DeSCENT: Deconvolutional Single-Cell RNA-seq Enhances Transcriptome-based Cancer Survival Analysis

Abstract

MotivationAccurate cancer survival prediction requires modeling tumor heterogeneity across both population and cell levels. Most cancer survival analyses use tumor transcriptomes only, since cohorts are usually measured with bulk RNA-seq but are rarely recorded with single-cell RNA-seq. This prevents the direct use of cell-level transcriptomes in cancer survival analysis. ResultsTo bridge this gap, we propose using bulk RNA-seq deconvolution algorithms to reconstruct each subjects scRNA-seq profile from their bulk data. Then, by combining both scRNA-seq and bulk RNA-seq together with their survival labels (paired to bulk), we perform multimodal transcriptome-based survival analysis. We built this framework as DeSCENT and evaluated it with common survival models on eight TCGA cancer cohorts. Results showed notable and consistent improvements in C-index over bulk-only models or models using cellular information alone. AvailabilityOur code is available at GitHub: https://github.com/YonghaoZhao722/DeSCENT. Contactzpluo@swjtu.edu.cn; y.he@imperial.ac.uk Supplementary informationSupplementary data are available at Bioinformatics online.