Gene expression profiling of the dorsolateral and medial orbitofrontal cortex in schizophrenia

Single-nucleus transcriptomic profiling of human orbitofrontal cortex reveals convergent effects of aging and psychiatric disease

Aging is a complex biological process and represents the largest risk factor for neurodegenerative disorders. The risk for neurodegenerative disorders is also increased in individuals with psychiatric disorders. Here, we characterized age-related transcriptomic changes in the brain by profiling ~800,000 nuclei from the orbitofrontal cortex from 87 individuals with and without psychiatric diagnoses and replicated findings in an independent cohort with 32 individuals. Aging affects all cell types, with LAMP5+LHX6+ interneurons, a cell-type abundant in primates, by far the most affected. Disrupted synaptic transmission emerged as a convergently affected pathway in aged tissue. Age-related transcriptomic changes overlapped with changes observed in Alzheimer's disease across multiple cell types. We find evidence for accelerated transcriptomic aging in individuals with psychiatric disorders and demonstrate a converging signature of aging and psychopathology across multiple cell types. Our findings shed light on cell-type-specific effects and biological pathways underlying age-related changes and their convergence with effects driven by psychiatric diagnosis.

Interaction between RNF4 and SART3 is associated with the risk of schizophrenia

The pathogenesis of schizophrenia (SCZ) is heavily influenced by genetic factors. Ring finger protein 4 (RNF4) and squamous cell carcinoma antigen recognized by T cells 3 (SART3) are thought to be involved in nervous system growth and development via oxidative stress pathways. Moreover, they have previously been linked to SCZ. Yet the role of RNF4 and SART3 in SCZ remains unclear. Here, we investigated how these two genes are involved in SCZ by studying their variants observed in patients. We first observed significantly elevated mRNA levels of RNF4 and SART3 in the peripheral blood in both first-episode (n = 30) and chronic (n = 30) SCZ patients compared to controls (n = 60). Next, we targeted-sequenced three single nucleotide polymorphisms (SNPs) in SART3 and six SNPs in RNF4 for association with SCZ using the genomic DNA extracted from peripheral blood leukocytes from SCZ participants (n = 392) and controls (n = 572). We observed a combination of SNPs that included rs1203860, rs2282765 (both in RNF4), and rs2287550 (in SART3) was associated with increased risk of SCZ, suggesting common pathogenic mechanisms between these two genes. We then conducted experiments in HEK293T cells to better understand the interaction between RNF4 and SART3. We observed that SART3 lowered the expression of RNF4 through ubiquitination and downregulated the expression of nuclear factor E2-related factor 2 (NRF2), a downstream factor of RNF4, implicating the existence of a possible shared regulatory mechanism for RNF4 and SART3. In conclusion, our study provides evidence that the interaction between RNF4 and SART3 contributes to the risk of SCZ. The findings shed light on the underlying molecular mechanisms of SCZ and may lead to the development of new therapies and interventions for this disorder.

Systematic discovery of signaling pathways linking immune activation to schizophrenia

Immune activation has been shown to play a critical role in the development of schizophrenia; however its underlying mechanism remains unknown. Our report demonstrates a high-quality protein interaction network for schizophrenia (SCZ Network), constructed using our “neighborhood walk” approach in combination with “random walk with restart”. The spatiotemporal expression pattern of the genes in this disease network revealed two developmental stages sensitive to perturbation by immune activation: mid-to late gestation, and adolescence. Furthermore, we induced immune activation at these stages in mice, carried out transcriptome sequencing on the mouse brains, and illustrated clear potential molecular pathways and key regulators correlating maternal immune activation during gestation and an increased risk for schizophrenia after a second immune activation at puberty. This work provides not only valuable resources for the study on molecular mechanisms underlying schizophrenia, but also a systematic strategy for the discovery of molecular pathways of complex mental disorders.

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A high-quality molecular network for schizophrenia (SCZ Network)

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A landscape of molecular pathways linking immune activation and schizophrenia

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The spatiotemporal network dynamics revealing stages susceptible to immune activation

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Identification of the molecular pathways and regulators in the immune-activated brain

Role of the lipid transport protein StarD7 in mitochondrial dynamics

Mitochondria are dynamic organelles crucial for cell function and survival implicated in oxidative energy production whose central functions are tightly controlled by lipids. StarD7 is a lipid transport protein involved in the phosphatidylcholine (PC) delivery to mitochondria. Previous studies have shown that StarD7 knockdown induces alterations in mitochondria and endoplasmic reticulum (ER) with a reduction in PC content, however whether StarD7 modulates mitochondrial dynamics remains unexplored. Here, we generated HTR-8/SVneo stable cells expressing the precursor StarD7.I and the mature processed StarD7.II isoforms. We demonstrated that StarD7.I overexpression altered mitochondrial morphology increasing its fragmentation, whereas no changes were observed in StarD7.II-overexpressing cells compared to the control (Ct) stable cells. StarD7.I (D7.I) stable cells were able to transport higher fluorescent PC analog to mitochondria than Ct cells, yield mitochondrial fusions, maintained the membrane potential, and produced lower levels of reactive oxygen species (ROS). Additionally, the expression of Dynamin Related Protein 1 (Drp1) and Mitofusin (Mfn2) proteins were increased, whereas the amount of Mitofusin 1 (Mfn1) decreased. Moreover, transfections with plasmids encoding Drp1-K38A, Drp1-S637D or Drp1-S637A mutants indicated that mitochondrial fragmentation in D7.I cells occurs in a fission-dependent manner via Drp1. In contrast, StarD7 silencing decreased Mfn1 and Mfn2 fusion proteins without modification of Drp1 protein level. These cells increased ROS levels and presented donut-shape mitochondria, indicative of metabolic stress. Altogether our findings provide novel evidence indicating that alterations in StarD7.I expression produce significant changes in mitochondrial morphology and dynamics.

Medial orbitofrontal cortex dopamine D1/D2 receptors differentially modulate distinct forms of probabilistic decision-making

Efficient decision-making involves weighing the costs and benefits associated with different actions and outcomes to maximize long-term utility. The medial orbitofrontal cortex (mOFC) has been implicated in guiding choice in situations involving reward uncertainty, as inactivation in rats alters choice involving probabilistic rewards. The mOFC receives considerable dopaminergic input, yet how dopamine (DA) modulates mOFC function has been virtually unexplored. Here, we assessed how mOFC D₁ and D₂ receptors modulate two forms of reward seeking mediated by this region, probabilistic reversal learning and probabilistic discounting. Separate groups of well-trained rats received intra-mOFC microinfusions of selective D₁ or D₂ antagonists or agonists prior to task performance. mOFC D₁ and D₂ blockade had opposing effects on performance during probabilistic reversal learning and probabilistic discounting. D₁ blockade impaired, while D₂ blockade increased the number of reversals completed, both mediated by changes in errors and negative feedback sensitivity apparent during the initial discrimination of the task, which suggests changes in probabilistic reinforcement learning rather than flexibility. Similarly, D₁ blockade reduced, while D₂ blockade increased preference for larger/risky rewards. Excess D₁ stimulation had no effect on either task, while excessive D₂ stimulation impaired probabilistic reversal performance, and reduced both profitable risky choice and overall task engagement. These findings highlight a previously uncharacterized role for mOFC DA, showing that D₁ and D₂ receptors play dissociable and opposing roles in different forms of reward-related action selection. Elucidating how DA biases behavior in these situations will expand our understanding of the mechanisms regulating optimal and aberrant decision-making.

Differential gene regulation in the anterior cingulate cortex and superior temporal cortex in schizophrenia: A molecular network approach

The closely connected anterior cingulate cortex (ACC) and superior temporal cortex (STC) are important for higher cognitive functions. Both brain regions are disturbed in schizophrenia, i.e., functional and structural alterations have been reported. This postmortem investigation in brains from patients with schizophrenia and controls compared gene expression in the left ACC and left STC. Most differentially expressed genes were unique to each brain region, but some clusters of genes were equally dysregulated in both, giving rise to a more general disease-specific pattern of gene regulation. The data was used to construct a molecular network of the genes identically expressed in both regions as primary nodes and the metabolically connected genes as secondary nodes. The network analysis identified downregulated clusters of immune-associated gene products and upregulated clusters belonging to the ubiquitin-proteasome system. These findings could help to identify new potential therapeutic targets for future approaches.

The RNA-Binding Protein HuD Regulates Alternative Splicing and Alternative Polyadenylation in the Mouse Neocortex

The neuronal Hu/ELAV-like proteins HuB, HuC and HuD are a class of RNA-binding proteins that are crucial for proper development and maintenance of the nervous system. These proteins bind to AU-rich elements (AREs) in the untranslated regions (3'-UTRs) of target mRNAs regulating mRNA stability, transport and translation. In addition to these cytoplasmic functions, Hu proteins have been implicated in alternative splicing and alternative polyadenylation in the nucleus. The purpose of this study was to identify transcriptome-wide effects of HuD deletion on both of these nuclear events using RNA sequencing data obtained from the neocortex of Elavl4-/- (HuD KO) mice. HuD KO affected alternative splicing of 310 genes, including 17 validated HuD targets such as Cbx3, Cspp1, Snap25 and Gria2. In addition, deletion of HuD affected polyadenylation of 53 genes, with the majority of significantly altered mRNAs shifting towards usage of proximal polyadenylation signals (PAS), resulting in shorter 3'-UTRs. None of these genes overlapped with those showing alternative splicing events. Overall, HuD KO had a greater effect on alternative splicing than polyadenylation, with many of the affected genes implicated in several neuronal functions and neuropsychiatric disorders.

Sorting Out Sorting Nexins Functions in the Nervous System in Health and Disease

Endocytosis is a fundamental process that controls protein/lipid composition of the plasma membrane, thereby shaping cellular metabolism, sensing, adhesion, signaling, and nutrient uptake. Endocytosis is essential for the cell to adapt to its surrounding environment, and a tight regulation of the endocytic mechanisms is required to maintain cell function and survival. This is particularly significant in the central nervous system (CNS), where composition of neuronal cell surface is crucial for synaptic functioning. In fact, distinct pathologies of the CNS are tightly linked to abnormal endolysosomal function, and several genome wide association analysis (GWAS) and biochemical studies have identified intracellular trafficking regulators as genetic risk factors for such pathologies. The sorting nexins (SNXs) are a family of proteins involved in protein trafficking regulation and signaling. SNXs dysregulation occurs in patients with Alzheimer’s disease (AD), Down’s syndrome (DS), schizophrenia, ataxia and epilepsy, among others, establishing clear roles for this protein family in pathology. Interestingly, restoration of SNXs levels has been shown to trigger synaptic plasticity recovery in a DS mouse model. This review encompasses an historical and evolutionary overview of SNXs protein family, focusing on its organization, phyla conservation, and evolution throughout the development of the nervous system during speciation. We will also survey SNXs molecular interactions and highlight how defects on SNXs underlie distinct pathologies of the CNS. Ultimately, we discuss possible strategies of intervention, surveying how our knowledge about the fundamental processes regulated by SNXs can be applied to the identification of novel therapeutic avenues for SNXs-related disorders.

Molecules, Mechanisms, and Disorders of Self-Domestication: Keys for Understanding Emotional and Social Communication from an Evolutionary Perspective

The neural crest hypothesis states that the phenotypic features of the domestication syndrome are due to a reduced number or disruption of neural crest cells (NCCs) migration, as these cells differentiate at their final destinations and proliferate into different tissues whose activity is reduced by domestication. Comparing the phenotypic characteristics of modern and prehistoric man, it is clear that during their recent evolutionary past, humans also went through a process of self-domestication with a simultaneous prolongation of the period of socialization. This has led to the development of social abilities and skills, especially language, as well as neoteny. Disorders of neural crest cell development and migration lead to many different conditions such as Waardenburg syndrome, Hirschsprung disease, fetal alcohol syndrome, DiGeorge and Treacher-Collins syndrome, for which the mechanisms are already relatively well-known. However, for others, such as Williams-Beuren syndrome and schizophrenia that have the characteristics of hyperdomestication, and autism spectrum disorders, and 7dupASD syndrome that have the characteristics of hypodomestication, much less is known. Thus, deciphering the biological determinants of disordered self-domestication has great potential for elucidating the normal and disturbed ontogenesis of humans, as well as for the understanding of evolution of mammals in general.

Time-Varying Gene Network Analysis of Human Prefrontal Cortex Development

The prefrontal cortex (PFC) constitutes a large part of the human central nervous system and is essential for the normal social affection and executive function of humans and other primates. Despite ongoing research in this region, the development of interactions between PFC genes over the lifespan is still unknown. To investigate the conversion of PFC gene interaction networks and further identify hub genes, we obtained time-series gene expression data of human PFC tissues from the Gene Expression Omnibus (GEO) database. A statistical model, loggle, was used to construct time-varying networks and several common network attributes were used to explore the development of PFC gene networks with age. Network similarity analysis showed that the development of human PFC is divided into three stages, namely, fast development period, deceleration to stationary period, and recession period. We identified some genes related to PFC development at these different stages, including genes involved in neuronal differentiation or synapse formation, genes involved in nerve impulse transmission, and genes involved in the development of myelin around neurons. Some of these genes are consistent with findings in previous reports. At the same time, we explored the development of several known KEGG pathways in PFC and corresponding hub genes. This study clarified the development trajectory of the interaction between PFC genes, and proposed a set of candidate genes related to PFC development, which helps further study of human brain development at the genomic level supplemental to regular anatomical analyses. The analytical process used in this study, involving the loggle model, similarity analysis, and central analysis, provides a comprehensive strategy to gain novel insights into the evolution and development of brain networks in other organisms.

Altered Cortical Thickness-Based Individualized Structural Covariance Networks in Patients with Schizophrenia and Bipolar Disorder

Structural covariance is described as coordinated variation in brain morphological features, such as cortical thickness and volume, among brain structures functionally or anatomically interconnected to one another. Structural covariance networks, based on graph theory, have been studied in mental disorders. This analysis can help in understanding the brain mechanisms of schizophrenia and bipolar disorder. We investigated cortical thickness-based individualized structural covariance networks in patients with schizophrenia and bipolar disorder. T1-weighted magnetic resonance images were obtained from 39 patients with schizophrenia, 37 patients with bipolar disorder type I, and 32 healthy controls, and cortical thickness was analyzed via a surface-based morphometry analysis. The structural covariance of cortical thickness was calculated at the individual level, and covariance networks were analyzed based on graph theoretical indices: strength, clustering coefficient (CC), path length (PL) and efficiency. At the global level, both patient groups showed decreased strength, CC and efficiency, and increased PL, compared to healthy controls. In bipolar disorder, we found intermediate network measures among the groups. At the nodal level, schizophrenia patients showed decreased CCs in the left suborbital sulcus and the right superior frontal sulcus, compared to bipolar disorder patients. In addition, patient groups showed decreased CCs in the right insular cortex and the left superior occipital gyrus. Global-level network indices, including strength, CCs and efficiency, positively correlated, while PL negatively correlated, with the positive symptoms of the Positive and Negative Syndrome Scale for patients with schizophrenia. The nodal-level CC of the right insular cortex positively correlated with the positive symptoms of schizophrenia, while that of the left superior occipital gyrus positively correlated with the Young Mania Rating Scale scores for bipolar disorder. Altered cortical structural networks were revealed in patients, and particularly, the prefrontal regions were more altered in schizophrenia. Furthermore, altered cortical structural networks in both patient groups correlated with core pathological symptoms, indicating that the insular cortex is more vulnerable in schizophrenia, and the superior occipital gyrus is more vulnerable in bipolar disorder. Our individualized structural covariance network indices might be promising biomarkers for the evaluation of patients with schizophrenia and bipolar disorder.

Predicting novel genomic regions linked to genetic disorders using GWAS and chromosome conformation data - a case study of schizophrenia

Genome-wide association studies identified numerous loci harbouring single nucleotide polymorphisms (SNPs) associated with various human diseases, although the causal role of many of them remains unknown. In this paper, we postulate that co-location and shared biological function of novel genes with genes known to associate with a specific phenotype make them potential candidates linked to the same phenotype (“guilt-by-proxy”). We propose a novel network-based approach for predicting candidate genes/genomic regions utilising the knowledge of the 3D architecture of the human genome and GWAS data. As a case study we used a well-studied polygenic disorder ‒ schizophrenia ‒ for which we compiled a comprehensive dataset of SNPs. Our approach revealed 634 novel regions covering ~398 Mb of the human genome and harbouring ~9000 genes. Using various network measures and enrichment analysis, we identified subsets of genes and investigated the plausibility of these genes/regions having an association with schizophrenia using literature search and bioinformatics resources. We identified several genes/regions with previously reported associations with schizophrenia, thus providing proof-of-concept, as well as novel candidates with no prior known associations. This approach has the potential to identify novel genes/genomic regions linked to other polygenic disorders and provide means of aggregating genes/SNPs for further investigation.

Breakdown of the Paracellular Tight and Adherens Junctions in the Gut and Blood Brain Barrier and Damage to the Vascular Barrier in Patients with Deficit Schizophrenia

Deficit schizophrenia is characterized by leaky intestinal tight and adherens junctions and bacterial translocation. Here we examine whether (deficit) schizophrenia is accompanied by leaky paracellular, transcellular, and vascular barriers in the gut and blood-brain barriers. We measured IgA responses to occludin, claudin-5, E-cadherin, and β-catenin (paracellular pathway, PARA); talin, actin, vinculin, and epithelial intermediate filament (transcellular pathway, TRANS); and plasmalemma vesicle-associated protein (PLVAP, vascular pathway) in 78 schizophrenia patients and 40 controls. IgA responses to claudin-5, E-cadherin, and β-catenin, the sum of the four PARA proteins, and the ratio PARA/TRANS were significantly higher in deficit schizophrenia patients than in nondeficit schizophrenia patients and controls. A large part of the variance in PHEMN (psychosis, hostility, excitation, mannerism, and negative) symptoms, psychomotor retardation, formal thought disorders, verbal fluency, word list memory, word list recall, and executive functions was explained by the PARA/TRANS ratio coupled with plasma IgA responses to Gram-negative bacteria, IgM to malondialdehyde, CCL-11 (eotaxin), IgA levels of the ratio of noxious to more protective tryptophan catabolites (NOX/PRO TRYCATs), and a plasma immune activation index. Moreover, IgA levels to Gram-negative bacteria were significantly associated with IgA to E-cadherin, β-catenin, and PLVAP, while IgA levels to claudin-5 were significantly predicted by IgA to E-cadherin, NOX/PRO TRYCAT ratio, Gram-negative bacteria, and CCL11. The phenomenology of the deficit syndrome is to a large extent explained by the cumulative effects of lowered natural IgM, breakdown of the paracellular and vascular pathways, increased bacterial translocation, peripheral immune-inflammatory responses, and indices of BBB breakdown.