Thalamic connectivity measured with fMRI is associated with a polygenic index predicting thalamo-prefrontal gene co-expression

The Left-Right Side-Specific Neuroendocrine Signaling from Injured Brain: An Organizational Principle

A neurological dogma is that the contralateral effects of brain injury are set through crossed descending neural tracts. We have recently identified a novel topographic neuroendocrine system (T-NES) that operates via a humoral pathway and mediates the left-right side-specific effects of unilateral brain lesions. In rats with completely transected thoracic spinal cords, unilateral injury to the sensorimotor cortex produced contralateral hindlimb flexion, a proxy for neurological deficit. Here, we investigated in acute experiments whether T-NES consists of left and right counterparts and whether they differ in neural and molecular mechanisms. We demonstrated that left- and right-sided hormonal signaling is differentially blocked by the δ-, κ- and µ-opioid antagonists. Left and right neurohormonal signaling differed in targeting the afferent spinal mechanisms. Bilateral deafferentation of the lumbar spinal cord abolished the hormone-mediated effects of the left-brain injury but not the right-sided lesion. The sympathetic nervous system was ruled out as a brain-to-spinal cord-signaling pathway since hindlimb responses were induced in rats with cervical spinal cord transections that were rostral to the preganglionic sympathetic neurons. Analysis of gene-gene co-expression patterns identified the left- and right-side-specific gene co-expression networks that were coordinated via the humoral pathway across the hypothalamus and lumbar spinal cord. The coordination was ipsilateral and disrupted by brain injury. These findings suggest that T-NES is bipartite and that its left and right counterparts contribute to contralateral neurological deficits through distinct neural mechanisms, and may enable ipsilateral regulation of molecular and neural processes across distant neural areas along the neuraxis.

Dopamine signaling enriched striatal gene set predicts striatal dopamine synthesis and physiological activity in vivo

The polygenic architecture of schizophrenia implicates several molecular pathways involved in synaptic function. However, it is unclear how polygenic risk funnels through these pathways to translate into syndromic illness. Using tensor decomposition, we analyze gene co-expression in the caudate nucleus, hippocampus, and dorsolateral prefrontal cortex of post-mortem brain samples from 358 individuals. We identify a set of genes predominantly expressed in the caudate nucleus and associated with both clinical state and genetic risk for schizophrenia that shows dopaminergic selectivity. A higher polygenic risk score for schizophrenia parsed by this set of genes predicts greater dopamine synthesis in the striatum and greater striatal activation during reward anticipation. These results translate dopamine-linked genetic risk variation into in vivo neurochemical and hemodynamic phenotypes in the striatum that have long been implicated in the pathophysiology of schizophrenia.

A miR-137-Related Biological Pathway of Risk for Schizophrenia Is Associated With Human Brain Emotion Processing

BACKGROUND

miR-137 is a microRNA involved in brain development, regulating neurogenesis and neuronal maturation. Genome-wide association studies have implicated miR-137 in schizophrenia risk but do not explain its involvement in brain function and underlying biology. Polygenic risk for schizophrenia mediated by miR-137 targets is associated with working memory, although other evidence points to emotion processing. We characterized the functional brain correlates of miR-137 target genes associated with schizophrenia while disentangling previously reported associations of miR-137 targets with working memory and emotion processing.

METHODS

Using RNA sequencing data from postmortem prefrontal cortex (N = 522), we identified a coexpression gene set enriched for miR-137 targets and schizophrenia risk genes. We validated the relationship of this set to miR-137 in vitro by manipulating miR-137 expression in neuroblastoma cells. We translated this gene set into polygenic scores of coexpression prediction and associated them with functional magnetic resonance imaging activation in healthy volunteers (n1 = 214; n2 = 136; n3 = 2075; n4 = 1800) and with short-term treatment response in patients with schizophrenia (N = 427).

RESULTS

In 4652 human participants, we found that 1) schizophrenia risk genes were coexpressed in a biologically validated set enriched for miR-137 targets; 2) increased expression of miR-137 target risk genes was mediated by low prefrontal miR-137 expression; 3) alleles that predict greater gene set coexpression were associated with greater prefrontal activation during emotion processing in 3 independent healthy cohorts (n1, n2, n3) in interaction with age (n4); and 4) these alleles predicted less improvement in negative symptoms following antipsychotic treatment in patients with schizophrenia.

CONCLUSIONS

The functional translation of miR-137 target gene expression linked with schizophrenia involves the neural substrates of emotion processing.

Copy Number Variation Informs fMRI-based Prediction of Autism Spectrum Disorder

The multifactorial etiology of autism spectrum disorder (ASD) suggests that its study would benefit greatly from multimodal approaches that combine data from widely varying platforms, e.g., neuroimaging, genetics, and clinical characterization. Prior neuroimaging-genetic analyses often apply naive feature concatenation approaches in data-driven work or use the findings from one modality to guide posthoc analysis of another, missing the opportunity to analyze the paired multimodal data in a truly unified approach. In this paper, we develop a more integrative model for combining genetic, demographic, and neuroimaging data. Inspired by the influence of genotype on phenotype, we propose using an attention-based approach where the genetic data guides attention to neuroimaging features of importance for model prediction. The genetic data is derived from copy number variation parameters, while the neuroimaging data is from functional magnetic resonance imaging. We evaluate the proposed approach on ASD classification and severity prediction tasks, using a sex-balanced dataset of 228 ASD and typically developing subjects in a 10-fold cross-validation framework. We demonstrate that our attention-based model combining genetic information, demographic data, and functional magnetic resonance imaging results in superior prediction performance compared to other multimodal approaches.

Dopamine and schizophrenia from bench to bedside: Discovery of a striatal co-expression risk gene set that predicts in vivo measures of striatal function

Schizophrenia (SCZ) is characterized by a polygenic risk architecture implicating diverse molecular pathways important for synaptic function. However, how polygenic risk funnels through these pathways to translate into syndromic illness is unanswered. To evaluate biologically meaningful pathways of risk, we used tensor decomposition to characterize gene co-expression in post-mortem brain (of neurotypicals: N=154; patients with SCZ: N=84; and GTEX samples N=120) from caudate nucleus (CN), hippocampus (HP), and dorsolateral prefrontal cortex (DLPFC). We identified a CN-predominant gene set showing dopaminergic selectivity that was enriched for genes associated with clinical state and for genes associated with SCZ risk. Parsing polygenic risk score for SCZ based on this specific gene set (parsed-PRS), we found that greater pathway-specific SCZ risk predicted greater in vivo striatal dopamine synthesis capacity measured by [ 18 F]-FDOPA PET in three independent cohorts of neurotypicals and patients (total N=235) and greater fMRI striatal activation during reward anticipation in two additional independent neurotypical cohorts (total N=141). These results reveal a 'bench to bedside' translation of dopamine-linked genetic risk variation in driving in vivo striatal neurochemical and hemodynamic phenotypes that have long been implicated in the pathophysiology of SCZ.

Thalamocortical connectivity and its relationship with symptoms and cognition across the psychosis continuum

BACKGROUND

Coordination between the thalamus and cortex is necessary for efficient processing of sensory information and appears disrupted in schizophrenia. The significance of this disrupted coordination (i.e. thalamocortical dysconnectivity) to the symptoms and cognitive deficits of schizophrenia is unclear. It is also unknown whether similar dysconnectivity is observed in other forms of psychotic psychopathology and associated with familial risk for psychosis. Here we examine the relevance of thalamocortical connectivity to the clinical symptoms and cognition of patients with psychotic psychopathology, their first-degree biological relatives, and a group of healthy controls.

METHOD

Patients with a schizophrenia-spectrum diagnosis (N = 100) or bipolar disorder with a history of psychosis (N = 33), their first-degree relatives (N = 73), and a group of healthy controls (N = 43) underwent resting functional MRI in addition to clinical and cognitive assessments as part of the Psychosis Human Connectome Project. A bilateral mediodorsal thalamus seed-based analysis was used to measure thalamocortical connectivity and test for group differences, as well as associations with symptomatology and cognition.

RESULTS

Reduced connectivity from mediodorsal thalamus to insular, orbitofrontal, and cerebellar regions was seen in schizophrenia. Across groups, greater symptomatology was related to less thalamocortical connectivity to the left middle frontal gyrus, anterior cingulate, right insula, and cerebellum. Poorer cognition was related to less thalamocortical connectivity to bilateral insula. Analyses revealed similar patterns of dysconnectivity across patient groups and their relatives.

CONCLUSIONS

Reduced thalamo-prefrontal-cerebellar and thalamo-insular connectivity may contribute to clinical symptomatology and cognitive deficits in patients with psychosis as well as individuals with familial risk for psychotic psychopathology.

Consensus molecular environment of schizophrenia risk genes in coexpression networks shifting across age and brain regions

Schizophrenia is a neurodevelopmental brain disorder whose genetic risk is associated with shifting clinical phenomena across the life span. We investigated the convergence of putative schizophrenia risk genes in brain coexpression networks in postmortem human prefrontal cortex (DLPFC), hippocampus, caudate nucleus, and dentate gyrus granule cells, parsed by specific age periods (total N = 833). The results support an early prefrontal involvement in the biology underlying schizophrenia and reveal a dynamic interplay of regions in which age parsing explains more variance in schizophrenia risk compared to lumping all age periods together. Across multiple data sources and publications, we identify 28 genes that are the most consistently found partners in modules enriched for schizophrenia risk genes in DLPFC; twenty-three are previously unidentified associations with schizophrenia. In iPSC-derived neurons, the relationship of these genes with schizophrenia risk genes is maintained. The genetic architecture of schizophrenia is embedded in shifting coexpression patterns across brain regions and time, potentially underwriting its shifting clinical presentation.

Lessons Learned From Parsing Genetic Risk for Schizophrenia Into Biological Pathways

The clinically heterogeneous presentation of schizophrenia is compounded by the heterogeneity of risk factors and neurobiological correlates of the disorder. Genome-wide association studies in schizophrenia have uncovered a remarkably high number of genetic variants, but the biological pathways they impact upon remain largely unidentified. Among the diverse methodological approaches employed to provide a more granular understanding of genetic risk for schizophrenia, the use of biological labels, such as gene ontologies, regulome approaches, and gene coexpression have all provided novel perspectives into how genetic risk translates into the neurobiology of schizophrenia. Here, we review the salient aspects of parsing polygenic risk for schizophrenia into biological pathways. We argue that parsed scores, compared to standard polygenic risk scores, may afford a more biologically plausible and accurate physiological modeling of the different dimensions involved in translating genetic risk into brain mechanisms, including multiple brain regions, cell types, and maturation stages. We discuss caveats, opportunities, and pitfalls inherent in the parsed risk approach.

Thalamocortical Development: A Neurodevelopmental Framework for Schizophrenia

Adolescence is a period of increased vulnerability for the development of psychiatric disorders, including schizophrenia. The prefrontal cortex (PFC) undergoes substantial maturation during this period, and PFC dysfunction is central to cognitive impairments in schizophrenia. As a result, impaired adolescent maturation of the PFC has been proposed as a mechanism in the etiology of the disorder and its cognitive symptoms. In adulthood, PFC function is tightly linked to its reciprocal connections with the thalamus, and acutely inhibiting thalamic inputs to the PFC produces impairments in PFC function and cognitive deficits. Here, we propose that thalamic activity is equally important during adolescence because it is required for proper PFC circuit development. Because thalamic abnormalities have been observed early in the progression of schizophrenia, we further postulate that adolescent thalamic dysfunction can have long-lasting consequences for PFC function and cognition in patients with schizophrenia.

Joint structural-functional magnetic resonance imaging features are associated with diagnosis and real-world functioning in patients with schizophrenia

OBJECTIVE

Earlier evidence suggested that structural-functional covariation in schizophrenia patients (SCZ) is associated with cognition, a predictor of functioning. Moreover, studies suggested that functional brain abnormalities of schizophrenia may be related with structural network features. However, only few studies have investigated the relationship between structural-functional covariation and both diagnosis and functioning in SCZ. We hypothesized that structural-functional covariation networks associated with diagnosis are related to real-world functioning in SCZ.

METHODS

We performed joint Independent Component Analysis on T1 images and resting-state fMRI-based Degree Centrality (DC) maps from 89 SCZ and 285 controls. Structural-functional covariation networks in which we found a main effect of diagnosis underwent correlation analysis to investigate their relationship with functioning. Covariation networks showing a significant association with both diagnosis and functioning underwent univariate analysis to better characterize group-level differences at the spatial level.

RESULTS

A structural-functional covariation network characterized by frontal, temporal, parietal and thalamic structural estimates significantly covaried with temporo-parietal resting-state DC. Compared with controls, SCZ had reduced structural-functional covariation within this network (p_FDR = 0.005). The same measure correlated positively with both social and occupational functioning (both p_FDR = 0.042). Univariate analyses revealed grey matter deviations in SCZ compared with controls within this structural-functional network in hippocampus, cerebellum, thalamus, orbito-frontal cortex, and insula. No group differences were found in DC.

CONCLUSIONS

Findings support the existence of a phenotypical association between group-level differences and inter-individual heterogeneity of functional deficits in SCZ. Given that only the joint structural/functional analysis revealed this association, structural-functional covariation may be a potentially relevant schizophrenia phenotype.

How recent learning shapes the brain: Memory-dependent functional reconfiguration of brain circuits

The process of storing recently encoded episodic mnestic traces so that they are available for subsequent retrieval is accompanied by specific brain functional connectivity (FC) changes. In this fMRI study, we examined the early processing of memories in twenty-eight healthy participants performing an episodic memory task interposed between two resting state sessions. Memory performance was assessed through a forced-choice recognition test after the scanning sessions. We investigated resting state system configuration changes via Independent Component Analysis by cross-modeling baseline resting state spatial maps onto the post-encoding resting state, and post-encoding resting state spatial maps onto baseline. We identified both persistent and plastic components of the overall brain functional configuration between baseline and post-encoding. While FC patterns within executive, default mode, and cerebellar circuits persisted from baseline to post-encoding, FC within the visual circuit changed. A significant session × performance interaction characterized medial temporal lobe and prefrontal cortex FC with the visual circuit, as well as thalamic FC within the executive control system. Findings reveal early-stage FC changes at the system-level subsequent to a learning experience and associated with inter-individual variation in memory performance.

Thalamic connectivity system across psychiatric disorders: Current status and clinical implications

The thalamic connectivity system, with the thalamus as the central node, enables transmission of the brain’s neural computations via extensive connections to cortical, subcortical, and cerebellar regions. Emerging reports suggest deficits in this system across multiple psychiatric disorders, making it a unique network of high translational and transdiagnostic utility in mapping neural alterations that potentially contribute to symptoms and disturbances in psychiatric patients. However, despite considerable research effort, it is still debated how this system contributes to psychiatric disorders. This review characterizes current knowledge regarding thalamic connectivity system deficits in psychiatric disorders, including schizophrenia, bipolar disorder, major depressive disorder, and autism spectrum disorder, across multiple levels of the system. We identify the presence of common and distinct patterns of deficits in the thalamic connectivity system in major psychiatric disorders and assess their nature and characteristics. Specifically, this review assembles evidence for the hypotheses of 1) thalamic microstructure, particularly in the mediodorsal nucleus, as a state marker of psychosis; 2) thalamo-prefrontal connectivity as a trait marker of psychosis; and 3) thalamo-somatosensory/parietal connectivity as a possible marker of general psychiatric illness. Furthermore, possible mechanisms contributing to thalamocortical dysconnectivity are explored. We discuss current views on the contributions of cerebellar-thalamic connectivity to the thalamic connectivity system and propose future studies to examine its effects at multiple levels, from the molecular (e.g., glutamatergic) to the behavioral (e.g., cognition), to gain a deeper understanding of the mechanisms that underlie the disturbances observed in psychiatric disorders.

Flexible and specific contributions of thalamic subdivisions to human cognition

The thalamus participates in multiple functional brain networks supporting different cognitive abilities. How thalamo-cortical connections map onto the architecture of human cognition remains an outstanding question. The aim of this meta-analysis is to map co-activation between thalamic and extra-thalamic brain regions onto separate cognitive domains and to assess thalamic subdivision specificity within each of the cognitive domains considered. We parsed 93 fMRI studies into twelve cognitive domains. Signed Differential Mapping served to obtain co-activation maps. We then projected the contribution of thalamic subdivisions onto a thalamic atlas to assess cognitive domain specificity. A set of brain regions was flexibly involved with thalamus in several cognitive domains. Thalamic subdivisions showed ample cognitive heterogeneity. Our proposed model represents thalamic involvement in cognition as an "ensemble" of functional subdivisions with common cell properties embedded in separate cortical circuits rather than a homogeneous functional unit.

Identification of Reproducible BCL11A Alterations in Schizophrenia Through Individual-Level Prediction of Coexpression

Previous studies have provided evidence for an alteration of genetic coexpression in schizophrenia (SCZ). However, such analyses have thus far lacked biological specificity for individual genes, which may be critical for identifying illness-relevant effects. Therefore, we applied machine learning to identify gene-specific coexpression differences at the individual subject level and compared these between individuals with SCZ, bipolar disorder, major depressive disorder (MDD), autism spectrum disorder (ASD), and healthy controls. Utilizing transcriptome-wide gene expression data from 21 independent datasets, comprising a total of 9509 participants, we identified a reproducible decrease of BCL11A coexpression across 4 SCZ datasets that showed diagnostic specificity for SCZ when compared with ASD and MDD. We further demonstrate that individual-level coexpression differences can be combined in multivariate coexpression scores that show reproducible illness classification across independent datasets in SCZ and ASD. This study demonstrates that machine learning can capture gene-specific coexpression differences at the individual subject level for SCZ and identify novel biomarker candidates.

A Pattern of Cognitive Deficits Stratified for Genetic and Environmental Risk Reliably Classifies Patients With Schizophrenia From Healthy Control Subjects

BACKGROUND

Schizophrenia risk is associated with both genetic and environmental risk factors. Furthermore, cognitive abnormalities are established core characteristics of schizophrenia. We aim to assess whether a classification approach encompassing risk factors, cognition, and their associations can discriminate patients with schizophrenia (SCZs) from healthy control subjects (HCs). We hypothesized that cognition would demonstrate greater HC-SCZ classification accuracy and that combined gene-environment stratification would improve the discrimination performance of cognition.

METHODS

Genome-wide association study-based genetic, environmental, and neurocognitive classifiers were trained to separate 337 HCs from 103 SCZs using support vector classification and repeated nested cross-validation. We validated classifiers on independent datasets using within-diagnostic (SCZ) and cross-diagnostic (clinically isolated syndrome for multiple sclerosis, another condition with cognitive abnormalities) approaches. Then, we tested whether gene-environment multivariate stratification modulated the discrimination performance of the cognitive classifier in iterative subsamples.

RESULTS

The cognitive classifier discriminated SCZs from HCs with a balanced accuracy (BAC) of 88.7%, followed by environmental (BAC = 65.1%) and genetic (BAC = 55.5%) classifiers. Similar classification performance was measured in the within-diagnosis validation sample (HC-SCZ BACs, cognition = 70.5%; environment = 65.8%; genetics = 49.9%). The cognitive classifier was relatively specific to schizophrenia (HC-clinically isolated syndrome for multiple sclerosis BAC = 56.7%). Combined gene-environment stratification allowed cognitive features to classify HCs from SCZs with 89.4% BAC.

CONCLUSIONS

Consistent with cognitive deficits being core features of the phenotype of SCZs, our results suggest that cognitive features alone bear the greatest amount of information for classification of SCZs. Consistent with genes and environment being risk factors, gene-environment stratification modulates HC-SCZ classification performance of cognition, perhaps providing another target for refining early identification and intervention strategies.

Multivariate classification of schizophrenia and its familial risk based on load-dependent attentional control brain functional connectivity

Patients with schizophrenia (SCZ), as well as their unaffected siblings (SIB), show functional connectivity (FC) alterations during performance of tasks involving attention. As compared with SCZ, these alterations are present in SIB to a lesser extent and are more pronounced during high cognitive demand, thus possibly representing one of the pathways in which familial risk is translated into the SCZ phenotype. Our aim is to measure the separability of SCZ and SIB from healthy controls (HC) using attentional control-dependent FC patterns, and to test to which extent these patterns span a continuum of neurofunctional alterations between HC and SCZ. 65 SCZ with 65 age and gender-matched HC and 39 SIB with 39 matched HC underwent the Variable Attentional Control (VAC) task. Load-dependent connectivity matrices were generated according to correct responses in each VAC load. Classification performances of high, intermediate and low VAC load FC on HC-SCZ and HC-SIB cohorts were tested through machine learning techniques within a repeated nested cross-validation framework. HC-SCZ classification models were applied to the HC-SIB cohort, and vice-versa. A high load-related decreased FC pattern discriminated between HC and SCZ with 66.9% accuracy and with 57.7% accuracy between HC and SIB. A high load-related increased FC network separated SIB from HC (69.6% accuracy), but not SCZ from HC (48.5% accuracy). Our findings revealed signatures of attentional FC abnormalities shared by SCZ and SIB individuals. We also found evidence for potential, SIB-specific FC signature, which may point to compensatory neurofunctional mechanisms in persons at familial risk for schizophrenia.

Prefrontal Coexpression of Schizophrenia Risk Genes Is Associated With Treatment Response in Patients

BACKGROUND

Gene coexpression networks are relevant to functional and clinical translation of schizophrenia risk genes. We hypothesized that schizophrenia risk genes converge into coexpression pathways that may be associated with gene regulation mechanisms and with response to treatment in patients with schizophrenia.

METHODS

We identified gene coexpression networks in two prefrontal cortex postmortem RNA sequencing datasets (n = 688) and replicated them in four more datasets (n = 1295). We identified and replicated (p values < .001) a single module enriched for schizophrenia risk loci (13 risk genes in 10 loci). In silico screening of potential regulators of the schizophrenia risk module via bioinformatic analyses identified two transcription factors and three microRNAs associated with the risk module. To translate postmortem information into clinical phenotypes, we identified polymorphisms predicting coexpression and combined them to obtain an index approximating module coexpression (Polygenic Coexpression Index [PCI]).

RESULTS

The PCI-coexpression association was successfully replicated in two independent brain transcriptome datasets (n = 131; p values < .05). Finally, we tested the association between the PCI and short-term treatment response in two independent samples of patients with schizophrenia treated with olanzapine (n = 167). The PCI was associated with treatment response in the positive symptom domain in both clinical cohorts (p values < .05).

CONCLUSIONS

In summary, our findings in 1983 samples of human postmortem prefrontal cortex show that coexpression of a set of genes enriched for schizophrenia risk genes is relevant to treatment response. This coexpression pathway may be coregulated by transcription factors and microRNA associated with it.