Researchers at Children’s Hospital of Philadelphia (CHOP) have identified a gene signature that distinguishes a high-risk subtype of acute lymphoblastic leukemia (ALL) associated with increased relapse rates. The study, published in Nature Cancer, utilized single-cell sequencing to analyze over 595,000 immature blood cells, revealing a specific subpopulation linked to treatment resistance.
Identifying the High-Risk Subtype
The research team focused on understanding the cellular and genetic factors contributing to treatment resistance and relapse in T-cell acute lymphoblastic leukemia (T-ALL). By employing single-cell sequencing, they pinpointed a subpopulation of bone marrow progenitor-like (BMP-like) T-ALL cells associated with poor survival rates. This BMP-like signature was previously undetected by bulk analysis methods.
“Generally, cancers like leukemia get stuck along a differentiation path, meaning that the blasts do not go on and form normal blood cells,” explained Kai Tan, PhD, a professor in the Department of Pediatrics and an investigator in the Center for Childhood Cancer Research at CHOP. “By using this technique and comparing cancerous cells to healthy control donor samples, single cell sequencing helped us identify which cells result in these high-risk cancers.”
Potential Therapeutic Intervention
Upon identifying the gene signature, the researchers conducted in silico and in vitro drug screenings to find potential therapies targeting these high-risk cells. Venetoclax, an FDA-approved drug for other forms of leukemia and lymphoma, demonstrated effectiveness in targeting the BMP-like cells. The team plans to initiate a clinical trial to evaluate venetoclax's efficacy in patients with the identified gene signature, particularly those with relapsed or refractory disease.
Clinical Significance
Acute lymphoblastic leukemia accounts for approximately 30% of pediatric cancers, making it the most common cancer in children. While modern therapies have improved outcomes, a significant percentage of patients still relapse, especially those with T-ALL. Identifying specific subtypes and therapeutic options is crucial for patients who relapse and have limited treatment alternatives.
“One of the major challenges in treating T-ALL is that we know certain drugs work for some patients who relapse, but these drugs are not effective for all patients who relapse. Identifying the patients who may benefit from new therapies is critical,” said David T. Teachey, MD, co-leader of the Immune Dysregulation Frontier Program at CHOP. “By identifying more gene signatures like what we describe in this study, we will have a much better idea of which therapeutic agents are most likely to help specific subsets of patients, which is the goal of precision medicine.”
