Journal Article

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

Greene, Jonathan R., Hastings, William D., Miret, Juan J., Liu, Derek, Kirschmeier, Paul T., Liu, David, Tani, Tetsuo, Gokhale, Prafulla C., Paweletz, Cloud P., Gurjao, Carino, Sehgal, Kartik, Lau, Christie J., Kitajima, Shunsuke, Teceno, Tyler, Mahadevan, Navin R., Thai, Tran C., Goldoni, Silvia, Noureddine, Moataz, Giannakis, Marios, Portell, Andrew, Taus, Luke J., Lizotte, Patrick H., Ivanova, Elena V., Vajdi, Amir, Barbie, David A., Jenkins, Russell W., Hammerman, Peter S., Pinzon-Ortiz, Maria

2021

Overview

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.

• Publisher: American Society for Clinical Investigation
• Subject: Animals / Antagonism / Apoptosis / Biomedical research / Cancer / Cancer cells / Carcinogenesis / Care and treatment / CD8 antigen / Cell death / Cell Line, Tumor / Collagen / Cytokines / Cytotoxicity / Drug resistance / Gene expression / IAP protein / Identification and classification / Immunotherapy / Interleukin 6 / Lymphocytes / Lymphocytes T / Mesenchyme / Mice / Neoplasm Proteins - genetics / Neoplasm Proteins - immunology / Neoplasms, Experimental - genetics / Neoplasms, Experimental - immunology / Neoplasms, Experimental - therapy / Oncology, Experimental / PD-1 protein / Programmed Cell Death 1 Receptor - antagonists & inhibitors / Programmed Cell Death 1 Receptor - genetics / Programmed Cell Death 1 Receptor - immunology / RNA sequencing / RNA-Seq / Single-Cell Analysis / Snail protein / Spheroids / Spheroids, Cellular - immunology / Spheroids, Cellular - pathology / Stem cell antigen 1 / Stem cells / Tumor necrosis factor-α / Tumors