High-Throughput Multiplexed Quantification of Molecules by Aptamer Sequencing (Apt-seq) in Single Cells

作者：Xiaoqiu Wu, Xinrui Lin, Xiaoxu Ma, Huidong Huang, Dengwei Zhang, Yuqing Liu, Rui Cheng, Jia Song, Lifei Zhang, Yamin Tan, Ruizi Peng, Tao Bing, Qin Wu, Weihong Tan · 发表于：Journal of the American Chemical Society · 年份：2025 · DOI：10.1021/jacs.5c01296 · 被引用次数：8 · 研究领域：Single-cell and spatial transcriptomics、Advanced biosensing and bioanalysis techniques、RNA and protein synthesis mechanisms

The advent of high-throughput sequencing technologies is transforming life sciences into a quantitative paradigm. However, existing sequencing technologies for nondirectly sequencable molecules, such as antibody-sequencing and glycan-sequencing, face certain challenges, including the complexity of antibody-oligonucleotide conjugation procedures, potential steric hindrance, and the labor-intensive chemoenzymatic labeling. Aptamers, as directly sequencable nucleic acids, offer exceptional specificity, broad target range, and small size, making them ideal tools for multimodal molecular profiling. In this work, we present Apt-seq, an aptamer-based, high-throughput platform for multimodal omics quantification at single-cell resolution. This integrative strategy─termed Aptomics─enables parallel profiling of cell surface proteins, glycans, and mRNA. The feasibility of the platform was validated using commercial cell lines, demonstrating strong concordance between sequencing data and flow cytometry results at both bulk and single-cell levels. When applied to complex clinical samples, Apt-seq exhibited exceptional sensitivity and enabled the precise profiling of tumor heterogeneity. Notably, the platform identified a subpopulation of tumor cells with elevated PTK7 surface expression, a marker of stemness. These findings underscore the role of PTK7 in tumor stemness and its potential as a stem-like biomarker. Moreover, using an aptamer targeting sialic acid, we tracked the dynamic chan...