|
| Status |
Public on Nov 01, 2016 |
| Title |
Alkylating pyrrole-imidazole polyamide KR12 binding in colorectal cancer genomes (SW480) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
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 endo-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.
|
| |
|
| Overall design |
For expression microarrays, samples were subject to 500 nM KR12 (treatment) or 0.05% DMSO (control) for 6 h followed by RNA extraction. For LS180, samples were prepared in 2 × 2 replicates for each treatment (DMSO as control compared to KR12 at 500 nM); for SW480, 3 replicates were performed for the control and treatment to determine effect of KR12 on gene expressions.
|
| |
|
| Contributor(s) |
Hiraoka K, Lin J, Hiroki N |
| Citation(s) |
27798693 |
| |
| Submission date |
Sep 08, 2016 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Jason Lin |
| Organization name |
Chiba Cancer Center Research Institute
|
| Street address |
666-2 Nitona-cho, Chuo-ku
|
| City |
Chiba |
| State/province |
Chiba |
| ZIP/Postal code |
260-8717 |
| Country |
Japan |
| |
|
| Platforms (1) |
| GPL16699 |
Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Feature Number version) |
|
| Samples (6)
|
|
| This SubSeries is part of SuperSeries: |
| GSE86599 |
Alkylating pyrrole-imidazole polyamide KR12 binding in colorectal cancer genomes |
|
| Relations |
| BioProject |
PRJNA342335 |
Less...
More...