Abstract: There are currently over 115 clinical trials worldwide using human pluripotent stem cells (hPSC)-derived cells. Culture conditions exert a selective pressure that can give an advantage to cells accumulating genomic alterations. Therefore, ensuring their genomic integrity is an important prerequisite. Seventeen years ago, using a-CGH and SNP array technologies, we identified, in hPSCs, a recurrent chromosomal defect (2.5 to 4.6 Mb) located on chromosome 20 at position q11.21. Cells carrying this amplification possess some features of neoplastic progression. 20q11.21 duplication is found in many cancers and is an important event in tumor progression. This anomaly is the most frequently observed worldwide in hPSCs. It is estimated that it represents more than 20% of the recurrent anomalies listed. However, this duplication is not well characterized. Only few studies have looked at the position of the extra copy of chromosome 20q11.21. Using fluorescence in situ hybridization we determined in 5 hPSC lines that the extra copy was inserted either at 1p36.3 region or as a tandem or inverted repeat at 20q11.21. Only one study analyzed the local genomic architecture and breakpoints of two samples using long-read next generation sequencing and found that in both cases, the duplications were arranged in a head-to-tail orientation. Optical genome mapping (OGM) has only rarely been used to monitor genomic integrity of hPSCs and their derivatives. Our study aims to evaluate in which way OGM could become a more sensitive and resolutive tool to qualify clinical-grade lines and might contribute to a better understanding of the mechanisms responsible for genomic instability. To this end, we analyzed 6 samples in which a 20q11.21 duplication has been previously identified with SNP arrays. Beyond the field of hPSC use in biotherapy, this study could also contribute to a better understanding of early events that play a role in tumor progression.
Funding Source: This study was supported by the Agence Nationale de la Recherche under the “Investissements d’avenir” program [ANR-10-IAHU-01]
