Brain Banks Spur New Frontiers in Neuropsychiatric Research and Strategies for Analysis and Validation

Brain eQTLs of European, African American, and Asian ancestry improve interpretation of schizophrenia GWAS

Research on brain expression quantitative trait loci (eQTLs) has illuminated the genetic underpinnings of schizophrenia (SCZ). Yet, the majority of these studies have been centered on European populations, leading to a constrained understanding of population diversities and disease risks. To address this gap, we examined genotype and RNA-seq data from African Americans (AA, n=158), Europeans (EUR, n=408), and East Asians (EAS, n=217). When comparing eQTLs between EUR and non-EUR populations, we observed concordant patterns of genetic regulatory effect, particularly in terms of the effect sizes of the eQTLs. However, 343,737 cis-eQTLs (representing ∼17% of all eQTLs pairs) linked to 1,276 genes (about 10% of all eGenes) and 198,769 SNPs (approximately 16% of all eSNPs) were identified only in the non-EUR populations. Over 90% of observed population differences in eQTLs could be traced back to differences in allele frequency. Furthermore, 35% of these eQTLs were notably rare (MAF < 0.05) in the EUR population. Integrating brain eQTLs with SCZ signals from diverse populations, we observed a higher disease heritability enrichment of brain eQTLs in matched populations compared to mismatched ones. Prioritization analysis identified seven new risk genes ( SFXN2 , RP11-282018.3 , CYP17A1 , VPS37B , DENR , FTCDNL1 , and NT5DC2 ), and three potential novel regulatory variants in known risk genes ( CNNM2 , C12orf65 , and MPHOSPH9 ) that were missed in the EUR dataset. Our findings underscore that increasing genetic ancestral diversity is more efficient for power improvement than merely increasing the sample size within single-ancestry eQTLs datasets. Such a strategy will not only improve our understanding of the biological underpinnings of population structures but also pave the way for the identification of novel risk genes in SCZ.

Epigenetics and ADHD: Reflections on Current Knowledge, Research Priorities and Translational Potential

Attention-deficit/hyperactivity disorder (ADHD) is a common and debilitating neurodevelopmental disorder influenced by both genetic and environmental factors, typically identified in the school-age years but hypothesized to have developmental origins beginning in utero. To improve current strategies for prediction, prevention and treatment, a central challenge is to delineate how, at a molecular level, genetic and environmental influences jointly shape ADHD risk, phenotypic presentation, and developmental course. Epigenetic processes that regulate gene expression, such as DNA methylation, have emerged as a promising molecular system in the search for both biomarkers and mechanisms to address this challenge. In this Current Opinion, we discuss the relevance of epigenetics (specifically DNA methylation) for ADHD research and clinical practice, starting with the current state of knowledge, what challenges we have yet to overcome, and what the future may hold in terms of methylation-based applications for personalized medicine in ADHD. We conclude that the field of epigenetics and ADHD is promising but is still in its infancy, and the potential for transformative translational applications remains a distant goal. Nevertheless, rapid methodological advances, together with the rise of collaborative science and increased availability of high-quality, longitudinal data make this a thriving research area that in future may contribute to the development of new tools for improved prediction, management, and treatment of ADHD.

Imaging Genetics in Epilepsy: Current Knowledge and New Perspectives

Epilepsy is a neurological network disease with genetics playing a much greater role than was previously appreciated. Unfortunately, the relationship between genetic basis and imaging phenotype is by no means simple. Imaging genetics integrates multidimensional datasets within a unified framework, providing a unique opportunity to pursue a global vision for epilepsy. This review delineates the current knowledge of underlying genetic mechanisms for brain networks in different epilepsy syndromes, particularly from a neural developmental perspective. Further, endophenotypes and their potential value are discussed. Finally, we highlight current challenges and provide perspectives for the future development of imaging genetics in epilepsy.

Biovalue in Human Brain Banking: Applications and Challenges for Research in Neurodegenerative Diseases

Brain banking occupies a central role for the advancement of the study of human neurodegenerative and neuropsychiatric diseases. The smooth functioning and effectiveness of a brain bank is largely a multidisciplinary effort and requires the cooperation and participation of several players including neurologists, neuropathologists, and research coordinators to guarantee that donated tissue is properly processed and archived. If properly run, brain banks can ultimately lay the foundation for new brain research and pioneer the discovery of new therapies for a variety of neurological diseases.

Psychiatric disorders in China: strengths and challenges of contemporary research and clinical services

China accounts for 17% of the global disease burden attributable to mental, neurological and substance use disorders. As a country undergoing profound societal change, China faces growing challenges to reduce the disease burden caused by psychiatric disorders. In this review, we aim to present an overview of progress in neuroscience research and clinical services for psychiatric disorders in China during the past three decades, analysing contributing factors and potential challenges to the field development. We first review studies in the epidemiological, genetic and neuroimaging fields as examples to illustrate a growing contribution of studies from China to the neuroscience research. Next, we introduce large-scale, open-access imaging genetic cohorts and recently initiated brain banks in China as platforms to study healthy brain functions and brain disorders. Then, we show progress in clinical services, including an integration of hospital and community-based healthcare systems and early intervention schemes. We finally discuss opportunities and existing challenges: achievements in research and clinical services are indispensable to the growing funding investment and continued engagement in international collaborations. The unique aspect of traditional Chinese medicine may provide insights to develop a novel treatment for psychiatric disorders. Yet obstacles still remain to promote research quality and to provide ubiquitous clinical services to vulnerable populations. Taken together, we expect to see a sustained advancement in psychiatric research and healthcare system in China. These achievements will contribute to the global efforts to realize good physical, mental and social well-being for all individuals.

Drug Response-Related DNA Methylation Changes in Schizophrenia, Bipolar Disorder, and Major Depressive Disorder

Pharmacotherapy is the most common treatment for schizophrenia (SCZ), bipolar disorder (BD), and major depressive disorder (MDD). Pharmacogenetic studies have achieved results with limited clinical utility. DNA methylation (DNAm), an epigenetic modification, has been proposed to be involved in both the pathology and drug treatment of these disorders. Emerging data indicates that DNAm could be used as a predictor of drug response for psychiatric disorders. In this study, we performed a systematic review to evaluate the reproducibility of published changes of drug response-related DNAm in SCZ, BD and MDD. A total of 37 publications were included. Since the studies involved patients of different treatment stages, we partitioned them into three groups based on their primary focuses: (1) medication-induced DNAm changes (n = 8); (2) the relationship between DNAm and clinical improvement (n = 24); and (3) comparison of DNAm status across different medications (n = 14). We found that only BDNF was consistent with the DNAm changes detected in four independent studies for MDD. It was positively correlated with clinical improvement in MDD. To develop better predictive DNAm factors for drug response, we also discussed future research strategies, including experimental, analytical procedures and statistical criteria. Our review shows promising possibilities for using BDNF DNAm as a predictor of antidepressant treatment response for MDD, while more pharmacoepigenetic studies are needed for treatments of various diseases. Future research should take advantage of a system-wide analysis with a strict and standard analytical procedure.

Man's best friend in life and death: scientific perspectives and challenges of dog brain banking

Biobanking refers to the systematic collection, storage, and distribution of pre- or post-mortem biological samples derived from volunteer donors. The demand for high-quality human specimens is clearly demonstrated by the number of newly emerging biobanking facilities and large international collaborative networks. Several animal species are relevant today in medical research; therefore, similar initiatives in comparative physiology could be fruitful. Dogs, in particular, are gaining increasing attention in translational research on complex phenomena, like aging, cancer, and neurodegenerative diseases. Therefore, biobanks gathering and storing dog biological materials together with related data could play a vital role in translational and veterinary research projects. To achieve these aims, a canine biobank should meet the same standards in sample quality and data management as human biobanks and should rely on well-designed collaborative networks between different professionals and dog owners. While efforts to create dog biobanks could face similar financial and technical challenges as their human counterparts, they can widen the spectrum of successful collaborative initiatives towards a better picture of dogs’ physiology, disease, evolution, and translational potential. In this review, we provide an overview about the current state of dog biobanking and introduce the “Canine Brain and Tissue Bank” (CBTB)—a new, large-scale collaborative endeavor in the field.

Agonal Factors Distort Gene-Expression Patterns in Human Postmortem Brains

Agonal factors, the conditions that occur just prior to death, can impact the molecular quality of postmortem brains, influencing gene expression results. Our study used gene expression data of 262 samples from ROSMAP with the detailed terminal state recorded for each donor, such as fever, infection, and unconsciousness. Fever and infection were the primary contributors to brain gene expression changes, brain cell-type-specific gene expression, and cell proportion changes. Furthermore, we also found that previous studies of gene expression in postmortem brains were confounded by agonal factors. Therefore, correction for agonal factors is important in the step of data preprocessing. Our analyses revealed fever and infection contributing to gene expression changes in postmortem brains and emphasized the necessity of study designs that document and account for agonal factors.

Bioinformatics analysis of immune infiltration in glioblastoma multiforme based on data using a methylation chip in the GEO database

Background

Glioblastoma multiforme (GBM) is the most aggressive and malignant tumor of the central nervous system. The study was to obtain the data of immune cell infiltration based on the data of a methylation chip in the GEO, and to clarify its prognostic significance for GBM.

Methods

The methylation data of glioblastoma was obtained by using the Illumina human methylation 450k BeadChip. The corrected expression was obtained by using edge R. Limma was used to correct the expression amount of the samples, and EpiDISH was used to translate the methylation expression data, so that the expression amount was transformed into the expression matrix of immune cells. The immune cells were then co-expressed, and the proportion and correlation of related immune cells was determined. The results of the cells in each of two groups were analyzed by enrichment and PCA mapping to establish the relevant differences.

Results

The data of GBM patients were obtained from the methylation chip of the GEO database. Patients were divided into a long-term (SNU-LTS) (21 cases), and short-term survival group (SNU-STS) (12 cases). There were 73 genes with significant individual differences between the two groups (P<0.05). EpiDISH was used to translate the methylation expression data into the expression matrix of immune cells, which showed that the highest proportion of cells in groups were mono cells, while Gran cells and CD8T appeared in a very small number of samples. The positive correlation between mono and B cells was the strongest, while the negative correlation between mono and Gran cells was the strongest. A violin chart shows that there was no significant difference in the infiltration degree of six kinds of immune cells between the two groups. Principal component analysis (PCA) showed that there was individual difference between the two groups, but the overall consistency was high.

Conclusions

Data on tumor immune cell infiltration can be obtained by using a methylation chip in the GEO database. This not only extends the application abilities of methylation chips but provides obvious individual differences. The study of tumor immune infiltrating cells may pave the way for targeted therapy in the treatment of GBM.

Parsing the Functional Impact of Noncoding Genetic Variants in the Brain Epigenome

The heritability of common psychiatric disorders has motivated global efforts to identify risk-associated genetic variants and elucidate molecular pathways connecting DNA sequence to disease-associated brain dysfunction. The overrepresentation of risk variants among gene regulatory loci instead of protein-coding loci, however, poses a unique challenge in discerning which among the many thousands of variants identified contribute functionally to disease etiology. Defined broadly, psychiatric epigenomics seeks to understand the effects of disease-associated genetic variation on functional readouts of chromatin in an effort to prioritize variants in terms of their impact on gene expression in the brain. Here, we provide an overview of epigenomic mapping in the human brain and highlight findings of particular relevance to psychiatric genetics. Computational methods, including convolutional neuronal networks, and other machine learning approaches hold great promise for elucidating the functional impact of both common and rare genetic variants, thereby refining the epigenomic architecture of psychiatric disorders and enabling integrative analyses of regulatory noncoding variants in the context of large population-level genome and phenome databases.

What a Clinician Should Know About the Neurobiology of Schizophrenia: A Historical Perspective to Current Understanding

The brain is no doubt the "organ" of psychiatry; yet, over the years, few evidence-based classifications of psychiatric disorders have been based on brain mechanisms. The National Institute of Mental Health notably proposed one such system, known as Research Domain Criteria, although it has not yet influenced any changes in the DSM. Of all the major psychiatric disorders, the brain has been studied most extensively in schizophrenia, with its speculative pathology first documented by Emil Kraepelin as early as the beginning of the 20th century. Subsequently, the revolution in technology over the past 50 years has changed how investigators are able to view the brain before death without performing biopsies. Schizophrenia is thus found to have both structural and functional widespread brain anomalies that likely lead to its clinical deterioration. At the onset of illness, acquiring an MRI scan could be part of the routine evaluation to determine how progressive the disease has so far been. However, this practice is not yet recognized by the American Psychiatric Association in any of its guidelines on the treatment of schizophrenia.