The power of CRISPR

Researchers around the world have quickly adopted the new gene-editing tool known as CRISPR to solve mysteries about the human body. At Stanford, scientists are refining the tool itself and putting it to work.

How hearts develop

“My lab focuses on discovering new drug targets to fight heart disease,” says Mark Mercola, PhD, a professor of cardiovascular medicine. “One of our biggest unsolved problems is figuring out which genes and proteins are involved in embryonic heart development.”

In 2015, Mercola’s team found evidence that a family of proteins called Id plays a key role in transforming human embryonic stem cells into heart muscle cells. But not everyone was convinced.

“We submitted our paper to the journal Genes & Development, but the editors told us we were wrong,” he recalls. “They wouldn’t even send the paper out for review.”

The editors pointed to a 2004 Cornell University study, where researchers knocked out the genes that make Id proteins in mouse embryos, yet the embryos developed tiny, beating hearts. The results seemed to prove that heart muscle cells can develop even after the Id proteins have been removed.

It would take more than a decade, and the discovery of CRISPR, for the full story to be told.

“There are actually four different Id genes, but the Cornell group only knocked out three of them,” says Mercola. “It required years of breeding generations of mice. Back then, a quadruple Id knockout would have been unthinkable. But with CRISPR, why not?”

Armed with CRISPR, Mercola and his co-workers returned to the lab and simultaneously knocked out all four Id genes in the embryos of mice. The results were dramatic: The quadruple knockout produced heartless embryos, confirming that Id is essential for early heart formation. The entire experiment took months to complete instead of years. “Five years ago, the idea of doing a quadruple knockout would have been crazy, but with CRISPR you don’t even do any breeding,” Mercola says.

He and his colleagues submitted their results to Genes & Development in 2017, and the study was published that year.

Gene toggler and chromosome bender

Stanley Qi, PhD, has invented an alternative version of CRISPR that lets scientists control a gene without destroying it. He calls the reversible system CRISPRa/i, shorthand for CRISPR activation and interference. In a few short years, it’s become a standard research tool in biomedicine.

“CRISPRa/i allows you to turn specific genes on and off repeatedly,” says Qi, an assistant professor of bioengineering and of chemical and systems biology. “You can simultaneously activate or repress a whole set of genes and see how different genes interact and affect the course of complex diseases, like cancers and Alzheimer’s.”

Kevin Wang, MD, PhD, an assistant professor of dermatology, is using a similar technique to study how the three-dimensional configuration of DNA — its various loops and curls — affects a gene’s function. His invention is the first technology capable of reversibly creating artificial loops in mammalian chromosomes to modulate gene expression. Wang predicts that many new applications will emerge as CRISPR matures.

“CRISPR is kind of like Legos,” he says. “You can add anything you want to it.”

Illustration by James LeVeque/Flickr