Alessia Fiorentino

Analysis of ANK3 and CACNA1C variants identified in bipolar disorder whole genome sequence data.

Genetic markers in the genes encoding ankyrin 3 (ANK3) and the α‐calcium channel subunit (CACNA1C) are associated with bipolar disorder (BP). The associated variants in the CACNA1C gene are mainly within intron 3 of the gene. ANK3 BP‐associated variants are in two distinct clusters at the ends of the gene, indicating disease allele heterogeneity.

Mutations in REEP6 Cause Autosomal-Recessive Retinitis Pigmentosa

Retinitis pigmentosa (RP) is the most frequent form of inherited retinal dystrophy. RP is genetically heterogeneous and the genes identified to date encode proteins involved in a wide range of functional pathways, including photoreceptor development, phototransduction, the retinoid cycle, cilia, and outer segment development. Here we report the identification of biallelic mutations in Receptor Expression Enhancer Protein 6 (REEP6) in seven individuals with autosomal-recessive RP from five unrelated families. REEP6 is a member of the REEP/Yop1 family of proteins that influence the structure of the endoplasmic reticulum but is relatively unstudied. The six variants identified include three frameshift variants, two missense variants, and a genomic rearrangement that disrupts exon 1. Human 3D organoid optic cups were used to investigate REEP6 expression and confirmed the expression of a retina-specific isoform REEP6.1, which is specifically affected by one of the frameshift mutations. Expression of the two missense variants (c.383C>T [p.Pro128Leu] and c.404T>C [p.Leu135Pro]) and the REEP6.1 frameshift mutant in cultured cells suggest that these changes destabilize the protein. Furthermore, CRISPR-Cas9-mediated gene editing was used to produce Reep6 knock-in mice with the p.Leu135Pro RP-associated variant identified in one RP-affected individual. The homozygous knock-in mice mimic the clinical phenotypes of RP, including progressive photoreceptor degeneration and dysfunction of the rod photoreceptors. Therefore, our study implicates REEP6 in retinal homeostasis and highlights a pathway previously uncharacterized in retinal dystrophy.

The functional GRM3 Kozak sequence variant rs148754219 affects the risk of schizophrenia and alcohol dependence as well as bipolar disorder

We previously reported that a Kozak sequence variant in the metabotropic glutamate receptor 3 gene (GRM3), rs148754219, is associated with bipolar disorder (BP) and affects gene transcription and translation (Kandaswamy et al., 2013). A marker near GRM3, rs12704290, is one of the top hits and reached genome-wide significance in a recently reported genome-wide association study of schizophrenia (SZ) (Ripke et al., 2014), and markers for GRM3 have also been reported to demonstrate association with alcohol dependence syndrome (ADS) (Levey et al., 2014). In our original sample, considering patients successfully genotyped for rs148754219, 19 out of 1062 BP cases and only four out of 932 controls were heterozygous [odds ratio (OR)=4.2 (1.4–12.3), P=0.005]. We have genotyped this variant in additional controls and cases diagnosed with BP, SZ and ADS with the same ancestry. Patients were assessed by trained clinicians as described previously (Kandaswamy et al., 2013; Way et al., 2014). Allele counts were compared and significance was tested using Fisher’s exact test. Thirteen out of 934 additional BP cases and three out of 377 additional controls were heterozygous [OR=1.8 (0.49–6.2), P=not significant]. Combined with the originally reported results (Kandaswamy et al., 2013), 32 out of 1964 BP cases and seven out of 1309 controls were heterozygous [OR=3.0 (1.3–6.8), P=0.003]. Out of 1235 SZ cases 16 were heterozygous and were compared with the total control sample [OR=2.4 (0.99–5.8), P=0.03]. Out of 1514 ADS cases 18 were heterozygous and one was homozygous for the variant allele [OR=2.5 (1.0–5.9), P=0.03]. If all case cohorts (BP, SZ and ADS) are combined together, there would be one homozygote and 66 heterozygotes out of 4971 cases compared with the seven heterozygotes out of 1309 controls [OR=2.7 (1.2–5.8), P=0.004]. Previous work has supported the view that some genetic risk factors may be common to different psychiatric diagnoses (Lydall et al., 2011; Lee et al., 2013). Although the individual results are of questionable significance, the magnitude and direction of effect are consistent across all the cohorts and thus suggest the possibility that this rare variant may have a direct, functional effect on the risk of developing any of these three disorders. Because of its rarity, large sample sizes would be needed to confirm these results. Doing this would be worthwhile because if this finding is confirmed it could provide molecular insight into a mechanism involving GRM3 leading to increased risk of mental disorders and could provide a basis for further functional and therapeutic studies.

Genetic association, mutation screening, and functional analysis of a Kozak sequence variant in the metabotropic glutamate receptor 3 gene in bipolar disorder.

IMPORTANCE Genetic markers at the gene encoding the metabotropic glutamate receptor 3 (GRM3) showed allelic association with bipolar disorder. OBJECTIVE To screen the GRM3 gene and adjacent control regions of genomic DNA in volunteers with bipolar affective disorder for mutations increasing susceptibility to bipolar disorder. DESIGN Sequencing and high-resolution melting curve analysis of DNA followed by genotyping was carried out in 1099 patients with bipolar affective disorder and 1152 healthy comparator individuals. SETTING Participants with bipolar disorder were recruited from National Health Service psychiatric services and from patient organizations. PARTICIPANTS Individuals were included if they had Research Diagnostic Criteria diagnoses of bipolar I and bipolar II disorder and were of British or Irish ancestry. MAIN OUTCOMES AND MEASURES Identification of base pair changes in the GRM3 gene that affected expression or function of the GRM3 receptor that also showed an allelic association with bipolar disorder. RESULTS A base pair variant (rs148754219) was found in the Kozak sequence of exon 1 of the GRM3 gene, 2 bases before the translation start codon of one of the receptor isoforms, in 23 of 2251 people who were screened and genotyped. Nineteen of the 1099 bipolar cases (1.7%) were mutation carriers compared with 4 of 1152 healthy comparators (0.3%). The variant was associated with bipolar disorder (P = .005; odds ratio, 4.20). Bioinformatic, electrophoretic mobility shift assay, and gene expression analysis found that the variant created a new transcription factor protein binding site and had a strong effect on gene transcription and translation. CONCLUSIONS AND RELEVANCE Confirmation of these findings is needed before the Kozak sequence variant can be accepted as a potential marker for personalized treatment of affective disorders with drugs targeting the metabotropic glutamate receptor 3.

Association of rare variation in the glutamate receptor gene SLC1A2 with susceptibility to bipolar disorder and schizophrenia

The SLC1A2 gene encodes the excitatory amino acid transporter 2 (EAAT2). Glutamate is the major mediator of excitatory neurotransmission and EAAT2 is responsible for clearing the neurotransmitter from the synaptic cleft. Genetic variation in SLC1A2 has been implicated in a range of neurological and neuropsychiatric conditions including schizophrenia (SZ), autism and in core phenotypes of bipolar disorder (BD). The coding and putative regulatory regions of SLC1A2 gene were screened for variants using high resolution melting or sequenced in 1099 or in 32 BD subjects. Thirty-two variants were detected in the SLC1A2 gene. Fifteen potentially etiological variants were selected for genotyping in 1099 BD and 1095 control samples. Five amino acid changing variants were also genotyped in 630 participants suffering from SZ. None of the variants were found to be associated with BD or SZ or with the two diseases combined. However, two recurrent missense variants (rs145827578:G>A, p.(G6S); rs199599866:G>A, p.(R31Q)) and one recurrent 5′-untranslated region (UTR) variant (ss825678885:G>T) were detected in cases only. Combined analysis of the recurrent-case-only missense variants and of the case-only missense and 5′-UTR variants showed nominal evidence for association with the combined diseases (Fisher’s P=0.019 and 0.0076). These findings are exploratory in nature and await replication in larger cohorts, however, they provide intriguing evidence that potentially functional rare variants in the SLC1A2 gene may confer susceptibility to psychotic disorders.

Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies

Pre-mRNA splicing factors play a fundamental role in regulating transcript diversity both temporally and spatially. Genetic defects in several spliceosome components have been linked to a set of non-overlapping spliceosomopathy phenotypes in humans, among which skeletal developmental defects and non-syndromic retinitis pigmentosa (RP) are frequent findings. Here we report that defects in spliceosome-associated protein CWC27 are associated with a spectrum of disease phenotypes ranging from isolated RP to severe syndromic forms. By whole-exome sequencing, recessive protein-truncating mutations in CWC27 were found in seven unrelated families that show a range of clinical phenotypes, including retinal degeneration, brachydactyly, craniofacial abnormalities, short stature, and neurological defects. Remarkably, variable expressivity of the human phenotype can be recapitulated in Cwc27 mutant mouse models, with significant embryonic lethality and severe phenotypes in the complete knockout mice while mice with a partial loss-of-function allele mimic the isolated retinal degeneration phenotype. Our study describes a retinal dystrophy-related phenotype spectrum as well as its genetic etiology and highlights the complexity of the spliceosomal gene network.

Recessive Retinopathy Consequent on Mutant G-Protein β Subunit 3 (GNB3).

IMPORTANCE Mutations in phototransduction and retinal signaling genes are implicated in many retinopathies. To our knowledge, GNB3 encoding the G-protein β subunit 3 (Gβ3) has not previously been implicated in human disease. OBSERVATIONS In this brief report, whole-exome sequencing was conducted on a patient with distinct inherited retinal disease presenting in childhood, with a phenotype characterized by nystagmus, normal retinal examination, and mild disturbance of the central macula on detailed retinal imaging. This sequencing revealed a homozygous GNB3 nonsense mutation (c.124C>T; p.Arg42Ter). Whole-exome sequencing was conducted from April 2015 to July 2015. CONCLUSIONS AND RELEVANCE Expressed in cone photoreceptors and ON-bipolar cells, Gβ3 is essential in phototransduction and ON-bipolar cell signaling. Knockout of Gnb3 in mice results in dysfunction of cone photoreceptors and ON-bipolar cells and a naturally occurring chicken mutation leads to retinal degeneration. Identification of further affected patients may allow description of the phenotypic and genotypic spectrum of disease associated with GNB3 retinopathy.

Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data.

Summary Phenopolis is an open-source web server providing an intuitive interface to genetic and phenotypic databases. It integrates analysis tools such as variant filtering and gene prioritization based on phenotype. The Phenopolis platform will accelerate clinical diagnosis, gene discovery and encourage wider adoption of the Human Phenotype Ontology in the study of rare genetic diseases. Availability and Implementation A demo of the website is available at https://phenopolis.github.io . If you wish to install a local copy, source code and installation instruction are available at https://github.com/phenopolis . The software is implemented using Python, MongoDB, HTML/Javascript and various bash shell scripts. Contact n.pontikos@ucl.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.

Whole-exome sequencing of individuals from an isolated population implicates rare risk variants in bipolar disorder

Bipolar disorder affects about 1% of the world’s population, and its estimated heritability is about 75%. Only few whole genome or whole-exome sequencing studies in bipolar disorder have been reported, and no rare coding variants have yet been robustly identified. The use of isolated populations might help finding variants with a recent origin, more likely to have drifted to higher frequency by chance. Following this approach, we investigated 28 bipolar cases and 214 controls from the Faroe Islands by whole exome sequencing, and the results were followed-up in a British sample of 2025 cases and 1358 controls. Seventeen variants in 16 genes in the single-variant analysis, and 3 genes in the gene-based statistics surpassed exome-wide significance in the discovery phase. The discovery findings were supported by enrichment analysis of common variants from genome-wide association studies (GWAS) data and interrogation of protein–protein interaction networks. The replication in the British sample confirmed the association with NOS1 (missense variant rs79487279) and NCL (gene-based test). A number of variants from the discovery set were not present in the replication sample, including a novel PITPNM2 missense variant, which is located in a highly significant schizophrenia GWAS locus. Likewise, PIK3C2A identified in the gene-based analysis is located in a combined bipolar and schizophrenia GWAS locus. Our results show support both for existing findings in the literature, as well as for new risk genes, and identify rare variants that might provide additional information on the underlying biology of bipolar disorder.

Genetic variation in the miR-708 gene and its binding targets in bipolar disorder.

rs12576775 was found to be associated with bipolar disorder (BD) in a genome‐wide association study (GWAS). The GWAS signal implicates genes for the microRNAs miR‐708 and miR‐5579 and the first exon of the Odd Oz/ten‐m homolog 4 gene (ODZ4). In the present study, miR‐708, its surrounding region, and its targets were analyzed for potential BD‐associated functional variants.