Cancer Cell Aptamer Screening Service

Core Concept: Aptamers vs. Antibodies

Aptamers are often called “chemical antibodies.” Their key advantages for cancer targeting include:

• Small size: Better tissue penetration.

• In vitro synthesis: Highly reproducible, no batch-to-batch variation.

• Ease of modification: Can be chemically tagged with dyes, drugs, or nanoparticles.

• Low immunogenicity.

• Target Range: Can bind to proteins, carbohydrates, lipids, or even complex molecular patterns on a whole cell’s surface.

The Screening Service Workflow (Cell-SELEX)

A typical service follows these steps:

1. Project Design & Target Selection

• Client Input: You define the target (e.g., “Aptamers for metastatic triple-negative breast cancer cell line MDA-MB-231”).

• Counter-Selection: Crucial step. To ensure specificity, the service provider will also use a control cell line (e.g., normal breast epithelial cells or a less aggressive cancer type) to remove aptamers that bind to common, non-target molecules.

• Library Design: The provider uses a vast random oligonucleotide library (e.g., 10^14 different sequences).

2. The SELEX Process
This is an iterative, multi-round biochemical “fishing” experiment:

• Incubation: The library is exposed to the target cancer cells.

• Washing: Weakly or unbound sequences are washed away.

• Elution: Bound aptamers are recovered (e.g., by heating or trypsinizing cells).

• Amplification: Recovered aptamers are amplified by PCR (for DNA) or RT-PCR (for RNA).

• Stringency Increase: In each subsequent round, conditions become stricter (more washing, shorter incubation, addition of counter-selection steps) to drive selection of the strongest, most specific binders.

3. Sequencing & Analysis

• High-Throughput Sequencing (NGS): After ~10-15 rounds, the enriched pool is sequenced.

• Bioinformatics: Clustering analysis identifies sequence “families” that have been enriched. The most frequent/interesting candidates are selected.

4. Characterization & Validation (Optional, often tiered)

• Synthesis: Selected aptamer candidates are chemically synthesized, often with modifications (e.g., Fluorescein for detection, PEGylation for stability).

• Binding Affinity (Kd): Measured via flow cytometry or similar, typically aiming for nM or even pM affinity.

• Specificity: Tested against a panel of related and unrelated cell lines.

• Internalization: Assessed if the aptamer is taken into the cell (critical for drug delivery applications).

• Target Identification (Optional): Some advanced services can help identify the actual protein/molecule the aptamer binds to (e.g., via aptamer pull-down followed by mass spectrometry).

Key Applications of the Resulting Aptamers

What to Look for in a Service Provider

1. Expertise in Cell-SELEX: Ask for proven experience, publications, or case studies.

2. Cell Culture Capabilities: They must be able to handle and maintain your specific cancer and control cell lines under proper conditions.

3. NGS & Bioinformatics: In-house capability is a major plus for efficient analysis.

4. Validation Suite: Clearly define what level of characterization is included (e.g., Kd, specificity panel) and what costs extra.

5. Turnaround Time & Cost: A full SELEX project typically takes 3-6 months and can cost $30,000 to $100,000+, depending on scope and validation.

6. Intellectual Property (IP) Terms: This is critical. Clearly establish who owns the discovered aptamer sequences. Options include full client ownership, joint IP, or a license-back arrangement.

Leading Providers & Models

• Specialized CROs: Several biotech companies focus exclusively on aptamer discovery (e.g., Aptamer Group, Aptus Biotech, Base Pair Biotechnologies).

• Academic Core Facilities: Some universities offer fee-for-service SELEX through core labs, often at a lower cost but with potentially less throughput.

• Full-Service CROs: Larger contract research organizations may have an aptamer discovery division.