Abstract 4411: A gene set enrichment analysis approach in single-cells along pseudotime trajectories reveals the dynamic activity of oncogenic pathways

Abstract

Abstract Single cell RNA-sequencing (scRNA-seq) has advanced studies of heterogeneous tissues and cell populations in both healthy and disease states. Dimensionality reduction methods leverage this highly granular data to identify cellular states not captured by “bulk” gene expression or to organize cells along ‘pseudotime' trajectories related to biological processes such as cell cycle or cellular differentiation. Cellular states and trajectories are often annotated using individual marker genes and not gene sets or pathways, despite their more reliable and interpretable association to biological processes. Gene Set Enrichment Analysis (GSEA) was designed to test the enrichment of gene sets in bulk transcriptomic data, but due to the sparsity of the expression data, has not been adapted to single cell analysis. We propose a method to compute gene set enrichment for scRNA-seq data, which calculates an enrichment score for each cell in the dataset. We apply this method to a set of matched ovarian cancer cell lines with acquired resistance to carboplatin. After aligning the cells to a cell-cycle derived pseudotime trajectory, the activity of pathways which were dysregulated in bulk expression profiles appeared to change with the cell cycle progression. The analysis further identified interferon alpha signaling induction in resistant cells, independent of differences in cell cycle progression. Hence, by quantifying and analyzing pathway-level transcriptional activity in the context of a single-cell pseudotime trajectory, the proposed method provides more interpretable annotation of biological processes altered in cancer progression and treatment. Citation Format: Alexander T. Wenzel, Devora Champa, Stephen B. Howell, Jill P. Mesirov, Olivier Harismendy. A gene set enrichment analysis approach in single-cells along pseudotime trajectories reveals the dynamic activity of oncogenic pathways [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4411.