Somatic mutation-associated risk index based on lncRNA expression for predicting prognosis in acute myeloid leukemia

References

• Siegel RL, Miller KD, Fuchs HE, et al. Cancer Statistics, 2021. CA Cancer J Clin. 2021;71(1):7–33.
   PubMed Web of Science ®Google Scholar
• Blum WG, Mims AS. Treating acute myeloid leukemia in the modern era: A primer. Cancer. 2020;126(21):4668–4677.
   PubMed Web of Science ®Google Scholar
• Negrini S, Gorgoulis VG, Halazonetis TD. Genomic instability--an evolving hallmark of cancer. Nat Rev Mol Cell Biol. 2010;11(3):220–228.
   PubMed Web of Science ®Google Scholar
• Sallmyr A, Fan J, Rassool FV. Genomic instability in myeloid malignancies: increased reactive oxygen species (ROS), DNA double strand breaks (DSBs) and error-prone repair. Cancer Lett. 2008;270(1):1–9.
   PubMed Web of Science ®Google Scholar
• Marcucci G, Haferlach T, Döhner H. Molecular genetics of adult acute myeloid leukemia: prognostic and therapeutic implications. J Clin Oncol. 2011;29(5):475–486.
   PubMed Web of Science ®Google Scholar
• Lischka A, Doberstein N, Freitag-Wolf S, et al. Genome Instability Profiles Predict Disease Outcome in a Cohort of 4,003 Patients with Breast Cancer. Clin Cancer Res. 2020;26(17):4606–4615.
   PubMed Web of Science ®Google Scholar
• Lin Y, Luo Y, Sun Y, et al. Genomic and transcriptomic alterations associated with drug vulnerabilities and prognosis in adenocarcinoma at the gastroesophageal junction. Nat Commun. 2020;11(1):6091.
   PubMed Web of Science ®Google Scholar
• Malihi PD, Graf RP, Rodriguez A, et al. Single-Cell Circulating Tumor Cell Analysis Reveals Genomic Instability as a Distinctive Feature of Aggressive Prostate Cancer. Clin Cancer Res. 2020;26(15):4143–4153.
   PubMed Web of Science ®Google Scholar
• Kronenwett U, Ploner A, Zetterberg A, et al. Genomic instability and prognosis in breast carcinomas. Cancer Epidemiol Biomarkers Prev. 2006;15(9):1630–1635.
   PubMed Web of Science ®Google Scholar
• Bao S, Hu T, Liu J, et al. Genomic instability-derived plasma extracellular vesicle-microRNA signature as a minimally invasive predictor of risk and unfavorable prognosis in breast cancer. J Nanobiotechnology. 2021;19(1):22.
   PubMed Web of Science ®Google Scholar
• Garzon R, Volinia S, Papaioannou D, et al. Expression and prognostic impact of lncRNAs in acute myeloid leukemia. Proc Natl Acad Sci U S A. 2014;111(52):18679–18684.
   PubMed Web of Science ®Google Scholar
• Cao L, Xiao PF, Tao YF, et al. Microarray profiling of bone marrow long non-coding RNA expression in Chinese pediatric acute myeloid leukemia patients. Oncol Rep. 2016;35(2):757–770.
   PubMed Web of Science ®Google Scholar
• Hu YP, Jin YP, Wu XS, et al. LncRNA-HGBC stabilized by HuR promotes gallbladder cancer progression by regulating miR-502-3p/SET/AKT axis. Mol Cancer. 2019;18(1):167.
   PubMed Web of Science ®Google Scholar
• Zuo X, Chen Z, Gao W, et al. M6A-mediated upregulation of LINC00958 increases lipogenesis and acts as a nanotherapeutic target in hepatocellular carcinoma. J Hematol Oncol. 2020;13(1):5.
   PubMed Web of Science ®Google Scholar
• Zheng ZQ, Li ZX, Zhou GQ, et al. Long Noncoding RNA FAM225A Promotes Nasopharyngeal Carcinoma Tumorigenesis and Metastasis by Acting as ceRNA to Sponge miR-590-3p/miR-1275 and Upregulate ITGB3. Cancer Res. 2019;79(18):4612–4626.
   PubMed Web of Science ®Google Scholar
• Hu WL, Jin L, Xu A, et al. Guardin is a p53-responsive long non-coding RNA that is essential for genomic stability. Nat Cell Biol. 2018;20(4):492–502.
   PubMed Web of Science ®Google Scholar
• Munschauer M, Nguyen CT, Sirokman K, et al. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Nature. 2018;561(7721):132–136.
   PubMed Web of Science ®Google Scholar
• Bartonicek N, Maag JL, Dinger ME. Long noncoding RNAs in cancer: mechanisms of action and technological advancements. Mol Cancer. 2016;15(1):43.
   PubMed Web of Science ®Google Scholar
• Huarte M. The emerging role of lncRNAs in cancer. Nat Med. 2015;21(11):1253–1261.
   PubMed Web of Science ®Google Scholar
• Pu C, Tao S, Xu J, et al. Harnessing Genomic Stress for Antitumor Immunity. Antioxid Redox Signal. 2021;34(14):1128–1150.
   PubMed Web of Science ®Google Scholar
• Vago L, Gojo I. Immune escape and immunotherapy of acute myeloid leukemia. J Clin Invest. 2020;130(4):1552–1564.
   PubMed Web of Science ®Google Scholar
• Tibshirani R. Regression shrinkage and selection via the lasso: a retrospective. J R Stat Soc Series B Stat Methodol. 2011;73(3):273–282.
   Web of Science ®Google Scholar
• Dohner H, Estey E, Grimwade D, et al. Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel. Blood. 2017;129(4):424–447.
   PubMed Web of Science ®Google Scholar
• Schumacher TN, Schreiber RD. Neoantigens in cancer immunotherapy. Science. 2015;348(6230):69–74.
   PubMed Web of Science ®Google Scholar
• Grivennikov SI, Greten FR, Karin M. Immunity, inflammation, and cancer. Cell. 2010;140(6):883–899.
   PubMed Web of Science ®Google Scholar
• Wilky BA. Immune checkpoint inhibitors: The linchpins of modern immunotherapy. Immunol Rev. 2019;290(1):6–23.
   PubMed Web of Science ®Google Scholar
• Liersch R, Muller-Tidow C, Berdel WE, et al. Prognostic factors for acute myeloid leukaemia in adults--biological significance and clinical use. Br J Haematol. 2014;165(1):17–38.
   PubMed Web of Science ®Google Scholar
• Grimwade D, Ivey A, Huntly BJ. Molecular landscape of acute myeloid leukemia in younger adults and its clinical relevance. Blood. 2016;127(1):29–41.
   PubMed Web of Science ®Google Scholar
• Li H, Mar BG, Zhang H, et al. The EMT regulator ZEB2 is a novel dependency of human and murine acute myeloid leukemia. Blood. 2017;129(4):497–508.
   PubMed Web of Science ®Google Scholar
• Carter SL, Eklund AC, Kohane IS, et al. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet. 2006;38(9):1043–1048.
   PubMed Web of Science ®Google Scholar
• Hieronymus H, Murali R, Tin A, et al. Tumor copy number alteration burden is a pan-cancer prognostic factor associated with recurrence and death. Elife. 2018;7:e37294.
   PubMed Web of Science ®Google Scholar
• Ling H, Spizzo R, Atlasi Y, et al. Ccat2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer. Genome Res. 2013;23(9):1446–1461.
   PubMed Web of Science ®Google Scholar
• Papaioannou D, Nicolet D, Ozer HG, et al. Prognostic and Biologic Relevance of Clinically Applicable Long Noncoding RNA Profiling in Older Patients with Cytogenetically Normal Acute Myeloid Leukemia. Mol Cancer Ther. 2019;18(8):1451–1459.
   PubMed Web of Science ®Google Scholar
• Sun J, Li W, Sun Y, et al. A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies. Nucleic Acids Res. 2014;42(15):9588–9601.
   PubMed Web of Science ®Google Scholar
• Wang G, Vasquez KM. Effects of Replication and Transcription on DNA Structure-Related Genetic Instability. Genes (Basel). 2017;8(1):17.
   PubMed Web of Science ®Google Scholar
• Sarek G, Marzec P, Margalef P, et al. Molecular basis of telomere dysfunction in human genetic diseases. Nat Struct Mol Biol. 2015;22(11):867–874.
   PubMed Web of Science ®Google Scholar
• Ley TJ, Ding L, Walter MJ, et al. Dnmt3a mutations in acute myeloid leukemia. N Engl J Med. 2010;363(25):2424–2433.
   PubMed Web of Science ®Google Scholar
• Kayser S, Levis MJ. Clinical implications of molecular markers in acute myeloid leukemia. Eur J Haematol. 2019;102(1):20–35.
   PubMed Web of Science ®Google Scholar
• Gale RE, Green C, Allen C, et al. The impact of FLT3 internal tandem duplication mutant level, number, size, and interaction with NPM1 mutations in a large cohort of young adult patients with acute myeloid leukemia. BLOOD. 2008;111(5):2776–2784.
   PubMed Web of Science ®Google Scholar
• Hellmann MD, Nathanson T, Rizvi H, et al. Genomic Features of Response to Combination Immunotherapy in Patients with Advanced Non-Small-Cell Lung Cancer. Cancer Cell. 2018;33(5):843–852.e4.
   PubMed Web of Science ®Google Scholar
• Rizvi NA, Hellmann MD, Snyder A, et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348(6230):124–128.
   PubMed Web of Science ®Google Scholar
• Chalmers ZR, Connelly CF, Fabrizio D, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med. 2017;9(1):34.
   PubMed Web of Science ®Google Scholar
• Zhang J, Hu X, Wang J, et al. Immune receptor repertoires in pediatric and adult acute myeloid leukemia. Genome Med. 2019;11(1):73.
   PubMed Web of Science ®Google Scholar
• van Galen P, Hovestadt V, Wadsworth IM, et al. Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity. Cell. 2019;176(6):1265–1281.e24.
   PubMed Web of Science ®Google Scholar
• Ustun C, Miller JS, Munn DH, et al. Regulatory T cells in acute myelogenous leukemia: is it time for immunomodulation? Blood. 2011;118(19):5084–5095.
   PubMed Web of Science ®Google Scholar
• Jia B, Wang L, Claxton DF, et al. Bone marrow CD8 T cells express high frequency of PD-1 and exhibit reduced anti-leukemia response in newly diagnosed AML patients. Blood Cancer J. 2018;8(3):34.
   PubMedGoogle Scholar
• Fife BT, Pauken KE, Eagar TN, et al. Interactions between PD-1 and PD-L1 promote tolerance by blocking the TCR-induced stop signal. Nat Immunol. 2009;10(11):1185–1192.
   PubMed Web of Science ®Google Scholar
• Keir ME, Liang SC, Guleria I, et al. Tissue expression of PD-L1 mediates peripheral T cell tolerance. J Exp Med. 2006;203(4):883–895.
   PubMed Web of Science ®Google Scholar
• Tan J, Yu Z, Huang J, et al. Increased PD-1+Tim-3+ exhausted T cells in bone marrow may influence the clinical outcome of patients with AML. Biomark Res. 2020;8:6.
   PubMed Web of Science ®Google Scholar
• Hobo W, Hutten T, Schaap N, et al. Immune checkpoint molecules in acute myeloid leukaemia: managing the double-edged sword. Br J Haematol. 2018;181(1):38–53.
   PubMed Web of Science ®Google Scholar
• Ghahremanloo A, Soltani A, Modaresi S, et al. Recent advances in the clinical development of immune checkpoint blockade therapy. Cell Oncol (Dordr). 2019;42(5):609–626.
   PubMed Web of Science ®Google Scholar
• Daver N, Garcia-Manero G, Basu S, et al. Efficacy, Safety, and Biomarkers of Response to Azacitidine and Nivolumab in Relapsed/Refractory Acute Myeloid Leukemia: A Nonrandomized, Open-Label, Phase II Study. Cancer Discov. 2019;9(3):370–383.
   PubMed Web of Science ®Google Scholar
• Ghosh A, Barba P, Perales MA. Checkpoint inhibitors in AML: are we there yet? Br J Haematol. 2020;188(1):159–167.
   PubMed Web of Science ®Google Scholar
• van der Lee DI, Reijmers RM, Honders MW, et al. Mutated nucleophosmin 1 as immunotherapy target in acute myeloid leukemia. J Clin Invest. 2019;129(2):774–785.
   PubMed Web of Science ®Google Scholar
• Perry JM, Tao F, Roy A, et al. Overcoming Wnt-beta-catenin dependent anticancer therapy resistance in leukaemia stem cells. Nat Cell Biol. 2020;22(6):689–700.
   PubMed Web of Science ®Google Scholar