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Dynamic single-cell RNA sequencing identifies immunotherapy persister cells following PD-1 blockade.

Sehgal, Kartik, Portell, Andrew, Ivanova, Elena, Lizotte, Patrick, Mahadevan, Navin R., Greene, Jonathan R., Vajdi, Amir, Gurjao, Carino, Teceno, Tyler, Taus, Luke J., Thai, Tran C., Kitajima, Shunsuke, Liu, Derek, Tani, Tetsuo, Noureddine, Moataz, Lau, Christie J., Kirschmeier, Paul T., Liu, David, Giannakis, Marios, Jenkins, Russell W., Gokhale, Prafulla C., Goldoni, Silvia, Pinzon-Ortiz, Maria, Hastings, Bill, Hammerman, Peter, Miret, Juan J., Paweletz, Cloud P. and Barbie, David A. (2021) Dynamic single-cell RNA sequencing identifies immunotherapy persister cells following PD-1 blockade. The Journal of clinical investigation, 131 (2). ISSN 1558-8238


Resistance to oncogene-targeted therapies involves discrete drug-tolerant persister cells, originally discovered through in vitro assays. Whether a similar phenomenon limits efficacy of programmed cell death 1 (PD-1) blockade is poorly understood. Here, we performed dynamic single-cell RNA-Seq of murine organotypic tumor spheroids undergoing PD-1 blockade, identifying a discrete subpopulation of immunotherapy persister cells (IPCs) that resisted CD8+ T cell-mediated killing. These cells expressed Snai1 and stem cell antigen 1 (Sca-1) and exhibited hybrid epithelial-mesenchymal features characteristic of a stem cell-like state. IPCs were expanded by IL-6 but were vulnerable to TNF-α-induced cytotoxicity, relying on baculoviral IAP repeat-containing protein 2 (Birc2) and Birc3 as survival factors. Combining PD-1 blockade with Birc2/3 antagonism in mice reduced IPCs and enhanced tumor cell killing in vivo, resulting in durable responsiveness that matched TNF cytotoxicity thresholds in vitro. Together, these data demonstrate the power of high-resolution functional ex vivo profiling to uncover fundamental mechanisms of immune escape from durable anti-PD-1 responses, while identifying IPCs as a cancer cell subpopulation targetable by specific therapeutic combinations.

Item Type: Article
Keywords: Animals Cell Line, Tumor Immunotherapy Mice Neoplasm Proteins Neoplasms, Experimental Programmed Cell Death 1 Receptor RNA-Seq Single-Cell Analysis Spheroids, Cellular
Date Deposited: 28 Oct 2022 00:45
Last Modified: 28 Oct 2022 00:45