Tag Archive for: CRISPR

RNA molecule

New deep learning system helps scientists edit RNA

RNA molecule

The Children’s National team built DeepCas13 on a newer and less studied CRISPR platform, called CRISPR-Cas13d, which instead focuses on RNA.

Children’s National Hospital scientists have created a revolutionary machine-learning system that predicts the effects of changing ribonucleic acid (RNA) molecules using a gene-editing tool built on CRISPR technology.

Called DeepCas13, the system is among the world’s first deep-learning frameworks to recognize the challenges of editing RNA – and then applying data science and machine learning to solve the intricate problems that stem from modifying biological code. Details of the DeepCas13 system were published recently in Nature Communications.

Born from an international collaboration, DeepCas13 could provide the backbone for treatments for diseases based on errors in RNA, including debilitating neurodegenerative diseases such as Huntington’s disease and muscular dystrophy.

“I am an optimistic person, so I expect to have treatments within five to 10 years,” said Wei Li, Ph.D., principal investigator at the Center for Genetic Medicine Research at Children’s National. “Of course, there are going to be lots of obstacles. If we have a very good system, like DeepCas13, with very good performance that can generate treatments, the next problem is how we deliver the system to the right tissue in the patients.”

The big picture

Most research in this space has focused on a version of CRISPR – or Clustered Regularly Interspaced Short Palindromic Repeats – that edits DNA, called CRISPR-Cas9. The Children’s National team built DeepCas13 on a newer and less studied CRISPR platform, called CRISPR-Cas13d, which instead focuses on RNA. In doing so, researchers are opening the door to treating a host of disorders of RNA, given its biological role in coding, decoding, regulating and supporting gene expression.

DeepCas13 combines hundreds of thousands of data points with considerable computing power to help scientists target errant pieces of RNA, while minimizing any off-target changes that could damage the health of cells.

“We only want to target the RNA molecule that is causing diseases, and we don’t want the system to edit normal RNA,” said Xiaolong Cheng, Ph.D., a member of the Li lab and the first author of the study. “With DeepCas13, we can design highly efficient, and highly specific, rules.”

What’s ahead

The FDA has approved one method for delivering RNA treatments to cells, using a virus known as AAV or adeno-associated virus. So far, the gene therapy method has had limited applications. But Li and other researchers see the potential for life-changing treatments in the coming years, built on DeepCas13 and other advances.

The system was developed with partners from around the world, including the University of Illinois Urbana-Champaign and Northeastern University in Shenyang, China. It is open source and available for free to researchers looking for targets to treat RNA-related diseases.

Li says this international partnership is leading the way: “We tested our DeepCas13 model over other methods, and we confirmed that our method has the highest prediction accuracy.”

DeepCas13 was funded by grants from NIH and the Children’s National Research Institute.

HIV virus

CRISPR gene editing identifies possible drug targets for HIV

HIV virus

Working with researchers at Johns Hopkins University, the Children’s National team used CRISPR gene technology to test drug targets that find and attack latent HIV, paving the way for drug treatments that may someday completely cure the virus.

Researchers at Children’s National Hospital have identified several new drug targets that may enhance the elimination of latent HIV in patients, a major bottleneck to the full treatment of the virus, according to new findings published in Science Translational Medicine.

Working with researchers at Johns Hopkins University, the Children’s National team used CRISPR gene technology to test drug targets that find and attack latent HIV, paving the way for drug treatments that may someday completely cure the virus. Currently, anti-retroviral therapies (ARTs) can only slow its progress.

Why we’re excited

“In less than one month, we were able to use CRISPR to test 20,000 gene candidates in one single experiment. It was an amazing application of the technology,” said Wei Li, Ph.D., a co-author of the study and assistant professor at the Center for Genetic Medicine Research at Children’s National. “The CRISPR technology provides a global, unbiased approach to understanding molecular aspects of HIV-1 infection, including the ways that HIV-1 enters cells and replicates. This research could someday revolutionize how we treat the virus pharmaceutically.”

The big picture

More than 30 million people worldwide live with HIV-1, the most common form of the virus that can eventually lead to AIDS. But no single agent can entirely eliminate HIV-1 in these patients.

Researchers have sought ways to attack this elusiveness and turned to the CRISPR gene-editing tool, which can locate specific bits of DNA inside a cell. They trained CRISPR screens on the HIV-1 genome to identify critical factors that allow or prevent the virus from lying latent. In the latter case, these pieces of DNA will be the ideal targets of a drug that will push the virus out of the latent stage so it can be targeted by therapies.

What’s ahead

The findings of the Children’s National and Johns Hopkins scientists point to novel drug therapies and validation systems that could someday eradicate HIV.

Bicna Song, a postdoctoral researcher in Li’s laboratory at the Center for Genetic Medicine, said that reversing HIV-1 latency will allow for the killing of infected cells and give researchers opportunities to actually cure patients with HIV.

“So far, no single latency-reversing agent – alone or in combination with another drug – has been shown to effectively reduce the latent reservoir size in persons living with HIV-1,” said Song, who contributed to the study. “With this work, we are meeting the urgent need to identify factors that can lead to new drug targets.”

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.