Str profiling for detecting contamination in ipsc lines with chromosomal abnormalities
Str profiling for detecting contamination in ipsc lines with chromosomal abnormalities Induced pluripotent stem cells (iPSCs) have revolutionized regenerative medicine and disease modeling due to their ability to differentiate into almost any cell type. However, maintaining the genetic integrity of iPSC lines is crucial for their reliable use in research and potential therapeutic applications. One of the persistent challenges in the cultivation of iPSCs is the occurrence of chromosomal abnormalities, which can lead to contamination, unpredictable behavior, and compromised experimental outcomes. Detecting such abnormalities early and accurately is essential for ensuring the safety and efficacy of iPSC-derived products.
One of the most effective methods for identifying chromosomal abnormalities in iPSC lines is short tandem repeat (STR) profiling, a technique traditionally used for cell line authentication. While STR profiling is primarily employed to verify the identity of cell lines, recent advancements have expanded its utility to include the detection of chromosomal abnormalities and contamination. This method involves analyzing specific repetitive DNA sequences scattered throughout the genome, which can reveal genetic discrepancies indicative of contamination or abnormal chromosomal structures.
The process begins with extracting DNA from the iPSC cultures, followed by PCR amplification of selected STR loci. These loci are chosen for their high polymorphism and stability, providing a genetic fingerprint unique to each cell line. When chromosomal abnormalities such as duplications, deletions, or translocations occur, they can alter the expected STR profile. For instance, an abnormality that results in extra copies of a chromosome may lead to increased signal intensity at corresponding STR loci, while deletions may cause missing or diminished signals. Such deviations from the baseline STR profile signal potential chromosomal irregularities.
Moreover, STR profiling can help identify cross-contamination with other cell lines, a common issue in cell culture laboratories. Contaminated cultures often harbor unintended cell populations, which can be distinguished based on their unique STR fingerprints. Regular STR analysis acts as a quality control measure, ensuring that the iPSC lines remain pure and free from contamination over successive passages.
While STR profiling is valuable, it is often complemented with other cytogenetic techniques such as karyotyping, fluorescence in situ hybridization (FISH), or comparative genomic hybridization (CGH) to confirm and characterize chromosomal abnormalities comprehensively. Nonetheless, STR profiling provides a rapid, cost-effective, and sensitive first-line screening tool to detect contamination and gross chromosomal alterations in iPSC lines.
In conclusion, as the use of iPSCs expands in both research and clinical contexts, developing reliable methods for routine screening of chromosomal integrity is vital. STR profiling offers a practical approach to detect contamination and abnormalities early, safeguarding the integrity of experimental data and ensuring the safety of potential therapeutic applications. Integrating STR analysis into standard quality control workflows enhances the reproducibility and safety of iPSC-based studies, ultimately advancing the field of regenerative medicine.
