Researchers from Penn Medicine and Children’s Hospital of Philadelphia (CHOP) have developed a CRISPR-based platform that can identify the genetic drivers of acute myeloid leukemia (AML) directly in patient cells. This new approach, described as the first of its kind, enables scientists to see how individual cancer cells respond to genetic changes, potentially leading to more precise drug targets and better understanding of treatment resistance.
Traditionally, CRISPR genome-editing tools have been used on preclinical models or long-established cancer cell lines. These models do not fully capture the genetic diversity found in actual patients. The research team aimed to apply these tools directly to tumor samples from patients with AML—a disease that accounts for about one-third of adult leukemias and is the second most common blood cancer among children in the United States.
The researchers improved methods for delivering CRISPR components into primary leukemia cells using optimized viral vectors. This allowed them to efficiently introduce gene edits into patient-derived AML cells and simultaneously test hundreds of genes for their impact on cancer growth and survival. They validated their findings both in laboratory settings and in preclinical models using transplanted patient-derived leukemia cells.
“This platform empowers scientists to test which genes and genetic elements really matter in human tumors,” said Junwei Shi, PhD, lead author of the study and associate professor at the Perelman School of Medicine at the University of Pennsylvania. “It helps identify drug-ready targets, shows how different tumor subpopulations within the same patient respond and speeds discovery of precision therapies.”
Single-gene edits were successful in about 86 percent of patient samples tested, while high-throughput screening worked in approximately 73 percent. The study confirmed many known leukemia “dependency” genes and uncovered vulnerabilities present only in certain patients or subtypes.
To further understand how edited genes affect cancer behavior, researchers combined CRISPR editing with single-cell RNA sequencing. This allowed them to observe diverse responses among different cell populations within each sample.
“We have learned that most leukemias are heterogeneous and may contain small subgroups of cells that may ultimately drive poor outcomes,” said Kai Tan, PhD, senior study author and professor at CHOP’s department of Pediatrics. “This clarified the results and revealed surprises. We validated previously reported genes that affect leukemia growth but also found that some edits caused cells to die while others halted growth and induced a dormant, therapy resistant state. These insights will help prioritize the best candidate genes for therapy development.”
The team plans to expand this work by studying other difficult-to-treat leukemias such as pediatric AML.
“Our hope is that this novel platform will identify new ways of developing precision therapies for patients who do not currently have promising options,” said Kathrin M. Bernt, MD, senior study author and pediatric oncologist at CHOP’s Cancer Center Leukemia and Lymphoma Program.
Funding for this research came from several sources including St. Jude Children’s Research Hospital Collaborative Research Consortium on Novel Therapies for Sickle Cell Disease; Mark Foundation for Cancer Research; FDA; Pediatric High-Risk Cancer Preclinical Model Resource; National Institutes of Health grants U54CA283759, CA226187, CA243072, CA233285, CA201230; and CA258904.
