WO2002044344A2 - Basal cell carcinoma cultures, methods related thereto and their use - Google Patents

Abstract

The present invention relates to the discovery of methods for culturing basal cell carcinomas. In one aspect the invention provides basal cell carcinoma cultures. In other aspects, the invention provides media, screening assays and methods for making BCC cultures. The cultures, media, assays and methods of the invention will be useful, in part, for finding BCC therapeutics and allowing more sophisticated in vitro studies of BCCs.

Description

Basal Cell Carcinoma Cultures, Compositions and Methods Related Thereto

Background of the Invention Basal cell carcinoma and BCNS:

Basal cell carcinoma (BCC) is the most common form of cancer in the United States. It is predicted that nearly 1 in 3 Caucasians born in the U.S. after 1994 will develop a BCC in their lifetimes (Miller et al. (1994) J. Am. Acad. Dermatol. 30: 774-778). While spontaneous cases of BCC are very common (and typically correlated with ultraviolet light exposure), there are also familial syndromes, such as the basal cell nevus syndrome (BCNS). BCNS is characterized by the presence of many basal cell cancers as well as developmental abnormalities including rib and craniofacial alterations, abnormalities of the hands and feet, and spina bifida. These features are indicative of abnormal embryonic development. The relationship between developmental defects and basal cell carcinoma was clarified by the discovery that the hedgehog signaling pathway, a pathway critical in development of many tissue types, was also involved in BCC and BCNS.

The putative hedgehog receptor, patched, has been implicated in BCC, familial BCNS, and several other cancers. A loss of heterozygosity of chromosome 9q alleles in both familial and sporadic basal cell carcinomas suggested the presence of a tumor suppressor gene in this region. The human homologue of the patched gene was recently cloned and mapped to chromosome 9q22.3 and patched mutations were identified in a variety of neoplasms including BCC. Of twelve tumors in which patched mutations were identified with a single strand conformational polymorphism screening assay, nine had chromosomal deletion of the second allele and the other three had inactivating mutations in both alleles (Gailani, supra). The alterations did not occur in the corresponding germline DNA.

Most of the identified mutations resulted in premature stop codons or frame shifts. Lench, N.J., et al, Hum. Genet. 1997 Oct; 100(5-6): 497-502. Several, however, were point mutations leading to amino acid substitutions in either extracellular or cytoplasmic domains. These sites of mutation may indicate functional importance for interaction with extracellular proteins or with cytoplasmic members of the downstream signaling pathway.

In addition, altered activity of other members of the hedgehog signaling pathway, including sonic hedgehog and smoothened, can also lead to the formation of BCCs (Xie et al. (1998) Nature 391 : 90-2).

Given the high incidence of BCC in the general population, BCC has been the subject of substantial research. However, as noted by Fan et al., "Progress towards therapies for BCC has been impeded by the lack of accurate model systems and the difficulty of growing human BCCs in vitro." (Fan et al. (1997) Nature Medicine 3:788-92). In general, basal cell carcinomas tend to undergo apoptosis and lose the characteristics of BCC when cultured in vitro. It has been a major challenge in the field to develop culturing methods that would allow the maintenance of BCCs in a laboratory setting. TJze hedgehog signaling pathway: The hedgehog pathway was first identified for its critical role in developmental pattern formation. Members of the hedgehog family of signaling molecules mediate many important short- and long-range patterning processes during invertebrate and vertebrate development. In the fly, a single hedgehog gene regulates segmental and imaginal disc patterning. In contrast, in vertebrates, a hedgehog gene family is involved in the control of left-right asymmetry, polarity in the CNS, somites and limb, organogenesis, chondrogenesis and spermatogenesis.

The first hedgehog gene was identified by a genetic screen in the fruitfly Drosophila melanogaster (Niisslein-Nolhard, C. and Wieschaus, E. (1980) Nature 287, 795-801). This screen identified a number of mutations affecting embryonic and larval development. In 1992 and 1993, the molecular nature of the Drosophila hedgehog {hh) gene was reported {C.F., Lee et al. (1992) Cell 71, 33-50), and since then, several hedgehog homologues have been isolated from various vertebrate species. While only one hedgehog gene has been found in Drosophila and other invertebrates, multiple Hedgehog genes are present in vertebrates. The vertebrate family of hedgehog genes includes at least four members, e.g., paralogs of the single drosophila hedgehog gene. Exemplary hedgehog genes and proteins are described in PCT publications WO 95/18856 and WO 96/17924. Three of these members, herein referred to as Desert hedgehog {Dhh), Sonic hedgehog {Shh) and Indian hedgehog {Ihh), apparently exist in all vertebrates, including fish, birds, and mammals. A fourth member, herein referred to as tiggie- winkle hedgehog {Thh), appears specific to fish. Desert hedgehog {Dhh) is expressed principally in the testes, both in mouse embryonic development and in the adult rodent and human; Indian hedgehog {Ihh) is involved in bone development during embryogenesis and in bone formation in the adult; and, Shh, which as described above, is primarily involved in morphogenic and neuroinductive activities. Given the critical inductive roles of hedgehog polypeptides in the development and maintenance of vertebrate organs, the identification of hedghog interacting proteins is of paramount significance in both clinical and research contexts.

The various Hedgehog proteins consist of a signal peptide, a highly conserved N-terminal region, and a more divergent C-terminal domain. In addition to signal sequence cleavage in the secretory pathway (Lee, J.J. et al. (1992) Cell 71:33-50; Tabata, T. et al. (1992) Genes Dev. 2635-2645; Chang, D.E. et al. (1994) Development 120:3339-3353), Hedgehog precursor proteins undergo an internal autoproteolytic cleavage which depends on conserved sequences in the C-terminal portion (Lee et al. (1994) Science 266:1528-1537; Porter et al. (1995) Nature 374:363-366). This autocleavage leads to a 19 kD N-terminal peptide and a C- terminal peptide of 26-28 kD (Lee et al. (1992) supra; Tabata et al. (1992) supra; Chang et al. (1994) supra; Lee et al. (1994) supra; Bumcrot, D.A., et al. (1995) Mol. Cell. Biol. 15:2294-2303; Porter et al. (1995) supra; Ekker, S.C. et al. (1995) Curr. Biol. 5:944-955; Lai, C.J. et al. (1995) Development 121:2349-23601 The N- terminal peptide stays tightly associated with the surface of cells in which it was synthesized, while the C-terminal peptide is freely diffusible both in vitro and in vivo (Porter et al. (1995) Nature 374:363; Lee et al. (1994) supra; Bumcrot et al. (1995) supra; Mart'. E. et al. (1995) Development 121:2537-2547; Roelink, H. et al. (1995) Cell 81:445-455). Interestingly, cell surface retention of the N-terminal peptide is dependent on autocleavage, as a truncated form of HH encoded by an RNA which terminates precisely at the normal position of internal cleavage is diffusible in vitro (Porter et al. (1995) supra) and in vivo (Porter, J.A. et al. (1996) Cell 86, 21-34). Biochemical studies have shown that the autoproteolytic cleavage of the HH precursor protein proceeds through an internal thioester intermediate which subsequently is cleaved in a nucleophilic substitution. It is likely that the nucleophile is a small lipophilic molecule which becomes covalently bound to the C-terminal end of the N-peptide (Porter et al. (1996) supra), tethering it to the cell surface. The biological implications are profound. As a result of the tethering, a high local concentration of N-terminal Hedgehog peptide is generated on the surface of the Hedgehog producing cells. It is this N-terminal peptide which is both necessary and sufficient for short- and long-range Hedgehog signaling activities in Drosophila and vertebrates (Porter et al. (1995) supra; Ekker et al. (1995) supra; Lai et al. (1995) supra; Roelink, H. et al. (1995) Cell 81:445-455; Porter et al. (1996) supra; Fietz. M.J. et al. (1995) Curr. Biol. 5:643-651; Fan, C.-M. et al. (1995) Cell 81 :457-465; Mart', E., et al. (1995) Nature 375:322-325; Lopez-Martinez et al. (1995) Curr. Biol 5:791-795; Ekker, S.C. et al. (1995) Development 121:2337-2347; Forbes, A.I. et al.(1996) Development 122:1125-11351. The expression of Shh starts shortly after the onset of gastrulation in the presumptive midline mesoderm, the node in the mouse (Chang et al. (1994) supra; Echelard, Y. et al. (1993) Cell 75:1417-1430), the rat (Roelink, H. et al. (1994) Cell 76:761-775) and the chick (Riddle, R.D. et al (1993) Cell 75:1401-1416), and the shield in the zebrafish (Ekker et al. (1995) supra; Krauss, S. et α/.(1993) Cell 75:1431-1444). In chick embyros, the Shh expression pattern in the node develops a left-right asymmetry, which appears to be responsible for the left-right situs of the heart (Levin, M. et al. (1995) Cell 82:803-814).

In the CNS, Shh from the notochord and the floorplate appears to induce ventral cell fates (Echelard et al. (1993) supra; Goodrich, L.V. et al. (1996) Genes Dev. 10:301-312; Roelinlc, H. et al. (1994) supra; Ruiz i Altaba, A. et al. (1995) Mol. Cell. Neurosci. 6:106-121; Ekker et al. (1995) supra; Krauss et al. (1993) supra; Hammerschmidt, M., et al. (1996) Genes Dev. 10:647-658). In explants of intermediate neuroectoderm at spinal cord levels, Shh protein induces floorplate and motor neuron development with distinct concentration thresholds, floor plate at high and motor neurons at lower concentrations (Roelink et al. (1995) supra; Mart' et al. (1995) supra; Tanabe, Y. et al. (1995) Curr. Biol. 5:651-658). Shh from the midline also patterns the paraxial regions of the vertebrate embryo, the somites in the trunk (Fan et al. (1995) supra) and the head mesenchyme rostral of the somites (Hammerschmidt et al. (1996) supra). In chick and mouse paraxial mesoderm explants, Shh promotes the expression of sclerotome specific markers like Paxl and Twist, at the expense of the dermamyotomal marker Pax3. Moreover, filter barrier experiments suggest that Shh mediates the induction of the sclerotome directly rather than by activation of a secondary signaling mechanism (Fan, C.-M. and Tessier-Lavigne, M. (1994) Cell 79, 1175-1186).

In the vertebrate limb buds, a subset of posterior mesenchymal cells, the "Zone of polarizing activity" (ZPA), regulates anteroposterior digit identity (reviewed in Honig, L.S. (1981) Nature 291:72-73). Ectopic expression of Shh or application of beads soaked in Shh peptide mimics the effect of anterior ZPA grafts, generating a mirror image duplication of digits (Chang et al. (1994) supra; Lopez- Martinez et al. (1995) supra; Riddle et al. (1993) supra) (Fig. 2g). Thus, digit identity appears to depend primarily on Shh concentration, although it is possible that other signals may relay this information over the substantial distances that appear to be required for AP patterning (100-150 μm). Similar to the interaction of HH and DPP in the Drosophila imaginal discs, Shh in the vertebrate limb bud activates the expression of Bmp2 (Francis, P.H. et al. (1994) Development 120:209- 218), a dpp homologue. However, unlike DPP in Drosophila, Bmp2 fails to mimic the polarizing effect of Shh upon ectopic application in the chick limb bud (Francis et al. (1994) supra). In addition to anteroposterior patterning, Shh also appears to be involved in the regulation of the proximodistal outgrowth of the limbs by inducing the synthesis of the fibroblast growth factor FGF4 in the posterior apical ectodermal ridge (Laufer, E. et al. (1994) Cell 79:993-1003; Niswander, L. et al{1994) Nature 371:609-612).

The close relationship between Hedgehog proteins and BMPs is likely to have been conserved at many, but probably not all sites of vertebrate Hedgehog expression. For example, in the chick hindgut, Shh has been shown to induce the expression of Bmp4, another vertebrate dpp homologue (Roberts, D.J. et al. (1995) Development 121:3163-3174). Furthermore, Shh and Bmp2, 4, or 6 show a striking correlation in their expression in epithelial and mesenchymal cells of the stomach, the urogenital system, the lung, the tooth buds and the hair follicles (Bitgood, M.J. and McMahon, A.P. (1995) Dev. Biol. 172:126-138). Further, Ihh, one of the two other mouse Hedgehog genes, is expressed adjacent to Bmp expressing cells in the gut and developing cartilage (Bitgood and McMahon (1995) supra). Ihh appears to play a crucial role in the regulation of chondrogenic development (Roberts et al. (1995) supra). During cartilage formation, chondrocytes proceed from a proliferating state via an intermediate, prehypertrophic state to differentiated hypertrophic chondrocytes. Ihh is expressed in the prehypertrophic chondrocytes and initiates a signaling cascade that leads to the blockage of chondrocyte differentiation. Its direct target is the perichondrium around the Ihh expression domain, which responds by the expression of GH and Patched {Ptc), conserved transcriptional targets of Hedgehog signals (see below). Most likely, this leads to secondary signaling resulting in the synthesis of parathyroid hormone- related protein (PTHrP) in the periarticular perichondrium. PTHrP itself signals back to the prehypertrophic chondrocytes, blocking their further differentiation. At the same time, PTHrP represses expression of Ihh, thereby forming a negative feedback loop that modulates the rate of chondrocyte differentiation.

Patched was originally identified in Drosophila as a segment polarity gene, one of a group of developmental genes that affect cell differentiation within the individual segments that occur in a homologous series along the anterior-posterior axis of the embryo. See Hooper, J.E. et al. (1989) Cell 59:751; and Nakano, Y. et al. (1989) Nature 341:508. Patterns of expression of the vertebrate homologue of patched suggest its involvement in the development of neural tube, skeleton, limbs, craniofacial structure, and skin. Genetic and functional studies demonstrate that patched is part of the hedgehog signaling cascade, an evolutionarily conserved pathway that regulates expression of a number of downstream genes. See Perrimon, N. (1995) Cell 80:517; and Perrimon, N. (1996) Cell 86:513. Patched participates in the constitutive transcriptional repression of the target genes; its effect is opposed by a secreted glycoprotein, encoded by hedgehog, or a vertebrate homologue, which induces transcriptional activation. Genes under control of this pathway include members of the Wnt and TGF-beta families. Patched proteins possess two large extracellular domains, twelve transmembrane segments, and several cytoplasmic segments. See Hooper, supra; Nakano, supra; Johnson, R.L. et al. (1996) Science 272:1668; and Hahn, H. et al. (1996) Cell 85:841. The biochemical role of patched in the hedgehog signaling pathway is unclear. Direct interaction with the hedgehog protein has, however, been reported (Chen, Y. et al. (1996) Cell 87:553). It is theorized that, in the absence of hedgehog, patched associates with another transmembrane protein encoded by the smoothened gene. See Perrimon, supra; and Chen, supra. When hedgehog binds to patched, smoothened is released and activates the downstream events in the hedgehog pathway, including increased expression of the gli-1 and patched genes. It is theorized that patched loss-of-function mutations allow increased and perhaps constitutive smoothened activity. Activating smoothened mutations occur in sporadic basal cell carcinoma, Xie et al. (1998) Nature 391: 90-2, and primitive neuroectodermal tumors of the central nervous system, Reifenberger et al. (1998) Cancer Res 58: 1798-803. Summary of the Invention

The present invention relates to the discovery of methods for culturing basal cell carcinomas. In one aspect the invention provides basal cell carcinoma cultures. In other aspects, the invention provides media, screening assays and methods for making BCC cultures. Basal cell carcinomas are known for being difficult to culture and also for being the most common form of cancer in the U.S. The cultures, media, assays and methods of the invention will be useful, in part, for finding BCC therapeutics and allowing more sophisticated in vitro studies of BCCs.

In one aspect, the invention features BCC cultures comprising cells exhibiting BCC microarchitecture. In one embodiment, the BCC culture is maintained in contact with the chorioallantoic membrane of a bird egg, and preferably a chicken egg. In preferred embodiments, BCC microarchitecture is characterized by nodes of cells with high nuclear/cytoplasmic ratios. BCC microarchitecture may also comprise retractions and/or peripheral palisades. In another aspect, the invention features ex vivo BCC cultures comprising epidermal cells and supporting cells. The epidermal cells preferably exhibit peripheral palisading and/or stromal epithelial clefting. Supporting cells may also be termed dermis or stromal cells.

BCC cultures of the invention are preferably stable, retaining BCC characteristics for at least 2 days, and preferably retaining such characteristics for at least 3, 4, 5, 6, or more days. In general, it is preferable to maintain BCC cultures at a liquid/air interface, and it is particularly preferable to do so by placing the BCC cultures on a support. Preferred supports include inserts that may be inserted into a medium-containing culture vessel, and such inserts may be coated with an organic material such as collagen I, collagen IN, or fibronectin. In certain embodiments, BCC cultures of the invention have epidermal cells with an active hedgehog signaling pathway. In a preferred embodiment, the epidermal cells of the culture comprise a hedgehog reporter gene construct. Preferred hedgehog reporter gene constructs include ptc-1 or gli-1 promoter portions operably linked to a reporter gene. In certain embodiments, the BCC culture comprises a sufficient amount of exogenous hedgehog protein and/or hedgehog agonist to promote or maintain BCC- like characteristics. In a particularly preferred embodiment, a sample of non- cancerous skin is provided and contacted with sufficient hedgehog protein and/or hedgehog agonist to cause the non-cancerous skin sample to develop one or more BCC characteristics. Skin samples are preferably embryonic and preferably include dermal (or stromal) and epidermal material.

In another aspect, a BCC culture comprises a BCC sample and dermis wherein said BCC sample exhibits peripheral palisading and/or stromal epithelial clefting and wherein the BCC sample and dermis are derived from different sources. Preferably, the BCC culture comprises growth medium and a substrate layer, wherein the substrate layer is most proximal to the growth medium, and the dermis is interposed between the substrate layer and the BCC sample. Optionally, a hydrated, organic matrix may be interposed between the dermis cells and the BCC sample. In other embodiments, the dermis and BCC sample may be held together by an inert ring placed around the sample.

In yet another aspect, the invention provides media that permit in vitro maintenance of BCC characteristics. In one embodiment, BCC culture media comprise a basal medium, such as DMEM, a source of growth factors, such as FBS, and a reducing agent. In a preferred embodiment, the medium comprises 0.8 - 1.2 x DMEM, 0 - 10 μg/ml hydrocortisone, 0.4 - 0.6% FBS, 100 - 500 mM and 2- mercaptoethanol. Corticosteroids such as hydrocortisone are also preferred media components. In another embodiment, BCC culture media comprise a basal medium, such as DMEM, a nutrient source, such as F 12, a source of growth factors, such as FBS, a corticosteroid. glutamine, insulin, epidermal growth factor (EGF), and a reducing agent. Preferred media comprise 0.8 - 1.2 x DMEM, 15 - 25% F12 nutrient supplement, 3 - 7% FBS, 0.5 - 10 μg/ml hydrocortisone, 100 - 500 μM 2- mercaptoethanol, glutamine, 5 - 20 mg/ml insulin and 5 - 20 μg/ml EGF. Fungizone™, are preferably included in all BCC culture media. In certain embodiments, BCC media may additionally comprise a hedgehog polypeptide and/or agonist in an amount sufficient to promote the formation of BCC characteristics in a non-cancerous skin sample. In yet another embodiment, the invention provides methods for making a stable BCC culture comprising obtaining a skin sample, comprising dermis and epidermis and placing the skin sample in contact with a culture medium, wherein the medium comprises a hedgehog agonist and/or hedgehog protein. Preferably, an insert is used to maintain the skin sample in contact with the medium at the liquid/air interface.

In a further embodiment, a method for making a stable BCC culture comprises obtaining a BCC sample and placing the BCC sample in close proximity to a sample of dermis. An organic matrix is optionally interposed between the BCC sample and the dermis. The BCC sample itself may or may not comprise stromal material. The BCC sample may be a Mohs shaving, which typically has little or no stromal material.

In one aspect, the invention provides screening assays for identifying BCC therapeutics, hedgehog agonists, and hedgehog antagonists. In one embodiment, the invention provides a method for identifying a hedgehog antagonist comprising contacting a test compound with a BCC culture and measuring a BCC characteristic, wherein a decrease in the presence of the BCC characteristic indicates that the test compound is a hedgehog antagonist. In a further embodiment, the BCC characteristic is a histological characteristic and preferably peripheral palisading or stromal epithelial clefting. In yet another embodiment, a BCC characteristic is a protein activity produced by a hedgehog reporter gene, wherein preferred hedgehog reporter genes are ptc-lacZ or gli-luc constructs. In a further embodiment, BCC therapeutics may be identified using essentially the same methods.

In another embodiment, the invention provides a method for identifying a hedgehog agonist comprising contacting a test compound with a BCC culture and measuring a BCC characteristic, wherein an increase in the presence of the BCC characteristic indicates that the test compound is a hedgehog agonist. In a further embodiment, the BCC characteristic is a histological characteristic and preferably peripheral palisading or stromal epithelial clefting. In yet another embodiment, a BCC characteristic is a protein activity produced by a hedgehog reporter gene, wherein preferred hedgehog reporter genes are ptc-lacZ or gli-luc constructs. The practice of the present invention will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D. N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Patent No: 4,683,195; Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Nols. 154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IN (D. M. Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, Ν.Y., 1986). Brief Description of Drawings

Figure 1 depicts the chemical structures for exemplary hedgehog antagonists AY9944, triparanol, jervine, cyclopamine, tomatidine and cholesterol.

Figure 2 depicts the chemical structure for compound A, an exemplary hedgehog antagonist.

Figure 3 shows the chemical structure for compound B, an exemplary hedgehog antagonist.

Figure 4 shows hematoxylin and eosin (H&E) staining of human BCCs cultured on the chorioallantoic membrane of a chicken embryo. Panel A is a culture of a nodular BCC sample. Panel B is a culture of a micronodular BCC sample. The section is within the dermis, parallel to the epidermal surface of the culture.

Figure 5 is a diagram of a BCC culture system with a dermis feeder, comprising a base support (1), a piece of dermis (2) overlaid with a hydrated organic matrix (3). The BCC sample (4) is placed on the matrix. Figure 6 H&E staining of three human basal cell carcinoma organotypic skin cultures grown with a dermis feeder. A. Nodular BCC. B. Micronodular BCC. C. Morpheaform BCC. BCC islands, clefting and peripheral palisading are all evident.

Figure 7 Organotypic culture of human basal cell carcinoma. A. Low- power views of histological sections of BCCs stained with hematoxylin and eosin show the presence of multiple basal cell islands in the dermis. B. In high-power view, the undifferentiated character of these cells is apparent, including, palisading of peripheral cells. Likewise, stromal clefting, is present. C. High-level expression of the transcription factor gli-1, a pivotal indicator of hedgehog signaling can be observed in the basal cell islands of the explant. D. The differentiation marker keratin 14 which is indicative of basal keratinocytes, continues to be expressed in the basal cell islands of the tumor. The section is within the dermis, parallel to the epidermal surface of the culture.

Figure 8 Organotypic culture of human basal cell carcinoma without dermis feeder. A. Nodular BCC. B. Micronodular BCC. BCC islands are evident intruding into the surrounding dermis. Stromal/epithelial clefting is also apparent. The section is within the dermis, parallel to the epidermal surface of the culture. Figure 9 Compound B treatment of human BCCs in short-term organotypic culture decreases gli-1 expression. BCCs were cultured without a dermis feeder. Quantitative radioactive in situ hybridizations was performed on paraformaldehyde- fixed, paraffin-embedded histological sections, using a protocol modified from Wilkinson et al. (1987). Briefly, 7mm sections were cleared, re-hydrated, digested with proteinase K, acetylated and hybridized with [33P]- labeled RNA probes over night. After high stringency post-hybridization washes, slides were exposed to a Phosphorlmager screen in the dark at room temperature for 4-5 days. After developing, the [33P]-signal was scanned using a Storm scanner (Molecular Dynamics). Individual basal cell islands were selected and the signal quantified and expressed in average counts/pixel using ImageQuant 1.0 software. The section is within the dermis, parallel to the epidermal surface of the culture.

Figure 10 Compound B treatment of human BCCs in short-term organotypic culture increases cell death. BCCs were cultured without a dermis feeder. For the detection of caspase 3, an early indicator of apoptosis, standard immunohistochemistry was performed using a monoclonal antibody specific for activate human caspase 3. The blue chromagen precipitate is X-gal. The section is within the dermis, parallel to the epidermal surface of the culture.

Figure 11 is a schematic ofa skin punch assay. Skin samples are removed from a mouse and placed on an insert at the air-liquid interface.

Figure 12 shows a skin punch culture system. A culture well 1 is partially filled with culture medium 4. An insert 2 is placed into the well such that the insert sits at the air-liquid interface. Skin samples 3 are placed on the insert.

Figure 13 Shh treatment induces BCC characteristics in skin punches. Skin punches were obtained from a ptc +/+ ptc-lacZ mouse, and β-galactosidase activity reflects expression of ptc. Skin samples were obtained from El 7 embryos and cultured on the presence or absence of Octyl-SHH. Top panels. Top view of skin punches showing β-galactosidase activity in Shh treated samples. Lower panels. Tissue sections running perpendicular to the epidermal surface and stained with H&E. The formation of BCC islands intruding into the dermis is evident, and the islands exhibit clefting and palisading. Figure 14 Compound B treatment inhibits BCC formation. Skin explants were treated with placebo, Shh, or Shh + Compound B. Ptc-lacZ activity is clear in the Shh-treated sample, wliile placebo and Shh + compound B do not elicit Ptc-lacZ expression. Figure 15 Compound B treatment inhibits BCC formation. Skin explants were treated with placebo, Shh, or Shh + Compound B. Sections are taken perpendicular to the epidermal surface and stained with H&E and X-Gal (for β- galactosidase activity). Compound B prevents the formation of BCC structures in the skin explants. Figure 16 Treatment with various hedgehog antagonists prevents BCC formation. Explants were exposed to Shh and forskolin (FK) or jervine. Shh alone stimulated ptc-lacZ expression as seen by X-gal staining. FK and jervine prevented ptc-lacZ expression. Best Mode for Carrying Out the Invention I. Overview

The present invention relates, in part, to the discovery of methods for promoting and maintaining basal cell carcinoma characteristics in ex vivo cultures. Basal cell carcinomas are a common form of cancer, and although rarely metastatic, BCCs can cause substantial local tissue destruction and disfigurement. As with most cancers, identification of BCCs is typically based on one or more distinctive ultrastructural, histological or molecular traits. BCCs are typified by an island of cells with a high nuclear/cytoplasmic ratio. This node often invades deeply into the dermis, such that sections through the dermis reveal BCC islands. Many BCC nodes are surrounded by a continuous band of type IN collagen, type V collagen, and laminin. These markers are characteristic of an intact basement membrane. In certain BCC forms, morpheaform and basosquamous types, the basement membrane shows large gaps. This may signify a BCC that is more likely to be invasive. BCCs typically have a tightly packed boundary layer of cells referred to as a peripheral palisade. In addition, during histological preparation, BCC nodes develop substantially larger retraction spaces than normal epidermis. Such retraction spaces may occur within the BCC node and also between the BCC and the stroma. Retraction spaces may occur because of decreased numbers of hemidesmosomes that provide strong cell-cell contacts. In addition, collagenase released by the BCC weakens its attachment to the underlying basement membranes and stromal cells, and thus clefts may form between the BCC and the underlying cells (called the stroma). (Miller (1991) J. Amer. Acad. Dermatol. 24:1-13) BCCs express keratins that are more typical of basal cells, keratin 5 and keratin 14 (Stoler et al. (1988) J. Cell Biol. 107:427-6). The stroma surrounding BCCs tends to produce hyaluronectin, a protein more typically found in fetal dermis and the perifollicular dermis of adult skin (Delpech et al. (1982) 106:561-8). Transferrin receptor is often a marker for proliferating cells, and is consistently found in BCCs (Gatter et al. (1984) Histopathology 8:209-27). BCCs tend to express a lower level of suprabasalar epidermal differentiation markers (keratin 10 and loricrin) and hemidesmosomal components (BP180, beta.4 integrin, a6 integrin, gamma.2 chain of LAM5). Also, diffuse staining of Bcl2 antigen can be seen within BCCs. BCCs are typically classified into types, based on overall morphology.

Nodular BCC is typified by large, nodular BCC islands. A BCC with many smaller nodules may be referred to as micronodular. Morpheaform BCC is typified by very small strands of neoplastic cells, instead of robust nodular islands. The strands typically extend deeply into the dermis, and morpheaform BCCs are the most likely to metastasize. Other classifications include superficial, cystic, adenoid, pigmented and metatypical. (Miller (1991) J. Amer. Acad. Dermatol. 24:1-13).

As described above, mutations that cause hyperactivation of the hedgehog signaling pathway are commonly associated with BCCs, and are probably causative. Thus, patched loss-of-function mutations lead to BCC formation, and overactivation of hedgehog or smoothened has a similar effect. Most BCCs show strong expression of hedgehog pathway-activated genes such as patched and gli.

BCCs are difficult to culture as an intact stracture. Most BCC cultures are actually cultures of individual cells dissociated from a BCC. Other BCC cultures are maintained only on a recipient animal, such as an immunocompromised mouse. When cultured incorrectly, BCCs tend to differentiate into normal epithelial cells, forming a stratified and keratinized epithelial structure. In one aspect, the invention relates to methods of causing skin samples that do not initially exhibit BCC characteristics to develop and maintain BCC characteristics in vitro. In one embodiment, this effect may be achieved by providing a stimulus to activate the hedgehog signaling pathway. In certain embodiments, such methods also depend upon the culture conditions disclosed herein.

In other aspects, the invention relates to methods of maintaining BCC! samples in an ex vivo culture. To our knowledge, these methods represent the first successful maintenance of BCC characteristics in an ex vivo culture system. Accordingly, the cultures themselves represent the first stable, in vitro BCC cultures. In certain aspects, BCC cultures provided herein may be used to screen for compounds that promote or diminish the formation of BCCs. Because the cultures exhibit the microarchitecture that is so typical of BCCs, the cultures may also be used to identify compounds that alter the architecture and cell-cell interactions in BCCs. In fact, such cultures may be used to examine essentially any aspect of BCC biology in vitro. This may lead to the discovery of valuable new therapeutics for the treatment of this most common cancer. Furthermore, because, in certain embodiments, BCC characteristics depend heavily upon hedgehog pathway activity, BCC cultures may be used to identify compounds that regulate the hedgehog signaling pathway. The hedgehog pathway has an important role in such biological functions as neural development, angiogenesis, lung development, bone and cartilage formation, pancreatic development, hair growth and various developmental defects, and therefore compounds that affect BCC growth and development may also be useful in treating a wide range of diseases, disorders and abnormalities. In a further aspect, the invention relates to the discovery that hedgehog antagonists are effective in preventing BCC formation and in causing apoptosis of existing BCCs. Accordingly, it is anticipated that hedgehog antagonists may be used to treat or prevent BCC. II. Definitions For convenience, certain terms employed in the specification, examples, and appended claims are collected here. The phrase "aberrant modification or mutation" ofa gene refers to such genetic lesions as, for example, deletions, substitution or addition of nucleotides to a gene, as well as gross chromosomal rearrangements of the gene and/or abnormal methylation of the gene. Likewise, mis-expression of a gene refers to aberrant levels of transcription of the gene relative to those levels in a normal cell under similar conditions, as well as non- wild-type splicing of mRNA transcribed from the gene.

"BCC Therapeutic" as used herein means a compound that alleviates at least one symptom associated with BCC or change or alters at least one BCC distinguishing feature or characteristic. For example, BCC Therapeutics include compounds that can inhibit the activity of at least one member of the hedgehog- signaling pathway or down-regulate the hedgehog signaling pathway.

"Basal cell carcinomas" exist in a variety of clinical and histological forms such as nodular, micronodular, nodular-ulcerative, superficial, pigmented, morphealike, fibroepithelioma and nevoid syndrome. Basal cell carcinomas are the most common cutaneous neoplasms found in humans. The majority of new cases of nonmelanoma skin cancers fall into this category. Basal cell carcinomas may be identified by histological features, particularly "peripheral palisading" and/or "stromal epithelial clefting". Peripheral palisading occurs when the cells at the edge of a BCC form a tightly packed boundary that resembles a palisade. Stromal epithelial clefting occurs in part because the BCC releases collagenase, loosening its attachment to the underlying stroma. During histological preparation, the BCC often lifts slightly off the stroma, giving rise to a cleft. BCCs may also be identified on the basis of the high nuclear/cytoplasmic ratio relative to the normal epidermal cells. BCC tends to form easily recognizable islands of such cells that have intruded into the dermis. BCCs also tend to express a high level (relative to neighboring epidermal cells) of keratin 14 and sbb-regulated genes such as ptc-1 and gli-1. BCCs tend to express a lower level of suprabasalar epidermal differentiation markers (keratin 10 and loricrin) and hemidesmosomal components (BP180, beta.4 integrin, a6 integrin, gamma.2 chain of LAM5). Also, diffuse staining of Bcl2 antigen can be seen within BCCs. The activity produced by a reporter gene that indicates a BCC-like expression level of any of the above genes may also be considered a BCC characteristic. A "basal cell carcinoma culture" or "BCC culture" is an ex vivo culture in which the tissue maintains at least one distinguishing feature of a basal cell carcinoma. For example, basal cell carcinomas may be identified by histological features, particularly "peripheral palisading" and/or "stromal epithelial clefting". Peripheral palisading occurs when the cells at the edge of a BCC form a tightly packed boundary that resembles a palisade. Stromal epithelial clefting occurs in part because the BCC releases collagenase, loosening its attachment to the underlying stroma. During histological preparation, the BCC often lifts slightly off the stroma, giving rise to a cleft. BCCs may also be identified on the basis of the high nuclear/cytoplasmic ratio relative to the normal epidermal cells. BCC tends to form easily recognizable islands of such cells that have intruded into the dermis. BCCs also tend to express a high level (relative to neighboring epidermal cells) of keratin 14 and sbb-regulated genes such as ptc-1 and gli-1. BCCs tend to express a lower level of suprabasalar epidermal differentiation markers (keratin 10 and loricrin) and hemidesmosomal components (BP180, beta.4 integrin, a6 integrin, gamma.2 chain of LAM5). Also, diffuse staining of Bcl2 antigen can be seen within BCCs. The activity produced by a reporter gene that indicates a BCC-like expression level of any of the above genes may also be considered a BCC characteristic. The BCC culture may have tissue from a BCC that was excised from an animal or human. The culture may comprise tissue that was originally non-neoplastic but has been stimulated to develop characteristics of a BCC.

The term "carcinoma" refers to a malignant new growth made up of epithelial cells tending to infiltrate surrounding tissues and to give rise to metastases. Exemplary carcinomas include: "basal cell carcinoma", which is an epithelial tumor of the skin that, while seldom metastasizing, has potentialities for local invasion and destruction; "squamous cell carcinoma", which refers to carcinomas arising from squamous epithelium and having cuboid cells; "carcinosarcoma", which include malignant tumors composed of carcinomatous and sarcomatous tissues; "adenocystic carcinoma", carcinoma marked by cylinders or bands of hyaline or mucinous stroma separated or surrounded by nests or cords of small epithelial cells, occurring in the mammary and salivary glands, and mucous glands of the respiratory tract; "epidermoid carcinoma", which refers to cancerous cells which tend to differentiate in the same way as those of the epidermis; i.e., they tend to form prickle cells and undergo cornification; "nasopharyngeal carcinoma", which refers to a malignant tumor arising in the epithelial lining of the space behind the nose; and "renal cell carcinoma", which pertains to carcinoma of the renal parenchyma composed of tubular cells in varying arrangements. Other carcinomatous epithelial growths are "papillomas", which refers to benign tumors derived from epithelium and having a papillomavirus as a causative agent; and "epidermoidomas", which refers to a cerebral or meningeal rumor formed by inclusion of ectodermal elements at the time of closure of the neural groove. The "corium" or "dermis" refers to the layer of the skin deep to the epidermis, consisting of a dense bed of vascular connective tissue, and containing the nerves and terminal organs of sensation. The hair roots, and sebaceous and sweat glands are structures of the epidermis which are deeply embedded in the dermis.

The term "ED50" means the dose of a drug which produces 50% of its maximum response or effect.

An "effective amount" of, e.g., a hedgehog antagonist, with respect to the subject method of treatment, refers to an amount of the antagonist in a preparation which, when applied as part of a desired dosage regimen brings about, e.g., a change in the rate of cell proliferation and/or the state of differentiation of a cell and/or rate of survival of a cell according to clinically acceptable standards for the disorder to be treated or the cosmetic purpose.

The terms "epithelia", "epithelial" and "epithelium" refer to the cellular covering of internal and external body surfaces (cutaneous, mucous and serous), including the glands and other structures derived therefrom, e.g., comeal, esophegeal, epidermal, and hair follicle epithelial cells. Other exemplary epithlelial tissue includes: olfactory epithelium, which is the pseudostratified epithelium lining the olfactory region of the nasal cavity, and containing the receptors for the sense of smell; glandular epithelium, which refers to epithelium composed of secreting cells; squamous epithelium, which refers to epithelium composed of flattened plate-like cells. The term epithelium can also refer to transitional epithelium, like that which is characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention, e.g., tissue which represents a transition between stratified squamous and columnar epithelium.

The term "epithelialization" refers to healing by the growth of epithelial tissue over a denuded surface. The- tenn "epidermal gland" refers to an aggregation of cells associated with the epidermis and specialized to secrete or excrete materials not related to their ordinary metabolic needs. For example, "sebaceous glands" are holocrine glands in the corium that secrete an oily substance and sebum. The term "sweat glands" refers to glands that secrete sweat, situated in the corium or subcutaneous tissue, opening by a duct on the body surface.

The term "epidermis" refers to the outermost and nonvascular layer of the skin, derived from the embryonic ectoderm, varying in thickness from 0.07-1.4 mm. On the palmar and plantar surfaces it comprises, from within outward, five layers: basal layer composed of columnar cells arranged perpendicularly; prickle-cell or spinous layer composed of flattened polyhedral cells with short processes or spines; granular layer composed of flattened granular cells; clear layer composed of several layers of clear, transparent cells in which the nuclei are indistinct or absent; and horny layer composed of flattened, cornified non-nucleated cells. In the epidermis of the general body surface, the clear layer is usually absent. "Excisional wounds" include tears, abrasions, cuts, punctures or lacerations in the epithelial layer of the skin and may extend into the dermal layer and even into subcutaneous fat and beyond. Excisional wounds can result from surgical procedures or from accidental penetration of the skin.

The term "ex vivo" as used herein in reference to BCC cultures, refers to a culture that is not in contact with a post-natal metazoan or a mammal of any sort, whether pre- or post-natal. A culture on an egg is therefore considered to be ex vivo, while a culture on a fetal mouse should not be considered ex vivo for the purposes of this invention.

The "growth state" of a cell refers to the rate of proliferation of the cell and/or the state of differentiation of the cell. An "altered growth state" is a growth state characterized by an abnormal rate of proliferation, e.g., a cell exhibiting an increased or decreased rate of proliferation relative to a normal cell. The term "hair" refers to a threadlike structure, especially the specialized epidermal structure composed of keratin and developing from a papilla sunk in the corium, produced only by mammals and characteristic of that group of animals. Also, "hair" may refer to the aggregate of such hairs. A "hair follicle" refers to one of the tubular-invaginations of the epidermis enclosing the hairs, and from which the hairs grow. "Hair follicle epithelial cells" refers to epithelial cells which surround the dermal papilla in the hair follicle, e.g., stem cells, outer root sheath cells, matrix cells, and inner root sheath cells. Such cells may be normal non-malignant cells, or transformed/immortalized cells. The term "hedgehog" is used to refer generically to any member of the hedgehog family, including sonic, indian, desert and tiggy winkle. The term may be used to indicate protein or gene and may include modified forms, such as forms with hydrophobic modifications.

The term "hedgehog signaling pathway", "hedgehog pathway" and "hedgehog signal transduction pathway" are all used to refer to the chain of events normally mediated by hedgehog, smoothened, ptc, and gli, among others, and resulting in a changes in gene expression and other phenotypic changes typical of hedgehog activity. The hedgehog pathway can be activated even in the absence of a hedgehog protein by activating a downstream component. For example, overexpression of smoothened will activate the pathway in the absence of hedgehog, gli (and particularly gli-1) and ptc gene expression are indicators of an active hedgehog signaling pathway.

The terms "hedgehog agonist" and "hedgehog antagonist" are essentially opposites and refer to an agents that potentiates or recapitulates the bioactivity of hedgehog or smoothened (agonist) or patched (antagonist). Agonists generally increase the activity of the hedgehog pathway while antagonists generally repress the activation of the hedgehog pathway. Preferred hedgehog antagonists can be used to overcome a ptc loss-of-function and/or a smoothened gain-of-function, the latter also being referred to as smoothened antagonists. Preferred hedgehog agonists can be used to overcome a hedgehog or smoothened loss-of-function, or a patched gain of function. The terms "hedgehog agonist" and "hedgehog antagonist" as used herein refers not only to any agent that may act by directly affecting the normal function of the hedgehog protein, but also to any agent that affects the hedgehog signaling pathway. A hedgehog agonist or antagonist may be a small molecule, an antibody (including but not restricted to: a diabody, single chain antibody, monoclonal antibody, IgG, IgM, IgA, IgD, IgE, or an antibody fragment comprising at least one pair of variable regions), an antisense nucleic acid, PNA or ribozyme, or a mutant hedgehog protein that can affect hedgehog signaling. An antibody may be directed to a protein encoded by any of the genes in the hedgehog pathway, including sonic, indian or desert hedgehog, smoothened, ptc-1, ptc-2, gli-1, gli-2, gli-3, etc. In most cases, the antibody would inhibit the activity of the target protein, but in certain cases an antibody could be an activator.

The term "hedgehog gain-of-function" refers to an aberrant modification or mutation of a ptc gene, hedgehog gene, or smoothened gene, or a decrease (or loss) in the level of expression of such a gene, which results in a phenotype which resembles contacting a cell with a hedgehog protein, e.g., aberrant activation of a hedgehog pathway. The gain-of-function may include a loss of the ability of the ptc gene product to regulate the level of expression of Ci genes, e.g., GUI, GH2, and GH3. The term 'hedgehog gain-of-function' is also used herein to refer to any similar cellular phenotype (e.g., exhibiting excess proliferation) which occurs due to an alteration anywhere in the hedgehog signal transduction pathway, including, but not limited to, a modification or mutation of hedgehog itself. For example, a tumor cell with an abnormally high proliferation rate due to activation of the hedgehog signalling pathway would have a 'hedgehog gain-of-function' phenotype, even if hedgehog is not mutated in that cell.

As used herein, "immortalized cells" refers to cells which have been altered via chemical and/or recombinant means such that the cells have the ability to grow through an indefinite number of divisions in culture.

The term "LD50" means the dose of a drug which is lethal in 50% of test subjects.

The term "microarchitecture" refers to the structural organization of a tissue or neoplastic growth (such as a BCC). The organization of a tissue or neoplasm usually depends on shape, size, characteristics and relative positioning of the cells that make up that tissue or neoplasm. Extracellular structures such as basement membranes, collagens and bone material can also have a substantial influence on microarchitecture. In the case of skin, varying structures such as the dermis, epidennis, nerves and capillaries interact to produce the microarchitecture. In a BCC, the cancerous cells and surrounding cells (the stroma) also contribute to the microarchitecture. Examples of BCC microarchitecture include the formation of islands of BCC cells that intrude into the dermis, the formation of peripheral palisading within those islands, and the tendency to form stromal epidermal clefts. In general, BCC microarchitecture refers to the general features that, upon microscopic examination allow one of skill in the art to determine that a BCC is present.

An "organotypic culture" with respect to BCC cultures, an organotypic culture maintains the overall organization of the BCC as it existed in the organism from which it was obtained. This contrasts with culturing methods that involve dispersing the tissue sample into single cells and then attempting to reconstitute the structure in vitro.

The term "overexpression" as used in reference to gene expression levels means any level of gene expression in cells of a tissue that is higher than the normal level of expression for that tissue. The normal level of expression for a tissue may be assessed by measuring gene expression in a healthy portion of that tissue. The term "patched" or "ptc" refers to members of the patched gene or protein family. Whether the term is intended to refer to one or many members of the family may be deduced from the context. Often the term is used to refer to the patched genes or proteins found in most mammals, ptc-1 and ptc-2.

The term "patched loss-of-function" refers to an aberrant modification or mutation of a ptc gene, or a decreased level of expression of the gene, which results in a phenotype which resembles contacting a cell with a hedgehog protein, e.g., aberrant activation of a hedgehog pathway. The loss-of-function may include a loss of the ability of the ptc gene product to regulate the level of expression of Ci genes, e.g., GUI, GH2 and GH3. A "patient" or "subject" to be treated by the subject method can mean either a human or non-human animal. The term "prodrag" is intended to encompass compounds which, under physiological conditions, are converted into the therapeutically active agents of the present invention. A common method for making a prodrag is to include selected moieties which are hydrolyzed under physiological conditions to reveal the desired molecule. In other embodiments, the prodrag is converted by an enzymatic activity of the host animal.

As used herein, "proliferating" and "proliferation" refer to cells undergoing mitosis.

Throughout this application, the term "proliferative skin disorder" refers to any disease/disorder of the skin marked by unwanted or aberrant proliferation of cutaneous tissue. These conditions are typically characterized by epidermal cell proliferation or incomplete cell differentiation, and include, for example, X-linked ichthyosis, psoriasis, atopic dermatitis, allergic contact dermatitis, basal cell carcinoma, epidermoiytic hyperkeratosis, and seborrheic dermatitis. For example, epidermodysplasia is a form of faulty development of the epidermis. Another example is "epidermolysis", which refers to a loosened state of the epidermis with formation of blebs and bullae either spontaneously or at the site of trauma.

The term "skin" refers to the outer protective covering of the body, consisting of the corium and the epidermis, and is understood to include sweat and sebaceous glands, as well as hair follicle structures. Throughout the present application, the adjective "cutaneous" may be used, and should be understood to refer generally to attributes of the skin, as appropriate to the context in which they are used.

The term "smoothened gain-of-function" refers to an aberrant modification or mutation of a smo gene, or an increased level of expression of the gene, which results in a phenotype which resembles contacting a cell with a hedgehog protein, e.g., aberrant activation of a hedgehog pathway. While not wishing to be bound by any particular theory, it is noted that ptc may not signal directly into the cell, but rather interact with smoothened, another membrane-bound protein located downstream of ptc in hedgehog signaling (Marigo et al., (1996) Nature 384: 177- 179). The gene smo is a segment-polarity gene required for the correct patterning of every segment in Drosophila (Alcedo et al, (1996) Cell 86: 221-232). Human homologs of smo have been identified. See, for example, Stone et al. (1996) Nature 384:129-134, and GenBank accession U84401. The smoothened gene encodes an integral membrane protein with characteristics of heterotrimeric G-protein-coupled receptors; i.e., 7-transmembrane regions. This protein shows homology to the Drosophila Frizzled (Fz) protein, a member of the wingless pathway. It was originally thought that smo encodes a receptor of the Hh signal. However, this suggestion was subsequently disproved, as evidence for ptc being the Hh receptor was obtained. Cells that express Smo fail to bind Hh, indicating that smo does not interact directly with Hh (Nusse, (1996) Nature 384: 119-120). Rather, the binding of Sonic hedgehog (SHH) to its receptor, PTCH, is thought to prevent normal inhibition by PTCH of smoothened (SMO), a seven-span transmembrane protein. A "support cell" as used herein refers to cells of the dermis or stroma. The term "therapeutic index" refers to the therapeutic index of a drag defined as LD50/ED50. As used herein, "transformed cells" refers to cells which have spontaneously converted to a state of unrestrained growth, i.e., they have acquired the ability to grow through an indefinite number of divisions in culture. Transformed cells may be characterized by such terms as neoplastic, anaplastic and/or hyperplastic, with respect to their loss of growth control.

III. BCC Cultures

In certain aspects, the invention relates to ex vivo BCC cultures. In certain embodiments, the cultures have BCC characteristics and/or microarchitecture. In certain embodiments, such cultures may be started with tissue comprising BCC characteristics. In other embodiments, such cultures may be started with tissue that does not exhibit BCC characteristics and such characteristics develop in culture. In particularly preferred embodiments, BCC cultures of the invention are stable, meaning that the culture conditions permit maintenance of BCC characteristics and/or microarchitecture for more that two days, or preferably more that three, four or five days.

In one embodiment, said culture comprises BCC and support cells, wherein said support cells include stroma or dermis. The BCC and support cells may be in direct or indirect contact. As used herein, indirect contact means that diffusible factors produced by the dermis are capable of reaching the BCC sample. Direct contact means that cells of the BCC sample are in physical contact with the dermis. In certain embodiments a BCC culture may comprise a tissue sample obtained from a basal cell carcinoma. A BCC sample may be obtained from a human, mouse or other vertebrate, including, for example a rat, guinea pig, rabbit, primate, hamster, pig, miniature swine, chicken or frog. In certain embodiments, BCC samples may be obtained from mice that are wild-type at the patched locus, mice having apatched-lacZ construct (or other patched reporter gene construct), ptc +/- mice, nude mice (preferrably hr/hr mice), ptc +/- hr/hr mice, mice overexpressing a hedgehog gene (Fan et al. 1997) in the epidermis or mice having a smoothened mutation associated with BCC (Xie et al. 1998), or any of the above mice that have been UV irradiated (Aszterbaum etal, 1997). In particularly preferred embodiments, BCCs are generated by UV-irradiating a mouse having a ptc +/- genotype. The UV irradiation causes an increased frequency of loss-of-function mutations in the sole functional ptc allele in epidermal cells. Such ptc -I- epidermal cells develop BCCs at a greatly accelerated rate. BCCs may be obtained directly from such mice, or BCCs may be transferred from the originating mouse to an immunocompromised mouse (such as a SCID mouse) for continued in vivo maintenance. BCC samples may be obtained from such transplanted BCCs.

A human BCC sample may be essentially any BCC sample obtained from a human, including the carcinomas found in individuals with BCNS. In certain embodiments, Mohs shavings may be used. Mohs surgery involves the progressive shaving of tissue from a BCC. Mohs shavings are thin and typically contain very little of the stroma surrounding the BCC nodule. In other embodiments, curettage samples may be used. Curettage involves cutting off large portion of the nodule. Curettage samples typically contain a larger portion of the stroma surrounding the BCC.

In other aspects, a sample may also be obtained from healthy skin or skin that does not have the distinguishing characteristics of a basal cell carcinoma. Such skin may be obtained from any vertebrate, including those listed above. In preferred embodiments, the skin sample includes a portion of the underlying dermis. In other preferred embodiments the skin sample is obtained from embryonic skin, although adult skin may also be used. In particularly preferred embodiments, the skin is peeled from the back of an E15.5-E17.5 mouse embryo and samples cut or punched from this peeled skin. It is further understood that skin can be reconstituted from keratinocytes.

Any such artificial skin may also be used as a tissue sample (Fan et al. 1997).

In certain embodiments, a BCC sample may be cultured on a part of an egg. Eggs may be essentially any bird egg and preferably chicken eggs. In preferred embodiments, the sample is cultured in contact with the chorioallantoic membrane. In other embodiments, a BCC sample may be cultured in direct or indirect contact with dermis (see for example Figure 5). Indirect contact means that diffusible factors produced by the dermis are capable of reaching the BCC sample. Direct contact means that cells of the BCC sample are in physical contact with the dermis. Dermis may be obtained from essentially any skin source, but preferably a human donor or a mouse. It is not necessary that the dermis and BCC sample derive from the same individual or even from the same species. In preferred embodiments, the dermis is proximal to the growth media relative to the BCC sample. In particularly preferred embodiments, the dermis is in contact with a support (such as any of those described above), and the BCC sample is placed on top of the dermis. The support is preferably positioned relative to the culture medium so as to maintain the tissue at the liquid/air interface. In a BCC culture comprising a BCC sample and heterologous dermis, it is preferable that a hydrated organic matrix be interposed between the BCC sample and the dermis. This may be achieved using any hydrated organic matrix such as collagens, laminins, proteoglycans, gelatins, chondroitin sulfates, agarose, polyacrylamide, sepharose, dextrans. In preferred embodiments, the matrix comprises growth factors typical of the basement membrane. In particularly preferred embodiments, the matrix comprises basement membrane components obtained from a cancerous cell type. For example, Mafrigel™ (Beckton-Dickinson Labware) is generated from the EHS mouse sarcoma, a tumor rich in extracellular matrix proteins. Mafrigel is composed of laminin, collagen IN, entactin, heparan sulfate proteoglycan, various growth factors, matrix metalloproteases and other components as described Kleinman et al, "Basement Membrane Complexes with Biological Activity", Biochemistry, Vol. 25 (1986), pages 312-318.

In certain aspects, BCC and skin samples are at an air-liquid interface. This is intended to mean that one portion of the cultured material is in contact with a liquid phase, while another portion of the cultured material is in contact with a gaseous phase. Preferably, a dermal or stromal portion of the culture is in contact with a liquid phase while an epidermal or BCC portion of the cultured material is in contact with a gaseous phase. In particularly preferred embodiments, many different stands, supports, platforms, grids, screens, filters etc. known in the art may be used for positioning a tissue sample at an air-liquid interface. In preferred embodiments, medium is placed in a culture receptacle (see, for example, Figure 12). The culture receptacle is designed such that it can accommodate an insert that acts as a support platform for the cultured samples. Samples may be loaded onto inserts and then lowered into culture receptacles. Alternatively the inserts may first be placed into the culture receptacles and then the samples placed onto the inserts. Inserts may have materials that are beneficial for the adherence and growth of the cultures, for example, collagens (eg. I, III or IV), fibronectins, merosins, tenascins or vitronectins.

Preferred culture media for the invention comprise a base medium, a source of growth factors, antibiotics, and a reducing agent. In certain aspects, preferred media comprise a nutritive supplement. In other aspects, preferred media further comprise a corticosteroid. In yet further aspects, preferred media further comprise an antifuiigal agent.

In certain embodiments, the preferred base medium comprises Dulbecco's Modified Eagle Medium (DMEM), however various equivalents are well known in the art. Exemplary base media include: BGJb Medium, Basal Media Eagle, Brinster's BMOC-3 Medium, CMRL Media, EHAA Medium, Fischer's Media, Gamborg's B-5 Medium, Glasgow Minimum Essential Media, HEPES Media, Iscove's Modified Dulbecco's Media, Leibovitz's L-15 Media, MCDB 131 Medium, McCoy's 5A Media, Media 199, Medium NCTC-109, Minimum Essential Media, Modified Eagle Medium, RPMI Media 1640, RPMI Media 1640 without L- glutamine, Waymouth's MB 752/1 Media and Williams' Media E eRDF Medium. RPMI media are a particularly preferred equivalent for DMEM.

Exemplary sources of growth factors include fetal bovine sera (FBS), bovine calf serum and newborn bovine calf serum. In addition, purified polypeptide growth factors may be included in the media. Preferred growth factors include insulin and epidermal growth factor (EGF). Other exemplary growth factors are acidic fibroblast growth factor, basic fibroblast growth factor, insulin-like growth factor 1 (IGF-1), insulin-like growth factor 2 (IGF-2), stem cell factor and keratinocyte growth factor (KGF). Exemplary antibiotics include carbenicillin, cefotaxime, gentamicin, hygromycin B, kanamycin, neomycin, polymyxin B, penicillins and streptomycin. In particularly preferred embodiments, the antibiotics comprise penicillin G and streptomycin.

2-mercaptoethanol is a preferred reducing agent. Equivalents include reduced gluathione, cysteine, and dithiothreitol.

Nutritive supplements of the invention include F-10 nutrient mixtures and F-12 nutrient mixtures. Nutritive supplements may also comprise one or more amino acids, including alanine, arginine, aspartic acid, asparagine, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, isoleucine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine.

Corticosteroids of the invention include hydrocortisone (17- hydroxycorticosterone), cortisone, 9-fluorohydrocortisone, 6.beta.-hydroxycortisone, and other equivalents.

Antifungal agents of the invention include amphotericin B (eg. Fungizone™) and nystatin.

In a preferred embodiment, culture media comprises OJx - 1.5x DMEM, 0 - 5 mg/ml hydrocortisone, 0.2 to 10% fetal bovine serum, 0.05 - 5 mg/ml streptomycin, 10 - 1000 units penicillin and 50 μM to 1 mM 2-mercaptoethanol. A particularly preferred culture medium comprises about lx DMEM, 0 - 0.5 mg/ml hydrocortisone, 0.2 to 1% FBS, 50 - 500 mg/ml streptomycin, 50 - 500 units penicillin and 100 - 500 μM 2-mercaptoethanol. In yet another preferred embodiment, culture comprises 0.7 - 1.5x DMEM, 10 - 30% F12 nutrient supplement, 2 - 10%) FBS, 0 - 5 mg/ml hydrocortisone, 0.05 - 5 mg/ml streptomycin, 10 - 1000 units penicillin, 50 μM to 1 mM 2- mercaptoethanol, glutamine, 5 - 20 mg/ml insulin and 5 - 20 μg/ml EGF. A particularly preferred culture medium comprises about lx DMEM, 12 - 25% F12 nutrient supplement, 3 - 7% FBS, 0.5 - 10 μg/ml hydrocortisone, 50 - 500 mg/ml streptomycin, 50 - 500 units penicillin and 100 - 500 μM 2-mercaptoethanol, glutamine, 5 - 20 mg/ml insulin and 5 - 20 μg/ml EGF. In a particularly preferred embodiment, culture media comprises at least 0.5 mg/ml hedgehog protein, preferably hydrophobically modified sonic hedgehog protein (see Genes and

Proteins of the Hedgehog Pathway, infra). A preferred hydrophobically modified sonic hedgehog protein is "Octyl-SHH". Octyl-SHH is the active N-terminal portion of SHH with an octanoyl maleimide moiety covalently bound to the amino terminal amino acid, (see US Patent Application 09/325,256, Pepinsky et al, filed June 3, 1999).

TV. Screening Assays

In certain aspects, the invention provides methods for identifying BCC therapeutics as well as hedgehog agonists and antagonists. In certain embodiments, methods for identifying such compounds comprise contacting a BCC culture with a test compound and measuring any change in at least one BCC distinguishing feature or characteristic. In general, a test compound that causes a decrease in a BCC characteristic is a potential BCC therapeutic and/or a hedgehog antagonist. A test compound that causes an increase in BCC characteristics is a potential hedgehog agonist. In one embodiment, a non-BCC skin sample may be contacted with a test compound. If the skin sample develops one or more BCC characteristic, then the test compound is a potential hedgehog agonist. In a preferred embodiment, the non- BCC skin sample is contacted with an amount of hedgehog protein normally insufficient to stimulate the production of a BCC characteristic. A test compound that can stimulate the production of a BCC characteristic in the presence of this low level of hedgehog protein is a potential hedgehog agonist. The presence of BCC characteristics or distinguishing features can easily be detected in BCC cultures. BCCs have a variety of distinguishing characteristics. Peripheral palisading and stromal epidermal rifts are histological markers of BCCs. Not all BCCs have both of these characteristics. Cells of BCCs also have a high nuclear/cytoplamic ratio. A variety of molecular markers for BCCs also exist. Markers that indicate activation of the hedgehog signaling pathway are typically overexpressed in BCCs. Such markers may include tc or gli-1 expression levels.

Expression of ptc and gli genes is activated by the hedgehog signaling pathway, including ptc-l,ptc-2, gli-1, gli-2 and gli-3. gli-1 expression is most consistently correlated with hedgehog signaling activity across a wide range of tissues and disorders, while gli-3 is somewhat less so. The gli genes encode transcription factors that activate expression of many genes needed to elicit the full effects of hedgehog signaling. However, the Gli-3 transcription factor can also act as a repressor of hedgehog effector genes, and therefore, expression of gli-3 can cause a decreased effect of the hedgehog signaling pathway. Whether Gli-3 acts as a transcriptional activator or repressor depends on post-translational events, and therefore it is expected that methods for detecting the activating form (versus the repressing form) of Gli-3 protein would also be a reliable measure of hedgehog pathway activation, gli-2 gene expression and activity are similar to gli-3. The gli-1 gene is strongly expressed in a wide array of cancers, hyperplasias and immature lungs, and serves as a marker for the relative activation of the hedgehog pathway. In addition, tissues, such as immature lung, that have high gli gene expression are strongly affected by hedgehog inl ibitors. Accordingly, it is contemplated that the detection of gli gene expression may be used as a powerful predictive tool to identify tissues and disorders that will particularly benefit from treatment with a hedgehog antagonist.

In preferred embodiments, gli-1 ox ptc expression levels are detected, either by direct detection of the transcript or by detection of protein levels or activity. Transcripts may be detected using any of a wide range of techniques that depend primarily on hybridization of probes to the gli-1 transcripts or to cDNAs synthesized therefrom. Gene expression may also be detected by measuring the expression ofa reporter gene fused to the enhancer or promoter region for a gene of interest. Reporter genes may be essentially any gene that produces an easily measurable product. Preferred reporter genes encode proteins such as luciferase {luc gene), beta-galactosidase {lacZ), beta-glucuronidase {GUS), and green fluorescent protein (and variants such as RFP, YFP, CFP and BFP). Other well known techniques for measuring gene expression include Northern blotting, reverse-transcriptase PCR and microarray analysis of transcript levels, as well as in situ hybridization assays. Methods for detecting Gli or Patched protein levels include Western blotting, immunoprecipitation, two-dimensional polyacrylamide gel electrophoresis (2D SDS-PAGE)(preferably compared against a standard wherein the position of the Gli proteins has been determined), and mass spectroscopy. Mass spectroscopy may be coupled with a series of purification steps to allow high-throughput identification of many different protein levels in a particular sample. Mass spectroscopy and 2D SDS-PAGE can also be used to identify post-transcriptional modifications to proteins including proteolytic events, ubiquitination, phosphorylation, lipid modification etc. Gli activity may also be assessed by analyzing binding to substrate DNA or in vitro transcriptional activation of target promoters. Gel shift assays, DNA footprinting assays and DNA-protein crosslinking assays are all methods that may be used to assess the presence of a protein capable of binding to Gli binding sites on DNA. BCCs also tend to express a very high level (relative to neighboring epidermal cells) of keratin 14. BCCs tend to express a lower level of suprabasalar epidermal differentiation markers (keratin 10 and loricrin) and hemidesmosomal components (BP180, beta.4 integrin, a6 integrin, gamma.2 chain of LAM5). Also, diffuse staining of Bcl2 antigen can be seen within BCCs. These markers may be detected by methods similar to those described for gli and patched above.

In certain embodiments, BCC cultures exhibit at least one of the above characteristics. In preferred embodiments, BCC cultures exhibit peripheral palisading and/or stromal epidermal rifting. In particularly preferred embodiments, BCC cultures also exhibit overexpression of a hedgehog-activated gene such as gli-1 oxptc-1. In other embodiments, BCC cultures exhibit at least one histological characteristic and a change in expression of at least three of the following genes: ptc-1, gli-1, keratin 14, keratin 10, loricrin, BP180, beta.4 integrin and a6 integrin. Test compounds of the invention comprise essentially any substance. In certain embodiments, the subject test compounds are organic molecules having a molecular weight less than 2500 amu, more preferably less than 1500 amu, and even more preferably less than 750 amu, and are capable of modulating at least some of the biological activities of the hedgehog signaling pathway, preferably specifically in target cells.

In other embodiments, subject test compounds are polypeptides. In particularly preferred embodiments, polypeptides of the invention are mutant forms of hedgehog that are either hyperactive or act as antagonists, inl ibiting the hedgehog pathway. In other embodiments, the subject polypeptides may be an antibody, including monoclonal antibodies, diabodies, single chain antibodies, etc. In yet a further embodiment, polypeptides can be expressed from a cDNA expression library or a phage display library. The subject methods may also be used to screen libraries of single chain antibodies or libraries of small oligopeptides. Methods for generating and screening cDNA expression libraries and phage display libraries are well known in the art. cDNA libraries of the invention may be generated from essentially any organism, tissue or cell type. The general principle for generating such libraries is well known and involves isolating mRNA from an organism, tissue or cell type. The mRNA is then converted into cDNA by reverse transcriptase. The resulting cDNA can then be cloned into any of various vectors for expression in a host cell type. Libraries of single chain antibodies with extraordinary diversity can also be generated by a variety of techniques. Specific methods are described in detail elsewhere (Sblattero et al. (2000) Nature Biotechnology 18: 75-80; U.S. Patent 4,946,778; U.S. Patent 5,969,108; U.S. 5,733,743; U.S. Patent 5,223,409).

In general, individual clones from the above libraries may be isolated and caused to produce the particular polypeptide. Many parallel BCC cultures are produced and placed in separate culture wells. Each of these can then be contacted with a different compound from the library, and each compound classified as an agonist, antagonist or neither based on its effect on BCC characteristics. For high throughput screening, it is preferable to measure a readily measurable BCC characteristic such as a reporter gene. The most widely used techniques for screening large gene libraries typically comprises cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates relatively easy isolation of the vector encoding the gene whose product was detected. Each of the illustrative assays described below are amenable to high through-put analysis as necessary to screen large numbers of clones.

In yet another screening assay, the candidate gene products are displayed on the surface of a cell or viral particle, and the ability of particular cells or viral particles to modulate BCC characteristics is detected. For instance, in the filamentous phage system, foreign peptide sequences can be expressed on the surface of infectious phage. Since each infectious phage displays the combinatorial gene product on its surface, if a particular phage is recovered from an assay, the phage can be amplified by another round of infection, and the protein of interest can easily be recovered. The group of almost identical E.coli filamentous phages Ml 3, fd, and f 1 are most often used in phage display libraries, as either of the phage glTT or gVIII coat proteins can be used to generate fusion proteins without disrupting the ultimate packaging of the viral particle (Ladner et al. PCT publication WO 90/02909; Garrard et al, PCT publication WO 92/09690; Marks et al. (1992) J. Biol. Chem. 267:16007-16010; Griffths et al. (1993) EMBO J 12:725-734; Clackson et al. (1991) Nature 352:624-628; and Barbas et al. (1992) PNAS 89:4457-4461).

Exemplary organic molecule hedgehog antagonists of the invention include cyclopamine, compound A, tomatidine, jervine, AY9944, triparanol, compound B, forskolin, cAMP, dibutyryl cAMP (and other hydrophobically modified cAMP variants) and fuctionally effective derivatives thereof. Functionally effective derivatives, compositions and methods for making such compounds are described in detail in the following co-pending U.S. Patent applications: Baxter et al., 09/663,835; Beachy et al. entitled "Inhibitors of hedgehog signaling pathways, compositions and uses related thereto" filed October 10, 2000; Baxter et al. "Mediators of hedgehog signaling pathway, compositions and uses related thereto" filed October 13, 2000; Philip Beachy, "Regulators of the hedgehog pathway, compositions and uses related thereto" filed October 13, 2000; Guicherit et al. "Mediators of Hedgehog Signaling Pathways, compositions and uses related thereto" filed November 9, 2000. These applications are incorporated by reference herein in their entirety.

In certain aspects, BCC therapeutics of the invention will cause cell death in BCC cultures. The ability of a BCC therapeutic to cause cell death may be monitored by detecting levels of any of various markers for apoptosis. Molecular markers for apoptosis may include expression of pro-apoptotic genes or proteins, or expression of other genes or proteins that are induced by apoptosis. Many of these latter are in fact anti-apoptotic factors induced to protect the dying cells. Examples of markers include caspases (eg. caspase 3), Bcl-2, p53, p65/RelA and other Bel and Bax proteins. V. Hedgehog Genes and Proteins

The polypeptide portion of the hedgehog compositions of the subject method can be generated by any of a variety of techniques, including purification of naturally occurring proteins, recombinantly produced proteins and synthetic chemistry. Polypeptide forms of the hedgehog therapeutics are preferably derived from vertebrate hedgehog proteins, e.g., have sequences corresponding to naturally occurring hedgehog proteins, or fragments thereof, from vertebrate organisms. However, it will be appreciated that the hedgehog polypeptide can correspond to a hedgehog protein (or fragment thereof) which occurs in any metazoan organism. The various naturally-occurring hedgehog proteins from which the subject therapeutics can be derived are characterized by a signal peptide, a highly conserved N-terminal region, and a more divergent C-terminal domain. In addition to signal sequence cleavage in the secretory pathway (Lee, J.J. et al. (1992) Cell 71 :33-50; Tabata, T. et al. (1992) Genes Dev. 2635-2645; Chang, D.E. et al. (1994)

Development 120:3339-3353), hedgehog precursor proteins naturally undergo an internal autoproteolytic cleavage which depends on conserved sequences in the C- terminal portion (Lee et al. (1994) Science 266:1528-1537; Porter et al. (1995) Nature 374:363-366). This autocleavage leads to a 19 kD N-tenninal peptide and a C-terminal peptide of 26-28 kD (Lee et al. (1992) supra; Tabata et al. (1992) supra; Chang et al. (1994) supra; Lee et al. (1994) supra; Bumcrot, D.A., et al. (1995) Mol. Cell. Biol. 15:2294-2303; Porter et al. (1995) supra; Ekker, S.C. et al. (1995) Curr. Biol. 5:944-955; Lai, C.J. et al. (1995) Development 121:2349-2360). The N- terminal peptide stays tightly associated with the surface of cells in which it was synthesized, while the C-terminal peptide is freely diffusible both in vitro and in vivo (Lee et al. (1994) supra; Bumcrot et al. (1995) supra; Mart', E. et al. (1995) Development 121:2531 -25 l; Roelink, H. et al. (1995) Cell 81:445-455). Cell surface retention of the N-terminal peptide is dependent on autocleavage, as a truncated form of hedgehog encoded by an RNA which terminates precisely at the normal position of internal cleavage is diffusible in vitro (Porter et al. (1995) supra) and in vivo (Porter, J.A. et al. (1996) Cell 86, 21-34). Biochemical studies have shown that the autoproteolytic cleavage of the hedgehog precursor protein proceeds through an internal thioester intermediate which subsequently is cleaved in a nucleophilic substitution. It is suggested that the nucleophile is a small lipophilic molecule, more particularly cholesterol, which becomes covalently bound to the C- terminal end of the N-peptide (Porter et al. (1996) supra), tethering it to the cell surface.

The vertebrate family of hedgehog genes includes at least four members, e.g., paralogs of the single drosophila hedgehog gene (SEQ ID No. 19). Three of these members, herein referred to as Desert hedgehog {Dhh), Sonic hedgehog {Shh) and Indian hedgehog {Ihh), apparently exist in all vertebrates, including fish, birds, and mammals. A fourth member, herein referred to as tiggie-winkle hedgehog {Thh), appears specific to fish. According to the appended sequence listing, (see also Table 1) a chicken Shh polypeptide is encoded by SEQ ID No: 1 ; a mouse Dhh polypeptide is encoded by SEQ ID No:2; a mouse Ihh polypeptide is encoded by SEQ ID No:3; a mouse Shh polypeptide is encoded by SEQ ID No: 4 a zebrafish Shh polypeptide is encoded by SEQ ID No:5; a human Shh polypeptide is encoded by SEQ ID No: 6; a human Ihh polypeptide is encoded by SEQ ID No:7; a human Dhh polypeptide is encoded by SEQ ID No. 8; and a zebrafish Thh is encoded by SEQ ID No. 9. Table 1 Guide to hedgehog sequences in Sequence Listing Nucleotide Amino Acid

Chicken Shh SEQ ID No. 1 SEQ ID No. 10

Mouse Dhh SEQ ID No. 2 SEQ ID No. 11

Mouse Ihh SEQ ID No. 3 SEQ ID No. 12

Mouse Shh SEQ ID No. 4 SEQ ID No. 13

Zebrafish Shh SEQ ID No. 5 SEQ ID No. 14

Human Shh SEQ ID No. 6 SEQ ID No. 15

Human Ihh SEQ ID No. 7 SEQ ID No. 16

Human Dhh SEQ ID No. 8 SEQ ID No. 17

Zebrafish Thh SEQ ID No. 9 SEQ ID No. 18

Drosophila HH SEQ ID No. 19 SEQ ID No. 20

In addition to the sequence variation between the various hedgehog homologs, the hedgehog proteins are apparently present naturally in a number of different forms, including a pro-form, a full-length mature form, and several processed fragments thereof. The pro-form includes an N-terminal signal peptide for directed secretion of the extracellular domain, while the full-length mature form lacks this signal sequence. As described above, further processing of the mature form occurs in some instances to yield biologically active fragments of the protein. For instance, sonic hedgehog undergoes additional proteolytic processing to yield two peptides of approximately 19 kDa and 27 kDa, the 19kDa fragment corresponding to an proteolytic N-terminal portion of the mature protein. In addition to proteolytic fragmentation and the addition of one or more lipophilic groups according to the present invention, the hedgehog proteins can be further modified, such as by glycosylation. Bioactive fragments of hedgehog polypeptides of the present invention have been generated and are described in great detail in, e.g., PCT publications WO 95/18856 and WO 96/17924. Moreover, mutagenesis can be used to create modified hh polypeptides, e.g., for such purposes as enhancing therapeutic or prophylactic efficacy, or stability (e.g., ex vivo shelf life and resistance to proteolytic degradation in vivo). Such modified peptides can be produced, for instance, by amino acid substitution, deletion, or addition. Modified hedgehog polypeptides can also include those with altered post-translational processing relative to a naturally occurring hedgehog protein, e.g., altered glycosylation, cholesterolization, prenylation and the like.

In one embodiment, the hedgehog therapeutic is a polypeptide encodable by a nucleotide sequence that hybridizes under stringent conditions to a hedgehog coding sequence represented in one or more of SEQ ID Nos: 1-7. Appropriate stringency conditions which promote DNA hybridization, for example, 6.0 x sodium chloride/sodium citrate (SSC) at about 45°C, followed by a wash of 2.0 x SSC at 50°C, are known to those skilled in the art or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. For example, the salt concentration in the wash step can be selected from a low stringency of about 2.0 x SSC at 50°C to a high stringency of about 0.2 x SSC at 50°C. In addition, the temperature in the wash step can be increased from low stringency conditions at room temperature, about 22°C, to high stringency conditions at about 65°C.

As described in the literature, genes for other hedgehog proteins, e.g., from other animals, can be obtained from mRNA or genomic DNA samples using techniques well known in the art. For example, a cDNA encoding a hedgehog protein can be obtained by isolating total mRNA from a cell, e.g. a mammalian cell, e.g. a human cell, including embryonic cells. Double stranded cDNAs can then be prepared from the total mRNA, and subsequently inserted into a suitable plasmid or bacteriophage vector using any one ofa number of known techniques. The gene encoding a hedgehog protein can also be cloned using established polymerase chain reaction techniques.

Preferred nucleic acids encode a hedgehog polypeptide comprising an amino acid sequence at least 60% homologous or identical, more preferably 70%> homologous or identical, and most preferably 80%) homologous or identical with an amino acid sequence selected from the group consisting of SEQ ID Nos: 8-14.

Nucleic acids which encode polypeptides at least about 90%, more preferably at least about 95%>, and most preferably at least about 98-99% homology or identity with an amino acid sequence represented in one of SEQ ID Nos: 8- 14 are also within the scope of the invention.

In addition to native hedgehog proteins, hedgehog polypeptides preferred by the present invention are at least 60% homologous or identical, more preferably 70% homologous or identical and most preferably 80% homologous or identical with an amino acid sequence represented by any of SEQ ID Nos:8-14. Polypeptides which are at least 90%, more preferably at least 95%, and most preferably at least about 98-

99% homologous or identical with a sequence selected from the group consisting of

SEQ ID Nos:8-14 are also within the scope of the invention.

Isolated hedgehog polypeptides can include all or a portion of the amino acid sequences represented in any of SEQ ID Nos: 10- 18 or 20, or a homologous sequence thereto. Preferred fragments of the subject hedgehog proteins correspond to the N-terminal and C-terminal proteolytic fragments of the mature protein. Bioactive fragments of hedgehog polypeptides are described in great detail in PCT publications WO 95/18856 and WO 96/17924.

With respect to bioactive fragments of hedgehog polypeptide, preferred hedgehog therapeutics include at least 50 (contiguous) amino acid residues of a hedgehog polypeptide, more preferably at least 100 (contiguous), and even more preferably at least 150 (contiguous) residues.

Another preferred hedgehog polypeptide which can be included in the hedgehog therapeutic is an N-terminal fragment of the mature protein having a molecular weight of approximately 19 kDa. There are a wide range of lipophilic moieties with which hedgehog polypeptides can be derivatized. The term "lipophilic group", in the context of being attached to a hedgehog polypeptide, refers to a group having high hydrocarbon content thereby giving the group high affinity to lipid phases. A lipophilic group can be, for example, a relatively long chain alkyl or cycloalkyl (preferably n-alkyl) group having approximately 7 to 30 carbons. The alkyl group may terminate with a hydroxy or primary amine "tail". To further illustrate, lipophilic molecules include naturally-occurring and synthetic aromatic and non- aromatic moieties such as fatty acids, esters and alcohols, other lipid molecules, cage structures such as adamantane and buclαninsterfullerenes, and aromatic hydrocarbons such as benzene, perylene, phenanthrene, anthracene, naphthalene, pyrene, chrysene, and naphthacene.

Particularly useful as lipophilic molecules are alicyclic hydrocarbons, saturated and unsaturated fatty acids and other lipid and phospholipid moieties, waxes, cholesterol, isoprenoids, terpenes and polyalicyclic hydrocarbons including adamantane and buckminsterfullerenes, vitamins, polyethylene glycol or oligoethylene glycol, (Cl-C18)-alkyl phosphate diesters, -O-CH2-CH(OH)-O-(C12- C18)-alkyl, and in particular conjugates with pyrene derivatives. The lipophilic moiety can be a lipophilic dye suitable for use in the invention include, but are not limited to, diphenylhexatriene, Nile Red, N-phenyl-1-naphthylamine, Prodan, Laurodan, Pyrene, Perylene, rhodamine, rhodamine B, tetramethylrhodamine, Texas Red, sulforhodamine, 1 , 1 '-didodecyl-3 ,3 ,3 ',3 'tetramethylindocarbocyanine perchlorate, octadecyl rhodamine B and the BODIPY dyes available from Molecular Probes Inc.

Other exemplary lipophilic moietites include aliphatic carbonyl radical groups include 1- or 2-adamantylacetyl, 3-methyladamant-l-ylacetyl, 3-methyl-3- bromo-1-adamantylacetyl, 1-decalinacetyl, camphoracetyl, camphaneacetyl, noradamantylacetyl, norbornaneacetyl, bicyclo[2.2.2.]-oct-5-eneacetyl, 1- methoxybicyclo[2.2.2.]-oct-5-ene-2-carbonyl, cis-5-norbornene-endo-2,3- dicarbonyl, 5-norbornen-2-ylacetyl, (lR)-( - )-myrtentaneacetyl, 2-norbornaneacetyl, anti-3-oxo-tricyclo[2.2.L0<2,6> ]-heptane-7-carbonyl, decanoyl, dodecanoyl, dodecenoyl, tetradecadienoyl, decynoyl or dodecynoyl. VII. Pharmaceutical compositions

While it is possible for a compound of the present invention to be administered alone, it is preferable to administer the compound as a pharmaceutical formulation (composition). The hedgehog agonists and antagonists according to the invention may be formulated for administration in any convenient way for use in human or veterinary medicine. In certain embodiments, the compound included in the pharmaceutical preparation may be active itself, or may be a prodrag, e.g., capable of being converted to an active compound in a physiological setting.

Thus, another aspect of the present invention provides pharmaceutically acceptable compositions comprising a therapeutically effective amount of one or more of the compounds described above, formulated together with one or more pharmaceutically acceptable carriers (additives) and/or diluents. As described in detail below, the pharmaceutical compositions of the present invention may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, boluses, powders, granules, pastes for application to the tongue; (2) parenteral administration, for example, by subcutaneous, intramuscular or intravenous injection as, for example, a sterile solution or suspension; (3) topical application, for example, as a cream, ointment or spray applied to the skin; or (4) intravaginally or intrarectally, for example, as a pessary, cream or foam. However, in certain embodiments he subject compounds may be simply dissolved or suspended in sterile water. In certain embodiments, the pharmaceutical preparation is non-pyrogenic, i.e., does not elevate the body temperature of a patient. The phrase "therapeutically effective amount" as used herein means that amount of a compound, material, or composition comprising a compound of the present invention which is effective for producing some desired therapeutic effect by overcoming a hedgehog gain-of-function phenotype in at least a sub-population of cells in an animal and thereby blocking the biological consequences of that pathway in the treated cells, at a reasonable benefit/risk ratio applicable to any medical treatment. The phrase "pharmaceutically acceptable" is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio. The phrase "pharmaceutically acceptable carrier" as used herein means a pharmaceutically acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in carrying or transporting the subject agonists and antagonists from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be "acceptable" in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient. Some examples of materials which can serve as pharmaceutically acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacantli; (5) malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) phosphate buffer solutions; and (21) other non-toxic compatible substances employed in pharmaceutical formulations.

As set out above, certain embodiments of the present hedgehog agonists and antagonists may contain a basic functional group, such as amino or alkylamino, and are, thus, capable of forming pharmaceutically acceptable salts with pharmaceutically acceptable acids. The term "pharmaceutically acceptable salts" in this respect, refers to the relatively non-toxic, inorganic and organic acid addition salts of compounds of the present invention. These salts can be prepared in situ during the final isolation and purification of the compounds of the invention, or by separately reacting a purified compound of the invention in its free base form with a suitable organic or inorganic acid, and isolating the salt thus formed. Representative salts include the hydrobromide, hydrochloride, sulfate, bisulfate, phosphate, nitrate, acetate, valerate, oleate, palmitate, stearate, laurate, benzoate, lactate, phosphate, tosylate, citrate, maleate, fumarate, succinate, tartrate, napthylate, mesylate, glucoheptonate, lactobionate, and laurylsulphonate salts and the like. (See, for example, Berge et al. (1977) "Pharmaceutical Salts", J Pharm. Sci. 66:1-19)

The pharmaceutically acceptable salts of the subject compounds include the conventional nontoxic salts or quaternary ammonium salts of the compounds, e.g., from non-toxic organic or inorganic acids. For example, such conventional nontoxic salts include those derived from inorganic acids such as hydrochloride, hydrobromic, sulfuric, sulfamic, phosphoric, nitric, and the like; and the salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, palmitic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicyclic, sulfanilic, 2-acetoxybenzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isothionic, and the like.

In other cases, the compounds of the present invention may contain one or more acidic functional groups and, thus, are capable of forming pharmaceutically acceptable salts with pharmaceutically acceptable bases. The term "pharmaceutically acceptable salts" in these instances refers to the relatively non-toxic, inorganic and organic base addition salts of compounds of the present invention. These salts can likewise be prepared in situ during the final isolation and purification of the compounds, or by separately reacting the purified compound in its free acid form with a suitable base, such as the hydroxide, carbonate or bicarbonate of a pharmaceutically acceptable metal cation, with ammonia, or with a pharmaceutically acceptable organic primary, secondary or tertiary amine. Representative alkali or alkaline earth salts include the lithium, sodium, potassium, calcium, magnesium, and aluminum salts and the like. Representative organic amines useful for the formation of base addition salts include ethylamine, diethylamine, ethylenediamine, ethanolamine, diethanolamine, piperazine and the like. (See, for example, Berge et al., supra)

Wetting agents, emulsifiers and lubricants, such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, release agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the compositions.

Examples of pharmaceutically acceptable antioxidants include: (1) water soluble antioxidants, such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like; (2) oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol, and the like; and (3) metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like. Formulations of the present invention include those suitable for oral, nasal, topical (including buccal and sublingual), rectal, vaginal and/or parenteral administration. The formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, the particular mode of administration. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound which produces a therapeutic effect. Generally, out of one hundred per cent, this amount will range from about 1 per cent to about ninety- nine percent of active ingredient, preferably from about 5 per cent to about 70 per cent, most preferably from about 10 per cent to about 30 per cent.

Methods of preparing these formulations or compositions include the step of bringing into association a compound of the present invention with the carrier and, optionally, one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association a compound of the present invention with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product.

Formulations of the invention suitable for oral administration may be in the form of capsules, cachets, pills, tablets, lozenges (using a flavored basis, usually sucrose and acacia or tragacanth), powders, granules, or as a solution or a suspension in an aqueous or non-aqueous liquid, or as an oil-in- water or water-in-oil liquid emulsion, or as an elixir or syrup, or as pastilles (using an inert base, such as gelatin and glycerin, or sucrose and acacia) and/or as mouth washes and the like, each containing a predetermined amount of a compound of the present invention as an active ingredient. A compound of the present invention may also be administered as a bolus, electuary or paste.

In solid dosage forms of the invention for oral administration (capsules, tablets, pills, dragees, powders, granules and the like), the active ingredient is mixed with one or more pharmaceutically acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and/or silicic acid; (2) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose and/or acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents, such as, for example, cetyl alcohol and glycerol monostearate; (8) absorbents, such as kaolin and bentonite clay; (9) lubricants, such a talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof; and (10) coloring agents. In the case of capsules, tablets and pills, the pharmaceutical compositions may also comprise buffering agents. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols and the like. A tablet may be made by compression or molding, optionally with one or more accessory ingredients. Compressed tablets may be prepared using binder (for example, gelatin or hydroxypropylmethyl cellulose), lubricant, inert diluent, preservative, disintegrant (for example, sodium starch glycolate or cross-linked sodium carboxymethyl cellulose), surface-active or dispersing agent. Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.

The tablets, and other solid dosage forms of the pharmaceutical compositions of the present invention, such as dragees, capsules, pills and granules, may optionally be scored or prepared with coatings and shells, such as enteric coatings and other coatings well known in the pharmaceutical-formulating art. They may also be formulated so as to provide slow or controlled release of the active ingredient therein using, for example, hydroxypropylmethyl cellulose in varying proportions to provide the desired release profile, other polymer matrices, liposomes and/or microspheres. They may be sterilized by, for example, filtration tlirough a bacteria- retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved in sterile water, or some other sterile injectable medium immediately before use. These compositions may also optionally contain opacifying agents and may be of a composition that they release the active ingredient(s) only, or preferentially, in a certain portion of the gastrointestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes. The active ingredient can also be in micro-encapsulated form, if appropriate, with one or more of the above-described excipients.

Liquid dosage forms for oral administration of the compounds of the invention include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredient, the liquid dosage forms may contain inert diluents commonly used in the art, such as, for example, water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (in particular, cottonseed, groundnut, com, germ, olive, castor and sesame oils), glycerol, tefrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, coloring, perfuming and preservative agents.

Suspensions, in addition to the active compounds, may contain suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.

It is known that sterols, such as cholesterol, will form complexes with cyclodextrins. Thus, in preferred embodiments, where the inhibitor is a steroidal alkaloid, it may be formulated with cyclodextrins, such as α-, β- and γ-cyclodextrin, dimethyl- β cyclodextrin and 2-hydiOxypropyl-β-cyclodextrin.

Formulations of the pharmaceutical compositions of the invention for rectal or vaginal administration may be presented as a suppository, which may be prepared by mixing one or more compounds of the invention with one or more suitable nonirritating excipients or carriers comprising, for example, cocoa butter, polyethylene glycol, a suppository wax or a salicylate, and which is solid at room temperature, but liquid at body temperature and, therefore, will melt in the rectum or vaginal cavity and release the active hedgehog antagonist.

Formulations of the present invention which are suitable for vaginal administration also include pessaries, tampons, creams, gels, pastes, foams or spray formulations containing such carriers as are known in the art to be appropriate.

Dosage forms for the topical or transdermal administration of a compound of this invention include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants. The active compound may be mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants which may be required.

The ointments, pastes, creams and gels may contain, in addition to an active compound of this invention, excipients, such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof. Powders and sprays can contain, in addition to a compound of this invention, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances. Sprays can additionally contain customary propellants, such as chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, such as butane and propane.

Transdermal patches have the added advantage of providing controlled delivery of a compound of the present invention to the body. Such dosage forms can be made by dissolving or dispersing the hedgehog agonists and antagonists in the proper medium. Absorption enhancers can also be used to increase the flux of the hedgehog agonists and antagonists across the skin. The rate of such flux can be controlled by either providing a rate controlling membrane or dispersing the compound in a polymer matrix or gel.

Ophthalmic formulations, eye ointments, powders, solutions and the like, are also contemplated as being within the scope of this invention. Pharmaceutical compositions of this invention suitable for parenteral administration comprise one or more compounds of the invention in combination with one or more pharmaceutically acceptable sterile isotonic aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, or sterile powders which may be reconstituted into sterile injectable solutions or dispersions just prior to use, which may contain antioxidants, buffers, bacteriostats, solutes which render the formulation isotonic with the blood of the intended recipient or suspending or thickening agents.

Examples of suitable aqueous and nonaqueous carriers which may be employed in the pharmaceutical compositions of the invention include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants. These compositions may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of the action of microorganisms may be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption such as aluminum monostearate and gelatin.

In some cases, in order to prolong the effect of a drug, it is desirable to slow the absorption of the drag from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material having poor water solubility. The rate of absorption of the drag then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the subject compounds in biodegradable polymers such as polylactide-polyglycolide. Depending on the ratio of drug to polymer, and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the drag in liposomes or microemulsions which are compatible with body tissue.

When the compounds of the present invention are administered as pharmaceuticals, to humans and animals, they can be given per se or as a pharmaceutical composition containing, for example, 0J to 99.5% (more preferably, 0.5 to 90%) of active ingredient in combination with a pharmaceutically acceptable carrier.

The addition of the active compound of the invention to animal feed is preferably accomplished by preparing an appropriate feed premix containing the active compound in an effective amount and incorporating the premix into the complete ration. Alternatively, an intermediate concentrate or feed supplement containing the active ingredient can be blended into the feed. The way in which such feed premixes and complete rations can be prepared and administered are described in reference books (such as "Applied Animal Nutrition", W.H. Freedman and CO., San Francisco, U.S.A., 1969 or "Livestock Feeds and Feeding" O and B books, Corvallis, Ore., U.S.A., 1977). Examples:

1. BCC chorioallantoic membrane culture: Materials & Equipment BL-2 lab, tissue culture hood and incubator, Hanlc's buffer (GIBCO 14175-095), Penicillin/Streptomycin (GIBCO 15140-122), Fungizone™ (GIBCO 15290-018), h.c. Fungizone™ (Sigma A 2411, 250mg), dissecting tools including curved scissors, chick incubator (with shaker and thermometer), fertilized chick eggs, 6x magnifying glass with light bulb, 20 gauge needles, 10 ml syringes, tuberculin syringes, Scotch tape, candler. Preparations:

Add 5ml penicillin/streptomycin and 1ml Fungizone™ to Hank's buffer. Add 50ml sterile ddH 0 to he. Fungizone™ powder in plastic tube (e.g. Falcon tube), keep in refrigerator. Start incubation of chick eggs (lay flat) 4-7 days before planned transplantation. Suction off 1.5ml of albumin each with 20g needle on day 2 or 3 , seal with Scotch tape. Methods:

1) Determine which eggs hold developing embryo using candler, make a window by tightly applying transparent tape (e.g. Scotch tape) cross-wise, then cutting a 0.5 inch circular hole using curved scissors; re-seal with tape, put back in incubator.

2) After incubation of mouse embryonic day 17 (E17) slcin, add several drops of serum, swirl dish and suction off de-activated dispase.

3) Upon arrival, rinse BCC sample (eg. Mohs shavings or curettage) once in buffer, then once briefly in 70% ethanol, then buffer and add 2 drops of h.c.

Fungizone™, followed by 2 rinses in buffer. 4) Under the dissecting microscope, trim off as much normal looking skin as possible. Remove hair follicles.

5) Record information on BCCs received, appearance etc.

6) Open windows and carefully tear two 3mm holes, each between 2 larger blood vessels of the chorioallantoic membrane (CAM) with a tuberculin syringe.

7) Transfer one transplant dermal-side down onto each CAM opening, seal and grow.

8) On day 5 dissect transplant out, rinse once in Hank's buffer, and fix in 4% paraformaldehe (PFA) overnight at 4 deg. C. 9) On day 6, rinse twice with PBS on nutator, then embed in 1% agarose for histology.

Results:

Using the above method, a BCC sample from a human or mouse can be maintained for five or more days (Figure 4). During this time, the typical histological indicators of BCC are maintained, as seen by the clusters of dark staining cells with high nuclear/cytoplasmic ratio, the palisading of cells at the edges of the clusters, and the clefts formed between the BCC clusters and the surrounding stroma (Figure 4). In addition, the high level of gli-1 expression is maintained. The method works well even with Mohs shavings, which are very thin shavings of tissue removed from BCCs. Mohs shavings often contain little or no stromal material. To our knowledge, this represents the first ex vivo culture system that permits maintenance of a BCC in the absence of stromal materials.

Potential therapeutics may be administered to the BCC culture, followed by histological examination to determine the effects of such test therapeutics. In addition expression of various BCC marker genes (e.g. ptc or gli) may be determined.

2. Human BCC explant assay:

With Dermis Feeder:

Material and equipment BL-2 lab, tissue culture hood and incubator, Hanlc's buffer (GIBCO 14175-095),

DMEM (GIBCO 11995-065), lOOOx Penicillin/Streptomycin (GIBCO 15140-122),

Fungizone™ (GIBCO 15290-018), h.c. Fungizone™ (Sigma A 2411, 250mg), dispase II (Roche 295 825), collagen inserts (Becton Dickinson, #40565), Mafrigel (Becton Dickinson 354592), hydrocortisone (Sigma H-0135), fetal bovine serum (Hyclone lot AGC 6341), dissecting tools, repeat pipettor + 2.5 and 12.5 ml tips. Preparations:

Order El 7 ptc.LacZ Dl 1 embryos on the day of the experiment or ahead of time. Pups can be kept in ice inside a plastic tube for up to 2 days. Add 5ml Pen/Strep and 1 ml Fungizone™ to Hank's buffer. Freeze dispase as aliquots of 5ml, Fungizone™ as 1ml aliquots. Add 50ml sterile ddH20 to h.c. Fungizone™.

Solutions:

Human explant culture medium (HEM) lx DMEM 50ml

5ug/ml hydrocortisone 250 ul

0.5% FBS 50 ul

Pen/Sfrep 0.5ml

Fungizone 50ul b-mercaptoethanol 0.5ul

Protocol:

I) Strip the back skin off of 2-3 mouse embryos and put the dermal side down in 5cm dish in cold Hank's buffer. 2) Rinse, suction off buffer and stretch skin out as flat as possible, pulling out the edges using tweezers.

3) Float the dish carefully with 10ml dispase (skin will float and remain stretched).

4) Incubate in TC incubator for 1 hr. 5) After incubation, add several drops of serum, swirl dish and suction off deactivated dispase.

6) Rinse 2x with Hank' s buffer, suction off supernatant.

7) Remove epidermal sheets completely (mesenchyme will be gooey).

8) Cut mesenchyme into 5x5mm pieces using a sterile scalpel. 9) Put on ice, covered; get BCC sample.

10) Take BCC curettage as is, do not rinse.

II) Thaw 1 Mafrigel well on ice, inside Petri dish 12) Trim off 2-3mm of edge on one side, fix overnight on PFA for preculture control

13) Under dissecting scope, trim off as much normal looking skin as possible (very flat) inside ethanol-washed and rinsed silicone elastomer plate. 14) Record information on BCC samples received, appearance, size, etc.

15) Cut BCCs in 2.5-4mm size pieces (depends upon thickness)

16) Put medium in well plate.

17) Put dermis pieces inside collagen plate and put 20ul Mafrigel on top of each piece of dermis. 18) Put one piece of BCC on top, epidermal side up where discernible, on dermis + Mafrigel.

19) Let culture gellify and incubate in 10% CO2/36 deg. C in incubator.

20) Change medium on day 2.

21) On day 3, collect and fix in 4% PFA O/N at 4 deg. C. On day 4, carefully rinse 2-3x with PBS on nutator, then transfer to 70% EtOH. Histology methods:

Standard paraffin-histology was performed on all specimens. Sections were cleared and counterstained with hematoxylin and eosin.

For g/z-1 in situ hybridization, sections were cleared, re-hydrated, digested with proteinase K, acetylated and hybridized with [33P]- labeled RNA probes over night. After high stringency post-hybridization washes, slides dipped in photoemulsion and incubated for 11 days. After development, sections were counter-stained with hematoxylin and imaged with dark-field and bright-field illumination. Using Photoshop software, the dark-field image was artificially colored in red and superimposed onto the bright-field image.

For the detection of keratin 14, standard immunohistochemistry was performed using a polyclonal antibody specific for keratin 14, followed by biotin- DAB detection.

For treatment with hedgehog antagonist, compound B, BCCs were grown and processed as described in protocol "Without dermis feeder". Quantitative radioactive in situ hybridizations was performed on paraformaldehyde-fixed, paraffin-embedded histological sections, using a protocol modified from Wilkinson et al. (1987). Briefly, 7mm sections were cleared, re-hydrated, digested with proteinase K, acetylated and hybridized with [33P]~ labeled RNA probes over night. After high stringency post-hybridization washes, slides were exposed to a Phosphorlmager screen in the dark at room temperature for 4-5 days. After developing, the [33 P] -signal was scanned using a Storm scanner (Molecular

Dynamics). Individual basal cell islands were selected and the signal quantified and expressed in average counts/pixel using ImageQuant 1.0 software.

For the detection of caspase 3, an early indicator of apoptosis, standard immunohistochemistry was performed using a monoclonal antibody specific for activate human caspase 3. The blue chromagen precipitate is X-gal. Results:

The method creates a sandwich of BCC with Mafrigel and a dermis feeder (Figure 5). Using the above method, a BCC sample from a human or mouse can be maintained for five or more days (Figure 6). During this time, the typical histological indicators of BCC are maintained, including the islands of dark staining cells with a high nuclear/cytoplasmic ratio intruded into the dermis. Peripheral palisading and clefting between the epidermal BCC islands and the surrounding stroma are also visible (see also Figure 7). In addition, the high level of gli-1 expression is maintained and the BCC marker keratin 14 continues to be expressed. The method works well even with Mohs shavings, which are very thin shavings of tissue removed from BCCs. Mohs shavings often contain little or no stromal material.

Without Dermis Feeder: Material and equipment BL-2 lab, tissue culture hood and incubator, Hanlc's buffer (GIBCO 14175-095), DMEM (GIBCO 11995-065), lOOOx Penicillin/Streptomycin (GIBCO 15140-122), Fungizone™ (GIBCO 15290-018), h.c. Fungizone™ (Sigma A 2411, 250mg), collagen inserts (Becton Dickinson, #40565), Mafrigel (Becton Dickinson 354592), hydrocortisone (Sigma H-0135), fetal bovine serum (FBS) (Hyclone lot AGC 6341), dissecting tools, repeat pipettor + 2.5 and 12.5 ml tips, sterile syringes and 30 gauge needles. Test compound (eg. hedgehog antagonist or agonist). Preparations:

Add 5ml Pen/Strep and 1 ml Fungizone™ to Hank's buffer. Freeze dispase as aliquots of 5ml, Fungizone™ as 1ml aliquots. Add 50ml sterile ddH20 to h.c.

Fungizone™ powder. Solutions:

Human explant culture medium 2 (HEM2) lx DMEM 50ml

0.5% FBS 50 ul

Pen/Strep 0.5ml Fungizone™ 50ul

2-mercaptoethanol 0.5ul

Protocol:

1) Rinse BCC specimen shavings once in Hank's buffer. Ifthere are a lot of hair follicles, rinse once briefly in 70% ethanol, then in buffer. 2) Under the dissecting microscope, trim off as much normal looking skin as possible; remove hair follicles and rinse, if necessary.

3) Record information on BCCs received, appearance, size etc.

4) In pefri dish with Hanks buffer, cut BCCs in 3-4 mm big pieces with roughly the same amount of basal cell islands in each, put on ice. 5) Put 800 μl medium w/ or w/o test compound (as desired) into each well of 12-well plate; record groups.

6) If desired, inject test compound in 0.9% NaCl into tissue and transfer dermal side down into collagen inserts.

7) Change medium on day 3. 8) The day of collection, rinse carefully from the insert with Hanlc's buffer, and fix in 4% PFA O N at 4 deg. C.

Results:

Using this method, BCC curettage specimens are grown in skin organotypic culture at the air-liquid interface, sitting on collagen I inserts. BCCs cultured in this manner maintain high levels of gli-1 expression as well as many histological characteristics of BCC. Figure 7 shows densely staining BCC islands maintained in culture or 3 or 4 days. Stromal/epithelial clefting is evident. Potential therapeutics may be administered to the BCC culture, whether cultured with or without the dermis feeder. BCC cultures may then be analyzed for histological features and hedgehog-regulated gene expression to determine the effects of such test therapeutics. For example, a human BCC explant was treated with Compound B, a hedgehog antagonist. This compound notably decreased gli-1 expression in the BCC explant (Figure 8). In addition, Compound B causes increased apoptosis in the BCC culture (Figure 9). Caspase 3 is a marker for apoptosis, and immunohistochemical staining shows increased caspase 3 in BCC islands exposed to compound B. This suggests that Compound B, as well as other hedgehog antagonists, would be useful as a therapy for BCC. In addition, this demonstrates the utility of the culture system for characterizing potential BCC therapeutics. 3. Skin punch assay Protocol for Skin Punch Assay 1. Collect E15.5-EI7.5 embryos and use tail for X-gal staining

2. Keep embryos in Hanlc's at 4 degree.

3. Pre-add 1 ml of culture medium to the insert and keep them in the incubator

4. 1-2 hrs later, identify transgenic embryos and peel off back skin.

5. Put skin on a flat surface (epidermis up) 5. Use 2 mm skin punch to cut out skin, you can easily get 15-20 pieces/embryo, pay attention to the orientation (epidermis up)

6. Suck off medium and gently place skin explant to the insert and press a little bit. Again epidermis up.

7. Add 1 ml culture medium with or w/o SHH to the well, not the insert. 8. Leave it at incubator, change medium every 2 days.

9. X-gal stain overnight. Note:

To make 500 ml culture media combine: DMEM(Cat. No. 11995-065, GIBCO): 360ml F12 (Cat. No. 11765-054, GIBCO): 120ml FBS (Hyclone): 25ml EGF (Clonetics 4107, 0. 1 lug/ml, dilute 10 ug,/ml with PBS) 0.5ml Insulin(Clonetics 4025, 10 mg/ml), 0.5 ml Hydrocortisone(Clonetics 4036, 1 mg/ml), 0.5 ml Glutamine: 5 ml penicillin/streptomycin: 5 ml 2-mercaptoethanol: 5 ul.

2. Octyl-SHH, 2ug/ml final.

3. 12-well collagen I inserts (Becton Dickinson or Collaborative Research, Cat. No 40565)

4. After a four day treatment with SHH, skin punch will exhibit features characteristic of BCC.

Results:

2mm circles of skin were put into a transwell and cultured in an air-liquid interface according to the protocol above (Figures 10, 11). Skin punches from mice of different stages were cultured in this system. Shh proteins, such as Shh modified with the hydrophobic moiety octyl maleimide are able to induce BCC-like moφhological change within 4-10 days depending on the stage in which skins were collected. Figure 12 shows that Shh treatment induced expression of the ptc-lacZ reporter gene, indicating activation of the hedgehog pathway. In addition, Shh promotes the formation of BCC islands intruding into the dermis. (Figure 12). These islands stain dark with H&E, show peripheral palisading and stromal/epithelial clefting, all characteristics of clinically occuring BCC. Generally speaking, the embryo skin was most responsive and the adult one was the least. Strikingly, BCC-like structures were formed in the 9 month old adult mouse skin at telogen stage which were treated with Shh for 10 days. Jervine, forskolin and compound B have all been found to inhibit Hh pathway and the formation of BCC- like structures in this assay.

5 μM compound B inhibits the ptc-lacZ expression that is normally stimulated by treatment with Shh (Figure 13). The compound B treatment also prevents formation of BCC islands and other histological BCC characteristics (Figure 14).

50 μM forskolin or 10 μM jervine had an effect similar to that of compound B. These hedgehog antagonists were sufficient to inhibit the formation of BCC characteristics in the skin punch assay, in the presence of 2 μg/ml Octyl-SHH. For example, ptc-lacZ expression was inhibited by forskolin (FK) and jervine (Figure 15).

We are now using this assay to test Hh agonists and antagonists as well as Hh agonists. Since this assay is very simple and manageable, it can be used to screen large numbers of small molecules as well as DNA expression libraries. 4. Mouse BCC model

A. UV irradiation of Ptc+/- mice

1). UVB irradiation of Ptc+/- adult mice UN irradiation was initiated on mice with C57B6/129/B6D2F1 mixed background.

We have finished UN irradiation on Ptc+/- mice with this genetic background and the mice are now set aside for following up BCC lesion development. The mice carrying visible BCC will be used for compound testing.

2). UNB irradiation of Ptc+/-;hr/hr double mutants We are now focusing on UV irradiation of Ptc+/-;hr/hr double mutants.. BCC lesions on those double mutants are easy to identify at earlier stage and to follow up since they do not have hair. Also, the double mutants make compound testing much well-controlled.

3). UVB irradiation of pups To accelerate the production of in vivo BCC models, we have started UV irradiation on neonatal Ptc+/- mice at various doses.

Starting with 109 Ptc+/- mice in the UN irradiation group, after several months, 8 mice have small visible BCC lesions (1 mm or bigger).

B. Transplantation of Murine BCC to SCID Mice While it is possible to study a BCC on the mouse on which it grew, it is preferable to transplant the BCC to a different mouse so that BCCs can continue to grow on the UN irradiated mouse. In addition, during transplantation, the BCC can be cut into multiple pieces. Alternatively, a BCC may be cultured as per the skin punch assay described above. A BCC of about 2mm in size is taken out from one of the UV-irradiated

Ptc+Λ mice, #249. The tumor was then cut into 9 small pieces ,and transplanted to SCID mice. Three mice were transplanted and each mouse received 3 pieces of transplants at 3 different sites subcutanously in the belly. Four weeks later, the transplantation sites formed small bumps. One of the bumps was cut out and X-gal stained. The transplant was easily recognized and blue, indicating it has activated Hh pathway. Histologically, the cells in the transplant have nuclear staining of X-gal. Most of them have the features of BCC cells, yet there are some degree of keratinocyte differentiation. With the success of this approach, we would like to expand our efforts and test compounds in the transplanted BCC in the future. 5. Cre-luc assay in keratinocytes for compound testing Using Cre-luc as a reporter, we have established a keratinocytes-based assay for screening PKA activators that may inhibit HH pathway. This assay has been working very well in primary human keratinocytes. To understand the mechanism of how compounds derived from Gli-luc HTS work, we are testing them in Cre-luc assay. If indeed some of compounds activate Cre-luc, it suggests that they may antagonize HH pathway by activating PKA pathway.

Claims

Claims:

1. An organotypic ex vivo BCC culture comprising cells exhibiting BCC microarchitecture.

2. The culture of claim 1, wherein said cells have an active hedgehog signaling pathway.

3. The culture of claim 2, wherein said cells express gli ox ptc.

4. The culture of claim 1 , wherein the cells exhibiting BCC microarchitecture do not form stratified, keratinized epithelial tissue.

5. The culture of claim 1, wherein the BCC microarchitecture comprises one or more of the following features: peripheral palisading, stromal epithelial clefting, invasion of the dermis, clustering of cells with a high nuclear/cytplasmic ratio.

6. The culture of claim 1, further comprising support cells in an amount effective to maintain BCC microarchitecture.

7. The culture of claim 1 wherein said culture is in contact with the chorioallantoic membrane of a bird egg.

8. The culture of claim 1, wherein said culture is in direct or indirect contact with a dermis feeder.

9. The culture of claim 1, wherein said cells are human cells.

10. The culture of claim 1, wherein said culture is at a liquid/air interface.

11. An ex vivo BCC culture comprising:

(a) epidermal cells; and

(b) supporting cells wherein a portion of said epidermal cells exhibit BCC microarchitecture.

12. The culture of claim 11, wherein said epidermal cells have an active hedgehog signaling pathway.

13. The culture of claim 11 , wherein said epidermal cells comprise a hedgehog reporter gene construct.

14. The culture of claim 13, wherein said hedgehog reporter gene construct comprises a ptc-1 or gli-1 promoter portion operably linked to a reporter gene.

15. The culture of claim 11 , wherein said culture is at a liquid/air interface.

16. The culture of claim 11 , wherein said culture retains BCC characteristics for at least 3 days.

17. The culture of claim 11 , further comprising a sufficient amount of exogenous hedgehog protein and/or hedgehog antagonist to promote or maintain BCC-like characteristics.

18. The culture of claim 17, wherein the supporting and epidermal cells derive from a non-cancerous skin sample.

19. The culture of claim 18, wherein the non-cancerous skin sample is an embryonic skin sample.

20. The culture of claim 11, wherein the supporting and epidermal cells are placed on an insert.

21. The culture of claim 20, wherein the insert comprises collagen I, collagen IV or fibronectin.

22. The culture of claim 11 , wherein the BCC microarchitecture comprises one or more of the following: peripheral palisading, sfromal/epithelial clefting, dermal invasion, clustering of cells with a high nuclear/cytplasmic ratio.

23. The culture of claim 11, wherein the epidermal cells are human cells.

24. The culture of claim 11, wherein the epidermal and supporting cells are obtained from a human BCC.

25. A stable BCC culture comprising: (a) a BCC sample; and

(b) dermis; wherein said BCC sample exhibits BCC microarchitecture.

26. The culture of claim 25, further comprising growth medium and a substrate layer, wherein the subsfrate layer is most proximal to the growth medium, and the dermis is interposed between the substrate layer and the epidermal cells.

27. The culture of claim 25 further comprising a hydrated, organic matrix interposed between the dermis and the epidermal cells.

28. The culture of claim 27, wherein the matrix is a basement membrane matrix produced by a cancerous cell line.

29. A method for preparing a BCC culture comprising:

-obtaining a non-cancerous skin sample, comprising dermis and epidermis; and -placing said skin sample in contact with a culture medium, wherein the medium comprises a hedgehog agonist and/or hedgehog protein.

30. The method of claim 29, wherein an insert is used to maintain the skin sample in contact with the medium and at the liquid/air interface.

31. A method for preparing a BCC culture comprising:

-obtaining a BCC sample; and

-placing the BCC sample in close proximity to a sample of dermis.

32. The method of claim 31 , wherein an organic matrix is interposed between said BCC sample and said dermis.

33. The method of claim 31 , wherein the BCC sample is a Mohs shaving.

34. A method for preparing a BCC culture comprising:

- obtaining a BCC sample comprising a portion of stromal cells sufficient to promote maintenance of BCC microarchitecture; and

- culturing the sample at a liquid/air interface.

35. A method for identifying a BCC therapeutic comprising contacting a test compound with a BCC culture of claim 11, and measuring a BCC characteristic, wherein a decrease in the presence of the BCC characteristic indicates that the test compound is a BCC therapeutic.

36. A method of claim 35, wherein said BCC characteristic is a histological characteristic.

37. A method of claim 36, wherein said histological characteristic is peripheral palisading, stromal epithelial clefting, dermal invasion or clustering of cells with a high nuclear/cytoplasmic ratio.

38. A method of claim 35, wherein said BCC characteristic is protein activity produced by a hedgehog reporter gene.

39. A method of claim 38, wherein said hedgehog reporter gene is a ptc-lacZ construct.

40. A method of claim 35, wherein said BCC therapeutic is a hedgehog antagonist.

41. A method for identifying a hedgehog agonist comprising contacting a test compound with a BCC culture and measuring a BCC characteristic, wherein an increase in the presence of the BCC characteristic indicates that the test compound is a hedgehog agonist.

42. A method for identifying a hedgehog antagonist comprising contacting a test compound with a BCC culture and measuring a BCC characteristic, wherein a decrease in the presence of the BCC characteristic indicates that the test compound is a hedgehog antagonist.

43. ^' A method of claim 41 or 42, wherein said BCC characteristic is a histological characteristic.

44. A method of claim 43, wherein said histological characteristic is peripheral palisading, stromal epithelial clefting, dermal invasion or clustering of cells with a high nuclear/cytoplasmic ratio.

45. A method of claim 43, wherein said BCC characteristic is protein activity produced by a hedgehog reporter gene.

46. A method of claim 43, wherein said hedgehog reporter gene is a ptc-lacZ construct.

47. A method of treating BCC comprising contacting a BCC with an effective amount of a hedgehog antagonist.

48. A method of treating BCC comprising contacting a BCC with an effective amount of a BCC therapeutic identified by the method of claim 35.

49. A method of causing apoptosis in a BCC comprising contacting a BCC with an effective amount of a hedgehog antagonist.