Antisense transcription from lentiviral gene targeting linked to an integrated stress response in colorectal cancer cells

Taekyu Ha; Michael DiPrima; Vishal Koparde; Parthav Jailwala; Hidetaka Ohnuki; Jing-Xin Feng; Murali Palangat; Daniel Larson; Giovanna Tosato

doi:10.1016/j.omtn.2022.05.029

Antisense transcription from lentiviral gene targeting linked to an integrated stress response in colorectal cancer cells

Mol Ther Nucleic Acids. 2022 May 18:28:877-891. doi: 10.1016/j.omtn.2022.05.029. eCollection 2022 Jun 14.

Authors

Taekyu Ha¹, Michael DiPrima¹, Vishal Koparde^{2

3}, Parthav Jailwala^{2

3}, Hidetaka Ohnuki¹, Jing-Xin Feng¹, Murali Palangat⁴, Daniel Larson⁴, Giovanna Tosato¹

Affiliations

¹ Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA.
² CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
³ Advanced Biomedical Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA.
⁴ Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

Abstract

Advances in gene therapy research have resulted in the successful development of new therapies for clinical use. Here, we explored a gene targeting approach to deplete ephrinB2 from colorectal cancer cells using an inducible lentiviral vector. EphrinB2, a transmembrane ephrin ligand, promotes colorectal cancer cell growth and viability and predicts poor patient survival when expressed at high levels in colorectal cancer tissues. We discovered that lentiviral vector integration and expression in the host DNA frequently drive divergent host gene transcription, generating antisense reads coupled with splicing events and generation of chimeric vector/host transcripts. Antisense transcription of host DNA was linked to development of an integrated stress response and cell death. Despite recent successes, off-target effects remain a concern in genetic medicine. Our results provide evidence that divergent gene transcription is a previously unrecognized off-target effect of lentiviral vector integration with built-in properties for regulation of gene expression.

Keywords: MT: Oligonucleotides; Therapies and Applications; antisense reads; colorectal cancer; ephrinB2; gene therapy; integrated stress response; lentiviral vector; shRNA; vector integration.