Abstract
Neuroblastoma (NB) is a childhood tumor arising from neural crest-derived progenitor cells. Cyclin dependent kinase 2 (CDK2) has been suggested to be a promising therapeutic target in NB especially MYCN-amplified tumors. How CDK2 contributes to the development of NB is not fully understood. Here, we demonstrate that high CDK2 expression in NB correlates with advanced and high-risk disease, MYCN-amplification, poor prognosis, and undifferentiated tumors. We uncovered that CDK2 genetic or pharmacological inhibition induces neuronal differentiation in human NB cell lines, which effect is in general more prominent in the MYCN-amplified subtype. Further, we establish CDK2 as a MYCN target gene that modulate the MYC-pathway in MYCN-amplified NB. Notably, pharmacological inhibition of CDK2 in combination with MYCN inhibition or all-trans-retinoic acid (ATRA) differentiation therapy enhances neuronal differentiation in vitro. These results reveal an important function of CDK2 in NB and highlight CDK2 inhibition alone or in combination with MYC inhibitors and retinoids as a potential strategy for differentiation therapy in NB.
Data availability
The NB primary tumor gene expression datasets: the SEQC-498, Westermann-579, Kocak-649, and TARGET-161 analyzed during the current study are available in the R2: Genomics Analysis and Visualization Platform repository ([http://r2.amc.nl](http:/r2.amc.nl)). The gene expression dataset following CDK2-KD in the MYCN-amplified cell line IMR32 is available at gene expression omnibus under the accession number GSE16480. The single cell RNA-seq data is available at NB atlas (https://single-cell.be/nbatlas/). No datasets were generated in this study.
References
Maris, J. M., Hogarty, M. D., Bagatell, R. & Cohn, S. L. Neuroblastoma Lancet 369, 2106–2120, doi:https://doi.org/10.1016/s0140-6736(07)60983-0 (2007).
Matthay, K. K. et al. Neuroblastoma. Nat. Rev. Dis. Primers. 2, 16078. https://doi.org/10.1038/nrdp.2016.78 (2016).
Chung, C. et al. Neuroblastoma. Pediatr. Blood Cancer. 68 Suppl 2, e28473. https://doi.org/10.1002/pbc.28473 (2021).
Cohn, S. L. et al. The international neuroblastoma risk group (INRG) classification system: an INRG task force report. J. Clin. Oncol. 27, 289–297. https://doi.org/10.1200/jco.2008.16.6785 (2009).
Pinto, N. R. et al. Advances in risk classification and treatment strategies for neuroblastoma. J. Clin. Oncol. 33, 3008–3017. https://doi.org/10.1200/jco.2014.59.4648 (2015).
Newman, E. A. & Nuchtern, J. G. Recent biologic and genetic advances in neuroblastoma: implications for diagnostic, risk stratification, and treatment strategies. Semin Pediatr. Surg. 25, 257–264. https://doi.org/10.1053/j.sempedsurg.2016.09.007 (2016).
Van Roy, N. et al. The emerging molecular pathogenesis of neuroblastoma: implications for improved risk assessment and targeted therapy. Genome Med. 1, 74. https://doi.org/10.1186/gm74 (2009).
Maris, J. M. Recent advances in neuroblastoma. N Engl. J. Med. 362, 2202–2211. https://doi.org/10.1056/NEJMra0804577 (2010).
Newman, E. A. et al. Update on neuroblastoma. J. Pediatr. Surg. 54, 383–389. https://doi.org/10.1016/j.jpedsurg.2018.09.004 (2019).
Zage, P. E. Novel therapies for relapsed and refractory neuroblastoma. Child. (Basel). 5 https://doi.org/10.3390/children5110148 (2018).
Wienke, J. et al. The immune landscape of neuroblastoma: challenges and opportunities for novel therapeutic strategies in pediatric oncology. Eur. J. Cancer. 144, 123–150. https://doi.org/10.1016/j.ejca.2020.11.014 (2020).
Yu, A. L. et al. Long-Term Follow-up of a phase III study of ch14.18 (Dinutuximab) + Cytokine immunotherapy in children with High-Risk neuroblastoma: COG study ANBL0032. Clin. Cancer Res. 27, 2179–2189. https://doi.org/10.1158/1078-0432.Ccr-20-3909 (2021).
Makimoto, A. et al. Retinoid therapy for neuroblastoma: historical Overview, regulatory Challenges, and prospects. Cancers (Basel). 16 https://doi.org/10.3390/cancers16030544 (2024).
Reynolds, C. P., Matthay, K. K., Villablanca, J. G. & Maurer, B. J. Retinoid therapy of high-risk neuroblastoma. Cancer Lett. 197, 185–192. https://doi.org/10.1016/s0304-3835(03)00108-3 (2003).
Valentijn, L. J. et al. Functional MYCN signature predicts outcome of neuroblastoma irrespective of MYCN amplification. Proc. Natl. Acad. Sci. U S A. 109, 19190–19195. https://doi.org/10.1073/pnas.1208215109 (2012).
Zimmerman, M. W. et al. MYC drives a subset of High-Risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification. Cancer Discov. 8, 320–335. https://doi.org/10.1158/2159-8290.Cd-17-0993 (2018).
Yang, X. H., Tang, F., Shin, J. & Cunningham, J. M. A c-Myc-regulated stem cell-like signature in high-risk neuroblastoma: A systematic discovery (Target neuroblastoma ESC-like signature). Sci. Rep. 7, 41. https://doi.org/10.1038/s41598-017-00122-x (2017).
Dang, C. V. MYC on the path to cancer. Cell 149, 22–35. https://doi.org/10.1016/j.cell.2012.03.003 (2012).
Cowling, V. H. & Cole, M. D. Mechanism of transcriptional activation by the Myc oncoproteins. Semin Cancer Biol. 16, 242–252. https://doi.org/10.1016/j.semcancer.2006.08.001 (2006).
Kress, T. R., Sabò, A. & Amati, B. MYC: connecting selective transcriptional control to global RNA production. Nat. Rev. Cancer. 15, 593–607. https://doi.org/10.1038/nrc3984 (2015).
Whitfield, J. R., Beaulieu, M. E. & Soucek, L. Strategies to inhibit Myc and their clinical applicability. Front. Cell. Dev. Biol. 5 https://doi.org/10.3389/fcell.2017.00010 (2017).
Duffy, M. J., O’Grady, S., Tang, M. & Crown, J. MYC as a target for cancer treatment. Cancer Treat. Rev. 94, 102154. https://doi.org/10.1016/j.ctrv.2021.102154 (2021).
Madden, S. K., de Araujo, A. D., Gerhardt, M., Fairlie, D. P. & Mason, J. M. Taking the Myc out of cancer: toward therapeutic strategies to directly inhibit c-Myc. Mol. Cancer. 20, 3. https://doi.org/10.1186/s12943-020-01291-6 (2021).
Wang, C. et al. Alternative approaches to target Myc for cancer treatment. Signal. Transduct. Target. Ther. 6, 117. https://doi.org/10.1038/s41392-021-00500-y (2021).
Llombart, V. & Mansour, M. R. Therapeutic targeting of undruggable MYC. EBioMedicine 75, 103756, (2022). https://doi.org/10.1016/j.ebiom.2021.103756
Whitfield, J. R. & Soucek, L. MYC in cancer: from undruggable target to clinical trials. Nat. Rev. Drug Discov. 24, 445–457. https://doi.org/10.1038/s41573-025-01143-2 (2025).
Han, H. et al. Small-Molecule MYC inhibitors suppress tumor growth and enhance immunotherapy. Cancer Cell. 36, 483–497e415. https://doi.org/10.1016/j.ccell.2019.10.001 (2019).
Castell, A. et al. A selective high affinity MYC-binding compound inhibits MYC:MAX interaction and MYC-dependent tumor cell proliferation. Sci. Rep. 8, 10064. https://doi.org/10.1038/s41598-018-28107-4 (2018).
Castell, A. et al. MYCMI-7: A small MYC-Binding compound that inhibits MYC: MAX interaction and tumor growth in a MYC-Dependent manner. Cancer Res. Commun. 2, 182–201. https://doi.org/10.1158/2767-9764.Crc-21-0019 (2022).
Soucek, L. et al. Omomyc, a potential Myc dominant negative, enhances Myc-induced apoptosis. Cancer Res. 62, 3507–3510 (2002).
Beaulieu, M. E. et al. Intrinsic cell-penetrating activity propels omomyc from proof of concept to viable anti-MYC therapy. Sci. Transl Med. 11 https://doi.org/10.1126/scitranslmed.aar5012 (2019).
Garralda, E. et al. MYC targeting by OMO-103 in solid tumors: a phase 1 trial. Nat. Med. 30, 762–771. https://doi.org/10.1038/s41591-024-02805-1 (2024).
Chayka, O., D’Acunto, C. W., Middleton, O., Arab, M. & Sala, A. Identification and Pharmacological inactivation of the MYCN gene network as a therapeutic strategy for neuroblastic tumor cells. J. Biol. Chem. 290, 2198–2212. https://doi.org/10.1074/jbc.M114.624056 (2015).
Durbin, A. D. et al. Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry. Nat. Genet. 50, 1240–1246. https://doi.org/10.1038/s41588-018-0191-z (2018).
Wang, J. et al. FDA-approved drug screen identifies proteasome as a synthetic lethal target in MYC-driven neuroblastoma. Oncogene 38, 6737–6751. https://doi.org/10.1038/s41388-019-0912-5 (2019).
Chen, L. et al. CRISPR-Cas9 screen reveals a MYCN-amplified neuroblastoma dependency on EZH2. J. Clin. Invest. 128, 446–462. https://doi.org/10.1172/JCI90793 (2018).
Lee, H. M. et al. A CRISPR-drug perturbational map for identifying compounds to combine with commonly used chemotherapeutics. Nat. Commun. 14, 7332. https://doi.org/10.1038/s41467-023-43134-0 (2023).
Sottile, F., Gnemmi, I., Cantilena, S., D’Acunto, W. C. & Sala, A. A chemical screen identifies the chemotherapeutic drug Topotecan as a specific inhibitor of the B-MYB/MYCN axis in neuroblastoma. Oncotarget 3, 535–545. https://doi.org/10.18632/oncotarget.498 (2012).
Ham, J. et al. Exploitation of the Apoptosis-Primed state of MYCN-Amplified neuroblastoma to develop a potent and specific targeted therapy combination. Cancer Cell. 29, 159–172. https://doi.org/10.1016/j.ccell.2016.01.002 (2016).
Cheung, B. B. et al. A novel combination therapy targeting ubiquitin-specific protease 5 in MYCN-driven neuroblastoma. Oncogene 40, 2367–2381. https://doi.org/10.1038/s41388-021-01712-w (2021).
Molenaar, J. J. et al. Inactivation of CDK2 is synthetically lethal to MYCN over-expressing cancer cells. Proc. Natl. Acad. Sci. U S A. 106, 12968–12973. https://doi.org/10.1073/pnas.0901418106 (2009).
Dolman, M. E. et al. Cyclin-Dependent kinase inhibitor AT7519 as a potential drug for MYCN-Dependent neuroblastoma. Clin. Cancer Res. 21, 5100–5109. https://doi.org/10.1158/1078-0432.Ccr-15-0313 (2015).
Poon, E. et al. Orally bioavailable CDK9/2 inhibitor shows mechanism-based therapeutic potential in MYCN-driven neuroblastoma. J. Clin. Invest. 130, 5875–5892. https://doi.org/10.1172/jci134132 (2020).
Geoerger, B. et al. A phase I study of the CDK4/6 inhibitor ribociclib (LEE011) in pediatric patients with malignant rhabdoid tumors, Neuroblastoma, and other solid tumors. Clin. Cancer Res. 23, 2433–2441. https://doi.org/10.1158/1078-0432.Ccr-16-2898 (2017).
Moreno, L. et al. Accelerating drug development for neuroblastoma: summary of the second neuroblastoma drug development strategy forum from innovative therapies for children with cancer and international society of paediatric oncology Europe neuroblastoma. Eur. J. Cancer. 136, 52–68. https://doi.org/10.1016/j.ejca.2020.05.010 (2020).
Chi, Y. et al. A novel landscape of nuclear human CDK2 substrates revealed by in situ phosphorylation. Sci. Adv. 6, eaaz9899. https://doi.org/10.1126/sciadv.aaz9899 (2020).
Chi, Y. et al. Identification of CDK2 substrates in human cell lysates. Genome Biol 9, R149, (2008). https://doi.org/10.1186/gb-2008-9-10-r149
Hydbring, P. et al. Phosphorylation by Cdk2 is required for Myc to repress Ras-induced senescence in cotransformation. Proc. Natl. Acad. Sci. U S A. 107, 58–63. https://doi.org/10.1073/pnas.0900121106 (2010).
Bazzar, W. et al. Pharmacological inactivation of CDK2 inhibits MYC/BCL-XL-driven leukemia in vivo through induction of cellular senescence. Cell. Cycle. 20, 23–38. https://doi.org/10.1080/15384101.2020.1855740 (2021).
Bolin, S. et al. Combined BET bromodomain and CDK2 Inhibition in MYC-driven Medulloblastoma. Oncogene 37, 2850–2862. https://doi.org/10.1038/s41388-018-0135-1 (2018).
Kanehisa, M., Furumichi, M., Sato, Y., Matsuura, Y. & Ishiguro-Watanabe, M. KEGG: biological systems database as a model of the real world. Nucleic Acids Res. 53, D672–d677. https://doi.org/10.1093/nar/gkae909 (2025).
Bonine, N. et al. NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors. Cell. Rep. 43, 114804. https://doi.org/10.1016/j.celrep.2024.114804 (2024).
Liaño-Pons, J. et al. Combined targeting of PRDX6 and GSTP1 as a potential differentiation strategy for neuroblastoma treatment. Proc. Natl. Acad. Sci. U S A. 122, e2427211122. https://doi.org/10.1073/pnas.2427211122 (2025).
Ruiz-Pérez, M. V. et al. Inhibition of fatty acid synthesis induces differentiation and reduces tumor burden in childhood neuroblastoma. iScience 24, 102128. https://doi.org/10.1016/j.isci.2021.102128 (2021).
Dzieran, J. et al. MYCN-amplified neuroblastoma maintains an aggressive and undifferentiated phenotype by deregulation of Estrogen and NGF signaling. Proc. Natl. Acad. Sci. U S A. 115, E1229–e1238. https://doi.org/10.1073/pnas.1710901115 (2018).
Kang, J. H. et al. MYCN Silencing induces differentiation and apoptosis in human neuroblastoma cells. Biochem. Biophys. Res. Commun. 351, 192–197. https://doi.org/10.1016/j.bbrc.2006.10.020 (2006).
Lutz, W. 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 13, 803–812 (1996).
Sears, R. et al. Multiple Ras-dependent phosphorylation pathways regulate Myc protein stability. Genes Dev. 14, 2501–2514. https://doi.org/10.1101/gad.836800 (2000).
Filippakopoulos, P. et al. Selective Inhibition of BET bromodomains. Nature 468, 1067–1073 (2010). http://www.nature.com/nature/journal/v468/n7327/abs/nature09504.html#supplementary-information
Agarwal, P. et al. MYCN amplification is associated with reduced expression of genes encoding γ-Secretase complex and NOTCH signaling components in neuroblastoma. Int. J. Mol. Sci. 24 https://doi.org/10.3390/ijms24098141 (2023).
Ianevski, A., Giri, A. K. & Aittokallio, T. SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples. Nucleic Acids Res. 50, W739–w743. https://doi.org/10.1093/nar/gkac382 (2022).
Fagundes, R., Teixeira, L. K. & Cyclin E/CDK2: DNA replication, replication stress and genomic instability. Front. Cell. Dev. Biol. 9, 774845. https://doi.org/10.3389/fcell.2021.774845 (2021).
Hydbring, P. & Larsson, L. G. Cdk2: a key regulator of the senescence control function of Myc. Aging (Albany NY). 2, 244–250. https://doi.org/10.18632/aging.100140 (2010).
Chen, S. et al. Cyclin-dependent kinases regulate epigenetic gene Silencing through phosphorylation of EZH2. Nat. Cell. Biol. 12, 1108–1114. https://doi.org/10.1038/ncb2116 (2010).
O’Connor, P. M. Mammalian G1 and G2 phase checkpoints. Cancer Surv. 29, 151–182 (1997).
Henriksen, J. R. et al. Conditional expression of retrovirally delivered anti-MYCN ShRNA as an in vitro model system to study neuronal differentiation in MYCN-amplified neuroblastoma. BMC Dev. Biol. 11, 1. https://doi.org/10.1186/1471-213X-11-1 (2011).
Valentijn, L. J. et al. Functional MYCN signature predicts outcome of neuroblastoma irrespective of < i>MYCN amplification. Proceedings of the National Academy of Sciences 109, 19190–19195, doi: (2012). https://doi.org/10.1073/pnas.1208215109
Fredlund, E., Ringnér, M., Maris, J. M. & Påhlman, S. High Myc pathway activity and low stage of neuronal differentiation associate with poor outcome in neuroblastoma. Proc. Natl. Acad. Sci. U S A. 105, 14094–14099. https://doi.org/10.1073/pnas.0804455105 (2008).
Ferguson, K. M. et al. Palbociclib releases the latent differentiation capacity of neuroblastoma cells. Dev Cell 58, 1967–1982.e (1968). https://doi.org/10.1016/j.devcel.2023.08.028 (2023).
Zhang, H. et al. Targeting CDK9 reactivates epigenetically silenced genes in cancer. Cell 175, 1244–1258e1226. https://doi.org/10.1016/j.cell.2018.09.051 (2018).
Chen, Z. et al. Multiple CDK inhibitor Dinaciclib suppresses neuroblastoma growth via inhibiting CDK2 and CDK9 activity. Sci. Rep. 6, 29090. https://doi.org/10.1038/srep29090 (2016).
Shokraie, F. et al. CDK inhibitors promote neuroblastoma cell differentiation and increase sensitivity to retinoic acid-a promising combination strategy for therapeutic intervention. Cell. Death Discov. 11, 363. https://doi.org/10.1038/s41420-025-02637-z (2025).
Kranenburg, O., Scharnhorst, V., Van der Eb, A. J. & Zantema, A. Inhibition of cyclin-dependent kinase activity triggers neuronal differentiation of mouse neuroblastoma cells. J. Cell. Biol. 131, 227–234. https://doi.org/10.1083/jcb.131.1.227 (1995).
Harbour, J. W., Luo, R. X., Santi, A. D., Postigo, A. A. & Dean, D. C. Cdk phosphorylation triggers sequential intramolecular interactions that progressively block Rb functions as cells move through G1. Cell 98, 859–869. https://doi.org/10.1016/S0092-8674(00)81519-6 (1999).
Farrell, A. S. & Sears, R. C. MYC degradation. Cold Spring Harb Perspect. Med. 4 https://doi.org/10.1101/cshperspect.a014365 (2014).
Gautier, L., Cope, L., Bolstad, B. M. & Irizarry, R. A. affy–analysis of affymetrix genechip data at the probe level. Bioinformatics 20, 307–315. https://doi.org/10.1093/bioinformatics/btg405 (2004).
Xie, Z. et al. Gene set knowledge discovery with enrichr. Curr. Protoc. 1, e90. https://doi.org/10.1002/cpz1.90 (2021).
Kuleshov, M. V. et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44, W90–97. https://doi.org/10.1093/nar/gkw377 (2016).
Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods. 18, 100–106. https://doi.org/10.1038/s41592-020-01018-x (2021).
Stirling, D. R. et al. CellProfiler 4: improvements in speed, utility and usability. BMC Bioinform. 22, 433. https://doi.org/10.1186/s12859-021-04344-9 (2021).
Acknowledgements
The authors express their great gratitude to all funding agencies, biomedicum imaging core facility and the biomedicum common virus laboratory BSL-2 at the Karolinska Institutet.
Funding
Open access funding provided by Karolinska Institute. This work was supported by grants from the Swedish Childhood Cancer Foundation (Barncancerfonden) (MA & LGL), O. E. och Edla Johanssons vetenskapliga stiftelse (MA), Stiftelsen Lars Hiertas Minne (MA), Fredrik och Ingrid Thurings Stiftelse (MA), and Lillian Sagens och Curt Ericssons Forskningsstiftelse (MA), The Swedish Cancer Foundation (Cancerfonden) (LGL), NovoNordisk Foundation (LGL), MyCural Therapeutics AB (LGL) and the Norwegian Cancer Society (216113, KL).
Author information
Authors and Affiliations
Contributions
MA and LGL conceptualized and supervised the study, acquired funding, and wrote the manuscript. MA, LM, ANT, MV, LZ, PV, FJ, and WB performed experiments, analyzed, interpreted, and visualized the data. KL provided resources, supervision of LM, analyzed and interpreted the data. All authors have read and approved the final draft of the manuscript.
Corresponding author
Ethics declarations
Competing interests
LGL is cofounder of MyCural Therapeutics AB and has ownership interests (including patents) in this company.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Alzrigat, M., Mahmoud, L., Topçu, A.N. et al. CDK2 inhibition promotes neuronal differentiation in neuroblastoma. Sci Rep (2026). https://doi.org/10.1038/s41598-026-38123-4
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/s41598-026-38123-4