A reference human induced pluripotent stem cell line for large-scale collaborative studies

• Published in: Cell stem cell 2022-12, Vol.29 (12), p.1685-1702.e22
• Main Authors: Pantazis, Caroline B., Yang, Andrian, Lara, Erika, McDonough, Justin A., Blauwendraat, Cornelis, Peng, Lirong, Oguro, Hideyuki, Kanaujiya, Jitendra, Zou, Jizhong, Sebesta, David, Pratt, Gretchen, Cross, Erin, Blockwick, Jeffrey, Buxton, Philip, Kinner-Bibeau, Lauren, Medura, Constance, Tompkins, Christopher, Hughes, Stephen, Santiana, Marianita, Faghri, Faraz, Nalls, Mike A., Vitale, Daniel, Ballard, Shannon, Qi, Yue A., Ramos, Daniel M., Anderson, Kailyn M., Stadler, Julia, Narayan, Priyanka, Papademetriou, Jason, Reilly, Luke, Nelson, Matthew P., Aggarwal, Sanya, Rosen, Leah U., Kirwan, Peter, Pisupati, Venkat, Coon, Steven L., Scholz, Sonja W., Priebe, Theresa, Öttl, Miriam, Dong, Jian, Meijer, Marieke, Janssen, Lara J.M., Lourenco, Vanessa S., van der Kant, Rik, Crusius, Dennis, Paquet, Dominik, Raulin, Ana-Caroline, Bu, Guojun, Held, Aaron, Wainger, Brian J., Gabriele, Rebecca M.C., Casey, Jackie M., Wray, Selina, Abu-Bonsrah, Dad, Parish, Clare L., Beccari, Melinda S., Cleveland, Don W., Li, Emmy, Rose, Indigo V.L., Kampmann, Martin, Calatayud Aristoy, Carles, Verstreken, Patrik, Heinrich, Laurin, Chen, Max Y., Schüle, Birgitt, Dou, Dan, Holzbaur, Erika L.F., Zanellati, Maria Clara, Basundra, Richa, Deshmukh, Mohanish, Cohen, Sarah, Khanna, Richa, Raman, Malavika, Nevin, Zachary S., Matia, Madeline, Van Lent, Jonas, Timmerman, Vincent, Conklin, Bruce R., Johnson Chase, Katherine, Zhang, Ke, Funes, Salome, Bosco, Daryl A., Erlebach, Lena, Welzer, Marc, Kronenberg-Versteeg, Deborah, Lyu, Guochang, Arenas, Ernest, Coccia, Elena, Sarrafha, Lily, Ahfeldt, Tim, Marioni, John C., Skarnes, William C., Cookson, Mark R., Ward, Michael E., Merkle, Florian T.
• Format: Article
• Language: English
• Subjects: Biological Assay; Cell Differentiation; CRISPR; differentiation; Gene Editing; Humans; Induced Pluripotent Stem Cells; iPSC; karyotype; p53; pluripotent; single-cell; stem cell; whole-genome
• ISSN: 1934-5909; 1875-9777; 1875-9777
• DOI: 10.1016/j.stem.2022.11.004

Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field. [Display omitted] •Deep genotyping and phenotyping identified KOLF2.1J as a reference human iPSC line•KOLF2.1J and its gene-edited derivates are readily obtainable with minimal restrictions•Human iPSC lines remain genetically stable after our CRISPR-Cas9-based gene editing•Our multifactorial pipeline serves as a blueprint to identify other lead iPSC lines Merkle and colleagues deeply characterized candidate human induced pluripotent stem cell (iPSC) lines to identify a common reference line. The KOLF2.1J line performed well across all tested assays and was therefore selected for large scale genomic engineering and distribution.