Increased H3K9me3 drives dedifferentiated phenotype via KLF6 repression in liposarcoma.

Liposarcoma (LPS) can be divided into 4 different subtypes, of which well-differentiated LPS (WDLPS) and dedifferentiated LPS (DDLPS) are the most common. WDLPS is typically low grade, whereas DDLPS is high grade, aggressive, and carries a worse prognosis. WDLPS and DDLPS frequently co-occur in patients. However, it is not clear whether DDLPS arises independently from WDLPS, or whether epigenomic alterations underly the histopathological differences of these subtypes. Here, we profiled 9 epigenetic marks in tumor samples from 151 patients with LPS and showed elevated trimethylation of histone H3 at Lys9 (H3K9me3) levels in DDLPS tumors. Integrated ChIP-seq and gene expression analyses of patient-derived cell lines revealed that H3K9me3 mediates differential regulation of genes involved in cellular differentiation and migration. Among these, Kruppel-like factor 6 (KLF6) was reduced in DDLPS, with increased H3K9me3 at associated regulatory regions. Pharmacologic inhibition of H3K9me3 with chaetocin decreased DDLPS proliferation and increased expression of the adipogenesis-associated factors PPARγ, CEBPα, and CEBPβ, suggesting that increased H3K9me3 may mediate DDLPS-associated aggressiveness and dedifferentiation properties. KLF6 overexpression partially phenocopied chaetocin treatment in DDLPS cells and induced phenotypic changes that were consistent with adipocytic differentiation, suggesting that the effects of increased H3K9me3 may be mediated through KLF6. In conclusion, we provide evidence of an epigenetic basis for the transition between WDLPS and DDLPS.

[1]  J. Park,et al.  Gankyrin is a predictive and oncogenic factor in well-differentiated and dedifferentiated liposarcoma , 2014, Oncotarget.

[2]  Adelina Rogowska-Wrzesinska,et al.  Transcription factor cooperativity in early adipogenic hotspots and super-enhancers. , 2014, Cell reports.

[3]  Anders K. Haakonsson,et al.  PPARγ and the global map of adipogenesis and beyond , 2014, Trends in Endocrinology & Metabolism.

[4]  Jian Peng,et al.  Role of histone acetyltransferases and histone deacetylases in adipocyte differentiation and adipogenesis. , 2014, European journal of cell biology.

[5]  Roland Eils,et al.  Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas , 2013, Genome Biology.

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

[7]  L. Qin,et al.  Phase II trial of the CDK4 inhibitor PD0332991 in patients with advanced CDK4-amplified well-differentiated or dedifferentiated liposarcoma. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[8]  A. Lazar,et al.  Novel Systemic Therapies in Advanced Liposarcoma: A Review of Recent Clinical Trial Results , 2013, Cancers.

[9]  J. Foekens,et al.  KLF6-SV1 Drives Breast Cancer Metastasis and Is Associated with Poor Survival , 2013, Science Translational Medicine.

[10]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[11]  Jean-Yves Blay,et al.  Effect of the MDM2 antagonist RG7112 on the P53 pathway in patients with MDM2-amplified, well-differentiated or dedifferentiated liposarcoma: an exploratory proof-of-mechanism study. , 2012, The Lancet. Oncology.

[12]  S. Friedman,et al.  Enhanced hepatocarcinogenesis in mouse models and human hepatocellular carcinoma by coordinate KLF6 depletion and increased messenger RNA splicing , 2012, Hepatology.

[13]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[14]  P. K. Bajpe,et al.  Targeting the epigenome for treatment of cancer , 2012, Oncogene.

[15]  Nir Friedman,et al.  A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. , 2012, Molecular cell.

[16]  Dina Lev,et al.  MiR-155 is a liposarcoma oncogene that targets casein kinase-1α and enhances β-catenin signaling. , 2012, Cancer research.

[17]  S. Singer,et al.  The Cyclin-Dependent Kinase Inhibitor Flavopiridol Potentiates Doxorubicin Efficacy in Advanced Sarcomas: Preclinical Investigations and Results of a Phase I Dose-Escalation Clinical Trial , 2012, Clinical Cancer Research.

[18]  N. Socci,et al.  Copy Number Losses Define Subgroups of Dedifferentiated Liposarcoma with Poor Prognosis and Genomic Instability , 2012, Clinical Cancer Research.

[19]  Martin Renqiang Min,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[20]  C. Sander,et al.  Frequent alterations and epigenetic silencing of differentiation pathway genes in structurally rearranged liposarcomas. , 2011, Cancer discovery.

[21]  Peter A. Jones,et al.  A decade of exploring the cancer epigenome — biological and translational implications , 2011, Nature Reviews Cancer.

[22]  C. Sander,et al.  Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma. , 2011, Cancer research.

[23]  S. Singer,et al.  Clinical and molecular approaches to well differentiated and dedifferentiated liposarcoma , 2011, Current opinion in oncology.

[24]  Joseph K. Pickrell,et al.  False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions , 2011, Bioinform..

[25]  K. Wilner,et al.  Phase I study of PD 0332991, a cyclin-dependent kinase inhibitor, administered in 3-week cycles (Schedule 2/1) , 2011, British Journal of Cancer.

[26]  M. Esteller,et al.  Cancer epigenetics reaches mainstream oncology , 2011, Nature Medicine.

[27]  Tao Ye,et al.  seqMINER: an integrated ChIP-seq data interpretation platform , 2010, Nucleic acids research.

[28]  A. Lazar,et al.  An experimental model for the study of well differentiated and dedifferentiated liposarcoma; deregulation of targetable tyrosine kinase receptors , 2010, Laboratory Investigation.

[29]  Eric S. Lander,et al.  Comparative Epigenomic Analysis of Murine and Human Adipogenesis , 2010, Cell.

[30]  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.

[31]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[32]  J. Rinn,et al.  Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature Biotechnology.

[33]  R. Blumenthal,et al.  Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. , 2010, Biochemistry.

[34]  J. Rinn,et al.  Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature biotechnology.

[35]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[36]  J. Coindre,et al.  Well-differentiated and dedifferentiated liposarcomas , 2010, Virchows Archiv.

[37]  S. Devries,et al.  Similarity in genetic alterations between paired well-differentiated and dedifferentiated components of dedifferentiated liposarcoma , 2009, Modern Pathology.

[38]  D. Leake,et al.  KLF6-SV1 is a novel antiapoptotic protein that targets the BH3-only protein NOXA for degradation and whose inhibition extends survival in an ovarian cancer model. , 2009, Cancer research.

[39]  H. Cedar,et al.  Linking DNA methylation and histone modification: patterns and paradigms , 2009, Nature Reviews Genetics.

[40]  J. Martignetti,et al.  The role of KLF6 and its splice variants in cancer therapy. , 2009, Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy.

[41]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[42]  H. Friess,et al.  Increased alternative splicing of the KLF6 tumour suppressor gene correlates with prognosis and tumour grade in patients with pancreatic cancer. , 2008, European journal of cancer.

[43]  S. Dhanasekaran,et al.  KLF6-SV1 overexpression accelerates human and mouse prostate cancer progression and metastasis. , 2008, The Journal of clinical investigation.

[44]  C. Sander,et al.  Gene expression profiling of liposarcoma identifies distinct biological types/subtypes and potential therapeutic targets in well-differentiated and dedifferentiated liposarcoma. , 2007, Cancer research.

[45]  Axel Imhof,et al.  Identification of a specific inhibitor of the histone methyltransferase SU(VAR)3-9 , 2005, Nature chemical biology.

[46]  J. Bocco,et al.  A new role for the Krüppel-like transcription factor KLF6 as an inhibitor of c-Jun proto-oncoprotein function , 2004, Oncogene.

[47]  S. Friedman,et al.  Cyclin-Dependent Kinase Inhibition by the KLF6 Tumor Suppressor Protein through Interaction with Cyclin D1 , 2004, Cancer Research.

[48]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[49]  S. Friedman,et al.  KLF6, a Candidate Tumor Suppressor Gene Mutated in Prostate Cancer , 2001, Science.

[50]  A. D. Tos.  Liposarcoma: new entities and evolving concepts. , 2000, Annals of diagnostic pathology.

[51]  Y. Masuho,et al.  Differential regulation of immediate early gene expression in preadipocyte cells through multiple signaling pathways. , 1999, Biochemical and biophysical research communications.