Comprehensive analysis identifies ubiquitin ligase FBXO42 as a tumor-promoting factor in neuroblastoma

Louis, C. U. & Shohet, J. M. Neuroblastoma: Molecular pathogenesis and therapy. Annu. Rev. Med. 66, 49–63 (2015).Article 
CAS 
PubMed 

Google Scholar 
Schleiermacher, G., Janoueix-Lerosey, I. & Delattre, O. Recent insights into the biology of neuroblastoma. Int. J. Cancer 135(10), 2249–2261 (2014).Article 
CAS 
PubMed 

Google Scholar 
Irwin, M. S. et al. Revised neuroblastoma risk classification system: A report from the Children’s Oncology Group. J. Clin. Oncol. 39(29), 3229–3241 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Park, J. R. et al. Effect of tandem autologous stem cell transplant vs single transplant on event-free survival in patients with high-risk neuroblastoma: A randomized clinical trial. JAMA. 322(8), 746–755 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Matthay, K. K. et al. Neuroblastoma. Nat. Rev. Dis. Primers 2, 16078 (2016).Article 
PubMed 

Google Scholar 
Halliwell, B. & Wasil, M. Tetracyclines as antioxidants in rheumatoid arthritis: Scavenging of hypochlorous acid. J. Rheumatol. 15(3), 530 (1988).CAS 
PubMed 

Google Scholar 
Song, L. & Luo, Z. Q. Post-translational regulation of ubiquitin signaling. J. Cell Biol. 218(6), 1776–1786 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Weissman, A. M. Themes and variations on ubiquitylation. Nat. Rev. Mol. Cell Biol. 2(3), 169–178 (2001).Article 
CAS 
PubMed 

Google Scholar 
Ikeda, F. & Dikic, I. Atypical ubiquitin chains: new molecular signals. Protein modifications: Beyond the usual suspects’ review series. EMBO Rep. 9(6), 536–542 (2008).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Komander, D., Clague, M. J. & Urbe, S. Breaking the chains: Structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol. 10(8), 550–563 (2009).Article 
CAS 
PubMed 

Google Scholar 
Muratani, M. & Tansey, W. P. How the ubiquitin-proteasome system controls transcription. Nat. Rev. Mol. Cell Biol. 4(3), 192–201 (2003).Article 
CAS 
PubMed 

Google Scholar 
Chen, L., Liu, S. & Tao, Y. Regulating tumor suppressor genes: Post-translational modifications. Signal Transduct. Target Ther. 5(1), 90 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhou, Y. et al. CCNB1IP1 prevents ubiquitination-mediated destabilization of MYCN and potentiates tumourigenesis of MYCN-amplificated neuroblastoma. Clin. Transl. Med. 13(7), e1328 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Dewson, G., Eichhorn, P. J. A. & Komander, D. Deubiquitinases in cancer. Nat. Rev. Cancer 23(12), 842–862 (2023).Article 
CAS 
PubMed 

Google Scholar 
Tavana, O. et al. HAUSP deubiquitinates and stabilizes N-Myc in neuroblastoma. Nat. Med. 22(10), 1180–1186 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Izumi, H. & Kaneko, Y. Trim32 facilitates degradation of MYCN on spindle poles and induces asymmetric cell division in human neuroblastoma cells. Cancer Res. 74(19), 5620–5630 (2014).Article 
CAS 
PubMed 

Google Scholar 
Becker, K., Marchenko, N. D., Maurice, M. & Moll, U. M. Hyperubiquitylation of wild-type p53 contributes to cytoplasmic sequestration in neuroblastoma. Cell Death Differ. 14(7), 1350–1360 (2007).Article 
CAS 
PubMed 

Google Scholar 
Yin, T. et al. An E3 ubiquitin-proteasome gene signature for predicting prognosis in patients with pancreatic cancer. Front. Immunol. 14, 1332626 (2023).Article 
CAS 
PubMed 

Google Scholar 
Zhang, J. et al. Ubiquitin-proteasome system-based signature to predict the prognosis and drug sensitivity of hepatocellular carcinoma. Front Pharmacol. 14, 1172908 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Luo, X. et al. Identification of a prognostic signature for ovarian cancer based on ubiquitin-related genes suggesting a potential role for FBXO9. Biomolecules. 13(12), 1724 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Tian, X. M. et al. A novel cuproptosis-related subtypes and gene signature associates with immunophenotype and predicts prognosis accurately in neuroblastoma. Front. Immunol. 13, 999849 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Shao, F. L., Liu, Q. Q. & Wang, S. Identify potential miRNA-mRNA regulatory networks contributing to high-risk neuroblastoma. Invest. New Drugs. 39(4), 901–913 (2021).Article 
CAS 
PubMed 

Google Scholar 
Shao, F., Wang, Z. & Wang, S. Identification of MYCN-related gene as a potential biomarker for neuroblastoma prognostic model by integrated analysis and quantitative real-time PCR. DNA Cell Biol. 40(2), 332–347 (2021).Article 
CAS 
PubMed 

Google Scholar 
Hartlieb, S. A. et al. Alternative lengthening of telomeres in childhood neuroblastoma from genome to proteome. Nat. Commun. 12(1), 1269 (2021).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wang, C. et al. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat. Biotechnol. 32(9), 926–932 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wang, X. et al. UbiBrowser 2.0: A comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. Nucleic Acids Res. 50(D1), D719–D728 (2022).Article 
CAS 
PubMed 

Google Scholar 
Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1), 27–30 (2000).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kanehisa, M. Toward understanding the origin and evolution of cellular organisms. Protein Sci. 28(11), 1947–1951 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M. & Ishiguro-Watanabe, M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 51(D1), D587–D592 (2023).Article 
CAS 
PubMed 

Google Scholar 
Subramanian, A. et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102(43), 15545–15550 (2005).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Liberzon, A. et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics. 27(12), 1739–1740 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Yoshihara, K. et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat. Commun. 4, 2612 (2013).Article 
ADS 
PubMed 

Google Scholar 
Newman, A. M. et al. Robust enumeration of cell subsets from tissue expression profiles. Nat. Methods 12(5), 453–457 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Racle, J., de Jonge, K., Baumgaertner, P., Speiser, D. E. & Gfeller, D. Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. Elife. 6, e26476 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Chen, Y., Li, Z. Y., Zhou, G. Q. & Sun, Y. An Immune-Related Gene Prognostic Index for head and neck squamous cell carcinoma. Clin. Cancer Res. 27(1), 330–341 (2021).Article 
PubMed 

Google Scholar 
Su, Z. et al. An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era. Genome Biol. 15(12), 523 (2014).Article 
PubMed 

Google Scholar 
Iasonos, A., Schrag, D., Raj, G. V. & Panageas, K. S. How to build and interpret a nomogram for cancer prognosis. J. Clin. Oncol. 26(8), 1364–1370 (2008).Article 
PubMed 

Google Scholar 
Sun, L. et al. Substrate phosphorylation and feedback regulation in JFK-promoted p53 destabilization. J. Biol. Chem. 286(6), 4226–4235 (2011).Article 
CAS 
PubMed 

Google Scholar 
Pickart, C. M. & Eddins, M. J. Ubiquitin: Structures, functions, mechanisms. Biochim. Biophys. Acta 1695(1–3), 55–72 (2004).Article 
CAS 
PubMed 

Google Scholar 
Cervia, L. D. et al. A ubiquitination cascade regulating the integrated stress response and survival in carcinomas. Cancer Discov. 13(3), 766–795 (2023).Article 
CAS 
PubMed 

Google Scholar 
Li, H. et al. Secreted LRPAP1 binds and triggers IFNAR1 degradation to facilitate virus evasion from cellular innate immunity. Signal Transduct. Target Ther. 8(1), 374 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Lu, X. et al. UBE2M-mediated neddylation of TRIM21 regulates obesity-induced inflammation and metabolic disorders. Cell Metab. 35(8), 1390–405 e8 (2023).Article 
CAS 
PubMed 

Google Scholar 
Bedekovics, T. et al. USP24 is a cancer-associated ubiquitin hydrolase, novel tumor suppressor, and chromosome instability gene deleted in neuroblastoma. Cancer Res. 81(5), 1321–1331 (2021).Article 
CAS 
PubMed 

Google Scholar 
Gu, Y. et al. The deubiquitinating enzyme UCHL1 is a favorable prognostic marker in neuroblastoma as it promotes neuronal differentiation. J. Exp. Clin. Cancer Res. 37(1), 258 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Meng, X., Li, H., Fang, E., Feng, J. & Zhao, X. Comparison of Stage 4 and Stage 4s neuroblastoma identifies autophagy-related gene and LncRNA signatures associated with prognosis. Front. Oncol. 10, 1411 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Hu, J. et al. Integrative analysis of multi-omics data for discovery of ferroptosis-related gene signature predicting immune activity in neuroblastoma. Front. Pharmacol. 14, 1162563 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Ma, K. et al. A signature based on five immune-related genes to predict the survival and immune characteristics of neuroblastoma. BMC Med. Genom. 15(1), 242 (2022).Article 
CAS 

Google Scholar 
Ren, J. et al. Lupiwighteone induces cell cycle arrest and apoptosis and activates the Nrf2/ARE pathway in human neuroblastoma cells. Biomed. Pharmacother. 69, 153–161 (2015).Article 
CAS 
PubMed 

Google Scholar 
Filomeni, G., Piccirillo, S., Rotilio, G. & Ciriolo, M. R. p38(MAPK) and ERK1/2 dictate cell death/survival response to different pro-oxidant stimuli via p53 and Nrf2 in neuroblastoma cells SH-SY5Y. Biochem. Pharmacol. 83(10), 1349–1357 (2012).Article 
CAS 
PubMed 

Google Scholar 
Chen, W., Lin, P., Bai, J., Fang, Y. & Zhang, B. Establishment and validation of a nomogram to predict cancer-specific survival in pediatric neuroblastoma patients. Front. Pediatr. 11, 1105922 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Xu, S. et al. Association of the CD4(+)/CD8(+) ratio with response to PD-1 inhibitor-based combination therapy and dermatological toxicities in patients with advanced gastric and esophageal cancer. Int. Immunopharmacol. 123, 110642 (2023).Article 
CAS 
PubMed 

Google Scholar 
Duchemann, B. et al. CD8(+)PD-1(+) to CD4(+)PD-1(+) ratio (PERLS) is associated with prognosis of patients with advanced NSCLC treated with PD-(L)1 blockers. J. Immunother. Cancer 10(2), e004012 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Wu, S. Y., Fu, T., Jiang, Y. Z. & Shao, Z. M. Natural killer cells in cancer biology and therapy. Mol. Cancer 19(1), 120 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cozar, B. et al. Tumor-infiltrating natural killer cells. Cancer Discov. 11(1), 34–44 (2021).Article 
CAS 
PubMed 

Google Scholar 
Skaar, J. R., Pagan, J. K. & Pagano, M. Mechanisms and function of substrate recruitment by F-box proteins. Nat. Rev. Mol. Cell Biol. 14(6), 369–381 (2013).Article 
CAS 
PubMed 

Google Scholar 
Jin, J. et al. Systematic analysis and nomenclature of mammalian F-box proteins. Genes Dev. 18(21), 2573–2580 (2004).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Veas-Perez de Tudela, M., Delgado-Esteban, M., Cuende, J., Bolanos, J. P. & Almeida, A. Human neuroblastoma cells with MYCN amplification are selectively resistant to oxidative stress by transcriptionally up-regulating glutamate cysteine ligase. J. Neurochem. 113(4), 819–825 (2010).Article 
CAS 
PubMed 

Google Scholar 
Zhang, W. et al. Comparative transcriptomic analysis of immune responses of the migratory locust, Locusta migratoria, to challenge by the fungal insect pathogen, Metarhizium acridum. BMC Genom. 16, 867 (2015).Article 

Google Scholar 
Teng, M. et al. A benchmark for RNA-seq quantification pipelines. Genome Biol. 17, 74 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Robert, C. & Watson, M. Errors in RNA-Seq quantification affect genes of relevance to human disease. Genome Biol. 16(1), 177 (2015).Article 
PubMed 
PubMed Central 

Google Scholar 
Everaert, C. et al. Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data. Sci. Rep. 7(1), 1559 (2017).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Pawlik, T. M. & Keyomarsi, K. Role of cell cycle in mediating sensitivity to radiotherapy. Int. J. Radiat. Oncol. Biol. Phys. 59(4), 928–942 (2004).Article 
PubMed 

Google Scholar 
Baskar, R., Dai, J., Wenlong, N., Yeo, R. & Yeoh, K. W. Biological response of cancer cells to radiation treatment. Front. Mol. Biosci. 1, 24 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Perez-Gonzalez, A., Bevant, K. & Blanpain, C. Cancer cell plasticity during tumor progression, metastasis and response to therapy. Nat. Cancer. 4(8), 1063–1082 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Liang, R. et al. Seleno-amino Acid metabolism reshapes the tumor microenvironment: From cytotoxicity to immunotherapy. Int. J. Biol. Sci. 20(7), 2779–2789 (2024).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Das, C. et al. A prismatic view of the epigenetic-metabolic regulatory axis in breast cancer therapy resistance. Oncogene 43, 1727 (2024).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar