A Novel M6A-Related Genes Signature Can Impact the Immune Status and Predict the Prognosis and Drug Sensitivity of Lung Adenocarcinoma

Identification of m6A-modified gene signatures in lung adenocarcinoma tumorigenesis and their potential role in drug resistance

BACKGROUND

Lung cancer is one of the most commonly diagnosed cancers. N6-methyladenosine (m6A) modification has a profound impact on RNA translation, splicing, transportation, and stability.

AIMS

This research aimed to identify and verify m6A-modified signatures for Lung adenocarcinoma (LUAD) tumorigenesis.

OBJECTIVE

Our previous mRNA-seq and m6A-seq data from 26 pairs of LUAD samples and tumor-adjacent normal tissues are used.

METHODS

Univariate Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) analysis were used to estimate the significance of 37 collected m6A regulators. WGCNA was constructed to identify the genes correlated with LUAD tumorigenesis. Pearson correlation analysis between mRNA-seq and m6A-seq data was used to identify the m6A-correlation genes.

RESULTS

LASSO-Cox analysis identified 18 m6A significant regulators. The top 3 regulators, including METTL16, FTO, and SRSF10, and their downstream genes which were reported in the literature were analysed to confirm their role in LUAD tumorigenesis. Blue and brown coexpression modules were chosen as key modules for LUAD tumorigenesis. At last, we intersected Lasso-downstream genes, m6A-correlation genes, with blue or brown module genes. As a result, 56 m6A-modified gene signatures were obtained. Among them, AKAP9, PLXNB2, BRPF3, HPS4, EXOC7, and KLF6 have an inconsistent expression in protein and mRNA levels, probably due to m6A modification. In addition, these genes may be involved in regulating drug resistance.

CONCLUSIONS

56 m6A-modified gene signatures for LUAD tumorigenesis were obtained from Pearson correlation analysis between mRNA-seq and m6A-seq data, along with LASSO and WGCNA analysis. Among them, AKAP9, PLXNB2, BRPF3, HPS4, EXOC7 and KLF6 play a crucial role in LUAD tumorigenesis in an m6A modification-dependent manner.

Prospective validation of ORACLE, a clonal expression biomarker associated with survival of patients with lung adenocarcinoma

Human tumors are diverse in their natural history and response to treatment, which in part results from genetic and transcriptomic heterogeneity. In clinical practice, single-site needle biopsies are used to sample this diversity, but cancer biomarkers may be confounded by spatiogenomic heterogeneity within individual tumors. Here we investigate clonally expressed genes as a solution to the sampling bias problem by analyzing multiregion whole-exome and RNA sequencing data for 450 tumor regions from 184 patients with lung adenocarcinoma in the TRACERx study. We prospectively validate the survival association of a clonal expression biomarker, Outcome Risk Associated Clonal Lung Expression (ORACLE), in combination with clinicopathological risk factors, and in stage I disease. We expand our mechanistic understanding, discovering that clonal transcriptional signals are detectable before tissue invasion, act as a molecular fingerprint for lethal metastatic clones and predict chemotherapy sensitivity. Lastly, we find that ORACLE summarizes the prognostic information encoded by genetic evolutionary measures, including chromosomal instability, as a concise 23-transcript assay.

Identification of a novel ADCC-related gene signature for predicting the prognosis and therapy response in lung adenocarcinoma

BACKGROUND

Previous studies have largely neglected the role of ADCC in LUAD, and no study has systematically compiled ADCC-associated genes to create prognostic signatures.

METHODS

In this study, 1564 LUAD patients, 2057 NSCLC patients, and more than 5000 patients with various cancer types from diverse cohorts were included. R package ConsensusClusterPlus was utilized to classify patients into different subtypes. A number of machine-learning algorithms were used to construct the ADCCRS. GSVA and ClusterProfiler were used for enrichment analyses, and IOBR was used to quantify immune cell infiltration level. GISTIC2.0 and maftools were used to analyze the CNV and SNV data. The Oncopredict package was used to predict drug information based on the GDSC1. Three immunotherapy cohorts were used to evaluate patient response to immunotherapy. The Seurat package was used to process single-cell data, the AUCell package was used to calculate cells' geneset activity scores, and the Scissor algorithm was used to identify ADCCRS-associated cells.

RESULTS

Through unsupervised clustering, two distinct subtypes of LUAD were identified, each exhibiting distinct clinical characteristics. The ADCCRS, consisted of 16 genes, was constructed by integrated machine-learning methods. The prognostic power of ADCCRS was validated in 28 independent datasets. Further, ADCCRS shows better predictive abilities than 102 previously published signatures in predicting LUAD patients' survival. A nomogram incorporating ADCCRS and clinical features was constructed, demonstrating high predictive performance. ADCCRS positively correlates with patients' gene mutation, and integrated analysis of bulk and single-cell transcriptome data revealed the association of ADCCRS with TME modulators. Cells representing high-ADCCRS phenotype exhibited more malignant features. LUAD patients with high ADCCRS levels exhibited sensitivity to chemotherapy and targeted therapy, while displaying resistance to immunotherapy. In pan-cancer analysis, ADCCRS still exhibited significant prognostic value and was found to be a risk factor for most cancer patients.

CONCLUSIONS

ADCCRS offers a critical prognostic insight for patients with LUAD, shedding light on the tumor microenvironment and forecasting treatment responsiveness.

The critical roles of m6A RNA methylation in lung cancer: from mechanism to prognosis and therapy

Lung cancer, a highly malignant disease, greatly affects patients' quality of life. N6-methyladenosine (m6A) is one of the most common posttranscriptional modifications of various RNAs, including mRNAs and ncRNAs. Emerging studies have demonstrated that m6A participates in normal physiological processes and that its dysregulation is involved in many diseases, especially pulmonary tumorigenesis and progression. Among these, regulators including m6A writers, readers and erasers mediate m6A modification of lung cancer-related molecular RNAs to regulate their expression. Furthermore, the imbalance of this regulatory effect adversely affects signalling pathways related to lung cancer cell proliferation, invasion, metastasis and other biological behaviours. Based on the close association between m6A and lung cancer, various prognostic risk models have been established and novel drugs have been developed. Overall, this review comprehensively elaborates the mechanism of m6A regulation in the development of lung cancer, suggesting its potential for clinical application in the therapy and prognostic assessment of lung cancer.

N6-methylandenosine-related immune genes correlate with prognosis and immune landscapes in gastric cancer

OBJECTIVES

This study aimed to probe into the significance of N6-methyladenosine (m6A)-related immune genes (m6AIGs) in predicting prognoses and immune landscapes of patients with gastric cancer (GC).

METHODS

The clinical data and transcriptomic matrix of GC patients were acquired from The Cancer Genome Atlas database. The clinically meaningful m6AIGs were acquired by univariate Cox regression analysis. GC patients were stratified into different clusters via consensus clustering analysis and different risk subgroups via m6AIGs prognostic signature. The clinicopathological features and tumor microenvironment (TME) in the different clusters and different risk subgroups were explored. The predictive performance was evaluated using the KM method, ROC curves, and univariate and multivariate regression analyses. Moreover, we fabricated a nomogram based on risk scores and clinical risk characteristics. Biological functional analysis was performed based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. The connectivity map was used to screen out potential small molecule drugs for GC patients.

RESULTS

A total of 14 prognostic m6AIGs and two clusters based on 14 prognostic m6AIGs were identified. A prognostic signature based on 4 m6AIGs and a nomogram based on independent prognostic factors was constructed and validated. Different clusters and different risk subgroups were significantly correlated with TME scores, the distribution of immune cells, and the expression of immune checkpoint genes. Some malignant and immune biological processes and pathways were correlated with the patients with poor prognosis. Ten small molecular drugs with potential therapeutic effect were screened out.

CONCLUSIONS

This study revealed the prognostic role and significant values of m6AIGs in GC, which enhanced the understanding of m6AIGs and paved the way for developing predictive biomarkers and therapeutic targets for GC.

A Novel Risk Model for lncRNAs Associated with Oxidative Stress Predicts Prognosis of Bladder Cancer

Background

Oxidative stress (OS) reactions are closely related to the development and progression of bladder cancer (BCa). This project aimed to identify new potential biomarkers to predict the prognosis of BCa and improve immunotherapy.

Methods

We downloaded transcriptomic information and clinical data on BCa from The Cancer Genome Atlas (TCGA). Screening for OS genes was statistically different between tumor and adjacent normal tissue. A coexpression analysis between lncRNAs and differentially expressed OS genes was performed to identify OS-related lncRNAs. Then, differentially expressed oxidative stress lncRNAs (DEOSlncRNAs) between tumors and normal tissues were identified. Univariate/multivariate Cox regression analysis was performed to select the lncRNAs for risk assessment. LASSO analysis was conducted to establish a prognostic model. The prognostic risk model could accurately predict BCa patient prognosis and reveal a close correlation with clinicopathological features. We analyzed the principal component analysis (PCA), immune microenvironment, and half-maximal inhibitory concentration (IC50) in the risk groups.

Results

We constructed a model containing eight DEOSlncRNAs (AC021321.1, AC068196.1, AC008750.1, SETBP1-DT, AL590617.2, THUMPD3-AS1, AC112721.1, and NR4A1AS). The prognostic risk model showed better results in predicting the prognosis of BCa patients and was strongly correlated with clinicopathological characteristics. We found great agreement between the calibration plots and prognostic predictions in this model. The areas under the receiver operating characteristic (ROC) curve (AUCs) at 1, 3, and 5 years were 0.792, 0.804, and 0.843, respectively. This model also showed good predictive ability regarding the tumor microenvironment and tumor mutation burden. In addition, the high-risk group was more sensitive to eight therapeutic agents, and the low-risk group was more responsive to five therapeutic agents. Sixteen immune checkpoints were significantly different between the two risk groups.

Conclusion

Our eight DEOSlncRNA risk models provide new insights into predicting prognosis and clinical progression in BCa patients.