redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-Cell RNA-Seq Data and Applications in Cancer

Abstract

The recent advancement of single-cell RNA sequencing (scRNA-seq) technologies facilitates the study of cell lineages in developmental processes and cancer. In this study, we developed a computational method, called redPATH, to reconstruct the pseudo developmental time of cell lineages using a consensus asymmetric Hamiltonian path algorithm. Besides, we developed a novel approach to visualize the trajectory development and implemented visualization methods to provide biological insights. We validated the performance of redPATH by segmenting different stages of cell development on multiple neural stem cell and cancer datasets, as well as other single-cell transcriptome data. In particular, we identified a stem cell-like subpopulation in malignant glioma cells. These cells express known proliferative markers, such as GFAP , ATP1A2 , IGFBPL1 , and ALDOC , and remain silenced for quiescent markers such as ID3 . Furthermore, we identified MCL1 as a significant gene that regulates cell apoptosis and CSF1R for reprogramming macrophages to control tumor growth. In conclusion, redPATH is a comprehensive tool for analyzing scRNA-seq datasets along the pseudo developmental time. redPATH is available at https://github.com/tinglabs/redPATH .

Advanced Single-Cell Omics Technologies and Informatics Tools for Genomics, Proteomics, and Bioinformatics Analysis

“…Liang et al proposed a novel single-cell clustering framework, SSRE, based on similarity learning [9] . Xie et al proposed redPATH, a comprehensive tool for reconstructing the pseudo development time of cell lineages based on scRNA-seq data [10] . Meanwhile, Wei et al developed DTFLOW, which can be applied in inference and visualization of single-cell pseudotime trajectory using diffusion propagation [11] .…”