DECEPTICON: a correlation-based strategy for RNA-seq deconvolution inspired by a variation of the Anna Karenina principle.

Abstract

Accurately deconvoluting cellular composition from bulk RNA-seq data is pivotal for understanding the tumor microenvironment and advancing precision medicine. Existing methods often struggle to consistently and accurately quantify cell types across heterogeneous RNA-seq datasets, particularly when ground truths are unavailable. In this study, we introduce DECEPTICON, a deconvolution strategy inspired by the Anna Karenina principle, which postulates that successful outcomes share common traits, while failures are more varied. DECEPTICON selects top-performing methods by leveraging correlations between different strategies and combines them dynamically to enhance performance. Our approach demonstrates superior accuracy in predicting cell-type proportions across multiple tumor datasets, improving correlation by 23.9% and reducing root mean square error by 73.5% compared to the best of 50 analyzed strategies. Applied to The Cancer Genome Atlas (TCGA) datasets for breast carcinoma, cervical squamous cell carcinoma, and lung adenocarcinoma, DECEPTICON-based predictions showed improved differentiation between patient prognoses. This correlation-based strategy offers a reliable, flexible tool for deconvoluting complex transcriptomic data and highlights its potential in refining prognostic assessments in oncology and advancing cancer biology.