Jae-Won Cho¹, Seyeon Park², Gamin Kim³, Heonjong Han¹, Hyo Sup Shim⁴, Sunhye Shin³, Yong-Soo Bae⁵, Seong Yong Park^6,*, Sang-Jun Ha^2,*, Insuk Lee^1,* & Hye Ryun Kim^3,*

¹Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea. ²Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea. ³Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul 03722, Korea. ⁴Department of Pathology, Yonsei University College of Medicine, Seoul 03722, Korea. ⁵Department of Biological Sciences, Science Research Center (SRC) for Immune Research on Non-lymphoid Organ (CIRNO), Sungkyunkwan University, Jangan-gu, Suwon, Gyeonggi-do 16419, Korea. ⁶Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul 03722, Korea.

^*Corresponding author.

Patients with non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations exhibit an unfavorable response to PD-1 inhibitor through unclear mechanisms. Hypothesizing that EGFR mutations alter tumor-immune interactions, we compare tumor-infiltrating lymphocytes between EGFR mutant (EGFR-MT) and wild type (EGFR-WT) tumors through single-cell transcriptomic analysis. We find that B cells, CXCL13-producing follicular helper CD4⁺ T (T_FH)-like cells, and tissue-resident memory CD8⁺ T (T_RM)-like cells decreased in EGFR-MT tumors. The NOTCH-RBPJ regulatory network, which is vital for persistence of T_RM state, is perturbed, and the interactions between T_FH and B cells through the CXCL13-CXCR5 axis disappear in EGFR-MT tumors. Notably, the proportion of T_RM-like cells is predictive for anti-PD-1 response in NSCLC. Our findings suggest that the impairment of T_FH-B-T_RM cooperation in tertiary lymphoid structure formation, accompanied by the dysregulation of T_RM homeostasis and the loss of T_FH-B crosstalk, underlies unfavorable anti-PD-1 response in EGFR-MT lung tumors.