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NIH Innovator Award Fuels New Tools for High Throughput Target Discovery

Published on
Mar 11, 2020
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Ophir Shalem, PhD, is the recipient of a National Institutes of Health Innovator Award.

By Jillian Rose Lim

Genetic screens form a fundamental tool for the discovery and functional annotation of genetic elements. Responsible for major discoveries in cancer, immunology, neurodegenerative disease, and beyond, these powerful methods allow researchers to identify genes within the massive human genome that can influence a whole number of physiological traits. By probing gene function, scientists have gained insights into a wide range of questions, from why some individuals resist certain drugs to what drives metastasis in cancer.

But despite the prevalent and powerful success of recent CRISPR-based screening, researchers now question how they might further optimize their toolbox of genomic technology. How can we increase the scope and specificity of genome-wide genetic screens?

Ophir Shalem, PhD, assistant professor of Genetics at Children’s Hospital of Philadelphia, works at the heart of such innovation. Alongside scientists in his lab, Dr. Shalem develops novel functional genomics tools to study neurogenerative diseases and other brain disorders. Dr. Shalem was one of the pioneers who, in 2014, used CRISPR to develop a genome-wide screening platform.

Now, as the recipient of a highly competitive National Institutes of Health (NIH) Director’s New Innovator Award, Dr. Shalem is working to develop an improved screening method that relies on more precise gene tagging via direct targeting of proteins. His award falls under the NIH Common Fund’s High-Risk, High-Rewards Program, which supports “exceptionally creative” scientists and “highly innovative research” according to the NIH website.

“This [research] is ‘high risk and high reward’ because it requires a significant amount of technological advances that currently do not exist – we need to develop a whole new set of tools,” said Dr. Shalem of his project, Direct and Rapid Control of Proteins at Scale. “Once everything is assembled together and successful, this novel screening method can be applied to a very, very wide range of possible questions.”

To understand the context of Dr. Shalem’s work, it helps to review existing approaches used to identify and investigate candidate genes.

Currently, scientists regularly use genome-wide loss-of-function screens that affect proteins indirectly – meaning that they inactivate protein function by targeting either the genome or the transcriptome. While this has led to valuable discoveries, Dr. Shalem said there are limitations: Depleting the target protein can often take several days – leaving time for adaptation mechanisms to influence a test’s results. In addition, many genes that are essential for cell growth cannot be studied for their involvement in other phenotypes.

The new screening system differs in that instead of inactivating proteins at the level of DNA (by introducing a mutation to the genes, for example), scientists will target proteins directly using a combination of sophisticated genome editing and biochemistry.

“The advantage of this novel screening method is that proteins are targeted in a very rapid manner,” Dr. Shalem said.

Through this method, Dr. Shalem and his lab will fuse thousands of proteins, directly in the cell’s genome, with small peptide tags. Then, using small molecules, they will be able to rapidly increase or decrease the stability of the fusion proteins and even follow the proteins localization. This method allows for a number of applications not possible in previous approaches: The team can conduct parallel measurements of gene expression dynamics for thousands of proteins, directly and rapidly control protein function, and study protein unfolding associated with human diseases.

With the NIH grant covering a total of five years, Dr. Shalem estimates his team will be in a good position in regards to developing the technology. In the meantime, he is excited to continue working in the exciting space that merges technological advances with the study of disease.

“I’m excited about combining technological development with translational and basic science,” Dr. Shalem said. “What really drives the lab is being able to drive both technology and disease research – associate them together, and use what we do in the technology development to ask the biology questions that we’re interested in.”

Learn more about Dr. Shalem’s research and lab.