Background: Brain metastasis (BrM) has been a challenge for lung cancer treatment, but the mechanisms underlying lung cancer BrM remain elusive. This study aims to dissect cellular components and their spatial distribution in human BrM tumors of lung adenocarcinoma (LUAD) and identify potential therapeutic targets. Methods: We performed single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) on three LUAD BrMs, and validated our findings using public scRNA-seq data of 10 LUAD BrMs. Western blotting, quantitative real-time polymerase chain reaction (qRT-PCR) and functional experiments were employed for experimental studies. Results: By combining scRNA-seq and ST, our analysis revealed the inter- and intra-tumoral heterogeneity of cellular components and their spatial localization within LUAD BrMs. Through RNA velocity and transcription factor (TF) regulatory activity analyses, we identified ATF3 as a potential regulator of the mesenchymal-epithelial transition (MET) program, which plays crucial roles in the colonization of tumor cells at metastatic sites. Furthermore, we demonstrated that knockdown of ATF3 significantly inhibited cancer cell proliferation while promoting cancer cell migration. Mechanistically, ATF3 knockdown could reverse the MET program. Additionally, we revealed that LGALS3/ANXA2-mediated cell-cell interaction between macrophage and tumor cells may also promote the MET program. Conclusions: Our study provides a single-cell atlas of the cellular composition in BrM of LUAD and identifies ATF3 as a potential therapeutic target for BrM treatment.

Most small cell lung cancers (SCLCs) exhibit low immunogenicity and intrinsic resistance to immunotherapy, yet the underlying mechanisms remain poorly understood. Here, we identify CREBBP loss, a frequent genetic alteration in SCLC, as a key suppressor of tumor cell-intrinsic immune responses that drives an immune-cold tumor microenvironment in Rb1/Trp53 -driven autochthonous mouse models. Consistently, Crebbp deletion promotes immune escape in syngeneic SCLC models. Mechanistically, Crebbp loss suppresses Sting and major histocompatibility complex class-I expression by reducing histone H3 acetylation. Notably, HDAC inhibition restores histone acetylation, reactivates these silenced genes, and induces tumor cell-intrinsic immune responses. Moreover, pharmacological HDAC inhibition synergizes with immune checkpoint blockade to suppress tumor growth in both Crebbp -mutant and Crebbp -wild-type SCLCs, with a more prominent effect in Crebbp -mutant tumors. Collectively, these findings establish CREBBP loss as a key mechanism of immune evasion and immunotherapy resistance in SCLC, highlighting HDAC inhibition as a promising strategy to enhance immunotherapy efficacy.

Background: Small cell lung cancer (SCLC) is an aggressive neuroendocrine tumor characterized by an intrinsic resistance to immunotherapy, primarily due to its low immunogenicity and immune-cold tumor microenvironment. The mechanisms underlying this resistance remain poorly understood. Methods: A systematic screen of 796 epigenetic regulators was performed to identify candidate genes associated with effector CD8⁺ T cell infiltration and clinical outcomes following chemoimmunotherapy in SCLC. This analysis integrated several public SCLC datasets, including single-cell RNA sequencing (scRNA-seq) data from 20 SCLC tumors, bulk RNA-seq data from the IMpower133 cohort, proteomic profiles from the TU-SCLC cohort, and an independent scRNA-seq dataset of 39 SCLC tumors. In vitro and in vivo functional experiments were conducted to investigate the role of the candidate genes in SCLC. Results: The epigenetic regulator TAF1 emerged as a key candidate, with its expression negatively correlating with effector CD8⁺ T cell infiltration in SCLC. Clinically, patients with low TAF1 expression in tumors showed better outcomes following atezolizumab-based chemoimmunotherapy, particularly in ASCL1-high tumors. Additionally, TAF1 expression was inversely correlated with MHC-I expression. Knockdown of TAF1 in SCLC cells restored MHC-I expression, suppressed tumor growth in immunocompetent mice, and increased CD8⁺ T cell infiltration. Conclusions: TAF1 functions as a potential epigenetic suppressor of MHC-I expression in SCLC. Targeting TAF1 may represent a promising therapeutic strategy to enhance immunotherapy efficacy in SCLC.