Chimeric Antigen Receptor T Cell Integration Site Analysis in Patients with B-cell Acute Lymphoblastic Leukemia
When CAR T cells fail to effectively treat a patient, there is often minimal CAR T cell proliferation. The site of CAR T vector integration has been identified as potentially influential in both CAR T proliferation and, thus, outcomes of CAR T treatment. EpiVIA is an existing computational tool that detects vector integration sites and a cell’s epigenetic landscape by analyzing data from ATAC-seq. In a novel application of EpiVIA we used it on in-house pediatric B-cell ALL sequencing data and performed downstream analyses. Integration sites were identified in CAR T cells right after being manufactured and in samples taken from patients several years after treatment. Computational metrics of EpiVIA were assessed as well. We sought to determine if EpiVIA could be used to elucidate patterns or identify factors that are associated with relapse. We found no overlap in integration sites between the post-manufacturer and long-term samples, and little correlation between expression-based clusters and cells with integration sites. While EpiVIA is a computationally efficient tool, as it runs in linear time, it lacks the sensitivity to detect enough integration sites to draw sufficient conclusions about the integration site’s role in the proliferative abilities, durability, and overall epigenetic profile of CAR T cells.
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