The Gene Fixer

 

For five decades, Stuart Orkin has harnessed new genetic tools to transform care for blood disorders – helping make sickle cell and beta thalassemia curable.

In the early 1970s, the field of genetics was confined to the study of bacteria and viruses. Conventional wisdom at the time was that the tools of molecular biology couldn't be used to study human diseases. Human cells were just too hard to access, and too slow to reproduce, but also, the technology available was too crude. Some experts in the field thought that molecular biology would never be done in humans.

Stuart Orkin, MD, and a small number of other scientists were undeterred, and through their persistent efforts upended that skepticism. Orkin, a physician-scientist at Dana-Farber/Boston Children's Cancer and Blood Disorders Center and the David G. Nathan Distinguished Professor of Pediatrics at Harvard Medical School, was chair of Dana-Farber's Pediatric Oncology department from 2000-2016. By adopting and mastering new molecular and genetic tools as quickly as they appeared, he produced a litany of firsts: the first mapping of the genetics of a disease, thalassemia, an inherited blood disorder; the discovery of the first mechanisms that enable blood stem cells to specialize into functional red blood cells; the science behind the first approved CRISPR-based gene therapy; and more.

"He has a great understanding of what could be learned if..." says David Nathan, MD, president emeritus of Dana-Farber and one of Orkin's earliest mentors. "I've never seen anybody like him."

Nathan hired Orkin in the late 1970s, giving him his own lab, a technician, and his mentorship. It was an unusual hire – Orkin had completed just two years of laboratory training at the National Institutes of Health (NIH) after earning his medical degree at Harvard Medical School – but 50 years later, Orkin's storied career has proven that it was a good one.

Two blood diseases – beta thalassemia and sickle cell disease – are now curable with approved gene therapy that is based on Orkin’s laboratory discoveries. Chronic granulomatous disease, a rare disease that leads to frequent and severe infections, is also being treated in clinical trials with gene therapy based on Orkin’s work. And molecular biology? It has become the foundation of modern cancer research.

Cracking the Thalassemia Code

One of the earliest projects in Orkin's lab focused on unraveling the genetic underpinnings of thalassemias, inherited blood diseases that impair formation of hemoglobin, which enables red blood cells to transport oxygen.

It was 1978, early days in molecular biology, and tools were scant. But Orkin embraced every possible bit of technology in his lab. So much so that, later in his career, he was known to quote the novelist Marcel Proust, who said, "The real voyage of discovery consists not in seeking new landscapes, but in having new eyes."

One of the earliest technologies to emerge was gene cloning. Scientists knew that genes could have mutations, but they had no good way of finding them. Gene cloning, the process of isolating a gene and replicating it, provided a sort of magnifying glass for scientists, enabling them to discover and catalog mutations. 

For Orkin, it wasn’t just this new technology that provided fresh eyes; it was also using the technology in a new way. Orkin recognized that these tools could be used to study human diseases caused by inherited mutations.

"This tool would get us where we wanted to go, to study disease in a way that really hadn’t been done before," says Orkin.

Orkin collaborated with a geneticist who had samples from patients with thalassemias from multiple areas of the world where the condition is frequent. The idea was that the disease had emerged through distinct mutations in different regions, varying much the same way other traits such as eye or hair color vary with ancestry. Some mutations affect alpha-globin and cause alpha thalassemia, for example, and others affect beta-globin and cause beta thalassemia. Orkin's team focused on beta thalassemia, which had a high need for new treatments.

He combined gene cloning with a technique called haplotype analysis, which helped the team narrow down which genes to clone from a collection of samples. This helped the team find not only the most common mutations, but also rarer disease mutations shared by only a few individuals. Once they cloned and sequenced the genes, they were able to understand how particular mutations affect production of beta-globin.

"We didn't want to go after just the most common mutation causing thalassemia," says Orkin. "We wanted to learn about the whole spectrum. In a couple of years, we basically mapped out and determined all the mutations of beta thalassemia. It was the first time that anyone had comprehensively done that for any genetic disease."

The work resulted in the creation of prenatal tests for the disease. But it didn't answer the question Orkin really wanted to answer.

"It told us how you can screw up a gene, but it didn’t tell us anything about red blood cells," says Orkin. "What I was interested in trying to figure out was how a red cell gets made."

How Red Blood Cells Form

In the late 1980s, Orkin embraced methods to identify transcription factors, which are proteins in the nucleus that regulate the expression of genes. He and his trainees found a new protein, GATA-1, which is a transcription factor that controls all genes in red blood cell development. 

To prove that GATA-1 acts as such a "master regulator," they turned to another new technology: gene knockouts. Knockout technology was very new and made it possible to remove a single gene in every cell of an organism to learn more about its function.

When the GATA1 gene was eliminated, no red cells were made, confirming its role as a master regulator. This approach of identifying a critical transcription factor and knocking it out became a standard approach and established a new discipline of molecular hematopoiesis.

"Stu was one of the first people to recognize that it was possible to apply molecular biology to hematology because you could access human blood cells easily," says David Williams, MD, president of Dana-Farber/Boston Children's and an early career mentee of Orkin’s. "And then he applied the tools of molecular biology as they evolved in a way that allowed him to make really big jumps in scientific understanding of blood diseases."

When Ramesh Shivdasani, MD, PhD, joined Orkin's lab in the early 1990s, Orkin was working toward uncovering the function of many transcription factors in blood cell development. A gene called TAL-1, or stem cell leukemia (SCL) was of special interest because it was a known leukemia oncogene.

Shivdasani and Orkin created a knockout of the gene to determine its normal role in blood development. Their next step was to identify clones in which the gene was correctly knocked out. The process used familiar technology but was challenging, nonetheless. Like quality control specialists in a factory, they were looking for a perfect match. The work was tedious and slow.

"We must have looked at more than 750 clones, and only one of them was correct," recalls Shivdasani, who is now a physician-scientist specializing in gastrointestinal cancers. He worked on the project with Erica Mayer, MD, MPH, then an undergraduate but now director of breast cancer clinical research at Dana-Farber.

From that one clone, they learned that the loss of this gene prevented formation of blood stem cells. The finding that a leukemia oncogene is also essential in normal blood cell development is now a recurrent theme in cancer research. Cancer results from misuse of such genes, either through mutation or rearrangement of chromosomes.

Alice Shaw, MD, PhD, now chair of Medical Oncology at Dana-Farber, joined Orkin's lab around the same time as a graduate student. Her work led to the discovery of FOG-1, a "friend" of GATA-1, helping to complete the picture of how different factors work together to tip a cell closer to becoming committed to being a red blood cell.

"Stu was already a professor, but he was in the lab every day of the week," says Shaw. "He would be standing there at 8 a.m. in the next bay over from me, and he would be pipetting. He worked tirelessly and never gave up."

Orkin's foundational work, says Williams, "set the stage for many discoveries that have come after it."

 

From Blood to Cancer Clues

Genetic links to cancer began to emerge, connecting aberrations in these regulatory transcription factors to acute lymphoblastic leukemia (ALL), to a subtype of acute myeloid leukemia (AML) that affects children, particularly those with Down syndrome, and to a predisposition to certain blood cancers.

Orkin’s findings also informed the work of Scott Armstrong, MD, PhD, chief research strategy officer, senior vice president for drug discovery, and Ted Williams Chair at Dana-Farber, who was mentored by Orkin while establishing his own lab about 20 years ago. Armstrong was looking at blood stem cells to learn more about leukemia, and some of the mouse models Orkin had developed ended up being critically important for Armstrong to begin to understand the formation of leukemia cells.

That work led to Armstrong's research uncovering how a normal protein called menin drives leukemia formation in blood stem cells. In the past year, based largely on that research, two menin inhibitors have been approved for the treatment of certain forms of acute myeloid leukemia and could reach approximately 40% of patients with the disease.

"Stu has the incredible ability to see where things are going and the best path to take to get there," says Armstrong. "And it seems effortless for him."

The Fetal Hemoglobin Switch

Not every path in the Orkin lab was effortless. For a long time, the challenge of finding the switch in red blood cells that flips at birth between fetal and adult hemoglobin was intractable. 

Before birth, red cells produce a different form of hemoglobin called fetal hemoglobin. People with higher levels of fetal hemoglobin as adults – perhaps due to an imperfect switch – fare better with diseases like beta thalassemia and sickle cell disease, which both cause adult hemoglobin to be faulty.

"We were interested in the problem of identifying this genetic switch, but after a decade or so, we gave up," says Orkin. "The field was in the doldrums for a long time."

In the early 2000s, Vijay Sankaran, MD, PhD, a physician-scientist at Dana-Farber and Boston Children's, joined Orkin's lab as an MD/PhD student and told Orkin he wanted to resume the search.

"Stu didn't say much, but his eyebrows went up," remembers Sankaran. "It's a testament to his style as a leader and mentor to be open to letting people pursue their passions."

Sankaran spent two years making little to no progress homing in on a molecular switch. There weren’t enough clues to guide him, until a new form of study emerged called genome-wide association studies. These studies, which only began to be used in the early 2000s, look across a large population of people and correlate traits with single changes in DNA sequences. 

Data from a study of a population in Sardinia, which has elevated rates of inherited blood disorders like thalassemia and sickle cell disease, enabled Sankaran and Orkin to focus on BCL11A as a gene that acts like a thermostat for fetal hemoglobin. Lower BCL11A expression results in higher levels of fetal hemoglobin.

The team built on that discovery, which was published in 2008, with studies of a mouse model of sickle cell disease showing that, indeed, knockout of BCL11A cured the disease by increasing levels of fetal hemoglobin. Fetal hemoglobin restored functions that faulty adult hemoglobin couldn’t carry out. They had found their therapeutic target. 

But that was not the end of the story. As cells differentiate from blood stem cells into increasingly specialized cells, they turn genes on and off to regulate their function. Some genes, such as BCL11A, work differently in different cell types. Turning off BCL11A in every cell would have effects beyond fetal hemoglobin levels and would disable essential biological functions. The team needed to find a more precise way to turn off BCL11A. 

By 2013, Dana-Farber and Boston Children's physician-scientist Daniel Bauer, MD, PhD, had joined the lab. He found a region of the gene containing an enhancer that controls the levels of BCL11A and is only used in red blood cells.

Around that same time, a new tool was entering the scene: CRISPR/Cas9 gene editing. Orkin and his lab teamed up with experts at the Broad Institute of MIT and Harvard to use it to begin editing different regions of the BCL11A enhancer to disable its function.

Soon after, Bauer and Orkin published and patented the instructions, in the form of a guide RNA, for a CRISPR/Cas9 gene editor to use to alter the enhancer and dial down BCL11A specifically in developing red blood cells. 

"That’s what is in Casgevy," says Orkin, referring to the CRISPR-based gene therapy used to cure sickle cell disease and beta thalassemia. The therapy was first tested in clinical trials in 2017 and approved in 2024. Dana-Farber treated and cured its first patient with beta thalassemia using Casgevy in 2025.

Williams also applied Orkin’s discoveries about BCL11A in an alternate approach to gene therapy using a viral vector. This technology is still being evaluated in a national multi-site clinical trial led by Boston Children’s Hospital.

The Next Fix

Casgevy delivers a one-time treatment but requires replacement of a patient’s bone marrow with gene-edited stem cells, making the treatment arduous and expensive. Its uptake after approval was anticipated to take time. So far, however, Casgevy has provided a functional cure for more than 90% of treated patients with either sickle cell disease or beta-thalassemia.

Meanwhile, Orkin is devoted to looking for other solutions. His lab is exploring the possibility that the BCL11A protein could be modulated using a small molecule drug, such as a protein degrader that clears it from cells before it has a chance to silence fetal hemoglobin. Such a medicine would likely require patients to take a pill indefinitely. But a pill could also be easy to distribute in regions of the world, such as in Africa, the Middle East, and India, where there are fewer medical resources and high rates of the hemoglobin diseases.

"The hemoglobin story has been a 40- to 50-year journey, and the basic problem is somewhat solved," says Orkin. "But we still have patients who need better therapy. The problem is never fully solved."

It could be that the technology needed to solve the next wave of challenges has not emerged yet. But more important are the minds of scientists like Orkin and those who have trained with him, who are able to embrace new approaches, see problems with fresh eyes, and carve out scientific landscapes that were previously unimaginable.

The Molecular Biology of a Rare Disease

The story behind the discovery of the genetic roots of chronic granulomatous disease begins years before David Nathan, MD, meets Stuart Orkin. It starts, as Nathan tells it, with two test tubes: one blue, and one white. 

One test tube contains normal white blood cells, called granulocytes. The other contains white blood cells from a patient of Nathan's with chronic granulomatous disease, a rare disease that results in frequent infections. Both test tubes start out blue.

It was known at the time that white blood cells pull bacteria into a sac inside themselves and then kill them with toxic chemicals. In an experiment, the test tube containing normal cells turned white due to the presence of these toxic chemicals. 

The tube containing the patient’s cells stayed blue, indicating an absence of these chemicals. The experiment confirmed the biological cause of the disease and showed for the first time that it was possible to diagnose it.

"It was thrilling," recalls Nathan. "I can still see my trainee running down the corridor with the two tubes. But we didn't know why this patient wasn’t producing these chemicals. Stuart found out why. He got to the bottom of it."

Getting to the bottom of it, however, took a decade. Finding a disease-related gene during that era was no small feat. 

Orkin used a process called positional gene cloning – a gradual narrowing down of the location of the gene in the genome using clues from experiments and patient samples. He and his collaborators were the first to use it to isolate a human disease gene. 

"If you cloned a gene back then, you got tenure," says Edward J. Benz Jr., MD, president and CEO emeritus of Dana-Farber and a contemporary of Orkin's. "That's how hard it was."

It isn't as hard now. Benz has a daughter who cloned a gene during a lunchtime activity at age 11. 

But now, scientists can do a lot more than clone a gene. It is now possible to edit the faulty gene and correct the disorder. 

"We successfully treated the first patient in the United States with gene therapy for chronic granulomatous disease here in Boston," says David Williams, MD, president of Dana-Farber/Boston Children's Cancer and Blood Disorders Center and an early career mentee of Orkin's.

By Elizabeth Dougherty