Linkage analysis of schizophrenia controlling for population substructure

Genetic Associations between Voltage-Gated Calcium Channels and Psychiatric Disorders

Psychiatric disorders are mental, behavioral or emotional disorders. These conditions are prevalent, one in four adults suffer from any type of psychiatric disorders world-wide. It has always been observed that psychiatric disorders have a genetic component, however, new methods to sequence full genomes of large cohorts have identified with high precision genetic risk loci for these conditions. Psychiatric disorders include, but are not limited to, bipolar disorder, schizophrenia, autism spectrum disorder, anxiety disorders, major depressive disorder, and attention-deficit and hyperactivity disorder. Several risk loci for psychiatric disorders fall within genes that encode for voltage-gated calcium channels (CaVs). Calcium entering through CaVs is crucial for multiple neuronal processes. In this review, we will summarize recent findings that link CaVs and their auxiliary subunits to psychiatric disorders. First, we will provide a general overview of CaVs structure, classification, function, expression and pharmacology. Next, we will summarize tools to study risk loci associated with psychiatric disorders. We will examine functional studies of risk variations in CaV genes when available. Finally, we will review pharmacological evidence of the use of CaV modulators to treat psychiatric disorders. Our review will be of interest for those studying pathophysiological aspects of CaVs.

A genome-wide screen for acrophobia susceptibility loci in a Finnish isolate

Acrophobia, an abnormal fear of heights, is a specific phobia characterized as apprehension cued by the occurrence or anticipation of elevated spaces. It is considered a complex trait with onset influenced by both genetic and environmental factors. Identification of genetic risk variants would provide novel insight into the genetic basis of the fear of heights phenotype and contribute to the molecular-level understanding of its aetiology. Genetic isolates may facilitate identification of susceptibility alleles due to reduced genetic heterogeneity. We took advantage of an internal genetic isolate in Finland in which a distinct acrophobia phenotype appears to be segregating in pedigrees originally ascertained for schizophrenia. We conducted parametric, nonparametric, joint linkage and linkage disequilibrium analyses using a microsatellite marker panel, genotyped in families to search for chromosomal regions correlated with acrophobia. Our results implicated a few regions with suggestive evidence for linkage on chromosomes 4q28 (LOD = 2.17), 8q24 (LOD = 2.09) and 13q21-q22 (LOD = 2.22). We observed no risk haplotypes shared between different families. These results suggest that genetic predisposition to acrophobia in this genetic isolate is unlikely to be mediated by a small number of shared high-risk alleles, but rather has a complex genetic architecture.

Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia

Background

Epigenetics of schizophrenia provides important information on how the environmental factors affect the genetic architecture of the disease. DNA methylation plays a pivotal role in etiology for schizophrenia. Previous studies have focused mostly on the discovery of schizophrenia-associated SNPs or genetic variants. As postmortem brain samples became available, more and more recent studies surveyed transcriptomics of the diseases. In this study, we constructed protein-protein interaction (PPI) network using the disease associated SNP (or genetic variants), differentially expressed disease genes and differentially methylated disease genes (or promoters). By combining the different datasets and topological analyses of the PPI network, we established a more comprehensive understanding of the development and genetics of this devastating mental illness.

Results

We analyzed the previously published DNA methylation profiles of prefrontal cortex from 335 healthy controls and 191 schizophrenic patients. These datasets revealed 2014 CpGs identified as GWAS risk loci with the differential methylation profile in schizophrenia, and 1689 schizophrenic differential methylated genes (SDMGs) identified with predominant hypomethylation. These SDMGs, combined with the PPIs of these genes, were constructed into the schizophrenic differential methylation network (SDMN). On the SDMN, there are 10 hypermethylated SDMGs, including GNA13, CAPNS1, GABPB2, GIT2, LEFTY1, NDUFA10, MIOS, MPHOSPH6, PRDM14 and RFWD2. The hypermethylation to differential expression network (HyDEN) were constructed to determine how the hypermethylated promoters regulate gene expression. The enrichment analyses of biochemical pathways in HyDEN, including TNF alpha, PDGFR-beta signaling, TGF beta Receptor, VEGFR1 and VEGFR2 signaling, regulation of telomerase, hepatocyte growth factor receptor signaling, ErbB1 downstream signaling and mTOR signaling pathway, suggested that the malfunctioning of these pathways contribute to the symptoms of schizophrenia.

Conclusions

The epigenetic profiles of DNA differential methylation from schizophrenic brain samples were investigated to understand the regulatory roles of SDMGs. The SDMGs interplays with SCZCGs in a coordinated fashion in the disease mechanism of schizophrenia. The protein complexes and pathways involved in SDMN may be responsible for the etiology and potential treatment targets. The SDMG promoters are predominantly hypomethylated. Increasing methylation on these promoters is proposed as a novel therapeutic approach for schizophrenia.

Electronic supplementary material

The online version of this article (doi:10.1186/s12920-016-0229-y) contains supplementary material, which is available to authorized users.

Genetic Evaluation of Schizophrenia Using the Illumina HumanExome Chip

INTRODUCTION

Schizophrenia is a genetically heterogeneous disorder that is associated with several common and rare genetic variants. As technology involved, cost advantages of chip based genotyping was combined with information about rare variants, resulting in the Infinium HumanExome Beadchip. Using this chip, a sample of 493 patients with schizophrenia or schizoaffective disorder and 484 healthy controls was genotyped.

RESULTS

From the initial 242901 SNVs, 88306 had at least one minor allele and passed quality control. No variant reached genomewide-significant results (p<10(-8)). The SNP with the lowest p-value was rs1230345 in WISP3 (p = 3.05*10(-6)), followed by rs9311525 in CACNA2D3 (p = 1.03*10(-5)) and rs1558557 (p = 3.85*10(-05)) on chromosome 7. At the gene level, 3 genes were of interest: WISP3, on chromosome 6q21, a signally protein from the extracellular matrix. A second candidate gene is CACNA2D3, a regulator of the intracerebral calcium pathway. A third gene is TNFSF10, associated with p53 mediated apoptosis.

Family with sequence similarity 107: A family of stress responsive small proteins with diverse functions in cancer and the nervous system (Review)

Under conditions of acute stress, rapid adaptation is crucial for maximizing biological survival. The responses to environmental stress are often complex, involving numerous genes and integrating events at the cellular and organismal levels. The heat shock proteins (HSPs) are a family of highly conserved proteins that play critical roles in maintaining cell homeostasis and protecting cells under chronic and acute stress conditions. The genes for these stress-responding proteins are widely distributed in organisms, tissues and cells. HSPs participate in a variety of physiological processes and are associated with various types of disease. In this review, we focused on family with sequence similarity 107 (FAM107), a novel unique protein family that exhibits functional similarity with HSPs during the cellular stress response. This review aimed to summarize the biological properties of FAM107 in cancer and the nervous system.

Does originating from a genetic isolate affect the level of cognitive impairments in schizophrenia families?

Earlier studies have detected differences in the prevalence, symptomatology and genetic risk variants of schizophrenia between a north-eastern Finnish genetic isolate and the rest of Finland. This study compared a population-based isolate sample (145 persons with schizophrenia, 304 first-degree relatives and 32 controls) with a rest of Finland sample (73 persons with schizophrenia, 100 first-degree relatives and 80 controls) in cognitive functioning. Persons from the isolate outperformed persons in the rest of Finland sample in verbal learning, verbal ability and cognitive flexibility in the schizophrenia groups and in verbal learning, speeded processing and attentional control in the relatives groups. The differences between the subsamples remained significant after taking into account an intragenic Reelin STR allele, previously associated with cognitive impairments and almost absent from the isolate, in addition to disorder characteristics and familial loading. In control groups, we observed no differences between the isolate and the rest of Finland. In conclusion, cognitive impairments were milder in schizophrenia patients and their first-degree relatives within than outside the isolate. An absence of differences between the control samples suggests that the differences in schizophrenia families may relate to genetic background, possibly to partly distinct variants affecting the liability inside and outside the isolate.

Emfit movement sensor in evaluating nocturnal breathing

Obstructive sleep apnea (OSA) diagnostics by the movement sensors static charge-sensitive bed (SCSB) and electromechanical film transducer (Emfit) is based on dividing the signal into different breathing patterns. The usage of non-invasive mattress sensors in diagnosing OSA is particularly tempting if patient has many other non sleep-related monitoring sensors. However, a systematic comparison of the apnea-hypopnea index (AHI) with Emfit-parameters is lacking. In addition to periodic breathing, SCSB and Emfit visualize episodes of sustained negative increases in intrathoracic pressure (increased respiratory resistance, IRR), of which relevance is still ambiguous. Our aim is to compare Emfit-parameters with the AHI and to provide a description of the patients suffering from IRR. Time percentage with all obstructive periodic Emfit breathing patterns (OPTotal%) showed the best correlation with the AHI. The OPTotal percentage of 21 yielded to excellent accuracy in detecting subjects with an AHI of 15/h or more. Patients with IRR received high scores in GHQ-12-questionnaire. An Emfit movement sensor might offer additional information in OSA diagnostics especially if nasal pressure transducer cannot be used.

MAGI1 copy number variation in bipolar affective disorder and schizophrenia

BACKGROUND

Bipolar affective disorder (BPAD) and schizophrenia (SZ) are devastating psychiatric disorders that each affect about 1% of the population worldwide. Identification of new drug targets is an important step toward better treatment of these poorly understood diseases.

METHODS

Genome-wide copy number variation (CNV) was assessed and variants were ranked by co-occurrence with disease in 48 BPAD families. Additional support for involvement of the highest-ranking CNV from the family-based analysis in psychiatric disease was obtained through analysis of 4084 samples with BPAD, SZ, or schizoaffective disorder. Finally, a pooled analysis of in-house and published datasets was carried out including 10,925 cases with BPAD, SZ, or schizoaffective disorder and 16,747 controls.

RESULTS

In the family-based analysis, an approximately 200 kilobase (kb) deletion in the first intron of the MAGI1 gene was identified that segregated with BPAD in a pedigree (six out of six affected individuals; parametric logarithm of the odds score = 1.14). In the pooled analysis, seven additional insertions or deletions over 100 kb were identified in MAGI1 in cases, while only two such CNV events were identified in the same gene in controls (p = .023; Fisher's exact test). Because earlier work had identified a CNV in the close relative MAGI2 in SZ, the study was extended to include MAGI2. In the pooled analysis of MAGI2, two large deletions were found in cases, and two duplications were detected in controls.

CONCLUSIONS

Results presented herein provide further evidence for a role of MAGI1 and MAGI2 in BPAD and SZ etiology.

Sex differences in cognition among persons with schizophrenia and healthy first-degree relatives

Previous research suggests differences between women and men in the clinical features of schizophrenia, but studies examining sex differences in neuropsychological functioning have reached inconsistent results. In the present study, sex differences in cognition and clinical features were investigated in population-based samples of participants with schizophrenia (n=218), their healthy first-degree relatives (n=438) and controls (n=123). Sex differences in illness features were small; nevertheless, women with schizophrenia had less negative symptoms and lived independently more often than men. The schizophrenia group had impairments in all studied neuropsychological domains, and the relatives were impaired in processing speed and set-shifting. In all groups, women performed better than men in processing speed, set-shifting and verbal episodic memory, whereas men outperformed women in visual working memory. The group-by-sex interaction was significant in two variables: women outperformed men in the relatives group in immediate verbal reproduction and in the use of semantic clustering as a learning strategy, while there was no sex difference in the schizophrenia group. In conclusion, sex differences in cognition are mostly similar in schizophrenia to those among controls, despite sex differences in illness features. The preservation of sex differences also in first-degree relatives supports the conclusion.

Familial transmission of schizophrenia in Palau: A 20-year genetic epidemiological study in three generations

Our genetic epidemiological studies of schizophrenia and other psychotic disorders (SCZ) in the isolated population of Palau have been ongoing for 20 years. Results from the first decade showed that Palau has an elevated prevalence of SCZ and that cases cluster in extended multigenerational pedigrees interconnected via complex genetic relationships after centuries of endogamous, but not consanguineous, marriages. The aim of our second decade of research, which extended data collection into a third generation of young, high-risk (HR) Palauans, was to identify significant predictors of intergenerational transmission of illness. Our findings revealed that degree of familial loading and gender effects on reproductive fitness are important modifiers of risk for transmission of SCZ. Among 45 distinct multiplex families, we identified 10 high-density (HD) Palauan families, each with 7-29 SCZ cases, which contain half of Palau's 260 SCZ cases and 80% of the 113 SCZ cases with one or more affected first-degree relatives, indicating that familial loading is a major risk factor for SCZ in Palau. Cases that belong to multiply affected sibships are more common than cases with an affected parent. Furthermore, only 6/38 multiply affected sibships have an affected parent, strong evidence that many unaffected parents are obligate carriers of susceptibility genes. Although reproductive fitness is dramatically reduced in affected males, the 30% minority who do become fathers are twice as likely as affected mothers to transmit SCZ to an offspring. As they evolve, these HD families can help to elucidate the genetic mechanisms that predict intergenerational transmission of SCZ.