Moving forward with chemical mutagenesis in the mouse

Biologia futura: animal testing in drug development-the past, the present and the future

Animal experiments have served to improve our knowledge on diseases and treatment approaches since ancient times. Today, animal experiments are widely used in medical, biomedical and veterinary research, and are essential means of drug development and preclinical testing, including toxicology and safety studies. Recently, great efforts have been made to replace animal experiments with in vitro organoid culture methods and in silico predictions, in agreement with the 3R strategy to "reduce, refine and replace" animals in experimental testing, as outlined by the European Commission. Here we present a mini-review on the development of animal testing, as well as on alternative in vitro and in silico methods, that may at least partly replace animal experiments in the near future.

Genomic Mutation Identification in Mice Using Illumina Sequencing and Linux-Based Computational Methods

Genetically modified mice are an essential tool for modeling disease-causing mechanisms and discovering gene function. SNP genotyping was traditionally used to associate candidate regions with traits in the mouse, but failed to reveal novel variants without further targeted sequencing. Using a robust set of computational protocols, we present a platform to enable scientists to detect variants arising from whole-genome and exome sequencing experiments. This article guides researchers on aligning reads to the mouse genome, quality-assurance strategies, mutation discovery, comparing mutations to previously discovered mouse SNPs, and the annotation of novel variants, in order to predict mutation consequences on the protein level. Challenges unique to the mouse are discussed, and two protocols use self-contained containers to maintain version control and allow users to adapt our approach to new techniques by upgrading container versions. Our protocols are suited for servers or office workstations and are usable by non-bioinformatics specialists. © 2019 by John Wiley & Sons, Inc.

Programmable Genome Editing Tools and their Regulation for Efficient Genome Engineering

Targeted genome editing has become a powerful genetic tool for studying gene function or for modifying genomes by correcting defective genes or introducing genes. A variety of reagents have been developed in recent years that can generate targeted double-stranded DNA cuts which can be repaired by the error-prone, non-homologous end joining repair system or via the homologous recombination-based double-strand break repair pathway provided a suitable template is available. These genome editing reagents require components for recognizing a specific DNA target site and for DNA-cleavage that generates the double-stranded break. In order to reduce potential toxic effects of genome editing reagents, it might be desirable to control the in vitro or in vivo activity of these reagents by incorporating regulatory switches that can reduce off-target activities and/or allow for these reagents to be turned on or off. This review will outline the various genome editing tools that are currently available and describe the strategies that have so far been employed for regulating these editing reagents. In addition, this review will examine potential regulatory switches/strategies that can be employed in the future in order to provide temporal control for these reagents.

Biology and Diseases of Mice

Today’s laboratory mouse, Mus musculus, has its origins as the ‘house mouse’ of North America and Europe. Beginning with mice bred by mouse fanciers, laboratory stocks (outbred) derived from M. musculus musculus from eastern Europe and M. m. domesticus from western Europe were developed into inbred strains. Since the mid-1980s, additional strains have been developed from Asian mice (M. m. castaneus from Thailand and M. m. molossinus from Japan) and from M. spretus which originated from the western Mediterranean region.

Zinc Finger Nucleases: A new era for transgenic animals

The rational engineering of eukaryotic genomes would facilitate the study of heritable changes in gene expression and offer enormous potential across basic research, drug-discovery, bioproduction and therapeutic development. A significant advancement toward this objective was achieved with the advent of a novel technology that enables high-frequency and high-fidelity genome editing via the application of custom designed zinc finger nucleases (ZFNs). A ZFN is a chimeric protein that consists of the non-specific endonuclease domain of FokI fused to a DNA-binding domain composed of an engineered zinc-finger motif. Within these chimeric proteins, the DNA binding specificity of the zinc finger protein determines the site of nuclease action. Once the engineered ZFNs recognize and bind to their specified locus, it leads to the dimerization of the two nuclease domains on the ZFNs to evoke a double-strand break (DSB) in the targeted DNA. The cell then employs the natural DNA repair processes of either non-homologous end joining (NHEJ) or homology-directed repair (HDR) to repair the targeted break. Due to the imperfect fidelity of NHEJ, a proportion of DSBs within a ZFN-treated cellular population will be misrepaired, leading to cells in which variable heterogeneous genetic insertions or deletions have been made at the target site. Alternatively, the HDR repair pathway enables precise insertion of a transgene or other defined alterations into the targeted region. By this approach, a donor template containing the transgene flanked by sequences that are homologous to the regions either side of the cleavage site is co-delivered into the cell along with the ZFNs. By creating a specific DSB, these cellular repair mechanisms are harnessed to generate precisely targeted genomic edits resulting in both cell lines and animal models with targeted gene deletions, integrations, or modifications. This review will discuss the development, mechanism of action, and applications of ZFN technology to genome engineering and the creation of animal models.

ENU mutation mapped to a distal region of chromosome 11 is a major determinant of bone size

Using a phenotype driven n-ethyl-nitrosourea (ENU) screen in growth hormone-deficient mice, we have identified a mutant (named 14104) that exhibited a smaller bone size. Phenotype measurements by microcomputed tomography revealed that mutant mice exhibited a 43 and 34% reduction in tissue area and bone area, respectively at the femur middiaphysis. Dynamic histomorphometry revealed a 30 and 15% lower bone formation rate at the periosteal and endosteal surface, respectively. Breaking strength of the femur was reduced by 30% in the mutant mice. To determine if the 14104 locus is involved in a mechanical loading signaling pathway, the skeletal anabolic response to tibia axial loading was evaluated. The increase in trabecular response in the loaded region was severely compromised by the 14014 mutation. To identify the location of mutation, we performed linkage analysis using 62 polymorphic markers in the B6-DBA/2J F2 mice. The genome-wide linkage analysis identified the location of the mutation to a 72 to 83 cM region on chromosome 11 with peak logarithm of the odds scores of 15 for periosteal circumference at marker D11mit338. Sequence analysis revealed no mutation in the coding region of 11 potential candidate genes. Based on these data and published data on the skeletal phenotype of genes in this region, we concluded that the 109-119 Mb region of chromosome 11 harbors a bone size gene that regulates periosteal bone formation. The mutant strain developed in this study provides an important tool to identify a novel mechanosensitive gene that determines bone size during postnatal development.

High throughput sequencing approaches to mutation discovery in the mouse

Phenotype-driven approaches in mice are powerful strategies for the discovery of genes and gene functions and for unravelling complex biological mechanisms. Traditional methods for mutation discovery are reliable and robust, but they can also be laborious and time consuming. Recently, high-throughput sequencing (HTS) technologies have revolutionised the process of forward genetics in mice by paving the way to rapid mutation discovery. However, successful application of HTS for mutation discovery relies heavily on the sequencing approach employed and strategies for data analysis. Here we review current HTS applications and resources for mutation discovery and provide an overview of the practical considerations for HTS implementation and data analysis.

Creating a "hopeful monster": mouse forward genetic screens

One of the most straightforward approaches to making novel biological discoveries is the forward genetic screen. The time is ripe for forward genetic screens in the mouse since the mouse genome is sequenced, but the function of many of the genes remains unknown. Today, with careful planning, such screens are within the reach of even small individual labs. In this chapter we first discuss the types of screens in existence, as well as how to design a screen to recover mutations that are relevant to the interests of a lab. We then describe how to create mutations using the chemical N-ethyl-N-nitrosourea (ENU), including a detailed injection protocol. Next, we outline breeding schemes to establish mutant lines for each type of screen. Finally, we explain how to map mutations using recombination and how to ensure that a particular mutation causes a phenotype. Our goal is to make forward genetics in the mouse accessible to any lab with the desire to do it.

An essential gene mutagenesis screen across the highly conserved piebald deletion region of mouse chromosome 14

The piebald deletion complex is a set of overlapping chromosomal deficiencies on distal mouse chromosome 14. We surveyed the functional genetic content of the piebald deletion region in an essential gene mutagenesis screen of 952 genomes to recover seven lethal mutants. The ENU-induced mutations were mapped to define genetic intervals using the piebald deletion panel. Lethal mutations included loci required for establishment of the left-right embryonic axis and a loss-of-function allele of Phr1 resulting in respiratory distress at birth. A functional map of the piebald region integrates experimental genetic data from the deletion panel, mutagenesis screen, and the targeted disruption of specific genes. A comparison of several genomic intervals targeted in regional mutagenesis screens suggests that the piebald region is characterized by a low gene density and high essential gene density with a distinct genomic content and organization that supports complex regulatory interactions and promotes evolutionary stability.

Mouse genetic models: an ideal system for understanding glaucomatous neurodegeneration and neuroprotection

Here we review how mouse studies are contributing to understanding glaucoma. We include discussion of aqueous humor drainage and intraocular pressure elevation, because new treatments to avoid exposure to high pressure will indirectly protect neurons from glaucoma, and complement direct neuroprotective strategies. We describe how mouse models are adding to both the understanding of glaucomatous neurodegeneration and the development of neuroprotective strategies.

Uses of forward and reverse genetics in mice to study gene function

As the focus of human genetics shifts from Mendelian traits to complex diseases, a sophisticated genetic tool kit-with space for genetics (classical, molecular, statistical, and quantitative), metabolics, proteomics, bioinformatics, and mathematics-is required to elucidate their multifactorial traits and regulatory processes. Importantly, mouse resources optimized to study the actions of isolated genetic loci on a fixed background are insufficient on their own for studying intact polygenic networks and genetic interactions, and researchers must work in the context of experimental model systems that optimally mimic the genetic structure of human populations. The success of such phenogenomic approaches depend on the efficacy by which specific mutations (gene targeting) and variability (recombinant inbreeding) can be introduced into the mouse genome, and on the optimization of phenotyping analyses of the mutant mouse lines. This unit describes the basic genetic approaches used to in the study of mouse model systems.

A chemical mutagenesis screen to identify modifier genes that interact with growth hormone and TGF-beta signaling pathways

We describe a phenotype-driven mutagenesis screen in which mice carrying a targeted mutation are bred with ENU-treated males in order to provide a sensitized system for detecting dominant modifier mutations. The presence of initial mutation renders the screening system more responsive to subtle changes in modifier genes that would not be penetrant in an otherwise wild type background. We utilized two mutant mouse models: 1) mice carrying a mutation in growth hormone releasing hormone receptor (Ghrhr) (denoted 'lit' allele, Ghrhr(lit)), which results in GH deficiency; and 2) mice lacking Smad2 gene, a signal transducer for TGF-beta, an important bone growth factor. The Smad2(-/-) mice are lethal and Ghrhr(lit/lit) mice are dwarf, but both Smad2(+/-) and Ghrhr(lit/)(+) mice exhibit normal growth. We injected 6-7 weeks old C57BL/6J male mice with ENU (100 mg/kg dose) and bred them with Ghrhr(lit/)(+) and Smad2(+/-) mice. The F1 mice with Ghrhr(lit/)(+) or Smad2(+/-) genotype were screened for growth and skeletal phenotypes. An outlier was identified as >3 SD units different from wild type control (n=20-30). We screened about 100 F1 mice with Ghrhr(lit/)(+) and Smad2(+/-) genotypes and identified nine outliers. A backcross established heritability of three mutant lines in multiple generations. Among the phenotypic deviants, we have identified a mutant mouse with 30-40% reduced bone size. The magnitude of the bone size phenotype was amplified by the presence of one copy of the disrupted Ghrhr gene as determined by the 2-way ANOVA (p<0.02 for interaction). Thus, a new mouse model has been established to identify a gene that interacts with GH signaling to regulate bone size. In addition, the sensitized screen also demonstrated higher recovery of skeletal phenotypes as compared to that obtained in the classical ENU screen in wild type mice. The discovery of mutants in a selected pathway will provide a valuable tool to not only to discover novel genes involved in a particular process but will also prove useful for the elucidation of the biology of that process.

Neurobehavioral mutants identified in an ENU-mutagenesis project

We report on a battery of behavioral screening tests that successfully identified several neurobehavioral mutants among a large-scale ENU-mutagenized mouse population. Large numbers of ENU-mutagenized mice were screened for abnormalities in central nervous system function based on abnormal performance in a series of behavior tasks. We developed and used a high-throughput screen of behavioral tasks to detect behavioral outliers. Twelve mutant pedigrees, representing a broad range of behavioral phenotypes, have been identified. Specifically, we have identified two open-field mutants (one displaying hyperlocomotion, the other hypolocomotion), four tail-suspension mutants (all displaying increased immobility), one nociception mutant (displaying abnormal responsiveness to thermal pain), two prepulse inhibition mutants (displaying poor inhibition of the startle response), one anxiety-related mutant (displaying decreased anxiety in the light/dark test), and one learning-and-memory mutant (displaying reduced response to the conditioned stimulus). These findings highlight the utility of a set of behavioral tasks used in a high-throughput screen to identify neurobehavioral mutants. Further analysis (i.e., behavioral and genetic mapping studies) of mutants is in progress with the ultimate goal of identification of novel genes and mouse models relevant to human disorders as well as the identification of novel therapeutic targets.

Understanding mammalian genetic systems: the challenge of phenotyping in the mouse

Understanding mammalian genetic systems is predicated on the determination of the relationship between genetic variation and phenotype. Several international programmes are under way to deliver mutations in every gene in the mouse genome. The challenge for mouse geneticists is to develop approaches that will provide comprehensive phenotype datasets for these mouse mutant libraries. Several factors are critical to success in this endeavour. It will be important to catalogue assay and environment and where possible to adopt standardised procedures for phenotyping tests along with common environmental conditions to ensure comparable datasets of phenotypes. Moreover, the scale of the task underlines the need to invest in technological development improving both the speed and cost of phenotyping platforms. In addition, it will be necessary to develop new informatics standards that capture the phenotype assay as well as other factors, genetic and environmental, that impinge upon phenotype outcome.

Potential and limitations of genetic manipulation in animals

Over the last decade, sequencing and characterisation of the mouse genome has been accompanied by unparalleled advances in functional genomics. In the context of drug action, we analyse the strengths and limitations of classical mutagenesis and gene targeting techniques, as well as alternative approaches such as chemical mutagenesis, gene trap, recombineering, transposon-mediated mutagenesis, chromosomal engineering, viral transgenesis and RNA interference. This review also focuses on the emerging importance of genetic manipulation in other species and related logistical issues of experimental work using mutants.:

Mouse phenogenomics: the fast track to "systems metabolism"

With the completion of the many genomes, genetics is positioned to meet physiology. In this review, we summarize the coming of "systems metabolism" in mammals through the use of the mouse, as a model system to study metabolism. Building on mouse genetics with increasingly sophisticated clinical and molecular phenotyping strategies has enabled scientists to now tackle complex biomedical questions, such as those related to the pathogenesis of the common metabolic disorders. The ultimate goal of such strategies will be to mimic human metabolism with the click of a mouse.

Magnetic resonance imaging for detection and analysis of mouse phenotypes

With the enormous and growing number of experimental and genetic mouse models of human disease, there is a need for efficient means of characterizing abnormalities in mouse anatomy and physiology. Adaptation of magnetic resonance imaging (MRI) to the scale of the mouse promises to address this challenge and make major contributions to biomedical research by non-invasive assessment in the mouse. MRI is already emerging as an enabling technology providing informative and meaningful measures in a range of mouse models. In this review, recent progress in both in vivo and post mortem imaging is reported. Challenges unique to mouse MRI are also identified. In particular, the needs for high-throughput imaging and comparative anatomical analyses in large biological studies are described and current efforts at handling these issues are presented.

Molecular characterization of ENU mouse mutagenesis and archives

The large-scale mouse mutagenesis with ENU has provided forward-genetic resources for functional genomics. The frozen sperm archive of ENU-mutagenized generation-1 (G1) mice could also provide a "mutant mouse library" that allows us to conduct reverse genetics in any particular target genes. We have archived frozen sperm as well as genomic DNA from 9224 G1 mice. By genome-wide screening of 63 target loci covering a sum of 197 Mbp of the mouse genome, a total of 148 ENU-induced mutations have been directly identified. The sites of mutations were primarily identified by temperature gradient capillary electrophoresis method followed by direct sequencing. The molecular characterization revealed that all the identified mutations were point mutations and mostly independent events except a few cases of redundant mutations. The base-substitution spectra in this study were different from those of the phenotype-based mutagenesis. The ENU-based gene-driven mutagenesis in the mouse now becomes feasible and practical.

Using microarrays to facilitate positional cloning: identification of tomosyn as an inhibitor of neurosecretion

Forward genetic screens have been used as a powerful strategy to dissect complex biological pathways in many model systems. A significant limitation of this approach has been the time-consuming and costly process of positional cloning and molecular characterization of the mutations isolated in these screens. Here, the authors describe a strategy using microarray hybridizations to facilitate positional cloning. This method relies on the fact that premature stop codons (i.e., nonsense mutations) constitute a frequent class of mutations isolated in screens and that nonsense mutant messenger RNAs are efficiently degraded by the conserved nonsense-mediated decay pathway. They validate this strategy by identifying two previously uncharacterized mutations: (1) tom-1, a mutation found in a forward genetic screen for enhanced acetylcholine secretion in Caenorhabditis elegans, and (2) an apparently spontaneous mutation in the hif-1 transcription factor gene. They further demonstrate the broad applicability of this strategy using other known mutants in C. elegans,Arabidopsis, and mouse. Characterization of tom-1 mutants suggests that TOM-1, the C. elegans ortholog of mammalian tomosyn, functions as an endogenous inhibitor of neurotransmitter secretion. These results also suggest that microarray hybridizations have the potential to significantly reduce the time and effort required for positional cloning.

Genetic screens are commonly used to figure out which genes are involved in a biological process. The first step in a genetic screen is to isolate mutant animals that are defective in the process being studied. The next step is to find which of the thousands of genes has the mutation that causes the observed defect. Positional cloning, the tried-and-true method for locating mutations, is slow and expensive. The authors propose using microarray hybridizations to speed the process. Their approach relies on the fact that a large fraction of the mutations found in screens are the results of premature stop codons, a particularly severe type of mutation. In cells, messages containing premature stop codons are rapidly destroyed by a protective pathway, called nonsense-mediated decay, thus making them directly detectable by microarray hybridization.

The authors apply this strategy retrospectively to known mutants in Caenorhabditis elegans, Arabidopsis, and mouse. They identify two uncharacterized mutations in C. elegans, including one, tom-1, found in a forward genetic screen for enhancers of neurotransmission. Interestingly, their characterization of tom-1 mutants suggests that the highly conserved protein tomosyn inhibits neurotransmission in neurons. This study shows that microarray hybridizations will help reduce the time and effort required for positional cloning.

Identification of a rat model for usher syndrome type 1B by N-ethyl-N-nitrosourea mutagenesis-driven forward genetics

The rat is the most extensively studied model organism and is broadly used in biomedical research. Current rat disease models are selected from existing strains and their number is thereby limited by the degree of naturally occurring variation or spontaneous mutations. We have used ENU mutagenesis to increase genetic variation in laboratory rats and identified a recessive mutant, named tornado, showing aberrant circling behavior, hyperactivity, and stereotypic head shaking. More detailed analysis revealed profound deafness due to disorganization and degeneration of the organ of Corti that already manifests at the onset of hearing. We set up a single nucleotide polymorphism (SNP)-based mapping strategy to identify the affected gene, revealing strong linkage to the central region of chromosome 1. Candidate gene resequencing identified a point mutation that introduces a premature stopcodon in Myo7a. Mutations in human MYO7A result in Usher syndrome type 1B, a severe autosomal inherited recessive disease that involves deafness and vestibular dysfunction. Here, we present the first characterized rat model for this disease. In addition, we demonstrate proof of principle for the generation and cloning of human disease models in rat using ENU mutagenesis, providing good perspectives for systematic phenotypic screens in the rat.

A method for the rapid automated assessment of olfactory function

We have developed a strategy for the rapid high-throughput screening of odor responsivity in genetically altered mice (in fact, any experimentally altered animal). Specifically, the report presents the development and validation of a fully automated procedure based on the evaluation of an animal's stimulus-induced reflexive breathing response (i.e. sniffing behavior) to both air and odorant stimuli. The method requires no training of the animal to be screened and the outcome of the evaluation yields an operationally defined measure. Briefly, using whole-body plethysmography, the procedure determines the numerical values for a set of 14 respiratory measures in response to the presentation of air and a well-above-threshold concentration of the odorant propanol. These measures of stimulus-induced sniffing are incorporated into a model that defines a single univariate measure of response behavior, or 'Sniffing Index', for each screened animal. The approach significantly discriminated between the reflexive sniffing response of a control group of mice and that of an experimentally defined manipulated group for which, a priori, we expected to observe a robust altered breathing response to odorant stimulation (i.e. non-odor-aversion-conditioned versus odor-aversion-conditioned C57BL/6J mice). Further, the procedure was able to significantly discriminate between a mutant phenotype with documented alterations in physiologic and behavioral function (namely, the OMP-null mutant), and their background strain. In addition, applying epidemiologic screening principles to the observed data, we established an operational procedure for the evaluation of unknown animals.