Evolution of Aptamer Materials Maps Exosomal Surface Proteins at the Nano-Bio Interface

Area of Science:

• Biochemistry
• Molecular Biology
• Nanotechnology

Background:

• Exosomes are crucial nanoscale vesicles for intercellular communication.
• Interrogating exosomal membrane proteins is challenging due to their properties.
• Existing methods struggle with the hydrophobicity, low abundance, and nanoscale curvature of exosomal proteins.

Purpose of the Study:

• To develop a novel strategy for direct discovery and quantification of exosomal membrane proteins under native conditions.
• To overcome the limitations of current methods in analyzing membrane-confined epitopes.
• To identify novel exosomal biomarkers for hepatocellular carcinoma and immunotherapy response.

Main Methods:

• AptEx-ID: A chemically guided aptamer evolution strategy using indole-modified nucleotides.
• Emulation of aromatic amino acid side chains to enhance DNA's molecular interaction space.
• Fluorescence-assisted microbead display integrated with machine learning for target-agnostic probe evolution.
• Multiplexed detection workflow for comprehensive exosomal profiling.

Main Results:

• AptEx-ID successfully enabled direct discovery and quantification of exosomal membrane proteins.
• A seven-aptamer membrane signature was resolved for plasma-derived exosomes from hepatocellular carcinoma.
• GTSE1 was identified as a novel exosomal surface protein associated with immunotherapy response.

Conclusions:

• Chemically augmented nucleic acids serve as adaptive molecular materials for probing nanoscale biological membranes.
• AptEx-ID provides a powerful platform for exosomal biomarker discovery and diagnostics.
• This approach advances the understanding of exosome biology and its role in disease.