Insertion/deletion and microsatellite alteration profiles in induced pluripotent stem cells

• Published in: Stem cell reports Vol. 16; no. 10; pp. 2503 - 2519
• Main Authors: Kamimura, Satoshi, Suga, Tomo, Hoki, Yuko, Sunayama, Misato, Imadome, Kaori, Fujita, Mayumi, Nakamura, Miki, Araki, Ryoko, Abe, Masumi
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 12.10.2021; Elsevier
• Subjects: Animals; Cells, Cultured; Cellular Reprogramming; Cellular Reprogramming Techniques - methods; cord blood erythroblasts; Genetic Profile; genome reprogramming; hotspots of microsatellite alteration; human iPSCs; Humans; INDEL Mutation; InDels; Induced Pluripotent Stem Cells - metabolism; Mice; Mice, Inbred C57BL; microsatellite alterations; Microsatellite Repeats; mouse iPSCs; mouse ntESCs; sister clones set; Whole Genome Sequencing; hotspots of microsatellite alteration; mouse iPSCs; genome reprogramming; whole-genome sequencing; microsatellite alterations; cord blood erythroblasts; InDels; human iPSCs; mouse ntESCs; sister clones set
• ISSN: 2213-6711; 2213-6711
• DOI: 10.1016/j.stemcr.2021.08.017

We here demonstrate that microsatellite (MS) alterations are elevated in both mouse and human induced pluripotent stem cells (iPSCs), but importantly we have now identified a type of human iPSC in which these alterations are considerably reduced. We aimed in our present analyses to profile the InDels in iPSC/ntESC genomes, especially in MS regions. To detect somatic de novo mutations in particular, we generated 13 independent reprogramed stem cell lines (11 iPSC and 2 ntESC lines) from an identical parent somatic cell fraction of a C57BL/6 mouse. By using this cell set with an identical genetic background, we could comprehensively detect clone-specific alterations and, importantly, experimentally validate them. The effectiveness of employing sister clones for detecting somatic de novo mutations was thereby demonstrated. We then successfully applied this approach to human iPSCs. Our results require further careful genomic analysis but make an important inroad into solving the issue of genome abnormalities in iPSCs. [Display omitted] •InDels and microsatellite alterations are elevated in iPSCs•These alterations are reduced in human iPSCs derived from cord blood erythroblasts•Employing sister clones is an effective way to detect somatic de novo mutations In this article, Abe and colleagues conclusively demonstrate that InDels and microsatellite alterations are elevated in reprogrammed pluripotent stem cells, both mouse and human, by employing sister clones and conducting large-scale validation experiments. Furthermore, they show that these alterations are considerably reduced in human iPSCs derived from cord blood erythroblasts.