Integrated Gene and Isoform-Level Transcriptomic Analysis of Adverse Childhood Experiences in the Human Prefrontal Cortex

Adverse childhood experiences (ACE) can lead to diverse outcomes, ranging from resilience to an increased risk of psychiatric disorders such as anxiety, depression, and posttraumatic stress disorder (PTSD). In mammals, most multiexon genes encode an average of 3.9 protein-coding isoforms, which amplify transcriptomic diversity and potentially exhibit distinct functional characteristics. Recent research has shown long-lasting transcriptomic changes associated with ACE, particularly in immune-related genes. However, differential isoform usage may not be captured when analyses are confined to gene-level expression. To date, no studies have explored isoform-level dysregulation in postmortem brains of individuals exposed to ACEs. Our study investigated transcriptomic dynamics across four prefrontal regions—the dorsolateral (dlPFC), dorsal Anterior Cingulate (dACC), orbitofrontal (OFC), and subgenual prefrontal (sgPFC) cortices—in a cohort of 22 donors with PTSD, comprising 11 with and 11 without ACE history. The OFC exhibited the highest number of differentially expressed genes (DEGs), followed by the sgPFC. Correspondingly, these regions also showed the most pronounced differential isoform usage, or “isoform switching”. Notably, our integrated transcriptomic analysis revealed that while PAQR6 was downregulated in the sgPFC among ACE-exposed individuals, its principal isoform (PAQR6-201) showed increased usage. Several genes exhibiting significant isoform switching did not display substantial differential gene expression. Functional pathway analysis revealed that genes with altered expression or isoform usage converged on neurogenesis regulation, with isoform-switching genes specifically enriched in gliogenesis. This study demonstrates that examining differential isoform usage unveils previously unrecognized genes potentially implicated in ACE. Future research should focus on characterizing the functional consequences of isoform-specific up-or downregulation to comprehensively understand transcriptomic dysregulation in complex psychiatric disorders.