Abstract 3352: A CRISPR-enabled function genomics profiling platform in acute leukemia: Updates from a pilot study of Function (Fx) Heme utilizing fresh patient samples
Authors: Dykes Kaitlyn C. , Tan Tuyet R. , Hodel Karl , Tran Kathleen , Meyers Maci , Hagmann Leonardo , Baltay Michele , Kilfeather Peter , Li Yali , Schmedt Christian , Sampath Srinath , Sampath Srihari , Tanaka Tiffany N. , Corbel Stephane 
Published: March 2024

Introduction: In this study we utilized a novel primary cell CRISPR/Cas9 profiling approach to identify gene dependencies in fresh acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL) patient samples. The primary aim of this prospective study was to demonstrate the feasibility of the CRISPR-based personalized functional genomic testing with fresh patient samples in the clinical setting.

Methods: AML and ALL patient peripheral blood samples (10-16 mL) were obtained at time of initial diagnosis and/or at relapse, and if feasible post-treatment. Primary cells were transduced with lentivirus harboring Cas9 enzyme and a ‘drug targets’ sgRNA panel. Transduced cells were harvested at early (input) and Day 8 timepoints, and sgRNA distribution was assessed by amplicon sequencing of DNA barcodes. Changes in barcode abundance were quantitated and aggregated to calculate gene-level phenotype scores, enabling identification of gene dependencies.

Results: 37 patients were included in the study, 23 with AML, 9 with Philadelphia (Ph) (+) ALL, 5 with Ph (-) ALL. The majority of patients had adverse or poor risk disease. The average age of patients was 52.6, range 18-84. 23 were male, 14 female; 20 identified as white, 17 as other. 20 patients were sampled at initial diagnosis, 12 were sampled at time of relapse and 5 at time of refractory disease. Serial samples were collected from 9 patients. 34 patients received treatment following sample collection. The majority of patients received intensive chemotherapy or a hypomethylating agent with venetoclax, however 15 patients received some form of targeted therapy. At the time of the abstract submission, Fx Heme results were available for 23 patients and among these, we identified potential treatment targets in 10 samples (43%). Importantly, 60% of the positive samples have a dependency on a gene clinically targetable by an approved leukemia drug. In addition, our profiling platform enabled the discovery of novel druggable dependencies in 100% of the positive samples.

Conclusions: With this pilot study we demonstrated that utilizing small volume fresh patient samples to assess CRISPR-defined gene dependencies on targeted therapies in AML and ALL is feasible, timely, and results in clear Fx Heme dependency gene output. Our data indicates that CRISPR-based comprehensive functional profiling has the potential to add valuable information beyond traditional NGS methods to determine the optimal therapy for patients with AML and ALL. Future directions include translating further into the clinical setting and correlating Fx Heme dependence with response to targeted treatment in acute leukemia patients.

Citation Format: Kaitlyn C. Dykes, Tuyet R. Tan, Karl Hodel, Kathleen Tran, Maci Meyers, Leonardo Hagmann, Michele Baltay, Peter Kilfeather, Yali Li, Christian Schmedt, Srinath Sampath, Srihari Sampath, Tiffany N. Tanaka, Stephane Corbel. A CRISPR-enabled function genomics profiling platform in acute leukemia: Updates from a pilot study of Function (Fx) Heme utilizing fresh patient samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3352.