History of the science of mutagenesis from a personal perspective

The mutagenic consequences of defective DNA repair

Multiple separate repair mechanisms safeguard the genome against various types of DNA damage, and their failure can increase the rate of spontaneous mutagenesis. The malfunction of distinct repair mechanisms leads to genomic instability through different mutagenic processes. For example, defective mismatch repair causes high base substitution rates and microsatellite instability, whereas homologous recombination deficiency is characteristically associated with deletions and chromosome instability. This review presents a comprehensive collection of all mutagenic phenotypes associated with the loss of each DNA repair mechanism, drawing on data from a variety of model organisms and mutagenesis assays, and placing greatest emphasis on systematic analyses of human cancer datasets. We describe the latest theories on the mechanism of each mutagenic process, often explained by reliance on an alternative repair pathway or the error-prone replication of unrepaired, damaged DNA. Aided by the concept of mutational signatures, the genomic phenotypes can be used in cancer diagnosis to identify defective DNA repair pathways.

Adopting duplex sequencing technology for genetic toxicity testing: A proof-of-concept mutagenesis experiment with N-ethyl-N-nitrosourea (ENU)-exposed rats

Duplex sequencing (DS) is an error-corrected next-generation sequencing method in which molecular barcodes informatically link PCR-copies back to their source DNA strands, enabling computational removal of errors in consensus sequences. The resulting background of less than one artifactual mutation per 107 nucleotides allows for direct detection of somatic mutations. TwinStrand Biosciences, Inc. has developed a DS-based mutagenesis assay to sample the rat genome, which can be applied to genetic toxicity testing. To evaluate this assay for early detection of mutagenesis, a time-course study was conducted using male Hsd:Sprague Dawley SD rats (3 per group) administered a single dose of 40 mg/kg N-ethyl-N-nitrosourea (ENU) via gavage, with mutation frequency (MF) and spectrum analyzed in stomach, bone marrow, blood, and liver tissues at 3 h, 24 h, 7 d, and 28 d post-exposure. Significant increases in MF were observed in ENU-exposed rats as early as 24 h for stomach (site of contact) and bone marrow (a highly proliferative tissue) and at 7 d for liver and blood. The canonical, mutational signature of ENU was established by 7 d post-exposure in all four tissues. Interlaboratory analysis of a subset of samples from different tissues and time points demonstrated remarkable reproducibility for both MF and spectrum. These results demonstrate that MF and spectrum can be evaluated successfully by directly sequencing targeted regions of DNA obtained from various tissues⁠, a considerable advancement compared to currently used in vivo gene mutation assays.

Adopting Duplex Sequencing™ Technology for Genetic Toxicity Testing: A Proof-of-Concept Mutagenesis Experiment with N-Ethyl-N-Nitrosourea (ENU)-Exposed Rats

Duplex sequencing (DuplexSeq) is an error-corrected next-generation sequencing (ecNGS) method in which molecular barcodes informatically link PCR-copies back to their source DNA strands, enabling computational removal of errors by comparing grouped strand sequencing reads. The resulting background of less than one artifactual mutation per 10 7 nucleotides allows for direct detection of somatic mutations. TwinStrand Biosciences, Inc. has developed a DuplexSeq-based mutagenesis assay to sample the rat genome, which can be applied to genetic toxicity testing. To evaluate this assay for early detection of mutagenesis, a time-course study was conducted using male Hsd:Sprague Dawley SD rats (3 per group) administered a single dose of 40 mg/kg N-ethyl-N-nitrosourea (ENU) via gavage, with mutation frequency (MF) and spectrum analyzed in stomach, bone marrow, blood, and liver tissues at 3 h, 24 h, 7 d, and 28 d post-exposure. Significant increases in MF were observed in ENU-exposed rats as early as 24 h for stomach (site of contact) and bone marrow (a highly proliferative tissue) and at 7 d for liver and blood. The canonical, mutational signature of ENU was established by 7 d post-exposure in all four tissues. Interlaboratory analysis of a subset of samples from different tissues and time points demonstrated remarkable reproducibility for both MF and spectrum. These results demonstrate that MF and spectrum can be evaluated successfully by directly sequencing targeted regions of DNA obtained from various tissues, a considerable advancement compared to currently used in vivo gene mutation assays.

HIGHLIGHTS

DuplexSeq is an ultra-accurate NGS technology that directly quantifies mutationsENU-dependent mutagenesis was detected 24 h post-exposure in proliferative tissuesMultiple tissues exhibited the canonical ENU mutation spectrum 7 d after exposureResults obtained with DuplexSeq were highly concordant between laboratoriesThe Rat-50 Mutagenesis Assay is promising for applications in genetic toxicology.

Does the combined free nitrous acid and electrochemical pretreatment increase methane productivity by provoking sludge solubilization and hydrolysis?

Free nitrous acid based pretreatments are novel and effective chemical strategies for enhancing waste activated sludge solubilization. In this study, the synergetic effects of the combined free nitrous acid and electrochemical pretreatment on sludge solubilization and subsequent methane productivity were evaluated. The results indicated that pretreatment with 10 V plus 14.17 mg N/L substantially enhanced sludge solubilization, with the highest soluble chemical oxygen demand concentration of 3296.7 mg/L, 25.6-time higher than that without pretreatment (128.9 mg/L). Due to the potential toxicity of NO₂^- and NO₃^- to microorganisms and its bioprocesses, the methane production of sludge pretreated by free nitrous acid was significantly deteriorated. The maximum methane yield (152.0 ± 9.6 mL/g-VS_added) was observed at 10 V pretreatment alone, only 1.7% higher than that of the control (149.4 ± 1.6 mL/g-VS_added). Combined pretreatment indeed enhances the sludge solubilization and hydrolysis, but does not always induce an improved anaerobic digestion efficiency.

Improving wastewater management using free nitrous acid (FNA)

Free nitrous acid (FNA), the protonated form of nitrite, has historically been an unwanted substance in wastewater systems due to its inhibition on a wide range of microorganisms. However, in recent years, advanced understanding of FNA inhibitory and biocidal effects on microorganisms has led to the development of a series of FNA-based applications that improve wastewater management practices. FNA has been used in sewer systems to control sewer corrosion and odor; in wastewater treatment to achieve carbon and energy efficient nitrogen removal; in sludge management to improve the sludge reduction and energy recovery; in membrane systems to address membrane fouling; and in wastewater algae systems to facilitate algae harvesting. This paper aims to comprehensively and critically review the current status of FNA-based applications in improving wastewater management. The underlying mechanisms of FNA inhibitory and biocidal effects are also reviewed and discussed. Knowledge gaps and current limitations of the FNA-based applications are identified; and perspectives on the development of FNA-based applications are discussed. We conclude that the FNA-based technologies have great potential for enhancing the performance of wastewater systems; however, further development and demonstration at larger scales are still required for their wider applications.

The mutagenesis moonshot: The propitious beginnings of the environmental mutagenesis and genomics society

A mutagenesis moonshot addressing the influence of the environment on our genetic wellbeing was launched just 2 months before astronauts landed on the moon. Its impetus included the discovery that X-rays (Muller HJ. [1927]: Science 64:84-87) and chemicals (Auerbach and Robson. [1946]: Nature 157:302) were germ-cell mutagens, the introduction of a growing number of untested chemicals into the environment after World War II, and an increasing awareness of the role of environmental pollution on human health. Due to mounting concern from influential scientists that germ-cell mutagens might be ubiquitous in the environment, Alexander Hollaender and colleagues founded in 1969 the Environmental Mutagen Society (EMS), now the Environmental Mutagenesis and Genomics Society (EMGS); Frits Sobels founded the European EMS in 1970. As Fred de Serres noted, such societies were necessary because protecting populations from environmental mutagens could not be addressed by existing scientific societies, and new multidisciplinary alliances were required to spearhead this movement. The nascent EMS gathered policy makers and scientists from government, industry, and academia who became advocates for laws requiring genetic toxicity testing of pesticides and drugs and helped implement those laws. They created an electronic database of the mutagenesis literature; established a peer-reviewed journal; promoted basic and applied research in DNA repair and mutagenesis; and established training programs that expanded the science worldwide. Despite these successes, one objective remains unfulfilled: identification of human germ-cell mutagens. After 50 years, the voyage continues, and a vibrant EMGS is needed to bring the mission to its intended target of protecting populations from genetic hazards. Environ. Mol. Mutagen. 61:8-24, 2020. © 2019 Wiley Periodicals, Inc.

Genotoxic activity of L-asparaginase produced by Streptomyces ansochromogenes UFPEDA 3420

L-asparaginase is an enzyme capable of hydrolyzing the substrate asparagine in aspartic acid and ammonia. Due to this mechanism of action observed, L-asparaginase is widely used in the treatment of Acute Lymphoblastic Leukemia, since these cells use asparagine for their survival. Because it is frequently used as an antineoplastic, it is necessary to evaluate its genotoxic effects. The aim of the present study was to evaluate cellular DNA damage after exposure to L-asparaginase produced by Streptomyces ansochromogenes UFPEDA 3420. NCIH-292, MCF-7 and MOLT-4 neoplastic cell lines and normal PBMC cells were used. L-Asparaginase used in this study was produced by actinobacteria S. ansochromogenes UFPEDA 3420, isolated and purified by chromatographic methods. L-Asparaginase induced micronucleus formation in PBMC cells and tumor lines when compared to the negative control. These data suggest that L-Asp appears to have a genotoxic effect very close to the positive control in normal cells (p < 0.05). The level of genomic damage measured by DNA breaks in alkaline SCGE assay was detected from the lowest concentration (12.5 µg/mL) to the highest concentration (50 µg/mL) for tumor cell lines and PBMC. In view of the above, new genotoxic studies will be carried out to better elucidate L-Asparaginase and its mutagenic potential, still unknown, enough for this drug to be safely used in conventional antineoplastic therapies.

Free nitrous acid pretreatment of wasted activated sludge to exploit internal carbon source for enhanced denitrification

Using internal carbon source contained in waste activated sludge (WAS) is beneficial for nitrogen removal from wastewater with low carbon/nitrogen ratio, but it is usually limited by sludge disintegration. This study presented a novel strategy based on free nitrous acid (FNA) pretreatment to intensify the release of organic matters from WAS for enhanced denitrification. During FNA pretreatment, soluble chemical oxygen demand (SCOD) production kept increasing when FNA increased from 0 to 2.04 mg HNO2-N/L. Compared with untreated WAS, the internal carbon source production increased by 50% in a simultaneous fermentation and denitrification reactor fed with WAS pretreated by FNA for 24 h at 2.04 mg HNO2-N/L. This also increased denitrification efficiency by 76% and sludge reduction by 87.5%. More importantly, greenhouse gas nitrous oxide production in denitrification was alleviated since more electrons could be provided by FNA pretreated WAS.

Free nitrous acid breaks down extracellular polymeric substances in waste activated sludge

The chemical breakdown of EPS components by FNA has been proved to account for the improvement of sludge biodegradability in addition to enhanced cell lysis in FNA-based sludge treatment technology.

N2O emissions: modeling the effect of process configuration and diurnal loading patterns

The objective of this research was to develop a mechanistic model for quantifying N2O emissions from activated sludge plants and demonstrate how this may be used to evaluate the effects of process configuration and diurnal loading patterns. The model describes the mechanistic link between the factors recognized to correlate positively with N2O emissions. The primary factors are the presence of ammonia and nitrite accumulation. Low dissolved oxygen concentrations also may be implicated through differential impacts on ammonia-oxidizing bacteria (AOB) versus nitrite-oxidizing bacteria (NOB) activity. Factors promoting N2O emissions at treatment plants are discussed below. The model was applied to data from laboratory and pilot-scale systems. From a practical standpoint, plant configuration (e.g., plug-flow versus complete-mix), influent loading patterns (and peak load), and certain operating strategies (e.g., handling of return streams) are all important in determining N2O emissions.

The strong biocidal effect of free nitrous acid on anaerobic sewer biofilms

Several recent studies showed that nitrite dosage to wastewater results in long-lasting reduction of the sulfate-reducing and methanogenic activities of anaerobic sewer biofilms. In this study, we revealed that the quick reduction in these activities is due to the biocidal effect of free nitrous acid (FNA), the protonated form of nitrite, on biofilm microorganisms. The microbial viability was assessed after sewer biofilms being exposed to wastewater containing nitrite at concentrations of 0-120 mg-N/L under pH levels of 5-7 for 6-24 h. The viable fraction of microorganisms was found to decrease substantially from approximately 80% prior to the treatment to 5-15% after 6-24 h treatment at FNA levels above 0.2 mg-N/L. The level of the biocidal effect has a much stronger correlation with the FNA concentration, which is well described by an exponential function, than with the nitrite concentration or with the pH level, suggesting that FNA is the actual biocidal agent. An increase of the treatment from 6 to 12 and 24 h resulted in only slight decreases in microbial viability. Physical disrupted biofilm was more susceptible to FNA in comparison with intact biofilms, indicating that the biocidal effect of FNA on biofilms was somewhat reduced by mass transfer limitations. The inability to achieve 2-log killing even in the case of disrupted biofilms suggests that some microorganisms may be more resistant to FNA than others. The recovery of biofilm activities in anaerobic reactors after being exposed to FNA at 0.18 and 0.36 mg-N/L, respectively, resembled the regrowth of residual sulfate-reducing bacteria and methanogens, further confirming the biocidal effects of FNA on microorganisms in biofilms.

Reflections on the origins and evolution of genetic toxicology and the Environmental Mutagen Society

This article traces the development of the field of mutagenesis and its metamorphosis into the research area we now call genetic toxicology. In 1969, this transitional event led to the founding of the Environmental Mutagen Society (EMS). The charter of this new Society was to "encourage interest in and study of mutagens in the human environment, particularly as these may be of concern to public health." As the mutagenesis field unfolded and expanded, new wording appeared to better describe this evolving area of research. The term "genetic toxicology" was coined and became an important subspecialty of the broad area of toxicology. Genetic toxicology is now set for a thorough reappraisal of its methods, goals, and priorities to meet the challenges of the 21st Century. To better understand these challenges, we have revisited the primary goal that the EMS founders had in mind for the Society's main mission and objective, namely, the quantitative assessment of genetic (hereditary) risks to human populations exposed to environmental agents. We also have reflected upon some of the seminal events over the last 40 years that have influenced the advancement of the genetic toxicology discipline and the extent to which the Society's major goal and allied objectives have been achieved. Additionally, we have provided suggestions on how EMS can further advance the science of genetic toxicology in the postgenome era. Any oversight or failure to make proper acknowledgment of individuals, events, or the citation of relevant references in this article is unintentional.

New approaches to assessing the effects of mutagenic agents on the integrity of the human genome

Heritable genetic alterations, although individually rare, have a substantial collective health impact. Approximately 20% of these are new mutations of unknown cause. Assessment of the effect of exposures to DNA damaging agents, i.e. mutagenic chemicals and radiations, on the integrity of the human genome and on the occurrence of genetic disease remains a daunting challenge. Recent insights may explain why previous examination of human exposures to ionizing radiation, as in Hiroshima and Nagasaki, failed to reveal heritable genetic effects. New opportunities to assess the heritable genetic damaging effects of environmental mutagens are afforded by: (1) integration of knowledge on the molecular nature of genetic disorders and the molecular effects of mutagens; (2) the development of more practical assays for germline mutagenesis; (3) the likely use of population-based genetic screening in personalized medicine.

Assessing human germ-cell mutagenesis in the Postgenome Era: a celebration of the legacy of William Lawson (Bill) Russell

Birth defects, de novo genetic diseases, and chromosomal abnormality syndromes occur in approximately 5% of all live births, and affected children suffer from a broad range of lifelong health consequences. Despite the social and medical impact of these defects, and the 8 decades of research in animal systems that have identified numerous germ-cell mutagens, no human germ-cell mutagen has been confirmed to date. There is now a growing consensus that the inability to detect human germ-cell mutagens is due to technological limitations in the detection of random mutations rather than biological differences between animal and human susceptibility. A multidisciplinary workshop responding to this challenge convened at The Jackson Laboratory in Bar Harbor, Maine. The purpose of the workshop was to assess the applicability of an emerging repertoire of genomic technologies to studies of human germ-cell mutagenesis. Workshop participants recommended large-scale human germ-cell mutation studies be conducted using samples from donors with high-dose exposures, such as cancer survivors. Within this high-risk cohort, parents and children could be evaluated for heritable changes in (a) DNA sequence and chromosomal structure, (b) repeat sequences and minisatellites, and (c) global gene expression profiles and pathways. Participants also advocated the establishment of a bio-bank of human tissue samples from donors with well-characterized exposure, including medical and reproductive histories. This mutational resource could support large-scale, multiple-endpoint studies. Additional studies could involve the examination of transgenerational effects associated with changes in imprinting and methylation patterns, nucleotide repeats, and mitochondrial DNA mutations. The further development of animal models and the integration of these with human studies are necessary to provide molecular insights into the mechanisms of germ-cell mutations and to identify prevention strategies. Furthermore, scientific specialty groups should be convened to review and prioritize the evidence for germ-cell mutagenicity from common environmental, occupational, medical, and lifestyle exposures. Workshop attendees agreed on the need for a full-scale assault to address key fundamental questions in human germ-cell environmental mutagenesis. These include, but are not limited to, the following: Do human germ-cell mutagens exist? What are the risks to future generations? Are some parents at higher risk than others for acquiring and transmitting germ-cell mutations? Obtaining answers to these, and other critical questions, will require strong support from relevant funding agencies, in addition to the engagement of scientists outside the fields of genomics and germ-cell mutagenesis.