TY - JOUR
T1 - Estimating genome-wide off-target effects for pyrrole-imidazole polyamide binding by a pathway-based expression profiling approach
AU - Lin, Jason
AU - Krishnamurthy, Sakthisri
AU - Yoda, Hiroyuki
AU - Shinozaki, Yoshinao
AU - Watanabe, Takayoshi
AU - Koshikawa, Nobuko
AU - Takatori, Atsushi
AU - Horton, Paul
AU - Nagase, Hiroki
N1 - Funding Information:
This work was supported by Grant-in-Aids for Scientific Research B and for Young Scientists B from Japan Society for the Promotion of Science (JP17H03602 to H.N. and JP17K15047 to J.L.) as well as Japan Agency for Medical Research and Development (AMED, JP17cm0106510, JP17ck0106263 and JP17ck0106356 to H.N., 15656919 to A.T. and JP18ck0106422 to H.N. and J.L.). Additional support was provided in part by Takeda Science Foundation (A.T.), Princess Takamatsu Cancer Research Fund (H.N.) and Grant-in-Aid for Scientific Research on Innovative Areas via the Platform for Supporting Cohort Study and Biospecimen Analysis (H.N. and J.L.) from the Ministry of Education, Culture, Sports, Science and Technology of Japan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We would like to thank Ms. Yuki Kaiho, Nina Matsuo and Yuki Nakamura as well as Drs. Takahiro Inoue, Kiriko Hiraoka and Yasutoshi Tatsumi at Chiba Cancer Center Research Institute for their experimental assistance. Dr. Tony Kuo at AIST Artificial Intelligence Research Center (AIST-AIRC) along with Drs. Etyan Ruppin and Itay Shaked at Tel Aviv University also provided insights and support during the initial period. High-performance computing was provided by the Institute of Medical Science at the University of Tokyo and AIST-AIRC. J.L. held a visiting appointment at AIST-AIRC for the duration of this project.
Publisher Copyright:
© 2019 Lin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2019/4
Y1 - 2019/4
N2 - In the search for new pharmaceutical leads, especially with DNA-binding molecules or genome editing methods, the issue of side and off-target effects have always been thorny in nature. A particular case is the investigation into the off-target effects of N-methylpyrrole-N-methylimidazole polyamides, a naturally inspired class of DNA binders with strong affinity to the minor-groove and sequence specificity, but at < 20 bases, their relatively short motifs also insinuate the possibility of non-unique genomic binding. Binding at non-intended loci potentially lead to the rise of off-target effects, issues that very few approaches are able to address to-date. We here report an analytical method to infer off-target binding, via expression profiling, based on probing the relative impact to various biochemical pathways; we also proposed an accompanying side effect prediction engine for the systematic screening of candidate polyamides. This method marks the first attempt in PI polyamide research to identify elements in biochemical pathways that are sensitive to the treatment of a candidate polyamide as an approach to infer possible off-target effects. Expression changes were then considered to assess possible outward phenotypic changes, manifested as side effects, should the same PI polyamide candidate be administered clinically. We validated some of these effects with a series of animal experiments, and found agreeable corroboration in certain side effects, such as changes in aspartate transaminase levels in ICR and nude mice post-administration.
AB - In the search for new pharmaceutical leads, especially with DNA-binding molecules or genome editing methods, the issue of side and off-target effects have always been thorny in nature. A particular case is the investigation into the off-target effects of N-methylpyrrole-N-methylimidazole polyamides, a naturally inspired class of DNA binders with strong affinity to the minor-groove and sequence specificity, but at < 20 bases, their relatively short motifs also insinuate the possibility of non-unique genomic binding. Binding at non-intended loci potentially lead to the rise of off-target effects, issues that very few approaches are able to address to-date. We here report an analytical method to infer off-target binding, via expression profiling, based on probing the relative impact to various biochemical pathways; we also proposed an accompanying side effect prediction engine for the systematic screening of candidate polyamides. This method marks the first attempt in PI polyamide research to identify elements in biochemical pathways that are sensitive to the treatment of a candidate polyamide as an approach to infer possible off-target effects. Expression changes were then considered to assess possible outward phenotypic changes, manifested as side effects, should the same PI polyamide candidate be administered clinically. We validated some of these effects with a series of animal experiments, and found agreeable corroboration in certain side effects, such as changes in aspartate transaminase levels in ICR and nude mice post-administration.
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U2 - 10.1371/journal.pone.0215247
DO - 10.1371/journal.pone.0215247
M3 - Article
C2 - 30964912
AN - SCOPUS:85064089235
SN - 1932-6203
VL - 14
JO - PloS one
JF - PloS one
IS - 4
M1 - e0215247
ER -