Abstract 260: Long RNA and DNA sequencing reveals HEK293 diversity between commercial sources

HEK293 cells are used extensively in cancer research, with more than 4800 articles between 2017 and 2022 (PubMed search “cancer[MeSH Major Topic] and hek293”). Studies involving transfection to overexpress, knock down, or modify proteins in these cells are common. While HEK293 cells are relatively easy to grow and maintain, early use of high throughput sequencing Yao-Cheng et. al. identified genomic variability between different sources of cell lines and revealed unexpected details about their developmental lineage (likely adrenal, not kidney)[1]. Genomic or transcriptomic reorganization may complicate interpretation of results from targeted intervention experiments. Here, we evaluate HEK293 cells from various commercial sources using long read sequencing technology. Oxford Nanopore direct cDNA profiling was used to compare isoform usage and examine gene fusions. Long DNA libraries were prepared using a high molecular weight isolation method, sequenced on Oxford Nanopore, and assembled to produce long contiguous fragments. Genome assemblies generated from long read sequencing support the genomic diversity reported by Yao-Cheng et.al, though the specific copy number variants are distinct from those previously reported. Assembled genomes and transcriptomes for these specific lots of HEK293 cells will be available at NCBI. Given the plastic nature of HEK293 cells, we recommend confirmation of genomic and transcriptomic structure of the specific cells in use before and after intervention. [1] Lin, Yao-Cheng, Morgane Boone, Leander Meuris, Irma Lemmens, Nadine Van Roy, Arne Soete, Joke Reumers, et al. “Genome Dynamics of the Human Embryonic Kidney 293 Lineage in Response to Cell Biology Manipulations.” Nature Communications 5, no. 1 (September 3, 2014): 4767. https://doi.org/10.1038/ncomms5767. Citation Format: Laura Blum, Brittany Sexton, Jonathan C. Sanford, Evan Janzen, Luo Sun, Paul A. Koetsier, Keerthana Krishnan, Lynne Apone, Bradley W. Langhorst. Long RNA and DNA sequencing reveals HEK293 diversity between commercial sources [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 260.