Ординатура / Офтальмология / Английские материалы / Eye, Retina, and Visual System of the Mouse_Chalupa, Williams_2008
.pdfSparrow, J. R., Nakanishi, K., and Parish, C. A. (2000). The lipofuscin fluorophore A2E mediates blue light-induced damage to retinal pigmented epithelial cells. Invest. Ophthalmol. Vis. Sci. 41:1981–1989.
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53 Beyond Positional Cloning
of Single Gene Mutations:
Use of Mouse Models to Examine Allelic Variance and to Identify Genetic Modifiers
PATSY M. NISHINA AND JUERGEN K. NAGGERT
Mouse models have proven to be extremely useful in the study of heritable ocular diseases. They have provided candidate genes for similar human diseases and whole animal systems to test potential therapeutic interventions. Environmental factors influencing vision, such as light and diet, can be easily studied in mice. In addition, as a robust renewable resource, they have allowed the systematic exploration of disease etiology, progression, and pathologies, which in turn has led to the generation of hypotheses about the functions of particular molecules and mechanisms underlying disease. Finally, mouse models can be an important tool for examining allelic effects (e.g., variability in phenotypes attributable to different mutations within a single gene) and for identifying genetic background modifiers (e.g., variability in phenotypes attributable to nonallellic interactions). Both are discussed in this chapter.
Four key factors make mouse models particularly effective for dissecting allelic effects and identifying modifier loci. First, mice are inbred, that is, all animals from a given strain are genetically identical. Therefore, phenotypic variability observed when comparing different mutations within the same molecule in the same inbred strain background would suggest allelic effects, barring differences in animal husbandry, whereas phenotypic variability observed in two different, genetically defined strains carrying the same mutant allele would suggest the presence of genetic modifier loci. Second, methods have been developed to induce mutations through chemical mutagenesis or by germ-line manipulation through genetic engineering. These approaches, particularly the latter, allow researchers to affect spatial or temporal expression to examine the function or roles of particular domains within genes. Third, the reagents and resources in the form of genomic information are tremendous, and new
data in the form of sequences and single nucleotide polymorphisms over multiple strains are forthcoming with ever increasing frequency (Pletcher et al., 2004; Rudd et al., 2005; Shifman et al., 2006; see also www.jax.org/phenome/ snp.html). These advances in particular will assist in the actual identification of the modifying genes and the pathways through which these genes function. Finally, a large number of noninvasive clinical tools have been adapted to the small eyes of the mouse, allowing for monitoring of phenotypic variability. These tools include slit lamp biomicroscopy, indirect ophthalmoscopy, fluorescein angiography, fundus photography, and electroretinography (ERG). In addition, methods to assess visually evoked potentials (VEPs; Ridder and Nusinowitz, 2006) and behavioral parameters such as visual acuity and contrast sensitivity (Douglas et al., 2005) are available. Finally, new noninvasive methods to access the morphological features of the retina by optical coherence tomography in a living animal are currently being developed by a number of groups. These methods will also extend our ability to carry out repeated measures to study disease progression and treatment modalities in a single mouse over time.
Allelic effects as a cause of phenotypic variation
Particular alleles may define clinical outcome or disease progression. They may also reveal the functional importance of a particular domain of a gene or protein and the response to environmental stresses or treatment modalities. The availability of mouse models bearing different alleles of the same gene is likely to increase as more animals are generated through chemical mutagenesis and targeted transgenesis to introduce clinically relevant disease alleles from human
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patients into the mouse genome. These models will be instrumental in elucidating the function of molecules and will provide an in vivo system in which to identify subpopulations of patients who harbor different mutations in the same molecule, and to test genotype-specific therapeutic modalities.
Defining Disease Progression, Clinical Outcome, or
Important Domains In general, loss-of-function alleles produce a different phenotype than do missense mutations effecting hypomorphic or gain-of-function alleles. It can be argued that insofar as most mutations identified in humans are generally not null mutations, to elucidate the role that molecules may play in vision an array of alleles for each protein should be studied.
The best example of an allelic series affecting disease progression was generated by chemical mutagenesis in the gene encoding phosphodiesterase 6b (Hart et al., 2005). Four of the seven mutations identified by the MRC Harwell ENU Mutagenesis program were phenotypically identical to the original Pdeb6brd1 mutation, which is found in many standard inbred strains (e.g., C3H/HeJ, SJL/J, FVB/N) and leads to a rapid panretinal rod photoreceptor degeneration by 3 weeks of age (Bowes et al., 1990). Three of the four predicted loss-of-function alleles were nonsense mutations leading to the introduction of premature stop codons, the fourth was a splice site mutation that would severely disrupt normal splicing. Two of the three remaining alleles that led to a slower progressing phenotype were missense mutations and the third was a splice site mutation that still allowed a small percentage of normal transcript to be formed. Interestingly, mice with the Pdeb6batrd3 allele, which carries an amino acid change from asparagine to serine in the highly conserved residue 606, near a putative catalytic domain, showed earlier impaired vision and a greater loss of rod photoreceptors than did Pdeb6batrd1 mice, which carry a histidine-620- glutamine mutation that occurs in a relatively conserved residue within a putative catalytic domain. Further study of these alleles may provide additional insight into the functional significance of the domains in which these missense mutations occur.
Although mutations in Pde6b can lead to photoreceptor degeneration, they can also lead to congenital stationary night blindness (CSNB) in humans without apparent morphological changes. Recently, Tsang et al. (2007) introduced a CSNB allele, Pde6bH258N, by transgenic means into the Pdeb6brd1 background and rescued the photoreceptors. ERG abnormalities were observed; however, the actual amplitude of the waveforms appeared to depend on the genetic background.
Another recent example of alternative alleles providing insight into the potential function of a gene similarly arose from a chemical mutagenesis screen (http://nmf.jax.org/
index.html). Through positional candidate cloning, nmf247 was identified as a point mutation in the splice acceptor site in intron 6 of Rpgrip1 that leads to a deletion of exon 7 and a premature stop codon in exon 9 (Won et al., 2007). Interestingly, the Rpgrip1nmf247 allele appeared to be more severe than the previously reported null allele (Zhao et al., 2003) in that outer segments were rarely observed and the rate of photoreceptor degeneration was extremely rapid, with most cell bodies gone by 3 weeks of age. In the rare case in which outer segments developed, they were enlarged and vertically oriented, as described in the null allele (Zhao et al., 2003). The recent report of a shorter murine splice variant of Rpgrip1 (Lu and Ferreira, 2005) and closer inspection of the null allele, which was an insertional mutation into exon 14, indicated that the original null allele potentially affected only the full-length form of Rpgrip1, whereas both splice variants would have been missing in Rpgrip1nmf247 mice. This observation suggests that the short form of RPGRIP1 or an otherwise unidentified splice variant may be important in the initiation of normal outer segment development, a hypothesis that is testable with the availability of the nmf247 mouse model.
Defining Responses to Environmental Influences It is perhaps not surprising that different alleles of the same gene produce different responses to environmental influences. Understanding these different responses to nongenetic factors such as light exposure may yield insights into clinical prognosis as well as the function of the molecules studied in relation to the environmental influence tested.
Four alleles of Rpe65, a molecule that is abundantly expressed in the retinal pigmented epithelium (RPE), have been described in mice (Hamel et al., 1993; Redmond et al., 1998; Pang et al., 2005). A targeted null mutation of the Rpe65 gene demonstrated that in the absence of functional RPE65 protein, outer segments become disorganized and a slow photoreceptor degeneration ensues (Redmond et al., 1998). The findings that Rpe65−/− mice do not have 11-cis- retinyl esters in their RPE and accumulate all-trans-retinyl esters suggested a disruption of the isomerization of all-trans- retinyl esters to 11-cis-retinal (Redmond et al., 1998). Moiseyev et al. (2005) hypothesized and provided evidence that RPE65 acts as an isomerohydrolase in the retinoid visual cycle. Perhaps it is not surprising, then, that alterations in RPE65 might affect retinal responses to light exposure. Danciger et al. (2000) noted that of nine albino mouse strains, the C57BL/6J-c2J (c2J) strain demonstrated marked resistance to light-induced photoreceptor damage. A genome-wide scan for the resistance/susceptibility alleles in progeny of a (c2J × BALB/c)F(1) × c2J backcross revealed a major locus (accounting for 50% of the protective effect) on chromosome 3 and three other weak but significant contributing regions on chromosomes 9, 12, and 14. The pro-
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tective effect observed in the c2J background was determined to result from a single nucleotide polymorphism (SNP) in the Rpe65 gene. The c2J strain has methionine at residue 450, while the other eight susceptible albino strains studied carried leucine at codon 450. BALB/cBy retinas, which were more susceptible to light damage, regenerate rhodopsin at a faster rate than retinas from c2J (Wenzel et al., 2001), indicating that the kinetics of regeneration, and not the absolute levels of rhodopsin, are important in light-induced degeneration. These observations are clinically relevant, as they suggest that naturally occurring variants that do not in themselves cause significant overt disease may influence visual outcome when challenged with environmental stresses.
Another example of allelic variants that affect different phenotypes on light exposure are those in the rhodopsin gene. Mutations in the rhodopsin gene, a G protein–coupled receptor, are responsible for 30% of autosomal dominant cases of retinitis pigmentosa (RP) in humans. Rhodopsindeficient mice generated by homologous recombination showed that the presence of rhodopsin is necessary for proper outer segment development and photoreceptor survival (Humphries et al., 1997). Panretinal loss of photoreceptor cell bodies was observed in Rho−/− mice by 3 months of age. Mutational screening of the rhodopsin gene in a dog model of RP found an amino acid change from threonine to arginine at residue 4 (Kijas et al., 2002). The dogs showed a very slow recovery after exposure to bleaching light levels and local areas of degeneration. Of direct clinical relevance is the observation that moderate levels of light, such as those used in clinical examinations, increased the rate of retinal degeneration in these dogs (Cideciyan et al., 2005). We have recently identified two new rhodopsin alleles in our Models for Translational Vision Research (MTVR) program, RhoMtvr1 and RhoMtvr4, which carry missense mutations induced by chemical mutagenesis that are phenotypically similar to the dog model (E. Budzynski, pers. comm., 2007). Degeneration of photoreceptors is focal and occurs only on direct light exposure. The observations from these models have important clinical implications, as individuals with this type of rhodopsin mutation may be more susceptible to lightinduced damage, and early identification of these individuals may delay vision impairment if a reduction in light exposure is included in their treatment plan.
Defining Response to Treatment Because particular mutations at similar sites in the rhodopsin gene result in different clinical outcomes, the response to treatment may also be genotype dependent. RHO P23H is one of the most frequently occurring mutations associated with autosomal dominant RP in humans. A transgenic mouse, VPP, made with mutations in three amino acids, including P23H, exhibits a slow degeneration of both rods and cones, as assessed by ERG amplitudes and histology (Naash et al.,
1993). Administration of recombinant human erythropoietin had no effect on the rate of photoreceptor degeneration in VPP mice but was able to protect mice from light-induced damage (Grimm et al., 2004). On the other hand, vitamin A supplementation slowed the rate of retinal degeneration in T17M transgenic mice but not in mice expressing the P347S allele of rhodopsin (Li et al., 1998).
Genetic modifiers as a cause of phenotypic variation
The phenotypic outcomes of a particular mutation may also be influenced by specific alleles of other genes in the genome, the so-called genetic modifiers. The phenomenon is also referred to as epistatic or nonlinear interaction between genes, so that the effects of variation in gene A are observed only in the presence of a particular variant of gene B. In mice, the existence of genetic modifiers was originally postulated from the variation in phenotype observed when spontaneous mutations were crossed onto different inbred backgrounds (Hummel et al., 1972). An early example of genetic modification in the visual system (LaVail et al., 1978) was demonstrated in mutants of the c locus in which differences in retinal ganglion cell projections could not be fully explained by allelic effects. Additionally, as large numbers of models with targeted mutations created on a 129Sv/J and C57BL/6 (B6) background have been generated, researchers have reported phenotypic variability, as the genetically engineered alleles were moved from the mixed 129/B6 background onto B6 (Ikeda et al., 1999; Humphries et al., 2001). In these cases, the effects of the modifier are observed only in the context of a primary mutation. The phenomenon of phenotypic modifications is currently recognized as a useful tool for identifying factors that interact with genes involved in known pathways or for providing entry points into the function of novel genes (Nadeau, 2003; Vincent, 2003; Linder, 2006). That is, they may provide additional information about genetic contributions to the phenotype for which treatment may already be available, or they may reveal additional steps in a biological pathway that may be more amenable to treatment. As more genes modifying the progression of ocular diseases caused by specific mutations are discovered, it is envisioned that these modifiers will unlock doors to new treatment modalities and help physicians make better diagnoses and treatment plans, perhaps by defining subgroups within a disease population. Examples of phenotypic variability in different genetic backgrounds where the primary mutation is the same are given in table 53.1. Examples of cases in which genetic modifier loci have been mapped or identified are less frequent; these are given in table 53.2. With the recent increase in available genomic information, the actual identification of genetic modifiers is expected to increase. Potential strategies for the identification of genetic modifiers are discussed later in the chapter.
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Table 53.1
Genetic modification of ocular phenotypes observed in different strain backgrounds
|
|
Strains Involved in Modification |
|
Model |
Effect of Genetic Modification |
(Resistant → Susceptible) |
References |
Retinal degeneration 3 (rd3) |
Variability in onset and progression of |
RBF/Dn, Meta-In(1)Rk, |
Heckenlively, 1993 |
|
photoreceptor degeneration |
Rb(11.13)4Bnr and In-30 |
|
Rhodopsin−/− |
Variable rate of photoreceptor |
C57BL/6 and 129/SvJ |
Humphries et al., |
|
degeneration |
|
2001 |
Nr2e3rd7 |
Suppression of retinal spotting and |
B6.Cg-rd7/rd7 and CAST/EiJ |
Akhmedov et al., |
|
photoreceptor degeneration |
|
2000 |
Trp53 |
Attenuation of vitreal opacity, retinal |
129/SvJ and C57BL/6 |
Ikeda et al., 1999 |
|
folds and retrolental fibroplasia in |
|
|
|
the 129/SvJ background |
|
|
Bmp4 |
Anterior segment dysgenesis with |
C57BL/6J, BliA |
Chang et al., 2001 |
|
elevated intraocular pressure |
CAST/Ei, C3H/HeJ |
|
|
|
AKR/J, BALB/C |
|
|
|
129/SvEvTac |
|
isa, iris stromal atrophy, DBA/2J ipd, iris pigment dispersion Nr2e1frc
Increased cell death |
AKXD-28/Ty |
Anderson et al., 2001 |
Milder phenotype |
AKXD-28/Ty |
Anderson et al., 2001 |
Thinning of optic layers, differences in |
B6129F1, 129P3/JEms, and |
Young et al., 2002 |
ERG responses, and retinal vascular |
C57BL/6 |
|
development |
|
|
Crb1rd8 |
Retinal dysplasia and photoreceptor |
C57BL/6 and C3H/HeJ |
Mehalow et al., 2003 |
|
degeneration |
|
|
|
|
|
|
Table 53.2
Genetic modifier loci that have been mapped and/or cloned
|
|
Strains Involved |
Map Location |
|
|
Effect of Genetic |
in Modification |
and/or Modifier |
|
Model |
Modification |
(Resistant → Susceptible) |
Identity |
References |
tubby (tub or rd5) |
Delay of photoreceptor |
AKR/J and C57BL/6 |
Chrs 11 (motr1), 2, |
Ikeda et al., 2002a |
|
degeneration |
|
and 8 |
|
Light-induced |
Resistance to light damage |
BALB/c2J and albino |
Rpe65 Leu450Met |
Danciger et al., 2000; |
photoreceptor |
|
strains |
|
Wenzel et al., 2001 |
damage model |
|
|
|
|
isa, iris stromal |
Increased cell death |
AKXD-28/Ty |
|
Anderson et al., 2001 |
atrophy, DBA/2J |
|
|
|
|
ipd, iris pigment |
Milder phenotype |
AKXD-28/Ty |
|
Anderson et al., 2001 |
dispersion |
|
|
|
|
Chx10orJ |
Partial recovery of visual |
CASA/Rk and 129/SvJ |
Chrs 6 and 14 |
Wong, et al., 2006 |
|
function |
|
|
|
VPP and Rpe65Leu450Met |
Reduced photoreceptor |
|
Rpe65 Leu450Met |
Naash et al., 1993; |
|
degeneration |
|
|
Samardzija et al., 2006 |
Examples of Genetic Modification of Retinal Degenerative Disease in Mice Recent figures indicate the existence of at least 181 cloned or mapped genes that, when mutated, lead to retinal disease in humans (Retnet: www. sph.uth.tmc.edu/Retnet/disease.htm). Although modifiers have been reported for a small percentage of these genes, because genes do not act in isolation, one would expect that most mutations are modified to some extent by inter-
action with other genes. In mice, an example of variable expressivity in photoreceptor degeneration as a result of genetic background was reported in 1993 for retinal degeneration 3 (rd3) mutant mice (Heckenlively, 1993). The onset and progression of degeneration differed among strains RBF/Dn, Meta-In(1)Rk, Rb(11.13)4Bnr, and In-30, all carrying the same rd3 allele. Scotopic ERGs were extinguished in the first two strains by 6 weeks of age, and
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outer nuclear layer (ONL) degeneration was observed as early as 14 days of age and progressed through 8 weeks. In contrast, mice homozygous for the rd3 mutation on strain In-30 manifested milder retinal dysfunction in which scotopic ERGs were not extinguished until 16 weeks of age, and ONL degeneration began at 3 weeks and progressed through 16 weeks of age (Heckenlively, 1993; Linberg et al., 2005). Since this first report of genetic modification, genetic background modification of photoreceptor degenerations has been reported for a number of models. Mice deficient in rhodopsin (Rho−/− mice) were protected by modifiers from the B6 genetic background when compared with the 129Sv background (Humphries et al., 2001). In the B6 background, Rho−/− mice were reported to have greater cone photoreceptor function and a greater number of photoreceptor nuclei. However, modification is specific for the mutant gene. Unlike the genetic modification observed for Rho−/− mice, in tubby mice (Ikeda et al., 2002a), the B6 background is more susceptible to photoreceptor degeneration and the AKR and CAST strain backgrounds afford some protection.
Modifier genes may also completely suppress a mutant phenotype (Ikeda et al., 1999; Akhmedov et al., 2000). In an intercross between strains B6.Cg-Nr2e3rd7/rd7 and CAST/ Ei, some F2 mice homozygous for the Nr2e3rd7 mutation were free of the characteristic retinal spotting phenotype (Akhmedov et al., 2000). Subsequent studies have shown that suppression of retinal spotting and subsequent photoreceptor degeneration correlates with suppression of the excess blue cone production that underlies the retinal whorls and folds (Haider et al., 2006). A similar suppression of the disease phenotype was observed in some F2 Nr2e3rd7 mice from intercrosses with the AKR/J and NON.NODn2b/J strains. Interestingly, none of the modifier regions identified from intercrosses between B6.Cg-Nr2e3rd7/Nr2e3rd7 and any of these strains overlapped (Haider et al., in press). Therefore, not only are genetic modifiers specific to mutations, as described with Rho−/− and tubby mice, they may also be different in different strain combinations.
Some modifiers have also demonstrated new phenotypes (Mehalow et al., 2003). The retinal degeneration 8 (rd8) mutation in crumbs1 (Crb1), originally identified in a mixed background between strains C57BL/6 and C3H/HeJ, exhibited large spots in the inferior nasal quadrant of the retina. These spots corresponded to areas of retinal dysplasia as shown by histological analysis. When the Crb1rd8 mutation was moved onto the C57BL/6 background by 10 backcross generations, the dysplastic phenotype disappeared, suggesting that unlinked C3H/HeJ alleles were lost during the process of introgressing the mutation onto the B6 background. Subsequent intercrosses with the B6.C3H-Crb1rd8/ Crb1rd8 mice and C3H/HeJ mice restored the dysplastic phenotype, indicating that the genetic modification is likely conferred by C3H/HeJ (M. M. Edwards, pers. comm., 2007).
In studies with mice where both environmental factors and allelic variability of primary mutations can be controlled, genetic modification may be more evident and tractable. However, genetic modification can still be complex, and for a given disorder, a combination of modifier genes may act together to create a cumulative effect on the expression of a phenotype. For example, in F2 tub/tub progeny of an intercross between B6.Cg-tub/tub and the AKR/J strain, a significant range of photoreceptor cell survival was observed. Several chromosomal regions were identified to cosegregate with the thickness of the ONL (Ikeda et al., 2002a). At 20 weeks of age, B6.Cg-tub/tub mice normally have 5%–10% of residual ONL thickness remaining, whereas ONL thickness in F2 mice from the intercross ranged from 5% to 80%. One modifier on chromosome 11, modifier of tubby retinal degeneration 1 (motr1), was detected with high statistical significance in a genome-wide scan, and two additional loci on chromosomes 2 and 8 showed suggestive linkage. Protective alleles came from both the AKR (motr1 and the chromosome 2 locus) and B6 backgrounds (the chromosome 8 locus). Interestingly, Williams et al. (1998) were able to map the natural variation in ganglion cell number in two recombinant inbred strain sets, BXD and BXH, to the same genomic regions containing the tubby modifiers. Identification of these and other modifier loci should offer insight into the particular pathways through which the primary mutant gene functions and into the pathways involved in degeneration.
Strategies for cloning genetic modifiers
As mentioned in the previous section, some genetic modifiers have been identified. The number is small when compared with the number of disease genes known to cause ocular disease, however. Therefore, it seems probable that many modifiers await discovery. Identifying these genes could help improve treatment for individuals affected by ocular diseases by defining pathways through which disease-causing genes function. At this juncture, it seems appropriate to consider methods that are evolving to identify variants that modify phenotypes or that have been used in other systems to identify modifier genes. An integrated approach using a combination of strategies is likely to provide the best opportunity for efficiently identifying genetic modifiers (Cervino et al., 2006).
Chromosomal Localization of Modified Traits The first step in identifying a genetic modifier is to establish a robust, reproducible method for phenotyping the modification, either qualitative (e.g., the presence or absence of a particular phenotype) or quantitative (e.g., the onset, rate, or severity of a particular phenotype). Because severity is characterized as a continuous distribution rather
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than in discrete subsets, it is grouped with the quantitative traits.
In the next step, the source of modification is chromosomally localized in progeny from backcrosses or intercrosses of mice that carry the primary mutation with another strain whose genetic makeup is able to modify the phenotype. Phenotypic modification that is observed only in mice carrying the primary mutation is mapped by comparing phenotypic variation to sequence variation throughout the genome (e.g., genome-wide scan). Once a region is found in which there is significant skewing of a genotype that correlates with the phenotypic modification, the region can be narrowed by further recombinational linkage analysis and testing for sequence differences among biologically relevant genes contained within the chromosomal area that might explain the modifying effects. If multiple regions are identified, candidate regions can be investigated individually for their ability to modify a given phenotype by construction of congenic strains in which the modifier region and the primary mutation are placed in the same genetic background by successive backcrossing. If the primary mutation is in the C57BL/6 background and modification is observed with strains A/J or PWD/Ph, then the congenic process may be hastened by intercrossing the primary mutation to the consomic or chromosomal substitution strain (Silver, 1995) bearing the chromosome on which the modification is observed. In addition, existing congenic lines that cover the modifier region in question can be used as a resource to verify or to identify the modifier (Ikeda et al., 2002a).
Segregating Crosses with Multiple Strains Although quantitative trait loci (QTL) mapping and recombinational linkage analysis are powerful tools, these traditional methods require large numbers of animals. It is important, therefore, that these methods be made more efficient. One way in which the efficiency of QTL mapping can be improved is by performing multiple crosses with different strains in which the primary mutation is segregating. Detecting the same modifier in multiple strains suggests that it may be derived from a common ancestral allele. Although recombinations were previously thought of as random events, hot spots for recombination have been shown in various strain combinations (Kelmenson et al., 2005); the use of multiple crosses narrows the confidence interval significantly by increasing the number of recombinations, both ancestral and new, within the region (Wang et al., 2004).
Haplotype Analysis A modifier region identified through multiple cross-mappings can be further narrowed by comparing the genomic sequences of the parental strains (reviewed in DiPetrillo et al., 2005; Flint et al., 2005). Haplotype analysis is one method used for such a comparison.
This method utilizes the fact that inbred mouse strains are derived from a limited set of ancestors, so that alleles of genes are shared between several inbred strains. These alleles are part of an ancestral haplotype surrounding that gene, and haplotype blocks can be identified by the identity of marker alleles within the haplotype between inbred strains. Since these haplotype blocks are on the order of 40 kb to 1.5 Mb long, the genomic area in which the modifier locus resides can be narrowed by identifying the shared ancestral haplotype block in the strains that modify the phenotype. Conversely, areas where no haplotype sharing is observed can be excluded as candidate regions for the modifier. Practically, a dense SNP map is compiled across the map position from the multiple strain cross and is compared between the strains that modify the phenotype and those that do not. Regions where all the modifying strains share the same SNP alleles and are different from the alleles of the nonmodifying strains can be considered candidate regions. The attraction of this technique is that it can reduce the necessity to generate large numbers of mice to narrow a region considerably, and in many cases the SNP information may already be available through the mouse resequencing project (www.informatics.jax.org/menus/strain_menu. shtml; http://genome.perlegen.com/browser/index.html). This technique has been used in mice to narrow modifier regions in studies investigating cancer (Wang and You, 2005) and cardiomyopathy (Wheeler et al., 2005). The power of haplotype analysis was shown in a study of hypertension, in which a QTL region was narrowed from 18 cM to 2.3 cM using haplotype analysis (DiPetrillo et al., 2004). Not all modifiers, however, are captured by ancestral haplotypes. Genetic variation is continually acquired, and at least some modifier alleles are due to mutations that occurred after the common inbred strains were established and are private to one or a few inbred strains (Ikeda et al., 2002b).
Gene Expression Profiling or Microarray Analysis A growing body of literature supports the usefulness of combining the mapping of modifier loci with expression profiling, especially in the identification of complex traits (Wayne and McIntyre, 2002; Tabakoff et al., 2003). In an elegant study, Dyck et al. (2003) combined these two techniques to understand the development of gallstones in C57L/J mice that carry the Lith1 gallstone-susceptibility locus. This study used expression profiling, through microarray analysis, to identify differences in gene expression between the C57L/J mice and gallstone-resistant AKR/J mice. Numerous genes involved in fatty acid metabolism were identified. Through literature searches of common regulatory elements within antioxidant systems, the nuclear transcription factor Nrf2, which maps to the Lith1 locus, was identified. Thus, the combination of modifier mapping and expression profiling in conjunction with pathway analysis is
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a powerful tool. Locus mapping identifies chromosomal regions that are associated with a known phenotype but may contain many genes. Expression profiling identifies genes whose expression levels differ between two populations (i.e., modified and unmodified) but whose association with the observed phenotype is unknown. By combining these two techniques, it is possible to use data acquired in the mapping phase to filter data acquired in the expression profiling phase, either by identifying a misregulated gene within the modifier region or by identifying a misregulated pathway, a component of which resides in the modifier region, suggesting it as a candidate gene.
Modifier Screens Using Mutagenesis Although mutagenesis screens have been used for years to identify modifiers in lower organisms (Carrera et al., 1998; Therrien et al., 2000; Mutsuddi et al., 2004), it has only recently been used for this purpose in mice. Mice with mutations in a gene that is believed to interact with genetic modifiers can be mutated using N-ethylnitrosurea (ENU), a chemical mutagen, and the resulting offspring screened for an altered phenotype. For example, an ENU modifier screen was used to identify genes that suppress thrombocytopenia (lack of blood platelets) in a mouse model Mpl−/− (Carpinelli et al., 2004). In this study, mutant males were treated with ENU and mated to untreated females. Blood collected from G1 progeny were assessed for platelet levels. Mice that showed improved platelet levels were backcrossed to Mpl −/− mice to verify heritability of suppression. DNA from males with heritable suppression was then used to map candidate modifiers. This study produced two candidate modifier alleles of the c-Myb gene. These alleles were shown to reduce c-MYB activity, subsequently suppressing the thrombocytopenia phenotype (Carpinelli et al., 2004). More recently, a sensitized screen to identify alterations in dopaminergic homeostasis was carried out in mice with a disrupted dopamine transporter (Speca et al., 2006). Seven phenodeviant lines with abnormal locomotor activity were identified, two of which were dependent on the presence of the DAT mutation and two others that affected dopamine neurotransmission. Hence, sensitized mutagenesis-driven modifier screens in mice could also be a powerful adjunct for identification of genetic modifiers for retinal disease genes.
Summary
The variability in onset, progression, severity, phenotypic expression, or response to treatment, which is a common observation for many diseases, may be due to interactions of mutant alleles with genetic modifiers, or alternatively to environmental or allelic effects. The heterogeneity within the human population makes it difficult to assess the underlying cause of the phenotypic disease variability. However,
understanding the nature of the variability may be important in effecting optimum treatment modalities. Model organisms, such as the mouse, can play an important and necessary role in elucidating the cause of variation in phenotype and in response to treatment.
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