Gene Age Gap Estimate (GAGE) for major depressive disorder: a penalized biological age model using gene expression.

Recent associations between Major Depressive Disorder (MDD) and measures of premature aging suggest accelerated biological aging as a potential biomarker for MDD susceptibility or MDD as a risk factor for age-related diseases. Statistical and machine learning regression models of biological age have been trained on various sources of high dimensional data to predict chronological age. Residuals or "gaps" between the predicted biological age and chronological age have been used for statistical inference, such as testing whether an increased age gap is associated with a given disease state. Recently, a gene expression-based model of biological age showed a higher age gap for individuals with MDD compared to healthy controls (HC). In the current study, we propose a machine learning approach that simplifies gene selection by using a least absolute shrinkage and selection operator (LASSO) penalty to construct an expression-based Gene Age Gap Estimate (GAGE) model. We construct the LASSO-GAGE (L-GAGE) model in an RNA-Seq study of 78 unmedicated individuals with MDD and 79 HC and then test for accelerated biological aging in MDD. When testing L-GAGE association with MDD, we account for factors such as sex and chronological age to mitigate regression to the mean effects. The L-GAGE shows higher biological aging in MDD subjects than HC, but the elevation is not statistically significant. However, when we dichotomize chronological age, the interaction between MDD status and age is significant in L-GAGE model. This effect remains statistically significant even after adjusting for chronological age and sex. We find cytomegalovirus (CMV) serostatus is associated with elevated L-GAGE. We also investigate feature selection methods Random Forest and nearest neighbor projected distance regression (NPDR) to characterize age related genes, and we find functional enrichment of infectious disease and SARS-COV pathways.

Differential expression of MDGA1 in major depressive disorder.

The identification of gene expression-based biomarkers for major depressive disorder (MDD) continues to be an important challenge. In order to identify candidate biomarkers and mechanisms, we apply statistical and machine learning feature selection to an RNA-Seq gene expression dataset of 78 unmedicated individuals with MDD and 79 healthy controls. We identify 49 genes by LASSO penalized logistic regression and 45 genes at the false discovery rate threshold 0.188. The MDGA1 gene has the lowest P-value (4.9e-5) and is expressed in the developing brain, involved in axon guidance, and associated with related mood disorders in previous studies of bipolar disorder (BD) and schizophrenia (SCZ). The expression of MDGA1 is associated with age and sex, but its association with MDD remains significant when adjusted for covariates. MDGA1 is in a co-expression cluster with another top gene, ATXN7L2 (ataxin 7 like 2), which was associated with MDD in a recent GWAS. The LASSO classification model of MDD includes MDGA1, and the model has a cross-validation accuracy of 79%. Another noteworthy top gene, IRF2BPL, is in a close co-expression cluster with MDGA1 and may be related to microglial inflammatory states in MDD. Future exploration of MDGA1 and its gene interactions may provide insights into mechanisms and heterogeneity of MDD.