Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders

Abnormal eye movement, brain regional homogeneity in schizophrenia and clinical high-risk individuals and their associated gene expression profiles

Clinical high-risk (CHR) is a prodromal period before psychosis characterized by attenuated, transient, or intermittent psychotic symptoms and declining functioning. They exhibit eye movement abnormalities and brain functional damage compared with schizophrenia, potentially increasing vulnerability to psychosis. This study investigates eye movement dysfunction and brain activity alterations in CHR and first-episode schizophrenia (FSZ) individuals to identify early biomarkers for psychosis progression. Twenty-seven drug-naïve FSZ, 25 CHR, and 28 healthy controls (HCs) were recruited for eye-tracking tasks and resting-state functional magnetic resonance imaging to evaluate eye movement and regional homogeneity (ReHo) differences. Machine-learning algorithms were used to differentiate FSZ from CHR. In combination with the Allen Human Brain Atlas (AHBA), transcriptome-neuroimaging analysis was applied to identify ReHo-related gene expression profiles. FSZ exhibited a wide range of eye movement abnormalities across multiple tasks, while certain abnormalities were already present in CHR. Abnormal ReHo alterations were found in orbitofrontal gyrus, temporal gyrus, and cingulum among three groups, associated with specific eye movement parameters. These differences in eye movement and ReHo allowed for high-accuracy discrimination between them. Genetic analysis identified significant genes in FSZ and CHR, enriched in various biological functions and pathways (all corrected p < 0.05). FSZ and CHR exhibited different eye movement and ReHo patterns, indicating potential as early biomarkers. Our findings reveal correlations between these ReHo patterns and gene expression profiles using AHBA database, shedding light on possible genetic mechanisms underlying brain function in FSZ and CHR.

Cognitive implications and associated transcriptomic signatures of distinct regional iron depositions in cerebral small vessel disease

INTRODUCTION

Regional brain iron dyshomeostasis is observed in cerebral small vessel disease (cSVD) and other neurodegeneration processes. However, its spatial patterns, cognitive impact, and underlying pathological mechanisms remain unclear.

METHODS

Voxel-based analysis of quantitative susceptibility mapping (QSM) was used to detect regional susceptibility changes, and their correlations with cognitive function were assessed using linear regression. We combined the microarray dataset from the Allen Human Brain Atlas (AHBA) to explore the pathological mechanisms of iron deposition patterns.

RESULTS

A total of 87 cSVD patients and 80 controls were included in the study. Increased QSM values in the bilateral putamen and caudate were associated with cognitive decline in cSVD. Gene set enrichment analysis revealed the enrichment of gene sets related to central nervous system integrity.

DISCUSSION

Iron deposition in deep gray matter may indicate cognitive changes in cSVD and could be linked to the disruption of brain structural and functional integrity.

HIGHLIGHTS

Increased susceptibility values, indicating focal iron deposition, were observed in the deep gray matter of patients with cerebral small vessel disease (cSVD). Regional iron concentration in the deep gray nuclei was associated with cognitive impairment in cSVD patients. Imaging transcriptomics suggests that cSVD-related iron deposition is linked to the structural and functional integrity of the brain. An open-source script for imaging transcriptomics focusing on regional gene expression was developed and proposed.

Biological mechanism of sex differences in mental rotation: Evidence from multimodal MRI, transcriptomic and receptor/transporter data

Sex differences in mental rotation are a well-documented phenomenon in cognitive research, with implications for the differing prevalence of neuropsychiatric disorders such as autism spectrum disorder (ASD), Alzheimer's disease (AD) and major depressive disorder (MDD) between the sexes. Despite extensive documentation, the biological mechanism underpinning these differences remain elusive. This study aimed to elucidate neural, genetic, and molecular bases of these disparities in mental rotation by integrating data from multimodal magnetic resonance imaging (MRI), transcriptomic and receptor/transporter. We first calculated the dynamic regional homogeneity (dReHo), gray matter volume (GMV) and fractional anisotropy (FA) in voxel-wise manner and parceled them into 246 brain regions based on Brainnetome Atlas. Subsequent analyses involved Pearson Correlations to examine the association between mental rotation performance and dReHo/GMV/FA and two-sample t-tests to delineate gender differences in these indices. Based on the above results, further mediation analysis was conducted to explore the relationship between sex, brain biomarkers and mental rotation. In addition, transcriptome-neuroimaging association analysis and correlation analysis between brain biomarkers and neurotransmitter receptor/transporter distribution were also performed to uncover genetic and molecular mechanisms contributing to the observed sex differences in mental rotation. We found correlations between mental rotation performance and dReHo, GMV and FA of the inferior parietal lobule (IPL) and superior temporal gyrus (STG) and sex effects on these brain biomarkers. Notably, the dReHo of the left IPL mediated the relationship between sex and mental rotation. Further correlation analysis revealed that the proton-coupled oligopeptide transporter PEPT2 (SLC15A2) and interleukin 17 receptor D (IL17RD) were associated with sex-related t-statistic maps and mental rotation-related r-statistic maps of dReHo. Moreover, γ-aminobutyric acid subtype A (GABAA) receptor availability was correlated with the r-statistic of dReHo, while norepinephrine transporter (NET) availability was correlated with its t-statistic. Serial mediation models revealed the indirect effect of these genes on the r-statistic maps through the transporter/receptor and t-statistic maps. Our findings provide novel insights into the biological mechanism underlying sex differences in mental rotation, identifying potential biomarkers for cognitive impairment and explaining variations in prevalence of certain mental disorders between the sexes. These results highlight the necessity of considering sex in research on mental health disorders.

Imaging Transcriptomics of Brain Functional Alterations in MS and Neuromyelitis Optica Spectrum Disorder

BACKGROUND AND PURPOSE

The underlying transcriptomic signatures driving brain functional alterations in MS and neuromyelitis optica spectrum disorder (NMOSD) are still unclear.

MATERIALS AND METHODS

Regional fractional amplitude of low-frequency fluctuation (fALFF) values were obtained and compared among 209 patients with MS, 90 patients with antiaquaporin-4 antibody (AQP4)+ NMOSD, 49 with AQP4- NMOSD, and 228 healthy controls from a discovery cohort. We used partial least squares (PLS) regression to identify the gene transcriptomic signatures associated with disease-related fALFF alterations. The biologic process and cell type-specific signature of the identified PLS genes were explored by enrichment analysis. The correlation between PLS genes and clinical variables was explored. A prospective independent cohort was used to validate the brain fALFF alterations and the repeatability of identified genes.

RESULTS

MS, AQP4+ NMOSD, and AQP4- NMOSD showed decreased fALFF in cognition-related regions and deep gray matter, while NMOSD (both AQP4+ and AQP4-) additionally demonstrated lower fALFF in the visual region. The overlapping PLS1- genes (indicating that the genes were overexpressed as regional fALFF decreased) were enriched in response to regulation of the immune response in all diseases, and the PLS1- genes were specifically enriched in the epigenetics profile in MS, membrane disruption and cell adhesion in AQP4+ NMOSD, and leukocyte activation in AQP4- NMOSD. For the cell type transcriptional signature, microglia and astrocytes accounted for the decreased fALFF. The fALFF-associated PLS1- genes directly correlated with Expanded Disability Status Scale of MS and disease duration across disorders.

CONCLUSIONS

We revealed the functional activity alterations and their underlying shared and specific gene transcriptional signatures in MS, AQP4+ NMOSD, and AQP4- NMOSD.

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.

Towards a neuroimaging biomarker for predicting cognitive behavioural therapy outcomes in treatment-naive depression: Preliminary findings

Clear prognostic indicators of cognitive behavioural therapy (CBT) are lacking for depression. This study aims to identify a biomarker that predicts CBT outcomes in depression. We developed a machine learning algorithm to predict post-CBT Hamilton Depression Rating Scale (HAMD) using pre-CBT regional homogeneity (ReHo). We examined transcriptomic signatures of regions with CBT-related ReHo changes. Twenty-five patients completed CBT and had increased ReHo in the dorsolateral prefrontal cortex (DLPFC) following CBT. Pre-CBT ReHo in left DLPFC was shown to be a predictor of post-HAMD scores. We identified left DLPFC ReHo as a neuroimaging biomarker for therapeutic effects of CBT in depression.

Toward Best Practices for Imaging Transcriptomics of the Human Brain

Modern brainwide transcriptional atlases provide unprecedented opportunities for investigating the molecular correlates of brain organization, as quantified using noninvasive neuroimaging. However, integrating neuroimaging data with transcriptomic measures is not straightforward, and careful consideration is required to make valid inferences. In this article, we review recent work exploring how various methodological choices affect 3 main phases of imaging transcriptomic analyses, including 1) processing of transcriptional atlas data; 2) relating transcriptional measures to independently derived neuroimaging phenotypes; and 3) evaluating the functional implications of identified associations through gene enrichment analyses. Our aim is to facilitate the development of standardized and reproducible approaches for this rapidly growing field. We identify sources of methodological variability, key choices that can affect findings, and considerations for mitigating false positive and/or spurious results. Finally, we provide an overview of freely available open-source toolboxes implementing current best-practice procedures across all 3 analysis phases.

Transcriptomic and cellular decoding of functional brain connectivity changes reveal regional brain vulnerability to pro- and anti-inflammatory therapies

BACKGROUND

Systemic inflammation induces acute changes in mood, motivation and cognition that closely resemble those observed in depressed individuals. However, the mechanistic pathways linking peripheral inflammation to depression-like psychopathology via intermediate effects on brain function remain incompletely understood.

METHODS

We combined data from 30 patients initiating interferon-α treatment for Hepatitis-C and 20 anti-tumour necrosis factor (TNF) therapy for inflammatory arthritis and used resting-state functional magnetic resonance imaging to investigate acute effects of each treatment on regional global brain connectivity (GBC). We leveraged transcriptomic data from the Allen Human Brain Atlas to uncover potential biological and cellular pathways underpinning regional vulnerability to GBC changes induced by each treatment.

RESULTS

Interferon-α and anti-TNF therapies both produced differential small-to-medium sized decreases in regional GBC. However, these were observed within distinct brain regions and the regional patterns of GBC changes induced by each treatment did not correlate suggesting independent underlying processes. Further, the spatial distribution of these differential GBC decreases could be captured by multivariate patterns of constitutive regional expression of genes respectively related to: i) neuroinflammation and glial cells; and ii) glutamatergic neurotransmission and neurons. The extent to which each participant expressed patterns of GBC changes aligning with these patterns of transcriptomic vulnerability also correlated with both acute treatment-induced changes in interleukin-6 (IL-6) and, for Interferon-α, longer-term treatment-associated changes in depressive symptoms.

CONCLUSIONS

Together, we present two transcriptomic models separately linking regional vulnerability to the acute effects of interferon-α and anti-TNF treatments on brain function to glial neuroinflammation and glutamatergic neurotransmission. These findings generate hypotheses about two potential brain mechanisms through which bidirectional changes in peripheral inflammation may contribute to the development/resolution of psychopathology.

Imaging transcriptomics: Convergent cellular, transcriptomic, and molecular neuroimaging signatures in the healthy adult human brain

The integration of transcriptomic and neuroimaging data, "imaging transcriptomics," has recently emerged to generate hypotheses about potential biological pathways underlying regional variability in neuroimaging features. However, the validity of this approach is yet to be examined in depth. Here, we sought to bridge this gap by performing transcriptomic decoding of the regional distribution of well-known molecular markers spanning different elements of the biology of the healthy human brain. Imaging transcriptomics identifies biological and cell pathways that are consistent with the known biology of a wide range of molecular neuroimaging markers. The extent to which it can capture patterns of gene expression that align well with elements of the biology of the neuroinflammatory axis, at least in healthy controls without a proinflammatory challenge, is inconclusive. Imaging transcriptomics might constitute an interesting approach to improve our understanding of the biological pathways underlying regional variability in a wide range of neuroimaging phenotypes.