytes, we treated the samples using the procedures described in the QIAamp DNA Blood Midi Kit protocol.

(iii) Gene screening, variation analysis and bioinformatics

All samples were treated with the Agilent SureSelect post-capture and enrichment protocols. Illumina HiSeq 2000 was used to sequence all samples with 100 bp paired end reads.

After quality control measures were performed, all reads were mapped against the human genome build hg19 using Bowtie2. Duplicated reads were removed with the Picard tool suite (version 1·136). We used two different variant calling algorithms (i.e., GATK2·8 and FreeBayes-VERS) for calling variants (McKenna et al., Reference McKenna, Hanna, Banks, Sivachenko, Cibulskis and Kernytsky2010; Garrison & Marth, Reference Garrison and Marth2012). For both calling algorithms, we followed the reported best practices and guidelines. Functional annotation of genetic variants was performed with SnpEff version 3·6 (Cingolani et al., Reference Cingolani, Platts, Wang, Coon, Nguyen and Wang2012). Finally, all annotated variants were loaded into a GEMINI database, and these were further used to explore the forms of human genetic variations (Paila et al., Reference Paila, Chapman, Kirchner and Quinlan2013).

We used an iterative strategy to obtain condense and meaningful variants. The strategy included the following steps: (i) quality of the reads; (ii) read depths (DP); (iii) exon-specific mutations; (iv) novel variants that were not present in the dbSNP database, etc.; and (v) comparison of our VCF files with the 1000 Genomes Project database (1000 Genomes Project Consortium, 2012), testing the significance with RStudio (version 7·7) Fisher's exact test.

(a) Tertiary and quaternary protein modelling

We built SWISS-MODEL tertiary and quaternary protein models using amino acid sequences from the National Center for Biotechnology Information (NCBI) database (FASTA format) and using a template with 25% (wild-type) and 18% (rs100666583 variation) sequence identities, respectively. For these models, the coverage was high. The SWISS-MODEL is an automated, non-profit, protein homology modelling server created by the Biozentrum at the University of Basel using evolutionary information (Schwede et al., Reference Schwede, Kopp, Guex and Peitsch2003; Biasini et al., Reference Biasini, Bienert, Waterhouse, Arnold, Studer and Schmidt2014).

3. Results

(i) Identification of disorder-specific mutations

Exome sequencing was performed for all family members (Fig. 1). We found a non-synonymous mutation that satisfied the high-impact quality demands (see ‘Gene screening, variation analysis and bioinformatics’ section), and it was detected only in the patients with psychotic disorders.

(a) Missense mutation in the GRIN3B gene

We found a missense mutation in the S1 domain of the GluN3B subunit, which was a single-nucleotide polymorphism on chromosome 19 position 1004897:1004898. This mutation is known as rs10666583 and is listed in the NCBI database dbSNP. The –/CGTT insertion causes an mRNA allele change and an amino acid residue frameshift. As a consequence of the mutation, guanine is replaced by alanine and an amino acid sequence is altered at position 466 within the glycine binding side of the S1 domain. The modified amino acid sequences are shown in Fig. 2.

Fig. 2. The GRIN3B rs10666583 mutation causes an altered amino acid structure. The GRIN3B rs10666583 mutation (box) on chromosome 19 in exon 3 [44] (a) requires an insertion variation –/GCTT (b) that causes an allele change on the mRNA strand (c), which lead to an amino acid change from guanine to alanine and an altered AAS of GluN3B (d) starting from position 466 (e).

(b) rs10666583 in the schizophrenic and healthy population of ReelinSys

Over the course of the ReelinSys project, we analysed the exome sequences of 17 out of 35 families containing at least one or more persons with a psychotic disorder, leading to a total of 22 patients. We found the rs10666583 mutation variant in 15 alleles, with an allele frequency (AF) of 0·51 in a total of 14 patients. Among the 34 corresponding healthy parents in the ReelinSys project, we found that 14 possessed this mutation, with an AF of 0·25. We did not find spontaneous rs10666583 mutations in any of the schizophrenic mutation carriers. This means there was no significant increase of the rs10666583 AF in patients compared with the healthy parents (p = 0·12).

(ii) rs10666583 in the schizophrenic patients compared with the 1000 Genomes Project population

We compared the genotype frequency (GF) – the quotient of individuals with a given genotype and the total number of individuals in a population – of rs10666583 in our ReelinSys study population with the 1000 Genomes Project database population (Table 3). We found that 14 out of 22 patients affected by psychotic disorder had this GRIN3B variant (GF = 0·63). From the 1000 Genomes Project population, 719 out of 2504 individuals had the rs10666583 variant (GF = 0·28). This represents a significant increase among patients (p = 0·0013), with an odds ratio of 4·3 (95% confidence interval [CI]: 1·8–10·4). We found 797 alleles with this variant out of 4211 in the 1000 Genomes Project population, with a AF of 0·18, and this represents a significant increase of rs10666583 in patients (p = 0·0018), with an odds ratio of 2·2 (95% CI: 1·2–4·3).

Table 3. rs10666583 variant mutation carriers.

a Significant increase (p < 0·05) of GF and AF in patients compared to WP.

WP: world population; AF: allele frequency; GF: genotype frequency; SZ: schizophrenic patients; Sib: siblings; SMR: spontaneous mutation rate.

(iii) SWISS protein model of the GluN3B wild-type and rs10666583 mutation variant

The 3D-SWISS protein model is shown in Fig. 3. As Fig. 3 indicates, the level of certainty of the structure ranges from high (blue) to low (orange). Because of the amino acid change and the frameshift of the amino acid structure at position 466, the model shows altered tertiary and quaternary structures for this region (Fig. 3(b), boxed region). The rs10666583 variant stops at position 482, and hence is significantly shorter than the wild-type GluN3B subunit, which is 1043 amino acids long.

Fig. 3. The SWISS model of wild-type Glu3B and the rs10666583 variation. The SWISS protein model shows the wild-type Glu3B subunit (a) of the N-methyl-D-aspartate receptor; the S1 region is boxed. The rs10666583 variation (b) shows truncated and altered protein tertiary and quaternary structures with the loss of its S1 region.

4. Discussion

Our main finding was of an autosomal dominant heterozygous frameshift mutation in the GRIN3B gene encoding the GluN3B subunit of the NMDA receptor that was present in all of the affected family members of our pedigree analysis and in 63·6% of all patients with schizophrenia in our ReelinSys study population. Compared to the 1000 Genomes Project database, we found a significantly increase in the quantity of this GRIN3B variant.

This frameshift causes an amino acid residue change at position 466 in the GluN3B subunit, which implies a displacement of the S1 binding domain primary structure that could reduce the affinity for glycine. A mutation analysis of the mouse GluN3B S1 domain and the critical amino acid residue sequences at positions 424, 504 and 505 revealed a distinct loss of the glycine binding site (Awobuluyi et al., Reference Awobuluyi, Yang, Ye, Chatterton, Godzik, Lipton and Zhang2007). Furthermore, we demonstrated altered tertiary and quaternary structures of the glycine binding site in the S1 region in our 3D-SWISS-MODEL; in addition, the mutant protein was significantly shorter than the wild-type protein. These findings are consistent with the subcellular findings of Matsuno and co-workers, who also described a truncated molecule with a lighter molecular weight and smaller bands than the major wild-type protein (Matsuno et al., Reference Matsuno, Ohi, Hashimoto, Yamamori, Yasuda and Fujimoto2015). Additionally, these authors found that the NMDA receptor rs10666583 mutation variant of the GluN3B subunit was not functioning upon electrophysiological verification (Matsuno et al., Reference Matsuno, Ohi, Hashimoto, Yamamori, Yasuda and Fujimoto2015). Glycine binding in the S1/S2 domain of GluN3B mediates the properties of the receptor pore. The GluN3/GluN2 and GluN1 heterotrimer leads to a reduction in Ca2+ permeability for the corresponding NMDA receptor, whereas the heterodimer GluN3/GluN1 leads to an increase in Ca2+ permeability (Chatterton et al., Reference Chatterton, Awobuluyi, Premkumar, Takahashi, Talantova and Shin2002; Matsuda et al., Reference Matsuda, Kamiya, Matsuda and Yuzaki2002, Reference Matsuda, Fletcher, Kamiya and Yuzaki2003; Low & Wee, Reference Low and Wee2010). Functional disturbances in these modulatory mechanisms could therefore lead to insufficient regulation of dendritic, spine or synaptic plasticity, or even cell death, induced by Ca2+ and a subsequent desynchronization of cortical microcircuits (Yuan et al., Reference Yuan, Lipinski and Degterev2003; Alvarez & Sabatini, Reference Alvarez and Sabatini2007; Zhang et al., Reference Zhang, Steijaert, Lau, Schütz, Delucinge-Vivier, Descombes and Bading2007; Konstantoudaki et al., Reference Konstantoudaki, Papoutsi, Chalkiadaki, Poirazi and Sidiropoulou2014). Interestingly, Spiros and colleagues found an inverse U-shaped dose–response correlation between glycine concentration and the negative symptoms of schizophrenia as a potential consequence of an imbalance in the ratio between excitation and inhibition (Spiros et al., 2014). Post-mortem histological analyses of cerebral brain tissue in patients with schizophrenia indicated a reduced pyramidal cell density and dendritic spine alterations in several regions of the cerebral cortex (Harrison, Reference Harrison1999; Benes et al., Reference Benes, Davidson and Bird1986; Glausier & Lewis, Reference Glausier and Lewis2013). The core symptoms of psychotic disorders, which include hallucinations, delusions and cognitive dysfunctions, are most likely due to dysfunctional neuronal circuits, unbalanced neurochemistry and reduced neuronal plasticity, and could therefore be linked to deregulated NMDA receptor functioning.

The rs10666583 frameshift was observed in 18% (AF) of the global population according to the 1000 Genomes Project, and in 25% (AF) of the healthy relatives in our study population. With a prevalence of psychotic disorders of less than 1% in the total population, these findings suggest that this polymorphism is not the only cause of the disease. Such a finding could also explain the increased rate of mutation carriers among the healthy relatives in the present study populations. We found distinctly higher rs10666583 AF and GF values among the patients in our population compared to the 1000 Genomes Project database. With odds ratios of 4·3 for the GF and 2·2 for the AF, this finding highlights the potential impact of this variant in the pathogenesis of schizophrenia, and we point out that a false allocation of pathogenicity could have severe consequences for patients and research enterprises.

Interestingly, we found rs10666583 only as a hereditary mutation and not as a de novo mutation. Referring to Matsuno et al. (Reference Matsuno, Ohi, Hashimoto, Yamamori, Yasuda and Fujimoto2015), we also demonstrated that this variant occurred within a family only for affected members, and that this variation is overrepresented in patients with psychotic disorder compared to in the 1000 Genomes Project. Because of the unbiased replication of this dbSNP based on undirected whole-exome sequencing, this provides added value beyond the specific genotyping of Matsuno et al. (Reference Matsuno, Ohi, Hashimoto, Yamamori, Yasuda and Fujimoto2015). In addition, an inherited mutation variant, which occurs only in diseased family members, represents a stronger indication of the development of the disease than a case–control study in the general population. It is precisely this biological importance that adds value to previous data, as it is a random finding.

An important limitation of this study is that, as the 1000 Genomes Project cannot rule out the future onset of a psychiatric disorder in previously healthy participants, it seems unlikely that all mutation carriers will eventually develop a psychiatric disease. Unknown protective genes and other modulating mechanisms may therefore be postulated in healthy mutation carriers. At the time of this writing, there were no genomic databases focusing on genetic variation among patients with psychiatric disorders and their siblings with which we could compare our results.

5. Conclusion

We found a frameshift mutation in the GluN3B subunit of the NMDA receptor that induces a degradation of the S1 glycine binding domain. This mutation could play a role in the deregulated neuronal circuits and neuronal plasticity in patients with psychotic disorders. Because of the high prevalence of this dbSNP in the non-affected population, we suggest that there is a complex interaction of further polymorphisms that causes the manifestation of psychotic symptoms. An important task for the future is to build a genomic database for psychiatric disorders in order to re-evaluate detected polymorphisms in patients with psychiatric disorders and to uncover the polygenetic causes of such disorders.

We thank all subjects who have participated in this study. This work was supported by the University Hospital of Freiburg, Department of Psychiatry and Psychotherapy.

The ReelinSys project was funded by the Federal Ministry of Education and Research.

6. Declaration of interest

The authors declare that they have no competing interests. We certify that there is no conflict of interest with any financial organization or non-financial competing interests regarding the material discussed in the manuscript.

No reimbursements, fees, funding or salary from an organization that could lose financially was received by any author in the past 5 years, nor any stocks or shares held. The authors do not hold any patents relating to the content of this manuscript.

7. Authors’ contributions

C. Normann and K. Biber designed the study, wrote the protocol and participated in data analysis and interpretation. T. Hornig managed patient recruitment and data collection, participated in data analysis and interpretation and wrote the final draft of the manuscript. R. Backofen, B. Grüning, K. Kundu and T. Houwaart participated in the design, analysis and interpretation of the data. All authors contributed to and have approved the final manuscript.

8. Ethics committee

Ethik-Kommission der Albert-Ludwigs-Universität

Engelbergerstr. 21

79106 Freiburg

(No. 94/13)

9. Availability of data and materials

After acceptance of BPSY-D-16-00377, a DNA database including a genomic variants archive will be set up online.

10. Consent to publish

All authors agree to the publication.

References

1000 Genomes Project Consortium (2012). An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422), 56–65.Google Scholar
Alvarez, V. A. & Sabatini, B. L. (2007). Anatomical and physiological plasticity of dendritic spines. Annual Review of Neuroscience 30, 79–97.Google Scholar
Andersson, O., Stenqvist, A., Attersand, A. & von Euler, G. (2001). Nucleotide Sequence, genomic organization, and chromosomal localization of genes encoding the human NMDA receptor subunits NR3A and NR3B. Genomics 78(3), 178–184.CrossRefGoogle ScholarPubMed
Armstrong, N., Sun, Y., Chen, G. Q. & Gouaux, E. (1998). Structure of a glutamate-receptor ligand-binding core in complex with kainate. Nature 395(6705), 913–917.Google Scholar
Awobuluyi, M., Yang, J., Ye, Y., Chatterton, J. E. Godzik, A., Lipton, S. A. & Zhang, D. (2007). Subunit-specific roles of glycine-binding domains in activation of NR1/NR3 N-methyl-D-aspartate receptors. Molecular Pharmacology 71(1), 112–122.Google Scholar
Balu, D. T. & Coyle, J. T. (2011). Neuroplasticity signaling pathways linked to the pathophysiology of schizophrenia. Neuroscience and Biobehavioral Reviews 35(3), 848–870.Google Scholar
Bauer, D., Gupta, D., Harotunian, V., Meador-Woodruff, J. H. & McCullumsmith, R. E. (2008). Abnormal expression of glutamate transporter and transporter interacting molecules in prefrontal cortex in elderly patients with schizophrenia. Schizophrenia Research 104(1–3), 108–120.Google Scholar
Benes, F. M., Davidson, J. & Bird, E. D. (1986). Quantitative cytoarchitectural studies of the cerebral cortex of schizophrenics. Arch Gen Psychiatry 43(1), 31–35.Google Scholar
Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T. et al. (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research 42(W1), W252–W258.CrossRefGoogle ScholarPubMed
Bitanihirwe, B. K. Y., Lim, M. P., Kelley, J. F., Kaneko, T. & Woo, T. U. W. (2009). Glutamatergic deficits and parvalbumin-containing inhibitory neurons in the prefrontal cortex in schizophrenia. BMC Psychiatry 9, 71.Google Scholar
Blot, K., Bai, J. & Otani, S. (2013). The effect of non-competitive NMDA receptor antagonist MK-801 on neuronal activity in rodent prefrontal cortex: an animal model for cognitive symptoms of schizophrenia. Journal of Physiology, Paris 107(6), 448–451.CrossRefGoogle ScholarPubMed
Chatterton, J. E., Awobuluyi, M., Premkumar, L. S., Takahashi, H., Talantova, M., Shin, Y. et al. (2002). Excitatory glycine receptors containing the NR3 family of NMDA receptor subunits. Nature 415(6873), 793–798.Google Scholar
Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L. et al. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6(2), 80–92.Google Scholar
Cioffi, C. L. (2013). Modulation of NMDA receptor function as a treatment for schizophrenia. Bioorganic & Medicinal Chemistry Letters 23(18), 5034–5044.CrossRefGoogle ScholarPubMed
Dalkara, T., Erdemli, G., Barun, S. & Onur, R. (1992). Glycine is required for NMDA receptor activation: electrophysiological evidence from intact rat hippocampus. Brain Research 576(2), 197–202.Google Scholar
de Bartolomeis, A., Latte, G., Tomasetti, C. & Iasevoli, F. (2014). Glutamatergic postsynaptic density protein dysfunctions in synaptic plasticity and dendritic spines morphology: relevance to schizophrenia and other behavioral disorders pathophysiology, and implications for novel therapeutic approaches. Molecular Neurobiology 49(1), 484–511.CrossRefGoogle ScholarPubMed
Dingledine, R., Borges, K., Bowie, D. & Traynelis, S. F. (1999). The glutamate receptor ion channels. Pharmacological Reviews 51(1), 7–61.Google Scholar
Fan, X., Jin, W. Y. & Wang, Y. T. (2014). The NMDA receptor complex: a multifunctional machine at the glutamatergic synapse. Frontiers in Cellular Neuroscience 8, 160.Google Scholar
Garrison, E. & Marth, G. (2012). Haplotype-based variant detection from short-read sequencing [www document]. URL https://arxiv.org/abs/1207·3907 Google Scholar
Geddes, A. E., Huang, X.-F. & Newell, K. A. (2011). Reciprocal signalling between NR2 subunits of the NMDA receptor and neuregulin1 and their role in schizophrenia. Progress in Neuro-Psychopharmacology & Biological Psychiatry 35(4), 896–904.Google Scholar
Giegling, I., Genius, J., Benninghoff, J. & Rujescu, D. (2010). Genetic findings in schizophrenia patients related to alterations in the intracellular Ca-homeostasis. Progress in Neuro-Psychopharmacology & Biological Psychiatry 34(8), 1375–1380.Google Scholar
Glausier, J. R. & Lewis, D. A. (2013). Dendritic spine pathology in schizophrenia. Neuroscience 251, 90–107.Google Scholar
Harris, E. W., Ganong, A. H. & Cotman, C. W. (1984). Long-term potentiation in the hippocampus involves activation of N-methyl-D-aspartate receptors. Brain Research 323(1), 132–137.Google Scholar
Harrison, P. J. (1999). The neuropathology of schizophrenia. A critical review of the data and their interpretation. Brain: A Journal of Neurology 122(Pt 4), 593–624.Google Scholar
Javitt, D. C. (2009). Glycine transport inhibitors for the treatment of schizophrenia: symptom and disease modification. Current Opinion in Drug Discovery & Development 12(4), 468–478.Google Scholar
Johnson, J. W. & Ascher, P. (1987). Glycine potentiates the NMDA response in cultured mouse brain neurons. Nature 325(6104), 529–531.CrossRefGoogle ScholarPubMed
Kay, S. R., Fiszbein, A. & Opler, L. A. (1987). The Positive and Negative Syndrome Scale (PANSS) for schizophrenia. Schizophrenia Bulletin 13(2), 261–276.Google Scholar
Kim, J. S., Kornhuber, H. H., Schmid-Burgk, W. & Holzmüller, B. (1980). Low cerebrospinal fluid glutamate in schizophrenic patients and a new hypothesis on schizophrenia. Neuroscience Letters 20(3), 379–382.Google Scholar
Kircher, T., Krug, A., Stratmann, M., Ghazi, S., Schales, C., Frauenheim, M. et al. (2014). A rating scale for the assessment of objective and subjective formal thought and language disorder (TALD). Schizophrenia Research 160(1–3), 216–221.Google Scholar
Konstantoudaki, X., Papoutsi, A., Chalkiadaki, K., Poirazi, P. & Sidiropoulou, K. (2014). Modulatory effects of inhibition on persistent activity in a cortical microcircuit model. Frontiers in Neural Circuits 8, 7.Google Scholar
Kornhuber, H. H., Kornhuber, J., Kim, J. S. & Kornhuber, M. E. (1984). [A biochemical theory of schizophrenia], Der Nervenarzt 55(11), 602–606.Google Scholar
Kristiansen, L. V., Huerta, I., Beneyto, M. & Meador-Woodruff, J. H. (2007). NMDA receptors and schizophrenia. Current Opinion in Pharmacology 7(1), 48–55.CrossRefGoogle ScholarPubMed
Laruelle, M. (2014). Schizophrenia: from dopaminergic to glutamatergic interventions. Current Opinion in Pharmacology 14, 97–102.Google Scholar
Li, N., Liu, R.-J., Dwyer, J. M., Banasr, M., Lee, B., Son, H. et al. (2011). Glutamate N-methyl-D-aspartate receptor antagonists rapidly reverse behavioral and synaptic deficits caused by chronic stress exposure. Biological Psychiatry 69(8), 754–61.Google Scholar
Lin, Y.-T., Hsieh, M. H., Liu, C.-C., Hwang, T.-J., Chien, Y.-L., Hwu, H.-G. & Liu, C.-M. (2014). A recently-discovered NMDA receptor gene, GRIN3B, is associated with duration mismatch negativity. Psychiatry Research 218(3), 356–58.CrossRefGoogle ScholarPubMed
Lipsky, R. H. & Goldman, D. (2003). Genomics and variation of ionotropic glutamate receptors. Annals of the New York Academy of Sciences 1003, 22–35.CrossRefGoogle ScholarPubMed
López-Gil, X., Babot, Z., Amargós-Bosch, M., Suñol, C., Artigas, F. & Adell, A. (2007). Clozapine and haloperidol differently suppress the MK-801-increased glutamatergic and serotonergic transmission in the medial prefrontal cortex of the rat. Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology 32(10), 2087–2097.Google Scholar
Low, C.-M. & Wee, K. S.-L. (2010). New insights into the not-so-new NR3 subunits of N-methyl-D-aspartate receptor: localization, structure, and function, Molecular Pharmacology 78(1), 1–11.Google Scholar
Matsuda, K., Fletcher, M. Kamiya, Y. & Yuzaki, M. (2003). Specific assembly with the NMDA receptor 3B subunit controls surface expression and calcium permeability of NMDA receptors. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience 23(31), 10064–10073.CrossRefGoogle ScholarPubMed
Matsuda, K., Kamiya, Y., Matsuda, S. & Yuzaki, M. (2002). Cloning and characterization of a novel NMDA receptor subunit NR3B: a dominant subunit that reduces calcium permeability. Molecular Brain Research 100(1–2), 43–52.CrossRefGoogle ScholarPubMed
Matsuno, H., Ohi, K., Hashimoto, R., Yamamori, H., Yasuda, Y., Fujimoto, M. et al. (2015). A naturally occurring null variant of the NMDA type glutamate receptor NR3B subunit is a risk factor of schizophrenia. PLoS One 10(3), e0116319.Google Scholar
Mátyás, T. (2006). [Gene polymorphism and gene expression in schizophrenia]. Psychiatria Hungarica: A Magyar Pszichiátriai Társaság Tudományos Folyóirata 21(6), 404–412.Google Scholar
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A. et al. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20(9), 1297–1303.Google Scholar
Moghaddam, B. & Adams, B. W. (1998). Reversal of phencyclidine effects by a group II metabotropic glutamate receptor agonist in rats. Science (New York, N.Y.) 281(5381), 1349–1352.CrossRefGoogle ScholarPubMed
Niemann, S., Kanki, H., Fukui, Y., Takao, K. Fukaya, M. Hynynen, M. N. et al. (2007). Genetic ablation of NMDA receptor subunit NR3B in mouse reveals motoneuronal and nonmotoneuronal phenotypes. The European Journal of Neuroscience 26(6), 1407–1420.Google Scholar
Normann, C. & Clark, K. (2005). Selective modulation of Ca2+ influx pathways by 5-HT regulates synaptic long-term plasticity in the hippocampus. Brain Research 1037(1–2), 187–193.Google Scholar
Normann, C., Peckys, D., Schulze, C. H., Walden, J., Jonas, P. & Bischofberger, J. (2000). Associative long-term depression in the hippocampus is dependent on postsynaptic N-type Ca2+ channels. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience 20(22), 8290–8297.Google Scholar
Paila, U., Chapman, B. A., Kirchner, R. & Quinlan, A. R. (2013). GEMINI: Integrative exploration of genetic variation and genome annotations. PLoS Computational Biology 9(7), e1003153.Google Scholar
Paoletti, P., Bellone, C. & Zhou, Q. (2013). NMDA receptor subunit diversity: impact on receptor properties, synaptic plasticity and disease. Nature Reviews Neuroscience 14(6), 383–400.CrossRefGoogle ScholarPubMed
Putnam, D. K., Sun, J. & Zhao, Z. (2011). Exploring schizophrenia drug–gene interactions through molecular network and pathway modeling. AMIA Annual Symposium Proceedings Archive 2011, 1127–1133.Google Scholar
Schwede, T., Kopp, J., Guex, N. & Peitsch, M. C. (2003). SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Research 31(13), 3381–3385.Google Scholar
Siegel, G. J. & Brady, S. T. (2011). Basic Neurochemistry: Principles of Molecular, Cellular, and Medical Neurobiology. 8th edition. Boston, MA: Academic Press.Google Scholar
Stern-Bach, Y., Bettler, B., Hartley, M., Sheppard, P. O., O'Hara, P. J. & Heinemann, S. F. (1994). Agonist selectivity of glutamate receptors is specified by two domains structurally related to bacterial amino acid-binding proteins. Neuron 13(6), 1345–1357.Google Scholar
Tarabeux, J., Kebir, O., Gauthier, J., Hamdan, F. F., Xiong, L., Piton, A. et al. (2011). Rare mutations in N-methyl-D-aspartate glutamate receptors in autism spectrum disorders and schizophrenia. Translational Psychiatry 1, e55.Google Scholar
Teyler, T. J. (1987). Long-term potentiation and memory. International Journal of Neurology 21–22, 163–171.Google ScholarPubMed
Vargas-Caballero, M. & Robinson, H. P. C. (2004). Fast and slow voltage-dependent dynamics of magnesium block in the NMDA receptor: the asymmetric trapping block model. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience 24(27), 6171–6180.Google Scholar
Wee, K. S.-L., Zhang, Y., Khanna, S. & Low, C.-M. (2008). Immunolocalization of NMDA receptor subunit NR3B in selected structures in the rat forebrain, cerebellum, and lumbar spinal cord. The Journal of Comparative Neurology 509(1), 118–135.CrossRefGoogle ScholarPubMed
Yao, Y. & Mayer, M. L. (2006). Characterization of a soluble ligand binding domain of the NMDA receptor regulatory subunit NR3A. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience 26(17), 4559–4566.Google Scholar
Yuan, J., Lipinski, M. & Degterev, A/ (2003). Diversity in the mechanisms of neuronal cell death, Neuron 40(2), 401–413.Google Scholar
Zarate, C. A., Singh, J. & Manji, H. K. (2006). Cellular plasticity cascades: targets for the development of novel therapeutics for bipolar disorder. Biological Psychiatry 59(11), 1006–1020.CrossRefGoogle ScholarPubMed
Zhang, S.-J., Steijaert, M. N., Lau, D., Schütz, G., Delucinge-Vivier, C., Descombes, P. & Bading, H. (2007). Decoding NMDA receptor signaling: identification of genomic programs specifying neuronal survival and death. Neuron 53(4), 549–562.Google Scholar
Zhou, Q. & Sheng, M. (2013). NMDA receptors in nervous system diseases. Neuropharmacology 74, 69–75.CrossRefGoogle ScholarPubMed
Figure 0

Table 1. N-methyl-D-aspartate receptor subunits, their main transmitter affinity and localization.

Figure 1

Fig. 1. Pedigree of the family, with affected members coloured black. Schizophrenic patients: 1–5; healthy family members: a–c.

Figure 2

Table 2. Demographic and clinical data of all family members.

Figure 3

Fig. 2. The GRIN3B rs10666583 mutation causes an altered amino acid structure. The GRIN3B rs10666583 mutation (box) on chromosome 19 in exon 3 [44] (a) requires an insertion variation –/GCTT (b) that causes an allele change on the mRNA strand (c), which lead to an amino acid change from guanine to alanine and an altered AAS of GluN3B (d) starting from position 466 (e).

Figure 4

Table 3. rs10666583 variant mutation carriers.

Figure 5

Fig. 3. The SWISS model of wild-type Glu3B and the rs10666583 variation. The SWISS protein model shows the wild-type Glu3B subunit (a) of the N-methyl-D-aspartate receptor; the S1 region is boxed. The rs10666583 variation (b) shows truncated and altered protein tertiary and quaternary structures with the loss of its S1 region.