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CRISPR-Cas9 Screen Points to Potential Vulnerabilities in KRAS-Mutated Colorectal Cancer

NEW YORK (GenomeWeb) – A team from the University of California, San Diego has uncovered potential vulnerabilities in KRAS-mutated colorectal cancer (CRC) using a CRISPR-Cas9 gene editing screen.

In a study published online today in Cancer Research, UCSD researchers systematically knocked out gene function across the genome in a tumor xenograft model of human CRC and in human CRC cell lines with or without KRAS mutations. In the CRCs containing KRAS mutations, they narrowed in on loss-of-function mutations that boosted or diminished CRC cell viability.

In particular, the team found that CRISPR-Cas9-based gene edits altering NAD kinase or ketohexokinase (KHK) metabolic enzymes could staunch KRAS-mutated CRC growth in the tumor xenograft system — an effect that the group subsequently recreated using pharmacologic inhibitors of these genes. In contrast, however, they did not see the same synthetic lethality in the CRC cell lines, suggesting that the in vivo gene editing method may pick up cancer contributors missed with strictly cell-based screening approaches.

"[T]he metabolic dependencies of tumor cells growing in a laboratory dish may differ dramatically compared to the same cells growing in a living system, underscoring potential limitations of standard laboratory-based cancer cell growth tests," senior author Tariq Rana, a pediatrics, genome medicine, and solid tumor therapeutics researcher at UCSD, said in a statement.

Rana and his colleagues focused on forms of CRC marked by alterations affecting KRAS, a gene that is mutated in roughly one-fifth of human cancer cases. Rather than targeting the KRAS mutations directly, however, they screened for synthetic genetic interactions across the genome using a library of nearly 65,400 pooled lentiviral single guide RNA constructs to produce loss-of-function mutations in more than 19,000 protein-coding genes and nearly 1,900 microRNAs.

After applying this knockout screen approach to CRC cells lines with or without KRAS mutations, the team considered synthetic lethality or synthetic enhancer mutations in human CRC xenograft tumors grown from the cell lines in mice.

The growth effect associated with the NAD kinase and KHK mutations turned up specifically in the tumor xenograft model of KRAS-mutated CRC. Among their follow up experiments, the researchers demonstrated that small molecule inhibitors of these metabolic enzymes could also curb KRAS-mutated CRC xenograft tumor growth.

Still other CRISPR-Cas9 mutations introduced in the screen seemed to enhance CRC tumor xenograft growth, highlighting potential tumor suppressor genes. For example, a gene coding for a large chromatin remodeling protein called INO80C appeared to act as a genome stabilizing tumor suppressor in the KRAS-mutated CRCs, the researchers reported. They saw a similar effect in a xenograft model of pancreatic adenocarcinoma as well.