Lost in the CRISPR Hype, a Gene-Editing Giant Is Fighting Back

February 21, 2018
Danny Funt

Sangamo’s ever-evolving zinc finger technology could catapult precision medicine. So why haven’t you heard about it?

Led by (from left to right) Chief Medical Officer Edward Conner, President and CEO Sandy Macrae, and Vice President of Technology Edward Rebar, Sangamo Therapeutics is looking to convert decades of research into a potentially transformative treatment for genetic diseases.

OVER THE PAST 23 YEARS, investigators at Sangamo have slowly been stocking freezers at their Bay Area headquarters with pairs of zinc fingers, the proteins that regulate gene expression. At one point, their technology was considered the cutting edge of genomic medicine, and Sangamo’s scientists were regarded as the best in the world at building it. Then simpler and more accessible gene-editing techniques came along, such as CRISPR, and many people dismissed Sangamo—as though it manufactured steam engines in an age of internal combustion. Still, the company’s 40 or so investigators continued to toil away at mastering zinc fingers and adding to their library, 1 pair after another.

Sangamo’s president and CEO, Sandy Macrae, PhD, imagines an enormous checkerboard of all the different zinc finger combinations necessary to target particular nucleotides. After investing hundreds of millions of dollars to refine this technology, the company has a proprietary library that now includes about 3000 such pairs, allowing the rapid preparation of medicine that can manipulate an ultra-specific DNA sequence: Targeting efficiency has gone from 2% to above 99.5%, and treatment that once took several months to assemble can now be ready in fewer than 10 days. In short, Macrae explains, “we can now target any nucleotide in the genome.”

At last, Sangamo is starting to take more of its medicine out of the freezer. The results of these early trials could help initiate the transformation in precision treatment—with wide-ranging implications for the cost of care—that the medical world has been waiting for.

In the past 18 months, Sangamo has overhauled its leadership team and revitalized its mission, changing its name from Sangamo Biosciences to Sangamo Therapeutics and planning a corporate relocation from the East Bay to San Francisco’s biotech hub as it strives to cash in on years of research. When Macrae took over, he had photographs installed throughout the company’s headquarters of people with the rare diseases that these first clinical trials seek to treat. The point was to refocus on patients, and the results of that seem promising.

In November, doctors in Oakland used Sangamo’s zinc finger nucleases to treat a man with the metabolic disease mucopolysaccharidosis type II (MPS II), or Hunter syndrome, the first person to receive treatment that edits genes within the body. With enzyme replacement therapy, the current treatment option, patients with MPS II require weekly transfusions. The patient in Oakland received a single 3-hour transfusion. If it works, he will produce the vital enzymes for the rest of his life.

Some investigators at Sangamo have spent their entire careers pursuing that medicine. For them, “seeing this go literally from the bench to the bedside has really been a life’s work realized,” says Russell DeKelver, PhD, who began working as a research associate and is now the rare diseases team leader at Sangamo.

Once the preeminent developer of gene-based medicine, Sangamo was overshadowed by the emergence of competitors, and biotech investors grew impatient with gene editing in general because of slowness in bringing it to market. If current trials are successful, Sangamo executives say, the medicine could be extended with relative ease to up to 1000 diseases that are also caused by a single gene mutation—they’ve already received $70 million up front from Pfizer to pursue such a treatment. The ultimate goal, however, is to be able to cure any genetic disease, permanently, at its source. Recent progress provides an infusion of optimism for genomic medicine and is no small triumph for a company seeking to reestablish itself at the forefront of its field.

Near the New Year, a family that has 2 sons with hemophilia visited Sangamo headquarters to describe their experience with the disease and to learn about Sangamo’s treatment, which is also entering clinical trials. Macrae recalls a topic of discussion: “What does it mean to change someone who has hemophilia to someone who doesn’t have hemophilia, and how do they feel about that?”

It’s a peculiar way of describing medicine, indicative of the fact that this treatment approach aspires to be, in the most literal sense, life-changing.

The Wait Is (Maybe Nearly) Over

DEBATE AROUND GENE EDITING tends to assume an intense gravity, and deservingly so, even if that kind of medicine has been almost entirely hypothetical. In his acclaimed 2016 book The Gene, the oncologist Siddhartha Mukherjee, MD, asks, “And what if we learned to change our genetic code intentionally? If such technologies were available, who would control them, and who would ensure their safety? Who would be the masters, and who the victims, of this technology?”

It’s fitting, in a way, that his warning echoes a prayer before the Jewish Day of Atonement: “How many shall pass away, and how many shall be born? Who shall live, and who shall die?”

Yet when asked to foresee the distant prospects of this medicine, Paul Harmatz, MD, betrays a polite frustration with that focus. Harmatz is a pediatric gastroenterologist at University of California, San Francisco, Benioff Children’s Hospital in Oakland, and he is most concerned about patients with metabolic diseases whom he has been treating for decades. As a principal investigator of the phase 1/2 clinical trials for Sangamo’s in vivo gene-editing treatment of Hunter syndrome, Harmatz describes this moment—cautiously—as “the forefront of a new paradigm in medicine.”

One of Harmatz’s longtime patients, Brian Madeux, a 44-year-old from Arizona, lacked a gene that produces an enzyme responsible for breaking down toxic carbohydrates in cells throughout the body. One of about 100,000 people, primarily men, has this debilitating disease. Madeux has required 26 operations throughout his life for all sorts of ailments, the Associated Press reported. (However expensive a onetime gene-editing treatment may turn out to be, it waits to be seen how that compares with a lifetime of recurring care.)

Under Harmatz’s supervision, Madeux received a transfusion with Sangamo’s medicine packaged in adeno-associated virus (AAV) vectors, a virus engineered to avoid bodily harm. The virus infects the albumin locus in the liver, where zinc fingers attach to a precise DNA sequence. A highly optimized nuclease makes a double-strand break, and the therapeutic genes are inserted. Billions of copies of this corrective gene are delivered, modifying less than 1% of the body’s vast surplus of albumin. As Sangamo’s chief medical officer, Edward Conner, PhD, puts it, “It’s almost like having a permanent transfusion pump based in the liver.”

“This treatment isn’t actually treating anything,” Harmatz explains. “It’s setting up a factory in the liver to produce a lot of this enzyme over a long time period.” About 6 months after Madeux’s treatment, a liver biopsy will reveal whether the enzyme is being produced successfully.

Doctors could, in theory, use that same process to implant corrective genes for any monogenic disease that involves a protein deficiency. Clinical trials are under way for MPS I, MPS II, and hemophilia B, with trials for Fabry disease forthcoming. There are altruistic reasons for focusing on ultrarare diseases but also practical ones: For novel technologies in particular, it’s extremely difficult to get FDA approval for diseases with huge patient populations, and those trials require elaborate designs to demonstrate efficacy. The MPS II phase 1/2 trials, by contrast, will treat up to 12 patients. These rare diseases have significant unmet need, largely because pharmaceutical and biotech companies don’t see the potential return on investment.

“We’re just exponentially grateful to Sangamo, recognizing that MPS diseases are so small compared with diseases everybody knows about,” says Terri Klein, president and CEO of the National MPS Society. “Brian is very brave, not knowing what to expect. Someone has to be on that front line.”

Indeed, the cutting edge brings risk. In 1999, 18-year-old Jesse Gelsinger died from complications after receiving gene therapy in a clinical trial at the University of Pennsylvania. An FDA investigation found several areas of negligence. Genomic medicine has advanced dramatically since then, but the lessons from that first “biotech death” are not forgotten.

A Long Time Coming

THE GENESIS OF SANGAMO was not so much a scientific breakthrough as it was a shrewd observation by its founder, Edward Lanphier. After graduating from Knox College with a degree in biochemistry, Lanphier entered the business side of biotech and by 1995 was in charge of building the “patent estate” of Somatix, a California-based gene-therapy company. He was captivated by research at 4 labs studying the impressive DNA-binding utility of zinc fingers, especially work out of the Medical Research Council in London led by the Nobel laureate Aaron Klug, PhD. Somatix wasn’t interested, but Lanphier was: He licensed intellectual property from those 4 labs and set up laboratory operations of his own.

In 1997, Lanphier moved his company from Colorado to Richmond, about 20 miles north of San Francisco, and after a couple of rounds of financing took it public in 2000. One of his first hires was Edward Rebar, then just a year removed from receiving his PhD at the Massachusetts Institute of Technology, where he’d worked on the first system for selecting zinc fingers to bind to new DNA sequences. Rebar has been the leading architect behind zinc finger optimization at Sangamo and is now its vice president of technology. Another pivotal early hire was Philip Gregory, PhD, who recalls Sangamo’s thriftiness at that stage: As Lanphier used to say, “we were throwing dimes around like manhole covers.”

Two months after Sangamo raised $48.8 million in its initial public offering (IPO), the former New York Times (NYT) biotech reporter Andrew Pollack offered this sobering check on the industry: “The sequencing of the human genome is often described as a triumph akin to landing on the moon. For investors, that might not be the most comforting analogy. Three decades after Apollo 11, no one has yet made a profit going to the moon.” Investors were apparently undeterred. Later that year, the Times quoted a joke going around Wall Street: “If you want to cause a buying stampede among investors, just insert the prefix ‘gen’ into a company’s name.”

Indeed, a year after its IPO, Sangamo acquired Gendaq in a transaction valued at $40 million. Wall Street may have sniggered, but Sangamo got the last laugh—that was almost certainly the most lucrative business move the company would ever make. Cofounded by Aaron Klug, Gendaq had been researching zinc fingers for 15 years. Sangamo added 16 scientists to its roster and acquired 22 patent applications, 2 issued patents, and $6 million in cash. “This consolidation of intellectual property and scientific assets catapults Sangamo into a unique position,” Klug said at the time. That leverage would go on to empower the company and embolden its critics.

Sangamo’s first decade was devoted to proving the efficacy of zinc fingers as a viable medicine, and Gregory led a team that sought to discover whether zinc finger nucleases could edit genes in human cells. After 2 years of research, their work led to a landmark 2005 paper in Nature revealing that site-specific gene modification with a nuclease was possible in a human T cell without suppressing anything else detectable in the genome.

“That was really the result everybody was waiting for,” Gregory says. “I have to say, we were very worried that we were getting tricked by the fantasy of the data. There had been a technology a few years earlier that had offered similar gene correction, but it turned out to be essentially an experimental artifact. So the supplementary data in our paper are just gigantic. We did every experiment imaginable to try to confirm that the data were real and not some artifact of the way we were measuring outcomes.

“To date,” he points out, “that’s still the most rigorous evaluation, from a data perspective, of gene correction.”

Three months after that article was published, Sangamo was accused of controlling a “zinc finger nuclease monopoly” in a Nature article by Christopher Thomas Scott, a graduate student at Stanford who went on to direct the university’s Program on Stem Cells in Society. “[T]he secrets of a cutting-edge technology that could transform gene therapy lie hidden in the intellectual property vaults of a small biotech company.” The strategy makes financial sense, Scott wrote, but it could hinder advancement of the science and antagonize investigators, who might then pursue alternate technologies.

“When zinc finger nucleases were the only game in town, it rankled a number of people that Sangamo was keeping their technology close to the chest,” Dana Carroll, PhD, one of the leading scientists in the field, tells Healthcare Analytics News™. “They developed the technology within their own company to a very, very high standard. Then they pursued practical applications that I think are admirable. It’s hard to criticize a company too severely for protecting their investment in the platform that they were developing.” (Sangamo licenses a patent from the University of Utah for a technology Carroll developed.)

During the mid-2000s, Sangamo did well over 100 material transfer agreements to make its technology available to other labs. “What people don’t talk about when discussing our control of the IP was that it’s extraordinarily difficult to make the kind of high-quality zinc finger proteins that we were making,” says Lanphier, who retired from Sangamo last year. “So yes, there was a patent barrier to entry, but in reality there was a much greater technical barrier.” The threat, the company believed, was not only competition but also the potential of second-rate experiments to sully their product’s reputation.

Sangamo’s breakthrough with zinc finger nucleases in 2005 eventually yielded 4 treatment approaches: gene regulation, in which genes are knocked out or activated; genome editing, in which a new gene is delivered to the nucleus of a cell; gene therapy, in which DNA is cut and a new gene is inserted; and cell therapy, in which T cells or stem cells are edited outside the body. Macrae argues that conflating the company’s original and current zinc finger technology “is like comparing the Model T Ford to a Porsche. The modern car still has 4 wheels and an engine, but it’s a very different beast.”

And so, with this optimized technology in hand, Sangamo and investigators at the University of Pennsylvania launched clinical trials in 2009 for a treatment of HIV. Doctors removed T cells from 102 patients and used zinc fingers to disable their CCR5 gene, making it harder for the virus to take hold. Those edited T cells were allowed to multiply and then were transfused back into patients. NYT reported on one such patient who, a month after being treated, stopped taking his antiviral drugs for 12 weeks as part of the experiment: “As expected, the amount of HIV in his blood shot up. But then it fell back to an undetectable level just before the end of the 12-week period. The patient’s immune cell counts also shot up. ‘I felt like Superman,’ he said in an interview.”

Although the treatment “worked,” in a technical sense, Sangamo realized it wasn’t a sufficient approach and has since diverted its focus. “What we didn’t know was how many of the T cells needed to mutate, and was it just T cells? Was it stem cells?” Macrae explains. “Now we need to work out whether other people could take this forward for us and look for that ultimate cure for HIV. It’s not something we’re going to do, because we just don’t have the bandwidth.”

Wall Street, meanwhile, is less bullish on genomic medicine than when Sangamo went public. “Genomics as a field has ebbed and flowed in terms of investor enthusiasm,” says Gregory, who left Sangamo as chief scientific officer in 2015. “Around the sequencing of the human genome, there was all this enthusiasm about how it would change medicine forever. That, of course, took a long time to happen, and the investor community lost patience. It turns out things are very complicated.”

With about 175 employees and $90 million to $100 million in operating expenses, Sangamo is relatively small for its field, and so it must be, in Macrae’s words, “ruthlessly strategic.” When developing a treatment would be unreasonably expensive and beyond the biological expertise of in-house scientists, Sangamo has formed partnerships with other companies; for example, with Bioverativ for treatment of beta-thalassemia and sickle cell disease, with Shire for treatment of Huntington disease, and with Pfizer for treatment of hemophilia A. That Pfizer deal included an initial $70 million for Sangamo to search for candidate zinc finger proteins, the largest up-front payment for a gene therapy to date.

In early January, Sangamo and Pfizer announced a collaboration to pursue treatment for a form of amyotrophic lateral sclerosis (ALS) that makes up about one-third of all ALS cases. Between its two deals with Pfizer, Sangamo is eligible to receive up to $625 million in milestone payments, along with royalties.

Counted Out

SANGAMO EXECUTIVES used to go into meetings and have to explain the basic principles of gene editing. That’s no longer a problem. The downside is that when people nowadays hear “gene editing,” they’re likely to respond, “Oh, you mean CRISPR?”

That presumption is hardly limited to lay people. Take Mukherjee’s book The Gene: It contains 495 pages on genetics, an extensive discussion of CRISPR, a footnote about another new gene-editing technology called TALEN, and not a word about Sangamo or its zinc finger proteins.

“If you are in an academic research lab and you want to do genome editing,” Carroll says, “you’d be a lunatic if you didn’t adopt the CRISPR technology at least initially because it’s easy

to employ.”

When Macrae makes a similar point, saying, “If I were doing my postdoc again, I would happily use CRISPR to knock out a cell or treat a mouse,” it has a slightly condescending air—as though someone who made grand pianos were to say, “If I were learning to play again, I would happily use a keyboard.”

Daniel Voytas, PhD, a specialist in the genomic engineering of plants at the University of Minnesota, cofounded the Zinc Finger Consortium, which offered open-source software for academic research. Later, he helped invent TALEN. “It was difficult to make zinc finger nucleases, and Sangamo was the best in the world at it,” Voytas says. “There was a tsunami of publications because everyone had access to new reagents, and Sangamo was sort of diluted by that.”

Sometimes an older technology has had more time to be perfected. Other times it has simply gone out of date. “There’s a perception that zinc fingers were slow and clumsy and large and expensive,” Macrae says. As for CRISPR, development was impeded by patent disputes among its 3 leading companies, and some say the technology is more susceptible to off-target mutations, which could potentially cause cancer. Crispr Therapeutics is seeking approval to pursue clinical trials this year for beta-thalassemia in Europe and sickle cell disease in the United States.

Perhaps the greatest obstacle for any gene therapy is delivering the medicine to the targeted part of the body. By that measure, Sangamo can be grateful that CRISPR and TALEN have dramatically expanded the search for an optimal delivery method.

“One of the things that Sangamo has in its favor is that zinc fingers are relatively small compared with the CRISPR-Cas9 protein and the TALENs,” Carroll says. “They can be packaged more easily into AAV vectors,” the virus that Sangamo is using to treat Hunter syndrome. “That’s not an insignificant thing.” In 2013, Sangamo acquired Ceregene, a private company developing the AAV vector platform, along with more than 120 issued, pending, or in-licensed patents.

“It’s all about delivery. Delivery will open up new diseases,” Macrae says. “That will be the future of the company.”

Reasonable Expectations

THE FIRST EVER IN VIVO GENE EDITING in Oakland attracted worldwide attention. A decade earlier, Sangamo had partnered with Sigma-Aldrich to sell its zinc fingers to investigators, but the medical availability of that technology is hardly imminent. Paul Harmatz notes how valuable enzyme replacement therapy has been to reduce the suffering of patients with MPS “for the past 15 years and probably for the next 10.”

Much of the ethical panic surrounding genomic medicine relates to embryonic gene therapy, but none of the treatments in development currently would be inheritable. Sangamo’s goal with MPS is eventually to treat young patients who’ve yet to experience irreversible tissue damage. The corrected gene would be integrated into the child’s DNA and produce enzymes as the liver grows.

“MPS is almost like Alzheimer’s for children,” explains Terri Klein, the National MPS Society president. “Many of our children can run, skip, kick soccer balls, and then they notice that something’s wrong and begin to regress very quickly. We just lost a child last week.”

Treating rare diseases could demonstrate this medicine’s safety and efficacy. “Sangamo has developed zinc finger nucleases into a real art,” Carroll says. “People have gotten excited about the CRISPR technology, and justifiably so, but Sangamo is still very much in the game.” In time, one of these technologies might prevail and transform the way we treat genetic diseases.

There is another possibility, however: that the best approach to gene editing has yet to be discovered.

Danny Funt is a freelance journalist based in New York. He can be reached on Twitter @dannyfunt.

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