No abstract

No abstract

Suicide attempt (SA) risk is elevated in individuals with bipolar disorder (BD), and DNA methylation patterns may serve as possible biomarkers of SA. We conducted epigenome-wide association studies (EWAS) of blood DNA methylation associated with BD and SA. DNA methylation was measured at > 700,000 positions in a discovery cohort of n = 84 adults with BD with a history of SA (BD/SA), n = 79 adults with BD without history of SA (BD/non-SA), and n = 76 non-psychiatric controls (CON). EWAS revealed six differentially methylated positions (DMPs) and seven differentially methylated regions (DMRs) between BD/SA and BD/non-SA, with multiple immune-related genes implicated. There were no epigenome-wide significant differences when BD/SA and BD/non-SA were each compared to CON, and patterns suggested that epigenetics differentiating BD/SA from BD/non-SA do not differentiate BD/non-SA from CON. Weighted gene co-methylation network analysis and trait enrichment analysis of the BD/SA vs. BD/non-SA contrast further corroborated immune system involvement, while gene ontology analysis implicated calcium signalling. In an independent replication cohort of n = 48 BD/SA and n = 47 BD/non-SA, fold-changes at the discovery cohort's significant sites showed moderate correlation across cohorts and agreement on direction. In both cohorts, classification accuracy for SA history among individuals with BD was highest when methylation at the significant CpG sites as well as information from clinical interviews were combined, with an AUC of 88.8% (CI = 83.8-93.8%) and 82.1% (CI = 73.6-90.5%) for the combined epigenetic-clinical predictor in the discovery and replication cohorts, respectively. Our results provide novel insight to the role of immune system functioning in SA and BD and also suggest that integrating information from multiple levels of analysis holds promise to improve risk assessment for SA in adults with BD.

There is a need for disentangling the role of transcriptional and epigenetic variation in mental health, disease, and mortality. Although alterations in DNA methylation patterns have been found to be particularly stable and highly concentrated in the brain, the study of bulk tissue, which contains several types of cells, can be limited and potentially significantly mask different alterations driven by specific cell types. Therefore, there is a need for methods to be able to purify specific cell-type populations that can be used in downstream molecular analyses. This protocol describes a methodology that uses fluorescence-activated nuclei sorting (FANS) to overcome these limitations and analyze, specifically, neuronal nuclei from frozen post-mortem prefrontal cortex tissue. Specifically, this protocol was based on recently-published protocols with the same goal with adaptations that have proven to improve yield and quality of the samples in our laboratory using the BD FACSJazzTM cell sorting system. To our knowledge, this is the only published protocol where a methodology for a flow cytometry instrument with a manual laser and sorting alignment is described in detail. This method can be used to purify populations of neuronal (NeuN+) and non-neuronal (NeuN-) nuclei from adult frozen post-mortem brain tissue, with tissue samples yielding purified populations of nuclei amenable to be able to perform analyses of DNA methylation, genotyping, and potentially, open chromatin analysis (via ATAC-seq).