Penn Medicine and Children’s Hospital of Philadelphia launch first CRISPR-based platform to pinpoint drivers of acute myeloid leukemia in patient cells

A new CRISPR-based tool that is directly used on patients’ cancer cells can identify genes and regulatory elements driving acute myeloid leukemia (AML), an aggressive blood cancer affecting the bone marrow and blood. This first-of-its-kind approach reveals how individual patient cells respond to genetic changes and makes it easier to identify drug targets and understand why some cancers stop responding to treatment. The findings were published today in Molecular Cell, by researchers from Penn Medicine and Children’s Hospital of Philadelphia (CHOP).

CRISPR genome-editing tools allow researchers to quickly test hundreds of genes at the same time to determine which ones are important for cancer growth and survival. These genetic toolkits have enabled the discovery and validation of new cancer drug targets. Until now, this approach has mostly been used in preclinical models or in long-established cancer cell lines grown in labs. These models do not fully represent the genetic diversity seen in patients. Researchers sought to apply CRISPR tools on heterogeneous tumor samples from patients to better understand which genetic elements cancer cells depend on and how they would respond to treatment.

AML accounts for about one in three leukemias in adults and is the second most common blood cancer in children in the U.S. While chemotherapy puts many patients with AML into remission, for those whose cancer does not respond to treatment or who experience relapse, treatment can be challenging, often due to certain gene or chromosome changes in the leukemia cells. This research aims to address that challenge. Because the new tool works on patient samples, the researchers hope it could one day be used not just as a research tool, but in the clinical setting to better prioritize treatment options based on each patient’s cancer’s unique biology.

New CRISPR platform provides more details, faster

In this study, the team developed a more efficient way to deliver CRISPR tools into AML cells taken from patients. They optimized viral vectors and delivery methods to introduce CRISPR components directly into primary leukemia cells, achieving high gene-editing efficiency. Using this platform, the team screened hundreds of gene edits simultaneously to find edits that reduced or increased cell growth, indicating genes that affect cancer survival. They tested edits both in vitro and in preclinical models using transplanted patient-derived leukemia cells to validate the findings.

“This platform empowers scientists to test which genes and genetic elements really matter in human tumors,” said Junwei Shi, PhD, the study’s lead author, and an associate professor of Cancer Biology in 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.”

Most patient samples were suitable for single-target evaluation: single-gene edits succeeded in about 86 percent of samples, and high-throughput screening of multiple genes worked in about 73 percent. The researchers also confirmed many known leukemia "dependency" genes and found vulnerabilities that show up only in some patients or subtypes.

For deeper insight, the team combined CRISPR edits with single-cell RNA sequencing. This approach highlighted how each cell responded with cell changes in its gene activity, cell state, and behavior. Combining CRISPR with single cell RNA sequencing captured the heterogeneous responses of different cells within the leukemia.

Findings could inform future AML therapy development

“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, a senior study author and a professor in the department of Pediatrics at CHOP. “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 research team plans to tackle other hard-to-treat leukemias next, including 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, a senior study author and a pediatric oncologist in the Cancer Center's Leukemia and Lymphoma Program at CHOP.

This work was supported by the St. Jude Children’s Research Hospital Collaborative Research Consortium on Novel Therapies for Sickle Cell Disease and the Mark Foundation for Cancer Research. Additional support was provided by FDA (75F40121C00137), “Pediatric High-Risk Cancer Preclinical Model Resource, National Institutes of Health of United States of America grants (U54CA283759), (CA226187), (CA243072), (CA233285), (CA201230) and (CA258904).