β-catenin-driven differentiation is a tissue-specific epigenetic vulnerability in adrenal cancer.

Adrenocortical carcinoma (ACC) is a rare cancer in which tissue-specific differentiation is paradoxically associated with dismal outcomes. The differentiated ACC subtype CIMP-high is prevalent, incurable, and routinely fatal. CIMP-high ACC possess abnormal DNA methylation and frequent β-catenin activating mutations. Here, we demonstrated that ACC differentiation is maintained by a balance between nuclear, tissue-specific β-catenin-containing complexes and the epigenome. On chromatin, β-catenin bound master adrenal transcription factor SF1 and hijacked the adrenocortical super-enhancer landscape to maintain differentiation in CIMP-high ACC; off chromatin, β-catenin bound histone methyltransferase EZH2. SF1/β-catenin and EZH2/β-catenin complexes present in normal adrenals persisted through all phases of ACC evolution. Pharmacologic EZH2 inhibition in CIMP-high ACC expelled SF1/β-catenin from chromatin and favored EZH2/β-catenin assembly, erasing differentiation and restraining cancer growth in vitro and in vivo. These studies illustrate how tissue-specific programs shape oncogene selection, surreptitiously encoding targetable therapeutic vulnerabilities.

[1]  G. Hammer,et al.  Update on Biology and Genomics of Adrenocortical Carcinomas: Rationale for Emerging Therapies. , 2022, Endocrine reviews.

[2]  Yoan Renaud,et al.  Sexually dimorphic activation of innate antitumor immunity prevents adrenocortical carcinoma development , 2022, bioRxiv.

[3]  Chris J. Stubben,et al.  Senescence-Induced Immune Remodeling Facilitates Metastatic Adrenal Cancer in a Sex-Dimorphic Manner , 2022, bioRxiv.

[4]  C. Lareau,et al.  Single-cell chromatin state analysis with Signac , 2021, Nature Methods.

[5]  Kyle J. Gaulton,et al.  A single-cell atlas of chromatin accessibility in the human genome , 2021, Cell.

[6]  Hannah R. Weisman,et al.  Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states , 2021, Nature Genetics.

[7]  M. Artyomov,et al.  Semi-supervised peak calling with SPAN and JBR genome browser , 2021, Bioinform..

[8]  Andrew J. Hill,et al.  A human cell atlas of fetal chromatin accessibility , 2020, Science.

[9]  G. Salles,et al.  Tazemetostat for patients with relapsed or refractory follicular lymphoma: an open-label, single-arm, multicentre, phase 2 trial. , 2020, The Lancet. Oncology.

[10]  A. Chinnaiyan,et al.  Abstract PR02: Integrated metabolic and epigenomic reprograming by H3K27M mutations in diffuse intrinsic pontine gliomas , 2020, Oral Presentations - Proffered Abstracts.

[11]  Jason D. Buenrostro,et al.  Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma. , 2020, Cancer cell.

[12]  F. Ramalho,et al.  Wnt/β-catenin activation cooperates with loss of p53 to cause adrenocortical carcinoma in mice , 2020, Oncogene.

[13]  Gabor Marth,et al.  MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate. , 2020, Cancer cell.

[14]  Ji Miao,et al.  Beta-Catenin Causes Adrenal Hyperplasia by Blocking Zonal Transdifferentiation , 2020, Cell reports.

[15]  Dan Zhang,et al.  Construction of a human cell landscape at single-cell level , 2020, Nature.

[16]  R. Auchus,et al.  Abiraterone acetate treatment lowers 11-oxygenated androgens. , 2020, European journal of endocrinology.

[17]  K. Nakano,et al.  Targeting Excessive EZH1 and EZH2 Activities for Abnormal Histone Methylation and Transcription Network in Malignant Lymphomas. , 2019, Cell reports.

[18]  A. Bracken,et al.  PRC2 functions in development and congenital disorders , 2019, Development.

[19]  N. Hannett,et al.  Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes. , 2019, Molecular cell.

[20]  Bing Ren,et al.  A Compendium of Promoter-Centered Long-Range Chromatin Interactions in the Human Genome , 2019, Nature Genetics.

[21]  J. Bertherat,et al.  EZH2 cooperates with E2F1 to stimulate expression of genes involved in adrenocortical carcinoma aggressiveness , 2019, British Journal of Cancer.

[22]  J. Pritchard,et al.  Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase , 2019, Cell.

[23]  T. Giordano,et al.  Targeted Assessment of G0S2 Methylation Identifies a Rapidly Recurrent, Routinely Fatal Molecular Subtype of Adrenocortical Carcinoma , 2019, Clinical Cancer Research.

[24]  Genevieve L. Stein-O’Brien,et al.  Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and BrafV600E-Induced Tumorigenesis. , 2019, Cancer cell.

[25]  R. Nusse,et al.  A ZNRF3-dependent Wnt/β-catenin signaling gradient is required for adrenal homeostasis , 2019, Genes & development.

[26]  Andrew J. Hill,et al.  The single cell transcriptional landscape of mammalian organogenesis , 2019, Nature.

[27]  V. Boeva,et al.  Steroidogenic differentiation and PKA signaling are programmed by histone methyltransferase EZH2 in the adrenal cortex , 2018, Proceedings of the National Academy of Sciences.

[28]  H. Munshi,et al.  Induction of MNK Kinase–dependent eIF4E Phosphorylation by Inhibitors Targeting BET Proteins Limits Efficacy of BET Inhibitors , 2018, Molecular Cancer Therapeutics.

[29]  Christoph Hafemeister,et al.  Comprehensive integration of single cell data , 2018, bioRxiv.

[30]  Mauro A. A. Castro,et al.  The chromatin accessibility landscape of primary human cancers , 2018, Science.

[31]  Karen E Gascoigne,et al.  Enhancer Activity Requires CBP/P300 Bromodomain-Dependent Histone H3K27 Acetylation. , 2018, Cell reports.

[32]  Daniel S. Day,et al.  Coactivator condensation at super-enhancers links phase separation and gene control , 2018, Science.

[33]  Judith B. Zaugg,et al.  Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors: diffTF , 2018, bioRxiv.

[34]  M. Perino,et al.  MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding , 2018, Nature Genetics.

[35]  G. Hammer,et al.  Sonic Hedgehog and WNT Signaling Promote Adrenal Gland Regeneration in Male Mice , 2018, Endocrinology.

[36]  J. Michael Cherry,et al.  The Encyclopedia of DNA elements (ENCODE): data portal update , 2017, Nucleic Acids Res..

[37]  H. Bourbon,et al.  Genome Regulation by Polycomb and Trithorax: 70 Years and Counting , 2017, Cell.

[38]  C. Zahnow,et al.  Chronic Cigarette Smoke-Induced Epigenomic Changes Precede Sensitization of Bronchial Epithelial Cells to Single-Step Transformation by KRAS Mutations. , 2017, Cancer cell.

[39]  Nicholas A. Sinnott-Armstrong,et al.  An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues , 2017, Nature Methods.

[40]  Hannah A. Pliner,et al.  Reversed graph embedding resolves complex single-cell trajectories , 2017, Nature Methods.

[41]  M. Bulyk,et al.  Polycomb-like proteins link the PRC2 complex to CpG islands , 2017, Nature.

[42]  Phillip G. Montgomery,et al.  Defining a Cancer Dependency Map , 2017, Cell.

[43]  William A. Flavahan,et al.  Epigenetic plasticity and the hallmarks of cancer , 2017, Science.

[44]  D. Johnston,et al.  Immunohistochemical analysis of H3K27me3 demonstrates global reduction in group-A childhood posterior fossa ependymoma and is a powerful predictor of outcome , 2017, Acta Neuropathologica.

[45]  R. Nusse,et al.  Wnt/β-Catenin Signaling, Disease, and Emerging Therapeutic Modalities , 2017, Cell.

[46]  R. Kemler,et al.  Trimethylation and Acetylation of β-Catenin at Lysine 49 Represent Key Elements in ESC Pluripotency. , 2017, Cell reports.

[47]  Andrew J. Hill,et al.  Single-cell mRNA quantification and differential analysis with Census , 2017, Nature Methods.

[48]  Richard C. McEachin,et al.  Lowered H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas , 2016, Science Translational Medicine.

[49]  Peter A. Jones,et al.  Epigenetic Determinants of Cancer. , 2016, Cold Spring Harbor perspectives in biology.

[50]  R. Kuick,et al.  EZH2 is overexpressed in adrenocortical carcinoma and is associated with disease progression. , 2016, Human molecular genetics.

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

[52]  Qing-Yu He,et al.  ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization , 2015, Bioinform..

[53]  Charles Y. Lin,et al.  Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers. , 2015, Molecular cell.

[54]  A. Gill,et al.  Immunohistochemical validation of overexpressed genes identified by global expression microarrays in adrenocortical carcinoma reveals potential predictive and prognostic biomarkers. , 2015, The oncologist.

[55]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[56]  J. Lieb,et al.  What are super-enhancers? , 2014, Nature Genetics.

[57]  P. Eline Slagboom,et al.  MethylAid: visual and interactive quality control of large Illumina 450k datasets , 2014, Bioinform..

[58]  P. Gestraud,et al.  Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes. , 2014, Cell reports.

[59]  R. Kuick,et al.  Wnt signaling inhibits adrenal steroidogenesis by cell-autonomous and non-cell-autonomous mechanisms. , 2014, Molecular Endocrinology.

[60]  Michael Kahn,et al.  Can we safely target the WNT pathway? , 2014, Nature Reviews Drug Discovery.

[61]  Rafael A. Irizarry,et al.  Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays , 2014, Bioinform..

[62]  Eric Baudin,et al.  Integrated genomic characterization of adrenocortical carcinoma , 2014, Nature Genetics.

[63]  Cole Trapnell,et al.  The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells , 2014, Nature Biotechnology.

[64]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[65]  H. Stunnenberg,et al.  Dnmt3L Antagonizes DNA Methylation at Bivalent Promoters and Favors DNA Methylation at Gene Bodies in ESCs , 2013, Cell.

[66]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[67]  G. Crabtree,et al.  Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy , 2013, Nature Genetics.

[68]  H. Franz,et al.  Wnt3a-dependent and -independent Protein Interaction Networks of Chromatin-bound β-catenin in Mouse Embryonic Stem Cells , 2013, Molecular & Cellular Proteomics.

[69]  Benjamin E. Gross,et al.  Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal , 2013, Science Signaling.

[70]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[71]  David A. Orlando,et al.  Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers , 2013, Cell.

[72]  H. Clevers,et al.  Intestinal Tumorigenesis Initiated by Dedifferentiation and Acquisition of Stem-Cell-like Properties , 2013, Cell.

[73]  Justin Guinney,et al.  GSVA: gene set variation analysis for microarray and RNA-Seq data , 2013, BMC Bioinformatics.

[74]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[75]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[76]  Benjamin E. Gross,et al.  The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.

[77]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[78]  Davis J. McCarthy,et al.  Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[79]  I. Ellis,et al.  Differential oestrogen receptor binding is associated with clinical outcome in breast cancer , 2011, Nature.

[80]  Michael R. Kennedy,et al.  The effects of ACTH on steroid metabolomic profiles in human adrenal cells. , 2011, The Journal of endocrinology.

[81]  Martin J. Aryee,et al.  A DNA hypermethylation module for the stem/progenitor cell signature of cancer , 2011, Genome research.

[82]  R. Copeland,et al.  Coordinated activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human B-cell lymphomas , 2010, Proceedings of the National Academy of Sciences.

[83]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[84]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[85]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[86]  D. Reinberg,et al.  Role of the polycomb protein EED in the propagation of repressive histone marks , 2009, Nature.

[87]  Robert Gentleman,et al.  rtracklayer: an R package for interfacing with genome browsers , 2009, Bioinform..

[88]  Gangning Liang,et al.  Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line , 2008, Proceedings of the National Academy of Sciences.

[89]  M. Fraga,et al.  The Polycomb group protein EZH2 directly controls DNA methylation , 2007, Nature.

[90]  P. Laird,et al.  Epigenetic stem cell signature in cancer , 2007, Nature Genetics.

[91]  Kelly M. McGarvey,et al.  A stem cell–like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing , 2007, Nature Genetics.

[92]  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.

[93]  Stormy J. Chamberlain,et al.  The Murine Polycomb Group Protein Eed Is Required for Global Histone H3 Lysine-27 Methylation , 2005, Current Biology.

[94]  Kristian Helin,et al.  Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity , 2004, The EMBO journal.

[95]  Yi Zhang,et al.  SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. , 2004, Molecular cell.

[96]  P. White,et al.  A Role for the NGFI‐B Family in Adrenal Zonation and Adrenocortical Disease , 2004, Endocrine research.

[97]  Kristian Helin,et al.  EZH2 is downstream of the pRB‐E2F pathway, essential for proliferation and amplified in cancer , 2003, The EMBO journal.

[98]  Anwar Hossain,et al.  Synergistic Cooperation between the β-Catenin Signaling Pathway and Steroidogenic Factor 1 in the Activation of the Mullerian Inhibiting Substance Type II Receptor* , 2003, Journal of Biological Chemistry.

[99]  Brian M. Gummow,et al.  Convergence of Wnt Signaling and Steroidogenic Factor-1 (SF-1) on Transcription of the Rat Inhibin α Gene* , 2003, Journal of Biological Chemistry.

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

[101]  A. Swain,et al.  Dax-1 (dosage-sensitive sex reversal-adrenal hypoplasia congenita critical region on the X chromosome, gene 1) gene transcription is regulated by wnt4 in the female developing gonad. , 2003, Molecular endocrinology.

[102]  J. Herman,et al.  CpG island methylator phenotype in colorectal cancer. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[103]  Fumiaki Ito,et al.  Cytoskeletal reorganization by soluble Wnt‐3a protein signalling , 1998, Genes to cells : devoted to molecular & cellular mechanisms.

[104]  J. Daly,et al.  Forskolin: unique diterpene activator of adenylate cyclase in membranes and in intact cells. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[105]  Benjamin J Raphael,et al.  Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. , 2016, Cancer cell.

[106]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[107]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[108]  R. Stark,et al.  DiffBind : Differential binding analysis of ChIP-Seq peak data , 2012 .

[109]  Cedric E. Ginestet.  ggplot2: Elegant Graphics for Data Analysis , 2011 .

[110]  O. MacDougald,et al.  T-cell factor 4N (TCF-4N), a novel isoform of mouse TCF-4, synergizes with beta-catenin to coactivate C/EBPalpha and steroidogenic factor 1 transcription factors. , 2003, Molecular and cellular biology.

[111]  M. Merika,et al.  Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription. , 1998, Molecular cell.