A Pipeline to Identify and Characterize Senescent Cells

Abstract

Senescence is a cell state that contributes to aging, as well as age-related diseases such as Alzheimer’s and heart disease. Through the use of bulk RNA-seq, several senescent markers have been identified. Despite the significance of these bulk RNA-seq senescence markers, these traditional markers are not efficient in determining senescence with precision. Another important issue is the method of analysis. While bulk RNA-seq has been useful in the initial discovery and characterization of traditional senescent cell markers, single cell RNA sequencing (scRNA-seq) may serve as a better alternative for precisely characterizing heterogeneous senescent cell expression profiles. Despite the widespread use and success of scRNA-seq in many areas of study since its advent in 2009, scRNA-seq has been used relatively little in the research field of senescence. Few studies have specifically single-cell-sequenced senescent cells. Even among these few studies, none have the necessary experimental design to allow for fool-proof annotation of senescent cells at single cell resolution, which leads to a catch-22: if there’s no consensus method of identifying individual senescent cells at the transcriptome level, there’s no reliable way of determining new markers. In this study, 64 different pipelines were assembled to determine consensus among different methods as well as build the best one for identifying and characterizing senescent cells in data provided from a previous study.