title: Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome.
abstract: Pyrrole-imidazole polyamides are versatile DNA minor groove binders and attractive therapeutic options against oncological targets, especially upon functionalization with an alkylating agent such as seco-CBI. These molecules also provide an alternative for oncogenes deemed "undruggable" at the protein level, where the absence of solvent-accessible pockets or structural crevices prevent the formation of protein-inhibitor ligands; nevertheless, the genome-wide effect of pyrrole-imidazole polyamide binding remain largely unclear to-date. Here we propose a next-generation sequencing-based workflow combined with whole genome expression arrays to address such issue using a candidate anti-cancer alkylating agent, KR12, against codon 12 mutant KRAS. Biotinylating KR12 enables the means to identify its genome-wide effects in living cells and possible biological implications via a coupled workflow of enrichment-based sequencing and expression microarrays. The subsequent computational pathway and expression analyses allow the identification of its genomic binding sites, as well as a route to explore a polyamide's possible genome-wide effects. Among the 3,343 KR12 binding sites identified in the human LS180 colorectal cancer genome, the reduction of KR12-bound gene expressions was also observed. Additionally, the coupled microarray-sequencing analysis also revealed some insights about the effect of local chromatin structure on pyrrole-imidazole polyamide, which had not been fully understood to-date. A comparative analysis with KR12 in a different human colorectal cancer genome SW480 also showed agreeable agreements of KR12 binding affecting gene expressions. Combination of these analyses thus suggested the possibility of applying this approach to other pyrrole-imidazole polyamides to reveal further biological details about the effect of polyamide binding in a genome.
authors: Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chuo-ku, Chiba, Japan.
authors: Jason
authors: J
authors: Lin
authors: Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chuo-ku, Chiba, Japan.
authors: Kiriko
authors: K
authors: Hiraoka
authors: Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chuo-ku, Chiba, Japan.
authors: Takayoshi
authors: T
authors: Watanabe
authors: Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan.
authors: Tony
authors: T
authors: Kuo
authors: Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chuo-ku, Chiba, Japan.|Department of Materials and Applied Chemistry, Nihon University, Chiyoda-ku, Tokyo, Japan.
authors: Yoshinao
authors: Y
authors: Shinozaki
authors: Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chuo-ku, Chiba, Japan.
authors: Atsushi
authors: A
authors: Takatori
authors: Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chuo-ku, Chiba, Japan.
authors: Nobuko
authors: N
authors: Koshikawa
authors: Department of Chemistry, Kyoto University, Sakyo-ku, Kyoto, Japan.
authors: Anandhakumar
authors: A
authors: Chandran
authors: Department of Materials and Applied Chemistry, Nihon University, Chiyoda-ku, Tokyo, Japan.
authors: Joe
authors: J
authors: Otsuki
authors: Department of Chemistry, Kyoto University, Sakyo-ku, Kyoto, Japan.
authors: Hiroshi
authors: H
authors: Sugiyama
authors: Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan.
authors: Paul
authors: P
authors: Horton
authors: Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, Chuo-ku, Chiba, Japan.
authors: Hiroki
authors: http://orcid.org/0000-0002-3992-5399
authors: H
authors: Nagase
mesh_terms: D018906:Antineoplastic Agents, Alkylating / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D001665:Binding Sites; D045744:Cell Line, Tumor; D002470:Cell Survival / Q000187:drug effects; D047369:Chromatin Immunoprecipitation; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D006801:Humans; D007093:Imidazoles / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D009154:Mutation; D009707:Nucleosomes / Q000378:metabolism; D059372:Nucleotide Motifs; D009757:Nylons / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D011485:Protein Binding; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018906:Antineoplastic Agents, Alkylating; D006657:Histones; D007093:Imidazoles; C000605800:KR12 compound; C117307:KRAS protein, human; D009707:Nucleosomes; D009757:Nylons; D004247:DNA; D016283:Proto-Oncogene Proteins p21(ras)