CHIMA: a correlation-aware high-dimensional mediation analysis with its application to the living brain project study

TL;DR

CHIMA is a novel correlation-aware high-dimensional mediation analysis method that improves mediator detection accuracy in correlated data and reveals gene mechanisms in Parkinson's disease from RNA-seq data.

Contribution

We introduce CHIMA, a new method that enhances high-dimensional mediation analysis by accounting for correlations, improving power and bias reduction.

Findings

CHIMA outperforms existing methods in simulations with correlated mediators.

Applied to RNA-seq data, CHIMA identified genes mediating Parkinson's disease effects.

Revealed cell-type-specific mechanisms in Parkinson's disease study.

Abstract

Mediation analysis examines the pathways through which mediators transmit the effect of an exposure to an outcome. In high-dimensional settings, the joint significance test is commonly applied using variable screening followed by statistical inference. However, when mediators are highly correlated, existing methods may experience reduced statistical power due to inaccurate screening and residual bias in asymptotic inference. To address these issues, we propose CHIMA (Correlation-aware High-dimensional Mediation Analysis), an extension of a recently developed high-dimensional mediation analysis framework that enhances performance under correlation by integrating two advances: (i) high-dimensional ordinary least squares projection for accurate screening under correlation; and (ii) approximate orthogonalization for bias reduction. Simulation studies demonstrate that CHIMA effectively identifies active mediators even in the presence of strong correlations and outperforms competing methods across various settings. We further apply CHIMA to ribonucleic acid sequencing (RNA-seq) from the Living Brain Project, identifying genes that mediate the effect of Parkinson's disease on brain cell composition, thereby revealing cell-type-specific mechanisms of disease.