Genetic Architecture Underlying Differential Resting-state Functional Connectivity of Subregions Within the Human Visual Cortex

Genetic mechanisms of dynamic functional connectivity density in diabetic retinopathy brains: a combined transcriptomic and resting-state functional magnetic resonance imaging study

Background

Diabetic retinopathy (DR) is a condition characterized by fundus lesions resulting from retinal microvascular leakage and obstruction linked to chronic progressive diabetes mellitus. Previous neuroimaging research has revealed both structural and functional changes in the brains of DR patients. Nevertheless, the variations in dynamic functional connectivity density (dFCD) within the brains of DR patients, along with the underlying molecular mechanisms connected to these changes, have yet to be fully understood.

Methods

Forty-seven diabetic retinopathy (DR) patients and 46 healthy controls (HCs) matched for sex, age, and education were recruited for this study from the Department of Ophthalmology at the Jiangxi Provincial People's Hospital. All subjects underwent resting-state functional magnetic resonance imaging scans to analyze the differences in dFCD between the two groups. Utilizing the Allen Human Brain Atlas, we conducted spatial correlation analyses integrating transcriptomic and neuroimaging data to pinpoint genes showing correlated expression levels with dFCD alterations in DR patients. Subsequently, we carried out gene enrichment, specific expression, and protein-protein interaction analyses.

Results

In comparison to the HC group, the DR group exhibited significantly reduced dFCD variability in the left anterior cingulum, left superior occipital gyrus, and right postcentral gyrus. The abnormal dFCD variability is linked to 1,318 positively and 1,318 negatively associated genes, primarily enriched for biological functions such as ion channels, synapses, and cellular junctions. Specific expression analysis revealed that these genes were distinctly expressed in Purkinje neurons, cortex, and striatum brain regions. Furthermore, protein-protein interaction (PPI) analyses indicated that these positive and negative genes could organize PPI networks with the support of respective hub genes.

Conclusion

our study identified altered dFCD variability in brain regions linked to visual and cognitive functions in DR patients. Moreover, transcriptome-neuroimaging correlation analyses revealed a spatial association between these dFCD changes and the genes with unique functional profiles. These genes were enriched in biologically significant functions and pathways, specific to certain cells and brain areas. Our research offers novel understandings of the genetic mechanisms influencing dFCD alterations in DR.

Altered spatiotemporal consistency and their genetic mechanisms in mild cognitive impairment: a combined neuroimaging and transcriptome study

The Four-dimensional (spatiotemporal) Consistency of local Neural Activities (FOCA) metric was utilized to assess spontaneous whole-brain activity. Despite its application, the genetic underpinnings of FOCA alterations in Alzheimer's Disease (AD)-related Mild Cognitive Impairment (MCI) remain largely unexplored. To elucidate these changes, we analyzed group FOCA differences in 41 MCI patients and 46 controls from the Alzheimer's Disease Neuroimaging Initiative database. Integrating the Allen Human Brain Atlas, we performed transcriptome-neuroimaging spatial association analyses to pinpoint genes correlating with MCI-related FOCA changes. We observed heightened FOCA in the frontal-parietal system and diminished FOCA in the temporal lobe and medium cingulate gyrus among MCI patients. These FOCA alterations were spatially linked to the expression of 384 genes, which were enriched in crucial molecular functions, biological processes, and cellular components of the cerebral cortex, as well as related pathways. These genes were specifically expressed in brain tissue and corticothalamic neurons, particularly during late cortical development. They also connected to various behavioral domains. Furthermore, these genes could form a protein-protein interaction network, supported by 34 hub genes. Our results suggest that local spatiotemporal consistency of spontaneous brain activity in MCI may stem from the complex interplay of a broad spectrum of genes with diverse functional features.

Regional brain iron correlates with transcriptional and cellular signatures in Alzheimer's disease

INTRODUCTION

The link between overload brain iron and transcriptional/cellular signatures in Alzheimer's disease (AD) remains inconclusive.

METHODS

Iron deposition in 41 cortical and subcortical regions of 30 AD patients and 26 healthy controls (HCs) was measured using quantitative susceptibility mapping (QSM). The expression of 15,633 genes was estimated in the same regions using transcriptomic data from the Allen Human Brain Atlas (AHBA). Partial least square (PLS) regression was used to identify the association between the healthy brain gene transcription and aberrant regional QSM signal in AD. The biological processes and cell types associated with the linked genes were evaluated.

RESULTS

Gene ontological analyses showed that the first PLS component (PLS1) genes were enriched for biological processes relating to the "protein phosphorylation" and "metal ion transport". Additionally, these genes were expressed in microglia (MG) and glutamatergic neurons (GLUs).

DISCUSSION

Our findings provide mechanistic insights from transcriptional and cellular signatures into regional iron accumulation measured by QSM in AD.

HIGHLIGHTS

Spatial patterns of iron deposition changes in AD correlate with cortical spatial expression genes in healthy subjects. The identified gene transcription profile underlies aberrant iron accumulation in AD was enriched for biological processes relating to "protein phosphorylation" and "metal ion transport". The related genes were predominantly expressed in MG and GLUs.

Molecular mechanisms and behavioral relevance underlying neural correlates of childhood neglect

BACKGROUND

Childhood neglect is associated with brain changes, yet the molecular mechanisms and behavioral relevance underlying such associations remain elusive.

METHODS

We calculated fractional amplitude of low-frequency fluctuations (fALFF) using resting-state functional MRI and tested their correlation with childhood neglect across a large sample of 510 healthy young adults. Then, we investigated the spatial relationships of the identified neural correlates of childhood neglect with gene expression, neurotransmitter, and behavioral domain atlases.

RESULTS

We found that more severe childhood neglect was correlated with higher fALFF in the bilateral anterior cingulate cortex. Remarkably, the identified neural correlates of childhood neglect were spatially correlated with expression of gene categories primarily involving neuron, synapse, ion channel, cognitive and perceptual processes, and physiological response and regulation. Concurrently, there were significant associations between the neural correlates and specific neurotransmitter systems including serotonin and GABA. Finally, neural correlates of childhood neglect were associated with diverse behavioral domains implicating mental disorders, emotion, cognition, and sensory perception.

LIMITATIONS

The cross-sectional study design cannot unequivocally establish causality.

CONCLUSIONS

Our findings may not only add to the current knowledge regarding the relationship between childhood neglect and mental health, but also have clinical implications for developing preventive strategies for individuals exposed to childhood neglect who are at risk for mental disorders.

Molecular mechanisms underlying the neural correlates of working memory

BACKGROUND

Working memory (WM), a core component of executive functions, relies on a dedicated brain system that maintains and stores information in the short term. While extensive neuroimaging research has identified a distributed set of neural substrates relevant to WM, their underlying molecular mechanisms remain enigmatic. This study investigated the neural correlates of WM as well as their underlying molecular mechanisms.

RESULTS

Our voxel-wise analyses of resting-state functional MRI data from 502 healthy young adults showed that better WM performance (higher accuracy and shorter reaction time of the 3-back task) was associated with lower functional connectivity density (FCD) in the left inferior temporal gyrus and higher FCD in the left anterior cingulate cortex. A combination of transcriptome-neuroimaging spatial correlation and the ensemble-based gene category enrichment analysis revealed that the identified neural correlates of WM were associated with expression of diverse gene categories involving important cortical components and their biological processes as well as sodium channels. Cross-region spatial correlation analyses demonstrated significant associations between the neural correlates of WM and a range of neurotransmitters including dopamine, glutamate, serotonin, and acetylcholine.

CONCLUSIONS

These findings may help to shed light on the molecular mechanisms underlying the neural correlates of WM.

Neural Correlates of Early-Life Urbanization and Their Spatial Relationships with Gene Expression, Neurotransmitter, and Behavioral Domain Atlases

Previous neuroimaging research has established associations between urban exposure during early life and alterations in brain function and structure. However, the molecular mechanisms and behavioral relevance of these associations remain largely unknown. Here, we aimed to address this question using a combined analysis of multimodal data. Initially, we calculated amplitude of low-frequency fluctuations (ALFF) and gray matter volume (GMV) using resting-state functional and structural MRI to investigate their associations with early-life urbanization in a large sample of 511 healthy young adults. Then, we examined the spatial relationships of the identified neural correlates of early-life urbanization with gene expression, neurotransmitter, and behavioral domain atlases. Results showed that higher early-life urbanization scores were correlated with increased ALFF of the right fusiform gyrus and decreased GMV of the left dorsal medial prefrontal cortex and left precuneus. Remarkably, the identified neural correlates of early-life urbanization were spatially correlated with expression of gene categories primarily involving immune system process, signal transduction, and cellular metabolic process. Concurrently, there were significant associations between the neural correlates and specific neurotransmitter systems including dopamine, acetylcholine, and serotonin. Finally, we found that the ALFF correlates were associated with behavioral terms including "perception," "sensory," "cognitive control," and "reasoning." Apart from expanding existing knowledge of early-life urban environmental risk for mental disorders and health in general, our findings may contribute to an emerging framework for integrating social science, neuroscience, genetics, and public policy to respond to the major health challenge of world urbanization.

Age-dependent functional development pattern in neonatal brain: An fMRI-based brain entropy study

The relationship between brain entropy (BEN) and early brain development has been established through animal studies. However, it remains unclear whether the BEN can be used to identify age-dependent functional changes in human neonatal brains and the genetic underpinning of the new neuroimaging marker remains to be elucidated. In this study, we analyzed resting-state fMRI data from the Developing Human Connectome Project, including 280 infants who were scanned at 37.5-43.5 weeks postmenstrual age. The BEN maps were calculated for each subject, and a voxel-wise analysis was conducted using a general linear model to examine the effects of age, sex, and preterm birth on BEN. Additionally, we evaluated the correlation between regional BEN and gene expression levels. Our results demonstrated that the BEN in the sensorimotor-auditory and association cortices, along the 'S-A' axis, was significantly positively correlated with postnatal age (PNA), and negatively correlated with gestational age (GA), respectively. Meanwhile, the BEN in the right rolandic operculum correlated significantly with both GA and PNA. Preterm-born infants exhibited increased BEN values in widespread cortical areas, particularly in the visual-motor cortex, when compared to term-born infants. Moreover, we identified five BEN-related genes (DNAJC12, FIG4, STX12, CETN2, and IRF2BP2), which were involved in protein folding, synaptic vesicle transportation and cell division. These findings suggest that the fMRI-based BEN can serve as an indicator of age-dependent brain functional development in human neonates, which may be influenced by specific genes.

Transcriptomic decoding of regional cortical vulnerability to major depressive disorder

Previous studies in small samples have identified inconsistent cortical abnormalities in major depressive disorder (MDD). Despite genetic influences on MDD and the brain, it is unclear how genetic risk for MDD is translated into spatially patterned cortical vulnerability. Here, we initially examined voxel-wise differences in cortical function and structure using the largest multi-modal MRI data from 1660 MDD patients and 1341 controls. Combined with the Allen Human Brain Atlas, we then adopted transcription-neuroimaging spatial correlation and the newly developed ensemble-based gene category enrichment analysis to identify gene categories with expression related to cortical changes in MDD. Results showed that patients had relatively circumscribed impairments in local functional properties and broadly distributed disruptions in global functional connectivity, consistently characterized by hyper-function in associative areas and hypo-function in primary regions. Moreover, the local functional alterations were correlated with genes enriched for biological functions related to MDD in general (e.g., endoplasmic reticulum stress, mitogen-activated protein kinase, histone acetylation, and DNA methylation); and the global functional connectivity changes were associated with not only MDD-general, but also brain-relevant genes (e.g., neuron, synapse, axon, glial cell, and neurotransmitters). Our findings may provide important insights into the transcriptomic signatures of regional cortical vulnerability to MDD.

Genetic mechanisms underlying local spontaneous brain activity in episodic migraine

Advances in neuroimaging techniques during the past few decades have captured impaired functional brain activity in migraine disorders, yet the molecular mechanisms accounting for its alterations in migraine remain largely unknown. A total of 27 patients with episodic migraine (EM) and 30 matched healthy controls (HCs) underwent resting-state functional and structural magnetic resonance imaging (MRI) scans. Regional homogeneity (ReHo), low-frequency fluctuations (ALFF), and fractional amplitude of low-frequency fluctuations (fALFF) of fMRI were compared between the two groups. Based on the Allen Human Brain Atlas and risk genes in migraine, we identified gene expression profiles associated with ReHo alterations in EM. Compared with HCs, patients with EM showed increased ReHo in the left orbital part of the superior frontal gyrus (P < 0.05, cluster-level FWE-corrected). The expression profiles of 16 genes were significantly correlated with ReHo alterations in EM (P < 0.05/5,013, Bonferroni corrected). These genes were mainly enriched for transcription regulation, synaptic transmission, energy metabolism, and migraine disorders. Furthermore, the neural activation was positively correlated with Hamilton Rating Scale for Anxiety (HAMA) scores. To test the stability of our results, we repeated our procedure by using ALFF and fALFF and found these results had a high degree of consistency. Overall, these findings not only demonstrated that regional brain activity was increased in patients with EM, which was associated with emotional regulation but also provided new insights into the genetic mechanisms underlying these changes in migraine.

Molecular mechanisms underlying resting-state brain functional correlates of behavioral inhibition

Previous literature has established the presence of sex differences in behavioral inhibition as well as its neural substrates and related disease risk. However, there is limited evidence that speaks directly to the question of whether or not there are sex-dependent associations between behavioral inhibition and resting-state brain function and, if so, how they are modulated by the underlying molecular mechanisms. We computed functional connectivity density (FCD) using resting-state functional MRI data to examine their associations with behavioral inhibition ability measured using a Go/No-Go task across a large cohort of 510 healthy young adults. Then, we examined the spatial relationships of the FCD correlates of behavioral inhibition with gene expression and neurotransmitter atlases to explore their potential genetic architecture and neurochemical basis. A significant negative correlation between behavioral inhibition and FCD in the left superior parietal lobule was found in females but not males. Further spatial correlation analyses demonstrated that the identified neural correlates of behavioral inhibition were associated with expression of gene categories predominantly implicating essential components of the cerebral cortex (glial cell, neuron, axon, dendrite, and synapse) and ion channel activity, as well as were linked to the serotonergic system. Our findings may not only yield important insights into the molecular mechanisms underlying the female-specific neural substrates of behavioral inhibition, but also provide a critical context for understanding how biological sex might contribute to variation in behavioral inhibition and its related disease risk.

Nodal properties of the resting-state brain functional network in childhood and adolescence

BACKGROUND AND PURPOSE

Changes in the topological properties of brain functional network nodes during childhood and adolescence can provide more detailed and intuitive information on the rules of brain development. This study aims to explore the characteristics of nodal attributes in child and adolescent brain functional networks and analyze the correlation between nodal attributes in different brain regions and age.

METHODS

Forty-two healthy volunteers aged 6-18 years who were right-handed primary and middle school students were recruited, and the subgroup analysis included children (6-12 years, n = 19) and adolescents (13-18 years, n = 23). Resting-state functional magnetic resonance imaging data were collected using a 3.0 Tesla MRI scanner. The topological properties of the functional brain network were analyzed using graph theory.

RESULTS

Compared with the children group, the degree centrality and nodal efficiency of multiple brain regions in the adolescent group were significantly increased, and the nodal shortest path was reduced (q<0.05, false discovery rate corrected). These brain regions were widely distributed in the whole brain and significantly correlated with age. Compared with the children group, reduced degree centralities were observed in the left dorsolateral fusiform gyrus, left rostral cuneus gyrus, and right medial superior occipital gyrus.

CONCLUSION

The transmission efficiency of the brain's core network gradually increased, and the subnetwork function gradually improved in children and adolescents with age. The functional development of each brain area in the occipital visual cortex was uneven and there was functional differentiation within the occipital visual cortex.

Cerebral blood flow changes and their genetic mechanisms in major depressive disorder: a combined neuroimaging and transcriptome study

BACKGROUND

Extensive research has shown abnormal cerebral blood flow (CBF) in patients with major depressive disorder (MDD) that is a heritable disease. The objective of this study was to investigate the genetic mechanisms of CBF abnormalities in MDD.

METHODS

To achieve a more thorough characterization of CBF changes in MDD, we performed a comprehensive neuroimaging meta-analysis of previous literature as well as examined group CBF differences in an independent sample of 133 MDD patients and 133 controls. In combination with the Allen Human Brain Atlas, transcriptome-neuroimaging spatial association analyses were conducted to identify genes whose expression correlated with CBF changes in MDD, followed by a set of gene functional feature analyses.

RESULTS

We found increased CBF in the reward circuitry and default-mode network and decreased CBF in the visual system in MDD patients. Moreover, these CBF changes were spatially associated with expression of 1532 genes, which were enriched for important molecular functions, biological processes, and cellular components of the cerebral cortex as well as several common mental disorders. Concurrently, these genes were specifically expressed in the brain tissue, in immune cells and neurons, and during nearly all developmental stages. Regarding behavioral relevance, these genes were associated with domains involving emotion and sensation. In addition, these genes could construct a protein-protein interaction network supported by 60 putative hub genes with functional significance.

CONCLUSIONS

Our findings suggest a cerebral perfusion redistribution in MDD, which may be a consequence of complex interactions of a wide range of genes with diverse functional features.

The lack of temporal brain dynamics asymmetry as a signature of impaired consciousness states

Life is a constant battle against equilibrium. From the cellular level to the macroscopic scale, living organisms as dissipative systems require the violation of their detailed balance, i.e. metabolic enzymatic reactions, in order to survive. We present a framework based on temporal asymmetry as a measure of non-equilibrium. By means of statistical physics, it was discovered that temporal asymmetries establish an arrow of time useful for assessing the reversibility in human brain time series. Previous studies in human and non-human primates have shown that decreased consciousness states such as sleep and anaesthesia result in brain dynamics closer to the equilibrium. Furthermore, there is growing interest in the analysis of brain symmetry based on neuroimaging recordings and since it is a non-invasive technique, it can be extended to different brain imaging modalities and applied at different temporo-spatial scales. In the present study, we provide a detailed description of our methodological approach, paying special attention to the theories that motivated this work. We test, for the first time, the reversibility analysis in human functional magnetic resonance imaging data in patients suffering from disorder of consciousness. We verify that the tendency of a decrease in the asymmetry of the brain signal together with the decrease in non-stationarity are key characteristics of impaired consciousness states. We expect that this work will open the way for assessing biomarkers for patients' improvement and classification, as well as motivating further research on the mechanistic understanding underlying states of impaired consciousness.

Resting-state brain functional alterations and their genetic mechanisms in drug-naive first-episode psychosis

Extensive research has established the presence of resting-state brain functional damage in psychosis. However, the genetic mechanisms of such disease phenotype are yet to be unveiled. We investigated resting-state brain functional alterations in patients with drug-naive first-episode psychosis (DFP) by performing a neuroimaging meta-analysis of 8 original studies comprising 500 patients and 469 controls. Combined with the Allen Human Brain Atlas, we further conducted transcriptome-neuroimaging spatial correlations to identify genes whose expression levels were linked to brain functional alterations in DFP, followed by a range of gene functional characteristic analyses. Meta-analysis revealed a mixture of increased and decreased brain function in widespread areas including the default-mode, visual, motor, striatal, and cerebellar systems in DFP. Moreover, these brain functional alterations were spatially associated with the expression of 1662 genes, which were enriched for molecular functions, cellular components, and biological processes of the cerebral cortex, as well as psychiatric disorders including schizophrenia. Specific expression analyses demonstrated that these genes were specifically expressed in the brain tissue, in cortical neurons and immune cells, and during nearly all developmental periods. Concurrently, the genes could construct a protein-protein interaction network supported by hub genes and were linked to multiple behavioral domains including emotion, attention, perception, and motor. Our findings provide empirical evidence for the notion that brain functional damage in DFP involves a complex interaction of polygenes with various functional characteristics.

Transcriptional substrates underlying functional connectivity profiles of subregions within the human sensorimotor cortex

The human sensorimotor cortex has multiple subregions showing functional commonalities and differences, likely attributable to their connectivity profiles. However, the molecular substrates underlying such connectivity profiles are unclear. Here, transcriptome-neuroimaging spatial correlation analyses were performed between transcriptomic data from the Allen human brain atlas and resting-state functional connectivity (rsFC) of 24 fine-grained sensorimotor subregions from 793 healthy subjects. Results showed that rsFC of six sensorimotor subregions were associated with expression measures of six gene sets that were specifically expressed in brain tissue. These sensorimotor subregions could be classified into the polygenic- and oligogenic-modulated subregions, whose rsFC were related to gene sets diverging on their numbers (hundreds vs. dozens) and functional characteristics. First, the former were specifically expressed in multiple types of neurons and immune cells, yet the latter were not specifically expressed in any cortical cell types. Second, the former were preferentially expressed during the middle and late stages of cortical development, while the latter showed no preferential expression during any stages. Third, the former were prone to be enriched for general biological functions and pathways, but the latter for specialized biological functions and pathways. Fourth, the former were enriched for neuropsychiatric disorders, whereas this enrichment was absent for the latter. Finally, although the identified genes were commonly associated with sensorimotor behavioral processes, the polygenic-modulated subregions associated genes were additionally related to vision and dementia. These findings may advance our understanding of the functional homogeneity and heterogeneity of the human sensorimotor cortex from the perspective of underlying genetic architecture.

Integrative Functional, Molecular, and Transcriptomic Analyses of Altered Intrinsic Timescale Gradient in Depression

The pathophysiology and pharmacology of depression are hypothesized to be related to the imbalance of excitation–inhibition that gives rise to hierarchical dynamics (or intrinsic timescale gradient), further supporting a hierarchy of cortical functions. On this assumption, intrinsic timescale gradient is theoretically altered in depression. However, it remains unknown. We investigated altered intrinsic timescale gradient recently developed to measure hierarchical brain dynamics gradient and its underlying molecular architecture and brain-wide gene expression in depression. We first presented replicable intrinsic timescale gradient in two independent Chinese Han datasets and then investigated altered intrinsic timescale gradient and its possible underlying molecular and transcriptional bases in patients with depression. As a result, patients with depression showed stage-specifically shorter timescales compared with healthy controls according to illness duration. The shorter timescales were spatially correlated with monoamine receptor/transporter densities, suggesting the underlying molecular basis of timescale aberrance and providing clues to treatment. In addition, we identified that timescale aberrance-related genes ontologically enriched for synapse-related and neurotransmitter (receptor) terms, elaborating the underlying transcriptional basis of timescale aberrance. These findings revealed atypical timescale gradient in depression and built a link between neuroimaging, transcriptome, and neurotransmitter information, facilitating an integrative understanding of depression.

Dissect Relationships Between Gene Co-expression and Functional Connectivity in Human Brain

Although recent evidence indicates an association between gene co-expression and functional connectivity in human brain, specific association patterns remain largely unknown. Here, using neuroimaging-based functional connectivity data of living brains and brain-wide gene expression data of postmortem brains, we performed comprehensive analyses to dissect relationships between gene co-expression and functional connectivity. We identified 125 connectivity-related genes (20 novel genes) enriched for dendrite extension, signaling pathway and schizophrenia, and 179 gene-related functional connections mainly connecting intra-network regions, especially homologous cortical regions. In addition, 51 genes were associated with connectivity in all brain functional networks and enriched for action potential and schizophrenia; in contrast, 51 genes showed network-specific modulatory effects and enriched for ion transportation. These results indicate that functional connectivity is unequally affected by gene expression, and connectivity-related genes with different biological functions are involved in connectivity modulation of different networks.