Common variants contribute to intrinsic human brain functional networks

The human brain forms functional networks of correlated activity, which have been linked with both cognitive and clinical outcomes. However, the genetic variants affecting brain function are largely unknown. Here, we used resting-state functional magnetic resonance images from 47,276 individuals to discover and validate common genetic variants influencing intrinsic brain activity. We identified 45 new genetic regions associated with brain functional signatures (P < 2.8 × 10^-11), including associations to the central executive, default mode, and salience networks involved in the triple-network model of psychopathology. A number of brain activity-associated loci colocalized with brain disorders (e.g., the APOE ε4 locus with Alzheimer's disease). Variation in brain function was genetically correlated with brain disorders, such as major depressive disorder and schizophrenia. Together, our study provides a step forward in understanding the genetic architecture of brain functional networks and their genetic links to brain-related complex traits and disorders.

Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae

Two years into the SARS-CoV-2 pandemic, the post-acute sequelae of infection are compounding the global health crisis. Often debilitating, these sequelae are clinically heterogeneous and of unknown molecular etiology. Here, a transcriptome-wide investigation of this new condition was performed in a large cohort of acutely infected patients followed clinically into the post-acute period. Gene expression signatures of post-acute sequelae were already present in whole blood during the acute phase of infection, with both innate and adaptive immune cells involved. Plasma cells stood out as driving at least two distinct clusters of sequelae, one largely dependent on circulating antibodies against the SARS-CoV-2 spike protein and the other antibody-independent. Altogether, multiple etiologies of post-acute sequelae were found concomitant with SARS-CoV-2 infection, directly linking the emergence of these sequelae with the host response to the virus.

Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children

Multisystem inflammatory syndrome in children (MIS-C) presents with fever, inflammation and pathology of multiple organs in individuals under 21 years of age in the weeks following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although an autoimmune pathogenesis has been proposed, the genes, pathways and cell types causal to this new disease remain unknown. Here we perform RNA sequencing of blood from patients with MIS-C and controls to find disease-associated genes clustered in a co-expression module annotated to CD56dimCD57+ natural killer (NK) cells and exhausted CD8+ T cells. A similar transcriptome signature is replicated in an independent cohort of Kawasaki disease (KD), the related condition after which MIS-C was initially named. Probing a probabilistic causal network previously constructed from over 1,000 blood transcriptomes both validates the structure of this module and reveals nine key regulators, including TBX21, a central coordinator of exhausted CD8+ T cell differentiation. Together, this unbiased, transcriptome-wide survey implicates downregulation of NK cells and cytotoxic T cell exhaustion in the pathogenesis of MIS-C.

Common genetic variation influencing human white matter microstructure

Brain regions communicate with each other through tracts of myelinated axons, commonly referred to as white matter. We identified common genetic variants influencing white matter microstructure using diffusion magnetic resonance imaging of 43,802 individuals. Genome-wide association analysis identified 109 associated loci, 30 of which were detected by tract-specific functional principal components analysis. A number of loci colocalized with brain diseases, such as glioma and stroke. Genetic correlations were observed between white matter microstructure and 57 complex traits and diseases. Common variants associated with white matter microstructure altered the function of regulatory elements in glial cells, particularly oligodendrocytes. This large-scale tract-specific study advances the understanding of the genetic architecture of white matter and its genetic links to a wide spectrum of clinical outcomes.

scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks

Understanding cell-type-specific gene regulatory mechanisms from genetic variants to diseases remains challenging. To address this, we developed a computational pipeline, scGRNom (single-cell Gene Regulatory Network prediction from multi-omics), to predict cell-type disease genes and regulatory networks including transcription factors and regulatory elements. With applications to schizophrenia and Alzheimer's disease, we predicted disease genes and regulatory networks for excitatory and inhibitory neurons, microglia, and oligodendrocytes. Further enrichment analyses revealed cross-disease and disease-specific functions and pathways at the cell-type level. Our machine learning analysis also found that cell-type disease genes improved clinical phenotype predictions. scGRNom is a general-purpose tool available at https://github.com/daifengwanglab/scGRNom .

The effects of the CACNA1C rs1006737 A/G on affective startle modulation in healthy males

Background:

The CACNA1C rs1006737 risk A allele has been associated with affective psychoses and functional studies indicate that it is associated with increased hippocampal/amygdala activity during emotional face-processing. Here we studied the impact of the risk A allele on affective startle modulation.

Methods:

Hundred and ninety-four healthy males stratified for their CACNA1C rs1006737 genotype (GG:111, GA:67, AA:16) were presented with 18 pleasant, 18 unpleasant and 18 neutral pictures with acoustic probes (104 dB) occurring during 12 pictures in each affective category. Baseline startle was assessed during blank screens. State mood was self-rated on arrival, pre- and post-test and the emotional valence and arousal of affective pictures at post-test.

Results:

Relative to the other genotypes, risk A allele homozygotes presented with higher anxiety/negative affect at pre-test, reduced and exaggerated physiological responses to the pleasant and negative pictures respectively, negative affect with reduced arousal at post-test and rated the affective pictures as less arousing and inconsistently to their physiological responses (all P < 0.05). Sustained contextual negative mood predicted reduced baseline and affective startle reactivity in the AA group.

Conclusions:

Healthy homozygous males for the risk A allele appear to have marked contextual sensitivity, affective reactivity akin to anxiety and depression and inefficient emotional appraisal. Our findings provide phenotypic detail of the CACNA1C AA genotype in non-symptomatic individuals, which suggest primary effects in emotional circuitry, consistent with previously documented alterations in hippocampal/amygdala processing.

A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons

BACKGROUND

Midbrain dopaminergic neurons (MDN) represent 0.0005% of the brain's neuronal population and mediate cognition, food intake, and metabolism. MDN are also posited to underlay the neurobiological dysfunction of schizophrenia (SCZ), a severe neuropsychiatric disorder that is characterized by psychosis as well as multifactorial medical co-morbidities, including metabolic disease, contributing to markedly increased morbidity and mortality. Paradoxically, however, the genetic risk sequences of psychosis and traits associated with metabolic disease, such as body mass, show very limited overlap.

METHODS

We investigated the genomic interaction of SCZ with medical conditions and traits, including body mass index (BMI), by exploring the MDN's "spatial genome," including chromosomal contact landscapes as a critical layer of cell type-specific epigenomic regulation. Low-input Hi-C protocols were applied to 5-10 × 103 dopaminergic and other cell-specific nuclei collected by fluorescence-activated nuclei sorting from the adult human midbrain.

RESULTS

The Hi-C-reconstructed MDN spatial genome revealed 11 "Euclidean hot spots" of clustered chromatin domains harboring risk sequences for SCZ and elevated BMI. Inter- and intra-chromosomal contacts interconnecting SCZ and BMI risk sequences showed massive enrichment for brain-specific expression quantitative trait loci (eQTL), with gene ontologies, regulatory motifs and proteomic interactions related to adipogenesis and lipid regulation, dopaminergic neurogenesis and neuronal connectivity, and reward- and addiction-related pathways.

CONCLUSIONS

We uncovered shared nuclear topographies of cognitive and metabolic risk variants. More broadly, our PsychENCODE sponsored Hi-C study offers a novel genomic approach for the study of psychiatric and medical co-morbidities constrained by limited overlap of their respective genetic risk architectures on the linear genome.

[The relationship of internet addiction with anxiety and depressive symptomatology]

Internet stimulates the user's senses causing a variety of subjective experiences and sensations, even though it has no inherent addictive quality. These experiences could be positive, as the improvement of education, or adverse, as the development of internet addiction. There are many people who prefer to invest their time and energy in the virtual world of the internet. They choose to withdraw their emotional investments from face to face communication, while in some cases the internet connection signifies the user's disconnection from the real life, as the person is isolated from the surrounding and lives in a virtual environment. Under these conditions the excessive use of internet may lead to addiction. The purpose of the present study was to investigate the relationship between internet addiction and anxiety and depressive symptomatology of the user. Participants were 203 internet users aged between 17 and 58 years (Mean=26.03, SD=7.92) who approached the Department For Problematic Use Of Internet, Addiction Unit "18ANO" in Psychiatric Hospital Of Attica to receive specialized help for their pathological internet use. Internet Addiction Test (IAT) was used for the assessment of internet addiction and Symptom Checklist- 90-R (SCL-90-R) was administered for the evaluation of anxiety and depressive symptomatology. The analysis of the survey data showed that gender difference is not observed as to the intensity internet dependence. Younger users are more likely to develop addictive behaviour (in relation to internet use). At this point it should be noted that although positive, this association does not present to be statistically significant. Finally, regarding the relationship between psychopathology and internet addiction, anxiety symptomatology, which was moderately correlated with the overall score at IAT, was found to predict in regression analysis the internet addiction. There was no statistically significant association between internet addiction and depressive symptomatology, with women however, who presented with depressive symptoms to appear more vulnerable than men (who requested therapy from the department). Exploration of the effects of sex and age on internet addiction is expected contribute to the design of the appropriate preventive and therapeutic programs, whereas the study of the relationship between internet addiction and other psychiatric disorders would contribute the understanding of the mechanisms underpinning the development and onset of the addiction.

GWAS meta-analysis reveals novel loci and genetic correlates for general cognitive function: a report from the COGENT consortium

This corrects the article DOI: 10.1038/mp.2016.244.

Winter birth, urbanicity and immigrant status predict psychometric schizotypy dimensions in adolescents

BACKGROUND

Urbanicity, immigration and winter-birth are stable epidemiological risk factors for schizophrenia, but their relationship to schizotypy is unknown. This is a first examination of the association of these epidemiological risk factors with positive schizotypy, in nonclinical adolescents, controlling for a range of potential and known confounders.

METHODS

We collected socio-demographics, life-style, family and school circumstances, positive schizotypy dimensions and other personality traits from 445 high school pupils (192 males, 158 immigrants) from 9 municipalities in Athens and Heraklion, Greece, which covered a range of host population and migrant densities. Using multivariate hierarchical linear regressions models, we estimated the association of schizotypy dimensions with: (1) demographics of a priori interest (winter-birth, immigrant status, urban characteristics), including family financial and mental health status; (2) factors resulting from principal component analysis (PCA) of the demographic and personal data; (3) factors resulting from PCA of the personality questionnaires.

RESULTS

Adolescent women scored higher on schizotypy than men. High anxiety/neuroticism was the most consistent and significant predictor of all schizotypy dimensions in both sexes. In the fully adjusted models, urbanicity predicted magical thinking and unusual experiences in women, while winter-birth and immigration predicted paranoid ideation and unusual experiences respectively in men.

CONCLUSIONS

These results support the continuum hypothesis and offer potential insights in the nature of risk conferred by winter-birth, urbanicity and immigration and the nature of important sex differences. Controlling for a wide range of potential confounding factors increases the robustness of these results and confidence that these were not spurious associations.

GWAS meta-analysis reveals novel loci and genetic correlates for general cognitive function: a report from the COGENT consortium

The complex nature of human cognition has resulted in cognitive genomics lagging behind many other fields in terms of gene discovery using genome-wide association study (GWAS) methods. In an attempt to overcome these barriers, the current study utilized GWAS meta-analysis to examine the association of common genetic variation (~8M single-nucleotide polymorphisms (SNP) with minor allele frequency ⩾1%) to general cognitive function in a sample of 35 298 healthy individuals of European ancestry across 24 cohorts in the Cognitive Genomics Consortium (COGENT). In addition, we utilized individual SNP lookups and polygenic score analyses to identify genetic overlap with other relevant neurobehavioral phenotypes. Our primary GWAS meta-analysis identified two novel SNP loci (top SNPs: rs76114856 in the CENPO gene on chromosome 2 and rs6669072 near LOC105378853 on chromosome 1) associated with cognitive performance at the genome-wide significance level (P<5 × 10^-8). Gene-based analysis identified an additional three Bonferroni-corrected significant loci at chromosomes 17q21.31, 17p13.1 and 1p13.3. Altogether, common variation across the genome resulted in a conservatively estimated SNP heritability of 21.5% (s.e.=0.01%) for general cognitive function. Integration with prior GWAS of cognitive performance and educational attainment yielded several additional significant loci. Finally, we found robust polygenic correlations between cognitive performance and educational attainment, several psychiatric disorders, birth length/weight and smoking behavior, as well as a novel genetic association to the personality trait of openness. These data provide new insight into the genetics of neurocognitive function with relevance to understanding the pathophysiology of neuropsychiatric illness.

Evidence for genetic heterogeneity between clinical subtypes of bipolar disorder

We performed a genome-wide association study of 6447 bipolar disorder (BD) cases and 12 639 controls from the International Cohort Collection for Bipolar Disorder (ICCBD). Meta-analysis was performed with prior results from the Psychiatric Genomics Consortium Bipolar Disorder Working Group for a combined sample of 13 902 cases and 19 279 controls. We identified eight genome-wide significant, associated regions, including a novel associated region on chromosome 10 (rs10884920; P=3.28 × 10-8) that includes the brain-enriched cytoskeleton protein adducin 3 (ADD3), a non-coding RNA, and a neuropeptide-specific aminopeptidase P (XPNPEP1). Our large sample size allowed us to test the heritability and genetic correlation of BD subtypes and investigate their genetic overlap with schizophrenia and major depressive disorder. We found a significant difference in heritability of the two most common forms of BD (BD I SNP-h2=0.35; BD II SNP-h2=0.25; P=0.02). The genetic correlation between BD I and BD II was 0.78, whereas the genetic correlation was 0.97 when BD cohorts containing both types were compared. In addition, we demonstrated a significantly greater load of polygenic risk alleles for schizophrenia and BD in patients with BD I compared with patients with BD II, and a greater load of schizophrenia risk alleles in patients with the bipolar type of schizoaffective disorder compared with patients with either BD I or BD II. These results point to a partial difference in the genetic architecture of BD subtypes as currently defined.

Genome-wide autozygosity is associated with lower general cognitive ability

Inbreeding depression refers to lower fitness among offspring of genetic relatives. This reduced fitness is caused by the inheritance of two identical chromosomal segments (autozygosity) across the genome, which may expose the effects of (partially) recessive deleterious mutations. Even among outbred populations, autozygosity can occur to varying degrees due to cryptic relatedness between parents. Using dense genome-wide single-nucleotide polymorphism (SNP) data, we examined the degree to which autozygosity associated with measured cognitive ability in an unselected sample of 4854 participants of European ancestry. We used runs of homozygosity-multiple homozygous SNPs in a row-to estimate autozygous tracts across the genome. We found that increased levels of autozygosity predicted lower general cognitive ability, and estimate a drop of 0.6 s.d. among the offspring of first cousins (P=0.003-0.02 depending on the model). This effect came predominantly from long and rare autozygous tracts, which theory predicts as more likely to be deleterious than short and common tracts. Association mapping of autozygous tracts did not reveal any specific regions that were predictive beyond chance after correcting for multiple testing genome wide. The observed effect size is consistent with studies of cognitive decline among offspring of known consanguineous relationships. These findings suggest a role for multiple recessive or partially recessive alleles in general cognitive ability, and that alleles decreasing general cognitive ability have been selected against over evolutionary time.

Glutamate transporter splice variant expression in an enriched pyramidal cell population in schizophrenia

Dysregulation of the glutamate transporters EAAT1 and EAAT2 and their isoforms have been implicated in schizophrenia. EAAT1 and EAAT2 expression has been studied in different brain regions but the prevalence of astrocytic glutamate transporter expression masks the more subtle changes in excitatory amino acid transporters (EAATs) isoforms in neurons in the cortex. Using laser capture microdissection, pyramidal neurons were cut from the anterior cingulate cortex of postmortem schizophrenia (n = 20) and control (n = 20) subjects. The messenger RNA (mRNA) levels of EAAT1, EAAT2 and the splice variants EAAT1 exon9skipping, EAAT2 exon9skipping and EAAT2b were analyzed by real time PCR (RT-PCR) in an enriched population of neurons. Region-level expression of these transcripts was measured in postmortem schizophrenia (n = 25) and controls (n = 25). The relationship between selected EAAT polymorphisms and EAAT splice variant expression was also explored. Anterior cingulate cortex pyramidal cell expression of EAAT2b mRNA was increased (P < 0.001; 67%) in schizophrenia subjects compared with controls. There was no significant change in other EAAT variants. EAAT2 exon9skipping mRNA was increased (P < 0.05; 38%) at region level in the anterior cingulate cortex with no significant change in other EAAT variants at region level. EAAT2 single-nucleotide polymorphisms were significantly associated with changes in EAAT2 isoform expression. Haloperidol decanoate-treated animals, acting as controls for possible antipsychotic effects, did not have significantly altered neuronal EAAT2b mRNA levels. The novel finding that EAAT2b levels are increased in populations of anterior cingulate cortex pyramidal cells further demonstrates a role for neuronal glutamate transporter splice variant expression in schizophrenia.

Integration of gene expression and GWAS results supports involvement of calcium signaling in Schizophrenia

The number of Genome Wide Association Studies (GWAS) of schizophrenia is rapidly growing. However, the small effect of individual genes limits the number of reliably implicated genes, which are too few and too diverse to perform reliable pathway analysis; hence the biological roles of the genes implicated in schizophrenia are unclear. To overcome these limitations we combine GWAS with genome-wide expression data from human post-mortem brain samples of schizophrenia patients and controls, taking these steps: 1) Identify 36 GWAS-based genes which are expressed in our dataset. 2) Find a cluster of 19 genes with highly correlated expression. We show that this correlation pattern is robust and statistically significant. 3) GO-enrichment analysis of these 19 genes reveals significant enrichment of ion channels and calcium-related processes. This finding (based on analyzing a small number of coherently expressed genes) is validated and enhanced in two ways: First, the emergence of calcium channels and calcium signaling is corroborated by identifying proteins that interact with those encoded by the cluster of 19. Second, extend the 19 cluster genes into 1028 genes, whose expression is highly correlated with the cluster's average profile. When GO-enrichment analysis is performed on this extended set, many schizophrenia related pathways appear, with calcium-related processes enriched with high statistical significance. Our results give further, expression-based validation to GWAS results, support a central role of calcium-signaling in the pathogenesis of schizophrenia, and point to additional pathways potentially related to the disease.

Sub-optimal parenting is associated with schizotypic and anxiety personality traits in adulthood

Part of the variation in personality characteristics has been attributed to the child-parent interaction and sub-optimal parenting has been associated with psychiatric morbidity. In the present study, an extensive battery of personality scales (Trait Anxiety Inventory, Behavioural Inhibition/Activation System questionnaire, Eysenck Personality Questionnaire-Revised, Temperament and Character Inventory, Schizotypal Traits Questionnaire, Toronto Alexithymia Scale) and the Parental Bonding Instrument (PBI) were administered in 324 adult healthy males to elucidate the effects of parenting on personality configuration. Personality variables were analysed using Principal Component Analysis (PCA) and the factors "Schizotypy", "Anxiety", "Behavioural activation", "Novelty seeking" and "Reward dependence" were extracted. Associations between personality factors with PBI "care" and "overprotection" scores were examined with regression analyses. Subjects were divided into "parental style" groups and personality factors were subjected to categorical analyses. "Schizotypy" and "Anxiety" were significantly predicted by high maternal overprotection and low paternal care. In addition, the Affectionless control group (low care/high overprotection) had higher "Schizotypy" and "Anxiety" compared with the Optimal Parenting group (high care/low overprotection). These results further validate sub-optimal parenting as an important environmental exposure and extend our understanding on the mechanisms by which it increases risk for psychiatric morbidity.

Azoles and antidepressants: a mini-review of the tolerability of co-administration

Depression is a common condition in chronically ill immunosuppressed patients on long-term antifungal therapy with azoles. As both azoles and more recent antifungals are metabolised by the P450 enzymatic system in the liver, here we review the potential of clinically meaningful interactions between antidepressants and azoles. Selective serotonin reuptake inhibitors are safer compared to tricycle antidepressants when co-administered with azoles. More pharmacovigilance is needed.

Prepulse inhibition of the startle reflex depends on the catechol O-methyltransferase Val158Met gene polymorphism

BACKGROUND

Recent evidence suggests that dopamine (DA) agonist-induced disruption of prepulse inhibition (PPI) depends on basal PPI values, in a manner that suggests an inverted U-shaped relationship between PPI and prefrontal DA levels. This is the first study to examine possible genetic determinants of PPI and the catechol O-methyltransferase (COMT) Val158Met polymorphism, the main catabolic pathway of released DA in the prefrontal cortex (PFC).

METHOD

PPI was measured in 93 healthy males presented with 75-dB and 85-dB prepulses at 60-ms and 120-ms prepulse-pulse intervals. Subjects were grouped according to their COMT status into a Val/Val, a Val/Met and a Met/Met group.

RESULTS

ANOVAs showed that at all prepulse and interval conditions, Val/Val individuals had the lowest PPI, Met/Met the highest, and Val/Met were intermediate.

CONCLUSIONS

These results suggest that PPI is regulated by DA neurotransmission in the PFC and its levels depend on the COMT Val158Met gene polymorphism. These findings enhance the value of the PPI paradigm in examining individual variability of early information processing in healthy subjects and psychiatric disorders associated with changes in PFC DA activity and attentional deficits such as schizophrenia.