Esoe, D.-P. | Search bioRxiv

bioRxiv2025

Single-cell profiling of EZH2-mediated immune signaling perturbations in NSCLC

Lung cancer, the leading cause of cancer-related death in the United States, remains a significant public health burden. One of the most personalized treatments to date uses a patients own tumor-infiltrating lymphocytes (TILs) as a cellular therapy to target the tumor. Endogenous TIL activity is also essential for immune checkpoint inhibitor (ICI) effectiveness. However, responses to immunotherapies vary due to immune-suppressive tumor microenvironments (TMEs) and limited antigen presentation. In this study, we computationally examine cell-cell signaling and transcriptional activity using single-cell RNA sequencing of lung cancer treated by inhibiting methyltransferase EZH2. We show that EZH2 inhibition shifts the TME to immunogenic signaling patterns conducive to increased T cell response, including antigen presentation and homing. T cells also showed more stem-like phenotypes. Importantly, inferred EZH2 activity showed it can still perform non-methyltransferase duties that are vital for T cell differentiation. Lastly, we tested our findings with patient-derived NSCLC TILs and found that transient EZH1/2 inhibition with valemetostat prior to harvest increases the CD8:CD4 ratio and T cell reactivity, but preferentially expands effector memory rather than central memory populations. These results indicate that transitory EZH2 inhibition could improve immunotherapies for lung cancer patients, with additional optimization needed to maximize TIL therapeutic benefit.

bioinformatics↗

bioRxiv2024

Methionine Restriction Reduces Lung Cancer Progression and Increases Chemotherapy Response

Targeting tumor metabolism through dietary interventions is an area of growing interest, and may help to improve the significant mortality of aggressive cancers, including non-small cell lung cancer (NSCLC). Here we show that the restriction of methionine in the aggressive KRAS/Lkb1-mutant NSCLC autochthonous mouse model drives decreased tumor progression and increased carboplatin treatment efficacy. Importantly, methionine restriction during early stages of tumorigenesis prevents the lineage switching known to occur in the model, and alters the tumor immune microenvironment (TIME) to have fewer tumor-infiltrating neutrophils. Mechanistically, mutations in LKB1 are linked to anti-oxidant production through changes to cystathionine-{beta}-synthase (CBS) expression. Human cell lines with rescued LKB1 show increased CBS levels and resistance to carboplatin, which can be partially rescued by methionine restriction. Furthermore, LKB1 rescued cells, but not mutant cells, show less G2- M arrest and apoptosis in high methionine conditions. Knock-down of CBS sensitized both LKB1 mutant and non-mutated lines to carboplatin, again rescuing the carboplatin resistance of the LKB1 rescued lines. Given that immunotherapy is commonly combined with chemotherapy for NSCLC, we next wanted to understand if T cells are impaired by MR. Therefore, we examined the ability of T cells from MR and control tumor bearing mice to proliferate in culture and found that T cells from MR treated mice had no defects in proliferation, even though we continued the MR conditions ex vivo. We also identified that CBS is most highly correlated with smoking, adenocarcinomas with alveolar and bronchiolar features, and adenosquamous cell carcinomas, implicating its roles in oxidative stress response and lineage fate in human tumors. Taken together, we have shown the importance of MR as a dietary intervention to slow tumor growth and improve treatment outcomes for NSCLC.

cancer biology↗