中国科学院杭州医学研究所吴芩团队近日实现了通过单细胞中的Aptamer测序（Apt-seq）对分子进行高通量多重定量。相关论文于2025年6月9日发表在《美国化学会志》上。
高通量测序技术的出现正在将生命科学转变为定量范式。然而，现有的非直接可测序分子的测序技术，如抗体测序和聚糖测序，面临着一定的挑战，包括抗体-寡核苷酸偶联程序的复杂性、潜在的空间位阻和劳动密集型的化学酶标记。适体作为一种可直接测序的核酸，具有特殊的特异性、广泛的靶标范围和小尺寸，使其成为多模态分子分析的理想工具。
研究组提出了Apt-seq，一个基于适配体的高通量平台，用于单细胞分辨率的多模态组学定量。这种整合策略──称为Aptomics──能够对细胞表面蛋白、聚糖和mRNA进行平行分析。该平台的可行性在商业细胞系主题化中得到了验证，在批量和单细胞水平上，测序数据和流式细胞术结果之间具有很强的一致性。当应用于复杂的临床样本时，Apt-seq表现出异常的敏感性，并能够精确地分析肿瘤异质性。值得注意的是，该平台发现了一个肿瘤细胞亚群，其PTK7表面表达升高，这是干细胞的标志。这些发现强调了PTK7在肿瘤干性中的作用及其作为干样生物标志物的潜力。
此外，该研究组设计了一种靶向唾液酸的适体，追踪了T细胞分化过程中唾液酸化的动态变化，观察到静息T细胞向功能T细胞过渡时唾液酸水平的增加，随后在成熟后下降。总的来说，课题组开发了一种新的多组学形式，称为Aptomics，它使用适体来对不能直接测序的分子进行测序，如蛋白质和聚糖等。Apt-seq能够同时定量直接和非直接测序的分子，为复杂生物系统中生命分子的全面定量和推进定量科学提供了一个多功能和可扩展的平台。
附：英文原文
Title: High-Throughput Multiplexed Quantification of Molecules by Aptamer Sequencing (Apt-seq) in Single Cells
Author: Xiaoqiu Wu, Xinrui Lin, Xiangqi Ma, Huidong Huang, Dengwei Zhang, Yuqing Liu, Rui Cheng, Jia Song, Lifei Zhang, Yamin Tan, Ruizi Peng, Tao Bing, Qin Wu, Weihong Tan
Issue&Volume: June 9, 2025
Abstract: 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 changes in sialylation during T cell differentiation, observing an increase in sialic acid levels as resting T cells transitioned into functional T cells, followed by a subsequent decline upon maturity. Collectively, we have developed a new form of multiomics, termed Aptomics, which employs aptamers to enable the sequencing of molecules that are not directly sequenceable, such as proteins and glycans, etc. Apt-seq enables the simultaneous quantitation of both directly and nondirectly sequencable molecules, offering a versatile and scalable platform for the comprehensive quantification of molecules of life in complex biological systems and advancing quantitative science.
DOI: 10.1021/jacs.5c01296
