Engineering vaccine-like protection without a vaccine

CRISPR gene-editing used on antibody-making B cells
An illustration of B-cell engineering

Scientists at Fred Hutchinson Cancer Research Center are reporting today how B cells, a type of blood cell critical to the immune system, can be efficiently engineered to make antibodies against specific diseases, working much like a vaccine.

Antibodies are tiny, Y-shaped proteins that lock onto bacteria, viruses and fungi encountered in the body. B cells are the natural factories that churn out these protective proteins by the billions.

The goal of nearly every successful vaccine — for diseases ranging from tetanus to hepatitis — is to coax B cells into making swarms of antibodies to block a specific microbial threat. Yet the process, which harkens back to the first smallpox vaccination in 1796, does not always work as well as doctors would like. Sometimes protection is partial; sometimes vaccines don’t work at all.

In research published online today in Science Immunology, a Hutch team led by Dr. Justin Taylor shows that B cells can be genetically engineered to make exactly the antibodies we want — demonstrating a potentially more precise and dependable way to generate protection without vaccines.

Dr. Justin Taylor in his lab
Dr. Justin Taylor is senior author of a paper on B-cell engineering published today in Science Immunology. Photos by Robert Hood / Fred Hutch News Service

DNA blueprints for antibodies

“What we really want to create is something where we take your B cells, engineer them to make the antibody you need, put them back in the body, and you are good for life,” Taylor said. “No vaccine required. We’ll just cut out the middleman.”

The report Friday describes in detail how Taylor and his team used the gene-editing technology known as CRISPR/cas9 to insert DNA blueprints for antibodies into B cells from mice and humans. Refined over a two-year period, their technique worked far better than expected, in some cases causing nearly two-thirds of the cultured cells to generate the antibodies desired.

In one experiment, the team engineered mouse B cells to make antibodies against respiratory syncytial virus, or RSV. The virus, which causes flu-like symptoms in humans, is particularly dangerous for infants, the elderly and people with weakened immunity, and there is no commercially available vaccine. The researchers infused those modified B cells into mice with defective immune systems, and then exposed them to RSV. The mice were protected from infection for at least 82 days.

“It’s not lifetime protection, but these results are a great first step,” Taylor said.

This new ability to engineer B cells is barely out of the lab dish, but if the technique can be applied to humans it could eventually become an important option for vulnerable patients. Instead of vaccine, they would get an infusion of their own, re-engineered B cells. It could be a lifesaver for recovering bone marrow transplants patients at high risk for infections, and it may offer an alternative approach to building antibody protection when vaccines are not up to the task.

B-cell engineering: 'A field that did not exist 3 years ago'

While it is way too early to try this in humans, Taylor and his team have proven a principle: This entirely new way of inducing protection against infectious diseases — “B-cell engineering,” as he calls it — is a plausible alternative to antibody production induced by vaccines.

“Other labs have seen these possibilities, so there is a lot of excitement in the field of B-cell engineering — a field that didn’t exist three years ago,” Taylor said.

That excitement blossomed this winter when Taylor’s and two other laboratories, working independently with CRISPR gene editing, disclosed their research in online, open-source websites favored by scientists who want to get their information out to the research community as quickly as possible.

“Justin’s work has progressed amazingly well,” said Dr. Larry Corey, a renowned virologist, the president and director emeritus of Fred Hutch, and a principal investigator of the HIV Vaccine Trials Network. “The ability to genetically engineer unique antibodies has enormous implications for preventing infections and delivering long-term therapies for treatment and prevention of a wide variety of diseases.”

Taylor first envisioned B-cell engineering nearly four years ago, while thinking about his new lab's primary focus: studying how the cells respond to vaccines. He knew that the idea was too unconventional for government grants, so he sought support from private foundations. In April 2016, he received a grant from The Hartwell Foundation, a Memphis philanthropy that specializes in funding innovative, early-stage biomedical research that might benefit children. 

"With the future direction of Justin's research focused upon achieving lifelong protection against infection, there is great expectation that, if successful, children recovering from cancer therapy would benefit immensely from his engineering strategy," said Fred Dombrose, president of the foundation.

Vir Biotechnology, a San Francisco firm that invests in technologies for the treatment and prevention of infectious diseases, also provided financial support for some of Taylor’s B-cell engineering research.

Dr. Larry Corey
Dr. Larry Corey, president and director emeritus of Fred Hutch

Grafting genes in just the right spot

B-cell engineering draws on some of the same gene-splicing science that has been used to tinker with T cells, another key blood cell that is a crucial component the immune system. Using various approaches, T cells are being rewired so that proteins on their surfaces can match and latch onto telltale proteins found on cancer cells. T-cell immunotherapies, such as CAR T, are now revolutionizing cancer treatment.

But until recently, no one has succeeded in engineering B cells. The reason: the antibody-making machinery of B cells is more complex. The genetic blueprints for making antibodies must be inserted into a very specific location on the B-cell genome or the antibodies will not fully function. That’s where the new molecular-scissors technology — CRISPR — made a difference. Favored for its ease of use and precision, it increases the chances that the two genes required for antibody production will be grafted in just the right spot.

Taylor credits much of the heavy lifting for the research to postdoctoral fellow Dr. Howell Moffett, the lead author of the paper, and research technician Carson Harms, both of whom joined his lab two years ago specifically to take on the B-cell engineering project. He praised them and team members Kristin Fitzpatrick, Marti Tooley and Jim Boonyaratanakorkit for their “creative thinking and tenacious attention to detail” as they fine-tuned their process.

The Hutch experiments stand out for their efficiencies — the high percentage of genetically engineered cells that yielded antibodies after the gene-splicing. Online reports by laboratories pursing similar ideas achieved efficiencies ranging from under 2% at Scripps Research Institute to 4% at The Rockefeller University.

“In our paper, the highest percentage we hit was 59% of cells yielding antibodies, which is remarkable,” Taylor said. “I was expecting our max would be 10%. They blew that out of the water.”

The Hutch researchers describe in their new paper how they used CRISPR in the lab to cut the genome of human B cells in a precisely determined location, near the spot holding genes for making antibodies. In a series of experiments, they inserted into that open part of the DNA chain the blueprints for making a specific antibody known to target a disease-causing virus.

Photo of Howell Moffet
Dr. Howell Moffet is lead author of the Science Immunology paper. He recently took a position at Lyell Immunopharma, a Seattle startup working on cancer immunotherapies.

An antibody to prevent HIV infection

They successfully generated antibodies for four different viruses: HIV, RSV, influenza and Epstein-Barr virus, which is implicated in mononucleosis and several cancers. For HIV, they chose a so-called broadly neutralizing antibody — one that the virus has a difficult time evading. That same antibody, known as VRC01, is being tested in the AMP Study, a pair of closely watched global trials in which more than 4,600 healthy participants will receive infusions of it or a placebo about every two months to see if the antibody can prevent HIV infection.

Taylor’s team also engineered B cells to produce an experimental broadly neutralizing antibody against influenza. With such an antibody, vaccine developers could create a flu shot that a patient might only need to receive once. If the antibody is found to work, but vaccines can’t stir up enough of them, B-cell engineering might be another way to confer such protection.

The RSV antibody is identical to one, known as palivizumab, that is infused into premature infants to protect them against the respiratory infection. To date, efforts to make an RSV vaccine have failed using traditional techniques meant to stimulate B cells with bits of the virus. Yet in Taylor’s mouse study, the engineered RSV antibody afforded roughly the same protection as a palivizumab infusion.

Given the early nature of B-cell engineering research, Taylor stressed several important caveats:

  • It really is early. There is an enormous difference between useful medical interventions and experiments in laboratory dishes or mice.
  • Safety. There is a possibility that CRISPR could cut the B-cell genome in the wrong place and cause unwanted or dangerous “off-target effects.” This is a major question that will need to be resolved before most CRISPR-based gene-splicing technology can be widely tested in humans.
  • Cost. Just like T-cell engineering, B-cell engineering is a costly, labor-intensive process. The first applications of this technology are likely to be extraordinarily expensive. Vaccines that work, on the other hand, are among the most cost-effective medical interventions in the world today.

B-cell engineering, if shown to be effective, would likely be targeted to patients at high risk of infection and unable to respond to vaccines, such as those undergoing transplants. It could become economically feasible if a single dose could contain a mixture of different B cells, each engineered to cover a broad range of infectious diseases.

As Taylor’s postdoctoral fellow Moffett noted, “In the near term, it is going to be a therapy for people in dire circumstances, such as a bone marrow transplant where a respiratory illness has a high mortality rate. In that case, it would totally be worth the cost.”

Much further down the road, B-cell engineering offers the intriguing possibility of replacing therapies that depend on lengthy, even lifelong, infusions of antibodies. There are now more than two dozen drugs that infuse laboratory-grown monoclonal antibodies to treat cancer and immune disorders. They are easily identified by the suffix “mab” at the end of their generic names, such as trastuzumab (Herceptin), pembrolizumab (Keytruda), rituximab (Rituxan) and ipilimumab (Yervoy). Instead of infusions of these antibodies, a single injection of engineered B cells might one day give patients the ability to churn out their own, personalized antibodies.

No drugs required.

Note: Scientists at Fred Hutch played a role in developing these discoveries, and Fred Hutch and certain of its scientists may benefit financially from this work in the future.

Sabin Russell is a former staff writer at Fred Hutchinson Cancer Center. For two decades he covered medical science, global health and health care economics for the San Francisco Chronicle, and he wrote extensively about infectious diseases, including HIV/AIDS. He was a Knight Science Journalism Fellow at MIT and a freelance writer for the New York Times and Health Affairs. 

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