DISC-seq: deciphering cell stress heterogeneity through joint mapping of cellular damage and transcriptomic landscapes in scRNA-seq [part 2]

Cell heterogeneity is a fundamental feature of biological systems, driving diverse responses to stimuli and stressors, including developmental cues, diseases, and drug treatments. While single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to characterize this diversity by profiling gene expression at single cell levels, a critical gap remains in that it cannot directly link transcriptional profiles to functional cellular outcomes, such as stress-induced damage. To bridge this gap, we developed DISC-seq (Damage Identification in Single-Cell RNA sequencing), a method compatible with standard scRNA-seq workflows that simultaneously quantifies transcriptome-wide gene expression and evaluates the extent of cell damage at single-cell resolution. Applied to both cancer cell lines and clinical peripheral blood mononuclear cells (PBMCs) from pediatric hematology patients, DISC-seq uncovered key molecular pathways and gene expression determinants that govern heterogeneous treatment and stress responses. Our approach enables the systematic discovery of regulatory mechanisms underlying heterogeneous cellular stress sensitivity within and across cell types, providing a powerful tool for dissecting the molecular basis of cell heterogeneity. Raw sequencing reads of scRNA-seq data can be accessed through GSA-human (https://ngdc.cncb.ac.cn/gsa-human/) with the accession number HRA014683. Processed matrices of cell line and PBMC samples can be found here.