CHOP and Penn Medicine Develop First CRISPR Platform for Direct Analysis of Patient AML Cells
核心洞察
Researchers from Children's Hospital of Philadelphia and Penn Medicine have created the first CRISPR (搜索)-based platform that works directly on patient acute myeloid leukemia cells to identify cancer-driving genes.
The platform achieved 86% success rate for single-gene edits and 73% for high-throughput screening across patient samples, revealing new therapeutic vulnerabilities.
Combined with single-cell RNA sequencing, the tool uncovered that some genetic edits cause cell death while others induce therapy-resistant dormant states.
Researchers from Children's Hospital of Philadelphia (CHOP) and the Perelman School of Medicine at the University of Pennsylvania have developed the first CRISPR (搜索)-based platform capable of identifying genes and regulatory elements driving acute myeloid leukemia (AML) directly in patient cancer cells. The findings, published in Molecular Cell, represent a significant advancement in precision oncology that could transform how clinicians approach treatment for this aggressive blood cancer.
The breakthrough addresses a critical limitation in cancer research. While CRISPR (搜索) genome-editing tools have enabled researchers to test hundreds of genes simultaneously to determine their importance for cancer growth and survival, these approaches have primarily relied on preclinical models or established cancer cell lines that do not fully represent the genetic diversity seen in patients.
Platform Achieves High Success Rates in Patient Samples
The research team developed an optimized delivery system using viral vectors to introduce CRISPR (搜索) components directly into primary leukemia cells from patients, achieving high gene-editing efficiency. The platform demonstrated robust performance across patient samples, with single-gene edits succeeding in approximately 86% of samples and high-throughput screening of multiple genes working in about 73% of cases.
"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 associate professor of Cancer Biology at Penn Medicine. "It helps identify drug-ready targets, shows how different tumor subpopulations within the same patient respond and speeds discovery of precision therapies."
Using this platform, the team screened hundreds of gene edits simultaneously to identify modifications that reduced or increased cell growth, indicating genes that affect cancer survival. They validated findings both in vitro and in preclinical models using transplanted patient-derived leukemia cells.
Single-Cell Analysis Reveals Therapeutic Insights
The researchers combined CRISPR (搜索) edits with single-cell RNA sequencing to gain deeper insights into cellular responses. This approach revealed how individual cells responded with changes in gene activity, cell state, and behavior, capturing the heterogeneous responses of different cells within the leukemia.
The analysis yielded unexpected findings about cellular responses to genetic modifications. "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," said Kai Tan, PhD, a senior study author and professor in the Department of Pediatrics at CHOP. "These insights will help prioritize the best candidate genes for therapy development."
Addressing Critical Medical Need
AML accounts for approximately one in three leukemias in adults and represents the second most common blood cancer in children in the United States. While chemotherapy achieves remission in many patients, those whose cancer does not respond to treatment or who experience relapse face significant challenges, often due to specific gene or chromosome changes in leukemia cells.
The researchers confirmed many known leukemia "dependency" genes and identified vulnerabilities that appear only in certain patients or subtypes. This heterogeneity insight is particularly valuable given that most leukemias contain small subgroups of cells that may ultimately drive poor outcomes.
Clinical Translation Potential
Because the platform works directly on patient samples, researchers envision its eventual use in clinical settings to prioritize treatment options based on each patient's unique cancer biology. "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 pediatric oncologist in the Cancer Center's Leukemia and Lymphoma Program at CHOP.
The research team plans to extend their approach to other hard-to-treat leukemias, including pediatric AML. The work was supported by multiple funding sources, including the St. Jude Children's Research Hospital Collaborative Research Consortium on Novel Therapies for Sickle Cell Disease, the Mark Foundation for Cancer Research, and various National Institutes of Health grants.