In a greenhouse on the campus of North Carolina State University, Rodolphe Barrangou walks me through a row of young poplar trees, some twelve feet high, all carrying CRISPR-edited genes. These are the first shoots of TreeCo, “the North Carolina Tree Company,” Barrangou’s latest commercial venture, launched with fellow faculty member Jack Wang, appropriately set in the wood basket of the world. Poplars are abundant trees used for plywood, furniture, and paper. Genome editing can improve the abundance of pulp and lower waste, with applications ranging from climate resilience to timber to bioenergy. Barrangou isn’t planning to feed the world just yet: first, he’d like to become the R&D engine for the lumber and forestry industry. But if not him, then surely someone else.
By the time we hit the edge of the petri dish, we’re going to need even better gene-editing tools. Fortunately, in this remarkably innovative arena, they’re already coming online.
I. The disease was originally called huanglengbing (“yellow shoot disease”), but differences in pronunciation resulted in a change to huanglongbing, which was made official in 1995.
II. Sadly Mirkov won’t see the fruits of his labors: he died after a short illness in 2018.
III. The Celtic polled variant is a duplication of 212 bases that replaces a ten-letter stretch in an intergenic region on cow chromosome 1. The resulting hornless trait is inherited in dominant fashion, although the precise mechanism is unknown.
IV. Pigs carry a UCP1 gene but it is nonfunctional. In the experiment, the Chinese team knocked in the mouse counterpart.
CHAPTER 22 CRISPR PRIME
In 1960, a tall, gentle man named Victor McKusick, a medical geneticist at Johns Hopkins University, published the first edition of a remarkable catalogue of genetic traits and disorders. Mendelian Inheritance in Man became the bible of geneticists around the world, the definitive source of information about human genetic diseases and their underlying mutations. After a dozen editions, the catalogue was moved online. It currently lists more than 7,000 discrete genetic disorders and traits. Of those, McKusick was most closely associated with Marfan syndrome, the genetics of which he first described in 1956. Thirty-five years later, McKusick’s colleagues at Hopkins identified the faulty gene alongside two other teams. I invited McKusick to write the accompanying commentary in Nature.1 It was only fitting. In it he discussed the notion that President Abraham Lincoln might have had Marfan syndrome.
If he were still alive, the father of medical genetics would be in awe at the progress we’ve made in documenting the myriad ways in which our genetic software can be corrupted, not to mention the potential of delivering a patch to fix those errors. The Welsh geneticist Steve Jones wrote that the book of life “has a vocabulary—the genes themselves—a grammar, the way in which the inherited information is arranged, and a literature, the thousands of instructions needed to make a human being.”2 The letters on the pages of our books are subject to a host of different insults—substitutions, deletions and insertions, expansions, duplications, and rearrangements. Building on McKusick’s legacy, the global genetic community has documented mutations in about one third of the total number of genes in the human genome. That number will increase.
Some genetic disorders are caused by the tiniest mutation imaginable—the swap of one letter in the genetic code for another. Sickle-cell disease results from an A shifting to a T in the beta-globin gene. Progeria, a genetic form of premature aging, is caused by a C to T substitution in the lamin A gene. Cystic fibrosis is caused by hundreds of different mutations in a single gene, the most prevalent being the loss of three bases coding for a single amino acid. Conversely, the most common mutation in patients with Tay-Sachs disease is the addition of four bases (TATC) in the beta-hexosaminidase gene. Huntington disease, fragile X mental retardation, and dozens of other disorders arise from the bizarre expansion of a tract of repetitive DNA. Other disorders arise from insertions, duplications, or deletions of longer stretches of DNA, including entire chromosomes such as trisomy 21, or Down syndrome. And there are many more subtle genetic defects, including epigenetic mutations that silence one copy of a gene, depending on which parent supplied the gene.
As genome engineers contemplate the plethora of genes and mutations that need to be corrected to treat or cure genetic disease, they will need a deluxe toolbox that will extend beyond CRISPR-Cas9. For all of the astonishing progress since 2012–13, there are strong signs that the CRISPR toolbox is receiving a major upgrade with a suite of new tools that riff on the original CRISPR gene editing machinery. Cas9 engineers a complete break in the DNA, and while the ability to stitch in the desired sequence or repair is improving rapidly, the process still lacks the requisite precision for most therapeutic applications. The classic CRISPR technology will only work therapeutically in a fraction of genetic diseases.
If you were to draw it up on a whiteboard, the Holy Grail of genome editing would be to develop a technology that can modify a single letter of the genetic code without cleaving the DNA in the process. Almost before the ink was dry on the classic CRISPR papers, researchers were studying the building blocks, seeking to modify and adapt them. That has been the goal of many investigators, but one in particular stands out in his mission to design a truly precise molecular editor. He’s a prodigiously talented scientist of Asian descent whose talent was on display in high school before enrolling at Harvard, excelling in his PhD in California, and hitting his prime at the Broad Institute. But this isn’t about Feng Zhang.
A decade older than Zhang, there are indeed some striking similarities in David Liu’s career. The son of Taiwanese parents, Liu was born and raised in Riverside, California. His mother was a physics professor, his father an engineer. Like Zhang, Liu’s scientific talent shone brightly in high school, driven by what he admits was some “immature competitiveness.” In 1990, he placed second in the national Westinghouse Science Talent Search competition, and first in his high school.
As a freshman at Harvard University, Liu’s interests gravitated toward physics rather than chemistry. But that changed in December 1990 when he traveled to Stockholm as one of five top US students to attend lectures by the newly minted Nobel laureates, including Harvard chemistry professor E. J. Corey. Liu was enthralled by Corey’s work on creating new molecules, like assembling Lego blocks. Afterwards, Liu told Corey he wanted to work in his lab. He got that opportunity and eventually graduated top of his class of more than 1,600 students in 1994. Years later, Corey told the Boston Globe that Liu was “going to be a superstar.”3
Liu moved back to California to take up a PhD at Berkeley with Peter Schultz, a talented molecular biologist who was literally rewriting the genetic code. Liu spent the next few years studying methods to expand the genetic alphabet—to encode and incorporate synthetic amino acids (beyond the twenty that occur naturally in the body) into proteins. A lecture on his groundbreaking graduate work back at Harvard turned into a de facto faculty interview. Occasionally scientists shine so spectacularly during their PhD that, like a professional basketball team drafting a high school prodigy, a university will offer them a faculty position. Harvard offered Liu a professorship, bypassing the usual four to five years of postdoctoral training. It was too tempting to refuse, but he doesn’t recommend others try it. “I had no idea what I was doing,” Liu admits.4