A MUTATION IN THE RAT ADENOMATOUS POLYPOSIS COLI GENE WITHIN THE HUMAN MUTATION HOTSPOT REGION

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This invention claims priority to U.S. Provisional Patent Application Serial No. 60/732,732 filed November 1 , 2005.

GOVERNMENT INTERESTS

[0002] This invention was made with United States government support under grant No. CA106216 awarded by the NIH. The United States may have certain rights in this invention.

FIELD OF THE INVENTION

[0003] This invention is related to tumor-susceptible non-human animals and to the use of such animals in identification of anti-tumor agents.

BACKGROUND OF THE INVENTION

[0004] Familial adenomatous polyposis (FAP) is an inherited condition in which numerous polyps form mainly in the epithelium of the large intestine. While these polyps start out benign, malignant transformation into colon cancer occurs when the polyps are not treated. FAP can occur due to mutations in the Adenomatous Polyposis CoIi (Ape) gene. The product of the Ape gene is a 300 kDa cytoplasmic protein associated with the adherence junction protein catenin. Humans with mutations in the Ape gene get hundreds to thousands of adenomas in the colon and typically develop colorectal cancer.

[0005] Experimental analysis of human colon cancer aims to develop an accurate model for studying tumor initiation, progression, and potential treatments. Much of modern cancer research is predicated on the establishment of animal tumor models, in particular rodent models. Murine (mouse) models are widely used. Traditionally, the rat has been favored for physiological studies while the mouse has been preferred for genetics.

[0006] One of the most widely distributed mouse models for studying human intestinal cancer is the Apc ^Mm (Min) mouse, with a two month growth period for macroscopically visible, countable tumors. The Apc^ ^m mouse was obtained through the use of chemical mutagenesis using N-ethyl-N- nitrosourea (ENU), and was described by Moser et al., 1993, Proc. Natl. Acad. Sci. USA 90: 8977-8981. The Apc ^mn mutant mice carry a single nonsense mutation in the adenomatosis polyposis coli {Ape) gene that results in a multiple intestinal neoplasia (Min) phenotype in affected mice - hence the name Apc ^Mn .

[0007] While the Ape gene is typically altered in humans similarly affected by colorectal tumors, there are important differences between the manifestations of the disease in humans and mice. The Min mouse and related mouse models including Apc ^1638N/+ and Apcf ⁷¹⁶ are not without their disadvantages. One of the main criticisms of the models is that the tumors arise primarily in the small intestine, in contrast to the colonic localization in human FAP patients. Mice are rarely used as models in major animal drug trials owing to their small size, short life span, and low amounts of recoverable plasma. Additionally, Min mice do not develop metastases to distant sites. Finally, mouse chromosomes are acrocentric, yet the analysis of mechanisms of loss of heterozygosity requires data on both arms of a metacentric chromosome. Although the Rb(7.18)9Lub metacentric fusion line of mice provides a means to confirm somatic recombination in the Min mouse (Haigis

and Dove, 2003, Nat. Genet. 33: 33-39), this translocation does not reflect the natural state, and the mice have a low colonic tumor incidence and multiplicity (21 % incidence, <0.4 tumors per mouse). These differences are sufficiently significant to have prompted many researchers to use an alternative model, namely rats fed the colon carcinogen azoxymethane (AOM), to more closely mimic the etiology of the disease in humans.

[0008] The laboratory rat presents several advantages over the mouse: an increased size and longevity, an increased tolerance of tumor burden, and an overwhelming use for large-scale chemoprevention studies. Most important, the metacentric structure of rat chromosome 18 provides new ways to study the mechanisms of Ape loss of heterozygosity (LOH) that cannot be studied endogenously in the mouse and that cannot be manipulated in the human. The importance of the rat centers around a debate on the role of genomic instability in colon cancer, and whether genomic instability is necessary for tumor initiation, or genomic instability is acquired afterwards and either stimulates neoplastic progression or simply accumulates as the neoplasm advances. The rat could thus provide a metacentric model on which to test these hypotheses. However, at present, no embryonic stem cell lines exist for the rat, precluding knockout technology via traditional homologous recombination.

[0009] It would be advantageous to create a new animal model system for mimicking disease progression, prevention, and treatment for evaluation of human therapeutics in human intestinal cancer, including colorectal cancer. Such model system could be used for screening compounds for carcinogenic activity, as well as screening compound for carcinogenesis inhibitory activity. The present invention addresses these and other related needs.

SUMMARY OF THE INVENTION

[0010] This invention provides a mutant rat having a disruption in its Ape gene that prevents expression of a functional Ape protein, which results in increased susceptibility to tumor development in the rat's colon compared to a wild-type rat. The disruption in the Ape gene may result in tumor development in the rat's colon compared to a wild-type rat.

[0011] This invention provides a mutant rat having a disrupted Ape gene having the nucleotide sequence of Rat Genome Database ID No. 1554322 (SEQ ID NO.-16).

[0012] The disruption in the Ape gene may result in a truncated Ape protein. The endogenous Ape gene may be disrupted by mutagenesis. The mutant rat may be an inbred line. The mutant rat may be heterozygous for the disruption in the Ape gene.

[0013] The disruption of the Ape gene in the mutant rat may be a germline mutation. The germline mutation may be passed to a somatic cell.

[0014] This invention provides the offspring or progeny of a mutant rat where the offspring or progeny has inherited the disrupted portion of the Ape gene. The offspring or progeny may include a disrupted Ape gene that has the nucleotide sequence of Rat Genome Database ID No. 1554322 (SEQ ID NO:16).

[0015] This invention provides a method for screening a compound for carcinogenic activity, which includes administering the compound to a mutant rat having a disruption in its Ape gene and comparing the incidence of tumors between the mutant rat administered with the compound and a mutant rat not administered with the compound. The disrupted Ape gene may have the nucleotide sequence of Rat Genome Database ID No. 1554322 (SEQ ID NO:16). The higher incidence of tumors may be indicative of the compound

having carcinogenic activity and the lower incidence of tumors may be indicative of the compound not having carcinogenic activity. The method may include administering a compound having carcinogenesis inhibitory activity to the mutant rat.

[0016] This invention provides a method for screening a compound for carcinogenesis inhibitory activity, which includes administering the compound to a mutant rat having a disruption in its Ape gene and comparing the incidence of tumors between the mutant rat administered with the compound and a mutant rat having a tumor but not administered with the compound. The disrupted Ape gene may have the nucleotide sequence of Rat Genome Database ID No. 1554322 (SEQ ID NO:16). Lower incidence of tumors may be indicative of the carcinogenesis inhibitory activity and a higher incidence of tumors may be indicative of the compound not having carcinogenesis inhibitory activity. The method may include administering to the mutant rat a compound having carcinogenic activity. Alternatively, the method may include administering to the mutant rat a compound suspected of having carcinogenic activity. The compound may be administered before tumor development. Alternatively, the compound may be administered after tumor development.

[0017] This invention provides a method of generating a mutant rat, which includes disrupting the rat's Ape gene, where the disruption prevents expression of the Ape gene and results in tumor development in the rat's colon. The disruption may include an A to T mutation in the Ape gene changing a lysine to a stop codon at codon position 1137. The disruption may be effected by mutagenesis. The mutagenesis may be chemical mutagenesis. The chemical mutagenesis may be effected using N-ethyl-N-nitrosourea. Alternatively, the mutagenesis may include mutagenesis using a transgenic

construct. The transgenic construct may include the nucleotide sequence deposited under ID 1554322 in the Rat Genome Database.

[0018] This invention provides an isolated nucleic acid comprising the nucleotide sequence of Rat Genome Database ID No. 1554322 (SEQ ID NO:16). The invention provides a vector that includes the isolated nucleic acid sequence SEQ ID NO:16. The invention also provides a rat embryo that includes the isolated nucleic acid sequence SEQ ID NO:16.

BRIEF DESCRIPTION OF THE DRAWINGS

[0019] Figure 1 depicts a schematic of the yeast-based screening protocol that was used for screening of DNA mutations in the ENU-mutagenized rats.

[0020] Figure 2 depicts sequence trace of the founder rat showing heterozygosity for the A→T transversion at nucleotide 3409 of Ape (top) compared to a wild-type littermate (bottom).

[0021] Figure 3 illustrates a cross-species alignment of 50 amino acids surrounding the Pirc mutation.

[0022] Figure 4 is a schematic diagram of the human APC (hAPC) protein domains.

[0023] Figure 5 shows images of colonic tumors that have developed in Pirc rats.

[0024] Figure 6 depicts images showing the histological and gross appearance of Pirc tumors.

[0025] Figure 7 illustrates LOH analysis for chromosome 18 on (F344xWF) F1 and F2 tumors.

[0026] Figure 8 illustrates aCGH analysis of colon tumor and normal genomes.

DETAILED DESCRIPTION OF THE INVENTION

[0027] The practice of the present invention employs, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry, immunology, protein kinetics, mass spectroscopy, and microscopy, which are within the skill of art. Such techniques are explained fully in the literature, e.g. in Sambrook et al., 2000, Molecular Cloning: A Laboratory Manual, 3rd ed., Cold Spring Harbor Laboratory Press; Current Protocols in Molecular Biology Volumes 1-3, John Wiley & Sons, Inc.; Kriegler, 1990, Gene Transfer and Expression: A Laboratory Manual. Stockton Press, New York; Dieffenbach et al., 1995, PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, each of which is incorporated herein by reference in its entirety.

[0028] Generally, the nomenclature and the laboratory procedures in recombinant DNA technology described below are those well known and commonly employed in the art. Standard techniques are used for cloning, DNA and RNA isolation, amplification and purification. Generally, enzymatic reactions involving DNA ligase, DNA polymerase, restriction endonucleases and the like are performed according to the manufacturer's specifications. Procedures employing commercially available assay kits and reagents are typically used according to manufacturer-defined protocols unless otherwise noted.

[0029] The terms "a", "an", "the" and the like, unless otherwise indicated, include plural forms.

[0030] The term "nucleic acid" or "polynucleotide sequence" refers to a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5' to the 3' end. Nucleic acids may also include modified nucleotides that permit correct read-through by a polymerase and do not alter expression of a polypeptide encoded by that nucleic acid.

[0031] The phrase "nucleic acid sequence encoding" refers to a nucleic acid which directs the expression of a specific protein or peptide. The nucleic acid sequences include both the DNA strand sequence that is transcribed into RNA and the RNA sequence that is translated into protein. The nucleic acid sequences include both the full length nucleic acid sequences as well as non- full length sequences derived from the full length sequences. It should be further understood that the sequence includes the degenerate codons of the native sequence or sequences which may be introduced to provide codon preference in a specific host cell.

[0032] The term "coding sequence" or "coding region" refers to a nucleic acid molecule having sequence information necessary to produce a gene product, when the sequence is expressed.

[0033] The term "genomic sequence" or "genome" refers to the complete DNA sequence of an organism.

[0034] The term "nucleic acid construct" or "DNA construct" is sometimes used to refer to a coding sequence or sequences operably linked to appropriate regulatory sequences so as to enable expression of the coding sequence, and inserted into a expression cassette for transforming a cell. This term may be used interchangeably with the term "transforming DNA" or "transgene". Such a nucleic acid construct may contain a coding sequence for a gene product of interest, along with a selectable marker gene and/or a reporter gene.

[0035] The term "label" refers to a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, useful labels include ³² P, fluorescent dyes, colorimetric labels, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or quantum dots. As used herein, the term "label" also includes indirect labeling of proteins using detectable labels bound to

other molecules or complexes of molecules that bind to a protein of interest, including antibodies and proteins to which antisera or monoclonal antibodies specifically bind. As used herein, the term "colorimetric label" includes a label that is detected using an enzyme-linked assay.

[0036] The phrases "disruption of the gene" and "gene disruption" refer to a mutation of the native, endogenous DNA sequence (usually one or more exons) and/or the promoter region of a gene so as to decrease or prevent expression of that gene in the cell as compared to the wild-type or naturally occurring sequence of the gene. Disruption of the Ape gene refers to a mutation of the Ape gene so as to decrease or prevent expression of the Ape gene. A mutant rat with a disrupted Ape gene is a rat that no longer expresses the Ape gene, or expresses the Ape gene at a decreased level as compared to the wild-type or naturally occurring sequence of the Ape gene.

[0037] The term "knockout" or "gene knockout" refers to partial or complete suppression of the expression of at least a portion of a protein encoded by an endogenous DNA sequence in a cell. The term "knockout rat" refers to a genetically engineered rat one or more of whose genes have been made inoperable through a gene knockout.

[0038] A "transgenic construct" is a recombinant construct that includes the disrupted Ape nucleotide sequence. For example, a "transgenic construct" may refer to a nucleic acid sequence that is designed to decrease or suppress expression of a protein encoded by endogenous DNA sequences in a cell. The nucleic acid sequence used as such transgenic construct is typically comprised of (1) DNA from some portion of the gene (exon sequence, intron sequence, and/or promoter sequence) to be suppressed and (2) a marker sequence used to detect the presence of the transgenic construct in the cell. The transgenic construct is inserted into a cell, and integrates with the genomic DNA so as to prevent or interrupt transcription of

the native DNA sequence. Such insertion usually occurs by homologous recombination (i.e., regions of the transgenic construct that are homologous to endogenous DNA sequences hybridize to each other when the transgenic construct is inserted into the cell and recombine so that the transgenic construct is incorporated into the corresponding position of the endogenous DNA). The transgenic construct nucleic acid sequence may include a full or partial sequence of one or more exons and/or introns of the gene to be suppressed, a full or partial promoter sequence of the gene to be suppressed, or combinations thereof. The transgenic construct can be inserted into a recombinant or expression vector. The transgenic construct can be inserted into an embryonic stem cell (ES cell) and is integrated into the ES cell genomic DNA, usually by the process of homologous recombination. This ES cell is then injected into, and integrates with, the developing embryo.

[0039] The terms "rodent" and "rodents" refer to all members of the phylogenetic order Rodentia including any and all progeny of all future generations derived therefrom.

[0040] The term "murine" refers to any and all members of the family Muridae, including rats and mice.

[0041] The term "isogenic" refers to an inbred line characterized by essentially identical genes.

[0042] The term "colon" refers to the part of the intestine that extends from the cecum to the rectum.

[0043] The terms "progeny" or "offspring" refer to any and all future generations derived and descending from a particular mammal, and in particular, to a rat containing a mutation in the Ape gene. Thus, progeny of any successive generation are included herein such that the progeny, the F1 , F2, F3, generations and so on indefinitely are included in this definition.

[0044] The term "germline mutation" is any detectable, heritable variation in the lineage of germ cells. Mutations in these cells are transmitted to offspring.

[0045] The term "congenic" refers to organisms that genetically differ in one locus. Foi^ example, congenic rats are generated by mating two inbred rat strains, and backcrossing the descendants a number of generations with one of the strains, the recipient strain. Conversely, the strain that contributes the smallest amount of genetic material is termed the donor strain.

[0046] The term "carcinogen" refers to any substance or agent that promotes cancer.

[0047] A compound "having carcinogenesis inhibitory activity" refers to a compound that is capable of preventing carcinogenesis and/or inhibiting growth of tumors.

[0048] Optimal alignment of sequences for comparison may be conducted by methods commonly known in the art, e.g., the local homology algorithm (Smith and Waterman, 1981 , Adv. Appl. Math. 2: 482-489), by the search for similarity method (Pearson and Lipman 1988, Proc. Natl. Acad. Sci. USA 85: 2444-2448), by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), Madison, Wl), or by inspection.

[0049] Protein and nucleic acid sequence identities are evaluated using the Basic Local Alignment Search Tool ("BLAST") which is well known in the art (Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. USA 87: 2267-2268; Altschul et al, 1997, Nucl. Acids Res. 25: 3389-3402). The BLAST programs can be used with the default parameters or with modified parameters provided by the user.

[0050] The particular gene that is the subject of the present invention is Ape (Adenomatous Polyposis CoIi), which is involved in familial colon cancer.

[0051] The present invention provides mutagenized rat that simulates or mimics human colon cancer, and can thus be used as a valuable model system for studying human colon cancer. This invention provides a Pirc rat (the terms "Pirc" - "Polyposis in the Rat Colon" or Apc ^Piro are used interchangeably herein), a rat knockout model of human familial adenomatous polyposis. The Pirc rat has a disrupted Ape gene. Preferably, the Pirc rat has a single point mutation with an A to T transversion changing a lysine to a stop codon at codon 1137 in the polypeptide encoded by the Ape gene. Thus, functional Ape protein is not expressed in somatic cells of the mutant rat.

[0052] This invention provides the isolation of a truncating mutation of the Ape gene in rats. The mutation of the Ape gene in rats can be somatic or germline. Preferably, the truncating mutation of the Ape gene in rats is a germline mutation.

[0053] Knockout (i.e. loss-of-function or change-in-function) rats can be produced by methods known in the art, such as somatic ENU treatment described in the examples below and in Moser et ai, 1993, Proc. Natl. Acad. Sci. USA 90: 8977-8981 , ENU mutagenesis followed by the screening of genes of interest by direct sequencing (Smits et ai, 2006, Trends Genet. 22: 232-240), or by a colorimetric yeast assay (Zan etal., 2003, Nat. Biotechnol. 21 : 645-651). A broad screen-based method of chemically mutagenizing rodents to produce either germline or autologus mutations can be used to obtain knockout rats, as disclosed in U.S. Patent Application No. 2003/0150001. This method is unusual in that animals are administered mutagen (e.g., by feeding), rather than produced transgenically, and then screened for the presence of mutations in desired genes rather than selected by virtue of their phenotype. A method of identifying a mutation in a gene of interest is then used, such as the method disclosed in US Patent No. 5,994,075. For example, a founder of the Pirc rat kindred can be identified by

screening. genomic DNAs from the progeny of λ/-ethyl-λ/-nitrosourea (ENU) treated males for truncating mutations in Ape. The mutagenized males can be selected from an inbred line of rats, e.g. the inbred Fisher-344 line of rats. Screening can be performed using a yeast gap-repair, ADE2-reporter truncation assay. Rats can also be mutagenized using target-selected mutagenesis (Smits et al., 2004, Genomics 83: 332-334).

[0054] Preferably, about 2530 bases of Ape exon 15 are amplified with chimeric primers for the rat Ape sequence carrying homology to a "universal vector" that accepts any such chimeric amplicon. The amplicon is then gap- repaired into the universal vector and transformed into ADE2-deficient yeast. Screening of the F1 progeny is performed to yield a single plate with half red, half white colonies; this is the expected ratio for a heterozygous mutant. The mutation in this Pirc rat is then confirmed by sequencing. Preferably, the mutation is at nucleotide position 3409 of the Ape gene, creating a K to X ^am (AAG to TAG) change, thereby creating a stop codon at position 1137. This Pirc (Apc ^Pιrc ) allele is registered in the Rat Genome Database (RGD) and RGDJD 1554322 has been assigned to it. It is shown here as SEQ ID NO:16.

[0055] The present invention also provides the offspring or progeny of the Pirc rat. The mutation in the Pirc rat of this invention has been successfully transmitted to more than 60 offspring, and to 5 progeny generations.

[0056] The Pirc rat can be used for screening of carcinogens and promoters of carcinogenesis. Thus, the present invention provides a method for screening a compound for carcinogenic activity using the Pirc rat of this invention.

[0057] The Pirc rat can also be used for screening of compound for carcinogenesis inhibitory activity. Thus, the present invention provides a

method for screening compound for carcinogenesis inhibitory activity, using the Pirc rat of this invention.

[0058] The screening of compounds for carcinogenesis activity and/or screening of compounds for carcinogenesis inhibitory activity can include longitudinal studies on a set of tumors within a rat, whose addresses are established by imaging (e.g. microCT, microPET) or endoscopy on the living rat. The endoscope permits to obtain pinch or snare biopsies from tumors. Sufficient DNA can be obtained from these biopsies to carry out Pyrosequencing using primers that flank the informative SNP sites in a heterozygote carrying the Pirc mutation. Tumor volume calculations can be done in Amira 4.1 (Mercury Computer Systems, Inc., Chelmsford, Massachusetts).

[0059] The inhibitory or the carcinogenic activity of compounds can be determined by the calculation of tumor multiplicity in experimental animals versus control untreated animals. Comparison between tumors at different stages can be performed. Furthermore, each rat provides in the range of 5 to 10 colonic tumors to study. If the tumors were independent across animals, this would reduce by a factor of 5 to 10 the number of animals needed. Independence will not be assumed, but even accounting for correlation within animals, the overall sample size required is reduced compared to a standard experimental design.

[0060] The analysis of tumor response on the basis of endoscopic, microCT, and microPET images can be validated by establishing the confidence limits of these measurements. The first step of validation is to measure the coefficient of variation in a series of replicate measurements on the same tumor by each modality. This coefficient of variation is expected to differ for different sizes of tumors, and perhaps for different biological classes. The microPET images can also vary with the batch of radiolabeled probe.

Overall, no rigorous conclusion can stand if it is based upon differences that are not significantly different from the salient coefficient of variation of the measurement. A precaution that can routinely be taken in measurements that could involve observer bias is to score blind to the identity of the sample.

[0061] To the inventors' knowledge this is the first mutant rat to be generated on a completely inbred line. The Pirc rat can be used as a cancer "test" model for multiple purposes. In principle, it is possible to treat the Pirc rat with various carcinogens, agents for treatment and prevention of carcinogenesis, biomarkers, labels, modifiers, or to subject the Pirc rat to various types of surgery, in order to study colorectal tumor initiation, progression, and potential treatments. These studies could then be used as bases for treatments of humans that have developed colorectal cancer, or are susceptible to developing one. One skilled in the art will know to cross the Pirc rat with other rat strains, transgenic rats, and knockouts, to generate a cross of the Pirc mutation into other desirable genetic backgrounds. The resulting progeny can be used for a variety of assays related to colorectal tumor initiation, progression, and potential treatments. Therefore, the Pirc rat kindred will enhance our ability to study the development, progression, physiology and treatment of disease.

Some advantages of the Pirc rat over prior models

[0062] Much of modern cancer research is predicated on the establishment of tractable and quantitative animal tumor models, in particular rodent models. (Nakagama et ai, 2005, Cancer Sci. 96: 627-636). Some of the reasons for the value of the Pirc rat are highlighted in a recent article that provides a systematic review and meta-analysis of colon chemoprevention in rats, mice, and men, and discusses the suitability of rodent models of carcinogenesis in predicting efficacy in humans (Corpet and Pierre, 2005, Eur. J. Cancer 41 :

1911-1922). Some of the advantages of the Pirc rat over prior models for colon chemoprevention are highlighted below. Pirc rats in accordance with this invention have one or more of these advantages.

[0063] Ape, the gene mutated in the Pirc rat, is the primary gene mutated in both sporadic and familial human colon tumors. Min, the analogous mouse model of colorectal cancer, the first mouse model of cancer that developed tumors that are easily observed, develops 0-4 colonic tumors, but has a short lifespan (3-6 months) owing to >40 small intestinal adenomas. In contrast, Pirc rats develop 3-6 colonic tumors with a long lifespan (>8 months) owing to <10 small intestinal adenomas, allowing for better assessment of tumor progression. In this respect at least, the Pirc rat is superior to the Min mouse. It is also the first knockout rat that develops such easily viewable tumors.

[0064] The Pirc rat is already on an inbred Fischer-344 background, which permits its study under genetically homogenous inbred conditions and a broad range of F344 /4pc ^Pιrc/+ x (i.e., other inbred) conditions. The heterozygous mutation is transmissible in normal Mendelian ratios.

[0065] Table 1 compares human /Ape-derived colorectal cancer, the Apc ^Mm mouse, the AOM rat models (rat + carcinogen), and the rat model of this invention (Pirc rat). Ranges are for strain averages, not for individual animals. The founding mutation in -100% of human FAP and Min mouse intestinal tumors is in the Ape gene, but -50% of carcinogen-induced rat tumors have the founding mutation in the beta-catenin gene. Chromosome status is important because it might affect the rate at which the Ape mutation undergoes loss of heterozygosity. The majority qf data for carcinogen-treated rats uses time points later than 10 months of age.

Table 1, Colorectal cancer phenotype comparisons

[0066] Current rat models of colon cancer induced by chemical carcinogens such as AOM, DMB, and PhiP have significant limitations: they require long-term (>8 months) time for development of tumors versus <6 months for the Pirc rat; they develop an average of less than one tumor per animal, versus an average of five tumors in the Pirc rat. The existence of more tumors per animal translates to fewer animals needed for statistical significance. Also, few of these chemically-induced tumors (<20%) develop from a mutation in the Ape gene, versus -100% of tumors in the Pirc rat. The current rat models also require administration of carcinogens for all rats, whereas Pirc rats require no treatment for the development of tumors, decreasing costs and time investments. Finally, they have inconsistent results due to differences in administration and dose responses, again requiring more animals to create a statistically significant result, versus a tight distribution of tumor multiplicity in Pirc rats.

[0067] Existing rodent models for colorectal cancer do not fully recapitulate progression of the disease in humans. The rat model affords a much greater opportunity to understand disease progression and potentially efficacy of new treatments envisioned for humans. In short, the new Ape rat model more effectively mimics the genotypic and phenotypic human disease than either the Apc ^Mm mouse or the AOM rat models. Shown in Table 2 are some of the phenotypic advantages that the Pirc rat provides in comparison to other known carcinogen-treated rats.

Table 2. Comparative advantages of known carcinogen-treated rats and the

Pirc rat of the present invention

[0068] The Pirc rat of this invention does not have to have all of the above advantages over prior models for colon chemoprevention. The Pirc rat has at least one of the above advantages over prior models.

[0069] The following examples are offered to illustrate, but not to limit the claimed invention.

EXAMPLES

[0070] Rats. Rats were maintained in standard, non-microisolator cages. Rats were fed either 5020 chow (Purina, St. Louis, MO) or 8604 chow (Teklad, Madison, Wl) with access to an automatic water supply. The following rat strains were used: F344/NTac; WF/NHsd; and SD/Hsd. The colons of 3 rats were perfused with PBS to stretch the muscularis into a flat sheet. The square area of each was measured with a ruler and used to normalize the square area of non-perfused colons to perfused ones. Tumors per square area were then calculated and averaged and the histology was assessed.

[0071] Colorimetric Yeast Assay. The N- Ethyl- /V- Nitrosourea (ENU) treatment of male rats for the mutagenesis screen was performed as previously described (Zan et al., 2003, Nat. Biotechnol. 21 : 645-651 ). F344 males were given an injection of 60 mg/kg of ENU once per week for two weeks.

[0072] Long-range PCR off of genomic DNA was performed using the following primers: Forward: GGC CAT CGA TAG CTC GAT GTA ACG TGC AGT TAA CGC CCA TGT CTC CTG GCT CAA GTT TGC (SEQ ID NO:1 ) and Reverse: CCT ACT AAC AGA TAC GCT ATG CAG GAC TCT GGA TTG CCC TGT TGG CAT GGC TGA AAT AA (SEQ ID NO:2). The final PCR reaction concentration mix was: 1 x Herculase Hotstart Buffer (Stratagene, La JoIIa, California), 0.2 mM dNTPs, 25 ng/μl of each primer, 0.15 U/μl Hotstart High Fidelity DNA Polymerase (Stratagene), 2 μl of genomic DNA, and ddH ₂ O to 10 μl. PCR conditions were: 94°C for 2 min, then 35 cycles of: (94°C for 45 min, 61 ⁰ C for 45 min, 72 ⁰ C for 2 min 30 sec) with a final elongation step of 72°C for 10 min. PCR products were confirmed by gel electrophoresis and cotransformed into yeast along with the universal vector (Chen and Gould, 2004, Biotechniques 37: 383-388).

[0073] Genotyping of λpc ^am1137/+ Animals. Two PCR/restriction enzyme digestion methods were developed to genotype the mutant SNP site of the Apc ^amU37 allele. One amplicon results in the mutant allele being cut by Nhe\ and one results in the wild type allele being cut by HincλU. Both work by introducing the restriction enzyme recognition sites into the primers. These complementary methods control for incomplete digests.

[0074] The primer sequences were as follows: for the Nhe\ amplicon, Forward: GGA AGA CGA CTA TGA AGA TGG (SEQ ID NO:3) and Reverse: TGC CCT GTA CTG ATG GAG (SEQ ID NO:4). For the HindUl amplicon, Forward: AAT AAC GTT CAC TGT AGT TGG TAA GCT (SEQ ID NO:5) and Reverse: AGG CAA TCA AGA AGC CAG AA (SEQ ID NO:6).

[0075] MicroCT and Endoscopy. Normal chow was replaced with a non- solid diet the night before microCT imaging. Anesthesia was administered through the regulated flow of isoflurane vapor (1-2%) through a nose cone. The colon was flushed with a warm PBS enema (40 cc). The colon was insufflated with air (20-40 cc), and microCT and endoscopic images were acquired on a Siemens MicroCAT-2 scanner. Acquisition proceeded for 8 minutes (80 kVp, 500 μA, 400 steps, 1 frame/view, 360 degree rotation, 93x93x100 μm voxel size) and reconstruction was done via Shepp-Logan filtered, back-projection. Amira (v 4.1 , TGS, Inc., San Diego, CA) software was used for 2- and 3-dimensionai image visualization and media production. Ex vivo imaging of excised colons was accomplished by filling the colon with barium as a contrast agent and tying off the ends.

[0076] Endoscopy was performed using an EG-1870K 6.0 mm color CCD chip videogastroscope and an EPK 1000 videoprocessor (Pentax Medical, Montvale, NJ). The image was captured on the workstation and photographed with an Olympus Camedia C-5050ZOOM digital camera using automatic exposure.

[0077] Somatic ENU treatment. ENU was dissolved in 95% EtOH and measured with a spectrophotometer at OD ₃ g _8mm to obtain a final concentration of 1 mg/ml. Either the ENU solution or 95% EtOH was injected intraperitoneal^ into 13-20 day old rats at 18 or 40 mg/kg of body mass. Treated animals were isolated in a laminar flow hood for at least three days before being returned to normal housing.

[0078] Immunofluorescence. Immunofluorescence was performed by first de-waxing the slides in xylene, rehydrating through an EtOH series, and boiling for 25 min in 0.01 M citrate buffer, pH 6.0. After washing in PBS, slides were incubated for 1 hour at 37 ⁰ C with the following primary antibodies: anti- mouse β-catenin-TRITC mAb (Transduction Laboratories, Lexington, KY) at 1 :200 and anti-human Ki-67 pAb (Novacastra, Newcastle, UK) at 1 :100. After washing in PBS, 0.1% Tween-20, slides were incubated for 1 hour at 37°C with the following secondary antibodies: goat anti-mouse Alexafluor-594 (Molecular Probes, Eugene, OR) at 1 :200 and donkey anti-rabbit Alexafluor- 488 (Molecular Probes) at 1 :200.

[0079] After washing in PBS, 0.1% Tween-20, slides were incubated for 5 min with DAPI, mounted, and sealed. Images were taken with a Zeiss Axiocam HRm camera mounted on a Zeiss Axiovert 200M inverted microscope. Images were taken with Axiovision software (v4.5.0.0).

[0080] Methylene Blue Staining. 0.5% methylene blue was heated until all particles were dissolved, then cooled to room temperature. Fixed intestines were placed into the methylene blue for 15-30 seconds, then washed in 70% methanol for 5-10 minutes.

[0081] Sanger Sequencing. Primers were digested away from the PCR amplicon of interest with Exonuclease I by adding the following mix to the PCR: 3.3 U/μl of Exonuclease I (Epicentre, Madison, Wl), 1.7 U/μl of shrimp alkaline phosphatase (Roche, Basel, Switzerland), and ddH ₂ O to 1.5 μl.

Reactions were incubated at 37 ⁰ C for 45 min and heat inactivated at 85°C for 15 min. Big Dye Terminator Mix (Applied Biosystems, Foster City, CA) and 5x sequencing buffer (Applied Biosystems) were added at a 2:3 ratio, along with 6.6 mM sequencing primer. The reaction was then purified on Sephadex G-50 columns (Roche) and submitted to the UW-Madison Biotechnology Center. Samples were run on an Applied Biosystems 373OxI automated DNA sequencing instrument and results were analyzed using the DNAstar (Madison, Wl) software.

[0082] Pyrosequencing. Formalin-fixed tumors were excised under a dissecting microscope to minimize contamination from non-tumor tissue. The bottom one-fourth of the polyp including the muscularis and any surrounding hyperplastic villi were excluded to enrich for tumor regions likely to exhibit Ape loss and β-catenin upregulation. Excised tissue was incubated overnight in distilled water at 65 ⁰ C to reverse formalin cross-links. 100 mM NaOH was added to a final concentration of 50 mM and samples were incubated at 95°C for at least four hours. Tris-HCI, pH 5.5 was then added to neutralize the solution and the samples were briefly centrifuged. The final PCR mix concentrations were as follows: 1X GoTaq clear buffer, 1.2 mM MgCI ₂ , 0.2 mM dNTPs, 264 pM of each primer, 0.6 U of GoTaq Flexi (Promega, Madison, Wl), 8 μl of DNA, and ddH ₂ O to 50 μl. The PCR cycling profile was: 94°C for 3 min, followed by 50 cycles of: (94°C for 15 sec, 57 ⁰ C for 1 min 30 sec, 72 ⁰ C for 2 min) with a final elongation step of 72 ⁰ C for 10 min.

[0083] Pyrosequencing was performed according to the manufacturer's protocols using Pyro Gold Reagents on a PSQ96MA machine and PSQ 96MA v2.1 software (Biotage, Uppsala, Sweden). 40 μl of PCR product were used per well and only sequence reads with single base peak heights of over 120 units were included.

[0084] Primer sequences were as follows: for the Apc ^am1137 SNP, Forward: ATG TGA ACC AGT CTT TGT GTC AG (SEQ ID NO:7); Reverse (biotinylated): ATG CTG TTC TTC CTC AGA ATA ACG (SEQ ID NO:8); Sequencing: GGA AGA CGA CTA TGA AGA T (SEQ ID NO:9). For the p arm SNP (dbSNP ss48531311), Forward: GTG GAA ACG AAG CAT CAT TCT GA (SEQ ID NO:10); Reverse (biotinylated): TGC TGT TCT AAA TTG CAC GTT TAC (SEQ ID NO:11); Sequencing: CGT ATT GGG TTG TGA GA (SEQ ID NO:12). For the c/ arm SNP (dbSNP ss48531727), Forward (biotinylated): TCA AAC AGA AGG CAG TTT ATT CAG (SEQ ID NO:13); Reverse: GGG GGT AAA ATA ATA TGC CGA GA (SEQ ID NO:14); Sequencing: TCT TAG TAA TGT ACC AGA TG (SEQ ID NO: 15).

[0085] An LOH/MOH cutoff value of 32.8% was determined by adapting the normal mixture technique from Shoemaker et al., 1998, Proc. Natl. Acad. Sci. USA 95: 10826-10831. Tumor data (n=114) were considered to arise either from an LOH normal component or an MOH normal component, according to some mixing probability. Control data came from a known MOH component (normal Pirc epithelium n=10). Then, using the fitted mixture model, a critical signal intensity value c was determined so that Prob[ intensity > c | LOH ] = .05 . In the estimated normal mixture, the LOH component had mean 16.2 and standard deviation 8.0; the MOH component had mean 43.2 and standard deviation 3.5; and an estimated fraction 84% of tumors were LOH. From this the critical signal value was c = 32.8. Modes of the likelihood surface at the boundary of the parameter space were avoided. Computations were done in R (R Development Core Team, 2005, R: A language and environment for statistical computing; available at http://www.R-project.org).

[0086] Identification of the λpc ^am1137 Mutation. The mutation was generated by treating a male Fischer-344 rat with ENU, and mating it to a female Fischer-344 rat. The resulting progeny carried a subset of the

mutations induced in the original male's sperm. The DNA was then extracted from these progeny (founders) and screened for mutations.

[0087] Figure 1 depicts how a segment of 2530 base pairs of exon 15 of the rat Ape gene from genomic DNA in the offspring of mutagenized Fisher- 344 inbred rats was screened. The method of screening for the mutant rats using a universal vector gap repair yeast truncation assay is described in Chen and Gould, 2004, Biotechniques 37: 383-388.

[0088] A 2.5 kb portion of the Ape gene was PCR amplified from the progeny and inserted into a yeast vector. The vector was transformed into yeast and plated on Ade2-indicator plates. If the Apc-Ade2 fusion transcript was normal, a large white colony was formed. If the fusion transcript was interrupted by an ENU-induced stop codon in Ape, then the loss of Ade2 allows the accumulation of a red substrate in the yeast, giving rise to a small red colony. The Pirc founder rat exhibited a yeast plate with -50% red colonies, indicating that a heterozygous stop codon mutation had been induced in the 2.5 kb region of the APC gene by ENU. The wild-type sibling rat used for comparison had a wild- type distribution of -13% red colonies (due to background "noise").

[0089] Screening of 1360 progeny yielded a single mutant with an A to T transversion changing a lysine to a stop codon at codon 1137 (see Apcf ^m1137 in Figure 2). The founder male successfully transmitted the mutation to progeny. Ten of the resulting mutant N1 animals were brother-sister mated and their offspring confirmed that the Pirc allele is homozygous lethal. Necropsy of three N1 Pirc heterozygotes, two at 90 days and one at 120 days of age, identified an average of 5 visible adenomatous polyps in the colon, while three wild type age-matched littermates were tumor-free.

[0090] The founder Pirc male rat harbored a heterozygous point mutation at nucleotide 3409 of Ape, creating a K→X ^am (AAG→TAG) change at codon

1137 (Figures 2 and 3). No other mutations were found after sequencing the entire coding region and intron-exon junctions 5' of the mutation. This allele was named Apc ^pirc or Apc ^amU37 . The predicted APC protein would be truncated at the third amino acid of the second 15-amino acid β-catenin binding domain (Figure 3), which is highly conserved among vertebrates.

[0091] Figure 3 shows a cross-species alignment of 50 amino acids surrounding the Pirc mutation. Note the conserved 15 amino acids (boxed) that indicate the β-catenin binding domain. The Pirc mutation (K to X, i.e. lysine to a stop codon) is located in that β-catenin binding domain.

[0092] A diagram of the known domains of the human Ape protein is shown in Figure 4 with the positions of the most well-known mutations in human and mouse (and the mutant Pirc rat, this invention) marked across the diagram. The 15 amino acid and 20 amino acid binding repeats circled are the beta- catenin binding regions. It is possible that loss of Ape function results in upregulation of the oncogenic beta-catenin protein, inducing tumors. The Pirc rat therefore has a nonsense mutation that results in truncation of the protein and loss of almost all of the beta-catenin binding domains.

[0093] Also shown in Figure 4, under the protein diagram, is a graph of modal tumor multiplicities from human familial adenomatous polyposis (FAP) patients as compared to where their truncating mutation lies. Thus, the Pirc rat mutation lies in an area analogous to a fairly severe FAP phenotype.

[0094] The Apc ^amλλ37 Mutation is not Lethal. Apc ^amV[37/+ animals were intercrossed on either an inbred F344/NTac (F344) or a [F344 x WF/NHsd (WF)] F1 background, to determine whether this Apcf ^mn37 mutation is homozygous lethal. No homozygous mutants were obtained out of 71 total progeny, with heterozygotes and wild-type progeny exhibiting a 2:1 Mendelian ratio (49:22). Thus, the Ap& ^mλλZ7 allele is homozygous lethal on two genetic backgrounds. In the formal possibility that this lethality is caused by a second

ENU-induced mutation, it would lie within 2.5cM (95% Cl) of the Apc ^amU37 mutation.

[0095] Consideration of the possibility that lethality is due to a second mutation X linked to Pirc. The data taken together strongly support the contention that Pirc is homozygous lethal; however, the possibility that the lethality is due to a second mutation X linked to Pirc was considered. If X is r recombination units from Pirc, the probability of observing a Pirc homozygote at the kth generation, conditional on non-XX parents (P(Pirc/Pirc | non-XX)), is

0.5α _k \ r- ^r / ₂ 1+ 0.25b _k + 0.5α _k b _k

0.15α _k +b _k +2α _k b _k

[0096] where a* = (1 - ή ^k and b _k = λ - a _k .

[0097] Using these probabilities, 95% confidence intervals for rcan be calculated. For example, consider the hypothesis test HO: r≥ iO against HA: r < tϋ. Each value of r0 determines P(Pirc/Pirc | non-XX), the expected proportion of Pirc homozygotes. Using this expected proportion, a Binomial test can be done assuming zero Pirc homozygotes are observed. By inverting the test (Bickel and Docksum 2001 , Mathematical Statistics Vol. I, 2nd edition, Prentice-Hall, NJ), a conservative 95% confidence interval for ris found. When k=1 and n=71 , the 95% confidence interval for r is (0, 0.0243).

[0098] Tumor phenotype segregates perfectly in 56 carriers and 23 non-carriers. Suppose the phenotype is due to a linked loci X, r recombination units from Pirc. The Binomial probability of observing no recombinations in 79 trials is 0.046 for r=0.038 and 0.00969 for r=0.057.

[0099] The phenotype of F344-Apc ^amU37/+ animals at the N1 -N3 generations was analyzed. Around 11 months of age, males became

moribund from rectal bleeding and weight loss. By contrast, females carrying this mutation have survived to over 14 months of age with no external signs of disease. Dissections at ages ranging from 88 to 397 days revealed multiple neoplasms in the small intestine and colon of both male and female heterozygotes.

[00100] The Pirc phenotype segregated perfectly with the >4pc ^am1137 allele in 56 carriers and 23 non-carriers. There is less than a 5% chance to observe this association if the phenotype were caused by a separate mutation more than 3.8cM from Ap<? ^mλm . Full necropsies of Pirc animals uncovered benign epidermoid cysts, but no other neoplasms or metastases. No significant differences in the multiplicity or phenotype of intestinal tumors were seen between successive backcross generations of the Pirc kindred on the inbred F344 background, indicating that any effects of ENU-induced modifying alleles are relatively minor.

[00101] Tumor multiplicities were determined for both adenomas and microadenomas (neoplasms less than 0.5mm in diameter). A significant dependence on gender was observed, with males developing more of both types of tumor in all regions of the intestinal tract. There was also a monotonic increase in tumor multiplicity with age, reaching an average of 14 colonic adenomas in males and 9 in females over eight months of age (Tables 3 and 4).

[00102] Shown in Table 3 are the tumor multiplicities in Pirc rats. Colonic microadenoma multiplicities could not be accurately measured without histopathological confirmation and were excluded from these analyses. Neoplasms less than 0.5 mm in size were classified as microadenomas.

Table 3. Tumor multiplicities in Pirc rats

[00103] Shown in Table 4 is the estimation of age and gender effects on tumor multiplicity. A Poisson regression was used to estimate the effects of age and gender on tumor multiplicity in F344 Pirc animals. The estimated age and gender coefficients are shown in Table 4 along with associated p- values and 95% confidence intervals for colon (C), small intestine (Sl), and small intestinal microadenomas (SITm). The results show that age and gender significantly affect each phenotype. The results were qualitatively similar when a Gaussian regression was used on a square root transformed phenotype. Results are shown for Poisson regression.

Table 4. Estimation of age and gender effects on tumor multiplicity

[00104] The incidence and multiplicity of colonic tumors is higher in the F344-Pirc rat than in carcinogen treated wild-type F344 rats or the Min mouse. Importantly, the Pirc rat addresses one of the major drawbacks of all genetic mouse models of intestinal cancer: the prominence of tumors in the small intestine. The ratio of tumor multiplicities in the colon to that in the small intestine in Pirc rats averages 1:1. By contrast, most lines of B6-Min mice have an average ratio of about 1 :40 (Table 1). The estimated polyp incidence

in the small intestine of human Familial Adenomatous Polyposis (FAP) patients ranges from 58-74% at first endoscopy and approaches 100% by 70 years (Bulow, 2004, Gut 53: 381-386), with multiplicities exceeding 80 in 17% of patients monitored with video capsule endoscopy. Thus, the distribution of intestinal tumors in the Pirc rat resembles that in FAP patients.

[00105] Thus, it was unexpectedly discovered that the rat mutation in Ape results primarily in colon tumors (Figure 5), as it does in humans. Figure 5 depicts tumors (shown in circles labeled A-D) developed in the colon. The expected result was tumor development similar to the Min mouse, which has a mutation in Ape and has tumors that occur primarily in the small intestine.

[00106] The histological and gross appearance of Pirc tumors was examined, and is depicted in Figure 6. Thus, Figure 6(a) shows H&E images of a focal adenocarcinoma with high-grade dysplasia, (b) Enlargement of the larger rectangle in panel a, showing invasion into the stalk, (c) Enlargement of the smaller rectangle in panel a, showing high grade dysplasia, as compared to normal crypts (d), from the same section, (e) H&E of a peduncular colonic adenoma, (f) β-catenin (red in original) and DAPI (blue in original) immunofluorescence of the same tumor. The dashed line delineates dysplastic tissue, i.e. tumor proper (above) and hyperplastic but non- tumorigenic tissue (below), (g) Magnification of the rectangle shown in panel f. (h, i, j) MicroCT, endoscopic, and dissection views, respectively, of three colonic tumors in an 11 -month old F344 Pirc male. Scale bars: a and e, 1 mm; j, 1 cm.

[00107] To characterize the intestinal lesions, histological examinations of sections of paraffin-embedded formalin-fixed tumors were performed. The neoplasms were identified as adenomas, adenocarcinomas in situ, or focal adenocarcinomas with invasion into the stalk (Figure 6a-d). The

histopathology and morphology of the tumors closely resembled that of the human. Tumors in the small intestine usually were flat, while colonic tumors were peduncular. Adenomas varied in size, frequently reaching 1cm in diameter in older animals, lmmunofluorescent staining of tumors revealed nuclear and cytoplasmic accumulation of β-catenin within dysplastic (abnormal) cells (Figure 6e-g) as well as upregulation of the proliferation marker Ki-67 (data not shown).

[00108] To determine whether longitudinal in vivo studies of intestinal tumorigenesis can be carried out, a 334-day old Pirc rat was anesthetized and its tumors visualized by endoscopy. A 6 mm-diameter endoscope provided clear images of three tumors with diameters 5.3 mm, 5.7 mm, and 6.8 mm. The same tumors were identified in three-dimensional microCT images and confirmed upon dissection (Figure 6h-j). This proof of principle paves the way for investigation into the sensitivity and specificity of endoscopy versus virtual colonoscopy. Endoscopy also enhances the statistical power of drug and genetic studies, minimizing the numbers of tumor-bearing rats required. Longitudinal studies of tumor progression and regression can be related to molecular profiles through endoscopic pinch biopsies of individual tumors.

[00109] The issue of whether genomic instability is necessary in early colonic neoplasms was also addressed. First, loss of heterozygosity at the Ap(? ^mU37 site on the inbred F344 background was quantitatively assayed by a novel Pyrosequencing assay. A majority of F344 tumors in the colon (87%, 34/39) and small intestine (100%, 24/24) showed loss of heterozygosity (LOH) of the wild-type Ape allele at codon 1137.

[00110] The metacentric karyotype of the rat was used to address whether the function of the wild-type Wistar-Furth (WF) allele of Ape in (F344 x WF) Pirc animals is lost through elimination of the entire WF chromosome, through homozygosis via somatic recombination, or through another genetic

or epigenetic process. Polymorphic single nucleotide polymorphisms (SNPs) on the p and q arms of chromosome 18 were assayed in tumors and in adjacent normal, heterozygous tissue from (F344xWF) F1 and F2 animals (Figure 7).

[00111] Shown in Figure 7 is LOH analysis for chromosome 18 on (F344xWF) F1 and F2 tumors. The three SNPs tested, ss48531311 (17Mb) and Apc ^amU37 (27Mb) on the p arm and ss48531727 (43Mb) on the q arm, were all heterozygous in the normal tissue. The centromere (open circle) lies at approximately the 38Mb position. LOH status at each SNP was assayed by quantitative Pyrosequencing. Five possible tumor genotypes are given (left to right): LOH involving only the two loci on the p arm, LOH involving only Apc ^amU37 , maintenance of heterozygosity at all three loci, hemizygosity for both arms (as assessed by aCGH), and homozygosis for all three loci.

[00112] If both chromosome arms exhibit LOH, whole chromosome loss with or without reduplication would be indicated. By contrast, if only one arm undergoes LOH, somatic recombination or terminal deletion would be supported. None of 22 colonic or 18 small intestinal tumors showed loss of both arms of the WF homolog. Of 16 colonic and 12 small intestinal tumors with arm-specific LOH, all loss events involved the Ape locus on the p arm, extending at least 10Mb distal in the majority of tumors. In all cases of LOH, the WF allele was lost while the F344 allele was maintained.

[00113] Array-based Comparative Genomic Hybridization (aCGH) analysis. The possibility of extended deletion of the q arm was tested by array comparative genomic hybridization (aCGH) analysis of two F344 colonic adenomas showing LOH at Ape (Figure 8). Immediately following necropsy, DNA was extracted from approximately 50 mg each of tumor and spleen tissue using the Qiagen DNeasy tissue kit. Comparative genomic hybridizations were performed by Nimblegen Systems (Madison, Wl) in their

Iceland manufacturing facilities using the Nimblegen RGSC 3.4 isothermal rat aCGH chip with 385,000 unique sequence features and a median probe density of 5303bp. Tumor and Pirc spleen DNA from the same animal were labeled with Cy5 or Cy3 and reciprocal hybridizations were performed for both tumor samples. Pirc spleen DNA was also hybridized against wild-type spleen DNA. CGH plots were generated using NimbleScan software and the data analyzed using SignalMap v1.8.

[00114] No allelic imbalance was detected over the entire genome of these tumors. Figure 8 shows aCGH analysis of colon tumor and normal genomes. Plots show the log ₂ ratio (y axis) calculated over 250 kb windows for the entire rat genome (RGSC 3.4, Nov 2004 build) by chromosome (x axis). The Pirc spleen and tumor samples were hybridized against each with Cy5 vs Cy3 labeling in both orientations. Tumors were determined to involve LOH by Pyrosequencing and calculated to be 70-80% pure. Figure 8(a) shows a Pirc spleen genomic DNA compared to wild-type spleen DNA. No significant difference is seen between the two, indicating the germline copy number variation. Figure 8(b, c) shows Pirc colon tumor genomic DNAs compared to spleen DNA from the same animal. Only one of the two labeling orientations is shown for each tumor. No statistically significant variation from the spleen was seen in either tumor sample.

[00115] The rat kindred for familial colon cancer of this invention has several features that can fuel investigations of colon cancer: the location of tumors resembles that in the human; the surface density of early neoplasms can reach the same level as in human FAP individuals; dominant polymorphic modifiers exist in rat genomes; and imaging by microCT and classical endoscopy gives access to statistically powerful longitudinal studies of tumor progression and regression.

[00116] Shown in Table 5 is an example of the use of a Pirc rat for screening a compound for carcinogenesis inhibitory activity. The effect of celecoxib on intestinal tumor multiplicity in F344 Pirc rats was tested. At about 40 days of age, Pirc rats backcrossed with F344-Tac and F334 control rats were fed celecoxib at 1200ppm diet. The rats were killed at about 22 weeks of age (about 150-160 days of age). Necropsy was performed to identify 1-2 mm tumors in the intestines.

Table 5. Use of the Pirc rat for screening the efficacy of celecoxib as a compound for carcinogenesis inhibitory activity

[00117] It is to be understood that this invention is not limited to the particular devices, methodology, protocols, subjects, or reagents described, and as such may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention, which is limited only by the claims. Other suitable modifications and adaptations of a variety of conditions and parameters normally encountered in clinical prevention and therapy, obvious to those skilled in the art, are within the scope of this invention. All publications, patents, and patent applications cited herein are incorporated by reference in their entirety for all purposes.