Detection of in vivo mutagenicity in rat liver samples using error-corrected sequencing techniques.

IF 2.7 4区 医学 Q2 GENETICS & HEREDITY Genes and Environment Pub Date : 2023-11-22 DOI:10.1186/s41021-023-00288-z
Kazuki Izawa, Masataka Tsuda, Takayoshi Suzuki, Masamitsu Honma, Kei-Ichi Sugiyama
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Abstract

Background: Mutagenicity, the ability of chemical agents to cause mutations and potentially lead to cancer, is a critical aspect of substance safety assessment for protecting human health and the environment. Metabolic enzymes activate multiple mutagens in living organisms, thus in vivo animal models provide highly important information for evaluating mutagenicity in human. Rats are considered suitable models as they share a similar metabolic pathway with humans for processing toxic chemical and exhibit higher responsiveness to chemical carcinogens than mice. To assess mutagenicity in rats, transgenic rodents (TGRs) are widely used for in vivo gene mutation assays. However, such assays are labor-intensive and could only detect transgene mutations inserted into the genome. Therefore, introducing a technology to directly detect in vivo mutagenicity in rats would be necessary. The next-generation sequencing (NGS) based error-corrected sequencing technique is a promising approach for such purposes.

Results: We investigated the applicability of paired-end and complementary consensus sequencing (PECC-Seq), an error-corrected sequencing technique, for detecting in vivo mutagenicity in the rat liver samples. PECC-Seq allows for the direct detection of ultra-rare somatic mutations in the genomic DNA without being constrained by the genomic locus, tissue, or organism. We tested PECC-Seq feasibility in rats treated with diethylnitrosamine (DEN), a mutagenic compound. Interestingly, the mutation and mutant frequencies between PECC-Seq and the TGR assay displayed a promising correlation. Our results also demonstrated that PECC-Seq could successfully detect the A:T > T:A mutation in rat liver samples, consistent with the TGR assay. Furthermore, we calculated the trinucleotide mutation frequency and proved that PECC-Seq accurately identified the DEN treatment-induced mutational signatures.

Conclusions: Our study provides the first evidence of using PECC-Seq for in vivo mutagenicity detection in rat liver samples. This approach could provide a valuable alternative to conventional TGR assays as it is labor- and time-efficient and eliminates the need for transgenic rodents. Error-corrected sequencing techniques, such as PECC-Seq, represent promising approaches for enhancing mutagenicity assessment and advancing regulatory science.

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使用错误校正测序技术检测大鼠肝脏样本的体内突变性。
背景:诱变性,即化学制剂引起突变并可能导致癌症的能力,是保护人类健康和环境的物质安全评估的一个重要方面。代谢酶在生物体中激活多种诱变剂,因此体内动物模型为评估人类的诱变性提供了非常重要的信息。大鼠被认为是合适的模型,因为它们与人类有相似的代谢途径来处理有毒化学物质,并且对化学致癌物的反应比小鼠更高。为了评估大鼠的诱变性,转基因啮齿动物(tgr)被广泛用于体内基因突变试验。然而,这种检测是劳动密集型的,并且只能检测插入基因组的转基因突变。因此,引入一种直接检测大鼠体内诱变性的技术是必要的。基于新一代测序(NGS)的错误校正测序技术是一种很有前途的方法。结果:我们研究了配对端和互补一致性测序(PECC-Seq)的适用性,这是一种错误校正测序技术,用于检测大鼠肝脏样本的体内突变性。PECC-Seq允许直接检测基因组DNA中超罕见的体细胞突变,而不受基因组位点、组织或生物体的限制。我们在致突变化合物二乙基亚硝胺(DEN)处理的大鼠中测试了PECC-Seq的可行性。有趣的是,PECC-Seq和TGR检测之间的突变和突变频率显示出很好的相关性。我们的研究结果还表明PECC-Seq可以成功检测大鼠肝脏样本中的A:T > T:A突变,与TGR检测一致。此外,我们计算了三核苷酸突变频率,并证明PECC-Seq准确地识别了DEN处理诱导的突变特征。结论:我们的研究提供了PECC-Seq用于大鼠肝脏样本体内突变性检测的第一个证据。这种方法可以为传统的TGR分析提供有价值的替代方法,因为它省力、省时,并且不需要转基因啮齿动物。纠错测序技术,如PECC-Seq,代表了加强诱变性评估和推进调控科学的有前途的方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Genes and Environment
Genes and Environment Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
4.00
自引率
0.00%
发文量
24
审稿时长
27 weeks
期刊介绍: Genes and Environment is an open access, peer-reviewed journal that aims to accelerate communications among global scientists working in the field of genes and environment. The journal publishes articles across a broad range of topics including environmental mutagenesis and carcinogenesis, environmental genomics and epigenetics, molecular epidemiology, genetic toxicology and regulatory sciences. Topics published in the journal include, but are not limited to, mutagenesis and anti-mutagenesis in bacteria; genotoxicity in mammalian somatic cells; genotoxicity in germ cells; replication and repair; DNA damage; metabolic activation and inactivation; water and air pollution; ROS, NO and photoactivation; pharmaceuticals and anticancer agents; radiation; endocrine disrupters; indirect mutagenesis; threshold; new techniques for environmental mutagenesis studies; DNA methylation (enzymatic); structure activity relationship; chemoprevention of cancer; regulatory science. Genetic toxicology including risk evaluation for human health, validation studies on testing methods and subjects of guidelines for regulation of chemicals are also within its scope.
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