Chapter 1
Mouse

Introduction

Apart from the many inbred strains, substrains, spontaneous mutants, and outbred stocks of laboratory mice, the mouse has been, and continues to be, central to molecular genomics, with worldwide efforts continuing to "knock out" every functional gene in the mouse genome and define the relationship between genotype and phenotype. Various mouse strains and stocks, as well as the genetically engineered mouse (GEM), play critical roles in hypothesis-driven biomedical research. Globally immunodeficient GEMs are currently popular for xenografting human stem cells and tumors. These trends have created rich opportunities and critical demand for comparative pathologists who are knowledgeable in mouse pathobiology. Unfortunately, the scientific literature is replete with erroneous interpretation of phenotype by scientists (as well as pathologists) lacking expertise in mouse pathology. Effective mouse pathology requires a global understanding of mouse biology.

It is impossible for the pathologist to command in-depth knowledge of all strains, stocks, and mutant types of mice, and often there are scant baseline data to draw upon. Nevertheless, the mouse pathologist must be cognizant of general patterns of mouse pathology, as well as strain- and GEM-specific nuances. The reader is referred to Sundberg et al. (2022) for a more comprehensive overview of GEM and mutant mouse pathology. The incidence and prevalence of strain-specific pathology are highly dependent upon genetic and environmental influences, including diet, bedding, microbial status, immunologic function, infectious disease, age, sex, and other factors. Our coverage of the esoterica of spontaneous mouse pathology is relatively superficial. We herein emphasize general patterns of disease, while attempting to address important strain-, mutant-, and GEM-specific diseases when appropriate. There are a growing number of internet-accessible resources for mouse phenotyping and pathology of strains, stocks, and GEMs. A listing of on-line web resources is available through several cited references, and reviewed in Sundberg et al. (2022).

The unique qualities of the laboratory mouse and the precision of mouse-related research make infectious agents, even those with minimal (or no) pathogenicity, major concerns due to their potential and sometimes significant impact upon research reproducibility, including phenotype. A challenge that is unique to the mouse is the difficulty in drawing the line between commensal, opportunistic, or overtly pathogenic microorganisms. Since the last edition, a variety of immune-deficient GEMs have been created, thereby raising the status of several relatively innocuous microorganisms to the level of pathogens. Immune-deficient mice and new molecular methods of microbial detection continue to reveal previously unrecognized mouse "pathogens," such as astrovirus, norovirus, parvovirus, Chlamydia, Clostridia, and Helicobacter. Furthermore, the unrestricted traffic of GEMs among institutions and the pressure to reduce costs of maintenance at the expense of quality control have resulted in the re-emergence of several infectious agents that have not been seen in several decades. We, therefore, unabashedly emphasize mouse infectious diseases in this chapter. Despite advances in husbandry and diagnostic surveillance, we are reluctant to discard entities that may seem to have disappeared from laboratory mouse populations because of their likelihood of return.

Mouse Genetics

The laboratory mouse is an artificial creation, and there is no true "wild-type" laboratory mouse. Furthermore, there is no such thing as "normal" microflora, since laboratory mice are often maintained in microbially pristine environments devoid of pathogens and opportunistic pathogens, as well as other commensal flora/fauna. This is especially true for globally immunodeficient mice, whose high microbial exclusion standards make them susceptible to dysbiosis. Laboratory mice are largely derived from domesticated "fancy mice" that arose from many years of trading mouse variants among fanciers in Europe, Asia, North America, and Australia. The laboratory mouse genome is, therefore, a mosaic derived from different subspecies of the Mus musculus (house mouse) complex, including M.m. domesticus, M.m. musculus, M.m. castaneus, M.m. molossinus (a natural hybrid of M.m. musculus and M.m. castaneus), and others. The genome of M.m. domesticus is the predominant contributor to most strains of mice. Many inbred strains share a common "Eve" with a mitochondrial genome of M.m. musculus origin and a common "Adam" that contributed the Y chromosome from M.m. castaneus. In addition, there is evidence that other Mus species, outside of the M. musculus complex, have contributed to the genome of some, but not all, laboratory mouse strains. For example, the C57BL mouse genome contains LINE 1 contributions from M. spretus, which make up to 6.5% of the C57BL genome. Some Mus species that are outside of the M. musculus complex, such as M. spretus, have been inbred. Thus, the laboratory mouse genome is not uniform among strains and some mouse strains are predominantly, but not entirely all within the M. musculus clade.

There are over 450 inbred strains of laboratory mice that have arisen during the last century, and these strains, which were selectively inbred to pan-genomic homozygosity for purposes entirely unrelated to modern research, are the foundation upon which literally thousands of spontaneous mutants and GEMs have been built. Additional inbred strains have been developed from wild mice (M.m. domesticus, M.m. castaneus, M. spretus, etc.). Furthermore, "outbred" mice (mostly so-called "Swiss" mice) are highly homozygous and nearly inbred. In addition to historical inbreeding that may be intentional or the inadvertent result of maintaining small populations of mice, rederivation of a mouse population results in genetic bottlenecks as well. There is no such thing as a truly "outbred" laboratory mouse with a fully heterozygous genome representative of wild-type M. musculus, and there is no wild mouse genetic counterpart of the laboratory mouse. An octaparental Diversity Outbred (DO) mouse stock has been developed from eight disparately related inbred strains of mice, but this stock is not extensively utilized. When working with mice, the pathologist must become facile with strains, substrains, sub-substrains, hybrids, congenics, insipient congenics, coisogenics, consomics, conplastics, recombinant inbreds, recombinant congenics, spontaneous mutants, random induced (radiation, chemical, retroviral, gene trap) mutants, transgenics (random insertions), and targeted mutant mice, each with relatively unique, predictable, and sometimes unpredictable phenotypes and patterns of disease whose expression is modified by environmental, immunological, and microbial variables.

The inherent value of the laboratory mouse is its inbred genome, but maintaining the genetic stability of inbred strains of mice is a challenge. Since the advent of GEMs, there has been widespread genetic mismanagement of mouse strains by investigators with considerable skill in mouse genomics but limited expertise in mouse genetics. Even with the best of intentions, continuous inbreeding leads to substrain divergence among different populations of the same parental origin due to spontaneous mutations, retrotransposon integrations, or residual heterozygosity. Genetic contamination is also a surprisingly frequent event in both commercial and academic breeding colonies of mice. Within a few generations, substrain divergence can result in significant differences in phenotype, including response to research variables. The variable genetic contributions of different origins of mice and selective inbreeding for strain characteristics, such as coat color or neoplasia, are especially important when considering retroelements, which make up 37% of the mouse genome. Retroelements are highly dynamic within the context of the inbred mouse genome. They are present in the genomes of all mammals but have become artificially important in the homozygous genome of the laboratory mouse, and in fact had much to do with development of original inbred strains of mice with unique phenotypes, especially coat color and neoplasia. It is difficult to ignore their impact on mouse pathology, and thus retroelements are discussed later in this chapter (see "Retroelements and Retroviral Infections").

Mouse Nomenclature

The details of mouse nomenclature are beyond the scope of this book, but it is critically important that the full and correct strain, substrain, and mutant allelic or transgene nomenclature be utilized when publishing, evaluating pathology, and judging the credibility of publications. Above all, pathologists involved in biomedical research should be fully cognizant of, and insist upon, using appropriate mouse nomenclature. Being able to "read" the nomenclature of a mouse that is submitted for evaluation is critical for interpreting pathology. Guidelines for mouse nomenclature are available at the International Mouse Nomenclature home page (http://www.informatics.jax.org/mgihome/nomen/strains.shtml). Pathology of Genetically Engineered and Other Mutant Mice (Sundberg et al. 2022), The Mouse in Biomedical Research: History, Genetics, and Wild Mice (Fox et al. 2007), the mouse chapter in Laboratory Animal Medicine (Fox et al. 2015, with new edition in press), and Mouse...