Identification of Three lncRNA-Related Prognostic Signatures in Gastric Cancer by Integrated Multi-Omics Analysis

References

• Sung H , FerlayJ , SiegelRLet al. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J. Clin.71(3), 209–249 (2021).
   PubMed Web of Science ®Google Scholar
• He Y , WangY , LuanFet al. Chinese and global burdens of gastric cancer from 1990 to 2019. Cancer Med.10(10), 3461–3473 (2021).
   PubMed Web of Science ®Google Scholar
• Yusefi AR , BagheriLankarani K , BastaniP , RadinmaneshM , KavosiZ. Risk factors for gastric cancer: a systematic review. Asian Pac. J. Cancer Prev.19(3), 591–603 (2018).
   PubMedGoogle Scholar
• Smyth EC , NilssonM , GrabschHI , Van GriekenNC , LordickF. Gastric cancer. Lancet396(10251), 635–648 (2020).
   PubMed Web of Science ®Google Scholar
• Fang C , WangW , DengJYet al. Proposal and validation of a modified staging system to improve the prognosis predictive performance of the 8th AJCC/UICC pTNM staging system for gastric adenocarcinoma: a multicenter study with external validation. Cancer Commun. (Lond)38(1), 67 (2018).
   PubMedGoogle Scholar
• Tang S , LinL , ChengJet al. The prognostic value of preoperative fibrinogen-to-prealbumin ratio and a novel FFC score in patients with resectable gastric cancer. BMC Cancer20(1), 382 (2020).
   PubMed Web of Science ®Google Scholar
• Steele CD , AbbasiA , IslamSMAet al. Signatures of copy number alterations in human cancer. Nature606(7916), 984–991 (2022).
   PubMed Web of Science ®Google Scholar
• Baldacchino S , GrechG. Somatic copy number aberrations in metastatic patients: the promise of liquid biopsies. Semin. Cancer Biol.60, 302–310 (2020).
   PubMed Web of Science ®Google Scholar
• Deng X , LiS , KongFet al. Long noncoding RNA PiHL regulates p53 protein stability through GRWD1/RPL11/MDM2 axis in colorectal cancer. Theranostics10(1), 265–280 (2020).
   PubMed Web of Science ®Google Scholar
• Deng X , KongF , LiSet al. A KLF4/PiHL/EZH2/HMGA2 regulatory axis and its function in promoting oxaliplatin-resistance of colorectal cancer. Cell Death Dis.12(5), 485 (2021).
   PubMed Web of Science ®Google Scholar
• Bond GL , HuW , LevineA. A single nucleotide polymorphism in the MDM2 gene: from a molecular and cellular explanation to clinical effect. Cancer Res.65(13), 5481–5484 (2005).
   PubMed Web of Science ®Google Scholar
• Wang Z , DaiJ , HuNet al. Identification of new susceptibility loci for gastric non-cardia adenocarcinoma: pooled results from two Chinese genome-wide association studies. Gut66(4), 581–587 (2017).
   PubMed Web of Science ®Google Scholar
• Hussain S , TulsyanS , DarSAet al. Role of epigenetics in carcinogenesis: recent advancements in anticancer therapy. Semin. Cancer Biol.83, 441–451 (2022).
   PubMed Web of Science ®Google Scholar
• Shahabi S , KumaranV , CastilloJet al. LINC00261 Is an epigenetically regulated tumor suppressor essential for activation of the DNA damage response. Cancer Res.79(12), 3050–3062 (2019).
   PubMed Web of Science ®Google Scholar
• Lian Q , WangB , FanL , SunJ , WangG , ZhangJ. DNA methylation data-based molecular subtype classification and prediction in patients with gastric cancer. Cancer Cell Int.20, 349 (2020).
   PubMed Web of Science ®Google Scholar
• Alabi N , ShekaD , SiddiquiA , WangE. Methylation-based signatures for gastroesophageal tumor classification. Cancers (Basel)12(5), 1208 (2020).
   PubMed Web of Science ®Google Scholar
• Xu Y , WuT , LiFet al. Identification and comprehensive characterization of lncRNAs with copy number variations and their driving transcriptional perturbed subpathways reveal functional significance for cancer. Brief. Bioinform.21(6), 2153–2166 (2020).
   PubMed Web of Science ®Google Scholar
• Tan H , ZhangS , ZhangJet al. Long non-coding RNAs in gastric cancer: new emerging biological functions and therapeutic implications. Theranostics10(19), 8880–8902 (2020).
   PubMed Web of Science ®Google Scholar
• Huang Z , ZhouJK , PengY , HeW , HuangC. The role of long noncoding RNAs in hepatocellular carcinoma. Mol. Cancer19(1), 77 (2020).
   PubMed Web of Science ®Google Scholar
• Dragomir MP , KopetzS , AjaniJA , CalinGA. Non-coding RNAs in GI cancers: from cancer hallmarks to clinical utility. Gut69(4), 748–763 (2020).
   PubMed Web of Science ®Google Scholar
• Goodall GJ , WickramasingheVO. RNA in cancer. Nat. Rev. Cancer21(1), 22–36 (2021).
   PubMed Web of Science ®Google Scholar
• Cabili MN , TrapnellC , GoffLet al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev.25(18), 1915–1927 (2011).
   PubMed Web of Science ®Google Scholar
• Cui Y , CaoW , LiQet al. Evaluation of prostate cancer antigen 3 for detecting prostate cancer: a systematic review and meta-analysis. Sci. Rep.6, 25776 (2016).
   PubMed Web of Science ®Google Scholar
• Yuan Q , DengD , PanCet al. Integration of transcriptomics, proteomics, and metabolomics data to reveal HER2-associated metabolic heterogeneity in gastric cancer with response to immunotherapy and neoadjuvant chemotherapy. Front. Immunol.13, 951137 (2022).
   PubMed Web of Science ®Google Scholar
• Kong W , WangZ , WangB. Unveiling DNA damage repair-based molecular subtypes, tumor microenvironment and pharmacogenomic landscape in gastric cancer. Front Genet14, 1118889 (2023).
   PubMed Web of Science ®Google Scholar
• Lu X , MengJ , ZhouY , JiangL , YanF. MOVICS: an R package for multi-omics integration and visualization in cancer subtyping. Bioinformatics36(22–23), 5539–5541 (2020).
   Web of Science ®Google Scholar
• Mayakonda A , LinDC , AssenovY , PlassC , KoefflerHP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res.28(11), 1747–1756 (2018).
   PubMed Web of Science ®Google Scholar
• Mermel CH , SchumacherSE , HillB , MeyersonML , BeroukhimR , GetzG. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol.12(4), R41 (2011).
   PubMed Web of Science ®Google Scholar
• Love MI , HuberW , AndersS. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol.15(12), 550 (2014).
   PubMed Web of Science ®Google Scholar
• Shannon P , MarkielA , OzierOet al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res.13(11), 2498–2504 (2003).
   PubMed Web of Science ®Google Scholar
• Wu T , HuE , XuSet al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (Camb.)2(3), 100141 (2021).
   PubMedGoogle Scholar
• Gu Z , GuL , EilsR , SchlesnerM , BrorsB. circlize Implements and enhances circular visualization in R. Bioinformatics30(19), 2811–2812 (2014).
   PubMed Web of Science ®Google Scholar
• Morris TJ , ButcherLM , FeberAet al. ChAMP: 450k chip analysis methylation pipeline. Bioinformatics30(3), 428–430 (2014).
   PubMed Web of Science ®Google Scholar
• Tian Y , MorrisTJ , WebsterAPet al. ChAMP: updated methylation analysis pipeline for Illumina BeadChips. Bioinformatics33(24), 3982–3984 (2017).
   PubMed Web of Science ®Google Scholar
• Zhou RS , ZhangEX , SunQFet al. Integrated analysis of lncRNA–miRNA–mRNA ceRNA network in squamous cell carcinoma of tongue. BMC Cancer19(1), 779 (2019).
   PubMed Web of Science ®Google Scholar
• Liu TT , LiR , HuoCet al. Identification of CDK2-related immune forecast model and ceRNA in lung adenocarcinoma, a pan-cancer analysis. Front. Cell Dev. Biol.9, 682002 (2021).
   PubMed Web of Science ®Google Scholar
• Friedman J , HastieT , TibshiraniR. Regularization paths for generalized linear models via coordinate descent. J. Stat Softw.33(1), 1–22 (2010).
   PubMed Web of Science ®Google Scholar
• Huang ML , HungYH , LeeWM , LiRK , JiangBR. SVM-RFE based feature selection and Taguchi parameters optimization for multiclass SVM classifier. Sci. World J.2014, 795624 (2014).
   Google Scholar
• Zhang M , QiC , WangZet al. Molecular characterization of ctDNA from Chinese patients with advanced gastric adenocarcinoma reveals actionable alterations for targeted and immune therapy. J. Mol. Med. (Berl.)99(9), 1311–1321 (2021).
   PubMed Web of Science ®Google Scholar
• Sukri A , HanafiahA , KosaiNR. The roles of immune cells in gastric cancer: anti-cancer or pro-cancer?Cancers (Basel)14(16), 3922 (2022).
   PubMed Web of Science ®Google Scholar
• Augustin JE , SoussanP , BassAJ. Targeting the complexity of ERBB2 biology in gastroesophageal carcinoma. Ann. Oncol.33(11), 1134–1148 (2022).
   PubMed Web of Science ®Google Scholar
• Wu J , ZhouZ , LiJet al. CHD4 promotes acquired chemoresistance and tumor progression by activating the MEK/ERK axis. Drug Resist. Update66, 100913 (2023).
   PubMed Web of Science ®Google Scholar
• Liang L , FangJY , XuJ. Gastric cancer and gene copy number variation: emerging cancer drivers for targeted therapy. Oncogene35(12), 1475–1482 (2016).
   PubMed Web of Science ®Google Scholar
• Serra O , GalánM , GinestaMM , CalvoM , SalaN , SalazarR. Comparison and applicability of molecular classifications for gastric cancer. Cancer Treat. Rev.77, 29–34 (2019).
   PubMed Web of Science ®Google Scholar
• Duan Y , GongK , XuS , ZhangF , MengX , HanJ. Regulation of cholesterol homeostasis in health and diseases: from mechanisms to targeted therapeutics. Signal Transduct. Target. Ther.7(1), 265 (2022).
   PubMed Web of Science ®Google Scholar
• Moore LD , LeT , FanG. DNA methylation and its basic function. Neuropsychopharmacology38(1), 23–38 (2013).
   PubMed Web of Science ®Google Scholar
• Sun M , NieF , WangYet al. LncRNA HOXA11-AS promotes proliferation and invasion of gastric cancer by scaffolding the chromatin modification factors PRC2, LSD1, and DNMT1. Cancer Res.76(21), 6299–6310 (2016).
   PubMed Web of Science ®Google Scholar
• Su J , ChenD , RuanYet al. LncRNA MBNL1-AS1 represses gastric cancer progression via the TGF-β pathway by modulating miR-424-5p/Smad7 axis. Bioengineered13(3), 6978–6995 (2022).
   PubMed Web of Science ®Google Scholar
• Teng F , ZhangJX , ChenYet al. LncRNA NKX2-1-AS1 promotes tumor progression and angiogenesis via upregulation of SERPINE1 expression and activation of the VEGFR-2 signaling pathway in gastric cancer. Mol. Oncol.15(4), 1234–1255 (2021).
   PubMed Web of Science ®Google Scholar
• Ghafouri-Fard S , EsmaeiliM , TaheriM. H19 lncRNA: roles in tumorigenesis. Biomed. Pharmacother.123, 109774 (2020).
   PubMed Web of Science ®Google Scholar
• Liu F , CuiJ , XueD. LncRNA TRHDE-AS1 and MiR-1275 as promising prognostic biomarkers and effects on tumor cell progression in gastric cancer. Tohoku J. Exp. Med.261(1), 13–23 (2023).
   PubMed Web of Science ®Google Scholar
• Wu H , GuJ , ZhouDet al. LINC00160 mediated paclitaxel- and doxorubicin-resistance in breast cancer cells by regulating TFF3 via transcription factor C/EBPβ. J. Cell Mol. Med.24(15), 8589–8602 (2020).
   PubMed Web of Science ®Google Scholar
• Zhu W , ShengD , ShaoY , ZhangQ , PengY. STAT3-regulated LncRNA LINC00160 mediates cell proliferation and cell metabolism of prostate cancer cells by repressing RCAN1 expression. Mol. Cell Biochem.477(3), 865–875 (2022).
   PubMed Web of Science ®Google Scholar
• Zhang Z , YuW , TangDet al. Epigenomics-based identification of oestrogen-regulated long noncoding RNAs in ER+ breast cancer. RNA Biol.17(11), 1590–1602 (2020).
   PubMed Web of Science ®Google Scholar
• Anderson DM , AndersonKM , NelsonBRet al. A myocardin-adjacent lncRNA balances SRF-dependent gene transcription in the heart. Genes Dev.35(11–12), 835–840 (2021).
   PubMed Web of Science ®Google Scholar