# Comparative aptamer profiling reveals cell surface remodeling and the emergence of a noncanonical cell surface protein under oncogenic signaling

## TL;DR

The paper introduces a new method using aptamers to study how cancer-related signals change the surface of cells, revealing unexpected protein movements.

## Contribution

A streamlined comparative aptamer profiling method is introduced to detect cell surface remodeling under oncogenic signaling.

## Key findings

- Mutant K-Ras expression dynamically alters cell surface composition.
- An aptamer identified abnormal translocation of a mitochondrial matrix protein to the cell surface.
- Aptamers showed specific binding to mutant K-Ras-expressing cells without sequence optimization.

## Abstract

Identifying cell type-specific molecular markers on the cancer cell surface is essential for understanding cancer progression and for discovering critical neoantigens relevant to immunotherapy. Nucleic acid aptamers serve as powerful tools for probing complex and dynamic cell surface characteristics. Here, we introduce a streamlined comparative aptamer profiling methodology that enables side-by-side analysis of cell surface remodeling. Using cell-SELEX (systematic evolution of ligands by exponential enrichment), we generated a modified base-incorporated aptamer library directly from cells, which was then employed to explore the surface states of normal and mutant protein-expressing cells. Differential analysis of aptamer enrichment using next-generation sequencing revealed distinct aptamer signatures that correlated with cell types. Our analysis demonstrated that mutant K-Ras expression dynamically altered cell surface composition. Individual aptamers showed specific binding to mutant K-Ras-expressing cells without requiring sequence optimization. Moreover, target identification of one aptamer revealed abnormal translocation of a mitochondrial matrix protein to the cell surface without detectable changes in mRNA or protein levels upon altered cellular signaling. These findings highlight the dynamic modulation of cell surface states by aberrant cellular signaling. Overall, we present a useful comparative strategy to investigate cell surface alterations. This approach may help uncover previously unrecognized cell surface markers associated with oncogenic signaling.

Comparative aptamer profiling was established to examine cell surface molecular states. This approach revealed bidirectional alterations and unexpected surface localization of a mitochondrial protein under oncogenic signaling.