LINE1 insertions as a genomic risk factor for schizophrenia: Preliminary evidence from an affected family.

Recent studies show that human-specific LINE1s (L1HS) play a key role in the development of the central nervous system (CNS) and its disorders, and that their transpositions within the human genome are more common than previously thought. Many polymorphic L1HS, that is, present or absent across individuals, are not annotated in the current release of the genome and are customarily termed "non-reference L1s." We developed an analytical workflow to identify L1 polymorphic insertions with next-generation sequencing (NGS) using data from a family in which SZ segregates. Our workflow exploits two independent algorithms to detect non-reference L1 insertions, performs local de novo alignment of the regions harboring predicted L1 insertions and resolves the L1 subfamily designation from the de novo assembled sequence. We found 110 non-reference L1 polymorphic loci exhibiting Mendelian inheritance, the vast majority of which are already reported in dbRIP and/or euL1db, thus, confirming their status as non-reference L1 polymorphic insertions. Four previously undetected L1 polymorphic loci were confirmed by PCR amplification and direct sequencing of the insert. A large fraction of our non-reference L1s is located within the open reading frame of protein-coding genes that belong to pathways already implicated in the pathogenesis of schizophrenia. The finding of these polymorphic variants among SZ offsprings is intriguing and suggestive of putative pathogenic role. Our data show the utility of NGS to uncover L1 polymorphic insertions, a neglected type of genetic variants with the potential to influence the risk to develop schizophrenia like SNVs and CNVs. © 2016 Wiley Periodicals, Inc.

Feed-forward hierarchical model of the ventral visual stream applied to functional brain image classification.

Functional brain imaging is a common tool in monitoring the progression of neurodegenerative and neurological disorders. Identifying functional brain imaging derived features that can accurately detect neurological disease is of primary importance to the medical community. Research in computer vision techniques to identify objects in photographs have reported high accuracies in that domain, but their direct applicability to identifying disease in functional imaging is still under investigation in the medical community. In particular, Serre et al. (: In: IEEE Conference on Computer Vision and Pattern Recognition (CVPR-05). pp 994-1000) introduced a biophysically inspired filtering method emulating visual processing in striate cortex which they applied to perform object recognition in photographs. In this work, the model described by Serre et al. [2005] is extended to three-dimensional volumetric images to perform signal detection in functional brain imaging (PET, SPECT). The filter outputs are used to train both neural network and logistic regression classifiers and tested on two distinct datasets: ADNI Alzheimer's disease 2-deoxy-D-glucose (FDG) PET and National Football League players Tc99m HMPAO SPECT. The filtering pipeline is analyzed to identify which steps are most important for classification accuracy. Our results compare favorably with other published classification results and outperform those of a blinded expert human rater, suggesting the utility of this approach.

Increased CNV-region deletions in mild cognitive impairment (MCI) and Alzheimer's disease (AD) subjects in the ADNI sample.

We investigated the genome-wide distribution of CNVs in the Alzheimer's disease (AD) Neuroimaging Initiative (ADNI) sample (146 with AD, 313 with Mild Cognitive Impairment (MCI), and 181 controls). Comparison of single CNVs between cases (MCI and AD) and controls shows overrepresentation of large heterozygous deletions in cases (p-value<0.0001). The analysis of CNV-Regions identifies 44 copy number variable loci of heterozygous deletions, with more CNV-Regions among affected than controls (p=0.005). Seven of the 44 CNV-Regions are nominally significant for association with cognitive impairment. We validated and confirmed our main findings with genome re-sequencing of selected patients and controls. The functional pathway analysis of the genes putatively affected by deletions of CNV-Regions reveals enrichment of genes implicated in axonal guidance, cell-cell adhesion, neuronal morphogenesis and differentiation. Our findings support the role of CNVs in AD, and suggest an association between large deletions and the development of cognitive impairment.

Transposable elements and psychiatric disorders.

Transposable Elements (TEs) or transposons are low-complexity elements (e.g., LINEs, SINEs, SVAs, and HERVs) that make up to two-thirds of the human genome. There is mounting evidence that TEs play an essential role in genomic architecture and regulation related to both normal function and disease states. Recently, the identification of active TEs in several different human brain regions suggests that TEs play a role in normal brain development and adult physiology and quite possibly in psychiatric disorders. TEs have been implicated in hemophilia, neurofibromatosis, and cancer. With the advent of next-generation whole-genome sequencing approaches, our understanding of the relationship between TEs and psychiatric disorders will greatly improve. We will review the biology of TEs and early evidence for TE involvement in psychiatric disorders.

Genetic modulation of the HTR2A gene reduces anxiety-related behavior in mice.

The expanding field of precision gene editing using CRISPR/Cas9 has demonstrated its potential as a transformative technology in the treatment of various diseases. However, whether this genome-editing tool could be used to modify neural circuits in the central nervous system (CNS), which are implicated in complex behavioral traits, remains uncertain. In this study, we demonstrate the feasibility of noninvasive, intranasal delivery of adeno-associated virus serotype 9 (AAV9) vectors containing CRISPR/Cas9 cargo within the CNS resulting in modification of the HTR2A receptor gene. In vitro, exposure to primary mouse cortical neurons to AAV9 vectors targeting the HT2RA gene led to a concentration-dependent decrease in spontaneous electrical activity following multielectrode array (MEA) analysis. In vivo, at 5 weeks postintranasal delivery in mice, analysis of brain samples revealed single base pair deletions and nonsense mutations, leading to an 8.46-fold reduction in mRNA expression and a corresponding 68% decrease in the 5HT-2A receptor staining. Our findings also demonstrate a significant decrease in anxiety-like behavior in treated mice. This study constitutes the first successful demonstration of a noninvasive CRISPR/Cas9 delivery platform, capable of bypassing the blood-brain barrier and enabling modulation of neuronal 5HT-2A receptor pathways. The results of this study targeting the HTR2A gene provide a foundation for the development of innovative therapeutic strategies for a broad range of neurological disorders, including anxiety, depression, attentional deficits, and cognitive dysfunction.

Behavioral and neuroanatomical investigation of Highly Superior Autobiographical Memory (HSAM).

A single case study recently documented one woman's ability to recall accurately vast amounts of autobiographical information, spanning most of her lifetime, without the use of practiced mnemonics (Parker, Cahill, & McGaugh, 2006). The current study reports findings based on eleven participants expressing this same memory ability, now referred to as Highly Superior Autobiographical Memory (HSAM). Participants were identified and subsequently characterized based on screening for memory of public events. They were then tested for personal autobiographical memories as well as for memory assessed by laboratory memory tests. Additionally, whole-brain structural MRI scans were obtained. Results indicated that HSAM participants performed significantly better at recalling public as well as personal autobiographical events as well as the days and dates on which these events occurred. However, their performance was comparable to age- and sex-matched controls on most standard laboratory memory tests. Neuroanatomical results identified nine structures as being morphologically different from those of control participants. The study of HSAM may provide new insights into the neurobiology of autobiographical memory.

fMRI Evidence for Default Mode Network Deactivation Associated with Rapid Eye Movements in Sleep.

System-specific brain responses-time-locked to rapid eye movements (REMs) in sleep-are characteristically widespread, with robust and clear activation in the primary visual cortex and other structures involved in multisensory integration. This pattern suggests that REMs underwrite hierarchical processing of visual information in a time-locked manner, where REMs index the generation and scanning of virtual-world models, through multisensory integration in dreaming-as in awake states. Default mode network (DMN) activity increases during rest and reduces during various tasks including visual perception. The implicit anticorrelation between the DMN and task-positive network (TPN)-that persists in REM sleep-prompted us to focus on DMN responses to temporally-precise REM events. We timed REMs during sleep from the video recordings and quantified the neural correlates of REMs-using functional MRI (fMRI)-in 24 independent studies of 11 healthy participants. A reanalysis of these data revealed that the cortical areas exempt from widespread REM-locked brain activation were restricted to the DMN. Furthermore, our analysis revealed a modest temporally-precise REM-locked decrease-phasic deactivation-in key DMN nodes, in a subset of independent studies. These results are consistent with hierarchical predictive coding; namely, permissive deactivation of DMN at the top of the hierarchy (leading to the widespread cortical activation at lower levels; especially the primary visual cortex). Additional findings indicate REM-locked cerebral vasodilation and suggest putative mechanisms for dream forgetting.

Identifying gene regulatory networks in schizophrenia.

The imaging genetics approach to studying the genetic basis of disease leverages the individual strengths of both neuroimaging and genetic studies by visualizing and quantifying the brain activation patterns in the context of genetic background. Brain imaging as an intermediate phenotype can help clarify the functional link among genes, the molecular networks in which they participate, and brain circuitry and function. Integrating genetic data from a genome-wide association study (GWAS) with brain imaging as a quantitative trait (QT) phenotype can increase the statistical power to identify risk genes. A QT analysis using brain imaging (DLPFC activation during a working memory task) as a quantitative trait has identified unanticipated risk genes for schizophrenia. Several of these genes (RSRC1, ARHGAP18, ROBO1-ROBO2, GPC1, TNIK, and CTXN3-SLC12A2) have functions related to progenitor cell proliferation, migration, and differentiation, cytoskeleton reorganization, axonal connectivity, and development of forebrain structures. These genes, however, do not function in isolation but rather through gene regulatory networks. To obtain a deeper understanding how the GWAS-identified genes participate in larger gene regulatory networks, we measured correlations among transcript levels in the mouse and human postmortem tissue and performed a gene set enrichment analysis (GSEA) that identified several microRNA associated with schizophrenia (448, 218, 137). The results of such computational approaches can be further validated in animal experiments in which the networks are experimentally studied and perturbed with specific compounds. Glypican 1 and FGF17 mouse models for example, can be used to study such gene regulatory networks. The model demonstrates epistatic interactions between FGF and glypican on brain development and may be a useful model of negative symptom schizophrenia.

Intranasal administration of PEGylated transforming growth factor-alpha improves behavioral deficits in a chronic stroke model.

We previously demonstrated that infusion of transforming growth factor (TGF)-alpha after chronic middle cerebral artery occlusion (MCAO) stimulates stem and progenitor cell proliferation, migration, and neuronal differentiation associated with the amelioration of neurologic impairment. But the use of TGF-alpha in humans is impeded by impracticality of intracranial infusion and the inability of intravenous TGF-alpha to cross the blood-brain barrier. Here we investigated whether intranasal delivery of PEGylated TGF-alpha (PEG-TGF-alpha) is a viable alternative. We found that intranasal PEG-TGF-alpha can also induce the proliferation of neural progenitors and their migration to the damaged striatum, and that this is associated with significant behavioral improvement in the MCAO model. This nonsurgical approach represents a potential therapeutic strategy for human patients.

fMRI evidence for multisensory recruitment associated with rapid eye movements during sleep.

We studied the neural correlates of rapid eye movement during sleep (REM) by timing REMs from video recording and using rapid event-related functional MRI. Consistent with the hypothesis that REMs share the brain systems and mechanisms with waking eye movements and are visually-targeted saccades, we found REM-locked activation in the primary visual cortex, thalamic reticular nucleus (TRN), 'visual claustrum', retrosplenial cortex (RSC, only on the right hemisphere), fusiform gyrus, anterior cingulate cortex, and the oculomotor circuit that controls awake saccadic eye movements (and subserves awake visuospatial attention). Unexpectedly, robust activation also occurred in non-visual sensory cortices, motor cortex, language areas, and the ascending reticular activating system, including basal forebrain, the major source of cholinergic input to the entire cortex. REM-associated activation of these areas, especially non-visual primary sensory cortices, TRN and claustrum, parallels findings from waking studies on the interactions between multiple sensory data, and their 'binding' into a unified percept, suggesting that these mechanisms are also shared in waking and dreaming and that the sharing goes beyond the expected visual scanning mechanisms. Surprisingly, REMs were associated with a decrease in signal in specific periventricular subregions, matching the distribution of the serotonergic supraependymal plexus. REMs might serve as a useful task-free probe into major brain systems for functional brain imaging.

Nicotine-induced brain metabolism associated with anger provocation.

Cortico-limbic brain activity associated with anger may be susceptible to nicotine and, thus, may contribute to smoking initiation and nicotine addiction. The purpose of the study was to identify the brain regions that are most reactive to nicotine and show the greatest association with anger task performance. Twenty adult nonsmokers (9 women, 11 men) participated in two laboratory sessions to assess brain metabolism with fluoro deoxy-glucose Positron Emission Topography (FDG-PET) in response to nicotine and placebo patches during an anger provocation task. Outcome variables for the anger provocation task were reaction time, intensity and length of retaliation. Reaction time was associated with nicotine-induced changes in the left thalamus. Length of retaliation was associated with a functionally linked set of cortical and subcortical structures such as right frontal lobe, right anterior cingulate (BA 24), right uncus, left parietal lobe, left BA 11, left cingulate, left BA 25, left amygdala, left BA 30, left BA 38 and BA 9. These findings reveal the underlying brain circuitry targeted by nicotine during anger provocation.

A genome-wide association study of schizophrenia using brain activation as a quantitative phenotype.

BACKGROUND: Genome-wide association studies (GWASs) are increasingly used to identify risk genes for complex illnesses including schizophrenia. These studies may require thousands of subjects to obtain sufficient power. We present an alternative strategy with increased statistical power over a case-control study that uses brain imaging as a quantitative trait (QT) in the context of a GWAS in schizophrenia. METHODS: Sixty-four subjects with chronic schizophrenia and 74 matched controls were recruited from the Functional Biomedical Informatics Research Network (FBIRN) consortium. Subjects were genotyped using the Illumina HumanHap300 BeadArray and were scanned while performing a Sternberg Item Recognition Paradigm in which they learned and then recognized target sets of digits in an functional magnetic resonance imaging protocol. The QT was the mean blood oxygen level-dependent signal in the dorsolateral prefrontal cortex during the probe condition for a memory load of 3 items. RESULTS: Three genes or chromosomal regions were identified by having 2 single-nucleotide polymorphisms (SNPs) each significant at P < 10(-6) for the interaction between the imaging QT and the diagnosis (ROBO1-ROBO2, TNIK, and CTXN3-SLC12A2). Three other genes had a significant SNP at <10(-6) (POU3F2, TRAF, and GPC1). Together, these 6 genes/regions identified pathways involved in neurodevelopment and response to stress. CONCLUSION: Combining imaging and genetic data from a GWAS identified genes related to forebrain development and stress response, already implicated in schizophrenic dysfunction, as affecting prefrontal efficiency. Although the identified genes require confirmation in an independent sample, our approach is a screening method over the whole genome to identify novel SNPs related to risk for schizophrenia.

A comparative analysis of completed suicide using high resolution brain SPECT imaging.

The authors compared regional cerebral blood flow in the brains of 12 psychiatric patients who completed the act of suicide with groups of healthy and nonsuicidal depressed subjects using statistical parametric mapping. Results were consistent with prior imaging studies on depression and were indicative of impaired impulse control and limbic dysregulation, including significant perfusion deficits in the medial prefrontal and subgenual areas (Brodmann's areas 11, 25) and ventral tegmentum. These results warrant further research.

Multivariate analyses suggest genetic impacts on neurocircuitry in schizophrenia.

We investigated the relationship of functional neurocircuitries and dopamine receptor D1 (DRD1) polymorphisms in schizophrenics during a working memory task. Participants performed the Serial Item Recognition Paradigm memory task during functional magnetic resonance imaging acquisition. We performed a data-driven multivariate analysis (partial least squares) to characterize brain network (covariance) patterns. Genetic testing identified two main genotypes. Accuracy did not differ between the groups. Covariance patterns of different areas (including the dorsolateral prefrontal cortex and the inferior parietal lobule) were inversely related between the two genotypes. Two groups of schizophrenic patients with similar symptomatology and performance on a working memory task, but with distinct dopamine receptor genotypes, may use distinct neural systems to retrieve information.

Sleep deprivation PET correlations of Hamilton symptom improvement ratings with changes in relative glucose metabolism in patients with depression.

BACKGROUND: This PET study is a continuing investigation of the effects of antidepressant medication and one night of total sleep deprivation on cerebral metabolism in depressed patients. This study was undertaken to confirm previous correlations between symptom improvement ratings and regional changes in glucose metabolism, using a higher resolution scanner than in previous investigations. In addition, we also studied the effect of concomitant antidepressant medication in conjunction with sleep depression. METHOD: Six depressed patients were administered the selective serotonin reuptake inhibitor sertraline for a week and then underwent positron emission tomography (FDG PET) before and after sleep deprivation. Changes in relative glucose metabolism were correlated with symptom improvement ratings in Hamilton Depression Rating Scale scores. RESULTS: Positive correlations (defined as reduced HDRS scores associated with areas having reduced relative cerebral glucose metabolism after TSD) were found in the inferior frontal gyrus and inferior frontal/orbital frontal cortex. Negative correlations (defined as reduced HDRS scores associated with areas of increased relative cerebral glucose metabolism after TSD) were found in the dorsolateral prefrontal cortex. LIMITATIONS: Limitations of this study are that the number of subjects was small (n=6) and they were scanned at a 7.6 mm resolution. CONCLUSIONS: The results of this study support previous findings on the effects of sleep deprivation and antidepressant medications in the treatment of unipolar and bipolar depression, with an emphasis on the significance of cerebral glucose metabolic changes in the ventral and DLPF cortex in mood regulation.

Corrigendum: Rapid Eye Movements in Sleep Furnish a Unique Probe Into Consciousness.

[This corrects the article DOI: 10.3389/fpsyg.2018.02087.].

Rapid Eye Movements in Sleep Furnish a Unique Probe Into Consciousness.

The neural correlates of rapid eye movements (REMs) in sleep are extraordinarily robust; including REM-locked multisensory-motor integration and accompanying activation in the retrosplenial cortex, the supplementary eye field and areas encompassing cholinergic basal nucleus (Hong et al., 2009). The phenomenology of REMs speaks to the notion that perceptual experience in both sleep and wakefulness is a constructive process - in which we generate predictions of sensory inputs and then test those predictions through actively sampling the sensorium with eye movements. On this view, REMs during sleep may index an internalized active sampling or 'scanning' of self-generated visual constructs that are released from the constraints of visual input. If this view is correct, it renders REMs an ideal probe to study consciousness as "an exclusively internal affair" (Metzinger, 2009). In other words, REMs offer a probe of active inference - in the sense of predictive coding - when the brain is isolated from the sensorium in virtue of the natural blockade of sensory afferents during REM sleep. Crucially, REMs are temporally precise events that enable powerful inferences based on time series analyses. As a natural, task-free probe, (REMs) could be used in non-compliant subjects, including infants and animals. In short, REMs constitute a promising probe to study the ontogenetic and phylogenetic development of consciousness and perhaps the psychopathology of schizophrenia and autism, which have been considered in terms of aberrant predictive coding.

Smoking to self-medicate attentional and emotional dysfunctions.

Individuals with attentional and emotional dysfunctions are most at risk for smoking initiation and subsequent nicotine addiction. This article presents converging findings from human behavioral research, brain imaging, and basic neuroscience on smoking as self-medication for attentional and emotional dysfunctions. Nicotine and other tobacco constituents have significant effects on neural circuitry underlying the regulation of attention and affect. Age, sex, early environment, and exposure to other drugs have been identified as important factors that moderate both the effects of nicotine on brain circuitry and behavior and the risk for smoking initiation. Findings also suggest that the effects of smoking differ depending on whether smoking is used to regulate attention or affect. Individual differences in the reinforcement processes underlying tobacco use have implications for the development of tailored smoking cessation programs and prevention strategies that include early treatment of attentional and emotional dysfunctions.

Frontal lobe metabolic decreases with sleep deprivation not totally reversed by recovery sleep.

We studied the effects of total sleep deprivation and recovery sleep in normal subjects using position emission tomography with 18F-deoxyglycose. Sleep deprivation resulted in a significant decrease in relative metabolism of the frontal cortex, thalamus, and striatum. Recovery sleep was found to have only a partial restorative effect on frontal lobe function with minimal reversal of subcortical deficits. Sleep may be especially important for maintenance of frontal lobe activity.

Imaging phenotypes and genotypes in schizophrenia.

Schizophrenia is associated with subtle structural and functional brain abnormalities. Both recent and classical data suggest that it is a heterogeneous disorder that is clearly heritable. The cause and course of schizophrenia are poorly understood, and classical categories of clinical symptoms have not been particularly useful in identifying its pathophysiology or predicting its treatment. The possible genetic risk factors for schizophrenia are numerous; however, the connection between the genotype and the time-course, or the multifaceted symptoms of the disease, has yet to be established. Brain imaging methods that study the structure or function of the cortical and subcortical regions have also identified distinct patterns that distinguish schizophrenics from controls, and that may identify meaningful subtypes of schizophrenia. The predictive relationship between these imaging phenotypes and disease characteristics such as treatment response is only beginning to be revealed. The emergence of the field of imaging genetics, combining genetic, and neuroimaging data, holds much promise for the deeper understanding and improved treatment of diseases such as schizophrenia. In this article we review some of the key findings in imaging phenotyping and genotyping of schizophrenia, and the initial endeavors at their combination into more meaningful and predictive patterns, or endophenotypes identifying the relationships among clinical symptoms, course, genes, and the underlying pathophysiology.