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tube labeled "CRISPR"

$2M from NIH to extract meaningful data from CRISPR screens

tube labeled "CRISPR"

Protein-coding genes comprise a mere 1% of DNA. While the other 99% of DNA was once derided as “junk,” it has become increasingly apparent that some non-coding genes enable essential cellular functions.

Wei Li, Ph.D., a principal investigator in the Center for Genetic Medicine Research at Children’s National in Washington, D.C., proposes to develop statistical and computational methods that sidestep existing hurdles that currently complicate genome-wide CRISPR/Cas9 screening. The National Institutes of Health has granted him $2.23 million in funding over five years to facilitate the systematic study of genes, non-coding elements and genetic interactions in various biological systems and disease types.

Right now, a large volume of screening data resides in the public domain, however it is difficult to compare data that is stored in one library with data stored at a different library. Over the course of the five-year project, Li aims to:

  • Improve functional gene identification from CRISPR screens.
  • Develop new analyses algorithms for screens targeting non-coding elements.
  • Study genetic interactions from CRISPR screens targeting gene pairs.

Ultimately, Li’s work will examine a range of disease types. Take cancer.

“There is abundant information already available in the public domain, like the Project Achilles  from the Broad Institute. However, no one is looking to see what is going in inside these tumors,” Li says. “Cancer is a disease of uncontrolled cell growth that makes tumors grow faster.”

Li and colleagues are going to ask which genes control this process by looking at genes that hit the brakes on cell growth as well as genes that pump the gas.

“You knock out one gene and then look: Does the cell grow faster or does it grow more slowly? If the cell grows more slowly, you know you are knocking out a gene that has the potential to stop tumor growth. If cells are growing faster, you know that you’re hitting genes that suppress cancer cell growth.”

In a nutshell, CRISPR (clustered regularly interspaced short palindromic repeats) screens knock out different genes and monitor changes in corresponding cell populations. When CRISPR first became popular, Li decided he wanted to do something with the technology. So, as a Postdoc at Harvard, he developed comprehensive computational algorithms for functional screens using CRISPR/Cas9.

To reach as many people as possible, he offered that MAGeCK/MAGeCK-VISPR software free to as many researchers as possible, providing source code and offering internet tutorials.

“So far, I think there are quite a lot of people using this. There have been more than 40,000 software downloads,” he adds. “It’s really exciting and revolutionary technology and, eventually, we hope the outcomes also will be exciting. We hope to find something really helpful for cancer patients.”

Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health under award number R01HG010753.

Cas9-mediated correction of metabolic liver disease

AAV.CRISPR-SaCas9

In vivo gene correction of the OTC locus in the mouse liver by AAV.CRISPR-SaCas9. Source: Nature Publishing Group copyright 2016.

What’s known

A deficiency of the enzyme ornithine transcarbamylase (OTC) in humans causes life-threatening hyperammonemic crises.  The OTC gene enables the body to make an enzyme that is a critical player in the urea cycle, a process that ensures excess nitrogen is excreted by the kidneys. Left unchecked, accumulating nitrogen becomes a toxic form of ammonia. Infants with OTC deficiency can suffer their first metabolic crisis as newborns. Up to 50 percent die or sustain severe brain injury, and survivors typically need a liver transplant by age 1. Gene therapy could cure OTC deficiency, but currently used viruses, such as adeno-associated virus (AAV), are not optimal in the neonatal setting.

What’s new

A research team led by Children’s National Health System and the University of Pennsylvania reasoned that the newborn liver may be an ideal setting for AAV-mediated gene correction using CRISPR-Cas9 gene editing. They intravenously infused two AAVs into two-day-old mice with partial OTC deficiency. One AAV expressed Cas9 and the other expressed a guide RNA and a donor OTC DNA. This resulted in correction of the mutation in 10 percent of liver cells and increased survival in mice challenged with a high-protein diet, which normally exacerbates disease. After consuming a high-protein diet for one week, the treated newborns had a 40 percent reduction in ammonia compared with the untreated group. The correction appears to last long term. The study “provides evidence for efficacy of gene editing in neonatal onset OTC deficiency,” says Mark L. Batshaw, M.D., Physician-In-Chief and Chief Academic Officer at Children’s National, and a study co-author. “This study provides convincing evidence for efficacy of in vivo genome editing in an authentic animal model of a lethal human metabolic disease,” the research team concludes.

Questions for future research

Q: More than 400 mutations can cause OTC deficiency, and each would require a separate gene-editing approach. Is it possible instead to insert the OTC genome using CRISPR-Cas9 to correct the disorder irrespective of the mutation?
Q: Will such gene editing also work in adult animal models of the OTC disorder?
Q: Do these encouraging results in animals translate to efficacy in infants?

Source: Yang, Y., L. Wang, P. Bell, D. McMenamin, Z. He, J. White, H. Yu, C. Xu, H. Morizono, K. Musunuru, M.L. Batshaw and J.M. Wilson. “A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice.” Published Feb. 1, 2016 by Nature Biotechnology.