title: Genome-wide ChIP-seq analysis of EZH2-mediated H3K27me3 target gene profile highlights differences between low- and high-grade astrocytic tumors.
abstract: Enhancer of zeste homolog-2(EZH2) is a key epigenetic regulator that functions as oncogene and also known for inducing altered trimethylation of histone at lysine-27 (H3K27me3) mark in various tumors. However, H3K27me3 targets and their precise relationship with gene expression are largely unknown in astrocytic tumors. In this study, we checked EZH2 messenger RNA and protein expression in 90 astrocytic tumors of different grades using quantitative PCR and immunohistochemistry, respectively. Further, genome-wide ChIP-seq analysis for H3K27me3 modification was also performed on 11 glioblastomas (GBMs) and 2 diffuse astrocytoma (DA) samples. Our results showed EZH2 to be highly overexpressed in astrocytic tumors with a significant positive correlation with grade. Interestingly, ChIP-seq mapping revealed distinct differences in genes and pathways targeted by these H3K27me3 modifications between GBM versus DA. Neuroactive ligand receptor pathway was found most enriched in GBM (P = 9.4 × 10-25), whereas DA were found to be enriched in metabolic pathways. Also, GBM showed a higher enrichment of H3K27me3 targets reported in embryonic stem cells and glioma stem cells as compared with DAs. Our results show majority of these H3K27me3 target genes were downregulated, not only due to H3K27me3 modification but also due to concomitant DNA methylation. Further, H3K27me3 modification-associated gene silencing was not restricted to promoter but also present in gene body and transcription start site regions. To the best of our knowledge, this is the first high-resolution genome-wide mapping of H3K27me3 modification in adult astrocytic primary tissue samples of human, highlighting the differences between grades. Interestingly, we identified SLC25A23 as important target of H3K27me3 modification, which was downregulated in GBM and its low expression was associated with poor prognosis in GBMs.
authors.affiliation: Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India.
authors.forename: Vikas
authors.initials: V
authors.lastname: Sharma
authors.affiliation: Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India.
authors.forename: Prit Benny
authors.initials: PB
authors.lastname: Malgulwar
authors.affiliation: Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India.
authors.forename: Suvendu
authors.initials: S
authors.lastname: Purkait
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, Karnataka, India.
authors.forename: Vikas
authors.initials: V
authors.lastname: Patil
authors.affiliation: Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Pathak
authors.affiliation: Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India.
authors.forename: Rahul
authors.initials: R
authors.lastname: Agrawal
authors.affiliation: Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India.
authors.forename: Ritu
authors.initials: R
authors.lastname: Kulshreshtha
authors.affiliation: Department of Radiation Oncology and.
authors.forename: Supriya
authors.initials: S
authors.lastname: Mallick
authors.affiliation: Department of Radiation Oncology and.
authors.forename: Pramod Kumar
authors.initials: PK
authors.lastname: Julka
authors.affiliation: Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi 110029, India.
authors.forename: Ashish
authors.initials: A
authors.lastname: Suri
authors.affiliation: Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi 110029, India.
authors.forename: Bhawani Shankar
authors.initials: BS
authors.lastname: Sharma
authors.affiliation: Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India.
authors.forename: Vaishali
authors.initials: V
authors.lastname: Suri
authors.affiliation: Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India.
authors.forename: Mehar Chand
authors.initials: MC
authors.lastname: Sharma
authors.affiliation: Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India.
authors.forename: Chitra
authors.initials: C
authors.lastname: Sarkar
mesh_terms: D017920:Antiporters / Q000235:genetics*; D001254:Astrocytoma / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D019175:DNA Methylation / Q000235:genetics*; D004742:Enhancer Elements, Genetic / Q000235:genetics; D000071221:Enhancer of Zeste Homolog 2 Protein / Q000235:genetics* / Q000378:metabolism; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D005909:Glioblastoma / Q000235:genetics* / Q000473:pathology; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D008297:Male; D024101:Mitochondrial Proteins / Q000235:genetics*; D060787:Neoplasm Grading; D011401:Promoter Regions, Genetic
chemical_list: C086357:ATP-Mg-Pi carrier proteins, mitochondria; D017920:Antiporters; D024101:Mitochondrial Proteins; C498409:EZH2 protein, human; D000071221:Enhancer of Zeste Homolog 2 Protein; D011495:Histone-Lysine N-Methyltransferase