Variation in DNA sequences that regulate gene expression identify neuropsychiatric disease mechanisms in the human brain

MEDIA ADVISORY  

UNDER EMBARGO UNTIL: Monday, September 26 at 11AM EST

Journal Name:  Nature Genetics  

Title of the Article: Population-level variation in enhancer expression identifies disease mechanisms in the human brain

Corresponding Author:  Panos Roussos, MD, MS, PhD, Director of Center for disease Neurogenomics, Icahn School of Medicine at Mount Sinai.

Bottom Line: Enhancers are DNA sequences that regulate gene expression and are themselves broadly expressed. By jointly analyzing population-level variation in gene and enhancer expression in the human brain, we characterized the enhancer-gene regulome and the regulatory mechanisms of transcribed enhancers in neuropsychiatric disease.

Results: It has been increasingly recognized that active enhancers are widely transcribed, and enhancer expression levels represent an essential signature of enhancer activation. Just like genes, active enhancer is also widely expressed. For this study, the research team generated comprehensive multi-omics references for neuronal and non-neuronal cells and developed a machine learning framework that accurately cataloged 30,795 neuronal and 23,265 non-neuronal transcribed enhancers. They then examined population-level variation in enhancer expression by analyzing 1382 RNA-sequence libraries from 774 schizophrenia (SCZ) and control postmortem brains to characterize the regulome and molecular mechanism of transcribed enhancers in neuropsychiatric disease. They found transcribed enhancers and transcribed enhancers-linked genes are strongly associated with neuropsychiatric disease, and transcribed enhancers mediate neuropsychiatric trait heritability in a manner that is complementary to gene expression. Lastly, they performed transcriptome-wide association analysis (TWAS) of joint gene-enhancer eQTL, which greatly facilitated the functional characterization of schizophrenia risk loci. Schizophrenia risk loci are the DNA alleles that can increase the probability of developing schizophrenia). However, the majority of such loci are outside the gene coding region and enriched with enhancer elements. Therefore, the study team focused on enhancer quantitative trait loci (QTL) analysis, a statistical method that links two types of information – molecular phenotypic data ( gene and enhancer expression) and genotypic data (molecular markers) – to characterize the genetic basis of schizophrenia loci.

Why the Research Is Interesting:  The majority of common neuropsychiatric disease-associated variants lie in the non-coding genome, where brain-associated enhancers are overrepresented both for risk alleles and the heritability of neuropsychiatric traits. However, a population-level analysis of enhancers is hampered by limited access to biospecimens and available molecular assays. Here, we dissect the enhancer function by analyzing the population-scale enhancer expression by total-RNA seq. We found >40,000 enhancers that are robustly expressed in two independent cohorts. Our approach also allows for the direct comparison between genes and enhancers, and the cis-coordination is validated by in vitro CRISPR inference. The transcribed enhancers are strongly associated with neuropsychiatric diseases and mediate neuropsychiatric trait heritability in a complementary manner to gene expression. We successfully identified 5,793 enhancer expression quantitative trait loci (eQTL), the majority of which are novel. We found the inclusion of enhancer eQTL in transcriptome-wide association studies enhanced functional interpretation of disease loci.

Who: enhancers in the human brain

When: postmortem brain (Age of death >17)

What: enhancer expression

How: We have generated comprehensive transcriptomic and epigenomic annotations, including histone modifications, chromatin accessibility, and chromosome spatial organization for neuronal and non-neuronal cells in the postmortem human brain. To catalog transcribed enhancers in the human brain, we have developed a machine learning scheme with multi-omics signals to annotate transcribed enhancers. In addition, as a part of the ongoing Commonmind Consortium(CMC) project, we have generated 1,382 total RNA-seq libraries from 774 schizophrenia (SCZ) and control postmortem brains. We examined the enhancer expression between cohorts and calculated the cis-coordination between the expression of gene and enhancer. To validate the cis-coordination, we performed CRISPR interference in neural progenitor cells between an enhancer and the cis-coordinated genes ~200kb away. We determined the enhancer expression quantitative trait loci (eQTL) and estimated the neuropsychiatric heritability mediated by enhancer expression. Lastly, we performed transcriptome-wide association studies to identify the potential causal enhancers for schizophrenia.

Study Conclusions: We found more than 40K enhancers were robustly expressed in the human brain,  and extensive cis-coordination between neighboring genes and enhancers, which is supported by the concordance with chromatin organization features, consistent allelic genetic effects, and in vitro CRISPR inference validation. The transcribed enhancers were strongly associated with neuropsychiatric disease risk variants and mediate neuropsychiatric trait heritability in a complementary manner to gene expression. Compared to gene expression, enhancer expressions were more exclusively associated with neuropsychiatric disease. Inclusion of enhancer eQTL enhanced functional interpretation of disease loci.

Paper Title:  Population-level variation in enhancer expression identifies disease mechanisms in the human brain

Said Mount Sinai's Dr. Panos Roussos of the research:“Overall, our study characterizes the enhancer-gene regulome and genetic mechanisms in the human cortex in both healthy and diseased states. Our results underscore the importance of enhancer elements in the etiology of neuropsychiatric disease. The framework described in this study provides an inexpensive and high-resolution approach to exploring active enhancer function in most human tissue and cell types. In future studies, integrating our enhancer expression framework with cell-type-, spatial-, and temporal-specific human brain multi-omic data will promise additional insights into the molecular mechanisms of neuropsychiatric diseases.”

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