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

Area of Science:

• Biotechnology
• Molecular Biology
• Genomics

Background:

• High-throughput sequencing transforms life sciences but faces challenges with nondirectly sequencable molecules like antibodies and glycans.
• Existing methods for antibody and glycan sequencing are complex, involve steric hindrance, and require labor-intensive labeling.
• Aptamers offer specificity, broad targeting, and small size, making them suitable for multimodal molecular profiling.

Purpose of the Study:

• To develop Apt-seq, an aptamer-based, high-throughput platform for multimodal omics quantification at single-cell resolution.
• To introduce Aptomics, an integrative strategy for parallel profiling of cell surface proteins, glycans, and mRNA.
• To demonstrate the platform's capability in analyzing complex biological samples and identifying novel biomarkers.

Main Methods:

• Developed Apt-seq, an aptamer-based sequencing platform for multimodal molecular profiling.
• Integrated aptamer selection and sequencing for simultaneous quantification of proteins, glycans, and mRNA.
• Validated the platform using cell lines and complex clinical samples, comparing results with flow cytometry.

Main Results:

• Apt-seq demonstrated strong concordance with flow cytometry for bulk and single-cell analyses.
• The platform precisely profiled tumor heterogeneity in clinical samples, identifying a PTK7-expressing subpopulation linked to stemness.
• Dynamic changes in sialylation during T cell differentiation were tracked, showing increased sialic acid in functional T cells.

Conclusions:

• Aptomics, powered by Apt-seq, enables sequencing of previously nondirectly sequencable molecules like proteins and glycans.
• The platform offers a versatile and scalable solution for comprehensive molecular quantification in complex biological systems.
• Apt-seq advances quantitative science by enabling simultaneous analysis of directly and indirectly sequencable molecules.