Wu Xiaoqiu, Lin Xinrui, Ma Xiangqi, Huang Huidong, Zhang Dengwei, Liu Yuqing, Cheng Rui, Song Jia, Zhang Lifei, Tan Yamin, Peng Ruizi, Bing Tao, Wu Qin, Tan Weihong
The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022 Hangzhou, Zhejiang, China.
Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 200240 Shanghai, China.
J Am Chem Soc. 2025 Jun 18;147(24):20394-20405. doi: 10.1021/jacs.5c01296. Epub 2025 Jun 9.
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.
高通量测序技术的出现正在将生命科学转变为一种定量范式。然而，现有的针对不可直接测序分子的测序技术，如抗体测序和聚糖测序，面临着一些挑战，包括抗体-寡核苷酸偶联程序的复杂性、潜在的空间位阻以及劳动密集型的化学酶标记。适体作为可直接测序的核酸，具有卓越的特异性、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。在这项工作中，我们展示了Apt-seq，这是一个基于适体的、用于单细胞分辨率下多组学定量的高通量平台。这种整合策略——称为适体组学——能够对细胞表面蛋白、聚糖和mRNA进行平行分析。该平台的可行性通过商业细胞系得到验证，在整体和单细胞水平上均证明了测序数据与流式细胞术结果之间的高度一致性。当应用于复杂的临床样本时，Apt-seq表现出卓越的灵敏度，并能够精确分析肿瘤异质性。值得注意的是，该平台鉴定出了一群PTK7表面表达升高的肿瘤细胞亚群，PTK7是一种干性标志物。这些发现强调了PTK7在肿瘤干性中的作用及其作为类似干细胞生物标志物的潜力。此外，使用靶向唾液酸的适体，我们追踪了T细胞分化过程中唾液酸化的动态变化，观察到静息T细胞转变为功能性T细胞时唾液酸水平升高，随后在成熟时下降。总体而言，我们开发了一种新的多组学形式，称为适体组学，它利用适体实现对不可直接测序分子（如蛋白质和聚糖等）的测序。Apt-seq能够同时对可直接和不可直接测序的分子进行定量，为复杂生物系统中生命分子的全面定量提供了一个通用且可扩展的平台，并推动定量科学的发展。
