MYCN driven oncogenesis involves cooperation with WDR5 to activate canonical MYC targets and G9a to repress differentiation genes

MYCN activates canonical MYC targets involved in ribosome biogenesis, protein synthesis and represses neuronal differentiation genes to drive oncogenesis in neuroblastoma (NB). How MYCN orchestrates global gene expression remains incompletely understood. Our study finds that MYCN binds promoters to up-regulate canonical MYC targets but binds to both enhancers and promoters to repress differentiation genes. MYCN-binding also increases H3K4me3 and H3K27ac on canonical MYC target promoters and decreases H3K27ac on neuronal differentiation gene enhancers and promoters. WDR5 is needed to facilitate MYCN promoter binding to activate canonical MYC target genes, whereas MYCN recruits G9a to enhancers to repress neuronal differentiation genes. Targeting both MYCN’s active and repressive transcriptional activities using both WDR5 and G9a inhibitors synergistically suppresses NB growth. We demonstrate that MYCN cooperates with WDR5 and G9a to orchestrate global gene transcription. The targeting of both these cofactors is a novel therapeutic strategy to indirectly target the oncogenic activity of MYCN.

[1]  C. Thiele,et al.  HAND2 assists MYCN enhancer invasion to regulate a noradrenergic neuroblastoma phenotype. , 2023, Cancer research.

[2]  Lin Wang,et al.  Discovery, evaluation and mechanism study of WDR5-targeted small molecular inhibitors for neuroblastoma , 2022, Acta Pharmacologica Sinica.

[3]  Brad T. Sherman,et al.  DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update) , 2022, Nucleic Acids Res..

[4]  M. Gessler,et al.  MYCN and MAX alterations in Wilms tumor and identification of novel N-MYC interaction partners as biomarker candidates , 2021, Cancer Cell International.

[5]  D. Andrews,et al.  MYC protein interactors in gene transcription and cancer , 2021, Nature Reviews Cancer.

[6]  G. Bejerano,et al.  WhichTF is functionally important in your open chromatin data? , 2021, PLoS Comput. Biol..

[7]  C. Thiele,et al.  Targeting MYCN in Pediatric and Adult Cancers , 2021, Frontiers in Oncology.

[8]  T. Aittokallio,et al.  SynergyFinder 2.0: visual analytics of multi-drug combination synergies , 2020, Nucleic Acids Res..

[9]  M. Eilers,et al.  Target gene-independent functions of MYC oncoproteins , 2020, Nature Reviews Molecular Cell Biology.

[10]  J. Khan,et al.  CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG , 2020, Nature Communications.

[11]  S. Fesik,et al.  Interaction of the oncoprotein transcription factor MYC with its chromatin cofactor WDR5 is essential for tumor maintenance , 2019, Proceedings of the National Academy of Sciences.

[12]  Anthony R. Dallosso,et al.  Increased Efficacy of Histone Methyltransferase G9a Inhibitors Against MYCN-Amplified Neuroblastoma , 2019, bioRxiv.

[13]  P. Fraser,et al.  Long-range enhancer–promoter contacts in gene expression control , 2019, Nature Reviews Genetics.

[14]  S. Fesik,et al.  Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity , 2019, Cell reports.

[15]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[16]  P. Boutros,et al.  MYC Interacts with the G9a Histone Methyltransferase to Drive Transcriptional Repression and Tumorigenesis. , 2018, Cancer cell.

[17]  Kathleen E. Houlahan,et al.  MYC dephosphorylation by the PP1/PNUTS phosphatase complex regulates chromatin binding and protein stability , 2018, Nature Communications.

[18]  M. Ferrer,et al.  MEK inhibition induces MYOG and remodels super-enhancers in RAS-driven rhabdomyosarcoma , 2018, Science Translational Medicine.

[19]  T. Hughes,et al.  The Human Transcription Factors , 2018, Cell.

[20]  D. Rickman,et al.  Association with Aurora-A Controls N-MYC-Dependent Promoter Escape and Pause Release of RNA Polymerase II during the Cell Cycle , 2017, Cell reports.

[21]  T. Golub,et al.  CRISPR-Cas9 screen reveals a MYCN-amplified neuroblastoma dependency on EZH2 , 2017, The Journal of clinical investigation.

[22]  M. Ferrer,et al.  PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability. , 2017, Cancer discovery.

[23]  A. Califano,et al.  HAUSP deubiquitinated and stabilizes N-Myc in neuroblastoma , 2016, Nature Medicine.

[24]  G. Cho,et al.  G9a inhibition promotes neuronal differentiation of human bone marrow mesenchymal stem cells through the transcriptional induction of RE-1 containing neuronal specific genes , 2016, Neurochemistry International.

[25]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[26]  R. C. Poulos,et al.  WDR5 Supports an N-Myc Transcriptional Complex That Drives a Protumorigenic Gene Expression Signature in Neuroblastoma. , 2015, Cancer research.

[27]  M. Surani,et al.  Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development , 2015, eLife.

[28]  C. Thiele,et al.  Zinc finger transcription factor CASZ1 interacts with histones, DNA repair proteins and recruits NuRD complex to regulate gene transcription , 2015, Oncotarget.

[29]  A. Harris,et al.  The role of histone demethylase KDM4B in Myc signaling in neuroblastoma. , 2015, Journal of the National Cancer Institute.

[30]  Qi Sun,et al.  Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC. , 2015, Molecular cell.

[31]  G. Perini,et al.  Lysine-specific demethylase (LSD1/KDM1A) and MYCN cooperatively repress tumor suppressor genes in neuroblastoma , 2015, Oncotarget.

[32]  J. Neuhaus,et al.  Clinical, biologic, and prognostic differences on the basis of primary tumor site in neuroblastoma: a report from the international neuroblastoma risk group project. , 2014, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[33]  Q. Xia,et al.  Inhibition of H3K9 Methyltransferase G9a Repressed Cell Proliferation and Induced Autophagy in Neuroblastoma Cells , 2014, PloS one.

[34]  L. Zender,et al.  Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles , 2014, Nature.

[35]  Yunhong Zha,et al.  The histone H3 methyltransferase G9A epigenetically activates the serine-glycine synthesis pathway to sustain cancer cell survival and proliferation. , 2013, Cell metabolism.

[36]  William A Weiss,et al.  Neuroblastoma and MYCN. , 2013, Cold Spring Harbor perspectives in medicine.

[37]  Michael A. Dyer,et al.  Neuroblastoma: developmental biology, cancer genomics and immunotherapy , 2013, Nature Reviews Cancer.

[38]  G. Perini,et al.  MYCN-mediated transcriptional repression in neuroblastoma: the other side of the coin , 2013, Front. Oncol..

[39]  Jan Koster,et al.  Functional MYCN signature predicts outcome of neuroblastoma irrespective of MYCN amplification , 2012, Proceedings of the National Academy of Sciences.

[40]  Chi V Dang,et al.  MYC on the Path to Cancer , 2012, Cell.

[41]  L. Penn,et al.  New model systems provide insights into Myc-induced transformation , 2011, Oncogene.

[42]  Y. Shinkai,et al.  H3K9 methyltransferase G9a and the related molecule GLP. , 2011, Genes & development.

[43]  G. Perini,et al.  A SP1/MIZ1/MYCN repression complex recruits HDAC1 at the TRKA and p75NTR promoters and affects neuroblastoma malignancy by inhibiting the cell response to NGF. , 2011, Cancer research.

[44]  B. H. Haug,et al.  Conditional expression of retrovirally delivered anti-MYCN shRNA as an in vitro model system to study neuronal differentiation in MYCN-amplified neuroblastoma , 2011, BMC Developmental Biology.

[45]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[46]  David S. Lapointe,et al.  ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data , 2010, BMC Bioinformatics.

[47]  D. Felsher,et al.  MYC as a regulator of ribosome biogenesis and protein synthesis , 2010, Nature Reviews Cancer.

[48]  L. Penn,et al.  Reflecting on 25 years with MYC , 2008, Nature Reviews Cancer.

[49]  Rainer König,et al.  Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas , 2008, Genome Biology.

[50]  C. Thiele,et al.  Use of RNA interference to elucidate the effect of MYCN on cell cycle in neuroblastoma , 2008, Pediatric blood & cancer.

[51]  G. Perini,et al.  Activation of tissue transglutaminase transcription by histone deacetylase inhibition as a therapeutic approach for Myc oncogenesis , 2007, Proceedings of the National Academy of Sciences.

[52]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[53]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[54]  M Schwab,et al.  N‐myc enhances the expression of a large set of genes functioning in ribosome biogenesis and protein synthesis , 2001, The EMBO journal.