N6-Methyladenosine-Regulated mRNAs: Potential Prognostic Biomarkers for Patients With Lung Adenocarcinoma

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.

Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans

BACKGROUND

Tibetans are genetically adapted to high-altitude environments. Though many studies have been conducted, the genetic basis of the adaptation remains elusive due to the poor reproducibility for detecting selective signatures in the Tibetan genomes.

RESULTS

Here, we present whole-genome sequencing (WGS) data of 1001 indigenous Tibetans, covering the major populated areas of the Qinghai-Tibetan Plateau in China. We identify 35 million variants, and more than one-third of them are novel variants. Utilizing the large-scale WGS data, we construct a comprehensive map of allele frequency and linkage disequilibrium and provide a population-specific genome reference panel, referred to as 1KTGP. Moreover, with the use of a combined approach, we redefine the signatures of Darwinian-positive selection in the Tibetan genomes, and we characterize a high-confidence list of 4320 variants and 192 genes that have undergone selection in Tibetans. In particular, we discover four new genes, TMEM132C, ATP13A3, SANBR, and KHDRBS2, with strong signals of selection, and they may account for the adaptation of cardio-pulmonary functions in Tibetans. Functional annotation and enrichment analysis indicate that the 192 genes with selective signatures are likely involved in multiple organs and physiological systems, suggesting polygenic and pleiotropic effects.

CONCLUSIONS

Overall, the large-scale Tibetan WGS data and the identified adaptive variants/genes can serve as a valuable resource for future genetic and medical studies of high-altitude populations.

Function and prognostic value of N6-methyladenosine-modified RNAs in lung adenocarcinoma

BACKGROUND

Aberrant regulation of N6-methyladenosine (m6A) modification is reportedly vital for cancer progression, including lung adenocarcinoma (LUAD). However, current studies mainly focus on the function and mechanism of m6A-modified regulators, such as m6A writers (METTL3 and METTL14), erasers (ALKBH5 and FTO), and readers (YTHDF1 and YTHDF2). The landscape, function, and prognostic value of RNAs by m6A-modified have not been fully clarified until now.

METHODS

The present study identified 57 RNAs with significantly different m6A-methylation levels in LUAD tissues using epitranscriptomic microarray analysis.

RESULTS

Among the 57 RNAs, 28 and 29 were hypermethylated and hypomethylated, respectively. The m6A-methylation level increased in mRNA and long non-coding RNA (lncRNA) but decreased in small non-coding RNA. After pathway enrichment analyses, RNA metabolism-associated pathways such as nucleotide metabolism were enriched in total and m6A-hypermethylated mRNAs. Furthermore, lncRNA networks were built using miRNet tools, revealing that the immune system was closed to m6A-modified lncRNAs. To evaluate the prognostic value of mRNAs with hypermethylated or hypomethylated, we calculated the risk scores, and constructed signatures to predict the survival time of patients with LUAD using multicox regression analysis. In addition, hypermethylated-mRNA and hypomethylated-mRNA signatures were established. The survival plotter showed that these two signatures effectively predicted the survival time of patients with LUAD.

CONCLUSIONS

The results of the present study support the evidence for understanding the expression, function, and potential prognostic values of m6A-modified RNAs, possibly promoting effective therapies for patients with LUAD.

Prognostic analysis of m6A-related genes as potential biomarkers in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options. N6-methyladenosine (m6A) is a reversible RNA modification and has been implicated in various biological processes. However, there are few studies on m6A in IPF. This project mainly explores the prognostic value of m6A-related genes as potential biomarkers in IPF, in order to establish a set of accurate prognostic prediction model. In this study, we used GSE28042 dataset in GEO database to screen out 218 m6A-related candidate genes with high IPF correlation and high differential expression through differentially expressed gene analysis, WGCNA and m6A correlation analysis. The genes associated with the prognosis of IPF were screened out by univariate Cox regression analysis, LASSO analysis, and multivariate Cox regression analysis, and the multivariate Cox model of prognostic risk of related genes was constructed. We found that RBM11, RBM47, RIC3, TRAF5 and ZNF14 were key genes in our model. Finally, the prognostic prediction ability and independent prognostic characteristics of the risk model were evaluated by survival analysis and independent prognostic analysis, and verified by the GSE93606 dataset, which proved that the prognostic risk model we constructed has a strong and stable prediction efficiency.

Development and validation of a m6A -regulated prognostic signature in lung adenocarcinoma

Lung adenocarcinoma (LUAD) is the most frequent subtype of lung cancer, with a 5-year survival rate of less than 20%. N6-methyladenosine (m6A) is the most prevalent RNA epigenetic modification in eukaryotic cells, and post-transcriptionally regulates gene expression and function by affecting RNA metabolism. The alterations of functionally important m6A sites have been previously shown to play vital roles in tumor initiation and progression, but little is known about the extent to which m6A-regulated genes play in prognostic performance for patients with LUAD. Here, we presented an overview of the m6A methylome in LUAD tissues using transcriptome-wide m6A methylation profiles, and found that differentially methylated transcripts were significantly enriched in tumor-related processes, including immune response, angiogenesis and cell-substrate adhesion. Joint analysis of m6A modification and gene expression suggested that 300 genes were regulated by m6A. Furthermore, we developed a m6A-regulated prognosis-associated signature (m6A-PPS) by performing a multi-step process. The m6A-PPS model, a 15-gene set, was qualified for prognosis prediction for LUAD patients. By regrouping the patients with this model, the OS of the high-risk group was shorter than that of the low-risk group across all datasets. Importantly, patients with high m6A-PPS scores respond better to immunotherapeutic. Our results provide a valuable resource for understanding the important role of epitranscriptomic modifications in the pathogenesis of LUAD, and obtain potential prognostic biomarkers.

m6A-binding protein IGF2BP1 promotes the malignant phenotypes of lung adenocarcinoma

BACKGROUND

Lung adenocarcinoma (LUAD), the most common type of lung cancer, poses a significant threat to the life of patients. N6-methyladenosine modification is the most abundant epigenetic modification and may play an important role in the lung carcinogenesis. IGF2BP1 is a newly discovered m6A-binding protein, but little is known about its role in LUAD.

METHODS

Data from TCGA, GEO, Kaplan-Meier Plotter, and GEPIA databases were systematically analyzed to access the expression and prognostic value of IGF2BP1 on LUAD. Real-time polymerase chain reaction, Western blot, and immunohistochemistry were performed to detect the mRNA and protein level of IGF2BP1 in LUAD tissues and para-carcinoma tissues. Functional cell experiments, including Cell Counting Kit-8 assay, Transwell invasion assay, wound healing assay, Annexin V-FITC/PI double-staining assay, and TUNEL assay, were used to investigate the functions of IGF2BP1 on LUAD cell proliferation, invasion, migration, and apoptosis, respectively. The top 50 genes that were positively or negatively related to the expression of IGF2BP1 were identified, and pathway enrichment analysis was performed. m⁶A modification sites within IGF2BP1-related genes were predicted by SRAMP.

RESULT

16 m⁶A regulators were significantly differentially expressed in LUAD tissues. IGF2BP1 was upregulated in LUAD tissues compared with para-carcinoma tissues. High expression of IGF2PB1 was significantly associated with higher clinical stages and poor prognosis of LUAD patients. Furthermore, our functional experiments indicated that IGF2BP1 facilitated cell proliferation, invasion, and migration and suppressed apoptosis in LUAD. Functional enrichment analysis of IGF2BP1-related genes indicated enrichment in several pathways related to oncogenesis. Additionally, m⁶A modification sites were detected within IGF2BP1-related genes.

CONCLUSIONS

Our findings demonstrate that IGF2BP1 plays a contributory role in the development and progression of LUAD. IGF2BP1 has the potential to become a prognostic predictor and therapeutic target for LUAD.

Development and Validation of Prognostic Model for Lung Adenocarcinoma Patients Based on m6A Methylation Related Transcriptomics

Existing studies suggest that m⁶A methylation is closely related to the prognosis of cancer. We developed three prognostic models based on m⁶A-related transcriptomics in lung adenocarcinoma patients and performed external validations. The TCGA-LUAD cohort served as the derivation cohort and six GEO data sets as external validation cohorts. The first model (mRNA model) was developed based on m⁶A-related mRNA. LASSO and stepwise regression were used to screen genes and the prognostic model was developed from multivariate Cox regression model. The second model (lncRNA model) was constructed based on m⁶A related lncRNAs. The four steps of random survival forest, LASSO, best subset selection and stepwise regression were used to screen genes and develop a Cox regression prognostic model. The third model combined the risk scores of the first two models with clinical variable. Variables were screened by stepwise regression. The mRNA model included 11 predictors. The internal validation C index was 0.736. The lncRNA model has 15 predictors. The internal validation C index was 0.707. The third model combined the risk scores of the first two models with tumor stage. The internal validation C index was 0.794. In validation sets, all C-indexes of models were about 0.6, and three models had good calibration accuracy. Freely online calculator on the web at https://lhj0520.shinyapps.io/LUAD_prediction_model/.

Comprehensive Analysis Revealed the Potential Implications of m6A Regulators in Lung Adenocarcinoma

Background: The biological significance of RNA N6-methyladenosine (m6A) decoration in tumorigenicity and progression has been highlighted in recent studies, but whether m6A modification plays a potential role in tumor microenvironment (TME) formation and immune regulation in lung adenocarcinoma (LUAD) remains unclear.

Methods: m6A modification features were evaluated by analyzing the multi-omics features of 17 m6A regulators in over 1900 LUAD samples, and at the same time, the correlation between these modification patterns and TME characteristics was analyzed. An m6A score signature–based principal component analysis (PCA) algorithm was constructed to assess the prognosis and responses of individual patients to immunotherapeutic and targeted therapies.

Results: Three different m6A modification patterns were determined in 1901 LUAD samples, which were found to be related to diverse clinical outcomes via different biological pathways. Based on the m6A score extracted from the m6A-associated signature genes, LUAD patients were separated into high- and low-m6A score groups. It was discovered that patients with high m6A scores had longer survival, lower tumor mutation loads, and low PD-L1/PDCD1/CTLA4/TAG3 expression level. In addition, LUAD patients with high m6A scores displayed lower IC₅₀ to some targeted drugs, including nilotinib, erlotinib, imatinib, and lapatinib.

Conclusion: m6A modification was significantly associated with the TME and clinical outcomes. These findings may help gain more insights into the role of m6A decoration in the molecular mechanism of LUAD, thus facilitating the development of more effective personalized treatment strategies.