Development of single cell sequencing technique that can simultaneously quantify proteome and transcriptome using aptamers

Abstract

Conventional bulk RNA sequencing (RNA-seq) provides only average information of the entire cell populations, so it had difficulties in distinguishing and analyzing various cell types. However, single-cell RNA sequencing (scRNA-seq) can identify cell type composition changes and cell type specific changes. In addition, scRNA-seq can perform cell trajectory analysis for cell differentiation and disease development. Therefore, the key genes can be revealed in the process of successive cell type changes. Like this, the importance and necessity of study using scRNA-seq, which can overcome the limitations of the existing technology and obtain genotypic and phenotypic heterogeneity information at a single cell level, is increasing. Nevertheless, studies that analyze only transcripts provide limited information on changes in cells. Therefore, the importance of analyzing single cells at various molecular levels is on the rise. In this study, I attempted to develop a technology that can simultaneously quantify transcripts and proteins by targeting not only cell surface proteins but also intracellular proteins using an aptamer called “chemical antibody”. First, the optimal binding conditions for aptamers and cells were set, and binding efficiency was confirmed for 11 aptamers. Based on these results, a scRNA-seq was performed using two cell lines. The result of analysis was contrary to expectations. There was no correlation between the transcriptome and the proteome, and the expression of the protein was similar for all aptamers. Further studies will be conducted on methods to block non-specifically bound aptamers and to confirm the specificity of aptamer binding. After further research, I intend to present new possibilities of single cell analysis technology capable of measuring various molecular levels.