Integrated bulk and single-cell RNA sequencing reveals peripheral immune dysregulation in adolescent major depressive disorder

• We integrated bulk and single-cell RNA sequencing to characterize peripheral transcriptional changes in adolescent major depressive disorder (MDD). • Bulk analyses revealed widespread transcriptional downregulation of immune-related genes, including key inflammatory regulators (e.g., NFKBIA , JUN , and JUND ). Single-cell profiling localized the strongest alterations to monocytes, with additional changes in T cells and neutrophils. • Comparisons between adolescent and adult MDD showed distinct expression patterns of immune-related genes and pathways. • The similar transcriptional profiles between drug-naïve and drug-treated adolescents suggested that monoamine-based antidepressants might not be associated with normalization of peripheral immune dysregulation in adolescent MDD. • These findings suggest a suppressed peripheral immune profile in adolescent MDD, and highlight the need for therapeutic strategies that more directly target the immune-related biological changes observed in depressed adolescents. Depression imposes severe psychological, social, and economic burdens, with its manifestations varying significantly across age groups. Adolescent major depressive disorder (MDD) presents unique challenges and remains poorly understood at the molecular level. This study aims to apply a multiomic approach to characterize peripheral transcriptional changes in adolescent MDD. Peripheral blood samples were collected from 180 MDD patients and 99 healthy controls (HC) for bulk RNA sequencing, with a subset of 4 MDD patients and 4 HC undergoing single-cell sequencing. We further explored the effect of drug therapy on transcriptional variations based on participants’ histories of antidepressant use. The EPIC analysis and flow cytometry were employed to predict and confirm the peripheral immune cell proportions within subgroups. Finally, the Connectivity Map platform identified potential drugs for adolescent MDD. Bulk analyses revealed widespread transcriptional downregulation of immune-related genes, including key inflammatory regulators (e.g., NFKBIA , JUN , and JUND ). Single-cell profiling localized the strongest alterations to monocytes, with additional changes in T cells and neutrophils. Notably, comparisons between adolescent and adult MDD showed distinct expression patterns of immune-related genes (e.g., NFKBIA , TNF , IL-12A , CCL2 , and CX3CR1 ) and pathways (e.g., the C-type lectin receptor signaling pathway, IL-17 signaling pathway, natural killer cell-mediated cytotoxicity, and toll-like receptor signaling pathway). The similar transcriptional profiles between drug-naïve and drug-treated adolescents indicated that monoamine-based antidepressants might not be associated with the normalization of peripheral immune dysregulation in adolescent MDD. Finally, the Connectivity Map analysis highlighted several compound classes, including tubulin-associated inhibitors, that may counteract the observed transcriptional pattern. These findings define a suppressed peripheral immune profile in adolescent MDD, and show limited modification of peripheral immune dysregulation by current treatments. Our study highlights the need for therapeutic strategies that more directly target the immune-related biological changes observed in depressed adolescents.