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Simple Summary: Monoclonal antibodies targeting the programmed death 1 (PD-1) receptor and its ligand (PD-L1) have demonstrated improved clinical response and survival in non-small cell lung cancer (NSCLC). Although extrinsic immunologic factors play important roles in the regulation of PD-L1 and PD-1, tumor intrinsic factors, including genetic alterations, epigenetic alterations, oncogenic and tumor suppressor signals, and transcription factors also play important roles in PD-L1 expression. There is an urgent need to investigate the intrinsic transcriptional profiles affecting the clinical response to PD-1 inhibitors in patients with non-small cell lung cancer. In our study, PD-1 inhibitor-associated intrinsic gene patterns were very different between lung adenocarcinoma and squamous cell carcinoma. In lung adenocarcinoma, the intrinsic gene signature was a very good predictive or prognostic biomarker. Our findings prove for the first time that an intrinsic gene signature is well predictive of responsiveness to PD-1 inhibitors in lung adenocarcinoma. Using a machine learning method, we investigated the intrinsic and extrinsic transcriptional profiles that affect the clinical response to PD-1 inhibitors in 57 patients with non-small cell lung cancer (NSCLC). Among the top 100 genes associated with the responsiveness to PD-1 inhibitors, the proportion of intrinsic genes in lung adenocarcinoma (LUAD) (69%) was higher than in NSCLC overall (36%) and lung squamous cell carcinoma (LUSC) (33%). The intrinsic gene signature of LUAD (mean area under the ROC curve (AUC) = 0.957 and mean accuracy = 0.9) had higher predictive power than either the intrinsic gene signature of NSCLC or LUSC or the extrinsic gene signature of NSCLC, LUAD, or LUSC. The high intrinsic gene signature group had a high overall survival rate in LUAD (p = 0.034). When we performed a pathway enrichment analysis, the cell cycle and cellular senescence pathways were related to the upregulation of intrinsic genes in LUAD. The intrinsic signature of LUAD also showed a positive correlation with other immune checkpoint targets, including CD274, LAG3, and PDCD1LG2 (Spearman correlation coefficient > 0.25). PD-1 inhibitor-related intrinsic gene patterns differed significantly between LUAD and LUSC and may be a particularly useful biomarker in LUAD. [ABSTRACT FROM AUTHOR]