Increased H3K9me3 drives dedifferentiated phenotype via KLF6 repression in liposarcoma
Emily Z. Keung, Kadir C. Akdemir, Ghadah A. Al Sannaa, Jeannine Garnett, Dina Lev, Keila E. Torres, Alexander J. Lazar, Kunal Rai, Lynda Chin
Emily Z. Keung, Kadir C. Akdemir, Ghadah A. Al Sannaa, Jeannine Garnett, Dina Lev, Keila E. Torres, Alexander J. Lazar, Kunal Rai, Lynda Chin
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Research Article Oncology

Increased H3K9me3 drives dedifferentiated phenotype via KLF6 repression in liposarcoma

Abstract

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.

Authors

Emily Z. Keung, Kadir C. Akdemir, Ghadah A. Al Sannaa, Jeannine Garnett, Dina Lev, Keila E. Torres, Alexander J. Lazar, Kunal Rai, Lynda Chin

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Figure 4

KLF6 is underexpressed in human DDLPS tumors compared with WDLPS tumors.

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KLF6 is underexpressed in human DDLPS tumors compared with WDLPS tumors....
(A) KLF6 expression levels in human DDLPS tumors (n = 17) compared with those detected in WDLPS tumors (n = 13) and normal fat (n = 6), as assessed by qRT-PCR normalized to GAPDH (mean ± SD; n = 3). Data were analyzed by Mann-Whitney U and Kruskal-Wallis tests. (B) KLF6 protein expression in human DDLPS tumors (n = 19) compared with levels detected in normal fat (n = 8) and WDLPS tumors (n = 14), as assessed by Western blot analysis. (C) Relative KLF6 copy numbers of WDLPS (n = 3) and DDLPS (n = 4) cell lines, as assessed by TaqMan CNV assay (RNaseP reference) (mean ± SD; n = 3). Data were analyzed by the Mann-Whitney U test. (D) Relative KLF6 copy numbers of WDLPS (n = 15) and DDLPS (n = 19) tumors, as assessed by TaqMan CNV assay (RNaseP reference) (mean ± SD; n = 3). Data were analyzed by Mann-Whitney U and Kruskal-Wallis tests. Mean KLF6 copy number: normal fat specimens, 1.99 (95% CI 1.60–2.37), DDLPS tumors, 2.04 (95% CI 1.84–2.24), and WDLPS tumors, 2.46 (95% CI 2.17–2.75). Data are representative of 2 experiments.