Abstract
During the past decade, the average 5-year survival rate of patients with Lung adenocarcinoma (LUAD) has remained < 20%, although the targeted therapies and novel immunotherapy approaches have held promise. Epigenetic modifications could provide prognostic value as molecular biomarkers, and we aimed to identify the independent risk of m6A-related lncRNAs to establish a risk model for the clinical prediction of prognoses in women with LUAD. In this study, we first assessed 31 N6-methyladenosine (m6A)-related lncRNAs associated with overall survival. Moreover, we evaluated the expression of the oncogenic driver and the tumor immune microenvironment (TIME) in two female LUAD subtypes (clusters 1 and 2) using consensus clustering. We also found 16 m6A-related lncRNAs as the independent prognostic indicator of women with LUAD and established a risk model developed from these lncRNAs. We comprehensively investigated the correlation between the TIME and m6A-related lncRNA and found that m6A-related lncRNA may significantly affect the immune cell infiltration level in LUAD. In conclusion, our study provides evidence on the prognostic prediction in women with LUAD and may help elucidate the processes and mechanisms of m6A-regulated lncRNAs.
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References
Camidge DR, Doebele RC, Kerr KM (2019) Comparing and contrasting predictive biomarkers for immunotherapy and targeted therapy of NSCLC. Nat Rev Clin Oncol 16(6):341–355
Campbell SL, Khosravi-Far R, Rossman KL, Clark GJ (1998) Der CJ, “Increasing complexity of Ras signaling,.” Oncogene 17(11):1395–1413
Choi YL, Soda M, Yamashita Y et al (2010) EML4-ALK mutations in lung cancer that confer resistance to ALK inhibitors. N Engl J Med 363(18):1734–1739
Gao C, Zhuang J, Li H et al (2021) Gene signatures of 6-methyladenine regulators in women with lung adenocarcinoma and development of a risk scoring system: a retrospective study using the cancer genome atlas database. Aging (albany NY) 13(3):3957–3968
Ghafouri-Fard S, Shoorei H, Branicki W, Taheri M (2020) Non-coding RNA profile in lung cancer. Exp Mol Pathol 114:104411
Han D, Liu J, Chen C et al (2019) Author correction: anti-tumour immunity controlled through mRNA m(6)A methylation and YTHDF1 in dendritic cells. Nature 568(7751):E3
He S, Song W, Cui S et al (2023) Modulation of miR-146b by N6-methyladenosine modification remodels tumor-associated macrophages and enhances anti-PD-1 therapy in colorectal cancer. Cell Oncol (dordr) 2023:1–16
Jing Z, Guo S, Zhang P, Liang Z (2020) LncRNA-associated ceRNA network reveals novel potential biomarkers of laryngeal squamous cell carcinoma. Technol Cancer Res Treat 19:1079253435
Li Y, Gu J, Xu F et al (2021) Molecular characterization, biological function, tumor microenvironment association and clinical significance of m6A regulators in lung adenocarcinoma. Brief Bioinform 22(4):bbaa225
Marchese FP, Raimondi I, Huarte M (2017) The multidimensional mechanisms of long noncoding RNA function. Genome Biol 18(1):206
Newman AM, Liu CL, Green MR et al (2015) Robust enumeration of cell subsets from tissue expression profiles. Nat Methods 12(5):453–457
Peng WX, Koirala P, Mo YY (2017) LncRNA-mediated regulation of cell signaling in cancer. Oncogene 36(41):5661–5667
Shulman Z, Stern-Ginossar N (2020) The RNA modification N(6)-methyladenosine as a novel regulator of the immune system. Nat Immunol 21(5):501–512
Sundar R, Soong R, Cho BC, Brahmer JR, Soo RA (2014) Immunotherapy in the treatment of non-small cell lung cancer. Lung Cancer 85(2):101–109
Tang H, Wang Z, Shao Q, Wang Y, Yang Q (2020) Comprehensive analysis of competing endogenous RNA (ceRNA) network based on RNAs differentially expressed in lung adenocarcinoma using the cancer genome atlas (TCGA) database. Med Sci Monit 26:e922676
Tian Y, Yu M, Sun L et al (2020) Distinct patterns of mRNA and lncRNA expression differences between lung squamous cell carcinoma and adenocarcinoma. J Comput Biol 27(7):1067–1078
Verma M (2015) The role of epigenomics in the study of cancer biomarkers and in the development of diagnostic tools. Adv Exp Med Biol 867:59–80
Wang A, Wang HY, Liu Y et al (2015) The prognostic value of PD-L1 expression for non-small cell lung cancer patients: a meta-analysis. Eur J Surg Oncol 41(4):450–456
Wang Y, Han D, Pan L, Sun J (2018) The positive feedback between lncRNA TNK2-AS1 and STAT3 enhances angiogenesis in non-small cell lung cancer. Biochem Biophys Res Commun 507(1–4):185–192
Wang H, Hu X, Huang M et al (2019) Mettl3-mediated mRNA m(6)A methylation promotes dendritic cell activation. Nat Commun 10(1):1898
Weber DG, Johnen G, Casjens S et al (2013) Evaluation of long noncoding RNA MALAT1 as a candidate blood-based biomarker for the diagnosis of non-small cell lung cancer. BMC Res Notes 6:518
Wilkerson MD, Hayes DN (2010) ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics 26(12):1572–1573
Xu JY, Zhang C, Wang X et al (2020) Integrative proteomic characterization of human lung adenocarcinoma. Cell 182(1):245–261
Xu F, Huang X, Li Y, Chen Y, Lin L (2021) m(6)A-related lncRNAs are potential biomarkers for predicting prognoses and immune responses in patients with LUAD. Mol Ther Nucleic Acids 24:780–791
Xue W, Wang Y, Gong Z et al (2021) A mirna-based signature is associated with tumor mutational burden in colon adenocarcinoma. Front Oncol. https://doi.org/10.3389/fonc.2021.634841
Xue W, Dong B, Wang Y et al (2022) A novel prognostic index of stomach adenocarcinoma based on immunogenomic landscape analysis and immunotherapy options. Exp Mol Pathol 128:104832
Xue W, Qiu K, Dong B et al (2023) Disulfidptosis-associated long non-coding RNA signature predicts the prognosis, tumor microenvironment, and immunotherapy and chemotherapy options in colon adenocarcinoma. Cancer Cell Int 23(1):1–15
Ye J, Wu S, Pan S, Huang J, Ge L (2020) Risk scoring based on expression of long non-coding RNAs can effectively predict survival in hepatocellular carcinoma patients with or without fibrosis. Oncol Rep 43(5):1451–1466
Yi L, Wu G, Guo L, Zou X, Huang P (2020) Comprehensive analysis of the PD-L1 and immune infiltrates of m(6)A RNA methylation regulators in head and neck squamous cell carcinoma. Mol Ther Nucleic Acids 21:299–314
Yoda S, Dagogo-Jack I, Hata AN (2019) Targeting oncogenic drivers in lung cancer: recent progress, current challenges and future opportunities. Pharmacol Ther 193:20–30
Yu J, Mao W, Sun S et al (2021) Identification of an m6A-related lncRNA signature for predicting the prognosis in patients with kidney renal clear cell carcinoma. Front Oncol 11:663263
Zhang R, Xia Y, Wang Z et al (2017) Serum long non coding RNA MALAT-1 protected by exosomes is up-regulated and promotes cell proliferation and migration in non-small cell lung cancer. Biochem Biophys Res Commun 490(2):406–414
Zhao BS, Roundtree IA, He C (2017) Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol 18(1):31–42
Zhou W, Bai C, Long C, Hu L, Zheng Y (2021) Construction and characterization of long non-coding RNA-associated networks to reveal potential prognostic biomarkers in human lung adenocarcinoma. Front Oncol 11:720400
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The authors report no conflicts of interest in this work. We would like to thank Editage (www.editage.com) for English language editing.
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This work was supported by the Changsha Natural Science Foundation of China (Grant Number: kq2014230).
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CH, ZW, and HY developed the idea of the study, participated in its design and coordination and helped to draft the manuscript. SW and WW contributed to the acquisition and interpretation of data. YY and CC provided critical review and substantially revised the manuscript. All authors read and approved the final manuscript.
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Wu, S., Tu, Q., Yuan, H. et al. Comprehensive Analysis for Predicting Prognoses and Immune Responses of m6A-Related lncRNAs in Women with Lung Adenocarcinoma. Biochem Genet (2023). https://doi.org/10.1007/s10528-023-10572-w
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DOI: https://doi.org/10.1007/s10528-023-10572-w