References
- Van Arendonk KJ, Chung DH. Neuroblastoma: tumor biology and its implications for staging and treatment. Children (Basel). 2019;6.
- Moreno L, Guo D, Irwin MS, et al. A nomogram of clinical and biologic factors to predict survival in children newly diagnosed with high-risk neuroblastoma: an International Neuroblastoma Risk Group project. Pediatr Blood Cancer. 2021;68:e28794.
- Bellini A, Bernard V, Leroy Q, et al. Deep sequencing reveals occurrence of subclonal ALK mutations in neuroblastoma at diagnosis. Clin Cancer Res. 2015;21:4913–4921.
- Pinto N, Mayfield JR, Raca G, et al. Segmental chromosomal aberrations in localized neuroblastoma can be detected in formalin-fixed paraffin-embedded tissue samples and are associated with recurrence. Pediatr Blood Cancer. 2016;63:1019–1023.
- Maleki Vareki S. High and low mutational burden tumors versus immunologically hot and cold tumors and response to immune checkpoint inhibitors. J Immunother Cancer. 2018;6:157.
- Pugh TJ, Morozova O, Attiyeh EF, et al. The genetic landscape of high-risk neuroblastoma. Nat Genet. 2013;45:279–284.
- Applebaum MA, Barr EK, Karpus J, et al. 5-Hydroxymethylcytosine profiles in circulating cell-free DNA associate with disease burden in children with neuroblastoma. Clin Cancer Res. 2020;26:1309–1317.
- Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science. 2009;324:929–930.
- Cao JZ, Hains AE, and Godley LA. Regulation of 5-hydroxymethylcytosine distribution by the TET enzymes. In: Jurga S, Barciszewski J, editors. The DNA, RNA, and histone methylomes. Cham, Switzerland: Soringer International Publishing; 2019. p. 229–263.
- Ficz G, Branco MR, Seisenberger S, et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature. 2011;473:398–402.
- Madzo J, Liu H, Rodriguez A, et al. Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis. Cell Rep. 2014;6:231–244.
- Mariani CJ, Vasanthakumar A, Madzo J, et al. TET1-mediated hydroxymethylation facilitates hypoxic gene induction in neuroblastoma. Cell Rep. 2014;7:1343–1352.
- He YF, Li BZ, Li Z, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science. 2011;333:1303–1307.
- Ito S, D’Alessio AC, Taranova OV, et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature. 2010;466:1129–1133.
- Rankin EB, Giaccia AJ. The role of hypoxia-inducible factors in tumorigenesis. Cell Death Differ. 2008;15:678–685.
- Iliopoulos O, Levy AP, Jiang C, et al. Negative regulation of hypoxia-inducible genes by the von Hippel-Lindau protein. Proc Natl Acad Sci U S A. 1996;93:10595–10599.
- Huertas-Castaño C, Gómez-Muñoz MA, Pardal R, et al. Hypoxia in the initiation and progression of neuroblastoma tumours. Int J Mol Sci. 2019;21:39.
- Lutz W, Stöhr M, Schürmann J, et al. Conditional expression of N-myc in human neuroblastoma cells increases expression of alpha-prothymosin and ornithine decarboxylase and accelerates progression into S-phase early after mitogenic stimulation of quiescent cells. Oncogene. 1996;13:803–812.
- Concordet JP, Haeussler M. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Res. 2018;46:W242–w245.
- Sanjana NE, Shalem O, Zhang F. Improved vectors and genome-wide libraries for CRISPR screening. Nat Methods. 2014;11:783–784.
- Moffat J, Grueneberg DA, Yang X, et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell. 2006;124:1283–1298.
- Camenisch G, Wenger RH, and Gassmann M. DNA binding activity of hypoxia-inducible factors. In: Armstrong D, editor. Oxidants and Antioxidants: ultrastructure and molecular biology protocols. Totowa, New Jersey: Humana Press; 2002. p. 117–129.
- Lignitto L, LeBoeuf SE, Homer H, et al. Nrf2 activation promotes lung cancer metastasis by inhibiting the degradation of Bach1. Cell. 2019;178:316–329.e318.
- Schneider CA, Rasband WS, Eliceiri KW. NIH image to imageJ: 25 years of image analysis. Nat Methods. 2012;9:671–675.
- Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–1760.
- Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9:R137.
- Robinson JT, Thorvaldsdóttir H, Winckler W, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–26.
- Song L, James SR, Kazim L, et al. Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry. Anal Chem. 2005;77:504–510.
- Song CX, Szulwach KE, Fu Y, et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol. 2011;29:68–72.
- Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–169.
- Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–842.
- Thomas PD, Campbell MJ, Kejariwal A, et al. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 2003;13:2129–2141.
- Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562–578.
- Souvorov A, Kapustin Y, Kiryutin B, et al. (2010) Gnomon–NCBI eukaryotic gene prediction tool. National Center for Biotechnology Information, 1–24.
- Justus CR, Leffler N, Ruiz-Echevarria M, et al. In vitro cell migration and invasion assays. J Vis Exp. 2014. DOI:10.3791/51046
- Chlenski A, Park C, Dobratic M, et al. Maternal embryonic leucine zipper kinase (MELK), a potential therapeutic target for neuroblastoma. Mol Cancer Ther. 2019;18:507–516.
- Gartlgruber M, Sharma AK, Quintero A, et al. Super enhancers define regulatory subtypes and cell identity in neuroblastoma. Nat Cancer. 2021;2:114–128.
- Harenza JL, Diamond MA, Adams RN, et al. Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines. Sci Data. 2017;4:170033.
- Zeid R, Lawlor MA, Poon E, et al. Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma. Nat Genet. 2018;50:515–523.
- Althoff K, Beckers A, Bell E, et al. A Cre-conditional MYCN-driven neuroblastoma mouse model as an improved tool for preclinical studies. Oncogene. 2015;34:3357–3368.
- Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576–589.
- Gao T, He B, Liu S, et al. EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types. Bioinformatics. 2016;32:3543–3551.
- Whyte WA, Orlando DA, Hnisz D, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013;153:307–319.
- Kent WJ, Sugnet CW, Furey TS, et al. The human genome browser at UCSC. Genome Res. 2002;12:996–1006.
- Neri F, Incarnato D, Krepelova A, et al. TET1 is controlled by pluripotency-associated factors in ESCs and downmodulated by PRC2 in differentiated cells and tissues. Nucleic Acids Res. 2015;43:6814–6826.
- Upton K, Modi A, Patel K, et al. Epigenomic profiling of neuroblastoma cell lines. Sci Data. 2020;7:116.
- Zhang W, Xia W, Wang Q, et al. Isoform switch of TET1 regulates DNA demethylation and mouse development. Mol Cell. 2016;64:1062–1073.
- Good CR, Madzo J, Patel B, et al. A novel isoform of TET1 that lacks a CXXC domain is overexpressed in cancer. Nucleic Acids Res. 2017;45:8269–8281.
- Greer CB, Wright J, Weiss JD, et al. Tet1 isoforms differentially regulate gene expression, synaptic transmission, and memory in the mammalian brain. J Neurosci. 2021;41:578–593.
- Van groningen T, Koster J, Valentijn LJ, et al. Neuroblastoma is composed of two super-enhancer-associated differentiation states. Nat Genet. 2017;49:1261–1266.
- Thienpont B, Steinbacher J, Zhao H, et al. Tumour hypoxia causes DNA hypermethylation by reducing TET activity. Nature. 2016;537:63–68.
- Laukka T, Mariani CJ, Ihantola T, et al. Fumarate and succinate regulate expression of hypoxia-inducible genes via TET enzymes. J Biol Chem. 2016;291:4256–4265.
- Costa Y, Ding J, Theunissen TW, et al. NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature. 2013;495:370–374.
- Lio CW, Zhang J, González-Avalos E, et al. Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility. Elife. 2016;5.
- Bhaskara VK, Mohanam I, Rao JS, et al. Intermittent hypoxia regulates stem-like characteristics and differentiation of neuroblastoma cells. PLoS One. 2012;7:e30905.
- Jögi A, Vallon-Christersson J, Holmquist L, et al. Human neuroblastoma cells exposed to hypoxia: induction of genes associated with growth, survival, and aggressive behavior. Exp Cell Res. 2004;295:469–487.
- Domanska UM, Kruizinga RC, Nagengast WB, et al. A review on CXCR4/CXCL12 axis in oncology: no place to hide. Eur J Cancer. 2013;49:219–230.
- Russell HV, Hicks J, Okcu MF, et al. CXCR4 expression in neuroblastoma primary tumors is associated with clinical presentation of bone and bone marrow metastases. J Pediatr Surg. 2004;39:1506–1511.
- Korbecki J, Kojder K, Kapczuk P, et al. The effect of hypoxia on the expression of CXC chemokines and CXC chemokine receptors-A review of literature. Int J Mol Sci. 2021;22:843.
- Cohn SL, Salwen H, Quasney MW, et al. Prolonged N-myc protein half-life in a neuroblastoma cell line lacking N-myc amplification. Oncogene. 1990;5:1821–1827.
- Meier R, Mühlethaler-Mottet A, Flahaut M, et al. The chemokine receptor CXCR4 strongly promotes neuroblastoma primary tumour and metastatic growth, but not invasion. PLoS One. 2007;2:e1016.
- Klein S, Abraham M, Bulvik B, et al. CXCR4 promotes neuroblastoma growth and therapeutic resistance through miR-15a/16-1-mediated ERK and BCL2/Cyclin D1 pathways. Cancer Res. 2018;78:1471–1483.
- Chatterjee S, Behnam Azad B, Nimmagadda S. The intricate role of CXCR4 in cancer. Adv Cancer Res. 2014;124:31–82.
- Hornbeck PV, Zhang B, Murray B, et al. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 2015;43:D512–520.
- Bauer C, Göbel K, Nagaraj N, et al. Phosphorylation of TET proteins is regulated via O-GlcNAcylation by the O-linked N-acetylglucosamine transferase (OGT). J Biol Chem. 2015;290:4801–4812.
- Jeong JJ, Gu X, Nie J, et al. Cytokine-regulated phosphorylation and activation of TET2 by JAK2 in hematopoiesis. Cancer Discov. 2019;9:778–795.
- Bland, JM , and Altman, DG. Multiple significance tests: the Bonferroni method. BMJ. 1995;310(6973):170. doi:10.1136/bmj.310.6973.170.
- Mi H, Muruganujan A, Casagrande JT, et al. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc. 2013;8:1551–1566.