A thorough interrogation of the immune landscape is crucial for immunotherapy strategy selection and prediction of clinical responses in non-small-cell lung cancer (NSCLC) patients. Single-cell RNA sequencing (scRNA-seq) techniques have prompted the opportunity to dissect the distinct immune signatures between lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), the two major subtypes of NSCLC. Here, we performed scRNA-seq on 72,475 immune cells from 40 samples of tumor and matched adjacent normal tissues spanning 19 NSCLC patients, and drew a systematic immune cell transcriptome atlas. Joint analyses of the distinct cellular compositions, differentially expressed genes (DEGs), cell–cell interactions, pseudotime trajectory, transcriptomic factors and prognostic factors based on The Cancer Genome Atlas (TCGA), revealed the central roles of cytotoxic and effector T and NK cells and the distinct functional macrophages (Mφ) subtypes in the immune microenvironment heterogeneity between LUAD and LUSC. The dominant subtype of Mφ was FABP4-Mφ in LUAD and SPP1-Mφ in LUSC. Importantly, we identified a novel lymphocyte-related Mφ cluster, which we named SELENOP-Mφ, and further established its antitumor role in both types, especially in LUAD. Our comprehensive depiction of the immune heterogeneity and definition of Mφ clusters could help design personalized treatment for lung cancer patients in clinical practice.

Post-operative recurrence rates of stage I non-small cell lung cancer (NSCLC) range from 20% to 40%. Nonetheless, the molecular mechanisms underlying recurrence hitherto remain largely elusive. Here, we generate genomic, epigenomic and transcriptomic profiles of paired tumors and adjacent tissues from 122 stage I NSCLC patients, among which 57 patients develop recurrence after surgery during follow-up. Integrated analyses illustrate that the presence of predominantly solid or micropapillary histological subtypes, increased genomic instability, and APOBEC-related signature are associated with recurrence. Furthermore, TP53 missense mutation in DNA-binding domain could contribute to shorter time to recurrence. DNA hypomethylation is pronounced in recurrent NSCLC, and PRAME is the significantly hypomethylated and overexpressed gene in recurrent lung adenocarcinoma (LUAD). Mechanistically, hypomethylation at TEAD1 binding site facilitates the transcriptional activation of PRAME. Inhibition of PRAME restrains the tumor metastasis via downregulation of epithelial–mesenchymal transition-related genes. We also identify that enrichment of AT2 cells with higher copy number variation burden, exhausted CD8 + T cells and Macro_SPP1, along with the reduced interaction between AT2 and immune cells, is essential for the formation of ecosystem in recurrent LUAD. Finally, multi-omics clustering could stratify the NSCLC patients into 4 subclusters with varying recurrence risk and subcluster-specific therapeutic vulnerabilities. Collectively, this study constitutes a promising resource enabling insights into the biological mechanisms and clinical management for post-operative recurrence of stage I NSCLC.

The neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) are easily obtained from routine blood tests. We investigated the associations of the NLR and PLR with the clinical parameters and prognoses of small cell lung cancer (SCLC) patients. Pre-treatment clinical and laboratory data from 139 patients with SCLC were retrospectively studied with univariate analyses. The NLR and PLR values were divided into two separate groups: high NLR (>4.55, n = 32) vs low NLR (≤4.55, n = 107) and high PLR (>148, n = 63) vs low PLR (≤148, n = 76). Kaplan-Meier survival analyses and Cox proportional hazard models were used to examine the effects of NLR and PLR on overall survival. Chi-square analyses revealed significant associations of high NLR with tumour stage, hepatic metastasis, radiotherapy and chemotherapy and significant associations of high PLR with tumour stage, bone and hepatic metastases, exposure to cooking oil fumes, and chemotherapy. Mann-Whitney U tests demonstrated an association of high NLR with smoking exposure, and high NLR and high PLR were correlated with several laboratory parameters. Kaplan-Meier analyses revealed that high NLR and high PLR conferred poor prognoses for SCLC patients. Moreover, multivariate analysis demonstrated that NLR, tumour stage, and hepatic metastasis were independent prognostic factors for survival. In this study, we found that NLR and PLR were associated with several factors that reflect the inflammatory (white blood cell count, WBC; lactate dehydrogenase, LDH) and nutritional (albumin, ALB; haemoglobin, HB; and cholesterol) status of SCLC patients at diagnosis. NLR is an independent prognostic factor and can be used to predict the mortality risk of SCLC patients.

Metabolic reprogramme was a key characteristic of malignant tumors. Increased evidences indicated that besides Warburg effect (abnormal glucose metabolism), abnormal lipid metabolism played more and more important in progression and metastasis of malignant tumors. MiR-15a-5p could inhibit development of lung cancer, while its regulating mechanism, especially the role in lipid metabolism still remained unclear. In this study, we confirmed that miR-15a-5p inhibited proliferation, migration and invasion of lung cancer cells. The online analysis of Mirpath v.3 predicted that miR-15a-5p was closely associated with fatty acid synthesis and lipid metabolism. In vitro cell experiments revealed that miR-15a-5p significantly suppressed fatty acid synthesis of lung cancer cells by inhibiting acetate uptake. Extensive analysis indicated that miR-15a-5p could suppress acetyl-CoA activity and decrease histone H4 acetylation by inhibiting ACSS2 expression. In addition, we also observed that ACSS2 located in nucleus under hypoxic conditions, while miR-15a-5p could be transported into nucleus to inhibit the function of ACSS2. Our study unveiled a novel mechanism of miR-15a-5p in inhibiting metastasis of lung cancer cells by suppressing lipid metabolism via suppression of ACSS2 mediated acetyl-CoA activity and histone acetylation.

Circulating molecules play important roles in lung cancer diagnosis. In addition, plasma lactate dehydrogenase (LDH) and creatine kinase (CK) have been shown to be closely related to tumor progression in breast cancer, prostate cancer, and colonel cancer. However, the relationships between LDH and CK levels with metastasis occurrence and the survival status of lung cancer patients remain unclear. A total of 1142 lung cancer patients were enrolled in this study and were separated into negative or positive groups, according to the plasma levels of CK or LDH. Patients in both groups were assessed for clinical characteristics, metastasis occurrence, and survival status. The Cox regression model was then introduced to confirm whether CK and LDH could act as independent factors for predicting a poor prognosis. The results indicated that CK had a close relationship with bone (p < 0.05) and lymph node (p < 0.05) metastases. In addition, LDH was strongly related with bone (p < 0.05), adrenal gland (p < 0.05), and lymph node (p < 0.05) metastases. CK and LDH were also correlated with the survival status of the lung cancer patients (all p < 0.001). According to specific histological classification analysis, it was found that CK was closely related to the survival status of adenocarcinoma (ADC) and squamous cell carcinoma (SCC) patients, while LDH was only correlated with that of ADC patients. Cox regression analysis confirmed that CK and LDH could act as independent factors for predicting a poor prognosis in ADC but not SCC patients. For the first time, our study confirmed the role of CK in metastasis occurrence and the survival status of lung cancer patients. In addition, it also demonstrated that CK and LDH could be used as independent factors to predict a poor prognosis in ADC patients. The identification of CK and LDH will play important roles in lung cancer diagnosis and poor outcome prediction in the future.