Multi-Omics analysis identifies a lncRNA-related prognostic signature to predict bladder cancer recurrence

References

• Bray F, Ferlay J, Soerjomataram I, et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68(6):394–424.
   PubMed Web of Science ®Google Scholar
• Kaufman DS, Shipley WU, Feldman AS. Bladder cancer. Lancet. 2009;374(9685):239–249.
   PubMed Web of Science ®Google Scholar
• Kamat AM, Hahn NM, Efstathiou JA, et al. Bladder cancer. Lancet. 2016;388(10061):2796–2810.
   PubMed Web of Science ®Google Scholar
• Del Bene G, Calabro F, Giannarelli D, et al. Neoadjuvant vs. Adjuvant chemotherapy in muscle invasive bladder cancer (MIBC): analysis from the RISC database. Front Oncol. 2018;8:463.
   PubMed Web of Science ®Google Scholar
• Hautmann RE, Gschwend JE, de Petriconi RC, et al. Cystectomy for transitional cell carcinoma of the bladder: results of a surgery only series in the neobladder era. J Urol. 2006;176(2):486–492. discussion 91–2.
   PubMed Web of Science ®Google Scholar
• Wosnitzer MS, Hruby GW, Murphy AM, et al. A comparison of the outcomes of neoadjuvant and adjuvant chemotherapy for clinical T2-T4aN0-N2M0 bladder cancer. Cancer. 2012;118(2):358–364.
   PubMed Web of Science ®Google Scholar
• Sylvester RJ, van der Meijden AP, Oosterlinck W, et al. Predicting recurrence and progression in individual patients with stage Ta T1 bladder cancer using EORTC risk tables: a combined analysis of 2596 patients from seven EORTC trials. Eur Urol. 2006;49(3): 466–5. discussion 75–7. DOI:10.1016/j.eururo.2005.12.031.
   PubMed Web of Science ®Google Scholar
• Patel VG, Oh WK, Galsky MD. Treatment of muscle-invasive and advanced bladder cancer in 2020. CA Cancer J Clin. 2020;70(5):404–423.
   PubMed Web of Science ®Google Scholar
• Dobruch J, Daneshmand S, Fisch M, et al. Gender and bladder cancer: a collaborative review of etiology, biology, and outcomes. Eur Urol. 2016;69(2):300–310.
   PubMed Web of Science ®Google Scholar
• Evans JR, Feng FY, Chinnaiyan AM. The bright side of dark matter: lncRNAs in cancer. J Clin Invest. 2016;126(8):2775–2782.
   PubMed Web of Science ®Google Scholar
• Zhan Y, Chen Z, He S, et al. Long non-coding RNA SOX2OT promotes the stemness phenotype of bladder cancer cells by modulating SOX2. Mol Cancer. 2020;19(1):25.
   PubMed Web of Science ®Google Scholar
• He W, Zhong G, Jiang N, et al. Long noncoding RNA BLACAT2 promotes bladder cancer-associated lymphangiogenesis and lymphatic metastasis. J Clin Invest. 2018;128(2):861–875.
   PubMed Web of Science ®Google Scholar
• Chen C, He W, Huang J, et al. LNMAT1 promotes lymphatic metastasis of bladder cancer via CCL2 dependent macrophage recruitment. Nat Commun. 2018;9(1):3826.
   PubMed Web of Science ®Google Scholar
• de Jong JJ, Liu Y, Robertson AG, et al. Long non-coding RNAs identify a subset of luminal muscle-invasive bladder cancer patients with favorable prognosis. Genome Med. 2019;11(1):60.
   PubMed Web of Science ®Google Scholar
• Du Y, Wang B, Jiang X, et al. Identification and validation of a stromal EMT related LncRNA signature as a potential marker to predict bladder cancer outcome. Front Oncol. 2021;11:620674.
   PubMed Web of Science ®Google Scholar
• Mao X, Chen S, Li G. Identification of a ten-long noncoding RNA signature for predicting the survival and immune status of patients with bladder urothelial carcinoma based on the GEO database: a superior machine learning model. Aging (Albany NY). 2021;13(5):6957–6981.
   PubMedGoogle Scholar
• Gao X, Zhang S, Chen Y, et al. Development of a novel six-long noncoding RNA signature predicting survival of patients with bladder urothelial carcinoma. J Cell Biochem. 2019;120(12):19796–19809.
   PubMed Web of Science ®Google Scholar
• Zhang S, Zhang J, An Y, et al. Multi-omics approaches identify SF3B3 and SIRT3 as candidate autophagic regulators and druggable targets in invasive breast carcinoma. Acta Pharm Sin B. 2021;11(5):1227–1245.
   PubMed Web of Science ®Google Scholar
• Gout AM, Arunachalam S, Finkelstein DB, et al. Data-driven approaches to advance research and clinical care for pediatric cancer. Biochim Biophys Acta Rev Cancer. 2021;1876(1):188571.
   PubMed Web of Science ®Google Scholar
• Lee D, Park Y, Kim S. Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches. Brief Bioinform. 2021;22:3.
   PubMed Web of Science ®Google Scholar
• Lewis JE, Kemp ML. Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance. Nat Commun. 2021;12(1):2700.
   PubMed Web of Science ®Google Scholar
• Murugesan M, Premkumar K. Systemic multi-omics analysis reveals amplified P4HA1 gene associated with prognostic and hypoxic regulation in breast cancer. Front Genet. 2021;12:632626.
   PubMed Web of Science ®Google Scholar
• Zhao Y, Gao Y, Xu X, et al. Multi-omics analysis of genomics, epigenomics and transcriptomics for molecular subtypes and core genes for lung adenocarcinoma. BMC Cancer. 2021;21(1):257.
   PubMed Web of Science ®Google Scholar
• Chaudhary K, Poirion OB, Lu L, et al. Deep learning-based multi-omics integration robustly predicts survival in liver cancer. Clin Cancer Res. 2018;24(6):1248–1259.
   PubMed Web of Science ®Google Scholar
• Harrow J, Denoeud F, Frankish A, et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7(Suppl 1):S4 1–9.
   PubMedGoogle Scholar
• Riester M, Taylor JM, Feifer A, et al. Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer. Clin Cancer Res. 2012;18(5):1323–1333.
   PubMed Web of Science ®Google Scholar
• Hicks SC, Irizarry RA. Quantro: a data-driven approach to guide the choice of an appropriate normalization method. Genome Biol. 2015;16:117.
   PubMed Web of Science ®Google Scholar
• Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4(2):249–264.
   PubMed Web of Science ®Google Scholar
• Mermel CH, Schumacher SE, Hill B, et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 2011;12(4):R41.
   PubMed Web of Science ®Google Scholar
• Lawrence MS, Stojanov P, Polak P, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499(7457):214–218.
   PubMed Web of Science ®Google Scholar
• Tibshirani R. The lasso method for variable selection in the Cox model. Stat Med. 1997;16(4):385–395.
   PubMed Web of Science ®Google Scholar
• Liu G, Locascio JJ, Corvol JC, et al. Prediction of cognition in Parkinson’s disease with a clinical-genetic score: a longitudinal analysis of nine cohorts. Lancet Neurol. 2017;16(8):620–629.
   PubMed Web of Science ®Google Scholar
• Fluss R, Faraggi D, Reiser B. Estimation of the Youden Index and its associated cutoff point. Biom J. 2005;47(4):458–472.
   PubMed Web of Science ®Google Scholar
• Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–15550.
   PubMed Web of Science ®Google Scholar
• Mootha VK, Lindgren CM, Eriksson KF, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34(3):267–273.
   PubMed Web of Science ®Google Scholar
• Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–457.
   PubMed Web of Science ®Google Scholar
• Yoshihara K, Shahmoradgoli M, Martinez E, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612.
   PubMed Web of Science ®Google Scholar
• Raposo CJ, McElroy KA, Fuchs SM. The Epithelial adhesin 1 tandem repeat region mediates protein display through multiple mechanisms. FEMS Yeast Res. 2020;20:3.
   Web of Science ®Google Scholar
• Luo WL, Luo MX, He RZ, et al. Reveals the pan-cancer landscape of bone morphogenetic proteins. Med Sci Monit. 2020;26:e920943.
   PubMed Web of Science ®Google Scholar
• Seal DB, Das V, Goswami S, et al. Estimating gene expression from DNA methylation and copy number variation: a deep learning regression model for multi-omics integration. Genomics. 2020;112(4):2833–2841.
   PubMed Web of Science ®Google Scholar
• Bao Z, Zhang W, Dong D. A potential prognostic lncRNA signature for predicting survival in patients with bladder urothelial carcinoma. Oncotarget. 2017;8(6):10485–10497.
   PubMedGoogle Scholar
• Barik GK, Sahay O, Behera A, et al. Keep your eyes peeled for long noncoding RNAs: explaining their boundless role in cancer metastasis, drug resistance, and clinical application. Biochim Biophys Acta Rev Cancer. 2021;1876(2):188612.
   PubMed Web of Science ®Google Scholar
• Ahmad S, Abbas M, Ullah MF, et al. Long non-coding RNAs regulated NF-kappaB signaling in cancer metastasis: micromanaging by not so small non-coding RNAs. Semin Cancer Biol. 2021. DOI:10.1016/j.semcancer.2021.07.015.
   Google Scholar
• Kong FE, Tang YQ, Gong YF, et al. Identification of prognostic claudins signature in hepatocellular carcinoma from a hepatocyte differentiation model. Hepatol Int. 2020;14(4):521–533.
   PubMed Web of Science ®Google Scholar
• Bo H, Zhu F, Liu Z, et al. Integrated analysis of high-throughput sequencing data reveals the key role of LINC00467 in the invasion and metastasis of testicular germ cell tumors. Cell Death Discov. 2021;7(1):206.
   PubMed Web of Science ®Google Scholar
• Unfried JP, Marin-Baquero M, Rivera-Calzada A, et al. Long noncoding RNA NIHCOLE promotes ligation efficiency of DNA double-strand breaks in hepatocellular carcinoma. Cancer Res. 2021;81(19):4910–4925.
   PubMed Web of Science ®Google Scholar
• Li RH, Tian T, Ge QW, et al. A phosphatidic acid-binding lncRNA SNHG9 facilitates LATS1 liquid-liquid phase separation to promote oncogenic YAP signaling. Cell Res. 2021;31(10):1088-1105.
   Web of Science ®Google Scholar
• Huang Z, Zhou JK, Peng Y, et al. The role of long noncoding RNAs in hepatocellular carcinoma. Mol Cancer. 2020;19(1):77.
   PubMed Web of Science ®Google Scholar
• Cheng J, Meng J, Zhu L, et al. Exosomal noncoding RNAs in Glioma: biological functions and potential clinical applications. Mol Cancer. 2020;19(1):66.
   PubMed Web of Science ®Google Scholar
• Cao Y, Tian T, Li W, et al. Long non-coding RNA in bladder cancer. Clin Chim Acta. 2020;503:113–121.
   PubMed Web of Science ®Google Scholar
• Liu Y, Zhang P, Wu Q, et al. Long non-coding RNA NR2F1-AS1 induces breast cancer lung metastatic dormancy by regulating NR2F1 and DeltaNp63. Nat Commun. 2021;12(1):5232.
   PubMed Web of Science ®Google Scholar
• Kikuchi Y, Tokita S, Hirama T, et al. CD8+ T-cell immune surveillance against a tumor antigen encoded by the oncogenic long non-coding RNA, PVT1. Cancer Immunol Res. 2021. DOI:10.1158/2326-6066.CIR-20-0964.
   PubMed Web of Science ®Google Scholar
• Ma L, Xu A, Kang L, et al. LSD1-Demethylated LINC01134 confers oxaliplatin resistance via SP1-induced p62 transcription in hepatocellular carcinoma. Hepatology 2021. DOI:10.1002/hep.32079.
   Web of Science ®Google Scholar
• Zhang MX, Zhang LZ, Fu LM, et al. Positive feedback regulation of lncRNA PVT1 and HIF2alpha contributes to clear cell renal cell carcinoma tumorigenesis and metastasis. Oncogene. 2021;40(37):5639–5650.
   PubMed Web of Science ®Google Scholar