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Amid Nobel Prize Suspense, Making Sense Of Latest Gene-Editing News

Xconomy National — 

There was a meeting Monday in Washington, D.C., to discuss some of the latest advances in gene editing, a field that has profound medical, agricultural, social, and ethical implications for society. At the lunch break, the webcast played over and over a genteel piece of classical music—Albinoni’s string concerto No. 4 in G major, to be exact—as if you’d called the offices of Masterpiece Theatre and got stuck on hold.

It was a short breather, one could say, from the chaotic pace that gene editing is undergoing at the moment. Or, in musical terms, perhaps it was a prelude to a Nobel Prize for some of the field’s pioneers, as Thomson Reuters predicted last month. (The prize for physics could be announced by the time you read this; the prize for chemistry, Wednesday.)

Convened by the U.S. National Academies, Monday’s meeting was also a warm-up for an international summit in December to hammer out ethical rules for gene editing in the germline—eggs, sperm, and embryos—which has spawned fears that babies will be designed for looks or intelligence, or new organisms will be unleashed into the wild with irreversible consequences.

“We live in remarkable times, and I salute the academies for taking steps to get ahead of this issue,” said Fyodor Urnov, senior scientist at Sangamo Biosciences (NASDAQ: SGMO), whose work has helped bring a treatment for HIV infection into clinical trials, the first and only gene editing program to get that far.

For those who can’t immerse themselves 24/7 in gene editing, following along can sometimes feel like watching multiple freight trains speed past while deciphering tiny print on the sides of each boxcar. The past few weeks have been particularly wild, with movement on the scientific, business, legal, and ethical fronts, so let’s dip into some of the most provocative and intriguing advances.

—New Tools For Gene Repair: The tools of gene editing all have one thing in common: scissors. That is, proteins called enzymes that cut DNA. How those scissors work, how accurately and deeply they cut, and how well they can get to their intended spot are all degrees of difference within the various gene editing systems. In CRISPR/Cas9, the ridiculously easy-to-use gene editing system that has taken the bioresearch world by storm, the Cas9 enzyme mainly comes from the bacterium S. pyogenes. It works pretty well in basic research labs, but as the technology moves toward human therapeutic uses, many researchers have been scrambling to find better versions of Cas9 from other bacteria or different enzymes entirely that might have different properties. (After all, you need more than one type of scissors for various household duties.)

Most recently, Feng Zhang of the Broad Institute of MIT and Harvard University and colleagues published details of an enzyme, Cpf1, which they found by searching through bacterial libraries. (CRISPR is based on the defense system bacteria and archaea use against invasive viruses.) When the paper came out in late September, I wrote about the potential benefits of Cpf1 over Cas9 that Zhang and colleagues outlined in the paper. They were careful to not to overstate those benefits, and outside observers were also circumspect in their appraisal.

Dana Carroll, considered a gene editing pioneer, called Cpf1 “a nice addition to the array of tools we have, but I’m not going to drop Cas9 and pick up the new platform.”

“We’ll have to see how things develop,” said Carroll, a biochemist at the University of Utah whose work on gene editing well predates the CRISPR/Cas9 discoveries. “Based on this paper, there doesn’t seem to be an immediate advantage to the Cpf1 system.”

(It should be noted that Carroll has backed the scientists, led by the University of California, Berkeley’s Jennifer Doudna, who are contesting Zhang and the Broad in the big CRISPR patent dispute. More on that fight, including a new development, later.)

However, Carroll noted one potential practical advantage to the Cpf1 discovery: Cpf1 requires a shorter guide than Cas9 to usher it to the right spot in the genome. Zhang and colleagues noted that the shorter guide could require less material to manufacture if and when Cpf1-based systems scale up into broader research and potentially therapeutic uses. Carroll agreed.

Another potential advantage Zhang and colleagues highlighted was Cpf1’s different cutting mechanism. Cas9 makes “blunt-end” cuts—it snips right through both strands of DNA at the same place. Cpf1 makes staggered cuts, as if the blades of its scissors were misaligned. Because of the different ways cells repair cuts in DNA, which they do all the time, the misaligned cuts are actually a good thing if you’re trying not just to snip out a gene but replace it with a new one.

For making new medicines, replacement is a big deal. It means far more genetic diseases, beyond the ones that can be cured by just snipping out a bad gene, could be treated.

“To repair genes is the holy grail of unlocking all the potential for this technology,” said Vic Myer, the chief technology officer of Editas Medicine, in an interview that took place before Zhang’s Cpf1 paper came out. (Zhang is a scientific cofounder of Editas, which is just a few blocks away from Zhang’s lab in Cambridge, MA.)

But cells prefer to fix themselves in a rather messy way at the cut site. (Imagine a wound healing with an ugly scar.)  This cellular preference makes fusing in a new gene very tricky. It’s proving difficult to do this replacement—or recombination, in gene-speak. Myer said Editas is working on making cells more amenable to recombination, things that “are too early to share.”

Many others are working on it, too. One group just made a big splash. Late last week, scientists at Seattle Children’s Research Institute and other Seattle-based entities published work that might make recombination a lot easier in an important subset of cells. SCRI pediatrician and immunologist Andrew Scharenberg and colleagues discovered that a workhorse of gene therapy—the adeno-associated virus (AAV), transformed into a gene delivery vehicle—is very good for shuttling genes into T cells and perhaps hematopoietic stem cells (HSCs). It was once generally considered too difficult, because those cells divide quickly, which would “wash out” the genetic material delivered by the invasive virus. They also defend themselves well against viral invaders.

The Seattle team was looking for a way to add new functions to T cells, a hot topic right now thanks to the early success of experimental T cell therapies, called CAR-T, for blood-borne cancers. T cell manipulation could also open up possibilities of using modified T cells in other cancers, autoimmune diseases, and—a primary focus of the Seattle Children’s team—making organ transplants easier and safer.

But nothing was working. “We had run out of ideas,” says Scharenberg. So they turned to AAV, which was long known to be an agent for splicing and mixing genes—but not in the cells Scharenberg’s group wanted to modify. They tested a panel of different forms of AAV, including new ones developed in recent years. They also made improvements to the gene they wanted to splice in—a piece of code called a promoter that helps the cell stitch the new gene into its DNA.

“We’ve demonstrated that it works in T cells,” says Scharenberg, adding that there’s still more work to show the same results in HSCs.

“It’s very exciting work,” says Jacob Corn, scientific director of the Innovative Genomics Initiative in Berkeley, CA (which was cofounded by Jennifer Doudna). IGI scientists are working on a gene editing treatment for sickle cell disease, as I reported this summer. They’re extracting HSCs from mice with an approximate version of the disease; using CRISPR/Cas9 to replace the faulty hemoglobin gene with a healthy one; and putting the edited cells back in the bone marrow. Data from the mouse study should be ready in five weeks and perhaps point toward a human clinical trial. Corn wants to see how Scharenberg’s team builds upon the HSC work, “but the approach looks very promising.”

Renier Brentjens, the director of cellular therapeutics at Memorial Sloan Kettering Cancer Center in New York, called the paper “beautiful” but had reservations. He has been modifying T cells with other forms of viral manipulation to make CAR-T therapies—Juno Therapeutics (NASDAQ: JUNO) has license to them—and “right now our cells work,” says Brentjens, using a gene transfer process as efficient as what Scharenberg and colleagues reported. His main worry is that the AAV method will take too long, leaving the cells in culture until they lose their potency or die, like a patient whose drawn-out surgery proves too traumatic.

Scharenberg acknowledges the time problem, but says “lots of labs” will work on making the process more efficient. In part, that’s because all are free to tinker with it. His team’s insights were based on a lot of other work hiding in plain sight, especially that of Arun Srivastava at the University of Florida. “The IP for AAV has been around so long, there’s not a lot of ground to grab,” said Scharenberg. “This is an advance that everyone will be able to adopt.”

—Steps Toward Human Testing: As IGI waits to see if its sickle cell work can become an experimental treatment, other groups are moving gene editing treatments toward the clinic. Editas is working on sickle cell disease, too, but its officials have spoken with greater detail about a program to treat a rare form of blindness, leber congenital amaurosis—taking care to say it’s not necessarily their lead program. Intellia Therapeutics, also in Cambridge, is working with Novartis on CAR-T cell therapies and genetic blood disorders.

Editas, Intellia, and a third company, CRISPR Therapeutics, have raised hundreds of millions of dollars in private funding as they race to the clinic with therapies created with CRISPR/Cas9.

For clinical work, however, CRISPR/Cas9 is well behind zinc finger nucleases, which are owned by Sangamo. As noted, Sangamo has already reached the clinic with an HIV treatment. At the National Academy meeting Monday, Sangamo’s Urnov outlined what would be another milestone: the first gene editing treatment where the editing happens without first removing the cells from the patient.

Sangamo has received a green light from a National Institutes of Health advisory committee to start a trial in hemophilia B patients. Despite losing its development partner Shire last month, the company still plans to ask for the FDA’s permission by the end of the year, Urnov said, which means a trial could start in 2016. (For more on the competition to treat hemophilia with gene therapy and gene editing, read Ben Fidler’s March feature.)

Sangamo also has sickle cell and beta-thalassemia programs partnered with Biogen (NASDAQ: BIIB) but with no publicly declared goals to start human testing.

One Step Closer To A Patent Showdown? There are no patent ambiguities with zinc fingers: Sangamo owns them, full stop. But the situation is far more unsettled with CRISPR/Cas9. In recent weeks, the big patent fight over ownership of CRISPR/Cas9, which I first wrote about here, saw a development.

The Patent and Trademark Office issued a memo on September 15 that seems to confirm what I’ve heard from sources close to the case. The camp associated with Jennifer Doudna and U.C. Berkeley appears to have built enough of a case to get the PTO to re-examine the patents granted to Zhang and the Broad in April 2014. Those were the first ever in the CRISPR field. Five months later, the Berkeley camp asked the PTO for interference—PTO-speak for a reconsideration of the patent in the face of a challenger—and has been building its case with thousands of documents, including positive testimony from Utah’s Dana Carroll.

The PTO doesn’t have to grant the Berkeley request, and to be clear, nothing’s been announced. But three weeks ago, the PTO released a review of the Berkeley group’s main patent application—which was originally deemed to have lost to the Broad side.

The review allowed many of the application’s claims and rejected others. I asked a biopharma patent attorney unaffiliated with the case if those rejections were an ominous sign for the Berkeley group. On the contrary, most of the rejections were for trivial or administrative reasons and are easily fixed, said Muna Abu-Shaar of Biospark Intellectual Property Law in Cambridge, who has been following the case.

There’s no guarantee that the PTO will open interference, but from the looks of the PTO memo, Abu-Shaar said, the Berkeley group should be able to make some tweaks and get its patent application in shape to go head-to-head with the Broad group’s applications.

Once that happens, each side will try to prove with lab notebooks, photographs, e-mail and other evidence that it was the first to invent this new gene-editing technology. (Since the Berkeley and Broad patent applications were filed, the U.S. patent system has switched to a “first to file” reward, likely making this the last great “first to invent” fight in U.S. patent history.)

The outcome of the bake-off, however, can be appealed up through the U.S. court system. “I’ve seen some of these things go through 10 years of interference and appeals,” said Abu-Shaar.

A settlement at some point is more likely. Meanwhile, the parties are making their cases in other ways: publishing scientific journals, sitting for profiles in the mainstream press, gathering awards, and helping drive the ethical debate, as Doudna has done.

Doudna and Zhang actually sat together on a panel at the NAS meeting Monday to discuss the underlying technology. It was unremarkable. The universe did not melt down. In fact, their joint appearance amid a whirlwind of presentations, debates, and criticism—one commenter at the end of the meeting warned that the field threatened to fall into a “dictatorship of commercial technical enterprise”—was a welcome reminder. They are now but small players among forces they’ve helped unleash but cannot control.