How the Discovery of an Early, Pre-Malignant State in Blood Cells Is Transforming Our Understanding of Human Biology, Aging, and Disease
April 26, 2023
CAR T-Cell Therapy
By Nicole Davis, PhD
In 2012, Benjamin Ebert, MD, PhD, and other researchers embarked on a bold exploration. While many scientists were studying genetic markers of cancer in people already diagnosed with the condition, the team had a very different question: Do the genetic mutations that drive the growth of leukemia and other blood cancers lurk in the bodies of people without cancer? If so, that might open the possibility of intercepting cancer even before it began.
These efforts were fueled by new technologies for decoding DNA — specifically, the fraction of the genetic code that encodes proteins, called the "exome." With exome sequencing, it is technically and financially feasible to conduct very large studies involving tens of thousands, even hundreds of thousands of patient samples.
"This led us to the surprising discovery that mutations in a handful of leukemia-causing genes become quite common with advancing age," said Ebert, chair of medical oncology at Dana-Farber, who spearheaded the study, published in 2014 in the New England Journal of Medicine.
This led us to the surprising discovery that mutations in a handful of leukemia-causing genes become quite common with advancing age.
He and his colleagues, in collaboration with the Broad Institute of Harvard and MIT, analyzed some 17,000 blood samples, searching for mutations in nearly 200 genes known to be associated with blood cancers. Remarkably, they found that more than 10% of people over age 70 carried mutations in a small subset of these genes, which include DNMT3A, TET2, and ASXL1. They also discovered that these mutated genes coincided with the abnormal expansion of the blood cells that harbor them — a phenomenon known as clonal hematopoiesis (CH).
Other research teams working independently, including one led by Steven McCarroll, PhD, at the Broad Institute and Harvard Medical School, made very similar discoveries. "We had incredibly identical findings, which really gave us confidence that what we were seeing was real," said Ebert, who is also the George P. Canellos, MD, and Jean S. Canellos Professor of Medicine at Harvard Medical School, an Institute Member of the Broad Institute, and a Howard Hughes Medical Institute Investigator.
After analyzing their data, Ebert's team recognized that individuals with this early pre-malignant state had a higher risk of developing blood cancer than those without it. "We also found that CH is associated with increased mortality overall," Ebert said. "But the puzzling thing was, we knew that couldn't be explained simply by blood cancer risk since the condition is relatively rare."
When the researchers dug more deeply into their findings, they unearthed a strong association with heart disease. They quickly launched follow-up studies in collaboration with Sekar Kathiresan, MD, then at Mass General Hospital and the Broad Institute, to unlock the basis of this link. They discovered that individuals with CH do carry an increased risk of heart disease, including heart attacks and strokes. In animal studies conducted in collaboration with Peter Libby, MD, at Brigham and Women's Hospital, they showed that blood cells carrying one of the commonly mutated genes associated with CH can accelerate the onset of heart disease in mice. Further experiments zeroed in on the likely culprits — malfunctioning white blood cells that release high levels of pro-inflammatory chemicals called cytokines.
"This became a robust field very quickly because of the volume of data we were looking at — first tens of thousands and now hundreds of thousands of exomes or genomes — and consistently finding the same genetic mutations and disease associations," said Ebert. Now, scientists are hoping to soon launch clinical trials of potential therapeutics that may be able to disrupt the inflammatory program spurred by clonal hematopoiesis of indeterminate potential (CHIP) and reduce the risk of heart disease.
Benjamin Ebert, MD, PhD (left), and Coleman Lindsley, MD, PhD, have led a number of research studies to help doctors and scientists better understand clonal hematopoiesis (CH).
Physician-scientist Lachelle Weeks, MD, PhD, treats patients with precursor conditions including clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS).
Inflammation and Clonal Hematopoiesis
Heart disease isn't the only age-related disease driven by inflammation; several others are also stoked by the fires of the immune system. Ebert and his colleagues have explored potential connections to CH for many of these conditions and so far have uncovered links to chronic obstructive pulmonary disease (COPD), gout, osteoporosis, and, most recently, chronic liver disease.
The biological mechanisms that underlie these associations are not yet clear. However, the impact on disease risk appears to be modest, and the findings add to an emerging picture of inflammation and aging — often called "inflammaging" — in which chronic, low-grade inflammation, without infection or other obvious causes, can help drive or exacerbate age-related diseases.
But that picture is still coming into focus and is likely more complex than imagined. For example, Siddartha Jaiswal, MD, PhD, a former postdoctoral fellow in Ebert's lab who led the early CH studies and is now a faculty member at Stanford University, spearheaded a recent study exploring potential connections between CH and Alzheimer's disease. The research, which has not yet been published but was presented at the annual meeting of the American Society of Hematology in December 2021, uncovered an extraordinary relationship: CH appears to protect against Alzheimer's. The biology behind this defensive maneuver is not yet clear, but the scientists speculate that key immune cells in the brain, called microglia, are likely involved. These cells arise from blood cells very early in development and take up residence in the brain. Microglia are now the focus of intense interest because of their roles in brain development and aging, including Alzheimer's disease.
"I've always been intrigued by hematology because it touches so many different organ systems," said Ebert. "And clonal hematopoiesis is definitely an example of that — when blood cells act abnormally, we're learning that they can cause, or even counteract, disease in a variety of ways."
Examining Clonal Hematopoiesis in Current Patients
The notion of CH grew from an effort to identify early, pre-malignant states in blood cells. Now, researchers at Dana-Farber and elsewhere are working to understand how that precursor condition unfolds, particularly in people who already have cancer.
"We know that clonal hematopoiesis is common in patients without cancer — but it's also common in patients with cancer, like breast cancer, lung cancer, multiple myeloma, and others," said Adam Sperling, MD, PhD, a hematologist and medical oncologist at Dana-Farber. "We also know that when those cancer patients receive chemotherapy, the risk of their CH evolving into leukemia goes up."
Sperling, who trained as a postdoctoral fellow in Ebert's lab and now runs his own lab at Brigham and Women's Hospital, is working to unravel the mechanisms by which cancer treatment drives the progression of CH into full-blown leukemia. Sperling and his colleagues published a study last year examining patients with advanced forms of multiple myeloma and non-Hodgkin's lymphoma. These patients typically receive extended chemotherapy treatment and often a stem cell transplant. "Whereas about 5 to 10% of the general population has CH, it's much higher in the group we examined — almost 50%."
Ultimately, the goal is to identify protective measures that can prevent or halt the evolution of CH into leukemia. "I see patients with multiple myeloma who have developed leukemia as a result of our therapy, and it's such a devastating complication," Sperling says. "Figuring out how to avoid that is a pressing need."
His team is also exploring CH from another angle: How does the biology of this precursor state influence an individual's risk of developing non-blood cancers? And if tumors do emerge, how does the body respond to them? Do patients with CH respond better — or worse — to cancer treatments than those without CH?
That latter question has formed the basis of several investigations by Sperling as well as other Dana-Farber researchers. In one study, Sperling examined how CH affects the response to CAR T-cell therapy, a form of treatment in which patients' own T-cells are engineered to more aggressively attack their tumors. Patients with advanced forms of multiple myeloma or non-Hodgkin's lymphoma seemed to respond better to CAR T-cell therapy if they also had CH.
"There may be other scenarios like this one where CH is beneficial," said Sperling. "If we can learn more about why that is, then we can then devise ways to harness the biology and make therapies more effective, regardless of whether patients have CH or not."
The Link Between Clonal Hematopoiesis and Stem Cell Transplant
Dana-Farber scientists have been studying CH in another important context — allogeneic hematopoietic cell transplants (HCTs), in which blood stem cells are harvested from a healthy donor and infused into a patient whose own stem cells have been eliminated using high-dose chemotherapy. This approach is often used to treat leukemia as well as other blood cancers.
About five years ago, Dana-Farber medical oncologists Christopher Gibson, MD, and Coleman Lindsley, MD, PhD, also former trainees of Ebert, sought to answer a fundamental question: Could HCT donors with CH transfer the pre-malignant condition to transplant recipients? In a proof-of-concept study involving over 500 transplants at Dana-Farber, they found their answer: Yes. In addition, they recognized that this scenario — commonly referred to as "donor CH"— was particularly common in recipients who developed low blood cell counts after their transplant.
"We then undertook a larger study to ask not just does donor CH happen, but how prevalent is it and what are the clinical consequences," said Lindsley, who is also an assistant professor at Harvard Medical School. In collaboration with a team at Johns Hopkins, the researchers analyzed over 1,700 stem cell transplants in which the donor was age 40 or older.
Two remarkable discoveries emerged. First, CH is common, present in about 25% of donors. In addition, the most common form of CH — resulting from mutations in the DNMT3A gene — is associated with improved transplant outcomes, including better survival and decreased rates of relapse. These cases did coincide with increased rates of a well-known complication of HCT, known as graft-versus-host disease, in which the donor's immune cells attack the recipient's cells.
"Reduced relapse and increased graft-versus-host disease are two sides of the same coin, because it's all a function of immune activation of the donor cells," said Gibson. "With CH, you seem to get more immune activation of the donor cells and therefore more activity against the malignancy after transplant, which means less risk of relapse, but the trade-off is you get some more graft-versus-host disease."
Lindsley added, "In other words, we believe the same altered inflammatory functions that result from CH and cause pathology in the aging population are actually essential for the positive functions in stem cell transplants."
Identifying Risk for Clonal Hematopoiesis
The flurry of research over the last several years to characterize CH and its myriad biological and clinical ramifications has carved a path for a new field — one that aims to not only detect blood cancers early, when CH is evident, but also to intervene and improve patient outcomes.
Dana-Farber medical oncologist Lachelle Weeks, MD, PhD, is one of the researchers pioneering this effort. As a postdoctoral researcher in Ebert's lab, she is developing ways to predict which patients with CH are at highest risk for progression to leukemia.
We're creating a tool that takes into account a variety of factors – including a patient's age, the genetic mutations they have, and whether or not they have low blood counts – and determines whether the person is at high, intermediate, or low risk for progression.
"We're creating a tool that takes into account a variety of factors – including a patient's age, the genetic mutations they have, and whether or not they have low blood counts – and determines whether the person is at high, intermediate, or low risk for progression," said Weeks. "This is something we've needed in the CH space for a long time, and I think it's going to be very helpful both in terms of caring for patients and also enabling clinical trials to test interventions for those patients who are at highest risk."
Together with researchers at Memorial Sloan Kettering, Johns Hopkins, and MD Anderson Cancer Center, Weeks and her colleagues are planning to launch such a trial in early 2023 for patients with clonal cytopenia of uncertain significance (CCUS), a term used to describe CH in patients who also have low numbers of blood cells. The study will test whether existing chemotherapy regimens, when administered at much lower doses and shorter durations than used for cancer patients, can delay or prevent the emergence of leukemia in CCUS patients.
Weeks also cares for patients who have CH and CCUS in Dana Farber's Center for Early Detection and Interception of Blood Cancers (formerly Center for Prevention of Progression), a unique clinic for patients with precursor conditions that can give rise to leukemia and other forms of blood cancer. Because there are no clinical interventions yet proven to improve outcomes for patients with CH, doctors do not recommend systematic screening for the condition. Most CH goes undiagnosed, but as blood sequencing becomes more commonly used to diagnose other conditions, the number of CH patients referred to the clinic is steadily increasing.
"Patients with CH should have the opportunity to discuss the condition with specialists who can help them understand their individual risk for leukemia, heart disease, and other conditions related to CH," said Weeks.
Finding effective therapeutics is now a major focus for the burgeoning field.
Ebert said, "Our goal now is really two-fold. We are working to identify the individuals with CH who are at greatest risk and to uncover therapeutic approaches that will significantly decrease that risk — whether that risk is attributed to cancer, heart disease, or another CH-driven disease."