Key differences in RNA editing between postmortem and live brains discovered

Recent research has shown that Nature CommunicationsThe researchers examined adenosine-to-inosine (A-to-I) nucleoside editing in postmortem and living prefrontal cortex tissue.

The researchers found that levels of RNA editing were significantly higher in postmortem brain tissue compared to live tissue. Psychiatry“Understanding these differences will improve our knowledge of brain function and disease in terms of correcting RNA editing, and may lead to better diagnostic and therapeutic approaches,” said Icahn Mount Sinai professor of Genetics and Genomic Sciences, Neuroscience and Neurosurgery and co-leader of the Living Brain Project.

background

Recent studies of molecular changes in response to ischemia exposure have helped us understand adenosine to inosine editing in the mammalian brain. Fresh brain tissue from live human donors eliminates the confounds of postmortem tissue analysis and allows for more accurate testing.

Adenosine to inosine editing is critical for central nervous system function and misregulation can lead to neurological disease. Deoxyribonucleic acid (DNA) is stable for long periods after death, but ribonucleic acid (RNA) is more fragile. Distinguishing between living and postmortem central nervous system (CNS) tissues is important for understanding brain disease and aging.

About the Research

In this study, we investigated adenosine-to-inosine editing changes in the dorsolateral prefrontal cortex (DLPFC) in living and postmortem humans.

The researchers proposed that molecular responses to ischemia exposure and the innate immune response may alter the adenosine-to-inosine editing landscape in postmortem brains.Using Live Brain Project (LBP) data, we investigated the effects of postmortem and live DLPFC tissue on the DLPFC. Al Editing activities. They analyzed genetic data from 164 living individuals and 233 partially matched postmortem DLPFC samples. They Al Editing index (AEI) for each study sample.

The researchers, from around the world, Al The variation in editing can be explained by biological and technical variables. They conducted two further studies to examine the effects of changes in PMI and RNA degradation on editing. Al Editing of biological and post-mortem tissue.

The researchers investigated RNA editing in live and postmortem DLPFC samples, sequencing 206,568 single nuclei from 21 postmortem and 31 live tissues. They also created pseudobulk pools of each cell type per donor and examined adenosine deaminase acting on RNA (ADAR) enzyme expression in live types and postmortem DLPFC. The researchers catalogued high-confidence RNA sites using two complementary site-calling approaches and extensive detection-based criteria to prevent false positives.

The researchers used gene set variation analysis (GSVA) ​​to discover biological pathways that could explain postmortem bias in RNA editing. They calculated single-sample scores of 10,493 Gene Ontology biological processes for each bulk RNA-seq sample and plotted it against AEI to discover predicted biological processes.

The researchers next investigated RNA editing quantitative trait loci (edQTLs) by identifying single nucleotide polymorphisms (SNPs) that could alter adenosine-to-inosine editing levels in 195 postmortem and 155 live DLPFC tissues. They conducted two cis-edQTL studies matching adenosine-to-inosine editing levels with SNPs, as well as an interaction analysis examining context-dependent effects in live and postmortem tissues.

result

The study found substantial changes in adenosine-to-inosine editing patterns between living and postmortem brains, especially in non-neuronal cells. Al The prefrontal cortex of postmortem samples showed significantly increased AEI and more advanced editing compared to live DLPFC. The levels of ADAR, adenosine deaminase RNA-specific B1 (ADARB1), and ADARB2 were increased in the postmortem dorsolateral prefrontal cortex. The ADAR gene was ranked 15th.^Number Correlations between differentially expressed genes in postmortem samples were found and were strongly associated with AEI.

Differences between postmortem and live tissues accounted for the greatest variation. Al Edit (72%). At the same time, other established factors such as medical diagnosis, brain bank, predicted neuronal percentage, RNA integrity (RIN), and prolonged postmortem interval (PMI) were the least explainable. Secondary postmortem studies revealed a moderate relationship between PMI and AEI, indicating that prolonged PMI is unlikely to cause an increased AEI. Al Editing of postmortem tissue.

The study found 193,195 editing sites per live DLPFC sample and 295,343 editing sites across postmortem tissues, suggesting ADAR-mediated RNA editing. These sites were mapped to A through I, Al These elements were well known, had moderate editing levels, and frequently mapped to introns or 3′ UTRs.

The team also found a significant over-representation of LIV-PM sites, which are highly edited and account for 15-31% of all A-to-I sites. In total, 1,688 biological activities were identified in the global Al Genes associated with the editing process distinguish living from postmortem samples and strongly predict changes in AEI.

Conclusion

Findings indicate that early biological responses to human death, including IFN-γ signaling and hypoxia, promote ADAR and ADARB1 expression and lead to a coordinated increase in adenosine to inosine editing across the transcriptome.Postmortem brain tissue exhibits increased ADAR and ADARB1 expression and widespread adenosine to inosine editing compared to live DLPFC.

This study presents a novel approach to prioritize regions important for brain function. We show genetic variants that differentially affect adenosine-to-inosine editing levels in postmortem and in vivo DLPFC. Biobiased sites are enriched in A-to-I regions, exhibit strict spatiotemporal control during brain development, and are associated with neurological disease.