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| Status |
Public on May 13, 2024 |
| Title |
Determine whether AsiDNA and belinostat alter chromatin accessbility genome-wide in glioblastoma cells. [NicE-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
An effective long-term inhibition of multiple DNA repair signals is required to design a novel and effective therapeutic for glioblastoma (GBM), a highly DNA repair ‘addicted’ cancer. AsiDNA, a double-strand DNA break (DSB) mimetic, is an innovative approach that shuts down the entire DNA repair system in cancer cells by sequestering DSB repair factors. We showed that inhibition of class I histone deacetylases (HDACs) dislodges repair factors from sites of DNA damage. We therefore tested whether AsiDNA and pan HDAC inhibitor Belinostat combination can impart a chromatin-based long-term DNA damage and impair DNA repair in GBM cells. We performed mass spectrometry with chromatin isolated from AsiDNA and Belinostat and found that Belinostat reduces histone H1.2 levels. To this end, we assessed whether AsiDNA and Belinostat alter histone H1.2 occupancy genome-wide. In order to understand the long-term effects of AsiDNA on DNA repair, we treated U87 cells with AsiDNA for 6 days followed by 6 days recovery from the drug. We used this protocol to create long-term AsiDNA treated cells (LTAU87) according to the clinical trial protocol. We performed NicE-seq with LTAU87 cells and MTU87 (mock treated U87; control) in the presence or absence of belinostat treatment in order to address whether they alter the global chromatin structure.
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| Overall design |
NicE-seq analysis following exposure of glioblastoma cells to AsiDNA and/or Belinostat. Library construction was performed as described by Ponnaluri et al [Genome Biology 18, 122 (2017)] by biotin labeling of chromatin digested with Nt.CviPII (NEB R0626S).
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| Contributor(s) |
Bhaskara S, Chandrasekharan M, Hang Gyeong C, Sagnik S, Sriharsa P |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 05, 2024 |
| Last update date |
May 13, 2024 |
| Contact name |
Mahesh Babu Chandrasekharan |
| E-mail(s) |
mahesh.chandrasekharan@hci.utah.edu
|
| Phone |
801-213-4220
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| Organization name |
University of Utah SOM
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| Department |
Radiation Oncology
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| Lab |
HCI Chandrasekharan Lab
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| Street address |
2000 circle of hope room 3715
|
| City |
salt lake city |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA1107962 |
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