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| Status |
Public on May 15, 2024 |
| Title |
Chemical genetics in Caenorhabditis elegans identifies anticancer compound chaetocin and p300/CBP as modulators of metal response genes |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We recently used a genome-wide screen to demonstrate that numr-1/2 is activated by disruption of RNA metabolism. To investigate numr-1/2 regulation and identify modulators of nucleic acid metabolism, we screened over 40,000 compounds and extracts from commercial and natural product libraries for numr-1/2p::GFP activation. Fungal toxin chaetocin was the most potent and least toxic numr-1/2 inducer. RT-qPCR demonstrates that chaetocin induces numr-1/2 and another stress-responsive SR-like protein gene (W03G1.5) in C. elegans over 50-fold within 45 minutes without affecting expression of canonical heat shock, osmotic stress, endoplasmic reticulum stress, mitochondrial stress, or detoxification response genes. Chaetocin does not activate other metal-responsive genes and actually reduces expression of metallothionein gene mtl-2 and fluorescence of mtl-2p::GFP consistent with repression of mtl-2 transcription. Along with a similar HMTase inhibitor from the same fungal origin - Chetomin, and two synthetic S-methyl-products of Chaetocin and Chetomin, respectively, we tested the expression profile at 5h and 12h post treatment at 500 nM concentration in HCT116 colorectal carcinoma cell line. Both S-methyl-products showed no significant activity or any detectable statistically significant changes in expression compared to the vehicle control. The parent compounds induced a number of expression changes consistent with effects on the stress-response genes in HCT116 cells.
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| Overall design |
HCT116 cells were seeded in 6-well plates at 2 × 10^5 cells/well in Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (Sigma) and 1% Antibiotic-Antimycotic solution (Gibco), left overnight to attach and acclimate and treated with solvent control (DMSO, 0.5%), chaetocin, chetomin or their respective sulfide-depleted analogs to final concentration of 500 nM . After 5 H or 12 H incubation with compounds or solvent, RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer instructions. Illumina RNA library construction and sequencing were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF) .
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| Contributor(s) |
Atanasova KR, Ratnayake R, Luesch H, Choe KP |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
May 16, 2023 |
| Last update date |
May 15, 2024 |
| Contact name |
Alberto Riva |
| E-mail(s) |
ariva@ufl.edu
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| Organization name |
University of Florida
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| Department |
ICBR
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| Lab |
Bioinformatics Core
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| Street address |
2033 Mowry Rd
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32605 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA973077 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE232639_diff_expr_genes_all_cpm1_12H.xlsx |
9.2 Mb |
(ftp)(http) |
XLSX |
| GSE232639_diff_expr_genes_all_cpm1_5H.xlsx |
8.4 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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