Using a technology that enables fast, easy editing of the genome, a research group led by Dr. Feng Zhang and Dr. Phillip Sharp at the Broad Institute and MIT’s David H. Koch Institute for Integrative Cancer Research systematically looked at the impact of each gene of the genome on lung cancer. Although the team conducted their studies using mouse models of non-small cell lung cancer, the results will be useful in determining how tumors evolve and metastasize in humans.
“Genome-scale guide RNA libraries are a powerful screening system, and we’re excited to start applying it to study gene function in animal models,” said Dr. Zhang in a news release from the Broad Institute. “This study represents a first step toward using Cas9 to identify important genes in cancer and other complex diseases in vivo.”
CRISPR-Cas9 sent a wave of excitement through the scientific community when it was first introduced as a tool to easily generate mouse models in a much shorter time than the time it takes using traditional methods of genetic manipulation. In Dr. Zhang and Sharp’s study, “Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis” published in Cell, the team knocked out genes one-by-one in mice and identified the effects on cancer. This study was unique from other studies using CRISPR-Cas9 at the Broad Institute because it considered the whole mouse, not just cells.
“Tumor evolution is an extremely complex set of processes, or hallmarks, controlled by networks of genes,” said Dr. Sharp. “The in vivo application of gene-editing is a powerful platform for functional genomic discovery, offering a novel means to investigate each step in tumor evolution and identify the genes that regulate these hallmarks.”
Using a mouse model of non-small cell lung cancer with whole-genome editing, the team identified through next-generation sequencing a number of genes that were knocked out in tumors and their metastatic cells. Among these genes were typical tumor suppressor genes (Pten, Cdkn2a, and Nf2), other genes not previously associated with lung cancer, and several microRNAs.
“After doing an unbiased, genome-wide screen, we designed a subpool library to quickly test many more targets than would otherwise be possible by targeting single genes in individual mice,” said co-first author Dr. Neville Sanjana. “The subpool also lets us see how these different genetic mutations compete within the same tumor.”
In addition to providing a proof-of-principle that in vivo knockout screening helps identify regulatory genes, the group at the Broad Institute may influence the practice of biopsying metastatic tumors in the clinic. Additional information from these biopsies would give more insight on the metastatic behavior of non-small cell lung cancer.