Gene therapy for sickle cell moves closer as scientists clear unexpected obstacle

Researchers have cleared the last scientific hurdle to a clinical trial of gene therapy to cure sickle cell disease, they reported on Tuesday, fueling hopes that they will begin enrolling patients early next year. But they dodged a bullet.

The new study, conducted in mice, addressed a sometimes calamitous risk in gene therapy: the difficulty of changing only one thing when tweaking the DNA of a cell. Past efforts to insert a healthy gene into patients with a defective version have led to such tragedies as a boy developing a rare form of leukemia, after a gene aimed at curing his immune-system disease inadvertently activated cancer-causing DNA. And knocking out a gene to eliminate its disease-causing effects can also KO unsuspected healthy functions.

Researchers at the Dana-Farber/Boston Children’s Cancer and Blood Disorders Center discovered that they, too, had a serious problem of unintended consequences as they tried to develop a gene therapy for sickle cell, which affects about 300,000 babies a year around the world. In this inherited disease, red blood cells curve into a sickly crescent, and their hemoglobin molecules cannot carry oxygen well. Patients suffer anemia, infections, tissue damage, strokes, excruciating pain, and even fatal organ failure.

The idea was to target a gene so that patients could keep producing a form of hemoglobin that human fetuses and newborns make. Normally, people stop making this fetal hemoglobin after birth. But some people with the mutation that causes sickle cell don’t actually develop the disease; their bodies continue to make fetal hemoglobin, which is healthy and adept at carrying oxygen, rather than switch to adult hemoglobin, which isn’t.

The solution seemed clear: block the fetal hemoglobin-to-adult hemoglobin switch, which is controlled by a gene called BCL11A that was discovered in 2008, and people with the sickle cell mutation won’t get the disease.

After decades without progress against sickle cell, scientists were well on their way to doing that. Disabling BCL11A in lab mice let the animals keep making fetal hemoglobin, found a 2011 study. Scientists led by Dr. David Williams of Dana-Farber/Children’s then launched additional mouse experiments to pave the way for a clinical trial of a gene therapy that would keep production of healthy fetal hemoglobin turned on.

He and his team removed blood stem cells (which make all kinds of blood cells) from mice, then infused the genetically altered cells back into the animals. If all went well, the altered mouse cells would make a beeline for their natural home — bone marrow — and set up shop there, producing an endless supply of red blood cells with healthy fetal hemoglobin rather than abnormal adult hemoglobin.

Three years ago, however, Williams got a shock: knocking out BCL11A didn’t just block the fetal-to-adult hemoglobin switch. It also kept the blood stem cells from successfully “engrafting,” or taking hold in the marrow. “When we knocked down BCL11A, the animals lost that engraftment very quickly,” Williams said. “It was totally unexpected.”

And it was a big problem. It meant that gene therapy disabling the fetal-to-adult hemoglobin BCL11A gene was fated to fail. The genetically engineered blood stem cells would indeed make healthy fetal hemoglobin. But after settling in the bone marrow, they would wither away like an orchid transplanted into the sands of the Sahara. That would not only doom the gene therapy itself, however. It would also cause serious problems for blood development, a toxic effect no one foresaw.

It turned out that BCL11A has many jobs beyond switching off production of fetal hemoglobin. This gene is a transcription factor, meaning it turns other genes on. Depending on what other molecules it partners with, BCL11A also activates genes essential for stem cell engraftment. Before the new study, published in the Journal of Clinical Investigation, “there was no hint of that role at all,” Williams said. The blood stem cells with disabled BCL11A, when transplanted back into mice, “were gone in two to four weeks instead of lasting forever.”

Gene therapy that targets a transcription factor such as BCL11A “is a little bit of a Pandora’s box, since you don’t know what other functions you’ll affect,” said Dr. Mitchell Weiss of St. Jude Children’s Research Hospital, who was not involved in the new study.

At least one leading gene-therapy company was moving toward a clinical trial disabling BCL11A; it would almost certainly have failed. Williams persuaded the company to pull back, likely averting another failed gene therapy trial.

For the last three years, Williams’ team worked on creating a way to silence BCL11A only in precursors of red blood cells, not in all blood stem cells. They succeeded. Cells from four sickle cell patients had their BCL11A silenced (via a molecule called “short hairpin RNA”) and kept making fetal hemoglobin, crowding out the sickling adult version.

Mice treated with the BCLA11A-silencing therapy produced red blood cells that had at least 80 percent healthy fetal hemoglobin rather than sickled adult hemoglobin. That is considered more than enough to cure sickle cell. And crucially, because BCL11A was KO’d only in some cells from the mice, blood stem cells successfully set up shop in the mice’s marrow.

Weiss said Williams’s results “showed that you can be precise in targeting [BCL11A’s] suppression,” apparently eliminating toxic side effects. “We’re getting closer to success” at finding a gene therapy for sickle cell, he said. Competing teams are pursuing at least three different approaches, he added, including using CRISPR genome editing, as he and colleagues reported last month.

“We think this is the data that will allow us to go into the first human gene therapy trial for sickle cell” using this approach, Williams said. The Food and Drug Administration has given the trial, which would assess the safety of the BCL11A gene therapy, a preliminary okay, and Williams expects to seek final FDA approval next month.

The BCL11A-suppressing molecule has been licensed to Bluebird Bio, which will pay for producing it. Williams has applied for a grant from the National Institutes of Health to run the trial, and is hoping a philanthropist steps up to provide the rest of the needed funding.