Tagmentation-based Analysis Reveals the Clonal Behavior of CAR-T Cells in Association with Lentivector Integration Sites

Overview

Journal Mol Ther Oncolytics

Publisher Cell Press

Date 2023 Jun 26

PMID 37360944

Authors

Jaeryuk Kim

Miyoung Park

Gyungwon Baek

Joo-Il Kim

Euna Kwon

Byeong-Cheol Kang

Jong-Il Kim

Hyoung Jin Kang

Affiliations

Soon will be listed here.

Abstract

Integration site (IS) analysis is essential in ensuring safety and efficacy of gene therapies when integrating vectors are used. Although clinical trials of gene therapy are rapidly increasing, current methods have limited use in clinical settings because of their lengthy protocols. Here, we describe a novel genome-wide IS analysis method, "detection of the integration sites in a time-efficient manner, quantifying clonal size using tagmentation sequencing" (DIStinct-seq). In DIStinct-seq, a bead-linked Tn5 transposome is used, allowing the sequencing library to be prepared within a single day. We validated the quantification performance of DIStinct-seq for measuring clonal size with clones of known IS. Using chimeric antigen receptor (CAR)-T cells, we revealed the characteristics of lentiviral IS. We then applied it to CAR-T cells collected at various times from tumor-engrafted mice, detecting 1,034-6,233 IS. Notably, we observed that the highly expanded clones had a higher integration frequency in the transcription units and vice versa in genomic safe harbors (GSH). Also, in GSH, persistent clones had more frequent IS. Together with these findings, the new IS analysis method will help to improve the safety and efficacy of gene therapies.

Citing Articles

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