Shared Genetic Architecture Among Gastrointestinal Diseases, Schizophrenia, and Brain Subcortical Volumes.

BACKGROUND AND HYPOTHESIS: The gut-brain axis plays important roles in both gastrointestinal diseases (GI diseases) and schizophrenia (SCZ). Moreover, both GI diseases and SCZ exhibit notable abnormalities in brain subcortical volumes. However, the genetic mechanisms underlying the comorbidity of these diseases and the shared alterations in brain subcortical volumes remain unclear. STUDY DESIGN: Using the genome-wide association studies data of SCZ, 14 brain subcortical volumes, and 8 GI diseases, the global polygenic overlap and local genetic correlations were identified, as well as the shared genetic variants among those phenotypes. Furthermore, we conducted multi-trait colocalization analyses to bolster our findings. Functional annotations, cell-type enrichment, and protein-protein interaction (PPI) analyses were carried out to reveal the critical etiology and pathology mechanisms. STUDY RESULTS: The global polygenic overlap and local genetic correlations informed the close relationships between SCZ and both GI diseases and brain subcortical volumes. Moreover, 84 unique lead-shared variants were identified. The associated genes were linked to vital biological processes within the immune system. Additionally, significant correlations were observed with key immune cells and the PPI analysis identified several histone-associated hub genes. These findings highlighted the pivotal roles played by the immune system for both SCZ and GI diseases, along with the shared alterations in brain subcortical volumes. CONCLUSIONS: These findings revealed the shared genetic architecture contributing to SCZ and GI diseases, as well as their shared alterations in brain subcortical volumes. These insights have substantial implications for the concurrent development of intervention and therapy targets for these diseases.

Cross-ancestry genome-wide association studies of brain imaging phenotypes.

Genome-wide association studies of brain imaging phenotypes are mainly performed in European populations, but other populations are severely under-represented. Here, we conducted Chinese-alone and cross-ancestry genome-wide association studies of 3,414 brain imaging phenotypes in 7,058 Chinese Han and 33,224 white British participants. We identified 38 new associations in Chinese-alone analyses and 486 additional new associations in cross-ancestry meta-analyses at P < 1.46 × 10-11 for discovery and P < 0.05 for replication. We pooled significant autosomal associations identified by single- or cross-ancestry analyses into 6,443 independent associations, which showed uneven distribution in the genome and the phenotype subgroups. We further divided them into 44 associations with different effect sizes and 3,557 associations with similar effect sizes between ancestries. Loci of these associations were shared with 15 brain-related non-imaging traits including cognition and neuropsychiatric disorders. Our results provide a valuable catalog of genetic associations for brain imaging phenotypes in more diverse populations.

Genome-wide association study of hippocampal blood-oxygen-level-dependent-cerebral blood flow correlation in Chinese Han population.

Correlation between blood-oxygen-level-dependent (BOLD) and cerebral blood flow (CBF) has been used as an index of neurovascular coupling. Hippocampal BOLD-CBF correlation is associated with neurocognition, and the reduced correlation is associated with neuropsychiatric disorders. We conducted the first genome-wide association study of the hippocampal BOLD-CBF correlation in 4,832 Chinese Han subjects. The hippocampal BOLD-CBF correlation had an estimated heritability of 16.2-23.9% and showed reliable genome-wide significant association with a locus at 3q28, in which many variants have been linked to neuroimaging and cerebrospinal fluid markers of Alzheimer's disease. Gene-based association analyses showed four significant genes (GMNC, CRTC2, DENND4B, and GATAD2B) and revealed enrichment for mast cell calcium mobilization, microglial cell proliferation, and ubiquitin-related proteolysis pathways that regulate different cellular components of the neurovascular unit. This is the first unbiased identification of the association of hippocampal BOLD-CBF correlation, providing fresh insights into the genetic architecture of hippocampal neurovascular coupling.

Covariation of preadult environmental exposures, adult brain imaging phenotypes, and adult personality traits.

Exposure to preadult environmental exposures may have long-lasting effects on mental health by affecting the maturation of the brain and personality, two traits that interact throughout the developmental process. However, environment-brain-personality covariation patterns and their mediation relationships remain unclear. In 4297 healthy participants (aged 18-30 years), we combined sparse multiple canonical correlation analysis with independent component analysis to identify the three-way covariation patterns of 59 preadult environmental exposures, 760 adult brain imaging phenotypes, and five personality traits, and found two robust environment-brain-personality covariation models with sex specificity. One model linked greater stress and less support to weaker functional connectivity and activity in the default mode network, stronger activity in subcortical nuclei, greater thickness and volume in the occipital, parietal and temporal cortices, and lower agreeableness, consciousness and extraversion as well as higher neuroticism. The other model linked higher urbanicity and better socioeconomic status to stronger functional connectivity and activity in the sensorimotor network, smaller volume and surface area and weaker functional connectivity and activity in the medial prefrontal cortex, lower white matter integrity, and higher openness to experience. We also conducted mediation analyses to explore the potential bidirectional mediation relationships between adult brain imaging phenotypes and personality traits with the influence of preadult environmental exposures and found both environment-brain-personality and environment-personality-brain pathways. We finally performed moderated mediation analyses to test the potential interactions between macro- and microenvironmental exposures and found that one category of exposure moderated the mediation pathways of another category of exposure. These results improve our understanding of the effects of preadult environmental exposures on the adult brain and personality traits and may facilitate the design of targeted interventions to improve mental health by reducing the impact of adverse environmental exposures.

Cross-ancestry genome-wide association meta-analyses of hippocampal and subfield volumes.

The hippocampus is critical for memory and cognition and neuropsychiatric disorders, and its subfields differ in architecture and function. Genome-wide association studies on hippocampal and subfield volumes are mainly conducted in European populations; however, other ancestral populations are under-represented. Here we conduct cross-ancestry genome-wide association meta-analyses in 65,791 individuals for hippocampal volume and 38,977 for subfield volumes, including 7,009 individuals of East Asian ancestry. We identify 339 variant-trait associations at P < 1.13 × 10-9 for 44 hippocampal traits, including 23 new associations. Common genetic variants have similar effects on hippocampal traits across ancestries, although ancestry-specific associations exist. Cross-ancestry analysis improves the fine-mapping precision and the prediction performance of polygenic scores in under-represented populations. These genetic variants are enriched for Wnt signaling and neuron differentiation and affect cognition, emotion and neuropsychiatric disorders. These findings may provide insight into the genetic architectures of hippocampal and subfield volumes.

Genes associated with spontaneous brain activity changes in clinically different patients with major depressive disorder: A transcription-neuroimaging association study.

AIMS: The amplitude of low-frequency fluctuations (ALFF) of resting-state functional MRI signals is a reliable neuroimaging measure of spontaneous brain activity. Inconsistent ALFF alterations have been reported in major depressive disorder (MDD) possibly due to clinical heterogeneity. This study was designed to investigate clinically sensitive and insensitive genes associated with ALFF alterations in MDD and the potential mechanisms. METHODS: Transcription-neuroimaging association analyses of case-control ALFF differences from two independent neuroimaging datasets with gene expression data from Allen Human Brain Atlas were performed to identify the two gene sets. Various enrichment analyses were conducted to characterize their preference in biological functions, cell types, temporal stages, and shared effects with other psychiatric disorders. RESULTS: Compared with controls, first-episode and drug-naïve patients showed more extensive ALFF alterations than patients with varied clinical features. We identified 903 clinically sensitive genes and 633 clinically insensitive genes, and the former was enriched for genes with down-regulated expression in the cerebral cortex of MDD patients. Despite shared functions of cell communication, signaling, and transport, clinically sensitive genes were enriched for cell differentiation and development whereas clinically insensitive genes were for ion transport and synaptic signaling. Clinically sensitive genes showed enrichment for microglia and macrophage from childhood to young adulthood in contrast to clinically insensitive genes for neurons before early infancy. Clinically sensitive genes (15.2%) were less likely correlated with ALFF alterations in schizophrenia than clinically insensitive genes (66.8%), and both were not relevant to bipolar disorder and adult attention deficit and hyperactivity disorder based on a third independent neuroimaging dataset. CONCLUSIONS: Present results provide novel insights into the molecular mechanisms of spontaneous brain activity changes in clinically different patients with MDD.

The impact of pre-adulthood urbanicity on hippocampal subfield volumes and neurocognitive abilities in young adults.

BACKGROUND: Urbanicity refers to the conditions that are particular to urban areas and is a growing environmental challenge that may affect hippocampus and neurocognition. This study aimed to investigate the effects of the average pre-adulthood urbanicity on hippocampal subfield volumes and neurocognitive abilities as well as the sensitive age windows of the urbanicity effects. PARTICIPANTS AND METHODS: We included 5,390 CHIMGEN participants (3,538 females; age: 23.69 ± 2.26 years, range: 18-30 years). Pre-adulthood urbanicity of each participant was defined as the average value of annual night-time light (NL) or built-up% from age 0-18, which were extracted from remote-sensing satellite data based on annual residential coordinates of the participants. The hippocampal subfield volumes were calculated based on structural MRI and eight neurocognitive measures were assessed. The linear regression was applied to investigate the associations of pre-adulthood NL with hippocampal subfield volumes and neurocognitive abilities, mediation models were used to find the underlying pathways among urbanicity, hippocampus and neurocognition, and distributed lag models were used to identify sensitive age windows of urbanicity effect. RESULTS: Higher pre-adulthood NL was associated with greater volumes in the left (ß = 0.100, 95%CI: [0.075, 0.125]) and right (0.078, [0.052, 0.103]) fimbria and left subiculum body (0.045, [0.020, 0.070]) and better neurocognitive abilities in information processing speed (-0.212, [-0.240, -0.183]), working memory (0.085, [0.057, 0.114]), episodic memory (0.107, [0.080, 0.135]), and immediate (0.094, [0.065, 0.123]) and delayed (0.087, [0.058, 0.116]) visuospatial recall, and hippocampal subfield volumes and visuospatial memory showed bilateral mediations for the urbanicity effects. Urbanicity effects were greatest on the fimbria in preschool and adolescence, on visuospatial memory and information processing from childhood to adolescence and on working memory after 14 years. CONCLUSION: These findings improve our understanding of the impact of urbanicity on hippocampus and neurocognitive abilities and will benefit for designing more targeted intervention for neurocognitive improvement.

Global diversity in individualized cortical network topography.

Individualized cortical network topography (ICNT) varies between people and exhibits great variability in the association networks in the human brain. However, these findings were mainly discovered in Western populations. It remains unclear whether and how ICNT is shaped by the non-Western populations. Here, we leveraged a multisession hierarchical Bayesian model to define individualized functional networks in White American and Han Chinese populations with data from both US and Chinese Human Connectome Projects. We found that both the size and spatial topography of individualized functional networks differed between White American and Han Chinese groups, especially in the heteromodal association cortex (including the ventral attention, control, language, dorsal attention, and default mode networks). Employing a support vector machine, we then demonstrated that ethnicity-related ICNT diversity can be used to identify an individual's ethnicity with high accuracy (74%, pperm < 0.0001), with heteromodal networks contributing most to the classification. This finding was further validated through mass-univariate analyses with generalized additive models. Moreover, we reveal that the spatial heterogeneity of ethnic diversity in ICNT correlated with fundamental properties of cortical organization, including evolutionary cortical expansion, brain myelination, and cerebral blood flow. Altogether, this case study highlights a need for more globally diverse and publicly available neuroimaging datasets.

Disrupted local functional connectivity in schizophrenia: An updated and extended meta-analysis.

Neuroimaging studies have shown that schizophrenia is associated with disruption of resting-state local functional connectivity. However, these findings vary considerably, which hampers our understanding of the underlying pathophysiological mechanisms of schizophrenia. Here, we performed an updated and extended meta-analysis to identify the most consistent changes of local functional connectivity measured by regional homogeneity (ReHo) in schizophrenia. Specifically, a systematic search of ReHo studies in patients with schizophrenia in PubMed, Embase, and Web of Science identified 18 studies (20 datasets), including 652 patients and 596 healthy controls. In addition, we included three whole-brain statistical maps of ReHo differences calculated based on independent datasets (163 patients and 194 controls). A voxel-wise meta-analysis was then conducted to investigate ReHo alterations and their relationship with clinical characteristics using the newly developed seed-based d mapping with permutation of subject images (SDM-PSI) meta-analytic approach. Compared with healthy controls, patients with schizophrenia showed significantly higher ReHo in the bilateral medial superior frontal gyrus, while lower ReHo in the bilateral postcentral gyrus, right precentral gyrus, and right middle occipital gyrus. The following sensitivity analyses including jackknife analysis, subgroup analysis, heterogeneity test, and publication bias test demonstrated that our results were robust and highly reliable. Meta-regression analysis revealed that illness duration was negatively correlated with ReHo abnormalities in the right precentral/postcentral gyrus. This comprehensive meta-analysis not only identified consistent and reliably aberrant local functional connectivity in schizophrenia but also helped to further deepen our understanding of its pathophysiology.

Total Brain Volumetric Measures and Schizophrenia Risk: A Two-Sample Mendelian Randomization Study.

Schizophrenia (SCZ) is an idiopathic psychiatric disorder with a heritable component and a substantial public health impact. Although abnormalities in total brain volumetric measures (TBVMs) have been found in patients with SCZ, it is still unknown whether these abnormalities have a causal effect on the risk of SCZ. Here, we performed a Mendelian randomization (MR) study to investigate the possible causal associations between each TBVM and SCZ risk. Specifically, genome-wide association study (GWAS) summary statistics of total gray matter volume, total white matter volume, total cerebrospinal fluid volume, and total brain volume were obtained from the United Kingdom Biobank database (33,224 individuals), and SCZ GWAS summary statistics were provided by the Psychiatric Genomics Consortium (150,064 individuals). The main MR analysis was conducted using the inverse variance weighted method, and other MR methods, including MR-Egger, weighted median, simple mode, and weighted mode methods, were performed to assess the robustness of our findings. For pleiotropy analysis, we employed three approaches: MR-Egger intercept, MR-PRESSO, and heterogeneity tests. No TBVM was causally associated with SCZ risk according to the MR results, and no significant pleiotropy or heterogeneity was found for instrumental variables. Taken together, this study suggested that alterations in TBVMs were not causally associated with the risk of SCZ.

Effects of INSR genetic polymorphism on hippocampal volume and episodic memory in chinese type 2 diabetes.

AIMS: We aimed to investigate the effect of the type 2 diabetes-specific insulin/IGF signaling genetic variants on the hippocampal volume and their relationships with episodic memory in Chinese patients with type 2 diabetes. METHODS: Analysis of variance was used to evaluate the genotype-by-diagnosis interaction effect on hippocampal volume in Chinese participants (109 patients with type 2 diabetes, 116 healthy controls). Mediation analysis was performed to test whether the hippocampal volume would mediate the association between genotype and episodic memory in patients with type 2 diabetes. RESULTS: INSR (rs8101064) exhibited a significant genotype-by-diagnosis interaction effect on the bilateral hippocampal volumes (left, P = 0.020; right, P = 0.004, PFDR < 0.05). The T allele carriers exhibited smaller bilateral hippocampal volumes than the CC homozygotes in patients with type 2 diabetes (left, P = 0.004; right, P = 0.002). Mediation analysis revealed the significant mediation effect of the left hippocampal volume on the association between INSR (rs8101064) genetic polymorphism and the short- and long-term memory scores in patients with type 2 diabetes (short-term memory: 95% CI, -2.716, -0.266; long-term memory: 95% CI, -0.823, -0.103). CONCLUSIONS: Hyperglycemia exposure and INSR (rs8101064) genetic polymorphism had an interaction effect on the hippocampal volume, and the T allele of the INSR (rs8101064) may serve as a risk factor for the decreased hippocampal volume in Chinese patients with type 2 diabetes. The left hippocampal volume mediated the effect of INSR (rs8101064) genetic polymorphism on episodic memory in Chinese patients with type 2 diabetes, which provided a biological pathway for understanding how the INSR (rs8101064) genetic polymorphism affects episodic memory in type 2 diabetes.

The morphometry of left cuneus mediating the genetic regulation on working memory.

Working memory is a basic human cognitive function. However, the genetic signatures and their biological pathway remain poorly understood. In the present study, we tried to clarify this issue by exploring the potential associations and pathways among genetic variants, brain morphometry and working memory performance. We first carried out association analyses between 2-back accuracy and 212 image-derived phenotypes from 1141 Human Connectome Project (HCP) subjects using a linear mixed model (LMM). We found a significantly positive correlation between the left cuneus volume and 2-back accuracy (T = 3.615, p = 3.150e-4, Cohen's d = 0.226, corrected using family-wise error [FWE] method). Based on the LMM-based genome-wide association study (GWAS) on the HCP dataset and UK Biobank 33 k GWAS summary statistics, we identified eight independent single nucleotide polymorphisms (SNPs) that were reliably associated with left cuneus volume in both UKB and HCP dataset. Within the eight SNPs, we found a negative correlation between the rs76119478 polymorphism and 2-back accuracy accuracy (T = -2.045, p = .041, Cohen's d = -0.129). Finally, an LMM-based mediation analysis elucidated a significant effect of left cuneus volume in mediating rs76119478 polymorphism on the 2-back accuracy (indirect effect = -0.007, 95% BCa CI = [-0.045, -0.003]). These results were also replicated in a subgroup of Caucasians in the HCP population. Further fine mapping demonstrated that rs76119478 maps on intergene CTD-2315A10.2 adjacent to protein-encoding gene DAAM1, and is significantly associated with L3HYPDH mRNA expression. Our study suggested this new variant rs76119478 may regulate the working memory through exerting influence on the left cuneus volume.

Prefrontal Granule Cell-Related Genes and Schizophrenia.

Although both the granular layer of the prefrontal cortex (PFC) and schizophrenia are unique in primates, especially humans, their linkage is unclear. Here, we tested whether schizophrenia is associated with expression profiles of the granule cell (GC)-related genes in the human PFC. We identified 14 candidate GC-related genes with gradually increased expression levels along the gradient of the agranular, dysgranular, light-granular, and granular prefrontal regions based on the densely sampled gene expression data of 6 postmortem human brains, and with more than 10-fold expression in neurons than other cell types based on the single-cell RNA-sequencing data of the human PFC. These GC-related genes were functionally associated with synaptic transmission and cell development and differentiation. The identified 14 GC-related genes were significantly enriched for schizophrenia, but not for depression and bipolar disorder. The expression levels of the 4 stable schizophrenia- and GC-related genes were spatially correlated with gray matter volume differences in the PFC between patients with schizophrenia and healthy controls. This study provides a set of candidate genes for the human prefrontal GCs and links expression profiles of the GC-related genes to the prefrontal structural impairments in schizophrenia.

Brain mRNA Expression Associated with Cortical Volume Alterations in Autism Spectrum Disorder.

Numerous studies report abnormal cerebral cortex volume (CCV) in autism spectrum disorder (ASD); however, genes related to CCV abnormalities in ASD remain largely unknown. Here, we identify genes associated with CCV alterations in ASD by performing spatial correlations between the gene expression of 6 donated brains and neuroimaging data from 1,404 ASD patients and 1,499 controls. Based on spatial correlations between gene expression and CCV differences from two independent meta-analyses and between gene expression and individual CCV distributions of 404 patients and 496 controls, we identify 417 genes associated with both CCV differences and individual CCV distributions. These genes are enriched for genetic association signals and genes downregulated in the ASD post-mortem brain. The expression patterns of these genes are correlated with brain activation patterns of language-related neural processes frequently impaired in ASD. These findings highlight a model whereby genetic risk impacts gene expression (downregulated), which leads to CCV alterations in ASD.

Individual-Level Identification of Gene Expression Associated with Volume Differences among Neocortical Areas.

The human cerebral cortex is the source of many complex behaviors and is a vulnerable target of various neuropsychiatric disorders, but transcriptional profiles linked to cerebral cortical volume (CCV) differences across brain areas remain unknown. Here, we screened CCV-related genes using an across-sample spatial correlation analysis in 6 postmortem brains and then individually validated these correlations in 1091 subjects with different ages and ethnicities. We identified 62 genes whose transcriptional profiles were repeatedly associated with CCV in more than 90% of individuals. CCV-related genes were specifically expressed in neurons and in developmental periods from middle childhood to young adulthood, were enriched in ion channels and developmental processes, and showed significant overlap with genes linked to brain functional activity and mental disorders. The identified genes represent the conserved transcriptional architecture of the human cerebral cortex, suggesting a link between conserved gene transcription and neocortical structural properties.

Left Parietal Functional Connectivity Mediates the Association Between COMT rs4633 and Verbal Intelligence in Healthy Adults.

In Chinese Han population, Catechol-O-methyltransferase gene (COMT) rs4633 is found to be associated with impaired cognitive process. We aimed to investigate the association between COMT rs4633 and verbal intelligence and the underlying neural mechanisms in Chinese Han healthy young adults. In 256 Chinese Han healthy young adults, we explored the modulatory effects of COMT rs4633 on verbal intelligence quotient (VIQ) and functional connectivity density (FCD) of the brain and the mediation effect of FCD on the association between COMT and VIQ. We further investigated the association between the expression patterns of dopamine receptor genes and the effect of COMT on FCD in the human brain. COMT rs4633 TT homozygotes exhibited lower VIQ than CC homozygotes and TC heterozygotes, higher long-range FCD (lrFCD) than CC homozygotes and TC heterozygotes in the left superior frontal gyrus. TT homozygotes and TC heterozygotes showed higher lrFCD than CC homozygotes in the left inferior parietal lobule. The lrFCD differences across genotypic subgroups were negatively associated with the expression of DRD2 and DRD3 genes. The left parietal lrFCD mediated the association between COMT rs4633 and VIQ. These findings provide a biological pathway that COMT rs4633 affects verbal intelligence via modulating the lrFCD of the left inferior parietal lobule.