Imaging genetics and psychiatric disorders

Bayesian pathway analysis over brain network mediators for survival data

Technological advancements in noninvasive imaging facilitate the construction of whole brain interconnected networks, known as brain connectivity. Existing approaches to analyze brain connectivity frequently disaggregate the entire network into a vector of unique edges or summary measures, leading to a substantial loss of information. Motivated by the need to explore the effect mechanism among genetic exposure, brain connectivity, and time to disease onset with maximum information extraction, we propose a Bayesian approach to model the effect pathway between each of these components while quantifying the mediating role of brain networks. To accommodate the biological architectures of brain connectivity constructed along white matter fiber tracts, we develop a structural model which includes a symmetric matrix-variate accelerated failure time model for disease onset and a symmetric matrix response regression for the network-variate mediator. We further impose within-graph sparsity and between-graph shrinkage to identify informative network configurations and eliminate the interference of noisy components. Simulations are carried out to confirm the advantages of our proposed method over existing alternatives. By applying the proposed method to the landmark Alzheimer's Disease Neuroimaging Initiative study, we obtain neurobiologically plausible insights that may inform future intervention strategies.

Integrating Multimodal Neuroimaging and Genetics: A Structurally-Linked Sparse Canonical Correlation Analysis Approach

Neuroimaging genetics represents a multivariate approach aimed at elucidating the intricate relationships between high-dimensional genetic variations and neuroimaging data. Predominantly, existing methodologies revolve around Sparse Canonical Correlation Analysis (SCCA), a framework we expand to 1) encompass multiple imaging modalities and 2) promote the simultaneous identification of structurally linked features across imaging modalities. The structurally linked brain regions were assessed using diffusion tensor imaging, which quantifies the presence of neuronal fibers, thereby grounding our approach in biologically well-founded prior knowledge within the SCCA model. In our proposed structurally linked SCCA framework, we leverage T1-weighted MRI and functional MRI (fMRI) time series data to delineate both the structural and functional characteristics of the brain. Genetic variations, specifically single nucleotide polymorphisms (SNPs), are also incorporated as a genetic modality. Validation of our methodology was conducted using a simulated dataset and large-scale normative data from the Human Connectome Project (HCP). Our approach demonstrated superior performance compared to existing methods on simulated data and revealed interpretable gene-imaging associations in the real dataset. Thus, our methodology lays the groundwork for elucidating the genetic underpinnings of brain structure and function, thereby providing novel insights into the field of neuroscience. Our code is available at https://github.com/mungegg.

Compositional structural brain signatures capture Alzheimer's genetic risk on brain structure along the disease continuum

INTRODUCTION

Traditional brain imaging genetics studies have primarily focused on how genetic factors influence the volume of specific brain regions, often neglecting the overall complexity of brain architecture and its genetic underpinnings.

METHODS

This study analyzed data from participants across the Alzheimer's disease (AD) continuum from the ALFA and ADNI studies. We exploited compositional data analysis to examine relative brain volumetric variations that (i) differentiate cognitively unimpaired (CU) individuals, defined as amyloid-negative (A-) based on CSF profiling, from those at different AD stages, and (ii) associated with increased genetic susceptibility to AD, assessed using polygenic risk scores.

RESULTS

Distinct brain signatures differentiated CU A-individuals from amyloid-positive MCI and AD. Moreover, disease stage-specific signatures were associated with higher genetic risk of AD.

DISCUSSION

The findings underscore the complex interplay between genetics and disease stages in shaping brain structure, which could inform targeted preventive strategies and interventions in preclinical AD.

Role of Imaging Genetics in Alzheimer's Disease: A Systematic Review and Current Update

BACKGROUND

Alzheimer's disease is a neurodegenerative disorder characterized by severe cognitive, behavioral, and psychological symptoms, such as dementia, cognitive decline, apathy, and depression. There are no accurate methods to diagnose the disease or proper therapeutic interventions to treat AD. Therefore, there is a need for novel diagnostic methods and markers to identify AD efficiently before its onset. Recently, there has been a rise in the use of imaging techniques like Magnetic Resonance Imaging (MRI) and functional Magnetic Resonance Imaging (fMRI) as diagnostic approaches in detecting the structural and functional changes in the brain, which help in the early and accurate diagnosis of AD. In addition, these changes in the brain have been reported to be affected by variations in genes involved in different pathways involved in the pathophysiology of AD.

METHODOLOGY

A literature review was carried out to identify studies that reported the association of genetic variants with structural and functional changes in the brain in AD patients. Databases like PubMed, Google Scholar, and Web of Science were accessed to retrieve relevant studies. Keywords like 'fMRI', 'Alzheimer's', 'SNP', and 'imaging' were used, and the studies were screened using different inclusion and exclusion criteria.

RESULTS

15 studies that found an association of genetic variations with structural and functional changes in the brain were retrieved from the literature. Based on this, 33 genes were identified to play a role in the development of disease. These genes were mainly involved in neurogenesis, cell proliferation, neural differentiation, inflammation and apoptosis. Few genes like FAS, TOM40, APOE, TRIB3 and SIRT1 were found to have a high association with AD. In addition, other genes that could be potential candidates were also identified.

CONCLUSION

Imaging genetics is a powerful tool in diagnosing and predicting AD and has the potential to identify genetic biomarkers and endophenotypes associated with the development of the disorder.

Effects of psychosis-associated genetic markers on brain volumetry: a systematic review of replicated findings and an independent validation

BACKGROUND

Given psychotic illnesses' high heritability and associations with brain structure, numerous neuroimaging-genetics findings have been reported in the last two decades. However, few findings have been replicated. In the present independent sample we aimed to replicate any psychosis-implicated SNPs (single nucleotide polymorphisms), which had previously shown at least two main effects on brain volume.

METHODS

A systematic review for SNPs showing a replicated effect on brain volume yielded 25 studies implicating seven SNPs in five genes. Their effect was then tested in 113 subjects with either schizophrenia, bipolar disorder, 'at risk mental state' or healthy state, for whole-brain and region-of-interest (ROI) associations with grey and white matter volume changes, using voxel-based morphometry.

RESULTS

We found FWER-corrected (Family-wise error rate) (i.e. statistically significant) associations of: (1) CACNA1C-rs769087-A with larger bilateral hippocampus and thalamus white matter, across the whole brain; and (2) CACNA1C-rs769087-A with larger superior frontal gyrus, as ROI. Higher replication concordance with existing literature was found, in decreasing order, for: (1) CACNA1C-rs769087-A, with larger dorsolateral-prefrontal/superior frontal gyrus and hippocampi (both with anatomical and directional concordance); (2) ZNF804A-rs11681373-A, with smaller angular gyrus grey matter and rectus gyri white matter (both with anatomical and directional concordance); and (3) BDNF-rs6265-T with superior frontal and middle cingulate gyri volume change (with anatomical and allelic concordance).

CONCLUSIONS

Most literature findings were not herein replicated. Nevertheless, high degree/likelihood of replication was found for two genome-wide association studies- and one candidate-implicated SNPs, supporting their involvement in psychosis and brain structure.

Differential association between the GLP1R gene variants and brain functional connectivity according to the severity of alcohol use

Growing evidence suggests that the glucagon-like peptide-1 (GLP-1) system is involved in mechanisms underlying alcohol seeking and consumption. Accordingly, the GLP-1 receptor (GLP-1R) has begun to be studied as a potential pharmacotherapeutic target for alcohol use disorder (AUD). The aim of this study was to investigate the association between genetic variation at the GLP-1R and brain functional connectivity, according to the severity of alcohol use. Participants were 181 individuals categorized as high-risk (n = 96) and low-risk (n = 85) alcohol use, according to their AUD identification test (AUDIT) score. Two uncommon single nucleotide polymorphisms (SNPs), rs6923761 and rs1042044, were selected a priori for this study because they encode amino-acid substitutions with putative functional consequences on GLP-1R activity. Genotype groups were based on the presence of the variant allele for each of the two GLP-1R SNPs of interest [rs6923761: AA + AG (n = 65), GG (n = 116); rs1042044: AA + AC (n = 114), CC (n = 67)]. Resting-state functional MRI data were acquired for 10 min and independent component (IC) analysis was conducted. Multivariate analyses of covariance (MANCOVA) examined the interaction between GLP-1R genotype group and AUDIT group on within- and between-network connectivity. For rs6923761, three ICs showed significant genotype × AUDIT interaction effects on within-network connectivity: two were mapped onto the anterior salience network and one was mapped onto the visuospatial network. For rs1042044, four ICs showed significant interaction effects on within-network connectivity: three were mapped onto the dorsal default mode network and one was mapped onto the basal ganglia network. For both SNPs, post-hoc analyses showed that in the group carrying the variant allele, high versus low AUDIT was associated with stronger within-network connectivity. No significant effects on between-network connectivity were found. In conclusion, genetic variation at the GLP-1R was differentially associated with brain functional connectivity in individuals with low versus high severity of alcohol use. Significant findings in the salience and default mode networks are particularly relevant, given their role in the neurobiology of AUD and addictive behaviors.

An Improved Fusion Paired Group Lasso Structured Sparse Canonical Correlation Analysis Based on Brain Imaging Genetics to Identify Biomarkers of Alzheimer’s Disease

Brain imaging genetics can demonstrate the complicated relationship between genetic factors and the structure or function of the humankind brain. Therefore, it has become an important research topic and attracted more and more attention from scholars. The structured sparse canonical correlation analysis (SCCA) model has been widely used to identify the association between brain image data and genetic data in imaging genetics. To investigate the intricate genetic basis of cerebrum imaging phenotypes, a great deal of other standard SCCA methods combining different interested structed have now appeared. For example, some models use group lasso penalty, and some use the fused lasso or the graph/network guided fused lasso for feature selection. However, prior knowledge may not be completely available and the group lasso methods have limited capabilities in practical applications. The graph/network guided approaches can use sample correlation to define constraints, thereby overcoming this problem. Unfortunately, this also has certain limitations. The graph/network conducted methods are susceptible to the sign of the sample correlation of the data, which will affect the stability of the model. To improve the efficiency and stability of SCCA, a sparse canonical correlation analysis model with GraphNet regularization (FGLGNSCCA) is proposed in this manuscript. Based on the FGLSCCA model, the GraphNet regularization penalty is imposed in our study and an optimization algorithm is presented to optimize the model. The structural Magnetic Resonance Imaging (sMRI) and gene expression data are used in this study to find the genotype and characteristics of brain regions associated with Alzheimer’s disease (AD). Experiment results shown that the new FGLGNSCCA model proposed in this manuscript is superior or equivalent to traditional methods in both artificially synthesized neuroimaging genetics data or actual neuroimaging genetics data. It can select essential features more powerfully compared with other multivariate methods and identify significant canonical correlation coefficients as well as captures more significant typical weight patterns which demonstrated its excellent ability in finding biologically important imaging genetic relations.

Imaging Transcriptomics of Brain Disorders

Noninvasive neuroimaging is a powerful tool for quantifying diverse aspects of brain structure and function in vivo, and it has been used extensively to map the neural changes associated with various brain disorders. However, most neuroimaging techniques offer only indirect measures of underlying pathological mechanisms. The recent development of anatomically comprehensive gene expression atlases has opened new opportunities for studying the transcriptional correlates of noninvasively measured neural phenotypes, offering a rich framework for evaluating pathophysiological hypotheses and putative mechanisms. Here, we provide an overview of some fundamental methods in imaging transcriptomics and outline their application to understanding brain disorders of neurodevelopment, adulthood, and neurodegeneration. Converging evidence indicates that spatial variations in gene expression are linked to normative changes in brain structure during age-related maturation and neurodegeneration that are in part associated with cell-specific gene expression markers of gene expression. Transcriptional correlates of disorder-related neuroimaging phenotypes are also linked to transcriptionally dysregulated genes identified in ex vivo analyses of patient brains. Modeling studies demonstrate that spatial patterns of gene expression are involved in regional vulnerability to neurodegeneration and the spread of disease across the brain. This growing body of work supports the utility of transcriptional atlases in testing hypotheses about the molecular mechanism driving disease-related changes in macroscopic neuroimaging phenotypes.

Co-sparse reduced-rank regression for association analysis between imaging phenotypes and genetic variants

MOTIVATION

The association analysis between genetic variants and imaging phenotypes must be carried out to understand the inherited neuropsychiatric disorders via imaging genetic studies. Given the high dimensionality in imaging and genetic data, traditional methods based on massive univariate regression entail large computational cost and disregard many-to-many correlations between phenotypes and genetic variants. Several multivariate imaging genetic methods have been proposed to alleviate the above problems. However, most of these methods are based on the l1 penalty, which might cause the over-selection of variables and thus mislead scientists in analyzing data from the field of neuroimaging genetics.

RESULTS

To address these challenges in both statistics and computation, we propose a novel co-sparse reduced-rank regression model that identifies complex correlations in a dimensional reduction manner. We developed an iterative algorithm based on a group primal dual-active set formulation to detect simultaneously important genetic variants and imaging phenotypes efficiently and precisely via non-convex penalty. The simulation studies showed that our method achieved accurate and stable performance in parameter estimation and variable selection. In real application, the proposed approach successfully detected several novel Alzheimer's disease-related genetic variants and regions of interest, which indicate that our method may be a valuable statistical toolbox for imaging genetic studies.

AVAILABILITY AND IMPLEMENTATION

The R package csrrr, and the code for experiments in this article is available in Github: https://github.com/hailongba/csrrr.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Neuroimaging PheWAS (Phenome-Wide Association Study): A Free Cloud-Computing Platform for Big-Data, Brain-Wide Imaging Association Studies

Large-scale, case-control genome-wide association studies (GWASs) have revealed genetic variations associated with diverse neurological and psychiatric disorders. Recent advances in neuroimaging and genomic databases of large healthy and diseased cohorts have empowered studies to characterize effects of the discovered genetic factors on brain structure and function, implicating neural pathways and genetic mechanisms in the underlying biology. However, the unprecedented scale and complexity of the imaging and genomic data requires new advanced biomedical data science tools to manage, process and analyze the data. In this work, we introduce Neuroimaging PheWAS (phenome-wide association study): a web-based system for searching over a wide variety of brain-wide imaging phenotypes to discover true system-level gene-brain relationships using a unified genotype-to-phenotype strategy. This design features a user-friendly graphical user interface (GUI) for anonymous data uploading, study definition and management, and interactive result visualizations as well as a cloud-based computational infrastructure and multiple state-of-art methods for statistical association analysis and multiple comparison correction. We demonstrated the potential of Neuroimaging PheWAS with a case study analyzing the influences of the apolipoprotein E (APOE) gene on various brain morphological properties across the brain in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Benchmark tests were performed to evaluate the system's performance using data from UK Biobank. The Neuroimaging PheWAS system is freely available. It simplifies the execution of PheWAS on neuroimaging data and provides an opportunity for imaging genetics studies to elucidate routes at play for specific genetic variants on diseases in the context of detailed imaging phenotypic data.

Effect of NEUROG3 polymorphism rs144643855 on regional spontaneous brain activity in major depressive disorder

PURPOSE

Our previous study identified a significant association between a single nucleotide polymorphism (SNP) located in the neurogenin3 (NEUROG3) gene and post-stroke depression (PSD) in Chinese populations. The present work explores whether polymorphism rs144643855 affects regional brain activity and clinical phenotypes in major depressive disorder (MDD).

METHOD

A total of 182 participants were included: 116 MDD patients and 66 normal controls. All participants underwent resting-state functional magnetic resonance imaging (rs-fMRI) scanning at baseline. Spontaneous brain activity was assessed using amplitude of low-frequency fluctuation (ALFF). The Hamilton Depression Scale-24 (HAMD-24) and Snaith-Hamilton Pleasure Scale (SHAPS) were used to assess participants at baseline. Two-way analysis of covariance (ANCOVA) was used to explore the interaction between diagnostic groups and NEUROG3 rs144643855 on regional brain activity. We performed correlation analysis to further test the association between these interactive brain regions and clinical manifestations of MDD.

RESULTS

Genotype and disease significantly interacted in the left inferior frontal gyrus (IFG-L), right superior frontal gyrus (SFG-R), and left paracentral lobule (PCL-L) (P < 0.05). ALFF values of the IFG-L were found to be significantly associated with anhedonia in MDD patients.

CONCLUSION

These findings suggest a potential relationship between rs144643855 variations and altered frontal brain activity in MDD. NEUROG3 may play an important role in the neuropathophysiology of MDD.

An expanding manifold in transmodal regions characterizes adolescent reconfiguration of structural connectome organization

Adolescence is a critical time for the continued maturation of brain networks. Here, we assessed structural connectome development in a large longitudinal sample ranging from childhood to young adulthood. By projecting high-dimensional connectomes into compact manifold spaces, we identified a marked expansion of structural connectomes, with strongest effects in transmodal regions during adolescence. Findings reflected increased within-module connectivity together with increased segregation, indicating increasing differentiation of higher-order association networks from the rest of the brain. Projection of subcortico-cortical connectivity patterns into these manifolds showed parallel alterations in pathways centered on the caudate and thalamus. Connectome findings were contextualized via spatial transcriptome association analysis, highlighting genes enriched in cortex, thalamus, and striatum. Statistical learning of cortical and subcortical manifold features at baseline and their maturational change predicted measures of intelligence at follow-up. Our findings demonstrate that connectome manifold learning can bridge the conceptual and empirical gaps between macroscale network reconfigurations, microscale processes, and cognitive outcomes in adolescent development.

Genome-wide association studies of brain imaging data via weighted distance correlation

MOTIVATION

Imaging genetics is mainly used to reveal the pathogenesis of neuropsychiatric risk genes and understand the relationship between human brain structure, functional and individual differences. Increasingly, the brain-wide imaging phenotypes in voxels are available to test the association with genetic markers. A challenge with analyzing such data is their high dimensionality and complex relationships.

RESULTS

To tackle this challenge, we introduce a weighed distance correlation (wdCor) that can assess the association between genetic markers and voxel-based imaging data. Importantly, the wdCor test takes the voxel-based data as a whole multivariate phenotype, which preserves the spatial continuity and might enhance the power. Besides, an adaptive permutation procedure is introduced to determine the P-values of the wdCor test and also alleviate the computational burden in GWAS. In extensive simulation studies, wdCor achieves much better performances compared to the original distance correlation. We also successfully apply wdCor to conduct a large-scale analysis on data from the Alzheimer's disease neuroimaging project (ADNI).

AVAILABILITY AND IMPLEMENTATION

Our wdCor method provides new research directions and ideas for multivariate analysis of high-dimensional data, it can also be used as a tool for scientific analysis of imaging genetics research in practical applications. The R package wdcor, and the code for reproducing all results in this article is available in Github: https://github.com/yangyuhui0129/wdcor.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Brain imaging genomics: influences of genomic variability on the structure and function of the human brain

Brain imaging genomics is an emerging discipline in which genomic and brain imaging data are integrated in order to elucidate the molecular mechanisms that underly brain phenotypes and diseases, including neuropsychiatric disorders. As with all genetic analyses of complex traits and diseases, brain imaging genomics has evolved from small, individual candidate gene investigations towards large, collaborative genome-wide association studies. Recent investigations, mostly population-based, have studied well-powered cohorts comprising tens of thousands of individuals and identified multiple robust associations of single-nucleotide polymorphisms and copy number variants with structural and functional brain phenotypes. Such systematic genomic screens of millions of genetic variants have generated initial insights into the genetic architecture of brain phenotypes and demonstrated that their etiology is polygenic in nature, involving multiple common variants with small effect sizes and rare variants with larger effect sizes. Ongoing international collaborative initiatives are now working to obtain a more complete picture of the underlying biology. As in other complex phenotypes, novel approaches – such as gene–gene interaction, gene–environment interaction, and epigenetic analyses – are being implemented in order to investigate their contribution to the observed phenotypic variability. An important consideration for future research will be the translation of brain imaging genomics findings into clinical practice.

Ethical issues in global neuroimaging genetics collaborations

Neuroimaging genetics is a rapidly developing field that combines neuropsychiatric genetics studies with imaging modalities to investigate how genetic variation influences brain structure and function. As both genetic and imaging technologies improve further, their combined power may hold translational potential in terms of improving psychiatric nosology, diagnosis, and treatment. While neuroimaging genetics studies offer a number of scientific advantages, they also face challenges. In response to some of these challenges, global neuroimaging genetics collaborations have been created to pool and compare brain data and replicate study findings. Attention has been paid to ethical issues in genetics, neuroimaging, and multi-site collaborative research, respectively, but there have been few substantive discussions of the ethical issues generated by the confluence of these areas in global neuroimaging genetics collaborations. Our discussion focuses on two areas: benefits and risks of global neuroimaging genetics collaborations and the potential impact of neuroimaging genetics research findings in low- and middle-income countries. Global neuroimaging genetics collaborations have the potential to enhance relations between countries and address global mental health challenges, however there are risks regarding inequity, exploitation and data sharing. Moreover, neuroimaging genetics research in low- and middle-income countries must address the issue of feedback of findings and the risk of essentializing and stigmatizing interpretations of mental disorders. We conclude by examining how the notion of solidarity, informed by an African Ethics framework, may justify some of the suggestions made in our discussion.

Neuroimaging studies within Cognitive Genetics Collaborative Research Organization aiming to replicate and extend works of ENIGMA

Reproducibility is one of the most important issues for generalizing the results of clinical research; however, low reproducibility in neuroimaging studies is well known. To overcome this problem, the Enhancing Neuroimaging Genetics through Meta‐Analysis (ENIGMA) consortium, an international neuroimaging consortium, established standard protocols for imaging analysis and employs either meta‐ and mega‐analyses of psychiatric disorders with large sample sizes. The Cognitive Genetics Collaborative Research Organization (COCORO) in Japan promotes neurobiological studies in psychiatry and has successfully replicated and extended works of ENIGMA especially for neuroimaging studies. For example, (a) the ENIGMA consortium showed subcortical regional volume alterations in patients with schizophrenia (n = 2,028) compared to controls (n = 2,540) across 15 cohorts using meta‐analysis. COCORO replicated the volumetric changes in patients with schizophrenia (n = 884) compared to controls (n = 1,680) using the ENIGMA imaging analysis protocol and mega‐analysis. Furthermore, a schizophrenia‐specific leftward asymmetry for the pallidum volume was demonstrated; and (b) the ENIGMA consortium identified white matter microstructural alterations in patients with schizophrenia (n = 1,963) compared to controls (n = 2,359) across 29 cohorts. Using the ENIGMA protocol, a study from COCORO showed similar results in patients with schizophrenia (n = 696) compared to controls (n = 1,506) from 12 sites using mega‐analysis. Moreover, the COCORO study found that schizophrenia, bipolar disorder (n = 211) and autism spectrum disorder (n = 126), but not major depressive disorder (n = 398), share similar white matter microstructural alterations, compared to controls. Further replication and harmonization of the ENIGMA consortium and COCORO will contribute to the generalization of their research findings.

CACNB2 rs11013860 polymorphism correlates of prefrontal cortex thickness in bipolar patients with first-episode mania

BACKGROUND

The β2 subunit of the voltage-gated l-type calcium channel gene(CACNB2) rs11013860 polymorphism is a putative genetic susceptibility marker for bipolar disorder (BD). However, the neural effects of CACNB2 rs11013860 in BD are largely unknown.

METHODS

Forty-six bipolar patients with first-episode mania and eighty-three healthy controls (HC) were genotyped for CACNB2 rs11013860 and were scanned with a 3.0 Tesla structural magnetic resonance imaging system to measure cortical thickness of prefrontal cortex (PFC) components (superior frontal cortex, orbitofrontal cortex, middle and inferior frontal gyri).

RESULTS

Cortical thickness was thinner in patients on all PFC measurements compared to HC (p < 0.050). Moreover, we found a significant interaction between CACNB2 genotype and diagnosis for the right superior frontal cortical thickness (F = 8.190, p = 0.040). Bonferroni corrected post-hoc tests revealed that, in CACNB2 A-allele carriers, patients displayed thinner superior frontal thickness compared to HC (p < 0.001). In patients, CACNB2 A-allele carriers also exhibited reduced superior frontal thickness compared to CACNB2 CC-allele carriers (p = 0.016).

LIMITATIONS

Lithium treatment may influence our results, and the sample size in our study is relatively small.

CONCLUSIONS

Our results suggest that the CACNB2 rs11013860 might impact PFC thickness in patients with first-episode mania. These findings provide evidence to support CACNB2 rs11013860 involvement in the emotion-processing neural circuitry abnormality in the early stage of BD, which will ultimately contribute to revealing the link between the variation in calcium channel genes and the neuropathological mechanism of BD.

Joint-Connectivity-Based Sparse Canonical Correlation Analysis of Imaging Genetics for Detecting Biomarkers of Parkinson's Disease

Imaging genetics is a method used to detect associations between imaging and genetic variables. Some researchers have used sparse canonical correlation analysis (SCCA) for imaging genetics. This study was conducted to improve the efficiency and interpretability of SCCA. We propose a connectivity-based penalty for incorporating biological prior information. Our proposed approach, named joint connectivity-based SCCA (JCB-SCCA), includes the proposed penalty and can handle multi-modal neuroimaging datasets. Different neuroimaging techniques provide distinct information on the brain and have been used to investigate various neurological disorders, including Parkinson's disease (PD). We applied our algorithm to simulated and real imaging genetics datasets for performance evaluation. Our algorithm was able to select important features in a more robust manner compared with other multivariate methods. The algorithm revealed promising features of single-nucleotide polymorphisms and brain regions related to PD by using a real imaging genetic dataset. The proposed imaging genetics model can be used to improve clinical diagnosis in the form of novel potential biomarkers. We hope to apply our algorithm to cohorts such as Alzheimer's patients or healthy subjects to determine the generalizability of our algorithm.

Genetic Advance in Depressive Disorder

Major depressive disorder (MDD) and bipolar disorder (BPD) are both chronic, severe mood disorder with high misdiagnosis rate, leading to substantial health and economic burdens to patients around the world. There is a high misdiagnosis rate of bipolar depression (BD) just based on symptomology in depressed patients whose previous manic or mixed episodes have not been well recognized. Therefore, it is important for psychiatrists to identify these two major psychiatric disorders. Recently, with the accumulation of clinical sample sizes and the advances of methodology and technology, certain progress in the genetics of major depression and bipolar disorder has been made. This article reviews the candidate genes for MDD and BD, genetic variation loci, chromosome structural variation, new technologies, and new methods.

A systematic review of associations between functional MRI activity and polygenic risk for schizophrenia and bipolar disorder

Genetic factors account for up to 80% of the liability for schizophrenia (SCZ) and bipolar disorder (BD). Genome-wide association studies have successfully identified several genes associated with increased risk for both disorders. This has allowed researchers to model the aggregate effect of genes associated with disease status and create a polygenic risk score (PGRS) for each individual. The interest in imaging genetics using PGRS has grown in recent years, with several studies now published. We have conducted a systematic review to examine the effects of PGRS of SCZ, BD and cross psychiatric disorders on brain function and connectivity using fMRI data. Results indicate that the effect of genetic load for SCZ and BD on brain function affects task-related recruitment, with frontal areas having a more prominent role, independent of task. Additionally, the results suggest that the polygenic architecture of psychotic disorders is not regionally confined but impacts on the task-dependent recruitment of multiple brain regions. Future imaging genetics studies with large samples, especially population studies, would be uniquely informative in mapping the spatial distribution of the genetic risk to psychiatric disorders on brain processes during various cognitive tasks and may lead to the discovery of biological pathways that could be crucial in mediating the link between genetic factors and alterations in brain networks.

The Association between DRD3 Ser9Gly Polymorphism and Depression Severity in Parkinson's Disease

More and more evidence suggests that dopamine receptor D3 gene (DRD3) plays an important role in the clinical manifestations and the treatment of Parkinson's disease (PD). DRD3 Ser9Gly polymorphism is the most frequently studied variant point. Our aim was to investigate the potential effect of DRD3 Ser9Gly polymorphism on modulating resting-state brain function and associative clinical manifestations in PD patients. We consecutively recruited 61 idiopathic PD patients and 47 healthy controls (HC) who were evaluated by clinical scales, genotyped for variant Ser9Gly in DRD3, and underwent resting-state functional magnetic resonance imaging. Based on DRD3 Ser9Gly polymorphism, PD patients and HCs were divided into four subgroups. Then, two-way analysis of covariance (ANCOVA) was applied to investigate main effects and interactions of PD and DRD3 Ser9Gly polymorphism on the brain function via amplitude of low-frequency fluctuations (ALFF) approach. The association between DRD3 Ser9Gly-modulated significantly different brain regions, and clinical manifestations were detected by Spearman's correlations. PD patients exhibited decreased ALFF values in the right inferior occipital gyrus, lingual gyrus, and fusiform gyrus. A significant difference in the interaction of “groups × genotypes” was observed in the right medial frontal gyrus. The ALFF value of the cluster showing significant interactions was positively correlated with HAMD-17 scores (r=0.489, p=0.011) and anhedonia scores (r=0.512, p=0.008) in PD patients with the Ser/Gly or Gly/Gly genotypes. Therefore, D3 gene Ser9Gly polymorphism might be associated with the severity of depression characterized by anhedonia in PD patients.

Effectiveness of imaging genetics analysis to explain degree of depression in Parkinson's disease

Depression is one of the most common and important neuropsychiatric symptoms in Parkinson's disease and often becomes worse as Parkinson's disease progresses. However, the underlying mechanisms of depression in Parkinson's disease are not clear. The aim of our study was to find genetic features related to depression in Parkinson's disease using an imaging genetics approach and to construct an analytical model for predicting the degree of depression in Parkinson's disease. The neuroimaging and genotyping data were obtained from an openly accessible database. We computed imaging features through connectivity analysis derived from tractography of diffusion tensor imaging. The imaging features were used as intermediate phenotypes to identify genetic variants according to the imaging genetics approach. We then constructed a linear regression model using the genetic features from imaging genetics approach to describe clinical scores indicating the degree of depression. As a comparison, we constructed other models using imaging features and genetic features based on references to demonstrate the effectiveness of our imaging genetics model. The models were trained and tested in a five-fold cross-validation. The imaging genetics approach identified several brain regions and genes known to be involved in depression, with the potential to be used as meaningful biomarkers. Our proposed model using imaging genetic features predicted and explained the degree of depression in Parkinson's disease appropriately (adjusted R2 larger than 0.6 over five training folds) and with a lower error and higher correlation than with other models over five test folds.

A practical guide to linking brain-wide gene expression and neuroimaging data

The recent availability of comprehensive, brain-wide gene expression atlases such as the Allen Human Brain Atlas (AHBA) has opened new opportunities for understanding how spatial variations on molecular scale relate to the macroscopic neuroimaging phenotypes. A rapidly growing body of literature is demonstrating relationships between gene expression and diverse properties of brain structure and function, but approaches for combining expression atlas data with neuroimaging are highly inconsistent, with substantial variations in how the expression data are processed. The degree to which these methodological variations affect findings is unclear. Here, we outline a seven-step analysis pipeline for relating brain-wide transcriptomic and neuroimaging data and compare how different processing choices influence the resulting data. We suggest that studies using the AHBA should work towards a unified data processing pipeline to ensure consistent and reproducible results in this burgeoning field.

Imaging Genetics Towards a Refined Diagnosis of Schizophrenia

Current diagnoses of schizophrenia and related psychiatric disorders are classified by phenomenological principles and clinical descriptions while ruling out other symptoms and conditions. Specific biomarkers are needed to assist the current diagnostic system. However, complicated gene and environment interactions induce great disease heterogeneity. This unclear etiology and heterogeneity raise difficulties in distinguishing schizophrenia-related effects. Simultaneously, the overlap in symptoms, genetic variations, and brain alterations in schizophrenia and related psychiatric disorders raises similar difficulties in determining disease-specific effects. Imaging genetics is a unique methodology to assess the impact of genetic factors on both brain structure and function. More importantly, imaging genetics builds a bridge to understand the behavioral and clinical implications of genetics and neuroimaging. By characterizing and quantifying the brain measures affected in psychiatric disorders, imaging genetics is contributing to identifying potential biomarkers for schizophrenia and related disorders. To date, candidate gene analysis, genome-wide association studies, polygenetic risk score analysis, and large-scale collaborative studies have made contributions to the understanding of schizophrenia with the potential to serve as biomarkers. Despite limitations, imaging genetics remains promising as more aggregative, clustering methods and imaging genetics-compatible clinical assessments are employed in future studies. We review imaging genetics' contribution to our understanding of the heterogeneity within schizophrenia and the commonalities across schizophrenia and other diagnostic borders, and we will discuss whether imaging genetics is ready to form its own diagnostic system.

Recent advances in functional genome analysis

At the beginning of this century, the Human Genome Project produced the first drafts of the human genome sequence. Following this, large-scale functional genomics studies were initiated to understand the molecular basis underlying the translation of the instructions encoded in the genome into the biological traits of organisms. Instrumental in the ensuing revolution in functional genomics were the rapid advances in massively parallel sequencing technologies as well as the development of a wide diversity of protocols that make use of these technologies to understand cellular behavior at the molecular level. Here, we review recent advances in functional genomic methods, discuss some of their current capabilities and limitations, and briefly sketch future directions within the field.

Interplay of Brain-Derived Neurotrophic Factor and Cytokines in Schizophrenia

Brain-derived neurotrophic factor (BDNF) is a member of the neurotrophin family and plays an important role in neuroplasticity, differentiation and survival of neurons, as well as their function. Neuroinflammation has been explored in the pathophysiology of many mental disorders, such as schizophrenia. Cytokines representing different types of immune responses have an impact on neurogenesis and BDNF expression. Cross-regulation of BDNF and cytokines is accomplished through several signalling pathways. Also, typical and atypical antipsychotic drugs variously modulate the expression of BDNF and serum levels of cytokines, which can possibly be used in evaluation of therapy effectiveness. Comorbidity of metabolic syndrome and atopic diseases has been considered in the context of BDNF and cytokines interplay in schizophrenia.

Imaging genetics in autism spectrum disorders: Linking genetics and brain imaging in the pursuit of the underlying neurobiological mechanisms

Autism spectrum disorders (ASD) include a wide range of heterogeneous neurodevelopmental conditions that affect an individual in several aspects of social communication and behavior. Recent advances in molecular genetic technologies have dramatically increased our understanding of ASD etiology through the identification of several autism risk genes, most of which serve important functions in synaptic plasticity and protein synthesis. However, despite significant progress in this field of research, the characterization of the neurobiological mechanisms by which common genetic risk variants might operate to give rise to ASD symptomatology has proven to be far more difficult than expected. The imaging genetics approach holds great promise for advancing our understanding of ASD etiology by bridging the gap between genetic variations and their resultant biological effects on the brain. This paper provides a conceptual overview of the contribution of genetics in ASD and discusses key findings from the emerging field of imaging genetics.

A Brief Assessment of Intelligence Decline in Schizophrenia As Represented by the Difference between Current and Premorbid Intellectual Quotient

Patients with schizophrenia elicit several clinical features, such as psychotic symptoms, cognitive impairment, and subtle decline of intelligence. The latter two features become evident around the onset of the illness, although they may exist even before the disease onset in a substantial proportion of cases. Here, we review the literature concerning intelligence decline (ID) during the progression of schizophrenia. ID can be estimated by comparing premorbid and current intellectual quotient (IQ) by means of the Adult Reading Test and Wechsler Adult Intelligence Scale (WAIS), respectively. For the purpose of brief assessment, we have recently developed the WAIS-Short Form, which consists of Similarities and Symbol Search and well reflects functional outcomes. According to the degree of ID, patients were classified into three distinct subgroups; deteriorated, preserved, and compromised groups. Patients who show deteriorated IQ (deteriorated group) elicit ID from a premorbid level (≥10-point difference between current and premorbid IQ), while patients who show preserved or compromised IQ do not show such decline (<10-point difference). Furthermore, the latter patients were divided into patients with preserved and compromised IQ based on an estimated premorbid IQ score >90 or below 90, respectively. We have recently shown the distribution of ID in a large cohort of schizophrenia patients. Consistent with previous studies, approximately 30% of schizophrenia patients had a decline of less than 10 points, i.e., normal intellectual performance. In contrast, approximately 70% of patients showed deterioration of IQ. These results indicate that there is a subgroup of schizophrenia patients who have mild or minimal intellectual deficits, following the onset of the disorder. Therefore, a careful assessment of ID is important in identifying appropriate interventions, including medications, cognitive remediation, and social/community services.

Psychiatric polygenic risk associates with cortical morphology and functional organization in aging

Common brain abnormalities in cortical morphology and functional organization are observed in psychiatric disorders and aging, reflecting shared genetic influences. This preliminary study aimed to examine the contribution of a polygenetic risk for psychiatric disorders (PRS_cross) to aging brain and to identify molecular mechanisms through the use of multimodal brain images, genotypes, and transcriptome data. We showed age-related cortical thinning in bilateral inferior frontal cortex (IFC) and superior temporal gyrus and alterations in the functional connectivity between bilateral IFC and between right IFC and right inferior parietal lobe as a function of PRS_cross. Interestingly, the genes in PRS_cross, that contributed most to aging neurodegeneration, were expressed in the functioanlly connected cortical regions. Especially, genes identified through the genotype-functional connectivity association analysis were commonly expressed in both cortical regions and formed strong gene networks with biological processes related to neural plasticity and synaptogenesis, regulated by glutamatergic and GABAergic transmission, neurotrophin signaling, and metabolism. This study suggested integrating genotype and transcriptome with neuroimage data sheds new light on the mechanisms of aging brain.

The association between gene variants and longitudinal structural brain changes in psychosis: a systematic review of longitudinal neuroimaging genetics studies

Evidence suggests that genetic variation might influence structural brain alterations in psychotic disorders. Longitudinal genetic neuroimaging (G-NI) studies are designed to assess the association between genetic variants, disease progression and brain changes. There is a paucity of reviews of longitudinal G-NI studies in psychotic disorders. A systematic search of PubMed from inception until November 2016 was conducted to identify longitudinal G-NI studies examining the link between Magnetic Resonance Imaging (MRI) and Diffusion Tensor Imaging (DTI)-based brain measurements and specific gene variants (SNPs, microsatellites, haplotypes) in patients with psychosis. Eleven studies examined seven genes: BDNF, COMT, NRG1, DISC1, CNR1, GAD1, and G72. Eight of these studies reported at least one association between a specific gene variant and longitudinal structural brain changes. Genetic variants associated with longitudinal brain volume or cortical thickness loss included a 4-marker haplotype in G72, a microsatellite and a SNP in NRG1, and individual SNPs in DISC1, CNR1, BDNF, COMT and GAD1. Associations between genotype and progressive brain changes were most frequently observed in frontal regions, with five studies reporting significant interactions. Effect sizes for significant associations were generally of small or intermediate magnitude (Cohen’s d < 0.8). Only two genes (BDNF and NRG1) were assessed in more than one study, with great heterogeneity of the results. Replication studies and studies exploring additional genetic variants identified by large-scale genetic analysis are warranted to further ascertain the role of genetic variants in longitudinal brain changes in psychosis.

G72 primate-specific gene: a still enigmatic element in psychiatric disorders

Numerous studies have demonstrated a link between genetic markers on chromosome 13 and schizophrenia, bipolar affective disorder, and other psychiatric phenotypes. The G72/G30 genes (transcribed in opposite directions) are located on chromosome 13q33, a region demonstrating strong evidence for linkage with various neuropsychiatric disorders. G72/G30 was identified in 2002 as a schizophrenia susceptibility locus; however, subsequent association studies did not reach consensus on single SNPs within the locus. Simultaneously, a new vision for the genetic architecture of psychiatric disorders suggested that schizophrenia was a quantitative trait, therefore ascribable to potentially hundreds of genes and subjected to the vagaries of the environment. The main protein product of G72 gene is named pLG72 or D-amino acid oxidase activator DAOA (153 amino acids) and its function is still debated. Functional analyses, also showing controversial results, indicate that pLG72 contributes to N-methyl-D-aspartate receptor modulation by affecting activity of the flavoprotein D-amino acid oxidase, the enzyme responsible for degrading the neuromodulator D-serine. In this review we, for the first time, summarize findings from molecular genetic linkage and association studies concerning G72 gene, cellular and molecular studies on pLG72, and investigations performed on G72/G30 transgenic mice. This will help elucidate the role of psychosis susceptibility genes, which will have a major impact on our understanding of disease pathophysiology and thus change classification and treatment.