Meta-analysis of sex differences in gene expression in schizophrenia

The impact of sex on gene expression in the brain of schizophrenic patients: a systematic review and meta-analysis of transcriptomic studies

BACKGROUND

Schizophrenia is a severe neuropsychiatric disorder characterized by altered perception, mood, and behavior that profoundly impacts patients and society despite its relatively low prevalence. Sex-based differences have been described in schizophrenia epidemiology, symptomatology and outcomes. Different studies explored the impact of schizophrenia in the brain transcriptome, however we lack a consensus transcriptomic profile that considers sex and differentiates specific cerebral regions.

METHODS

We performed a systematic review on bulk RNA-sequencing studies of post-mortem brain samples. Then, we fulfilled differential expression analysis on each study and summarized their results with regions-specific meta-analyses (prefrontal cortex and hippocampus) and a global all-studies meta-analysis. Finally, we used the consensus transcriptomic profiles to functionally characterize the impact of schizophrenia in males and females by protein-protein interaction networks, enriched biological processes and dysregulated transcription factors.

RESULTS

We discovered the sex-based dysregulation of 265 genes in the prefrontal cortex, 1.414 genes in the hippocampus and 66 genes in the all-studies meta-analyses. The functional characterization of these gene sets unveiled increased processes related to immune response functions in the prefrontal cortex in male and the hippocampus in female schizophrenia patients and the overexpression of genes related to neurotransmission and synapses in the prefrontal cortex of female schizophrenia patients. Considering a meta-analysis of all brain regions available, we encountered the relative overexpression of genes related to synaptic plasticity and transmission in females and the overexpression of genes involved in organizing genetic information and protein folding in male schizophrenia patients. The protein-protein interaction networks and transcription factors activity analyses supported these sex-based profiles.

CONCLUSIONS

Our results report multiple sex-based transcriptomic alterations in specific brain regions of schizophrenia patients, which provides new insight into the role of sex in schizophrenia. Moreover, we unveil a partial overlapping of inflammatory processes in the prefrontal cortex of males and the hippocampus of females.

Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus

Schizophrenia is a complex neuropsychiatric disorder with sexually dimorphic features, including differential symptomatology, drug responsiveness, and male incidence rate. Prior large-scale transcriptome analyses for sex differences in schizophrenia have focused on the prefrontal cortex. Analyzing BrainSeq Consortium data (caudate nucleus: n = 399, dorsolateral prefrontal cortex: n = 377, and hippocampus: n = 394), we identified 831 unique genes that exhibit sex differences across brain regions, enriched for immune-related pathways. We observed X-chromosome dosage reduction in the hippocampus of male individuals with schizophrenia. Our sex interaction model revealed 148 junctions dysregulated in a sex-specific manner in schizophrenia. Sex-specific schizophrenia analysis identified dozens of differentially expressed genes, notably enriched in immune-related pathways. Finally, our sex-interacting expression quantitative trait loci analysis revealed 704 unique genes, nine associated with schizophrenia risk. These findings emphasize the importance of sex-informed analysis of sexually dimorphic traits, inform personalized therapeutic strategies in schizophrenia, and highlight the need for increased female samples for schizophrenia analyses.

Fatty acid desaturase 1/2 (FADS1 and FADS2), fatty acid desaturase indices, and their relationships with metabolic syndrome in female adults with first-episode schizophrenia after antipsychotic medications

OBJECTIVE

Although antipsychotics constitute the best treatment for patients with schizophrenia, this treatment class carries a high risk of metabolic disarrangements thus developing metabolic syndrome (MetS). Altered fatty acid (FA) composition and desaturase indices have been associated with several metabolic diseases, including MetS. Herein, we determined fatty acid desaturase 1 (FADS1) and FADS2 gene expressions, serum delta-5 desaturase (D5D) and D6D indices in female adults with first-episode schizophrenia after olanzapine medication, as well as their relationship with the incidence of MetS.

METHODS

This study prospectively recruited 120 female patients with first-episode schizophrenia who completed 6-month olanzapine medication. Among these female patients, 31 patients developed MetS and 89 patients did not.

RESULTS

The mRNA expression levels of FADS1 and FADS2 in patients were analyzed according to the presence of MetS and evaluation times with results of two-way ANOVAs (FADS1: PMetS = 0.0006, Ptime = 0.004, Pinteraction = 0.010; FADS2: PMetS = 0.012, Ptime < 0.0001, Pinteraction = 0.001). The D5D and D6D indices in patients were analyzed according to the presence of MetS and evaluation times with results of two-way ANOVAs (D5D: PMetS = 0.002, Ptime = 0.009, Pinteraction = 0.014; D6D: PMetS = 0.011, Ptime = 0.006, Pinteraction = 0.0001). The SCD-16 and SCD-18 indices in patients were analyzed according to the presence of MetS and evaluation times (SCD-16: PMetS = 0.005, Ptime = 0.009, Pinteraction = 0.016; SCD-18: PMetS = 0.037, Ptime = 0.382, Pinteraction = 0.163). The following multiple comparisons test showed the MetS exhibited reduced FADS1 mRNA expression and D5D index, increased FADS2 mRNA expression and D6D index, concomitant with an enhanced SCD-16 index, compared to the non-MetS did not after 6-month olanzapine medication.

CONCLUSION

The study suggests changes of FADS1, FADS2 expressions, and fatty acid desaturase indices including D5D, D6D, and SCD-16 may be associated with the development of MetS in female adults with first-episode schizophrenia after olanzapine medication.

Sex differences in brain cell-type specific chromatin accessibility in schizophrenia

Our understanding of the sex-specific role of the non-coding genome in serious mental illness remains largely incomplete. To address this gap, we explored sex differences in 1,393 chromatin accessibility profiles, derived from neuronal and non-neuronal nuclei of two distinct cortical regions from 234 cases with serious mental illness and 235 controls. We identified sex-specific enhancer-promoter interactions and showed that they regulate genes involved in X-chromosome inactivation (XCI). Examining chromosomal conformation allowed us to identify sex-specific cis- and trans-regulatory domains (CRDs and TRDs). Co-localization of sex-specific TRDs with schizophrenia common risk variants pinpointed male-specific regulatory regions controlling a number of metabolic pathways. Additionally, enhancers from female-specific TRDs were found to regulate two genes known to escape XCI, (XIST and JPX), underlying the importance of TRDs in deciphering sex differences in schizophrenia. Overall, these findings provide extensive characterization of sex differences in the brain epigenome and disease-associated regulomes.

Exploring the Genetic Landscape of Mild Behavioral Impairment as an Early Marker of Cognitive Decline: An Updated Review Focusing on Alzheimer's Disease

The clinical features and pathophysiology of neuropsychiatric symptoms (NPSs) in dementia have been extensively studied. However, the genetic architecture and underlying neurobiological mechanisms of NPSs at preclinical stages of cognitive decline and Alzheimer's disease (AD) remain largely unknown. Mild behavioral impairment (MBI) represents an at-risk state for incident cognitive impairment and is defined by the emergence of persistent NPSs among non-demented individuals in later life. These NPSs include affective dysregulation, decreased motivation, impulse dyscontrol, abnormal perception and thought content, and social inappropriateness. Accumulating evidence has recently begun to shed more light on the genetic background of MBI, focusing on its potential association with genetic factors related to AD. The Apolipoprotein E (APOE) genotype and the MS4A locus have been associated with affective dysregulation, ZCWPW1 with social inappropriateness and psychosis, BIN1 and EPHA1 with psychosis, and NME8 with apathy. The association between MBI and polygenic risk scores (PRSs) in terms of AD dementia has been also explored. Potential implicated mechanisms include neuroinflammation, synaptic dysfunction, epigenetic modifications, oxidative stress responses, proteosomal impairment, and abnormal immune responses. In this review, we summarize and critically discuss the available evidence on the genetic background of MBI with an emphasis on AD, aiming to gain insights into the potential underlying neurobiological mechanisms, which till now remain largely unexplored. In addition, we propose future areas of research in this emerging field, with the aim to better understand the molecular pathophysiology of MBI and its genetic links with cognitive decline.

Exploring sex differences: insights into gene expression, neuroanatomy, neurochemistry, cognition, and pathology

Increased knowledge about sex differences is important for development of individualized treatments against many diseases as well as understanding behavioral and pathological differences. This review summarizes sex chromosome effects on gene expression, epigenetics, and hormones in relation to the brain. We explore neuroanatomy, neurochemistry, cognition, and brain pathology aiming to explain the current state of the art. While some domains exhibit strong differences, others reveal subtle differences whose overall significance warrants clarification. We hope that the current review increases awareness and serves as a basis for the planning of future studies that consider both sexes equally regarding similarities and differences.

Microglia-neuron interactions in prefrontal gray matter in schizophrenia: a postmortem ultrastructural morphometric study

This study addressed the question of whether the interaction between neurons and satellite microglia (SatMg) is abnormal in schizophrenia. SatMg-neuron communication at direct contacts between neuronal soma is essential for neuroplasticity as SatMg can regulate neuronal activity. A postmortem ultrastructural morphometric study was performed to investigate SatMg and adjacent neurons in layer 5 of the prefrontal cortex in 21 cases of schizophrenia and 20 healthy controls. Density of SatMg was significantly higher in the young schizophrenia group and in the group with illness duration ≤ 26 years as compared to controls. We found lower volume fraction (Vv) and the number (N) of mitochondria and higher Vv and N of lipofuscin granules and vacuoles in endoplasmic reticulum in SatMg in the schizophrenia compared to the control brain. These changes progressed with age and illness duration. A significantly higher soma area and Vv of vacuoles of endoplasmic reticulum were revealed in neurons in schizophrenia as compared to controls. Negative significant correlations between N of vacuoles in neurons and N of mitochondria in SatMg were found in the control group but not in the schizophrenia group. Area of vacuole in neurons was significantly positively correlated with Vv and area of mitochondria in SatMg in the control group and negatively in the schizophrenia group. Correlation coefficients between these parameters differed significantly between the groups. These results indicate disturbed SatMg-neuron interactions in the schizophrenia brain and suggest a key role of mitochondrial abnormalities in SatMg in these disturbances.

Maternal Immune Activation Induces Adolescent Cognitive Deficits Preceded by Developmental Perturbations in Cortical Reelin Signalling

Exposure to maternal immune activation (MIA) in utero significantly elevates the risk of developing schizophrenia and other neurodevelopmental disorders. To understand the biological mechanisms underlying the link between MIA and increased risk, preclinical animal models have focussed on specific signalling pathways in the brain that mediate symptoms associated with neurodevelopmental disorders such as cognitive dysfunction. Reelin signalling in multiple brain regions is involved in neuronal migration, synaptic plasticity and long-term potentiation, and has been implicated in cognitive deficits. However, how regulation of Reelin expression is affected by MIA across cortical development and associated cognitive functions remains largely unclear. Using a MIA rat model, here we demonstrate cognitive deficits in adolescent object-location memory in MIA offspring and reductions in Reln expression prenatally and in the adult prefrontal cortex. Further, developmental disturbances in gene/protein expression and DNA methylation of downstream signalling components occurred subsequent to MIA-induced Reelin dysregulation and prior to cognitive deficits. We propose that MIA-induced dysregulation of Reelin signalling contributes to the emergence of prefrontal cortex-mediated cognitive deficits through altered NMDA receptor function, resulting in inefficient long-term potentiation. Our data suggest a developmental window during which attenuation of Reelin signalling may provide a possible therapeutic target.

Meta-analysis of brain samples of individuals with schizophrenia detects down-regulation of multiple ATP synthase encoding genes in both females and males

Schizophrenia is a chronic and debilitating mental disorder, with unknown pathophysiology. Converging lines of evidence suggest that mitochondrial functioning may be compromised in schizophrenia. Postmortem brain samples of individuals with schizophrenia showed dysregulated expression levels of genes encoding enzyme complexes comprising the mitochondrial electron transport chain (ETC), including ATP synthase, the fifth ETC complex. However, there are inconsistencies regarding the direction of change, i.e., up- or down-regulation, and differences between female and male patients were hardly examined. We have performed a systematic meta-analysis of the expression of 16 ATP synthase encoding genes in postmortem brain samples of individuals with schizophrenia vs. healthy controls of three regions: Brodmann Area 10 (BA10), BA22/Superior Temporal Gyrus (STG) and the cerebellum. Eight independent datasets were integrated (overall 294brain samples, 145 of individuals with schizophrenia and 149 controls). The meta-analysis was applied to all individuals with schizophrenia vs. the controls, and also to female and male patients vs. age-matched controls, separately. A significant down-regulation of two ATP synthase encoding genes was detected in schizophrenia, ATP5A1 and ATP5H, and a trend towards down-regulation of five further ATP synthase genes. The down-regulation tendency was shown for both females and males with schizophrenia. Our findings support the hypothesis that schizophrenia is associated with reduced ATP synthesis via the oxidative phosphorylation system, which is caused by reduced cellular demand of ATP. Abnormal cellular energy metabolism can lead to alterations in neural function and brain circuitry, and thereby to the cognitive and behavioral aberrations characteristic of schizophrenia.

Molecular Abnormalities in BTBR Mice and Their Relevance to Schizophrenia and Autism Spectrum Disorders: An Overview of Transcriptomic and Proteomic Studies

Animal models of psychopathologies are of exceptional interest for neurobiologists because these models allow us to clarify molecular mechanisms underlying the pathologies. One such model is the inbred BTBR strain of mice, which is characterized by behavioral, neuroanatomical, and physiological hallmarks of schizophrenia (SCZ) and autism spectrum disorders (ASDs). Despite the active use of BTBR mice as a model object, the understanding of the molecular features of this strain that cause the observed behavioral phenotype remains insufficient. Here, we analyzed recently published data from independent transcriptomic and proteomic studies on hippocampal and corticostriatal samples from BTBR mice to search for the most consistent aberrations in gene or protein expression. Next, we compared reproducible molecular signatures of BTBR mice with data on postmortem samples from ASD and SCZ patients. Taken together, these data helped us to elucidate brain-region-specific molecular abnormalities in BTBR mice as well as their relevance to the anomalies seen in ASDs or SCZ in humans.

In-depth investigations of the molecular basis underlying sex differences among middle-aged and elderly schizophrenia populations

Sex can influence almost all aspects of schizophrenia. However, the molecular mechanisms underlying sex differences in schizophrenia remain poorly understood. In this project, the dataset GSE107638 containing neuronal RNA-seq data and age/sex information of individuals with or without schizophrenia were retrieved. Schizophrenia samples were divided into young male (M-1), young female (F-1), middle-aged and elderly male (M-2) and middle-aged and elderly female (F-2) groups. Next, green/yellow/turquoise modules related to the M-2 trait and turquoise module correlated with the F-2 trait were identified by weighted correlation network analysis (WGCNA) analysis (soft thresholding power: 13; min module size: 200). Crucial genes in the M-2 green, M-2 turquoise and F-2 turquoise modules were identified by WGCNA, gene significance/module membership, and protein-protein interaction (PPI) analysis. Moreover, 2067 and 934 differentially expressed genes (|log2 fold-change| ≥0.58 and P-value < 0.05) in M-2 and F-2 schizophrenia subgroups versus same-age and same-sex counterparts were identified, respectively. Additionally, 82 core genes in the M-2 turquoise module and 4 hub genes in the F-2 turquoise module were differentially expressed in M-2 and F-2 schizophrenia subgroups versus their counterparts, respectively. Among the 82 hub genes, 15 genes were found to be correlated with neuronal development by the Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Also, 2 potential PPI networks related to neuronal development were identified. Taken together, multiple potential hub genes and 2 potential neurobiological networks related to schizophrenia sex differences and disease progression were identified among middle-aged and elderly schizophrenia populations.

Sex Differences in Psychosis: Focus on Animal Models

Most psychiatric illnesses, such as schizophrenia, show profound sex differences in incidence, clinical presentation, course, and outcome. Fortunately, more recently the literature on sex differences and (to a lesser extent) effects of sex steroid hormones is expanding, and in this review we have focused on such studies in psychosis, both from a clinical/epidemiological and preclinical/animal model perspective. We begin by briefly describing the clinical evidence for sex differences in schizophrenia epidemiology, symptomatology, and pathophysiology. We then detail sex differences and sex hormone effects in behavioral animal models of psychosis, specifically psychotropic drug-induced locomotor hyperactivity and disruption of prepulse inhibition. We expand on the preclinical data to include developmental and genetic models of psychosis, such as the maternal immune activation model and neuregulin transgenic animals, respectively. Finally, we suggest several recommendations for future studies, in order to facilitate a better understanding of sex differences in the development of psychosis.

Sex Differences in the Human Brain Transcriptome of Cases With Schizophrenia

BACKGROUND

While schizophrenia differs between males and females in the age of onset, symptomatology, and disease course, the molecular mechanisms underlying these differences remain uncharacterized.

METHODS

To address questions about the sex-specific effects of schizophrenia, we performed a large-scale transcriptome analysis of RNA sequencing data from 437 controls and 341 cases from two distinct cohorts from the CommonMind Consortium.

RESULTS

Analysis across the cohorts identified a reproducible gene expression signature of schizophrenia that was highly concordant with previous work. Differential expression across sex was reproducible across cohorts and identified X- and Y-linked genes, as well as those involved in dosage compensation. Intriguingly, the sex expression signature was also enriched for genes involved in neurexin family protein binding and synaptic organization. Differential expression analysis testing a sex-by-diagnosis interaction effect did not identify any genome-wide signature after multiple testing corrections. Gene coexpression network analysis was performed to reduce dimensionality from thousands of genes to dozens of modules and elucidate interactions among genes. We found enrichment of coexpression modules for sex-by-diagnosis differential expression signatures, which were highly reproducible across the two cohorts and involved a number of diverse pathways, including neural nucleus development, neuron projection morphogenesis, and regulation of neural precursor cell proliferation.

CONCLUSIONS

Overall, our results indicate that the effect size of sex differences in schizophrenia gene expression signatures is small and underscore the challenge of identifying robust sex-by-diagnosis signatures, which will require future analyses in larger cohorts.

Genome-wide Gene-by-Sex Interaction Studies Identify Novel Nonsyndromic Orofacial Clefts Risk Locus

Risk loci identified through genome-wide association studies have explained about 25% of the phenotypic variations in nonsyndromic orofacial clefts (nsOFCs) on the liability scale. Despite the notable sex differences in the incidences of the different cleft types, investigation of loci for sex-specific effects has been understudied. To explore the sex-specific effects in genetic etiology of nsOFCs, we conducted a genome-wide gene × sex (GxSex) interaction study in a sub-Saharan African orofacial cleft cohort. The sample included 1,019 nonsyndromic orofacial cleft cases (814 cleft lip with or without cleft palate and 205 cleft palate only) and 2,159 controls recruited from 3 sites (Ethiopia, Ghana, and Nigeria). An additive logistic model was used to examine the joint effects of the genotype and GxSex interaction. Furthermore, we examined loci with suggestive significance (P < 1E-5) in the additive model for the effect of the GxSex interaction only. We identified a novel risk locus on chromosome 8p22 with genome-wide significant joint and GxSex interaction effects (rs2720555, p_2df = 1.16E-08, p_GxSex = 1.49E-09, odds ratio [OR] = 0.44, 95% CI = 0.34 to 0.57). For males, the risk of cleft lip with or without cleft palate at this locus decreases with additional copies of the minor allele (p < 0.0001, OR = 0.60, 95% CI = 0.48 to 0.74), but the effect is reversed for females (p = 0.0004, OR = 1.36, 95% CI = 1.15 to 1.60). We replicated the female-specific effect of this locus in an independent cohort (p = 0.037, OR = 1.30, 95% CI = 1.02 to 1.65), but no significant effect was found for the males (p = 0.29, OR = 0.86, 95% CI = 0.65 to 1.14). This locus is in topologically associating domain with craniofacially expressed and enriched genes during embryonic development. Rare coding mutations of some of these genes were identified in nsOFC cohorts through whole exome sequencing analysis. Our study is additional proof that genome-wide GxSex interaction analysis provides an opportunity for novel findings of loci and genes that contribute to the risk of nsOFCs.

Changes of Hypocretin (Orexin) System in Schizophrenia: From Plasma to Brain

Hypocretin (also called orexin) regulates various functions, such as sleep-wake rhythms, attention, cognition, and energy balance, which show significant changes in schizophrenia (SCZ). We aimed to identify alterations in the hypocretin system in SCZ patients. We measured plasma hypocretin-1 levels in SCZ patients and healthy controls and found significantly decreased plasma hypocretin-1 levels in SCZ patients, which was mainly due to a significant decrease in female SCZ patients compared with female controls. In addition, we measured postmortem hypothalamic hypocretin-1-immunoreactivity (ir), ventricular cerebrospinal fluid (CSF) hypocretin-1 levels, and hypocretin receptor (Hcrt-R) mRNA expression in the superior frontal gyrus (SFG) in SCZ patients and controls We observed a significant decrease in the amount of hypothalamic hypocretin-1 ir in SCZ patients, which was due to decreased amounts in female but not male patients. Moreover, Hcrt-R2 mRNA in the SFG was decreased in female SCZ patients compared with female controls, while male SCZ patients showed a trend of increased Hcrt-R1 mRNA and Hcrt-R2 mRNA expression compared with male controls. We conclude that central hypocretin neurotransmission is decreased in SCZ patients, especially female patients, and this is reflected in the plasma.

Gene expression meta-analysis reveals the down-regulation of three GABA receptor subunits in the superior temporal gyrus of patients with schizophrenia

One of the main theories accounting for the underlying pathophysiology of schizophrenia posits alterations in GABAergic neurotransmission. While previous gene expression studies of postmortem brain samples typically report the down-regulation of GABA related genes in schizophrenia, the results are often inconsistent and not uniform across studies. We performed a systematic gene expression analysis of 22 GABA related genes in postmortem superior temporal gyrus (STG) samples of 19 elderly subjects with schizophrenia (mean age: 77) and 14 matched controls from the Icahn school of Medicine at Mount Sinai (MSSM) cohort. To test the validity and robustness of the resulting differentially expressed genes, we then conducted a meta-analysis of the MSSM and an independent dataset from the Stanley Consortium of 14 STG samples of relatively young subjects with schizophrenia (mean age: 44) and 15 matched controls. For the first time, the findings showed the down-regulation of three GABA-receptor subunits of type A, GABRA1, GABRA2 and GABRB3, in the STG samples of subjects with schizophrenia, in both the elderly and the relatively young patients. These findings, as well as previous results, lend weight to the notion of a common upstream pathology that alters GABAergic neurotransmission in schizophrenia. GABRA1, GABRA2 and GABRB3 down-regulation may contribute to the pathophysiology and clinical manifestations of schizophrenia through altered oscillation synchronization in the STG.

Molecular windows into the human brain for psychiatric disorders

Delineating the pathophysiology of psychiatric disorders has been extremely challenging but technological advances in recent decades have facilitated a deeper interrogation of molecular processes in the human brain. Initial candidate gene expression studies of the postmortem brain have evolved into genome wide profiling of the transcriptome and the epigenome, a critical regulator of gene expression. Here, we review the potential and challenges of direct molecular characterization of the postmortem human brain, and provide a brief overview of recent transcriptional and epigenetic studies with respect to neuropsychiatric disorders. Such information can now be leveraged and integrated with the growing number of genome-wide association databases to provide a functional context of trait-associated genetic variants linked to psychiatric illnesses and related phenotypes. While it is clear that the field is still developing and challenges remain to be surmounted, these recent advances nevertheless hold tremendous promise for delineating the neurobiological underpinnings of mental diseases and accelerating the development of novel medication strategies.

A Novel Joint Gene Set Analysis Framework Improves Identification of Enriched Pathways in Cross Disease Transcriptomic Analysis

Motivation: Gene set enrichment analysis is a widely accepted expression analysis tool which aims at detecting coordinated expression change within a pre-defined gene sets rather than individual genes. The benefit of gene set analysis over individual differentially expressed (DE) gene analysis includes more reproducible and interpretable results and detecting small but consistent change among gene set which could not be detected by DE gene analysis. There have been many successful gene set analysis applications in human diseases. However, when the sample size of a disease study is small and no other public data sets of the same disease are available, it will lead to lack of power to detect pathways of importance to the disease. Results: We have developed a novel joint gene set analysis statistical framework which aims at improving the power of identifying enriched gene sets through integrating multiple similar disease data sets. Through comprehensive simulation studies, we demonstrated that our proposed frameworks obtained much better AUC scores than single data set analysis and another meta-analysis method in identification of enriched pathways. When applied to two real data sets, the proposed framework could retain the enriched gene sets identified by single data set analysis and exclusively obtained up to 200% more disease-related gene sets demonstrating the improved identification power through information shared between similar diseases. We expect that the proposed framework would enable researchers to better explore public data sets when the sample size of their study is limited.

Mental health profile and its relation with parental alcohol use problems and/or the experience of abuse in a sample of Moroccan high school students: an explorative study

BACKGROUND

Studies on mental health are scarce from Arab countries, especially studies focusing on adolescents. In addition to the neurobiological and physiological changes that occur during adolescent development, psychological, societal and cultural influences have strong effects on adolescents' behavior and on their somatic and mental health. The present study aimed (1) to describe the mental health profile, operationalized as psychological distress, of a sample of Moroccan adolescents, and (2) to investigate how specific psychosocial factors (parental alcohol use problems and the experience of physical and/or psychological abuse) may affect adolescents' mental health.

METHODS

The sample included 375 adolescents from conveniently selected classes of four high schools in the city of Tetouan in Morocco. The participants responded to an anonymous survey containing, beside other inventories, the Brief Symptom Inventory (BSI) and identified those reporting parental alcohol use problems and/or the previous experience of abuse. The sample characteristics were defined using descriptive statistics. The effects of the defined psychosocial factors were identified using the Kruskal-Wallis test, followed by the post hoc Fisher's least significant difference test.

RESULTS

The most common problems found in high school students from an urban region of Morocco were memory problems, concentration difficulties, restlessness, fear, nervosity and feelings of inadequacy during interpersonal interactions. The female students reported significantly higher psychological distress levels when compared to the male students (p < 0.001). The adolescents reporting parental alcohol use problems and the experience of physical/psychological abuse showed significantly higher levels of psychological distress (p = 0.02), especially symptoms of somatization (p < 0.001), hostility (p = 0.005) and anxiety (p = 0.01), than those not reporting any of these psychosocial factors.

CONCLUSION

The mental health profile of female adolescents from an urban area of Morocco is worse than that of their male fellow students. Adolescents reporting parental alcohol use problems and/or the experience of physical/psychological abuse need synchronized support from social- and healthcare services.

Association study of the excitatory amino acid transporter 2 (EAAT2) and glycine transporter 1 (GlyT1) gene polymorphism with schizophrenia in a Polish population

Background: Excitatory amino acid transporter 2 encoded by SLC1A2 is responsible for approximately 90% of glutamate uptake. Glycine transporter 1, encoded by SLC6A9, is responsible for maintaining a low concentration of the N-methyl-D-aspartate receptor (NMDAR) co-agonist - glycine in the synaptic cleft, suggesting its participation in the development of the NMDARs hypofunction described in schizophrenia. Aim: The aim of this study was to evaluate whether the functional polymorphism-181 A/C (rs4354668) of the SLC1A2 and the rs2486001 (IVS3+411 G/A) in the SLC6A9 are involved in schizophrenia development and its clinical picture in the Polish population. Methods: The study group consisted of 393 unrelated Caucasian patients (157 [39.9%] females and 236 [60.1%] males; mean age 41±12) diagnosed with schizophrenia according to the DSM-5, and 462 healthy controls. The results of the Positive and Negative Syndrome Scale (PANSS) were presented in the five-dimensional model. Polymorphisms of SLC1A2 and SLC6A9 were genotyped with the use of PCR-RFLP assay. Results: There were no statistically significant differences in the frequency of genotypes and alleles between the patients and controls for SLC1A2 and SLC6A9 polymorphisms in either the entire sample or after stratification according to gender. In the haplotype analysis, men with CA haplotype had more than 1.5 higher risk to develop schizophrenia than women (OR=1.63 [95% CI=1.17-2.27, p<0.05]). The influence of gender, genotypes of both analyzed polymorphisms and gender x genotype interactions on individual dimensions of the PANSS scale has not been observed. Also, there was no association of either polymorphism with suicide attempts. Conclusion: The results of the present study did not indicate an association of polymorphism-181 A/C (rs4354668) in SLC1A2 and rs2486001 in SLC6A9 with onset of schizophrenia and its psychopathology in a Polish population.

A novel joint analysis framework improves identification of differentially expressed genes in cross disease transcriptomic analysis

Motivation

Detecting differentially expressed (DE) genes between disease and normal control group is one of the most common analyses in genome-wide transcriptomic data. Since most studies don’t have a lot of samples, researchers have used meta-analysis to group different datasets for the same disease. Even then, in many cases the statistical power is still not enough. Taking into account the fact that many diseases share the same disease genes, it is desirable to design a statistical framework that can identify diseases’ common and specific DE genes simultaneously to improve the identification power.

Results

We developed a novel empirical Bayes based mixture model to identify DE genes in specific study by leveraging the shared information across multiple different disease expression data sets. The effectiveness of joint analysis was demonstrated through comprehensive simulation studies and two real data applications. The simulation results showed that our method consistently outperformed single data set analysis and two other meta-analysis methods in identification power. In real data analysis, overall our method demonstrated better identification power in detecting DE genes and prioritized more disease related genes and disease related pathways than single data set analysis. Over 150% more disease related genes are identified by our method in application to Huntington’s disease. We expect that our method would provide researchers a new way of utilizing available data sets from different diseases when sample size of the focused disease is limited.

Electronic supplementary material

The online version of this article (10.1186/s13040-018-0163-y) contains supplementary material, which is available to authorized users.

A disease similarity matrix based on the uniqueness of shared genes

Background

Complex diseases involve many genes, and these genes are often associated with several different illnesses. Disease similarity measurement can be based on shared genotype or phenotype. Quantifying relationships between genes can reveal previously unknown connections and form a reference base for therapy development and drug repurposing.

Methods

Here we introduce a method to measure disease similarity that incorporates the uniqueness of shared genes. For each disease pair, we calculated the uniqueness score and constructed disease similarity matrices using OMIM and Disease Ontology annotation.

Results

Using the Disease Ontology-based matrix, we identified several interesting connections between cancer and other disease and conditions such as malaria, along with studies to support our findings. We also found several high scoring pairwise relationships for which there was little or no literature support, highlighting potentially interesting connections warranting additional study.

Conclusions

We developed a co-occurrence matrix based on gene uniqueness to examine the relationships between diseases from OMIM and DORIF data. Our similarity matrix can be used to identify potential disease relationships and to motivate further studies investigating the causal mechanisms in diseases.

Toxoplasma gondii infection in schizophrenia and associated clinical features

The belief that latent toxoplasmosis is asymptomatic has been questioned, in particular due to the repeated highlighted link between the Toxoplasma gondii infection and an increased incidence of schizophrenia. However, to understand this relationship, the effect of infection with Toxoplasma gondii on the severity of schizophrenia has been poorly studied. Our work focused on comparing the prevalence of Toxoplasma infection between schizophrenic patients and healthy controls, as well as comparing the clinical features and the demographic characteristics between Toxoplasma-seronegative and Toxoplasma-seropositive patients with schizophrenia. The rate of IgG antibody in the schizophrenia patients was 74.8% compared 53.8% in controls. Patients with schizophrenia had a significantly higher mean of serum IgG antibodies to T. gondii compared to controls. The seropositive male patients had a higher age of disease onset, a higher BPRS score, a greater negative PANSS score and a lower GAF score than the seronegative male patients. These results suggest a higher severity of clinical symptoms in the male patients with schizophrenia. This study provides further evidence to the hypothesis that exposure to Toxoplasma may be a risk factor for schizophrenia. Moreover, toxoplasmosis in men with schizophrenia may lead to more severe negative and cognitive symptoms and a less favorable course of schizophrenia.

Classification of Benign and Malignant Thyroid Nodules Using a Combined Clinical Information and Gene Expression Signatures

BACKGROUND

A key challenge in thyroid carcinoma is preoperatively diagnosing malignant thyroid nodules. A novel diagnostic test that measures the expression of a 3-gene signature (DPP4, SCG5 and CA12) has demonstrated promise in thyroid carcinoma assessment. However, more reliable prediction methods combining clinical features with genomic signatures with high accuracy, good stability and low cost are needed.

METHODOLOGY/PRINCIPAL FINDINGS

25 clinical information were recorded in 771 patients. Feature selection and validation were conducted using random forest. Thyroid samples and clinical data were obtained from 142 patients at two different hospitals, and expression of the 3-gene signature was measured using quantitative PCR. The predictive abilities of three models (based on the selected clinical variables, the gene expression profile, and integrated gene expression and clinical information) were compared. Seven clinical characteristics were selected based on a training set (539 patients) and tested in three test sets, yielding predictive accuracies of 82.3% (n = 232), 81.4% (n = 70), and 81.9% (n = 72). The predictive sensitivity, specificity, and accuracy were 72.3%, 80.5% and 76.8% for the model based on the gene expression signature, 66.2%, 81.8% and 74.6% for the model based on the clinical data, and 83.1%, 84.4% and 83.8% for the combined model in a 10-fold cross-validation (n = 142).

CONCLUSIONS

These findings reveal that the integrated model, which combines clinical data with the 3-gene signature, is superior to models based on gene expression or clinical data alone. The integrated model appears to be a reliable tool for the preoperative diagnosis of thyroid tumors.

Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans

The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analyzed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes), followed by the heart (375 genes), kidney (224 genes), colon (218 genes), and thyroid (163 genes). More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs, and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.