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CRISPR as a Screening Tool for Drug Targets

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Once again the quality of research presented at the annual American Association for Cancer Research (AACR) meeting transcends excellence. Researchers from around the globe have descended on the city of New Orleans to exchange ideas that they all hope will lead them down the path toward the next impactful cancer therapeutic. There is certainly no shortage of innovative presentations that vary in topics from cancer epigenetics to the latest molecular diagnostic techniques that are poised to reshape clinical medicine.

Yet, genome editing still continues to lead the pack as one of the most exciting revolutions in cancer research over the past several decades. In particular, the CRISPR/Cas9 system has been associated with an extraordinary number of research publications since its initial use as a genome engineering tool in 2012. Now, genome editing using the CRISPR/Cas9 nuclease is empowering real genetic analyses within human cell cultures. Because this technique can be used to inactivate a set of genes completely or regulate their expression, it becomes feasible to identify the molecular mechanisms that control a particular pathway, especially as it relates to disease states, such as cancer.

Researchers are continually looking for new ways to apply CRISPR technology, and identifying synthetic lethal mutations of oncogenic targets holds enormous potential for the development of novel drug targets. Moreover, identifying genes that mediate the sensitivity of cancer cells to existing drugs may also provide valuable insight into possible drug resistance mechanisms.

In one of the major symposiums at AACR—titled CRISPR in Drug Discovery—a group of investigators presented data that showed how the genome editing technology could be employed as a screening tool for identifying or validating druggable cancer genes. Chairperson of the session and initial presenter David Sabatini, M.D., Ph.D., member of the Whitehead Institute and professor of biology at MIT, led the audience through his work on genetic screens of human cells for studying cancer. One of the primary goals of Dr. Sabatini’s work is to identify the absolutely essential genes that cancer cells need to survive.

Dr. Sabatini discussed his laboratory’s work on developing large libraries [approximately 180,000 single guide RNAs (sgRNAs)] for CRISPR/Cas9 genetic screens, which his group used on a variety of cancer cell lines in association studies to determine which genes and pathways were most important. Interestingly, he found that pathologically similar cancer lines had very distinct molecular signatures, with only a few genes being absolutely essential among all cancer types. The Whitehead team found that the search to find genes indispensable for a single type pf cancer is often very useful for drug target identification.

Next, Christopher Vakoc, M.D., Ph.D., associate professor at Cold Spring Harbor Laboratory (CSHL), discussed his work using CRISPR/Cas9 as a scanning and screening tool for mapping functional protein domains. Dr. Vakoc accomplished his work studying chromosome biology and using CRISPR to find essential chromatin regulators. Moreover, with the power of the CRISPR screening and scanning, Dr. Vakoc and his laboratory team are continuing to annotate methodically the functional relevance of protein domains associated with gene regulation and signal transduction for various forms of cancer.

Specifically, Dr. Vakoc showed previously that inhibition of the transcriptional coactivator BRD4 had a positive effect on leukemia in mice. Using CRISPR technology, he has been able to reveal the precise 3D binding domains of various proteins that are essential to cancer cells, including BRD4. The CSHL team is now beginning to use this powerful genome editing tool to uncover fundamental cancer control mechanisms, as well as possible new drug targets.

The final presentation of the CRISPR in Drug Discovery session was given by Johnathan Weissman, Ph.D., professor at the University of California, San Francisco (UCSF) School of Medicine. Dr. Weissman provided data on his work using catalytically inactive Cas9 as a CRISPR inhibition and activation tool—in other words “breaking” the DNA cutting mechanism. This afforded the UCSF team precise and fine-tuned gene expression. In essence, an inactive Cas9 enzyme is often fused to the guide RNA and recruited to the target DNA sequence. Instead of cutting the DNA strands, the fusion molecule manipulates transcription of the target DNA.

Dr. Weissman and his team have generated a vastly improved CRISPRi/a library from almost 2700 genes that helps them define the relationship between gene expression and phenotype. Using CRISPRi/a, Dr. Weissman’s laboratory was able to modulate gene expression over approximately a 1000-fold range, which enables them to identify essential genes and regulators of complex pathways.

Using CRISPRi/a for drug discovery allows researchers to identify drug targets rapidly and validate them. With this approach, Dr. Weismann’s lab has begun work on developing antichaperone cancer therapeutics. Chaperones, like heat shock protein 70 (HSP70), have been linked to the development of cancer drug resistance, and new therapeutics could help to resensitize the cancer cells to existing chemotherapy compounds.

Common wisdom often points to the idea that those at the top for an extended time will falter sooner or later. There may come a day when that is true for CRISPR, although it doesn’t seem to be anytime soon, as the potential this technology possesses is just too great not to tap into or ignore.

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