Genetically engineered cell lines, a cornerstone of biomedical research, have long faced challenges of misidentification and unauthorized use. These issues not only threaten the reproducibility of research but also risk billions of dollars and valuable intellectual property annually. Now, researchers at The University of Texas at Dallas have pioneered a groundbreaking method that embeds unique genetic identifiers in engineered cell lines, effectively eliminating identification errors and safeguarding innovations with tamper-proof genomic tags.
Dr. Leonidas Bleris, a professor of bioengineering at the Erik Jonsson School of Engineering and Computer Science, emphasized the significance of this advancement. “There are thousands of genetically engineered cell lines in use today, yet we often have no reliable way to verify their identity and origin,” Bleris stated. “Our team has been tackling this challenge by developing innovative solutions that embed unique genetic IDs — essentially barcodes — directly into cells.”
Revolutionizing Cell Line Authentication
The announcement comes as Bleris and his team published their findings in the August 7 issue of the journal Advanced Science. Custom-designed cell lines are crucial for developing vaccines and targeted therapies for a wide array of diseases. However, the rapid growth of gene-editing tools like CRISPR has outpaced current authentication capabilities. “Existing methods can’t reliably distinguish between cell lines that share the same origin but carry different genetic modifications,” Bleris explained. “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 security technology used in microchips, UT Dallas researchers have developed a patent-pending method applying the concept of physical unclonable functions (PUFs) to living cells. This creates unique, tamper-proof genetic “fingerprints” that are impossible to replicate. “Biotechnology companies can now ‘barcode’ their cell lines to protect their product,” Bleris added.
From Concept to Implementation
In 2022, UT Dallas researchers introduced a two-step version of the genetic PUFs technology to safeguard engineered cell lines. The latest research streamlines this process into a single step, simplifying implementation. The method utilizes CRISPR to guide the Cas9 enzyme, which acts like scissors to cut DNA at specific locations. Researchers target a “safe-harbor” location in the genome, where modifications can occur without affecting the cell’s function.
To repair the break, another enzyme, terminal deoxynucleotidyl transferase, adds random extra DNA sequences into the safe-harbor area. These sequences create a unique pattern across the cell population, serving as a distinct identifier. The researchers have also developed machine learning tools to 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, PhD’23, a bioengineering researcher at UT Dallas and co-lead author of the study.
Collaborative Efforts and Future Implications
The UT Dallas team collaborated with Dr. Alexander Pertsemlidis, a professor of pediatrics and cell systems at UT San Antonio. Pertsemlidis and Bleris co-founded SyntaxisBio Inc. to commercialize the technology. Other contributors included Zikun Zhou, a doctoral student in biomedical engineering; Jie Chen, a computer science graduate; and Yesh Doctor, a former member of Bleris’ lab. Jocelyn G. Camposagrado, a biomedical engineering graduate, and Dr. Yiorgos Makris, a SyntaxisBio advisor, also played pivotal roles.
The research received support from UT Dallas, the National Science Foundation, and a Small Business Technology Transfer grant from the National Human Genome Research Institute, part of the National Institutes of Health.
This development represents a significant leap forward in the field of biomedical research, offering a robust solution to longstanding issues of cell line authentication. As the technology becomes more widely adopted, it promises to enhance the integrity and reliability of scientific research, ensuring that innovations are protected and accurately attributed.
