redPATH:Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer
- Author:
Xie KAIKUN
1
,
2
;
Liu ZEHUA
;
Chen NING
;
Chen TING
Author Information
1. Institute for Artificial Intelligence,State Key Lab of Intelligent Technology and Systems,Department of Computer Science and Technology,Tsinghua University,Beijing 100084,China
2. Tsinghua-Fuzhou Institute of Digital Technology,Beijing National Research Center for Information Science and Technology,Tsinghua University,Beijing 100084,China
- Keywords:
Single-cell pseudotime reconstruction;
Consensus Hamiltonian path;
Cell differentiation;
Cell proliferation;
Cell development and diseases
- From:
Genomics, Proteomics & Bioinformatics
2021;19(2):292-305
- CountryChina
- Language:Chinese
-
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 malig-nant 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 reprogram-ming 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.
