Abstract
Forward genetic screens across hundreds of cancer cell lines have started to define the genetic dependencies of proliferating human cells. However, most such screens have been performed in vitro with little consideration into how medium composition might affect gene essentiality. This protocol describes a method to use CRISPR/Cas9-based loss-of-function screens to ask how gene essentiality in human cell lines varies with medium composition. First, a single-guide RNA (sgRNA) library is packaged into lentivirus, and an optimal infection titer is determined for the target cells. Following selection, genomic DNA (gDNA) is extracted from an aliquot of the transduced cells. The remaining transduced cells are then screened in at least two distinct cell culture media. At the conclusion of the screening period, gDNA is collected from each cell population. Next, high-throughput sequencing is used to determine sgRNA barcode abundances from the initial and each of the final populations. Finally, an analytical pipeline is used to identify medium-essential candidate genes from these screen results.
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Acknowledgements
This work was supported by grant and fellowship support from the NIH (T32HG002760 to K.S.H. and K22CA225864 to J.R.C.). J.R.C. is an inventor on a patent application for HPLM (PCT/US2017/061377) assigned to the Whitehead Institute. Kimberly S. Huggler and Nicholas J. Rossiter contributed equally to this manuscript.
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Huggler, K.S., Rossiter, N.J., Flickinger, K.M., Cantor, J.R. (2022). CRISPR/Cas9 Screening to Identify Conditionally Essential Genes in Human Cell Lines. In: Zhang, R. (eds) Essential Genes and Genomes. Methods in Molecular Biology, vol 2377. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1720-5_2
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DOI: https://doi.org/10.1007/978-1-0716-1720-5_2
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Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1719-9
Online ISBN: 978-1-0716-1720-5
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