Establishment of ganglioside GD2-expressing extranodal NK/T-cell lymphoma cell line with scRNA-seq analysis

• Published in: Experimental hematology Vol. 130; p. 104132
• Main Authors: Sato, Shoko, Ishii, Midori, Tachibana, Kota, Furukawa, Yoshiki, Toyota, Tokuko, Kinoshita, Shintaro, Azusawa, Yoko, Ando, Jun, Ando, Miki
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Inc 01.02.2024
• ISSN: 0301-472X; 1873-2399
• DOI: 10.1016/j.exphem.2023.11.006

•A novel GD2+ extranodal NK/T-cell lymphoma cell line, ENKL-J1, was established.•GD2-CART cells exhibited robust cytotoxicity for ENKL-J1 cells in vitro and in vivo.•scRNA-seq analysis in ENKL-J1 cells uncovered therapeutic targets.•Eprenetapopt, tazemetostat, and vorinostat induced apoptosis in ENKL-J1 in vitro.•In vivo efficacy of eprenetapopt against ENKL-J1 was also demonstrated. Extranodal natural killer (NK)/T-cell lymphoma, nasal type (ENKL), is characterized by Epstein-Barr virus infection and poor prognosis. We established a novel cell line, ENKL-J1, from bone marrow cells of an ENKL patient. We found that ENKL-J1 cells express the ganglioside GD2 (GD2) and that GD2-directed chimeric antigen receptor T cells exhibit cytotoxicity against ENKL-J1 cells, indicating that GD2 would be a suitable target of GD2-expressing ENKL cells. Targeted next-generation sequencing revealed TP53 and TET2 variants in ENKL-J1 cells. Furthermore, single-cell RNA sequencing in ENKL-J1 cells showed high gene-expression levels in the oncogenic signaling pathways JAK-STAT, NF-κB, and MAPK. Genes related to multidrug resistance (ABCC1), tumor suppression (ATG5, CRYBG1, FOXO3, TP53, MGA), anti-apoptosis (BCL2, BCL2L1), immune checkpoints (CD274, CD47), and epigenetic regulation (DDX3X, EZH2, HDAC2/3) also were expressed at high levels. The molecular targeting agents eprenetapopt, tazemetostat, and vorinostat efficiently induced apoptosis in ENKL-J1 cells in vitro. Furthermore, GD2-directed chimeric antigen receptor T cells showed cytotoxicity against ENKL-J1 cells in vivo. These findings not only contribute to understanding the molecular and genomic characteristics of ENKL; they also suggest new treatment options for patients with advanced or relapsed ENKL.