TRAIN (Transcription of Repeats Activates INterferon) in response to chromatin destabilization induced by small molecules in mammalian cells
- Roswell Park Cancer Institute, United States
- Ariel University, Israel
- Buffalo BioLabs, United States
- Institute of Carcinogenesis, Blokhin Cancer Research Center RAMS, Russia
Figures
Figure 1 with 1 supplement
Effect of CBL0137 on transcription of genes in FACT-positive and -negative mouse tissues.
(A) IHC staining with SSRP1 antibody of liver and lung tissues with no detectable SSRP1 and spleen and testis expressing SSRP1. (B, C) Analyses of changes in genes expression in different tissues of …
Figure 1—figure supplement 1
Effects of different doses of CBL0137 in tumor growth and gene expression in mice.
(A) Change in a volume of subcutaneous HepG2 tumors in SCID mice treated once a week with IV with vehicle (5% dextrose) or 30, 60 and 90 mg/kg of CBL0137 for 4 weeks. (B) Dendrogram of gene …
Figure 2 with 1 supplement
Activation of IFN response is detected in response to CBL0137 in different tissues of mice via GSEA.
(A) Venn diagrams showing the number of up (red font) or down (blue font) regulated genes in response to CBL0137 together with gene set names enriched for these genes. The p-value of overlap is …
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Figure 2—source data 1
GSEA analysis of genes downregulated in response to treatment with 30 mg/kg (sheet 1), 60 mg/kg (sheet 2) and 90 mg/kg (sheet 3) of CBL0137 in liver.
- https://doi.org/10.7554/eLife.30842.006
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Figure 2—source data 2
GSEA analysis of genes upregulated in response to treatment with 30 mg/kg (sheet 1), 60 mg/kg (sheet 2) and 90 mg/kg (sheet 3) of CBL0137 in liver.
- https://doi.org/10.7554/eLife.30842.007
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Figure 2—source data 3
GSEA analysis of genes downregulated in response to treatment with 30 mg/kg (sheet 1), 60 mg/kg (sheet 2) and 90 mg/kg (sheet 3) of CBL0137 in lung.
- https://doi.org/10.7554/eLife.30842.008
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Figure 2—source data 4
GSEA analysis of genes upregulated in response to treatment with 30 mg/kg (sheet 1), 60 mg/kg (sheet 2) and 90 mg/kg (sheet 3) of CBL0137 in lung.
- https://doi.org/10.7554/eLife.30842.009
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Figure 2—source data 5
GSEA analysis of genes downregulated in response to treatment with 30 mg/kg (sheet 1), 60 mg/kg (sheet 2) and 90 mg/kg (sheet 3) of CBL0137 in spleen.
- https://doi.org/10.7554/eLife.30842.010
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Figure 2—source data 6
GSEA analysis of genes upregulated in response to treatment with 30 mg/kg (sheet 1), 60 mg/kg (sheet 2) and 90 mg/kg (sheet 3) of CBL0137 in spleen.
- https://doi.org/10.7554/eLife.30842.011
Figure 2—figure supplement 1
GSEA analysis of genes upregulated in liver (A), lung (B) and spleen (C) of mice treated with CBL0137.
https://doi.org/10.7554/eLife.30842.005
Figure 3 with 2 supplements
CBL0137 causes increased expression of IFN-responsive genes in different tissues of mice.
Quantitation of RT-PCR data (A, B, D, E, F, G) shown as fold change upon treatment with different doses of CBL0137 (mg/kg) comparing to vehicle-treated control. Mean values from three mice ± SD. …
Figure 3—figure supplement 1
Images of RT-PCR reactions used for quantitation on Figure 3.
https://doi.org/10.7554/eLife.30842.013
Figure 3—figure supplement 2
Images of RT-PCR reactions used for quantitation for Figure 3.
https://doi.org/10.7554/eLife.30842.014
Figure 4 with 1 supplement
Induction of IFN response in human and mouse cells treated with CBL0137.
(A) RT-PCR and immunoblotting of mRNA and lysates from human normal diploid fibroblasts (NDF). ISG56 is a product of the human IFIT3 gene. (B) RT-PCR of mRNA from MEF, wild type or Trp53 (p53) …
Figure 4—figure supplement 1
Comparison of the sensitivity of ISRE reporter assay with detection of the transcript of endogenous ISG, IFIT3 in human tumor cell line HCT116 transduced with lentiviral ISRE-Luc reporter.
Cells were treated for 36 hr with indicated doses of IFNα or CBL0137 and then either used for reporter assay (A) of for RNA isolation and RT-PCR (B).
Figure 5
Induction of IFN-responsive gene by CBL0137 depends on IFN signaling.
(A) RT-PCR of RNA from MEF cells of different genotype or wild type MEF transduced with control shRNA or shRNA to Irf7 and treated for 24 hr with 0.5 μM of CBL0137. (B) Immunoblotting of tissue …
Figure 6 with 1 supplement
Elevated presence of double-stranded RNA in cells and tissues of mice treated with CBL0137.
Immunofluorescent staining of MEF (A) and human HT1080 (B) cells with antibody to dsRNA (red) and Hoeschst (blue). (C) Northern blotting of RNA from MEF (Trp53-/-) treated with either 5-Aza for 72 …
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Figure 6—source data 1
Analysis of expression of repetitive elements in control and CBL0137 treated wild type of Trp53-/- MEF cells of lungs of wild-type mice via RNA-seq.
- https://doi.org/10.7554/eLife.30842.020
Figure 6—figure supplement 1
INF induction by CBL0137 does not depend on ZBP1.
(A) RT-PCR with primers to ZBP1 of mRNA from Hela cells in which ZBP1 gene was inactivated with CRISP-Cas9 recombinase. Two different gRNA to ZBP1 and one control were used. (B) Fluorescent …
Figure 7 with 1 supplement
Chromatin opening is accompanied by TRAIN.
(A) Increase in the proportion of cells expressing GFP from silenced viral promoter in Hela cells treated with either TSA (250 nM) or CBL0137 (500 nM). (B) Changes in the abundance of Ifit3 and Irf7 …
Figure 7—figure supplement 1
Abundance of transcripts corresponding to major (GSAT) or minor (SATMIN) satellites or LINE1 per millions of reads of RNA-seq of total RNA from MEF cells from Trp53 wild type (p53+/+) or Trp53-null (p53-/-) mice or lung tissue of Trp53 wild-type mice treated with either 1 μM or 60 mg/kg of CBL0137 for 24 hr.
https://doi.org/10.7554/eLife.30842.022
Figure 8
CBL0137 treatment leads to displacement of histone H1.
Live cell imaging of HT1080 cells expressing mCherry-tagged H1.5 and GFP-tagged SSRP1. (A) Images of nuclei of the same cells at different moments after addition of 1 μM CBL0137 to cell culture …
Figure 9
Input of IFN response into anti-cancer activity of CBL0137.
(A) Treatment of cells transduced with H-RasV12 with CBL0137 leads to the reduction in the number of transformed foci in Ifnar-dependent manner. MEF of different background were transduced with …
Figure 10
Proposed scheme of nucleosome states in the absence and presence of increasing concentrations of CBL0137 (A) and associated biological processes in cells (B).
https://doi.org/10.7554/eLife.30842.025Additional files
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Transparent reporting form
- https://doi.org/10.7554/eLife.30842.026
