Defining neural molecular features and their functional significance in lung cancer

Background: Lung cancer remains the leading cause of cancer-related mortality, accounting for over 150,000 deaths annually in the US. Although genomic characterization and immunotherapy have significantly reshaped the treatment landscape, overall 5-year survival remains low at ~29.7%, partially due to the heterogeneity across and within histologic subtypes. Lung cancers with neuroendocrine (NE) features exhibit particularly aggressive clinical behavior, including high rates of brain metastasis and poor responsiveness to immunotherapy. Emerging evidence suggests that a subset of LUAD acquires neural traits independent of NE identity. Acquisition of intrinsic neuron-like electrical activity in NE-SCLC drives tumorigenic capability and metastatic potential has been also reported. These neural features may represent an unrecognized biological axis associated with lineage plasticity, metastasis, and immune escape. Rationale and hypothesis: Our previous epigenomic studies identified neural-like lineage subclasses within LUSC (nLUSC) signified by SOX2/BRN2 circuitry in contrast to classical subset signified by SOX2/TP63 circuitry. Neural factors were unexpectedly co-opted in lung cancer to establish enhancer landscapes consistent with neural developmental pathways. We hypothesize that co-opted neural circuitries establish neural-like epigenomic programs in lung cancers, conferring enhanced neural affinity and intrinsic immune privilege that facilitate metastasis and resistance to immunotherapy. Experimental procedures: First, we cultured nLUSC cell lines with or without ectopic dNp63 expression that suppresses neural program and quantified migration toward differentiated human glutamatergic neurons in transwell, along with profiling transcriptomic and epigenomic remodeling upon interaction with neurons. Second, we stimulated a panel of classical and neural LUSC cells with IFN-gamma to measure the antigen presentation activity. We co-cultured T cells with LUSC lines and measured intracellular and released Granzyme B and perforin levels to quantify T cell-mediated cytotoxicity, along with profiling transcriptomes and enhancer landscapes to identify enrichment of neural signatures. Results: nLUSC exhibits functionally distinct behaviors compared to their classical counterparts. nLUSC cells demonstrated enhanced migratory capacity towards neurons. Classical cells maintained stronger antigen-presenting potential by both MHC-I and MHC-II markers at baseline and predominantly upregulated APM and enhanced their immunogenicity, whereas nLUSC cells exhibited a more immunosuppressive response; e.g., upregulation of PD-L1 , CD95 and HLA-E upon IFNgamma stimulation. Conclusions: The study reveals that neural and classical lung cancer subtypes are not only transcriptionally divergent but also functionally distinct in behaviors relevant to neural affinity and immune escape.