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Concordance of hydrogen peroxide-induced 8-oxoguanine patterns with two cancer mutation signatures of upper GI tract tumors

ABSTRACT: Concordance of hydrogen peroxide-induced 8-oxoguanine patterns with two cancer mutation signatures of upper GI tract tumors

PROVIDER: PRJNA766602 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16085651_1.fastq.gz	Fastqsanger.gz
	SRR16085651_2.fastq.gz	Fastqsanger.gz
	SRR16085652_1.fastq.gz	Fastqsanger.gz
	SRR16085652_2.fastq.gz	Fastqsanger.gz
	SRR16085653_1.fastq.gz	Fastqsanger.gz

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Concordance of hydrogen peroxide-induced 8-oxoguanine patterns with two cancer mutation signatures of upper GI tract tumors

Project description:Oxidative DNA damage has been linked to cancer, aging, inflammation, and other pathological conditions. Although the chemical nature of the damaged bases is well understood, the precise distribution of oxidatively damaged DNA bases in the human genome is not known. Here we have used the recently developed circle-damage-sequencing method to map two types of oxidative DNA damage, oxidized guanines produced by hydrogen peroxide and oxidized thymines created by treatment of cells with potassium permanganate, at single base resolution. We show that oxidized guanines, chiefly 8-oxo-G, occur strictly dependent on the G/C sequence context and show a pronounced peak at transcription start sites (TSS). We determined the trinucleotide sequence pattern of guanine oxidation. This pattern shows high similarity to the cancer-associated single base substitution signatures SBS18 and SBS36. SBS36 is found in colorectal cancers that carry mutations in MUTYH, encoding a DNA repair enzyme that operates on 8-oxo-G mispairs. SBS18 is common in inflammation-associated upper GI tract tumors including esophageal and gastric adenocarcinomas. Oxidized thymines induced by permanganate occur with a distinct dinucleotide specificity, 5’T-A/C, and are depleted at the TSS. Collectively, our data provides a comprehensive analysis of two types of oxidized DNA bases in the human genome and suggests that two cancer mutational signatures, SBS18 and SBS36, are caused by reactive oxygen species.

2022-04-12 | GSE184820 | GEO

Concordance of hydrogen peroxide-induced 8-oxo-guanine patterns with two cancer mutation signatures of upper GI tract tumors.

Project description:Oxidative DNA damage has been linked to inflammation, cancer, and aging. Here, we have mapped two types of oxidative DNA damage, oxidized guanines produced by hydrogen peroxide and oxidized thymines created by potassium permanganate, at a single-base resolution. 8-Oxo-guanine occurs strictly dependent on the G/C sequence context and shows a pronounced peak at transcription start sites (TSSs). We determined the trinucleotide sequence pattern of guanine oxidation. This pattern shows high similarity to the cancer-associated single-base substitution signatures SBS18 and SBS36. SBS36 is found in colorectal cancers that carry mutations in MUTYH, encoding a repair enzyme that operates on 8-oxo-guanine mispairs. SBS18 is common in inflammation-associated upper gastrointestinal tract tumors including esophageal and gastric adenocarcinomas. Oxidized thymines induced by permanganate occur with a distinct dinucleotide specificity, 5'T-A/C, and are depleted at the TSS. Our data suggest that two cancer mutational signatures, SBS18 and SBS36, are caused by reactive oxygen species.

| S-EPMC9166614 | biostudies-literature

Adaptation to hydrogen peroxide

Project description:Adaptation to hydrogen peroxide in Saccharomyces cerevisiae is profiled with expression arrays. Adaptation describes the process in which a mild dose of toxin (in this case, hydrogen peroxide) is able to protect against a later acute dose. Here, we study two adaptive protocols (0.1 mM H2O2 and 0.1 + 0.4 mM H2O2) and one acute protocol (0.4 mM H2O2) to identify processes uniquely involved in adaptation. Predictions from these studies are validated in expression profiling of deletion mutants of the transcription factors Yap1, Mga2, and Rox1.

2009-04-23 | GSE12602 | GEO

Response of Bacillus pumilus to hydrogen peroxide

Project description:Reactive oxygen species such as hydrogen peroxide occur in all aerobically living organisms. Oxidative stress during fermentation can impair the fitness of the production host and the quality of the product. B. pumilus has been described as highly resistant to hydrogen peroxide. The response of exponentially growing B. pumilus cells to hydrogen peroxide was studied.

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Funil Reservoir and hydrogen peroxide

Project description:Hydrogen Peroxide applied to funil reservoir water

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Hydrogen peroxide Stress in Desulfovibrio vulgaris Hildenborough

Project description:Using data from microarray experiments, we investigated the effects of excess hydrogen peroxide on D. vulgaris. Keywords: stress response, time course

2011-07-04 | GSE21438 | GEO

Hyperthermophilic archaeon Pyrococcus furiosus response to hydrogen peroxide

Project description:Oxidative Stress Protection and the Repair Response To Hydrogen Peroxide in the Hyperthermophilic Archaeon Pyrococcus furiosus Pyrococcus furiosus is a shallow marine, anaerobic archaeon that grows optimally at 100°C. Addition of H2O2 (0.5 mM) to a growing culture resulted in cessation of growth with a 2 hour lag before normal growth resumed. Whole genome transcriptional profiling revealed that the main response occurs within 30 min of peroxide addition, with the up-regulation of 62 open reading frames (ORFs), 36 of which are part of 10 potential operons. More than half of the up-regulated ORFs are of unknown function while some others encode proteins that are involved potentially in sequestering iron and sulfide, in DNA repair and in generating NADPH. This response is thought to involve primarily damage repair rather than protection, since cultures exposed to sub-toxic levels of H2O2 were not more resistant to the subsequent addition of H2O2 (0.5 – 5.0 mM). Consequently, there is little if any induced protective response to peroxide, rather, the organism maintains a constitutive protective mechanism involving high levels of oxidoreductase-type enzymes such as superoxide reductase, rubrerythrin and alkyl hydroperoxide reductase I. The related hyperthermophiles P. woesei and Thermococcus kodakaraensis were more sensitive to peroxide than P. furiosus, apparently due to the lack of several of its peroxide-responsive ORFs.

2010-02-25 | GSE20470 | GEO

Response of Bacillus pumilus to hydrogen peroxide

2014-05-17 | E-GEOD-57735 | biostudies-arrayexpress

RNA-seq of Microcystis aeruginosa PCC7806: on hydrogen peroxide

Project description:Comparison for gene expression of Microcystis aeruginosa PCC7806 after hydrogen peroxide treatment

2021-01-07 | GSE164328 | GEO

Transcriptome profiling of H. polymorpha in response to hydrogen peroxide exposure

Project description:To gain insight into the basic mechanism of Hydrogen peroxide detoxification in the methylotrophic yeast, H. polymorpha, we analyzed changes in transcriptional profiles in response to hydrogen peroxide exposure.

2015-02-28 | GSE43048 | GEO

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