A Quasi-Regression Method for the Mediation Analysis of Zero-Inflated Single-Cell Data

TL;DR

QuasiMed is a novel quasi-regression framework designed for causal mediation analysis in single-cell data, addressing distributional assumptions and demonstrating high power and efficiency.

Contribution

It introduces a three-step mediation method specifically tailored for single-cell data, relaxing distributional assumptions and enabling causal pathway identification.

Findings

High power and false discovery rate control in simulations

Efficient computation demonstrated in real data analysis

Successfully identified mediating pathways in single-cell data

Abstract

Recent advances in single-cell technologies have advanced our understanding of gene regulation and cellular heterogeneity at single-cell resolution. Single-cell data contain both gene expression levels and the proportion of expressing cells, which makes them structurally different from bulk data. Currently, methodological work on causal mediation analysis for single-cell data remains limited and often requires specific distributional assumptions. To address this challenge, we present QuasiMed, a mediation framework specialized for single-cell data. Our proposed method comprises three steps, including (i) screening mediator candidates through penalized regression and marginal models (similar to sure independence screening), (ii) estimation of indirect effects through the average expression and the proportion of expressing cells, (iii) and hypothesis testing with multiplicity control. The key benefit of QuasiMed is that it specifies only the mean functions of the mediation models through a quasi-regression framework, thereby relaxing strict distributional assumptions. The method performance was evaluated through the real-data-inspired simulations, and demonstrated high power, false discovery rate control, and computational efficiency. Lastly, we applied QuasiMed to ROSMAP single-cell data to illustrate its potential to identify mediating causal pathways. R package is freely available on GitHub repository at https://github.com/sjahnn/QuasiMed.