Depression proteomic profiling in adolescents with transcriptome analyses in independent cohorts

Abstract

Introduction: Depression is a major global burden with unclear pathophysiology and poor treatment outcomes. Diagnosis of depression continues to rely primarily on behavioral rather than biological methods. Investigating tools that might aid in diagnosing and treating early-onset depression is essential for improving the prognosis of the disease course. While there is increasing evidence of possible biomarkers in adult depression, studies investigating this subject in adolescents are lacking.

Methods: In the current study, we analyzed protein levels in 461 adolescents assessed for depression using the Development and Well-Being Assessment (DAWBA) questionnaire as part of the domestic Psychiatric Health in Adolescent Study conducted in Uppsala, Sweden. We used the Proseek Multiplex Neuro Exploratory panel with Proximity Extension Assay technology provided by Olink Bioscience, followed by transcriptome analyses for the genes corresponding to the significant proteins, using four publicly available cohorts.

Results: We identified a total of seven proteins showing different levels between DAWBA risk groups at nominal significance, including RBKS, CRADD, ASGR1, HMOX2, PPP3R1, CD63, and PMVK. Transcriptomic analyses for these genes showed nominally significant replication of PPP3R1 in two of four cohorts including whole blood and prefrontal cortex, while ASGR1 and CD63 were replicated in only one cohort.

Discussion: Our study on adolescent depression revealed protein-level and transcriptomic differences, particularly in PPP3R1, pointing to the involvement of the calcineurin pathway in depression. Our findings regarding PPP3R1 also support the role of the prefrontal cortex in depression and reinforce the significance of investigating prefrontal cortex-related mechanisms in depression.

Keywords: adolescents; depression; proteome; psychiatry; transcriptome.

Figure 1

Results graph. This figure shows the main results obtained in the PSY cohort and their replications in the transcriptome cohorts. Red nodes indicate differentially expressed genes, blue nodes indicate probes or plasma proteins, orange nodes indicate the analyses. Arrows indicate relationships between the nodes. Brick-red edges indicate upregulation of the protein/probe in depression, whereas green edges indicate respective downregulation. Gray edges show relationships between gene names and probes. The thickness of the red and green edges edges is proportional to the sizes of β-coefficients in the linear models.

Figure 2

PPP3R1 expression. (A) PPP3R1 plasma NPX in the PSY cohort depending on the DAWBA risk group. Asterisk indicates a nominal p<0.05. (B) The expression levels of PPP3R1-related probe ILMN_1796962 in whole blood in depression versus controls in GSE64930. Asterisk indicates a nominal p<0.05. (C) The expression levels of PPP3R1-related probe 204506_at in prefrontal cortex in several psychiatric conditions and controls in the dataset GSE53987. Asterisk indicates a nominal p<0.05. DAWBA, Development and Well-Being Assessment; NPX, Normalized Protein Expression; SCZ, schizophrenia; BD, bipolar disorder; MDD, major depressive disorder.

Figure 3

Hypothetical model of blood proteome relation with depression. This figure represents a hypothetical model explaining observed associations between depression and the blood levels of PPP3R1, CD63, and ASGR1. I Several studies indicate links between platelet activation and depression (60, 61). However, this mechanism is not fully established. II. The activation of platelets could be indirectly indicated by increase of CD63 levels, as this protein is abundant in exosomes (62) and release of exosomes could be attributed to platelet activation (63). The levels of CD63 platelets were positively associated with depression (60, 61). III. PPP3R1, a regulatory component of calcineurin complex mediating phosphatase activity, has been shown to bind platelets and prevent their aggregation (64, 65), and thus its increase may indicate disturbances in platelet homeostasis. The disturbances of calcineurin signaling may be indicated by changes in blood and prefrontal cortex as observed in this study. However, we observed increased plasma levels of PPP3R1 in depressed individuals. IV. The ASGR1 contribution to depression is not clear, however it is related to platelet phagocytosis by liver sinusoidal endothelial cells (66, 67).