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Development of single chain antibodies for targeting Ewing sarcoma surface marker CD99
Yogalakshmi Sabapathy1, Priya Ramanathan1, Rajkumar Thangarajan2
1Cancer Institute (WIA), Chennai, India.
Biochemical and Biophysical Research Communications
|April 5, 2026
Summary
Researchers engineered CD99-targeting single-chain variable fragments (scFvs) for Ewing sarcoma (ES). A shorter 15-mer linker improved scFv binding affinity and specificity, showing promise for new cancer therapies.
Area of Science:
- Oncology
- Immunology
- Biotechnology
Background:
- Recombinant antibodies are crucial therapeutics for cancer treatment.
- CD99 is a glycoprotein overexpressed in malignancies like Ewing sarcoma (ES).
- Current ES therapies have significant toxicity and late complications, necessitating novel treatments.
Purpose of the Study:
- To develop CD99-targeting single-chain antibodies (scFvs) for improved cancer therapy.
- To engineer and characterize two scFvs with different linker lengths for CD99 targeting.
- To evaluate the impact of linker length on scFv performance and specificity.
Main Methods:
- Isolated variable regions from a hybridoma-derived anti-CD99 antibody.
- Engineered two scFvs with distinct 15-mer and 18-mer linkers.
- Expressed and purified scFvs in Escherichia coli.
- Performed in vitro binding analyses to compare scFv affinity and specificity.
Main Results:
- Both engineered scFvs were successfully expressed and purified.
- The scFv with the shorter 15-mer linker showed significantly enhanced affinity and specificity.
- The 15-mer scFv demonstrated superior binding to CD99-overexpressing Ewing sarcoma cells compared to the 18-mer variant.
- Linker length was identified as a critical factor influencing scFv performance.
Conclusions:
- A rational design principle for optimizing CD99-targeting scFvs was established.
- The 15-mer scFv holds potential for CAR-T cell development in Ewing sarcoma.
- This scFv may also be applicable for targeting other CD99-overexpressing carcinomas.

