In 2008, a team of scientists at Washington University School of Medicine in St. Louis became the first to decode the DNA of a patient’s cancer cells and trace the disease to its genetic roots. The patient, a woman in her 50s, suffered from acute myeloid leukemia (AML), an aggressive and often deadly cancer of the blood and bone marrow. The findings garnered the research team worldwide acclaim and paved the way for more personalized approaches for the treatment of cancer based on the clusters of mutations in patients’ tumors.
One of the most unusual mutations discovered in that patient’s AML cells was in the gene DNMT3A. The gene had never been linked to cancer, so the significance of the gene’s mutations was unknown. But it was a fascinating candidate gene to consider. DNMT3A was known to encode an enzyme that can methylate DNA at very specific places in the genome, a process that can change patterns of gene expression and that was known to be very important for normal development.
In the year that followed, the Washington University team sequenced the DNMT3A gene in 280 additional AML patients and found that it was indeed one of the most common initiating mutations for this disease — and that mutations in one particular site, at the 882nd amino acid in the DNMT3A protein, was more common than all of the others. This “hot spot” for mutations suggested that something special was going on there, and further studies from the lab of Timothy J. Ley, MD, clarified what that something was. Ley, the university’s Lewis T. and Rosalind B. Apple Professor of Medicine and chief of the Section of Stem Cell Biology in the Division of Oncology, helped lead the first sequencing of the AML patient’s genome.
The mutations at amino acid 882 changed the way the protein normally interacted with itself to make a functional enzyme, and reduced the activity of the enzyme by about 80% — essentially rendering it inactive. When Ley and his then-trainees David Russler-Germain, MD, PhD, and David Spencer, MD, PhD, looked at the DNA methylation patterns in AML samples with this mutation, they found a very distinct signature, with pinpoint areas of reduced DNA methylation at very specific regions of the genome in every patient who had the mutation.
This knowledge framed an essential chicken vs. egg question: Were these areas with reduced DNA methylation important for causing AML, or were they just a byproduct of cancer transformation? The only way to find out would be to get a sample of blood cells from a person with the same exact DNMT3A mutation but who did not have AML, to see whether the changes in DNA methylation were already there.
But there was no obvious way to find such a patient.
On a bright winter afternoon in 2015, serendipity graced the investigators and the families of a group of patients with a rare genetic syndrome that had been discovered the year before.
As Ley sat in his office mulling over the conundrum that was confounding the field, his phone rang.
The caller — Shashikant Kulkarni, PhD, then-head of the Department of Pathology & Immunology’s Cytogenetics and Molecular Pathology Laboratory — bombarded Ley with a staccato of facts: A patient at St. Louis Children’s Hospital. A 9-year-old boy named Ayden, with a newly described genetic syndrome associated with a mutation in the DNMT3A gene — but his blood counts were normal. And, Kulkarni noted, the boy and his parents had consented to donating his blood and tissue samples for research.
“I couldn’t believe it,” Ley recalled.
Shortly after that conversation, Ley received a call from Marwan Shinawi, MD, a professor of pediatrics in the Department of Pediatrics’ Division of Genetics & Genomic Medicine. Shinawi had just diagnosed Ayden with DNMT3A Overgrowth Syndrome, also known as Tatton Brown Rahman Syndrome (TBRS), a syndrome first identified in 2014 by a pediatric geneticist in London, Kate Tatton-Brown. The condition can cause individuals to be taller than average, overweight and have a large head circumference and distinctive facial features. People with the disorder also may have intellectual disabilities, behavioral difficulties and decreased muscle tone.
In 2014, there were only 13 patients in the world with a known diagnosis of the syndrome.
“You’re not going to believe this,” Shinawi told Ley over the phone, “but the patient has the R882H mutation that you’ve been studying, and his father works here in pathology.”
“It was truly incredible,” Ley said. “There were 13 known patients in the world who had this syndrome. None of them to date had the mutation at position 882 that was so strongly associated with AML. This created a remarkable opportunity to learn more about how DNMT3A mutations contributed to TBRS and how they initiated AML.
Ley’s prior research on the mutation and blood cancers also triggered concern for Ayden. “I worried that Ayden and these other children might be at increased risk of leukemia,” Ley said. “I knew that it was essential to monitor Ayden’s health while determining whether there is an increased risk of leukemia for patients with this syndrome.”
Thanks to Ayden’s contribution to scientific research — as well as similar contributions from dozens of other families from around the world — the Washington University Medical Campus is now a global beacon for patient care and research for TBRS. Now, the syndrome is known to affect about 250 children and young adults worldwide, according to the TBRS Community, a family-led rare-disease organization founded by Jill Kiernan. Her daughter, Aevary, was one of the first to be diagnosed with the syndrome, in 2014.
The nonprofit, which emphasizes advocacy, education and research, is collecting information from families in a clinical registry to study the genetics, development and health of children with DNMT3A Overgrowth Syndrome and of their families.
“Dr. Ley has been amazing about talking directly to families whose children have DNMT3A variants,” Kiernan said. “He says, ‘We’ll do what we can. We’ll coordinate with their team. We’ll tell them what we know and what we don’t know.’ And he does. It’s not only Dr. Ley, but everyone we’ve worked with at Washington University has a sincere interest in helping these children and their families.”
The children’s blood and tissue samples continue to be studied in laboratories across the School of Medicine, from oncology and genomics to neuroscience and pediatrics. In conjunction with the studies of clinical samples, genetically modified mouse models are proving to be an important new tool for understanding how DNMT3A mutations work. Mouse and human genomes share common genes that typically function in the same way. Such similarities make mice ideal for simulating human disorders to study how a single mutation can cause all of the features of a complex disease like TBRS. Remarkably, when the amino acid 882 mutation is created in mouse germline cells that make eggs and sperm, the animals develop virtually all of the features of the human syndrome — including the reductions in DNA methylation noted in the AML patients. They also have an increased likelihood of developing blood cancers, including AML. These findings were published last year in Nature Communications.
“The key to understanding genetic conditions such as TBRS is having both clinical data and samples, as well as mouse models,” explained the paper’s first author, Amanda M. Smith, PhD, a former researcher in Ley’s lab who led the development of the mouse model with the amino acid 882 mutation.
Harrison Gabel, PhD, an assistant professor in the Department of Neuroscience, has created additional DMNT3A mouse models and focused on how they affect brain function. “We’re looking at it from a molecular level, how genes get turned on and off, and how that affects development to drive the overgrowth, obesity and neurologic dysfunction that occur in the disorder,” he said. “The collaborative environment and resources at Washington University position us to attack this particular disorder from all sides. Dr. Ley and I are working side by side, studying the gene in blood cells and in the brain. Combining our efforts with Dr. Shinawi, who understands the clinical aspects of this disorder, and adding in the remarkable relationship with patients and their families, it all adds up to a powerful synergistic approach.”
Gabel is a member of the TBRS Community’s scientific advisory committee, and Ley and Shinawi serve on the medical advisory board. This nonprofit recently secured a three-year, $600,000 grant from the Chan Zuckerberg Initiative. “It is a total game changer for our little organization that’s been fueled by parent volunteers,” said Kerry Grens, the group’s vice president and the Department of Neuroscience’s new marketing administrator. Her son Adrian was diagnosed with TBRS in 2019, when he was 3 years old.
Shortly after Adrian was born, Grens and her husband noticed their son was delayed on milestones such as holding up his head and sitting. He also had strabismus (crossed eyes) and a congenital heart defect. “We saw a lot of doctors before we came to Washington University, underwent genetic sequencing and received an official diagnosis from Dr. Shinawi,” Grens said. “It can feel hopeless to have a child with an incurable rare disease, and volunteering with the organization gives me a chance to feel like I’m making progress, making a difference. A lot still needs to be answered about this genetic mutation and the associated risks for other diseases such as leukemia.”
Research led by Margaret Ferris, MD, PhD, an instructor of pediatrics at Washington University and an oncologist at St. Louis Children’s Hospital, recently confirmed the scientists’ initial concerns: Patients with TBRS are at an increased risk — about 250 times more than the general population — for blood cancers, including acute myeloid leukemia. The study was published in November in Blood, the journal of the American Society of Hematology.
“This can be difficult news to tell the families, obviously, but it’s the truth, and they need the truth,” said Ley, the study’s senior author. “Do we need to monitor these children for early signs of the development of leukemia? The answer is, clearly, yes, we do.”
Ayden’s dad, Michael Isaacs, said the truth, no matter what it may be, gives him hope. “Not knowing is the biggest burden,” said Isaacs, director of informatics and of external affairs for the Department of Pathology & Immunology. “Knowing, and having a diagnosis, help set expectations for what the future may look like, but most of all, it gives me hope. The research being done, the dedication of the parents, and the collaborations at Washington University all give me hope.”