Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide Article Swipe

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Kokiladevi Alagarswamy , Ken‐ichi Shinohara , Shihori Takayanagi , Masaki Fukuyo , Atsushi Okabe , Bahityar Rahmutulla , Natsumi Yoda , Rui Qin , Naoki Shiga , Masahiro Sugiura , Hiroaki Sato , K Kita , Takayoshi Suzuki , Tetsuhiro Nemoto , Atsushi Kaneda ·

YOU? · · 2018 · Open Access · · DOI: https://doi.org/10.18632/oncotarget.25451

Epigenome regulates gene expression to determine cell fate, and accumulation of epigenomic aberrations leads to diseases, including cancer. NCD38 inhibits lysine-specific demethylase-1 (LSD1), a histone demethylase targeting H3K4me1 and H3K4me2, but not H3K4me3. In this study, we conjugated NCD38 with a potent small molecule called pyrrole (Py) imidazole (Im) polyamide, to analyze whether targets of the inhibitor could be regulated in a sequence-specific manner. We synthesized two conjugates using β-Ala (β) as a linker, i.e., NCD38-β-β-Py-Py-Py-Py (NCD38-β₂P₄) recognizing WWWWWW sequence, and NCD38-β-β-Py-Im-Py-Py (NCD38-β₂PIPP) recognizing WWCGWW sequence. When RKO cells were treated with NCD38, H3K4me2 levels increased in 103 regions with significant activation of nearby genes (P = 0.03), whereas H3K4me3 levels were not obviously increased. H3K27ac levels were also increased in 458 regions with significant activation of nearby genes (P = 3 × 10^-10), and these activated regions frequently included GC-rich sequences, but less frequently included AT-rich sequences (P < 1 × 10^-15) or WWCGWW sequences (P = 2 × 10^-13). When treated with NCD38-β₂P₄, 234 regions showed increased H3K27ac levels with significant activation of nearby genes (P = 2 × 10^-11), including significantly fewer GC-rich sequences (P < 1 × 10^-15) and significantly more AT-rich sequences (P < 1 × 10^-15) compared with NCD38 treatment. When treated with NCD38-β₂PIPP, 82 regions showed increased H3K27ac levels, including significantly fewer GC-rich sequences (P = 1 × 10^-11) and fewer AT-rich sequences (P = 0.005), but significantly more WWCGWW sequences (P = 0.0001) compared with NCD38 treatment. These indicated that target regions of epigenomic inhibitors could be modified in a sequence-specific manner and that conjugation of Py-Im polyamides may be useful for this purpose.

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Conjugated system Histone Imidazole Polyamide Medicine Cancer research Pyrrole Histone deacetylase inhibitor Pharmacology Chemistry Biochemistry Histone deacetylase DNA Organic chemistry Polymer

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Type: article
Language: en
Landing Page: https://doi.org/10.18632/oncotarget.25451
PDF: https://www.oncotarget.com/article/25451/pdf/
OA Status: diamond
Cited By: 6
References: 60
Related Works: 10
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DOI: https://doi.org/10.18632/oncotarget.25451

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Title: Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide

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Language: en

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Publication year: 2018

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Publication date: 2018-06-29

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Authors: Kokiladevi Alagarswamy, Ken‐ichi Shinohara, Shihori Takayanagi, Masaki Fukuyo, Atsushi Okabe, Bahityar Rahmutulla, Natsumi Yoda, Rui Qin, Naoki Shiga, Masahiro Sugiura, Hiroaki Sato, K Kita, Takayoshi Suzuki, Tetsuhiro Nemoto, Atsushi Kaneda

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Landing page: https://doi.org/10.18632/oncotarget.25451

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Concepts: Conjugated system, Histone, Imidazole, Polyamide, Medicine, Cancer research, Pyrrole, Histone deacetylase inhibitor, Pharmacology, Chemistry, Biochemistry, Histone deacetylase, DNA, Organic chemistry, Polymer

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