Single-Cell Differentiation Trajectory Inference Algorithm with Iterative Feature Selection

The construction of cell differentiation trajectories from single-cell transcriptomic data or proteomic data by single-cell trajectory inference methods can help to understand the developmental process of normal tissues or provide pathologically relevant information. However, the accuracy and robustness of current single-cell trajectory inference algorithms are still a challenge, one of the reasons is the noise caused by the detection of a large number of unrelated genes in single-cell sequencing. In order to solve this problem, a trajectory inference method iterTIPD (iterative trajectory inference based on probability distribution) based on iterative feature selection is proposed. Its innovation lies in iteratively applying feature selection methods widely used for screening differentially expressed genes to linear or branching single-cell RNA sequencing data, and improving the accuracy and robustness of cell pseudotime ordering by selecting the gene subset that contributes the most to the constructed differentiation trajectory. Experimental results on four scRNA-seq datasets show that iterTIPD can effectively improve the accuracy and robustness of the single-cell trajectory inference algorithm. IterTIPD also improves the performance of other trajectory inference algorithms, proving generalization of iterTIPD. The differentiation trajectory of neural stem cells is reconstructed by iterTIPD algorithm, and the comparison shows that the differentiation trajectory is highly consistent with the known neural stem cell differentiation trajectory. Meanwhile, Top2a and Gja1 may be novel markers defining activated neural stem cell subpopulations.