Thirteen years of manipulating the mouse genome: a personal history

In 1974, Dr. Ralph Brinster published a paper describing the consequences of injecting embryonal carcinoma cells, the predecessors of embryonic stem cells, into mouse blastocysts. Despite their early promise, embryonal carcinoma cells would not efficiently populate the germ line of mice. A decade later Elizabeth Robertson and I described the efficient generation of germline chimaeras from cultured embryonic stem cells and shortly afterwards the genetic manipulation of the mouse germline using ES cells. Our demonstration of the potency of Embryonic Stem cells gave birth to a new era in manipulative mouse genetics, one in which endogenous genes can now be mutated at will using gene targeting of retroviral mutagenesis. This review focuses on the development and testing of concepts and techniques during the thirteen years after we knew germline modification of endogenous genes in the mouse would be possible. This period is one in which more and more sophisticated tools for manipulating the mouse germline were developed and implemented. In this review I have taken the rare opportunity to reveal some of my thought processes, frustrations, successes and failures as we moved through this exciting period of rapid technological change. As I look forward to the next thirteen years, I feel that this will be an equally exciting period for manipulative genetics as we struggle to formulate concepts and design experiments that enable us to understand gene function in an era when the sequence of all genes will be known.

An anchored framework BAC map of mouse chromosome 11 assembled using multiplex oligonucleotide hybridization

Despite abundant library resources for many organisms, physical mapping of these organisms has been seriously limited due to lack of efficient library screening techniques. We have developed a highly efficient strategy for large-scale screening of genomic libraries based on multiplex oligonucleotide hybridization on high-density genomic filters. We have applied this strategy to generate a bacterial artificial chromosome (BAC) anchored map of mouse chromosome 11. Using the MIT mouse SSLP data, 320 pairs of oligonucleotide probes were designed with an "overgo" computer program that selects new primer sequences that avoid the microsatellite repeat. BACs identified by these probes are automatically anchored to the chromosome. Ninety-two percent of the probes identified positive clones from a 5.9-fold coverage mouse BAC library with an average of 7 positive clones per marker. An average of 4.2 clones was confirmed for 204 markers by PCR. Our data show that a large number of clones can be efficiently isolated from a large genomic library using this strategy with minimal effort. This strategy will have wide application for large-scale mapping and sequencing of human and other large genomes.

Embryonic lethality and tumorigenesis caused by segmental aneuploidy on mouse chromosome 11

Chromosome engineering in mice enables the construction of models of human chromosomal diseases and provides key reagents for genetic studies. To begin to define functional information for a small portion of chromosome 11, deficiencies, duplications, and inversions were constructed in embryonic stem cells with sizes ranging from 1 Mb to 22 cM. Two deficiencies and three duplications were established in the mouse germline. Mice with a 1-Mb duplication developed corneal hyperplasia and thymic tumors, while two different 3- to 4-cM deficiencies were embryonically lethal in heterozygous mice. A duplication corresponding to one of these two deficiencies was able to rescue its haplolethality.

Functional characterization of BRCA1 and BRCA2: clues from their interacting proteins

The familial breast and ovarian cancer susceptibility genes, BRCA1 and BRCA2 have been the subject of extensive functional analysis studies since their cloning. Clues to their biological role in maintaining the genomic integrity were provided by studies that revealed their interaction with the recombination repair protein HsRad51. The first clue of an interaction between HsRad51 and BRCA1 came from the colocalization of the characteristic nuclear foci formed by these two proteins during S phase of the cell cycle. An interaction between murine Brca2 and MmRad51 was detected by the yeast two hybrid system. Utilizing the yeast two hybrid system and other techniques several other Brca1 and Brca2 interacting proteins have been identified like, BARD1, importin-alpha, BIPs, RNA polymerase II holoenzyme, BRAP2 etc. Recently, mutations suggesting a role as a tumor suppressor have been identified in the BARD1 gene in primary human tumors. The identification of molecules that interact with Brca1 and Brca2 has greatly enhanced our knowledge of how BRCA1 and BRCA2 may function as tumor suppressors.

Entoptic image quality of the retinal vasculature

Spatial details of entoptically visible retinal vessels were investigated using transcleral and Maxwellian-view stimulators. Nine normal subjects provided detailed drawings of the entoptic images which were digitized and superimposed onto digitized fundus photographs and fluorescein angiograms from the same eyes. Subjects also used a tracing method to locate visible entoptic features. The trans-scleral method provided images similar in detail to standard fundus photography (lacking capillary detail, but capturing larger arteries, veins, arterioles and venules) in the macula and around the disk. The Maxwellian-view method illuminated the fovea (7.7 degree field) and provided foveola capillary detail (capillaries traversing the foveola, the capillary arcade forming the FAZ) as well as the larger foveal vessels supplying the foveola, and often contained more foveal detail that available with fluorescein angiography.

Predicting the effects of optical defocus on human contrast sensitivity

We used diffraction modulation transfer functions and model eyes to predict the effect of defocus on the contrast sensitivity function (CSF) and compared these predictions with previously published experimental data. Using the principle that optically induced changes in the modulation transfer function should be paralleled by identical changes in the CSF, we used the modulation transfer function calculations with the best-focus CSF measurements to predict the defocused CSF. An aberration-free model predicted the effects of defocus well when the CSF was measured with small pupils (e.g., 2 mm) but not with larger pupils (6-8 mm). When the model included average aberrations, prediction of the defocused CSF with large pupils was better but remained inaccurate, failing, in particular, to reflect differences between individual subjects. Inclusion of measured aberrations for individual subjects provided accurate predictions in the shape of the monochromatic CSF of two of three subjects with hyperopic defocus and good predictions of the polychromatic CSF of two subjects with hyperopic defocus. Prediction of the effects of myopic defocus by use of measured individual aberrations of one subject were less successful. Hence a diffraction optics model can provide good predictions of the effects of defocus on the human CSF, given that one has knowledge of the individual ocular aberrations. These predictions are dependent on the quality of the aberration measurements.

Comparison of the eye's wave-front aberration measured psychophysically and with the Shack-Hartmann wave-front sensor

The Shack-Hartmann wave-front sensor offers many theoretical advantages over other methods for measuring aberrations of the eye; therefore it is essential that its accuracy be thoroughly tested. We assessed the accuracy of a Shack-Hartmann sensor by directly comparing its measured wave-front aberration function with that obtained by the Smirnov psychophysical method for the same eyes. Wave-front profiles measured by the two methods agreed closely in terms of shape and magnitude with rms differences of approximately lambda/2 and approximately lambda/6 (5.6-mm pupil) for two eyes. Primary spherical aberration was dominant in these profiles, and, in one subject, secondary coma was opposite in sign to primary coma, thereby canceling its effect. Discovery of an unusual, subtle wave-front anomaly in one individual further demonstrated the accuracy and sensitivity of the Shack-Hartmann wave-front sensor for measuring the optical quality of the human eye.

Chromosomal transposition of a Tc1/mariner-like element in mouse embryonic stem cells

Mouse has become an increasingly important organism for modeling human diseases and for determining gene function in a mammalian context. Unfortunately, transposon-tagged mutagenesis, one of the most valuable tools for functional genomics, still is not available in this organism. On the other hand, it has long been speculated that members of the Tc1/mariner-like elements may be less dependent on host factors and, hence, can be introduced into heterologous organisms. However, this prediction has not been realized in mice. We report here the chromosomal transposition of the Sleeping Beauty (SB) element in mouse embryonic stem cells, providing evidence that it can be used as an in vivo mutagen in mice.

Retention of wild-type p53 in tumors from p53 heterozygous mice: reduction of p53 dosage can promote cancer formation

Tumor suppressor genes are generally viewed as being recessive at the cellular level, so that mutation or loss of both tumor suppressor alleles is a prerequisite for tumor formation. The tumor suppressor gene, p53, is mutated in approximately 50% of human sporadic cancers and in an inherited cancer predisposition (Li-Fraumeni syndrome). We have analyzed the status of the wild-type p53 allele in tumors taken from p53-deficient heterozygous (p53+/-) mice. These mice inherit a single null p53 allele and develop tumors much earlier than those mice with two functional copies of wild-type p53. We present evidence that a high proportion of the tumors from the p53+/- mice retain an intact, functional, wild-type p53 allele. Unlike p53+/- tumors which lose their wild-type allele, the tumors which retain an intact p53 allele express p53 protein that induces apoptosis following gamma-irradiation, activates p21(WAF1/CIP1) and Mdm2 expression, represses PCNA expression (a negatively regulated target of wild-type p53), shows high levels of binding to oligonucleotides containing a wild-type p53 response element and prevents chromosomal instability as measured by comparative genomic hybridization. These results indicate that loss of both p53 alleles is not a prerequisite for tumor formation and that mere reduction in p53 levels may be sufficient to promote tumorigenesis.

The role of neural and optical factors in limiting visual resolution in myopia

The myopic growth process has the potential to modify both the optical and neural performance of the eye. We provide three simple models, based on different types of retinal stretching, to predict changes in neural resolution resulting from axial length increases in myopia. These predictions are compared to visual acuity (VA) measures in 34 subjects with refractive errors ranging from plano to -14 D. Our results show a reduction in VA with increasing myopia but not in a manner predicted by our models. We discuss the relative contribution of optical and neural factors to the reduction in visual resolution in myopia.

Tumour susceptibility and spontaneous mutation in mice deficient in Mlh1, Pms1 and Pms2 DNA mismatch repair

Germline mutations in the human MSH2, MLH1, PMS2 and PMS1 DNA mismatch repair (MMR) gene homologues appear to be responsible for most cases of hereditary non-polyposis colorectal cancer (HNPCC; refs 1-5). An important role for DNA replication errors in colorectal tumorigenesis has been suggested by the finding of frequent alterations in the length of specific mononucleotide tracts within genes controlling cell growth, including TGF-beta receptor type II (ref. 6), BAX (ref. 7) and APC (ref. 8). A broader role for MMR deficiency in human tumorigenesis is implicated by microsatellite instability in a fraction of sporadic tumours, including gastric, endometrial and colorectal malignancies. To better define the role of individual MMR genes in cancer susceptibility and MMR functions, we have generated mice deficient for the murine homologues of the human genes MLH1, PMS1 and PMS2. Surprisingly, we find that these mice show different tumour susceptibilities, most notably, to intestinal adenomas and adenocarcinomas, and different mutational spectra. Our results suggest that a general increase in replication errors may not be sufficient for intestinal tumour formation and that these genes share overlapping, but not identical functions.

Building effective partnerships: a national evaluation of the Cancer Information Service outreach program. Part 2

The Cancer Information Service's (CIS) nationally coordinated, regionally focused outreach program establishes partnerships with government, nonprofit, and private organizations to reach underserved and minority populations. A national random sample telephone survey, conducted with 867 partner organizations who had contact with the CIS in early 1996, assessed the types of CIS assistance used, satisfaction with and usefulness of these services, organizational characteristics, and the overall impact on partners' cancer-related programs. CIS partners provide programs for the medically underserved (79%) and specific racial and ethnic groups (72%) and address a range of cancer control issues. Partners use and highly value an array of CIS assistance. Over 90% are satisfied with the CIS services. Diffusion of accurate and science-based information, materials and resources is a key element of the outreach assistance. Two out of three partners are receiving late-breaking news and scientific information from the CIS and 86% are disseminating it to their constituents. The majority of those partners surveyed reported that they rely on the CIS to assist with their most important cancer programs. Sixty-eight percent of the partners rated the CIS assistance as important or very important to their cancer-related programs. These survey results indicate that the CIS outreach program provides key support to partners' cancer programs and has an impact on their efforts. The results support the effectiveness of a regionally based outreach program working in partnership with existing organizations at the state, county, and local level who are addressing the needs of underserved populations.

Novel monosaccharides as potent inhibitors of cell proliferation

The effects of several novel monosaccharides upon thymidine incorporation into both normal and tumour cells were investigated. The monosaccharide 2-deoxy-3-[1-(R)-(ethoxycarbonyl)ethyl]- alpha-D-allo-pyranose had the most inhibitory effect on proliferation, with the (S)-enantiomer having less inhibitory effects. The chiral centre at carbon-7 was found to be an important part of the molecule, as 2-deoxy-3-[methoxycarbonyl methyl]-alpha-D-allo-pyranose had greatly decreased anti-proliferative properties in comparison with the parent compound. In addition, the 2-deoxy structure at carbon-2 was also found to be important, as 3-[1-(S)-(ethoxycarbonyl)ethyl]-alpha-D-allo-hexopyranose had greatly decreased inhibitory properties in comparison with the parent compound. The results indicate that these novel monosaccharides possess potent anti-proliferative properties, related to their chiral carbon-7 and 2-deoxy carbon-2 structure and suggest that further substitutions of the functional group at carbon-7 may improve these properties and possibly produce inhibitor selectivity for tumour cells in preference to normal cells.

Using targeted large deletions and high-efficiency N-ethyl-N-nitrosourea mutagenesis for functional analyses of the mammalian genome

The Human Genome Project has generated nucleotide sequences from an estimated 80,000 to 100,000 genes, only a small fraction of which have a known role. Nucleotide sequence information alone is insufficient to predict gene function. One of the most powerful ways of revealing gene function, as demonstrated in bacteria, worms, yeast, and flies, is to generate mutations and characterize them at both the phenotypic and the molecular levels. Given the physiological and anatomical parallels between mouse and human, genotype-phenotype relationships established in mice can be extrapolated to human syndromes. A new method is described for functional genetic analyses in the mouse that uses loxP/Cre engineering to generate coat color-tagged large deletions. The haploid regions can then be dissected by mutagenesis with N-ethyl-N-nitrosourea in phenotype-driven screens to obtain functional information on genes in any desired region of the mouse genome.

Role of DNA mismatch repair in the cytotoxicity of ionizing radiation

The DNA mismatch repair (MMR) system in mammalian cells not only serves to correct base mispairs and other replication errors, but it also influences the cellular response to certain forms of DNA damage. Cells that are deficient in MMR are relatively resistant to alkylation damage because, in wild-type cells, the MMR system is thought to promote toxicity via futile repair of alkylated mispairs. Conversely, MMR-deficient cells are sensitive to UV light, possibly due to the requirement for MMR factors in transcription-coupled repair of active genes. MMR deficiency has been associated with familial and sporadic carcinomas of the colon and other sites, and so, we sought to determine the influence of MMR status on cellular response to ionizing radiation, an agent commonly used for cancer therapy. Fibroblast cell lines were established from transgenic mice carrying targeted disruptions of one of three MMR genes in mammalian cells: Pms2, Mlh1, or Msh2. In comparison to wild-type cell lines from related mice, the Pms2-, Mlh1-, or Msh2-nullizygous cell lines were found to exhibit higher levels of clonogenic survival following exposure to ionizing radiation. Because ionizing radiation generates a variety of lesions in DNA, the differences in survival may reflect a role for MMR in processing a subset of these lesions, such as damaged bases. These results both identify a new class of DNA-damaging agents whose effects are modulated by the MMR system and may help to elucidate pathways of radiation response in cancer cells.

Effects of refractive error on detection acuity and resolution acuity in peripheral vision

PURPOSE

To evaluate the effect of refractive error on detection acuity and resolution acuity in peripheral vision.

METHODS

Detection acuity, defined as the highest spatial frequency for which luminance gratings can be discriminated from a uniform field, and resolution acuity, defined as the highest spatial frequency for which spatial patterns are perceived veridically, was determined for vertical and horizontal gratings located at 20 degrees, 30 degrees, and 40 degrees of eccentricity. Resolution was also measured for tumbling-E discrimination at these locations. Refractive state of the eye for test targets was manipulated by introducing an ophthalmic trial lens into the line of sight for the stimulus while holding accommodative state fixed.

RESULTS

Detection acuity in the periphery varied significantly with the amount of optical defocus, whereas acuity for grating resolution or letter discrimination was unaffected by defocus over a large range (up to 6 D). These results are consistent with the working hypothesis that detection acuity in the periphery is limited by contrast insufficiency under normal viewing conditions, but resolution is limited by ambiguity because of neural undersampling.

CONCLUSIONS

The large depth of focus for resolution acuity measured for peripheral vision indicates that spatial resolution is likely to remain sampling-limited even when peripheral refractive errors are not fully corrected, thus relaxing the methodologic requirements for obtaining noninvasive estimates of neural sampling density of the living eye in a clinical setting.

Interaction between sub- and supra-Nyquist spatial frequencies in peripheral vision

In peripheral vision, high-frequency gratings beyond the Nyquist limit are visible as aliased patterns but, as shown previously, their visibility can be masked by superimposed sub-Nyquist gratings. Is the converse also true? Can supra-Nyquist gratings affect the detectability of sub-Nyquist gratings? In this study, we investigated the masking effect of high contrast, supra-Nyquist components of a compound grating on the contrast detection of sub-Nyquist components by employing a temporal three-alternative, forced-choice (3AFC) masking paradigm. We found that high-frequency, aliased gratings with contrast just 2 or 3 times above threshold can have a powerful masking effect on low-frequency, resolved gratings in peripheral vision. This result was surprising because prior results from sub-Nyquist masking studies in the fovea and the periphery have indicated that masking occurs only when the mask contrast is at least 5 times greater than threshold. Strong masking by supra-Nyquist gratings that are only just visible may be accounted for by an irregular sampling model in which the alias of the mask is distributed over a band of frequencies in the sub-Nyquist range. Furthermore, if undersampling is the explanation for the results of this study, then masking must occur after spatial sampling.

Use of liquid-crystal adaptive-optics to alter the refractive state of the eye

We evaluated the potential of wavefront shaping with liquid-crystals for modulating the eye's refractive state. A spatial light modulator with 127 liquid crystals cells was imaged in the entrance pupil of the eye and programmed to induce prismatic, spherical, and astigmatic refractive changes. Psychophysical evaluation of these optical effects was in agreement with expectations for prisms up to approximately 0.08 D and for lenses up to approximately 1.5 D. These maximum dioptric values represent wavefront retardation of about 3 to 4 wavelengths of 584 nm light across a 3-mm diameter pupil. Optical aliasing of high-power prisms was traced to spatial undersampling of the wavefront retardation function by the discrete array of liquid crystal cells. Undersampling may also be the factor which limits the useful dioptric range of the technique.

Spherical aberration of the reduced schematic eye with elliptical refracting surface

We extend the single-surface schematic-eye model of ocular chromatic aberration to account for spherical aberration of the eye. This extension is accomplished by allowing the model's single refracting surface to be a member of the family of ellipses with variable shape parameter (eccentricity). The resulting model, dubbed the "Indiana Eye," may have either positive or negative spherical aberration of varying degree, depending upon the numerical value of the shape parameter. Spherical aberration of the model eye is well described by third-order optical theory for shape parameters in the range 0 < or = p < or = 0.7, but requires fifth-order theory for an accurate description over the parametric range 0.7 < p < or = 1.0. An improved technique was devised for fitting the model to published measurements of ray aberrations while avoiding errors of estimation of the degree of spherical aberration present in eyes which also manifest odd-symmetric aberrations, such as coma. A shape parameter value of approximately p = 0.6 provided the best fit of the model to selected data from the literature.

Wavelength-dependent magnification and polychromatic image quality in eyes corrected for longitudinal chromatic aberration

Theoretical calculations using a simple model eye in combination with achromatizing lenses or artificial pupils show that correcting wavelength-dependent refractive error or its effects can exaggerate wavelength-dependent magnification by up to a factor of 7. These calculations are confirmed experimentally, and their effects on retinal image quality are modeled. Because of the increased wavelength-dependent magnification, gains in polychromatic image quality produced by correcting wavelength-dependent refractive error (or minimizing its effects with small pupils) are generally restricted to a small region of the retina.