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Genetically engineered cell lines used in biomedical research have long been prone to misidentification and unauthorized use, wasting billions of dollars each year and jeopardizing critical scientific discoveries. These problems not only undermine reproducibility of research results, but also put valuable intellectual property at risk.

Now, researchers at The University of Texas at Dallas have developed a novel method to embed unique genetic identifiers in engineered cell lines, eliminating identification errors and safeguarding innovations with tamper-proof genomic tags.

"There are thousands of genetically engineered cell lines in use today, yet we often have no reliable way to verify their identity and origin," said Dr. Leonidas Bleris, professor of bioengineering in the Erik Jonsson School of Engineering and Computer Science. "Our team has been tackling this challenge by developing innovative solutions that embed unique genetic IDs—essentially barcodes—directly into cells."

Bleris is corresponding author of a study in the journal Advanced Science demonstrating the technology.

Custom-designed cell lines are essential for developing vaccines and targeted therapies across a wide range of diseases. The widespread use of the gene-editing tool CRISPR has accelerated the creation of new research models, but this rapid growth has outpaced current authentication capabilities, Bleris said.

"Existing methods can't reliably distinguish between cell lines that share the same origin but carry different genetic modifications," Bleris said. "This leaves biomedical research vulnerable due to misidentification, cross-contamination and unauthorized use, and can result in the loss of valuable intellectual property."

Inspired by a security technology used to protect microchips, UT Dallas researchers have developed a patent-pending method that applies the concept of physical unclonable functions, or PUFs, to living cells—creating unique, tamper-proof genetic "fingerprints" that can't be copied.

"Biotechnology companies can now 'barcode' their cell lines to protect their product," Bleris said.

In 2022, UT Dallas researchers developed a two-step version of the genetic PUFs technology to protect the authenticity of engineered cell lines. Their new research reduces the process to one step, making the technology easier to implement.

The process uses CRISPR to guide Cas9, an enzyme that acts like a pair of scissors to cut DNA at specific locations. The researchers target the area of the genome called a "safe-harbor" location, where modifications can be made without affecting the cell's function.

The method leverages another enzyme, terminal deoxynucleotidyl transferase, to repair the break while adding random extra DNA sequences into the safe-harbor area. The added sequences form a unique pattern across the cell population that serves as the unique identifier.

The researchers also developed machine learning tools that can verify cell lines' identity.

"The machine learning-based method we developed allows us to fully utilize the space of genetic fingerprints and improve the resolution of cell-line identification," said Taek Kang Ph.D.'23, a bioengineering researcher at UT Dallas, a former Eugene McDermott Graduate Fellow and the study's co-lead author.