Whole-genome DNA methylation and DNA methylation-based biomarkers in lung squamous cell carcinoma.

Exploring early detection methods through comprehensive evaluation of DNA methylation for lung squamous cell carcinoma (LUSC) patients is of great significance. By using different machine learning algorithms for feature selection and model construction based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, five methylation biomarkers in LUSC (along with mapped genes) were identified including cg14823851 (TBX4), cg02772121 (TRIM15), cg10424681 (C6orf201), cg12910906 (ARHGEF4), and cg20181079 (OR4D11), achieving extremely high sensitivity and specificity in distinguishing LUSC from normal samples in independent cohorts. Pyrosequencing assay verified DNA methylation levels, meanwhile qRT-PCR and immunohistochemistry results presented their accordant methylation-related gene expression statuses in paired LUSC and normal lung tissues. The five methylation-based biomarkers proposed in this study have great potential for the diagnosis of LUSC and could guide studies in methylation-regulated tumor development and progression.

Real-world comprehensive diagnosis and "Surgery + X" treatment strategy of early-stage synchronous multiple primary lung cancer.

BACKGROUND: Diagnosing and treating synchronous multiple primary lung cancers (sMPLC) are complex and challenging. This study aimed to report real-world data on the comprehensive diagnosis and treatment of patients with early-stage sMPLC. MATERIALS AND METHODS: A single-center cohort study was carried out and a large number of patients with early-stage sMPLC were included. A single- or two-stage surgery was performed to remove the primary and co-existing lesions. The "X" strategies, including ablation, SBRT, and EGFR-TKIs treatment, were applied to treat the high-risk residual lesions. Wide panel-genomic sequencing was performed to assess the genetic heterogeneity of the co-existing lesions. RESULTS: A total of 465 early-stage sMPLC patients with 1198 resected lesions were included. Despite most patients being histologically different or harboring different genetic alternations, about 7.5% of the patients had the same histological type and driver gene mutation changes, comprehensive re-evaluation is thus needed. The "Surgery + X" strategy showed remarkable efficacy and safety in treating multiple lesions. Follow-up data revealed that the T2 stage (p = 0.014) and the solid presence of a primary lesion (p < 0.001) were significantly related to tumor recurrence. And a T2-stage primary tumor had a significantly higher rate of developing new lesions after the initial surgery (p < 0.001). CONCLUSIONS: In real-world practice, histopathological and radiological evaluation combined with genetic analyses could be a robust diagnostic approach for sMPLC. The "Surgery + X" treatment strategy showed remarkable efficacy, superiority, and safety in the clinical treatment of early-stage sMPLC.

Genetic, DNA methylation, and immune profile discrepancies between early-stage single primary lung cancer and synchronous multiple primary lung cancer.

BACKGROUND: To explore the possible carcinogenesis and help better diagnose and treat patients with synchronous multiple primary lung cancers (sMPLC), we systematically investigated the genetic and DNA methylation profiles of early-stage sMPLC and single primary lung cancer (SPLC) and explored the immune profiles in the tumor microenvironment. METHODS: Hundred and ninety-one patients with 191 nodules in the SPLC group and 132 patients with 295 nodules in the sMPLC group were enrolled. All the samples were subjected to wide panel-genomic sequencing. Genome-wide DNA methylation was assessed using the Infinium Human Methylation 850 K BeadChip. RNA-seq and CIBERSORT analyses were performed to identify the immune characteristics in these two groups. RESULTS: Lesions from sMPLC patients had lower TMB levels than that from SPLC patients. sMPLC had a similar genetic mutational landscape with SPLC, despite some subgroup genetic discrepancies. Distinct DNA methylation patterns were identified between the two groups. The differentially methylated genes were related to immune response pathways. RNA-seq analyses revealed more immune-related DEGs in sMPLC. Accordingly, more immune-related biological processes and pathways were identified in sMPLC. Aberrant DNA methylation was associated with the abnormal expression of immune-related genes. CIBERSORT analysis revealed the infiltration of immune cells was different between the two groups. CONCLUSION: Our study for the first time demonstrated genetic, epigenetic, and immune profile discrepancies between sMPLC and SPLC. Relative to the similar genetic mutational landscape, the DNA methylation patterns and related immune profiles were significantly different between sMPLC and SPLC, indicating their essential roles in the initiation and development of sMPLC.

Immune Microenvironment Signatures as Biomarkers to Predict Early Recurrence of Stage Ia-b Lung Cancer.

INTRODUCTION: Approximately 30% of patients diagnosed with stage Ia-b NSCLC die of recurrent disease after surgery. This study aimed to identify immune-related biomarkers that might predict tumor recurrence in stage Ia-b NSCLC within 40 months after curative resection. METHODS: Gene expression data of stage Ia-b NSCLC samples was retrieved from the TCGA database, the GEO databases, and the Second Xiangya hospital (XXEYY) database. 22 types of tumors infiltrating immune cells and the expression of immune-associated genes were investigated using CIBERSORT, immunohistochemical staining, and GSEA analyses in a total of 450 patients (80 in the training cohort and 370 in the validation cohorts). Recurrence-related immune features were selected based on the LASSO Cox regression model. RESULTS: High density of Tregs, Macrophages M0 and M1 cell could be observed in recurrence group while the memory B cell was more frequently enriched in controls, yet Tregs alone was significantly associated with tumor early recurrence in TCGA cohort, XYEYY cohort and GSE37745 dataset. A handful of immune-related genes were identified in the recurrence group. Based on Lasso regression analysis, the expressions of five immune-related genes, RLTPR, SLFN13, MIR4500HG, HYDIN and TPRG1 were closely correlated with tumor early recurrence. In the training cohort (TCGA), the combination of these five genes has sensitivity and specificity of 85% and 85%, with AUC of 0.91 (95% CI 0.84-0.98) for lung cancer early recurrence prediction, whereas in validation cohorts, the sensitivity and specificity using this panel was 61-89% and 54-82%, with AUC of 0.62-0.84. CONCLUSION: Our study demonstrated that the immune microenvironment signatures were closely related to tumor early recurrence. Compared to tumor-infiltrating lymphocytes, the expression of five immune-related genes could be robust biomarkers to predict early recurrence of stage Ia-b NSCLC after curative resection.

Annotation and cluster analysis of long noncoding RNA linked to male sex and estrogen in cancers.

The sex difference in cancer occurrence is a consistent finding in cancer epidemiology. Several solid tumors, including lung cancer, colorectal cancer, hepatic carcinoma, and renal carcinoma, are generally more common in males. Although sexual dimorphism is attributed to hormonal or behavioral differences, evidence for the function of lncRNA is lacking in sex-specific cancers. We show here that LINC00263 is one of the most dysregulated lncRNAs in lung adenocarcinomas and is upregulated in lung adenocarcinoma, colorectal cancer, and renal carcinoma, especially in male patients compared to females. LINC00263 functions as an oncogene by promoting translocation of p65 into the nucleus to activate the NF-κB-signaling pathway through interaction with IKKα in the cytoplasm. The expression of LINC00263 is strongly correlated with ESR1, and it is decreased after treatment with estrogen. Ligand-activated ER could inhibit the function of LINC00263 by inhibiting NF-κB from cytoplasmic translocation into the nucleus. The inhibitory effect of estrogen on LINC00263 indicates its differential expression in male and female patients. Our findings indicate that LINC00263 is linked to male sex and estrogen as an oncogene, and these findings might help in the exploration of the mechanisms of differential gene regulation in sex-specific cancers.

Aryl hydrocarbon receptor activated by benzo (a) pyrene promotes SMARCA6 expression in NSCLC.

Recent studies suggest that individual subunits of chromatin-remodeling complexes generate epigenetically specific signaling in tumorigenicity. The impact of environmental factors on the chromatin-remodeling factor has not been thoroughly elucidated to date. We detected the expression level of SMARCA6 (SWI/SNF2-Related, Matrix-Associated, Actin-Dependent Regulator of Chromatin, Subfamily A, Member 6) in NSCLC (Non-small-cell lung carcinoma) and measured it through quantitative real-time PCR (qRT-PCR) and immunohistochemistry. The effects of BaP on proliferation and cell cycle progression were evaluated using MTT, colony formation and FACS analyses. Tumor growth in vivo was observed in a xenograft model. ChIP and qPCR were performed to validate that SMARCA6 was a potential target of AhR in NSCLC. As a result, BaP increased SMARCA6 expression. Smoking was linked with elevated SMARCA6 expression in NSCLC. BaP promoted cancer progression in vitro and in vivo. ChIP assay confirmed that BaP increases SMARCA6 expression via recruitment of AhR and induces SMARCA6 expression by facilitating AhR translocation to the nucleus. Furthermore, inhibition of AhR expression decreases SMARCA6 expression in NSCLC. Finally, knockdown of SMARCA6 attenuates BaP-induced cancer progression. This study demonstrates that BaP promotes proliferation by activation of AhR, which promotes SMARCA6 expression, and may identify new diagnostic and therapeutic targets in lung cancer.

Long non-coding RNA linc01433 promotes migration and invasion in non-small cell lung cancer.

BACKGROUND: For many years, lung cancer has been the most common and deadly cancer worldwide. Early diagnosis of non-small cell lung cancer (NSCLC) in particular is very difficult because the symptoms are often ignored. The five-year survival rate is very low despite great improvements to therapy. Thus, there is an urgent need to identify prognostic biomarkers and target molecules for the clinical diagnosis and individualized treatment of NSCLC. METHODS: We performed quantitative real-time PCR to determine the expression levels of the long non-coding RNA (lncRNA) linc01433 in NSCLC and normal matched lung tissue. Subsequently, we established cell lines with overexpression or knockdown of linc01433 to evaluate the effects on proliferation and metastasis in vitro. Epithelial-to-mesenchymal transition was examined using Western blot. RESULTS: Linc01433 was significantly overexpressed in NSCLC tissues compared to normal lung tissues. In addition, linc01433 levels were associated with smoking history. Linc01433 overexpression in lung cancer cells increased proliferation, migration, and invasion abilities, as well as epithelial-to-mesenchymal transition. CONCLUSIONS: Linc01433 is a cancer-related lncRNA that may have an oncogene-like effect in NSCLC.