The present invention discloses polynucleotides which identify and encode DP119, DP444, DP810, DP685, WE474, DP160, RA977, or RA770 as well as novel functions for these proteins of the inventions. The invention provides for compositions for disorders associated with the expression of the proteins of the invention, such as for the treatment, alleviation and/or prevention of pancreatic dysfunction (for example diabetes, hyperglycemia, and impaired glucose tolerance), and related disorders, and other disease and disorders.
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This invention relates to the use of nucleic acid and amino acid sequences of proteins specifically expressed in certain tissues including pancreatic tissues and to the use of effectors/modulators in the diagnosis, study, prevention, and treatment of diseases and disorders, for example, but not limited to, of the pancreas including metabolic disorders such as diabetes and related disorders like obesity, adipositas, and/or metabolic syndrome, as well as liver diseases, neurodegenerative disorders, and others. In addition, these sequences can be used for beta cell regeneration.
There are worldwide more than 151 million people having diabetes, 10% of those in the United States and about 20% in Europe (see, for example, Zimmet et al., 2001, Nature 414:782-787). Diabetes is among the leading causes of death and considered to be one of the main threats to human health in the 21 st century. There are two main forms of diabetes. Type I autoimmune diabetes (IDDM) results from the destruction of insulin producing beta-cells in the pancreatic islets of Langerhans. The adult pancreas has very limited regenerative potential, and so these islets are not replaced after they are destroyed. The patient's survival then depends on exogenous administration of insulin. The risk of developing type I diabetes is higher than for virtually all other severe chronic diseases of childhood. Type II diabetes is characterized by a progression from moderate to severe insulin-resistance and glucose intolerance, leading eventually to beta cell failure and dependence on exogenous insulin. High body weight and a sedentary live style are major risk factors for type II diabetes. Recently, LADA (latent autoimmune diabetes in adults) has been recognized as a form of diabetes distinct from Type I and Type II diabetes. Patients with LADA are usually first diagnosed later than most Type I diabetics, are initially not dependent on exogenous insulin and are characterized by the presence of islet autoantibodies, particularly against GAD65. It is estimated that about 10% of all patients which are currently diagnosed as Type II diabetics are actually LADA patients.
In about 4% of all pregnancies, elevated blood glucose levels can be observed in the mother. While this type of diabetes (“gestational diabetes”) usually resolves after birth it represents a health risk for both mother and baby and therefore needs to be treated.
It should be noted, that not only early phase type II diabetics but also type I and LADA patients retain some beta cell activity. Therefore, in most if not all forms of diabetes, beneficial treatments can be obtained by improving insulin secretion by the beta cells still present in the patient.
Although since the availability of injectable insulin diabetes is no longer an acutely live-threatening disease, it imposes a significant burden on the patient. This is because administration of insulin and other cannot prevent excursions to high or low blood glucose levels. Acute hypoglycemia can lead to coma and death. Frequent hyperglycemia causes complications, including diabetic ketoacidosis, end-stage renal disease, diabetic neuropathy, diabetic retinopathy and amputation. There are also a host of related conditions, such as obesity, hypertension, heart disease, peripheral vascular disease, and infections, for which persons with diabetes are at substantially increased risk. These and other complications account for a major proportion of the high cost of treating diabetic patients and contribute to overall lower quality of life and a reduced life expectancy. In order to cure diabetes, the lost beta cells would have to be replaced. This is currently done during islet or pancreas transplantation. However, donor organs are not available in sufficient numbers to transplant even a significant proportion of insulin dependent diabetic patients. Furthermore, patients have to undergo immunosuppressive therapy after transplantation, leading to a different set of side effects and long term complications.
Transplantable material could be generated from stem cells differentiated in vitro before transplantation into the patient. Progress has been made towards the differentiation of beta cells in vitro, however, additional factors promoting differentiation will have to be identified in order to enhance the performance of the differentiated cells.
A different approach can be regeneration through differentiation of somatic stem cells contained within the patient's body. These stem cells could be those which mediate the normal replacement of lost beta cells within the pancreas. However, it is also possible to treat diabetes by appropriate differentiation of stem cells in other tissues such as the liver, the intestine, or other organs.
Thus, there is a need in the art for the identification of novel factors which can promote the differentiation and/or function of beta cells in vitro and/or in vivo.
The pancreas is an essential organ possessing both an exocrine function involved in the delivery of enzymes into the digestive tract and an endocrine function by which various hormones are secreted into the blood stream. The exocrine function is assured by acinar and centroacinar cells that produce various digestive enzymes (for example, amylase, proteases, nuclease, etc.) and intercalated ducts that transport these enzymes in alkaline solution to the duodenum. The functional unit of the endocrine pancreas is the islet of Langerhans. Islets are scattered throughout the exocrine portion of the pancreas and are composed of four cell types: alpha-, beta-, delta- and PP-cells, reviewed for example in Kim & Hebrok, 2001, Genes & Development 15:111-127, and in Slack, Development 121 (1995), 1569-1580. Beta-cells produce insulin, represent the majority of the endocrine cells and form the core of the islets, while alpha-cells secrete glucagon and are located in the periphery. Delta-cells and PP-cells are less numerous and secrete somatostatin and pancreatic polypeptide, respectively.
Early pancreatic development has been well studied in different species, including chicken, zebrafish, and mice (for an detailed review, see Kim & Hebrock, 2001, supra). The pancreas develops from distinct dorsal and ventral anlagen. Pancreas development requires specification of the pancreas anlage along both anterior-posterior and dorsal-ventral axes. Within the developing anlage, a number of important regulatory factors important for proper organ development have been described, although a recapitulation of the different developmental programs in vitro has so far proven to be difficult.
Later in life, the acinar and ductal cells retain a significant proliferative capacity that can ensure cell renewal and growth, whereas the islet cells become mostly mitotically inactive. During embryonic development, and probably later in life, pancreatic islets of Langerhans originate from differentiating epithelial stem cells. These stem cells are situated in the pancreatic ducts or appear to form duct-like structures during development but are otherwise poorly characterized. The early progenitor cells to the pancreatic islets are multipotential and coactivate an early endocrine gene expression program. As development proceeds, expression of islet-specific hormones becomes restricted to the pattern of expression characteristic for mature islet cells. Pancreatic islet formation is dynamic and responds to changes in insulin demand, such as during pregnancy, or during childhood and adolescence.
Many pancreas diseases are associated with defects in pancreatic architecture or insufficient cellular regeneration, but the molecular mechanisms underlying these defects are basically unknown. However, studies have identified a number of signaling pathways which influence pancreatic cell fate as well as the morphogenesis of pancreatic structures, for example FGF signaling, activin signaling, the Hedgehog pathway, notch signaling, VEGF signaling, and the TGF-beta signaling pathway. There is a need in the prior art for the identification of candidate genes that are specifically expressed in early development in certain pancreatic tissues. These genes and the thereby encoded proteins can provide tools to the diagnosis and treatment of severe pancreatic disorders and related diseases. Therefore, this invention describes proteins that are specifically expressed in pancreatic tissues early in the development. The invention relates to the use of these genes and proteins in the diagnosis, prevention and/or treatment of pancreatic dysfunctions, such as diabetes, and other diseases.
So far, a function in the regulation of metabolic diseases such as diabetes has not been described in the prior art for the proteins of the invention. This invention describes novel functions for the DP119, DP444, DP810, DP685, WE474, DP160, RA977, or RA770 genes and proteins encoded thereby (referred to as proteins of the invention herein) that are involved in the development of the pancreas.
The identification of polynucleotides encoding molecules specifically expressed in the pancreatic tissues such as embryonic pancreatic epithelium, islet cells of the pancreas, pancreatic mesenchyme, as well as other tissues like forebrain, hindbrain, ganglia, branchial arches, stomach, intestinal region, lung, and mesonephrons, and the molecules themselves, presents the opportunity to investigate diseases and disorders of the pancreas, including diabetes. The identification of the proteins of the invention and antibodies against these proteins as well as effector molecules of said polypeptides or proteins, e.g. aptamers or other receptors satisfies a need in the art by providing new compositions useful in diagnosis, treatment, and prognosis of pancreatic diseases, adipositas and other metabolic disorders, as well as neurodegenerative disorders and other diseases.
DP119, DP444, DP810, DP685, WE474, DP160, RA977, or RA770 proteins and nucleic acid molecules coding therefor are obtainable from vertebrate species, e.g. mammals or birds. Particularly preferred are human homolog nucleic acids or polypeptides (see
Accordingly, the invention features a substantially purified protein which has the amino acid sequence shown in SEQ ID NO: 2, 4, 6, 8, 10, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42 or 44 respectively. One aspect of the invention features isolated and substantially purified polynucleotides that encode the proteins of the invention. In a particular aspect, the polynucleotide is the nucleotide sequence of SEQ ID NO: 1, 3, 5, 7, 9, 11, 12, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41 or 43. The invention also relates to a polynucleotide sequence comprising the complement of SEQ ID NO: 1, 3, 5, 7, 9, 11, 12, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41 or 43, or variants thereof. In addition, the invention features polynucleotide sequences which hybridize under stringent conditions to SEQ ID NO: 1, 3, 5, 7, 9, 11, 12, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41 or 43 and/or the complement thereof. The invention additionally features polypeptides or peptides comprising fragments or portions of the above amino acid sequences and polynucleotides or oligonucleotides comprising fragments or portions of the above nucleic acid sequences and nucleic acid analogs, e.g. peptide nucleic acids (PNA), morpholinonucleic acids, locked nucleic acids (LNA), or antisense molecules thereof, and expression vectors and host cells comprising polynucleotides that encode the proteins of the invention. The length of polypeptide or peptide fragments is preferably at least 5, more preferably at least 6 and most preferably at least 8 amino acids. The length of nucleic acid fragments and nucleic acid analogs is preferably at least 10, more preferably at least 15 and most preferably at least 20 nucleotides.
The present invention also features antibodies which bind specifically to the proteins of the invention, and pharmaceutical compositions comprising substantially purified proteins of the invention. The invention also features the use of effectors, e.g. agonists and antagonists of the proteins of the invention. Effectors are preferably selected from antibodies, aptamers, low molecular weight molecules, antisense-molecules, ribozymes capable of modulating the function of the nucleic acids and proteins of the invention. The nucleic acids that encode the proteins of the invention are used in identifying: homologous or related genes; in producing compositions that modulate the expression or function of the encoded proteins; for gene therapy; mapping functional regions of the proteins; and in characterizing associated physiological pathways.
Before the present proteins, nucleotide sequences, and methods are described, it is understood that this invention is not limited to the particular methodology, protocols, cell lines, vectors, and reagents described as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims.
It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, reference to “a host cell” includes a plurality of such host cells, reference to the “antibody” is a reference to one or more antibodies and equivalents thereof known to those skilled in the art, and so forth. Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods, devices, and materials are now described. All publications mentioned herein are incorporated herein by reference for the purpose of describing and disclosing the cell lines, vectors, and methodologies which are reported in the publications which might be used in connection with the invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.
The invention is based on the finding of novel functions for DP119, DP444, DP810, DP685, WE474, DP160, RA977, or RA770 proteins and particularly based on the finding that these proteins are expressed specifically in early pancreatic tissues and in other tissues.
The invention is further based on polynucleotides encoding the proteins of the invention, functional fragments of said genes, polypeptides encoded by said genes or fragments thereof, and effectors/modulators, e.g. antibodies, biologically active nucleic acids, such as antisense molecules, RNAi molecules or ribozymes, aptamers, peptides or low-molecular weight organic compounds recognizing said polynucleotides or polypeptides, and the use of these compositions for the diagnosis, study, prevention, or treatment of diseases and disorders related to such cells, including metabolic diseases, such as diabetes and obesity, neurodegenerative disorders, heart diseases, intestinal diseases, liver disorders, and others.
Nucleic acids encoding the chicken proteins of the present invention were first identified from the pancreas tissue cDNA library (day 6) through a whole-mount in situ screen for genes expressed in the embryonic pancreatic bud (see EXAMPLES).
Zebrafish have gained importance as model organism during the recent years. The embryos of this species are transparent and available in large numbers, develop quickly outside of their mother and allow both forward and reverse genetic analysis of gene function. Published data on pancreatic development in zebrafish shows that islet formation occurs extremely rapid (within 24 hrs) and suggest that this process requires the same regulatory genes as in mammals (see Biemar et al., Dev Biol. 2001 Feb. 15; 230(2):189-203). Suppressing gene function in zebrafish embryos using morpholino antisense oligonucleotides (Mos), modified Peptide Nucleic Acids (mPNAs) or other antisense compounds with good efficiency and specificity yields phenotypes which are usually indistinguishable from genetic mutants in the same gene (Nasevicius et al., Nat Genet. 2000 October; 26(2):216-20; Effimov et al., NAR 26; 566-575; Urtishak et al., 5th international conference on zebrafish development and genetics, Madison/Wis. 2002, abstr. #17). Therefore, this approach allows rapid assessment of gene function in a model vertebrate.
Microarrays are analytical tools routinely used in bioanalysis. A microarray has molecules distributed over, and stably associated with, the surface of a solid support. The term “microarray” refers to an arrangement of a plurality of polynucleotides, polypeptides, antibodies, or other chemical compounds on a substrate. Microarrays of polypeptides, polynucleotides, and/or antibodies have been developed and find use in a variety of applications, such as monitoring gene expression, drug discovery, gene sequencing, gene mapping, bacterial identification, and combinatorial chemistry. One area in particular in which microarrays find use is in gene expression analysis (see Example 4). Array technology can be used to explore the expression of a single polymorphic gene or the expression profile of a large number of related or unrelated genes. When the expression of a single gene is examined, arrays are employed to detect the expression of a specific gene or its variants. When an expression profile is examined, arrays provide a platform for identifying genes that are tissue specific, are affected by a substance being tested in a toxicology assay, are part of a signaling cascade, carry out housekeeping functions, or are specifically related to a particular genetic predisposition, condition, disease, or disorder.
Microarrays may be prepared, used, and analyzed using methods known in the art (see for example, Brennan, T. M. et al. (1995) U.S. Pat. No. 5,474,796—Schena, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93:10614-10619; Baldeschweiler et al. (1995) PCT application WO95/251116; Shalon, D. et al. (1995) PCT application WO95/35505; Heller, R. A. et al. (1997) Proc. Natl. Acad. Sci. USA 94:21502155; Heller, M. J. et al. (1997) U.S. Pat. No. 5,605,662). Various types of microarrays are well known and thoroughly described in Schena, M., ed. (1999; DNA Microarrays: A Practical Approach, Oxford University Press, London).
In further embodiments, oligonucleotides or longer fragments derived from any of the polynucleotides described herein may be used as elements on a microarray. The microarray can be used in transcript imaging techniques which monitor the relative expression levels of large numbers of genes simultaneously as described below. The microarray may also be used: to identify genetic variants, mutations, and polymorphisms. This information may be used to determine gene function, to understand the genetic basis of a disorder, to diagnose a disorder, to monitor progression/regression of disease as a function of gene expression, and to develop and monitor the activities of therapeutic agents in the treatment of disease. In particular, this information may be used to develop a pharmacogenomic profile of a patient in order to select the most appropriate and effective treatment regimen for that patient. For example, therapeutic agents, which are highly effective and display the fewest side effects may be selected for a patient based on his/her pharmacogenomic profile.
DP119: In one embodiment, the invention encompasses the chicken DP119 protein, a polypeptide comprising the amino acid sequence of SEQ ID NO:2, as presented using the one-letter code in
The predicted amino acid sequence was searched in the publicly available GenBank database. In search of sequence databases, it was found, for example, that DP119 has homology with a human hypothetical protein (Genbank Accession Number AL050137.1 for the cDNA and CAB43286.1 for the protein) and to mouse hypothetical protein (Genbank Accession Number BC025654.1 for the cDNA and AAH25654.1 for the protein, see
The C-terminus of DP119 contains an olfactomedin-like domain; the N-terminus is characterized by a cystein-rich domain reminiscent of certain cytokines. These two domains may represent functional subdomains of the protein.
DP444: In one embodiment, the invention encompasses the chicken DP444 protein, a polypeptide comprising the amino acid sequence of SEQ ID NO: 8, as presented using the one-letter code in
The predicted amino acid sequence was searched in the publicly available GenBank database. In search of sequence databases, it was found, for example, that DP444 has homology with the human protein BAC03521, nucleotide GenBank Accession no. AK090815 (see EXAMPLE 10 for more detail). Highly homologous mouse and fish proteins could also be identified (see
Knockdown of DP444 gene function in zebrafish using antisense-Morpholino-oligos specific for DP444 leads to an islet convergence defect in 20-30% of all injected embryos (see
Expression analysis in adult mouse tissues reveals that DP444 transcripts are restricted to brain (particularly hypothalamus) and islets, suggesting an important function of DP444 in beta cells.
DP810: In one embodiment, the invention encompasses the chicken DP810-like protein, a polypeptide comprising the amino acid sequence of SEQ ID NO: 18, as presented using the one-letter code in
The predicted amino acid sequence was searched in the publicly available GenBank database. In search of sequence databases, it was found, for example, that DP810 has homology with human likely ortholog of mouse polydom protein (GenBank Accession Number NM—024500.1 for the cDNA (
Polydom was described first in 2000 (Gilges D. et al., 2000, Biochem J. 352 Pt 1:49-59). It was shown that a C-terminally tagged form of the protein is secreted when expressed in Cos7 cells. Sites for N-glycosylation in the primary sequence and a slightly reduced mobility on SDS-PAGE gels suggest postranslational modification by glycosylation. Strong expression of polydom was found in human placenta and lung, weaker expression was seen in spleen, skeletal muscle and heart. Pancreatic expression was not analyzed. The human homolog of Polydom was mapped by FISH to chromosome 9q32. Polydom contains a number of protein domains. Most notable are EGF—(epidermal growth factor) like repeats, a von Willebrand factor type A domain, and 34 complement control protein (CCP) modules, suggesting a potential function in cell signalling or cell adhesion.
DP685: In one embodiment, the invention encompasses the chicken DP685 protein, a polypeptide encoded by the nucleic acid sequence of SEQ ID NO: 21, as presented in
The predicted amino acid sequence was searched in the publicly available GenBank database. In search of sequence databases, it was found, for example, that DP685 has homology with a human autotaxin-t (synonym Ectonucleotide pyrophosphatase/Pyrophosphatase 2 (ENPP2); Genbank Accession Number L46720.1 and AAB00855.1; SEQ ID NO: 23 and 24). Based upon homology, DP685 protein and each homologous protein or peptide may share at least some activity.
The bifunctional enzyme phosphodiesterase I (EC 18.104.22.168)/nucleotide pyrophosphatase (EC 22.214.171.124) (refered to as PD-I (alpha)) was cloned from rat brain by Narita et al. (1994) J. Biol. Chem. 269: 28235-28242. The human PD-I alpha homologue is an 863-amino acid protein with 89% identity to the rat protein (Kawagoe et al. (1995) Genomics 30: 380-384). Northern blot analysis detected a 3-kb transcript in brain, placenta, kidney and lung. An apparent splice variant of PD-I (alpha) lacking 52 amino acids, but otherwise identical, has been described as autotaxin, a tumor cell motility-stimulating factor (Murata et al., 1994 J. Biol. Chem. 269: 30479-30484). Kawagoe et al. (1995), supra, obtained a genomic clone for the 5′-end of the gene which contained a variety of potential DNA-binding sites as well as intron 1.
However, two recent publications have identified that autotaxin has lysophospholipase D activity and that it synthesizes lysophosphatidic acid (LPA) (Tokumura et al., 2002, J Biol Chem. 2002 Aug 9; Umezu-Goto et al., 2002, J Cell Biol. 158(2):227-33; reviewed in Moolenaar, 2002, J Cell Biol. 158(2):197-9). LPA is a potent signalling compound with effects on cytoskeletal organization, cell proliferation and cell migration. Its activity is mediated by a family of G-protein coupled receptors belonging to the edg-family. The different members of this family show differences in expression and downstream signalling partners (reviewed e.g. in Takuwa et al., 2002, J Biochem (Tokyo). 131(6):767-71).
As shown in this invention, the expression pattern of autotaxin in the day 4 and day 5 chicken embryo suggests that autotaxin and/or LPA synthesized by autotaxin plays an important and up to now unknown role in animal development. This is especially striking when the patterning of the limbs, the central nervous system and growth, differentiation and morphogenesis of the pancreas are considered (see
The expression of autotaxin in the embryonic pancreatic bud suggests a novel function of insulin secreting cells from other cell types such as stem cells.
The expression of autotaxin in neural tissues, e.g. the neural tube and the brain, and in the limbs suggests a novel function and a use of autotaxin, LPA, or other reaction products generated by autotaxin in the generation of neural cells and cells of the motility apparatus from other cell types such as stem cells.
It also raises the possibility that agonists specific for LPA-receptors expressed in specific cell types or their precursors can modulate the growth, differentiation, or organ-specific organization of these cells. For example, stimulation of an LPA-receptor more or less specifically expressed in certain cell types such as pancreatic stem cells, other stem cells or other cells that can be used to generate new insulin-secreting cells might yield relatively specific responses in spite of the many effects described in the literature for LPA.
WE474: In one embodiment, the invention encompasses the chicken WE474 protein, a polypeptide comprising the amino acid sequence of SEQ ID NO:28, as presented using the one-letter code in
The predicted amino acid sequence was searched in the publicly available GenBank database. In search of sequence databases, it was found, for example, that WE474 has homology with a human collectin sub-family member 10 (Genbank Accession Number NM—006438.2 for the cDNA and NP—006429.1 for the protein; SEQ ID. NO: 29 and 30). Based upon homology, WE474 protein and each homologous protein or peptide may share at least some activity.
Collectins are a C-lectin family with collagen-like sequences and carbohydrate recognition domains. These proteins can bind to carbohydrate antigens of microorganisms and inhibit their infection by direct neutralization and agglutination, the activation of complement through the lectin pathway, and opsonization by collectin receptors (Ohtani K. et al., 1999, J Biol Chem 274(19):13681-13689). A cDNA encoding human collectin from liver (CL-L1 (collectin liver 1)) has typical collectin structural characteristics, consisting of an N-terminal cysteine-rich domain, a collagen-like domain, a neck domain, and a carbohydrate recognition domain. This collectin has a unique repeat of four lysine residues in its C-terminal area. CL-L1 is present mainly in liver as a cytosolic protein and at low levels in placenta. More sensitive analyses showed that most tissues (except skeletal muscle) have CL-L1 mRNA. Zoo-blot analysis indicated that CL-L1 is limited to mammals and birds. A chromosomal localization study indicated that the CL-L1 gene localizes to chromosome 8q23-q24.1. CL-L1 binds mannose weakly (see, for example, Ohtani K. et al., 1999, J Biol Chem 274(19):13681-13689). Analysis of the WE474 protein sequence using suitable software (such as SignalP, Nielsen et al., Protein Engineering 10, 1-6) reveals the presence of a secretion signal. Thus, WE474 is likely to have a role in cell-cell or autocrine signalling.
DP160: In one embodiment, the invention encompasses the chicken DP160 protein, a polypeptide comprising the amino acid sequence of SEQ ID NO:32, as presented using the one-letter code in
The predicted amino acid sequence was searched in the publicly available GenBank database. In search of sequence databases, it was found, for example, that DP160 has homology with a human CCR4 carbon catabolite repression 4-like protein (CCRN4L; Nocturnin) (Genbank Accession Number XP—003343.3 and XP—003343.2; SEQ ID NO: 33 and 34). Based upon homology, or DP160 protein and each homologous protein or peptide may share at least some activity.
Nocturnin was originally identified by differential display as a circadian clock regulated gene with high expression at night in photoreceptors of the African clawed frog, Xenopus laevis. Although encoding a novel protein, the nocturnin cDNA had strong sequence similarity with a C-terminal domain of the yeast transcription factor CCR4, and with mouse and human ESTs. Since its original identification several homologues of nocturnin/CCR4 were cloned, including from human and mouse. Northern analysis of mRNA in C3H/He and C57/BI6 mice revealed that the mNoc gene is expressed in a broad range of tissues, with greatest abundance in liver, kidney and testis as well as in multiple brain regions. Furthermore, mNoc exhibits circadian rhythmicity of mRNA abundance with peak levels at the time of light offset in the retina, spleen, heart, kidney and liver (Wang et al., 2001, BMC Dev Biol 1(1):9).
RA977: In one embodiment, the invention encompasses the chicken RA977 protein, a polypeptide comprising the amino acid sequence of SEQ ID NO:36, as presented using the one-letter code in
The predicted amino acid sequence was searched in the publicly available GenBank database. In search of sequence databases, it was found, for example, that RA977 has homology with a human epithelial membrane protein 2 (EMP2; Genbank Accession Number XM—030218.1 for the cDNA and P54851 for the protein; SEQ ID NO: 37 and 38, see
The epithelial membrane protein-2 (EMP-2) is a member of the peripheral myelin protein 22 gene family (PMP22/EMP/MP20 gene family). Mutations affecting the PMP22 gene are associated with hereditary motor and sensory neuropathies. In human, EMP-2 mRNA transcripts are found in most tissues including liver. EMP-2 is most prominently expressed in the adult ovary, heart, lung and intestine and in fetal lung. Since PMP22 has been implicated in the regulation of cell proliferation and apoptosis, it appears likely that EMP-2 is involved in similar regulatory processes in a variety of tissues (Taylor V. and Suter U., 1996, Gene 175(1-2):115-120).
Charcot-Marie-Tooth (CMT) neuropathy represents a genetically heterogeneous group of diseases affecting the peripheral nervous system. Autosomal dominant CMT type 1C (CMT1C). was mapped genetically to chromosome 16p13.1-p12.3. The epithelial membrane protein 2 gene (EMP2), which maps to chromosome 16p13.2, is a candidate gene for CMT1C (Street V. A., 2002, Am J Hum Genet 70(1):244-250).
Epithelial membrane protein 2, a 4-transmembrane protein, might suppress B-cell lymphoma tumorigenicity through a functional tumor suppressor phenotype (Wang C. X., 2001, Blood 97(12):3890-3895).
RA770: In one embodiment, the invention encompasses the chicken RA770-like protein, a polypeptide comprising the amino acid sequence of SEQ ID NO: 40, as presented using the one-letter code in
The predicted amino acid sequence was searched in the publicly available GenBank database. In search of sequence databases, it was found, for example, that RA770 has homology with human neurturin precursor (GenBank Accession Number NM—004558 (
Neurturin (or NRTN), a potent neurotrophic factor, was purified from Chinese hamster ovary cell-conditioned media by Kotzbauer et al. (1996) Nature 384: 467-470. The protein is closely related to glial cell line-derived neurotrophic factor (GDNF). Neurturin and GDNF form a distinct TGF-beta subfamily, referred to as TRNs (for ‘TGF-beta-related neurotrophins’; see review by Takahashi, 2001, Cytokine Growth Factor Rev 12(4):361-73). Members of this protein family signal through a unique multicomponent receptor system consisting of RET tyrosine kinase and glycosyl-phosphatidylinositol-anchored coreceptor (GFRalpha1-4)). These neurotrophic factors promote the survival of various neurons including peripheral autonomic and sensory neurons as well as central motor and dopamine neurons, and have been expected as therapeutic agents for neurodegenerative diseases. In addition, the GDNF/RET signaling plays a crucial role in renal development and regulation of spermatogonia differentiation. RET mutations cause several human diseases such as papillary thyroid carcinoma, multiple endocrine neoplasia types 2A and 2B, and Hirschsprung's disease. The mutations resulted in RET activation or inactivation by various mechanisms and the biological properties of mutant proteins appeared to be correlated with disease phenotypes. The signaling pathways activated by GDNF or mutant RET are being extensively investigated to understand the molecular mechanisms of disease development and the physiological roles of the GDNF family ligands.
Heuckeroth et al. (1997) Genomics 44:137-140 stated that inactivating mutations in GDNF or Ret in knockout mice cause intestinal aganglionosis and renal dysplasia. Neurturin also signals through RET and a GPI-linked coreceptor. Like GDNF, neurturin can promote the survival of numerous neuronal populations, including sympathetic, nodose, and dorsal root ganglion sensory neurons. Heuckeroth et al. (1997), supra, isolated mouse and human genomic neurturin clones and showed that preproneurturin is encoded by 2 exons. Mouse and human clones have common intron/exon boundaries. They used interspecific backcross analysis to localize neurturin to mouse chromosome 17 and fluorescence in situ hybridization to localize human neurturin to the syntenic region of 19p13.3.
Considering that RET and glial cell line-derived neurotrophic factor mutations had been reported in Hirschsprung disease, Doray et al. (1998) Hum. Molec. Genet. 7: 1449-1452 regarded the other RET ligand, neurturin, as an attractive candidate gene, especially as it shares large homologies with GDNF. Doray et al. (1998), supra, reported a heterozygous missense Neurturin mutation in a large nonconsanguineous family including 4 children affected with a severe aganglionosis phenotype extending up to the small intestine. It appeared that the Neurturin mutation they found was not sufficient to cause HSCR, and this multiplex family also segregated a RET mutation. This cascade of independent and additive genetic events fits well with the multigenic pattern of inheritance expected in HSCR, and further supports the role of RET ligands in the development of the enteric nervous system.
The invention also encompasses variants of the proteins of the invention. A preferred variant is one having at least 80%, and more preferably 90%, amino acid sequence similarity to the amino acid sequence of the proteins of the invention (SEQ ID NO: 2, 4, 6, 8, 10, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42 or 44 respectively). A most preferred variant is one having at least 95% amino acid sequence similarity to SEQ ID NO: 2, 4, 6, 8, 10, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42 or 44 respectively.
The invention also encompasses polynucleotides which encode the proteins of the invention. Accordingly, any nucleic acid sequence which encodes the amino acid sequence of the proteins of the invention can be used to generate recombinant molecules which express the proteins of the invention. In a particular embodiment, the invention encompasses the polynucleotide comprising the nucleic acid sequence of SEQ ID NO: 1, 3, 5, 7, 9, 11, 12, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41 or 43. It will be appreciated by those skilled in the art that as a result of the degeneracy of the genetic code, a multitude of nucleotide sequences encoding the proteins of the invention, some bearing minimal homology to the nucleotide sequences of any known and naturally occurring gene, may be produced. Thus, the invention contemplates each and every possible variation of nucleotide sequence that could be made by selecting combinations based on possible codon choices.
Also encompassed by the invention are polynucleotide sequences that are capable of hybridizing to the claimed nucleotide sequences, and in particular, those shown in SEQ ID NO: 13, 5, 7, 9, 11, 12, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41 or 43, and/or the complement thereof under various conditions of stringency. Hybridization conditions are based on the melting temperature (Tm) of the nucleic acid binding complex or probe, as taught in Wahl, G. M. and S. L. Berger (1987, Methods Enzymol. 152:399-407) and Kimmel, A. R. (1987, Methods Enzymol. 152:507-511), and may be used at a defined stringency. Preferably, hybridization under stringent conditions means that after washing for 1 h with 1×SSC and 0.1. % SDS at 50° C., preferably at 55° C., more preferably at 62° C. and most preferably at 68° C., particularly for 1 h in 0.2×SSC and 0.1% SDS at 50° C., preferably at 55° C., more preferably at 62° C. and most preferably at 68° C., a positive hybridization signal is observed. Altered nucleic acid sequences encoding the proteins of the invention which are encompassed by the invention include deletions, insertions, or substitutions of different nucleotides resulting in polynucleotides that encode the same or functionally equivalent proteins of the invention. The encoded proteins may also contain deletions, insertions, or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent protein of the invention.
Also included within the scope of the present invention are alleles of the genes encoding the proteins of the invention. As used herein, an “allele” or “allelic sequence” is an alternative form of the gene which may result from at least one mutation in the nucleic acid sequence. Alleles may result in altered mRNAs or polypeptides whose structures or function may or may not be altered. Any given gene may have none, one, or many allelic forms. Common mutational changes which give rise to alleles are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence. Methods for DNA sequencing which are well known and generally available in the art may be used to practice any embodiments of the invention. The nucleic acid sequences encoding the proteins of the invention may be extended utilizing a partial nucleotide sequence and employing various methods known in the art to detect upstream sequences such as promoters and regulatory elements. For example, one method which may be employed, “restriction-site” PCR, uses universal primers to retrieve unknown sequence adjacent to a known locus (Sarkar, G. (1993) PCR Methods Applic. 2:318-322). In particular, genomic DNA is first amplified in the presence of primer to linker sequence and a primer specific to the known region. The amplified sequences are then subjected to a second round of PCR with the same linker primer and another specific primer internal to the first one. Products of each round of PCR are transcribed with an appropriate RNA polymerase and sequenced using reverse transcriptase. Inverse PCR may also be used to amplify or extend sequences using divergent primers based on a known region (Triglia, T. et al. (1988) Nucleic Acids Res. 16:8186). The primers may be designed using OLIGO 4.06 primer analysis software (National Biosciences Inc., Plymouth, Minn.), or another appropriate program, to 22-30 nucleotides in length, to have a GC content of 50% or more, and to anneal to the target sequence at temperatures about 68° C.-72° C. The method uses several restriction enzymes to generates suitable fragment. The fragment is then circularized by intramolecular ligation and used as a PCR template.
Another method which may be used is capture PCR which involves PCR amplification of DNA fragments adjacent to a known sequence in human and yeast artificial chromosome DNA (Lagerstrom, M. et al. (PCR Methods Applic. 1:111-119). In this method, multiple restriction enzyme digestions and ligations also be used to place an engineered double-stranded sequence into an unknown portion of the DNA molecule before performing PCR. Another method which may be used to retrieve unknown sequences is that of Parker, J. D. et al. (1991; Nucleic Acids Res. 19:3055-3060). Additionally, one may use PCR, nested primers, and PROMOTERFINDER libraries to walk in genomic DNA (Clontech, Palo Alto, Calif.). This process avoids the need to screen libraries and is useful in finding intron/exon junctions. When screening for full-length cDNAs, it is preferable to use libraries that have been size-selected to include larger cDNAs. Also, random-primed libraries are preferable, in that they will contain more sequences which contain the 5′ regions of genes. Use of a randomly primed library may be especially preferable for situations in which an oligo d(T) library does not yield a full-length cDNA. Genomic libraries may be useful for extension of sequence into the 5′ and 3′ non-transcribed regulatory regions. Capillary electrophoresis systems which are commercially available may be used to analyze the size or confirm the nucleotide sequence of sequencing or PCR products. In particular, capillary sequencing may employ flowable polymers for electrophoretic separation, four different fluorescent dyes (one for each nucleotide) which are laser activated, and detection of the emitted wavelengths by a charge coupled devise camera. Output/light intensity may be converted to electrical signal using appropriate software (e.g. GENOTYPER and SEQUENCE NAVIGATOR, Perkin Elmer) and the entire process from loading of samples to computer analysis and electronic data display may be computer controlled. Capillary electrophoresis is especially preferable for the sequencing of small pieces of DNA which might be present in limited amounts in a particular sample.
In another embodiment of the invention, polynucleotide sequences or functional fragments thereof which encode the proteins of the invention, or fusion proteins or functional equivalents thereof, may be used in recombinant DNA molecules to direct expression of the proteins of the invention in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences which encode substantially the same or a functionally equivalent amino acid sequence may be produced and these sequences may be used to clone and express the proteins of the invention. As will be understood by those of skill in the art, it may be advantageous to produce the protein-encoding nucleotide sequences possessing non-naturally occurring codons. For example, codons preferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce a recombinant RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence. The nucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter the proteins of the invention encoding sequences for a variety of reasons, including but not limited to, alterations, which modify the cloning, processing, and/or expression of the gene product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. For example, site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, or introduce mutations, and so forth. Such mutated genes may be used to study structure-function relationships of the proteins of the invention, or to alter properties of the proteins that affect their function or regulation.
In another embodiment of the invention, natural, modified, or recombinant nucleic acid sequences encoding the proteins of the invention may be ligated to a heterologous sequence to encode a fusion protein. For example, to screen peptide libraries for inhibitors of the proteins of the invention activity, it may be useful to encode chimeric proteins of the invention that can be recognized by a commercially available antibody. A fusion protein may also be engineered to contain a cleavage site located between the proteins of the invention encoding sequence and the heterologous protein sequence, so that the proteins of the invention may be cleaved and purified away from the heterologous moiety. A fusion protein between the DP444 protein and a protein transduction peptide (reviewed e.g. in Lindsay, M. A.; Curr Opin Pharmacol 2002 October; 2(5):587-94) may be engineered to allow the uptake of recombinant fusion protein by mammalian cells. In another embodiment, sequences encoding the proteins of the invention may be synthesized, in whole or in part, using chemical methods well known in the art (see Caruthers, M. H. et al. (1980) Nuc. Acids Res. Symp. Ser. 7:215-223, Horn, T. et al. (1980) Nucl. Acids Res. Symp. Ser. 7:225-232). Alternatively, the protein itself may be produced using chemical methods to synthesize the amino acid sequence of the proteins of the invention, or a portion thereof. For example, peptide synthesis can be performed using various solid-phase techniques (Roberge, J. Y. et al. (1995) Science 269:202-204) and automated synthesis may be achieved, for example, using the ABI 431A peptide synthesizer (Perkin Elmer). The newly synthesized peptide may be substantially purified by preparative high performance liquid chromatography (e.g. Creighton, T. (1983) proteins, Structures and Molecular Principles, WH Freeman and Co., New York, N.Y.) The composition of the synthetic peptides may be confirmed by amino acid analysis or sequencing (e.g. the Edman degradation procedure; Creighton, supra). Additionally, the amino acid sequence of the proteins of the invention, or any part thereof, may be altered during direct synthesis and/or combined using chemical methods with sequences from other proteins, or any part thereof, to produce a variant polypeptide.
In order to express a biologically active protein of the invention, the nucleotide sequences encoding the proteins of the invention or functional equivalents, may be inserted into appropriate expression vector, i.e. a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding the proteins of the invention and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described in Sambrook, J. et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview, N.Y., and Ausubel, F. M. et al. (1989) Current Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y.
A variety of expression vector/host systems may be utilized to contain and express sequences encoding the proteins of the invention. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g. baculovirus); plant cell systems transformed with virus expression vectors (e.g. cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g. Ti or PBR322 plasmids); or animal cell systems.
The presence of polynucleotide sequences encoding the proteins of the invention can be detected by DNA-DNA or DNA-RNA hybridization and/or amplification using probes or portions or functional fragments of polynucleotides encoding the proteins of the invention. Nucleic acid amplification based assays involve the use of oligonucleotides or oligomers based on the sequences encoding the proteins of the invention to detect transformants containing DNA or RNA encoding the proteins of the invention. As used herein “oligonucleotides” or “oligomers” refer to a nucleic acid sequence of at least about 10 nucleotides and as many as about 60 nucleotides, preferably about 15 to 30 nucleotides, and more preferably about 20-25 nucleotides, which can be used as a probe or amplimer.
A variety of protocols for detecting and measuring the expression of the proteins of the invention, using either polyclonal or monoclonal antibodies specific for the protein are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescence activated cell sorting (FACS). A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on the proteins of the invention is preferred, but a competitive binding assay may be employed. These and other assays are described, among other places, in Hampton, R. et al. (1990; Serological Methods, a Laboratory Manual, APS Press, St Paul, Minn.) and Maddox, D. E. et al. (1983; J. Exp. Med. 158:1211-1216).
Compounds that bind the proteins of the invention, e.g. antibodies, are useful for the identification or enrichment of cells, which are positive for the expression of the proteins of the invention, from complex cell mixtures. Such cell populations are useful in transplantation, for experimental evaluation, and as source of lineage and cell specific products, including mRNA species useful in identifying genes specifically expressed in these cells, and as target for the identification of factors of molecules that can affect them. The pancreatic progenitor cell population, which is positive for the expression of the proteins of the invention, is useful in transplantation to provide a recipient with pancreatic islet cells, including insulin producing beta cells; for drug screening; experimental models of islet differentiation and interaction with other cell types; in vitro screening assays to define growth and differentiation factors, and to additionally characterize genes involved in islet development and regulation; and the like. The native cells may be used for these purposes, or they may be genetically modified to provide altered capabilities. Cells from a regenerating pancreas, from embryonic foregut, stomach and duodenum, or other sources of pancreatic progenitor cells may be used as a starting population. The progenitor cells may be obtained from any mammalian species, e.g. equine, bovine, porcine, canine, feline, rodent, e.g. mice, rats, hamster, primate, etc. particularly human.
A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides encoding the proteins of the invention include oligolabeling, nick translation, end-labeling or PCR amplification using a labeled nucleotide.
Alternatively, the sequences encoding the proteins of the invention, or any portions thereof may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides. These procedures may be conducted using a variety of commercially available kits (Pharmacia & Upjohn, (Kalamazoo, Mich.); Promega (Madison Wis.); and U.S. Biochemical Corp., (Cleveland, Ohio). Suitable reporter molecules or labels, which may be used, include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
Host cells transformed with nucleotide sequences encoding the proteins of the invention may be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The protein produced by a recombinant cell may be secreted or contained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides which encode the proteins of the invention may be designed to contain signal sequences which direct secretion of the proteins of the invention through a prokaryotic or eukaryotic cell membrane. Other recombinant constructions may be used to join sequences encoding the proteins of the invention to nucleotide sequence encoding a polypeptide domain which will facilitate purification of soluble proteins. Such purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAG extension/affinity purification system (Immunex Corp., Seattle, Wash.) The inclusion of cleavable linker sequences such as those specific for Factor XA or enterokinase (Invitrogen, San Diego, Calif.) between the purification domain and the proteins of the invention may be used to facilitate purification. One such expression vector provides for expression of a fusion protein containing the proteins of the invention and a nucleic acid encoding 6 histidine residues preceding a thioredoxin or an enterokinase cleavage site. The histidine residues facilitate purification on IMIAC (immobilized metal ion affinity chromotagraphy as described in Porath, J. et al. (1992, Prot. Exp. Purif. 3: 263-281) while the enterokinase cleavage site provides a means for purifying the proteins of the invention from the fusion protein. A discussion of vectors which contain fusion proteins is provided in Kroll, D. J. et al. (1993; DNA Cell Biol. 12:441-453). In addition to recombinant production, fragments of the proteins of the invention may be produced by direct peptide synthesis using solid-phase techniques (Merrifield J. (1963) J. Am. Chem. Soc. 85:2149-2154). protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be achieved, for example, using Applied Biosystems 431A peptide synthesizer (Perkin Elmer). Various fragments of the proteins of the invention may be chemically synthesized separately and combined using chemical methods to produce the full length molecule.
The nucleic acids encoding the proteins of the invention can be used to generate transgenic animal or site specific gene modifications in cell lines. Transgenic animals may be made through homologous recombination, where the normal locus of the genes encoding the proteins of the invention is altered. Alternatively, a nucleic acid construct is randomly integrated into the genome. Vectors for stable integration include plasmids, retrovirusses and other animal virusses, YACs, and the like. The modified cells or animal are useful in the study of the function and regulation of the proteins of the invention. For example, a series of small deletions and/or substitutions may be made in the genes that encode the proteins of the invention to determine the role of particular domains of the protein, functions in pancreatic differentiation, etc. Specific constructs of interest include anti-sense molecules, which will block the expression of the proteins of the invention, or expression of dominant negative mutations. A detectable marker, such as lac Z may be introduced in the locus of the genes of the invention, where upregulation of expression of the genes of the invention will result in an easily detected change in phenotype. One may also provide for expression of the genes of the invention or variants thereof in cells or tissues where it is not normally expressed or at abnormal times of development. In addition, by providing expression of the proteins of the invention in cells in which they are not normally produced, one can induce changes in cell behavior. DNA constructs for homologous recombination will comprise at least portions of the genes of the invention with the desired genetic modification, and will include regions of homology to the target locus. DNA constructs for random integration need not include regions of homology to mediate recombination. Conveniently, markers for positive and negative selection are included. Methods for generating cells having targeted gene modifications through homologous recombination are known in the art. For embryonic stem (ES) cells, an ES cell line may be employed, or embryonic cells may be obtained freshly from a host, e.g. mouse, rat, guinea pig etc. Such cells are grown on an appropriate fibroblast-feeder layer or grown in presence of leukemia inhibiting factor (LIF). When ES or embryonic cells have been transformed, they may be used to produce transgenic animals. After transformation, the cells are plated onto a feeder layer in an appropriate medium. Cells containing the construct may be detected by employing a selective medium. After sufficient time for colonies to grow, they are picked and analyzed for the occurrence of homologous recombination or integration of the construct. Those colonies that ate positive may then be used for embryo manipulation and blastocyst injection. Blastocysts are obtained from 4 to 6 week old superovulated females. The ES cells are trypsinized, and the modified cells are injected into the blastocoel of the blastocyst. After injection, the blastocysts are returned to each uterine horn of pseudopregnant females. Females are then allowed to go to term and the resulting offspring screened for the construct. By providing for a different phenotype of the blastocyst and the genetically modified cells, chimeric progeny can be readily detected. The chimeric animals are screened for the presence of the modified gene and males and females having the modification are mated to produce homozygous progeny. If the gene alterations cause lethality at some point in development, tissues or organs can be maintained as allogenic or congenic grafts or transplants, or in vitro culture. The transgenic animals may be any non-human mammal, such as laboratory animal, domestic animals, etc. The transgenic animals may be used in functional studies, drug screening, etc.
Diagnostics and Therapeutics
From the in situ expression patterns obtained by using the proteins of this invention it can be concluded that the proteins described in this invention are specifically expressed in pancreatic cells such as islet cells (for example DP685; DP160; RA770), pancreatic mesenchyme (RA770), cells of the pancreatic epithelium (for example DP685; DP160), pancreatic duct cells (DP160) as well as in other cells such as ganglia along the neural tube (DP160; DP444), somites (DP444), dorsal hindbrain (DP444), liver (DP685), heart (DP685), stomach (DP444) and intestinal cells (DP685; DP444). Therefore, the nucleic acids and proteins of the invention and effectors/modulators thereof are useful in diagnostic and therapeutic applications implicated, for example but not limited to, in metabolic disorders and dysfunctions associated with the above organs or tissues like diabetes and obesity, liver diseases and neural diseases, e.g. neuro-degenerative disorders and other diseases and disorders. Hence the proteins of the invention could be useful as a diagnostic markers or as a target for small molecule screening, and in prevention or treatment of diabetes and/or obesity and other metabolic disorders and other diseases such as neurodegenerative disorders, heart, liver, stomach, or intestinal disorders.
Therapeutic uses for the invention(s) are, for example but not limited to, the following: (i) tissue regeneration in vitro and in vivo (regeneration for all these tissues and cell types composing these tissues and cell types derived from these tissues); (ii) protein therapeutic, (iii) small molecule drug target, (iv) antibody target (therapeutic, diagnostic, drug targeting/cytotoxic antibody), (v) diagnostic and/or prognostic marker, (vi) gene therapy (gene delivery/gene ablation), and (vii) research tools.
The nucleic acids and proteins of the invention are useful in therapeutic applications implicated in various diseases and disorders described below and/or other pathologies and disorders. For example, but not limited to, a cDNA encoding one of the proteins of the invention may be useful in gene therapy, and the proteins of the invention may be useful when administered to a subject in need thereof. By way of non-limiting example, the compositions of the present invention will have efficacy for treatment of patients suffering from, for example, but not limited to, in metabolic disorders like diabetes and obesity, and other diseases and disorders. The novel nucleic acids encoding the proteins of the invention, or functional fragments thereof, may further be useful in diagnostic applications, wherein the presence or amount of the nucleic acid or the protein are to be assessed. These materials are further useful in the generation of antibodies that bind immunospecifically to the novel substances of the invention for use in therapeutic or diagnostic methods. In other embodiments of the invention, the compositions of the invention e.g. the proteins or functional fragments thereof may be used for therapeutic purposes. For example, the compositions, such as the pancreas specific proteins described in this invention, can be used for promoting the differentiation and/or function of beta cells in vitro and/or in vivo. Further, the compositions, such as the proteins, can be used for the regeneration of β-cells, e.g. of partially or completely dysfunctional β-cells in vitro and/or in vivo.
For example, in one aspect, antibodies which are specific for the proteins of the invention may be used directly as an antagonist, or indirectly as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissue which express the proteins of the invention. The antibodies may be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, Fab fragments, and fragments produced by a Fab expression library. Neutralizing antibodies, (i.e. those which inhibit biological function) are especially preferred for therapeutic use.
For the production of antibodies, various hosts including goats, rabbits, rats, mice, humans, and others, may be immunized by injection with the proteins of the invention or any fragment or oligopeptide thereof which has immunogenic properties. Depending on the host species, various adjuvants may be used to increase immunological response. It is preferred that the peptides, fragments or oligopeptides used to induce antibodies to the proteins of the invention have an amino acid sequence consisting of at least five amino acids, and more preferably at least 10 amino acids.
Monoclonal antibodies to the proteins of the invention may be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique (Köhler, G. et al. (1975) Nature 256:495-497; Kozbor, D. et al. (1985) J. Immunol. Methods 81:31-42; Cote, R. J. et al. (Proc. Natl. Acad. Sci. 80:2026-2030; Cole, S. P. et al. (1984) Mol. Cell Biol. 62:109-120). In addition, techniques developed for the production of “chimeric antibodies”, the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity can be used (Morrison, S. L. et al. (1984) Proc. Natl. Aced. Sci. 81:6851-6855; Neuberger, M. S. et al. (1984) Nature 312:604-608; Takeda, S. et al. (1985) Nature 314:452-454). Alternatively, techniques described for the production of single chain antibodies may be adapted, using methods known in the art, to produce the proteins of the invention-specific single chain antibodies. Antibodies with related specificity, but of distinct idiotypic composition, may be generated by chain shuffling from random combinatorial immunoglobulin libraries (Burton, D. R. (1991) Proc. Natl. Acad. Sci. 88:11120-3). Antibodies may also be producing by inducing in vivo production in the lymphocyte population or by screening recombinant immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature (Orlandi, R. et al. (1989) Proc. Natl. Acad. Sci. 86:3833-3837; Winter, G. et al. (1991) Nature 349:293-299).
Antibody fragments which contain specific binding sites for the proteins of the invention may also be generated. For example, such fragments include, but are not limited to, the F(ab′)2 fragments which can be produced by pepsin digestion of the antibody molecule and the Fab fragments which can be generated by reducing the disulfide bridges of F(ab′)2 fragments. Alternatively, Fab expression libraries may be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity (Huse, W. D. et al. (1989) Science 254:1275-1281).
Various immunoassays may be used for screening to identify antibodies having the desired specificity. Numerous protocols for competitive binding and immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificities are well known in the art. Such immunoassays typically involve the measurement of complex formation between the proteins of the invention and its specific antibody. A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering the proteins of the invention epitopes is preferred, but a competitive binding assay may also be employed (Maddox, supra).
In another embodiment of the invention, the polynucleotides, or any fragment thereof, such as aptamers, antisense molecules, RNAi molecules or ribozymes may be used for therapeutic purposes. In one aspect, aptamers i.e. nucleic acid molecules which are capable of binding to a protein of the invention and modulating its activity, may be generated by a screening and selection procedure involving the use of combinatorial nucleic acid libraries.
In a further aspect, antisense molecules to the polynucleotide encoding the proteins of the invention may be used in situations in which it would be desirable to block the transcription of the mRNA. In particular, cells may be transformed with sequences complementary to polynucleotides encoding the proteins of the invention. Thus, antisense molecules may be used to modulate the activity of the proteins of the invention, or to achieve regulation of gene function. Such technology is now well know in the art, and sense or antisense oligomers or larger fragments, can be designed from various locations along the coding or control regions of sequences encoding the proteins of the invention. Expression vectors derived from retroviruses, adenoviruses, herpes or vaccinia viruses, or from various bacterial plasmids may be used for delivery of nucleotide sequences to the targeted organ, tissue or cell population. Methods which are well known to those skilled in the art can be used to construct recombinant vectors which will express antisense molecules complementary to the polynucleotides of the gene encoding the proteins of the invention. These techniques are described both in Sambrook et al. (supra) and in Ausubel et al. (supra). Genes encoding the proteins of the invention can be turned off by transforming a cell or tissue with expression vectors which express high levels of a polynucleotide or fragment thereof which encodes the proteins of the invention. Such constructs may be used to introduce untranslatable sense or antisense sequences into a cell. Even in the absence of integration into the DNA, such vectors may continue to transcribe RNA molecules until they are disabled by endogenous nucleases. Transient expression may last for a month or more with a non-replicating vector and even longer if appropriate replication elements are part of the vector system.
As mentioned above, modifications of gene expression can be obtained by designing antisense molecules, DNA, RNA, or nucleic acid analogues such as PNA, to the control regions of the gene encoding the proteins of the invention, i.e., the promoters, enhancers, and introns. Oligonucleotides derived from the transcription initiation site, e.g. between positions −10 and +10 from the start site, are preferred. Similarly, inhibition can be achieved using “triple helix” base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules. Recent therapeutic advances using triplex DNA have been described in the literature (Gee, J. E. et al. (1994) In; Huber, B. E. and B. I. Carr, Molecular and Immunologic Approaches, Futura Publishing Co., Mt. Kisco, N.Y.). The antisense molecules may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.
Ribozymes, enzymatic RNA molecules, may also be used to catalyze the specific cleavage of RNA. The mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage. Examples which may be used include engineered hammerhead motif ribozyme molecules that can be specifically and efficiently catalyze endonucleolytic cleavage of sequences encoding the proteins of the invention. Specific ribozyme cleavage sites within any potential RNA target are initially identified by scanning the target molecule for ribozyme cleavage sites which include the following sequences: GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides corresponding to the region of the target gene containing the cleavage site may be evaluated for secondary structural features which may render the oligonucleotide inoperable. The suitability of candidate targets may also be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays.
Effector nucleic acid molecules, e.g. antisense molecules and ribozymes of the invention may be prepared by any method known in the art for the synthesis of nucleic acid molecules. These include techniques for chemically synthesizing oligonucleotides such as solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules may be generated by in vitro and in vivo transcription of DNA sequences encoding the proteins of the invention. Such DNA sequences may be incorporated into a variety of vectors with suitable RNA polymerase promoters such as T7 or SP6. Alternatively, these cDNA constructs that synthesize antisense RNA constitutively or inducibly can be introduced into cell lines, cells, or tissues. RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5′ and/or 3′ ends of the molecule or the use of phosphorothioate or 2′ O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of nontraditional bases such as inosine, queosine, and wybutosine, as well as acetyl-, methyl-, thio- and similarly modified forms of adenine, cytidine, guanine, thymine, and uridine which are not as easily recognized by endogenous endonucleases.
Gene function can also be suppressed using small interfering RNAs. These are short (18 to 25 bp) RNA duplexes (the RNA may be modified for stabilization). The small interfering RNAs can be made either synthetically, by in vitro transcription procedures or using suitable vectors which express the desired RNA duplex as a hairpin structure inside the target cell. Applications include functional gene suppression in tissue culture, in model organisms such as mice or therapeutically (see e.g. Shi, Y. Trends Genet 19(1):9-12; Shuey, D. J., Drug Discov Today. 7(20):1040-6). The presence of longer (>30 bp) antisense RNAs inside of eukaryotic cells can also lead to gene silencing under certain circumstances.
Many methods for introducing vectors into cells or tissues are available and equally suitable for use in vivo, in vitro, and ex vivo. For ex vivo therapy, vectors may be introduced into stem cells taken from the patient and clonally propagated for autologous transplant back into that same patient. Delivery by transfection and by liposome injections may be achieved using methods which are well known in the art. Any of the therapeutic methods described above may be applied to any suitable subject including, for example, mammals such as dogs, cats, cows, horses, rabbits, monkeys, and most preferably, humans.
An additional embodiment of the invention relates to the administration of a pharmaceutical composition, in conjunction with a pharmaceutically acceptable carrier, for any of the therapeutic effects discussed above. Such pharmaceutical compositions may consist of the proteins of the invention, antibodies to the proteins of the invention, mimetics, agonists, antagonists, or inhibitors of the proteins of the invention. The compositions may be administered alone or in combination with at least one other agent, such as stabilizing compound, which may be administered in any sterile, biocompatible pharmaceutical carrier, including, but not limited to, saline, buffered saline, dextrose, and water. The compositions may be administered to a patient alone, or in combination with other agents, drugs or hormones. The pharmaceutical compositions utilized in this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal means.
In addition to the active ingredients, these pharmaceutical compositions may contain suitable pharmaceutically-acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Further details on techniques for formulation and administration may be found in the latest edition of Remington's Pharmaceutical Sciences (Maack Publishing Co., Easton, Pa.).
The pharmaceutical compositions of the present invention may be manufactured in a manner that is known in the art, e.g. by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes. After pharmaceutical compositions have been prepared, they can be placed in an appropriate container and labeled for treatment of an indicated condition. For administration of the proteins of the invention, such labeling would include amount, frequency, and method of administration.
Pharmaceutical compositions suitable for use in the invention include compositions wherein the active ingredients are contained in an effective amount to achieve the intended purpose. The determination of an effective dose is well within the capability of those skilled in the art. For any compounds, the therapeutically effective does can be estimated initially either in cell culture assays, e.g. of preadipoctic cell lines, or in animal models, usually mice, rabbits, dogs, or pigs. The animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. A therapeutically effective dose refers to that amount of active ingredient, for example the proteins of the invention or fragments thereof, antibodies of the proteins; of the invention, which is effective for the treatment of a specific condition. Therapeutic efficacy can toxicity may be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g. ED50 (the does therapeutically effective in 50% of the population) and LD50 (the dose lethal to 50% of the population). The dose ratio between therapeutic and toxic effects is the therapeutic index, and it can be expressed as the ratio, LD50/ED50. Pharmaceutical compositions which exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies is used in formulating a range of dosage for human use. The dosage contained in such compositions is preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage varies within this range depending upon the dosage from employed, sensitivity of the patient, and the route of administration. The exact dosage will be determined by the practitioner, in light of factors related to the subject that requires treatment. Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Factors which may be taken into account include the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or once every two weeks depending on half-life and clearance rate of the particular formulation. Normal dosage amounts may vary from 0.1 to 100,000 micrograms, up to a total dose of about 1 g, depending upon the route of administration. Guidance as to particular dosages and methods of delivery is provided in the literature and generally available to practitioners in the art. Those skilled in the art employ different formulations for nucleotides than for proteins or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc.
In another embodiment, antibodies which specifically bind the proteins of the invention may be used for the diagnosis of conditions or diseases characterized by expression of the proteins of the invention, or in assays to monitor patients being treated with the proteins of the invention, agonists, antagonists or inhibitors. The antibodies useful for diagnostic purposes may be prepared in the same manner as those described above for therapeutics. Diagnostic assays for the proteins of the invention include methods which utilize the antibody and a label to detect the proteins of the invention in human body fluids or extracts of cells or tissues. The antibodies may be used with or without modification, and may be labeled by joining them, either covalently or non-covalently, with a reporter molecule. A wide variety of reporter molecules which are known in the art may be used several of which are described above.
A variety of protocols including ELISA, RIA, and FACS for measuring the proteins of the invention are known in the art and provide a basis for diagnosing altered or abnormal levels of the proteins of the invention expression. Normal or standard values for the proteins of the invention expression are established by combining body fluids or cell extracts taken from normal mammalian subjects, preferably human, with antibody to the proteins of the invention under conditions suitable for complex formation. The amount of standard complex formation may be quantified by various methods, but preferably by photometric means. Quantities of the proteins of the invention expressed in control and disease samples from biopsied tissues, for example, are compared with the standard values. Deviation between standard and subject values establishes the parameters for diagnosing disease.
In another embodiment of the invention, the polynucleotides of the invention may be used for diagnostic purposes. The polynucleotides which may be used include oligonucleotide sequences, antisense RNA and DNA molecules, and PNAs. The polynucleotides may be used to detect and quantitate gene expression in biopsied tissues in which expression of the proteins of the invention may be correlated with disease. The diagnostic assay may be used to distinguish between absence, presence, and excess expression of the proteins of the invention, and to monitor regulation of the proteins of the invention levels during therapeutic intervention.
In one aspect, hybridization with PCR probes which are capable of detecting polynucleotide sequences, including genomic sequences, encoding the proteins of the invention or closely related molecules, may be used to identify nucleic acid sequences which encode the proteins of the invention. The specificity of the probe, whether it is made from a highly specific region, or a less specific region, and the stringency of the hybridization or amplification (maximal, high, intermediate, or low) will determine whether the probe identifies only naturally occurring sequences encoding the proteins of the invention, alleles, or related sequences. Probes may also be used for the detection of related sequences, and should preferably contain at least 50% of the nucleotides from any of the proteins of the invention encoding sequences. The hybridization probes of the subject invention may be DNA or RNA and derived from the nucleotide sequence of SEQ ID NO: 1, 3, 5, 7, 9, 11, 12, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41 or 43, or from a genomic sequence including promoter, enhancer elements, and introns of the naturally occurring the proteins of the invention. Means for producing specific hybridization probes for DNAs encoding the proteins of the invention include the cloning of nucleic acid sequences encoding the proteins of the invention or the proteins of the invention derivatives into vectors for the production of mRNA probes. Such vectors are known in the art, commercially available, and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerases and the appropriate labeled nucleotides. Hybridization probes may be labeled by a variety of reporter groups, for example, radionuclides such as 32P or 35S, or enzymatic labels, such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems, and the like.
Polynucleotide sequences may be used for the diagnosis of conditions or diseases which are associated with expression of the proteins of the invention. Examples of such conditions or diseases include, but are not limited to, pancreatic diseases and disorders, including diabetes. Polynucleotide sequences may also be used to monitor the progress of patients receiving treatment for pancreatic diseases and disorders, including diabetes. The polynucleotide sequences may be used in Southern or northern analysis, dot blot, or other membrane-based technologies; in PCR technologies; or in dip stick, pin, ELISA or chip assays utilizing fluids or tissues from patient biopsies to detect altered the proteins of the invention expression. Such qualitative or quantitative methods are well known in the art.
In a particular aspect, the nucleotide sequences may be useful in assays that detect activation or induction of various pancreatic diseases and disorders, including diabetes, particularly those mentioned above. The nucleotide sequences may be labeled by standard methods, and added to a fluid or tissue sample from a patient under conditions suitable for the formation of hybridization complexes. After a suitable incubation period, the sample is washed and the signal is quantitated and compared with a standard value. The presence of altered levels of nucleotide sequences in the sample compared to the standard, e.g. a control sample indicates the presence of the associated disease. Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials, or in monitoring the treatment of an individual patient.
In order to provide a basis for the diagnosis of disease associated with expression of the proteins of the invention, a normal or standard profile for expression is established. This may be accomplished by combining body fluids or cell extracts taken from normal subjects, either animal or human, with a sequence, or a fragment thereof, which encodes the proteins of the invention, under conditions suitable for hybridization or amplification. Standard hybridization may be quantified by comparing the values obtained from normal subjects with those from an experiment where a known amount of a substantially purified polynucleotide is used. Standard values obtained from normal samples may be compared with values obtained from samples from patients who are symptomatic for disease. Deviation between standard and subject values is used to establish the presence of disease. Once disease is established and a treatment protocol is initiated, hybridization assays may be repeated on a regular basis to evaluate whether the level of expression in the patient begins to approximate that which is observed in the normal patient. The results obtained from successive assays may be used to show the efficacy of treatment over a period ranging from several days to months.
With respect to pancreatic diseases and disorders, including diabetes, the presence of a relatively high amount of transcript in biopsied tissue from an individual may indicate a predisposition for the development of the disease, or may provide a means for detecting the disease prior to the appearance of actual clinical symptoms. A more definitive diagnosis of this type may allow health professionals to employ preventative measures or aggressive treatment earlier thereby preventing the development or further progression of the pancreatic diseases and disorders. Additional diagnostic uses for oligonucleotides designed from the sequences encoding the proteins of the invention may involve the use of PCR. Such oligomers may be chemically synthesized, generated enzymatically, or produced from a recombinant source. Oligomers will preferably consist of two nucleotide sequences, one with sense orientation (5′.fwdarw.3′) and another with antisense (3′.rarw.5′), employed under optimized conditions for identification of a specific gene or condition. The same two oligomers, nested sets of oligomers, or even a degenerate pool of oligomers may be employed under less stringent conditions for detection and/or quantitation of closely related DNA or RNA sequences.
Methods, which may also be used to quantitate the expression of the proteins of the invention, include various labels, e.g. radioisotopes, fluorescers, chemiluminescers, enzymes, specific binding molecules, particles, e.g. magnetic particles or the like. Specific binding molecules include pairs, such as biotin and streptavidin, digoxin and antidigoxin etc. For the specific binding members, the complementary member would normally be labeled with a molecule that provides for detection, in accordance with known procedures. The methods include coamplification of a control nucleic acid, and standard curves onto which the experimental results are interpolated (Melby, P. C. et al. (1993) J. Immunol. Methods, 159:235-244; Duplaa, C. et al. (1993) Anal. Biochem. 212:229-236. The speed of quantitation of multiple samples may be accelerated by running the assay in an ELISA format where the oligomer of interest is presented in various dilutions and a spectrophotometric or colorimetric response gives rapid quantitation.
In another embodiment of the invention, the nucleic acid sequences which encode the proteins of the invention may also be used to generate hybridization probes which are useful for mapping the naturally occurring genomic sequence. The sequences may be mapped to a particular chromosome or to a specific region of the chromosome using well known techniques. Such techniques include FISH, FACS, or artificial chromosome constructions, such as yeast artificial chromosomes, bacterial artificial chromosomes, bacterial P1 constructions or single chromosomencDNA libraries as reviewed in Price, C. M. (1993) Blood Rev. 7:127-134, and Trask, B. J. (1991) Trends Genet. 7:149-154. FISH (as described in Verma et al. (1988) Human Chromosomes: A Manual of Basic Techniques, Pergamon Press, New York, N.Y.) may be correlated with other physical chromosome mapping techniques and genetic map data. Examples of genetic map data can be found in the 1994 Genome Issue of Science (265:1981f). Correlation between the location of the gene encoding the proteins of the invention on a physical chromosomal map and a specific disease, or predisposition to a specific disease, may help delimit the region of DNA associated with that genetic disease.
The nucleotide sequences of the subject invention may be used to detect differences in gene sequences between normal, carrier, or affected individuals. In situ hybridization of chromosomal preparations and physical mapping techniques such as linkage analysis using established chromosomal markers may be used for extending genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of a particular human chromosome is not known. New sequences can be assigned to chromosomal arms, or parts thereof, by physical mapping. This provides valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once the disease or syndrome has been crudely localized by genetic linkage to a particular genomic region, for example, AT to 11q22-23 (Gatti, R. A. et al. (1988) Nature 336:577-580), any sequences mapping to that area may represent associated or regulatory genes for further investigation. The nucleotide sequence of the subject invention may also be used to detect differences in the chromosomal location due to translocation, inversion, etc. among normal, carrier, or affected individuals.
In another embodiment of the invention, the proteins of the invention, its catalytic or immunogenic fragments or oligopeptides thereof, an in vitro model, a genetically altered cell or animal, can be used for screening libraries of compounds in any of a variety of drug screening techniques. One can identify ligands or substrates that bind to, modulate or mimic the action of one or more of the proteins of the invention. A protein of the invention or a fragment thereof employed in such screening may be free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly. The formation of binding complexes, between the proteins of the invention and the agent tested, may be measured. Of particular interest are screening assays for agents that have a low toxicity for mammalian cells. The term “agent” as used herein describes any molecule, e.g. protein, peptide or pharmaceutical, with the capability of altering or mimicking the physiological function of one or more of the proteins of the invention. Candidate agents encompass numerous chemical classes, though typically they are organic molecules, preferably small organic compounds having a molecular weight of more than 50 and less than about 2,500 Daltons. Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof. Candidate agents are obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, etc. to produce structural analogs. Where the screening assay is a binding assay, one or more of the molecules may be joined to a label, where the label can directly or indirectly provide a detectable signal.
Another technique for drug screening which may be used provides for high throughput screening of compounds having suitable binding affinity to the protein of interest as described in published PCT application WO84/03564. In this method, as applied to the proteins of the invention large numbers of different small test compounds are provided or synthesized on a solid substrate, such as plastic pins or some other surface. The test compounds are reacted with the proteins of the invention, or fragments thereof, and washed. Bound the proteins of the invention is then detected by methods well known in the art. Purified the proteins of the invention can also be coated directly onto plates for use in the aforementioned drug screening techniques. Alternatively, non-neutralizing antibodies can be used to capture the peptide and immobilize it on a solid support. In another embodiment, one may use competitive drug screening assays in which neutralizing antibodies capable of binding the proteins of the invention specifically compete with a test compound for binding the proteins of the invention. In this manner, the antibodies can be used to detect the presence of any peptide which shares one or more antigenic determinants with the proteins of the invention. In additional embodiments, the nucleotide sequences which encode the proteins of the invention may be used in any molecular biology techniques that have yet to be developed, provided the new techniques rely on properties of nucleotide that are currently known, including, but not limited to, such properties as the triplet genetic code and specific base pair interactions.
The nucleic acids encoding the proteins of the invention can be used to generate transgenic cell lines and animals. These transgenic non-human animals are useful in the study of the function and regulation of the proteins of the invention in vivo. Transgenic animals, particularly mammalian transgenic animals, can serve as a model system for the investigation of many developmental and cellular processes common to humans. A variety of non-human models of metabolic disorders can be used to test modulators of the protein of the invention. Misexpression (for example, overexpression or lack of expression) of the protein of the invention, particular feeding conditions, and/or administration of biologically active compounts can create models of metablic disorders.
In one embodiment of the invention, such assays use mouse models of insulin resistance and/or diabetes, such as mice carrying gene knockouts in the leptin pathway (for example, ob (leptin) or db (leptin receptor) mice). Such mice develop typical symptoms of diabetes, show hepatic lipid accumulation and frequently have increased plasma lipid levels (see Bruning et al, 1998, Mol. Cell. 2:449-569). Susceptible wild type mice (for example C57BI/6) show similiar symptoms if fed a high fat diet. In addition to testing the expression of the proteins of the invention in such mouse strainns, these mice could be used to test whether administration of a candidate modulator alters for example lipid accumulation in the liver, in plasma, or adipose tissues using standard assays well known in the art, such as FPLC, calorimetric assays, blood glucose level tests, insulin tolerance tests and others.
Transgenic animals may be made through homologous recombination in non-human embryonic stem cells, where the normal locus of the gene encoding the protein of the invention is mutated. Alternatively, a nucleic acid construct encoding the protein is injected into oocytes and is randomly integrated into the genome. One may also express the genes of the invention or variants thereof in tissues where they are not normally expressed or at abnormal times of development. Furthermore, variants of the genes of the invention like specific constructs expressing anti-sense molecules or expression of dominant negative mutations, which will block or alter the expression of the proteins of the invention may be randomly integrated into the genome. A detectable marker, such as lac Z or luciferase may be introduced into the locus of the genes of the invention, where upregulation of expression of the genes of the invention will result in an easily detectable change in phenotype. Vectors for stable integration include plasmids, retroviruses and other animal viruses, yeast artificial chromosomes (YACs), and the like.
DNA constructs for homologous recombination will contain at least portions of the genes of the invention with the desired genetic modification, and will include regions of homology to the target locus. Conveniently, markers for positive and negative selection are included. DNA constructs for random integration do not need to contain regions of homology to mediate recombination. DNA constructs for random integration will consist of the nucleic acids encoding the proteins of the invention, a regulatory element (promoter), an intron and a poly-adenylation signal. Methods for generating cells having targeted gene modifications through homologous recombination are known in the field. For embryonic stem (ES) cells, an ES cell line may be employed, or embryonic cells may be obtained freshly from a host, e.g. mouse, rat, guinea pig, etc. Such cells are grown on an appropriate fibroblast-feeder layer and are grown in the presence of leukemia inhibiting factor (LIF).
When ES or embryonic cells or somatic pluripotent stem cells have been transformed, they may be used to produce transgenic animals. After transformation, the cells are plated onto a feeder layer in an appropriate medium. Cells containing the construct may be selected by employing a selective medium. After sufficient time for colonies to grow, they are picked and analyzed for the occurrence of homologous recombination or integration of the construct. Those colonies that are positive may then be used for embryo transfection and blastocyst injection. Blastocysts are obtained from 4 to 6 week old superovulated females. The ES cells are trypsinized, and the modified cells are injected into the blastocoel of the blastocyst. After injection, the blastocysts are returned to each uterine horn of pseudopregnant females. Females are then allowed to go to term and the resulting offspring is screened for the construct. By providing for a different phenotype of the blastocyst and the genetically modified cells, chimeric progeny can be readily detected. The chimeric animals are screened for the presence of the modified gene and males and females having the modification are mated to produce homozygous progeny. If the gene alterations cause lethality at some point in development, tissues or organs can be maintained as allogenic or congenic grafts or transplants, or in vitro culture. The transgenic animals may be any non-human mammal, such as laboratory animal, domestic animals, etc. The transgenic animals may be used in functional studies, drug screening, etc.
Finally, the invention also relates to a kit comprising at least one of
- (a) a nucleic acid molecule or a functional fragment thereof;
- (b) a amino acid molecule or a functional fragment or an isoform thereof;
- (c) a vector comprising the nucleic acid of (a);
- (d) a host cell comprising the nucleic acid of (a) or the vector of (b);
- (e) a polypeptide encoded by the nucleic acid of (a);
- (f) a fusion polypeptide encoded by the nucleic acid of (a);
- (g) an antibody, an aptamer or another receptor against the nucleic acid of (a) or the polypeptide of (d) or (e) and
- (h) an anti-sense oligonucleotide of the nucleic acid of (a).
The kit may be used for diagnostic or therapeutic purposes or for screening applications as described above. The kit may further contain user instructions.BRIEF DESCRIPTION OF THE FIGURES
The examples below are provided to illustrate the subject invention and are not included for the purpose of limiting the invention.EXAMPLES Example 1 DPd6 Chick cDNA Library Construction
The Chick DPd6 cDNA library was constructed from dorsal pancreatic buds dissected from 6 day old chick embryos. The frozen tissue was homogenized and lysed using a Brinkmann POLYTRON homogenizer PT-3000 (Brinkman Instruments, Westbury, N.J.) in guanidinium isothiocyanate solution. The lysates were centrifuged over a 5.7 M CsCl cushion using as Beckman SW28 rotor in a Beckman L8-70M ultracentrifuge (Beckman Instruments, Fullerton, Calif.) for 18 hours at 25,000 rpm at ambient temperature. The RNA was extracted with acid phenol pH 4.7, precipitated using 0.3 M sodium acetate and 2.5 volumes of ethanol, resuspended in RNase-free water, and DNase treated at 37° C. The RNA extraction was repeated with acid phenol pH 4.7 and precipitated with sodium acetate and ethanol as before. The mRNA was then isolated using the Micro-FastTrack 2.0 mRNA isolation kit (Invitrogen, Groningen, Netherlands) and used to construct the cDNA libraries. The mRNAs were handled according to the recommended protocols in the SUPERSCRIPT cDNA synthesis and plasmid cloning system (Gibco/BRL). Following transformation into DH10B host cells, single colonies were picked and the subjected to PCR in order to amplify the cloned cDNA insert. Amplified PCR fragments representing single cDNA inserts were subsequently in vitro transcribed to generate Digoxygenin labelled RNA probes (Roche). The RNA probes were used in a whole-mount in situ screen to determine the expression of their respective gene products in early chick embryos. Plasmids containing the genes encoding the proteins of the invention were identified because of their high expression in pancreatic tissues.Example 2 In Situ Hybridizations
Whole-mount in situ hybridizations were performed according to standard protocols as known to those skilled in the art and as described previously (for example, Pelton, R. W. et al., (1990) Development 110,609-620; Belo, J. A. et al., (1997) Mech. Dev. 68, 45-57).Example 3 Isolation and Sequencing of cDNA Clones
Plasmid DNA was released from the cells and purified using the REAL PREP 96-well plasmid isolation kit (QIAGEN). This kit enabled the simultaneous purification of 96 samples in a 96-well block using multi-channel reagent dispensers. The protocol recommended by the manufacturer was employed except for the following changes, as indicated below: (i) the bacteria were cultured in 1 ml of sterile Terrific Broth (LIFE TECHNOLOGIES™, Gaithersburg, Md., USA) with carbenicillin at 25 mg/L and glycerol at 0.4%; (ii) after inoculation, the cultures were incubated for 19 hours and at the end of incubation, the cells were lysed with 0.3 ml of lysis buffer; and (iii) following isopropanol precipitation, the plasmid DNA pellet was resuspended in 0.1 ml of distilled water. After the last step in the protocol, samples were transferred to a 96-well block for storage at 4° C. The cDNAs were sequenced by GATC Biotech AG (Konstanz, Germany) accoding to standard protocols known to those skilled in the art.Example 4 Homology Searching of cDNA Clones and Their Deduced Proteins
After the reading frame was determined, the nucleotide sequences of the invention as well as the amino acid sequences deduced from them were used as query sequences against databases such as GenBank, SwissProt, BLOCKS, and Pima II. These databases, which contain previously identified and annotated sequences, were searched for regions of homology (similarity) using BLAST, which stands for Basic Local Alignment Search Tool (Altschul S. F. (1993) J. Mol. Evol. 36:290-300; Altschul, S. F. et al. (1990) J. Mol. Biol. 215:403-10). BLAST produced alignments of both nucleotide and amino acid sequences to determine sequence similarity. Because of the local nature of the alignments, BLAST was especially useful in determining exact matches or in identifying homologs which may be of prokaryotic (bacterial) or eukaryotic (animal, fungal, or plant) origin. Other algorithms such as the one described in Smith et al. (1992, protein Engineering 5:35-51), incorporated herein by reference, could have been used when dealing with primary sequence patterns and secondary structure gap penalties. The BLAST approach, as detailed in Karlin et al. (supra) and incorporated herein by reference, searched formatches between a query sequence and a database sequence. BLAST evaluated the statistical significance of any matches found, and reported only those matches that satisfy the user-selected threshold of significance. In this application, threshold was set at 10-25 for nucleotides and 10-14 for peptides. Nucleotide sequences were searched against the GenBank databases for primate, rodent, and other mammalian sequences; and deduced amino acid sequences from the same clones were then searched against GenBank functional protein databases, mammalian, vertebrate, and eukaryote for homology.Example 5 Extension of Polynucleotides to Full Length or to Recover Regulatory Sequences
Full length nucleic acid sequences encoding the proteins of the invention are used to design oligonucleotide primers for extending a partial nucleotide sequence to full length or for obtaining 5′ or 3′, intron or other control sequences from genomic libraries. One primer is synthesized to initiate extension in the antisense direction and the other is synthesized to extend sequence in the sense direction. Primers are used to facilitate the extension of the known sequence “outward” generating amplicons containing new, unknown nucleotide sequence for the region of interest. The initial primers are designed from the cDNA using OLIGO 4.06 primer analysis software (National Biosciences), or another appropriate program, to be 22-30 nucleotides in length, to have a GC content of 50% or more, and to anneal to the target sequence at temperatures about 68° C.-72° C. Any stretch of nucleotides which would result in hairpin dimerizations is avoided. The original, selected cDNA libraries, or a human genomic library are used to extend the sequence, the latter is most useful to obtain 5′ upstream regions. If more extension is necessary or desired, additional sets of primers are designed to further extend the known region. By following the instructions for the XL-PCR kit (Perkin Elmer) and thoroughly mixing the enzyme and reaction mix, high fidelity amplification is obtained. Beginning with 40 pmol of each primer and the recommended concentrations of all other components of the kit, PCR is performed using the Peltier thermal cycler (PTC200; M. J. Research, Watertown, Mass.) and the following parameters:
- Step 1 94° C. for 1 min (initial denaturation)
- Step 2 65° C. for 1 min
- Step 3 68° C. for 6 min
- Step 4 94° C. for 15 sec
- Step 5 65° C. for 1 min
- Step 6 68° C. for 7 min
- Step 7 Repeat step 4-6 for 15 additional cycles
- Step 8 94° C. for 15 sec
- Step 9 65° C. for 1 min
- Step 10 68° C. for 7-15 min
- Step 11 Repeat step 8-10 for 12 cycles
- Step 12 72° C. for 8 ml
- Step 13 4° C. (and holding)
A 5-10 μl aliquot of the reaction mixture is analyzed by electrophoresis on a low concentration (about 0.6-0.8% agarose mini-gel to determine which reactions were successful in extending the sequence. Bands thought to contain the largest products are selected and removed from the gel. Further purification involves using a commercial gel extraction method such as the QIAQUICK DNA purification kit (QIAGEN). After recovery of the DNA, Klenow enzyme is used to trim single-stranded, nucleotide overhangs creating blunt ends which facilitate religation and cloning. After ethanol precipitation, the products are redissolved in 13 μl of ligation buffer, 1 μl T4-DNA ligase (15 units) and 1 μl T4 polynucleotide kinase are added, and the mixture is incubated at room temperature for 2-3 hours or overnight at 16° C. Competent E. coli cells (in 40 μl of appropriate media) are transformed with 3 μl of ligation mixture and cultured in 80 μl of SOC medium (Sambrook et al., supra). After incubation for one hour at 37° C. the whole transformation mixture is plated on Luria Bertani (LB)-agar (Sambrook et al., supra) containing 2×Carb. The following day, several colonies are randomly picked from each plate and cultured in 150 μl of liquid LB/2×Carb medium placed in an individual well of an appropriate, commercially-available, sterile 96-well microtiter plate. The following day, 5 μl of each overnight culture is transferred into a non-sterile 96-well plate and after dilution 1:10 with water, 5 μl of each sample is transferred into a PCR array. For PCR amplification, 18 μl of concentrated PCR reaction mix (3.3×) containing 4 units of rTth DNA polymerase, a vector primer, and one or both of the gene specific primers used for the extension reaction are added to each well. Amplification is performed using the following conditions:
- Step 1 94° C. for 60 sec
- Step 2 94° C. for 20 sec
- Step 3 55° C. for 30 sec
- Step 4 72° C. for 90 sec
- Step 5 Repeat steps 2-4 for an additional 29 cycles
- Step 6 72° C. for 180 sec
- Step 7 4° C. (and holding)
Aliquots of the PCR reactions are run on agarose gels together with molecular weight markers. The sizes of the PCR products are compared to the original partial cDNAs, and appropriate clones are selected, ligated into plasmid, and sequenced.Example 6 Labeling and Use of Hydridization Probes
Hybridization probes derived from nucleic acids described in this invention were employed to screen cDNAs, genomic DNAs, or mRNAs. Although the labeling of oligonucleotides, consisting of about 20 base-pairs, is specifically described, essentially the same procedure is used with larger cDNA fragments. Oligonucleotides are designed using state-of-the-art software such as OLIGO 4.06 primer analysis software (National Biosciences, labeled by combining 50 pmol of each oligomer and 250 μCi Of γ-32P adenosine triphosphate (Amersham) and T4 polynucleotide kinase (DuPont Nen(r), Boston, Mass.). The labelled oligonucleotides are substantially purified with SEPHADEX G-25 superfine resin column (Pharmacia & Upjohn). A portion containing 107 counts per minute of each of the sense and antisense oligonucleotides is used in a typical membrane based hybridization analysis of human genomic DNA digested with one of the following membranes (Ase I, Bgl II, EcoRI, Pst I, Xba I, or Pvu II; DuPont NEN(r)). The DNA from each digest is fractionated on a 0.7 percent agarose gel and transferred to nylon membranes (NYTRAN PLUS membrane, Schleicher & Schuell, Durham, N.H.). Hybrization is carried out for 16 hours at 40° C. To remove nonspecific signals, blots are sequentially washed at room temperature under increasingly stringent conditions up to 0.1×saline solution citrate (SSC) and 0.5% sodium dodecyl sulfate. After XOMAI AR Autoradiography film (Kodak Rochester, N.Y.) is exposed to the blots, or the blots are placed in a PHOSPHOIMAGER (Molecular Dynamics, Sunnyvale, Calif.) for several hours, hybridization patterns are compared visually.Example 7 Antisense Molecules
Antisense molecules to the sequences encoding proteins of the invention, or any part thereof, are used to inhibit in vivo or in vitro expression of naturally occurring the proteins of the invention. Although use of antisense oligonucleotides, comprising about 20 base-pairs, is specifically described, essentially the same procedure is used with larger cDNA fragments. An oligonucleotide is used to inhibit expression of naturally occurring proteins of the invention. Antisense oligonucleotides can inhibit gene function in multiple ways. They can bind to the 5′UTR of a transcript and block translation. Alternatively, binding of the antisense oligonucleotide can induce cleavage of the transcript by RNAseH. Antisense oligos have also been shown to block splicing of a pre-mRNA, thereby either blocking formation of specific splice forms or leading to the accumulation of unspliced messages which cannot give rise to mature protein, are unstable, or both. The mechanism of action of a particular antisense oligonucleotide is determined by the chemical composition of the oligonucleotide and/or by the binding site within the targeted transcript.
Antisense oligonucleotides can be applied to tissue culture cells, used in animals or therapeutically in humans. Injection into early zebrafish or xenopus embryos allows convenient analysis of gene function in these species.Example 8 Expression of the Proteins of the Invention
Expression of the proteins of the invention, such as the proteins of the invention and homologous proteins, is accomplished by subcloning the cDNAs into appropriate vectors and transforming the vectors into host cells. In this case, the cloning, vector, PSPORT 1, previously used for the generation of the cDNA library is used to express the proteins of the invention in E. coli. Upstream of the cloning site, this vector contains a promoter for β-galactosidase, followed by sequence containing the amino-terminal Met, and the subsequent seven residues of β-galactosidase. Immediately following these eight residues is a bacteriophage promoter useful for transcription and a linker containing a number of unique restriction sites. Induction of an isolated, transformed bacterial strain with IPTG using standard methods produces a fusion protein which consists of the first eight residues of β-galactosidase, about 5 to 15 residues of linker, and the full length protein. The signal residues direct the secretion of the proteins of the invention into the bacterial growth media which can be used directly in the following assay for activity.Example 9 Production of Antibodies Specific for the Proteins of the Invention
The proteins of the invention that are substantially purified using PAGE electrophoresis (Sambrook, supra), or other purification techniques, is used to immunize rabbits and to produce antibodies using standard protocols. The amino acid sequences are analyzed using DNASTAR software (DNASTAR Inc) to determine regions of high immunogenicity and a corresponding oligopolypeptide is synthesized and used to raise antibodies by means known to those of skill in the art. Selection of appropriate epitopes, such as those near the C-terminus or in hydrophilic regions, is described by Ausubel et al. (supra), and others.
Typically, the oligopeptides are 15 residues in length, synthesized using an Applied Biosystems 431A peptide synthesizer 431A using Fmoc-chemistry, and coupled to keyhole limpet hemocyanin (KLH, Sigma, St. Louis, Mo.) by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS; Ausubel et al., supra). Rabbits are immunized with the oligopeptide-KLH complex in complete Freund's adjuvant. The resulting antisera are tested for antipeptide activity, for example, by binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radioiodinated, goat anti-rabbit IgG.
The proteins of the invention or biologically active fragments thereof are labeled with 125I Bolton-Hunter reagent (Bolton et al. (1973) Biochem. J. 133:529). Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled proteins of the invention, washed and any wells with labeled proteins of the invention complex are assayed. Data obtained using different concentrations of proteins of the invention are used to calculate values for the number, affinity, and association of proteins of the invention with the candidate molecules. All publications and patents mentioned in the above specification are herein incorporated by reference.Example 10 Identification of Human Homologous Genes and Proteins
Homologous proteins and nucleic acid molecules coding therefore are obtainable from insect or vertebrate species, e.g. mammals or birds. Sequences homologous to the chicken proteins and nucleic acid molecules were identified using the publicly available program BLASTP 2.2.3 of the non-redundant protein data base of the National Center for Biotechnology Information (NCBI) (see, Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402).
Chicken DP119 (SEQ ID NO: 2) showed 93% identities and 98% homologies to amino acids 251 to 432 of human CAB43286.1 (SEQ ID NO: 4; encoded by AL050137.1—SEQ ID NO:3) and 93% identities and 97% homologies to amino acids 565 to 746 of mouse AAH25654.1 (SEQ ID NO: 5; encoded by BC025654.1; SEQ ID NO: 6). BLAST searches using human in the Derwent GenSeq Database using human CAB43286.1 or mouse AAH25654.1 as querys revealed the following entries: WO200153312-A1 with claimed applications include diseases of the peripheral nervous system and Immune system suppression, and others; WO200018922-A2 describing novel carbohydrate-associated proteins used for the prevention and treatment of autoimmune/inflammatory disorders, the gastrointestinal and reproductive systems; and WO200155320-A2 with uses in prevention and treatment of reproductive system disorders, including cancer.
Chicken DP444 (SEQ ID: 8 encoded by SEQ ID: 7) showed 93% identity and 97% homology to the polypeptide encoded by human BI035296 (SEQ ID: 9,
Chicken DP810 (SEQ ID NO: 17, see
Chicken DP685 (SEQ ID NO:22, see
Chicken WE474 (SEQ ID NO: 27 encoding SEQ ID NO: 28, see
Chicken DP160 (SEQ ID NO:32, see
Chicken RA977 (SEQ ID NO: 35; encoded protein SEQ ID NO: 36, see
Chicken RA770 (SEQ ID NO:40, see.
A complete mDG770 Open Reading Frame (ORF) was cloned under the control of the rat insulin promoter II (Lomedico et al., (1979) Cell 18: 545-558) using the Gateway system (Invitrogen). For the structure of the transgenic construct, see also
Transgenic construct DNA (see Example 11) was injected into C57/BL6×CBA embryos (Harlan Winkelmann, Borchen, Germany) using standard techniques (see, for example, Brinster et al. (1985), Proc. Natl. Acad. Sci. USA 82: 4438-4442). The mDG770 transgene (see Example 11) was expressed under the control of the rat insulin promoter II (Lomedico et al., supra) using techniques known to those skilled in the art (for example, see, Gunnig et al. (1987), Proc. Natl. Acad. Sci. USA 84, 4831-4835). Using this technique, several independent founderlines were generated.Example 13 Genotype Analysis of rIP-mDG770 Transgenic Mice
Genotyping was performed by PCR using genomic DNA isolated from the tail tip. To detect the mDG770 transgene a transgene specific forward primer (5′ tgc tat ctg tct gga tgt gcc 3′ and a mDG770 transgene specific reverse primer (5′ aag gac acc tcg tcc tca tag 3′) was used.Example 14 mDG770 Expression Analysis Via TaqMan Analysis
The expression of the mDG770 transgene in islets was monitored by TaqMan analysis. For this analysis, 25 ng cDNA derived from pancreatic islet RNA isolated from transgenic mice and their littermates and a mDG770 specifc primer/probe pair were used to detect endogenous as well as transgenic mDG770 expression (mDG770-1 forward primer: 5′ GCC TAT GAG GAC GAG GTG TCC 3′, mDG770 reverse primer: 5′ AGC TCT TGC AGC GTG TGG T 3′, mDG770 probe: 5′ TCC TGG ACG TGC ACA GCC GC 3′). TaqMan analysis was performed using standard techniques known to those skilled in the art. Ectopic transgene expression was detected in 3 of 4 rIP-mDG770 transgenic founderlines analysed. The two founderlines showing highest transgene expression levels were used for further analysis.Example 15 Bodyweight, Body Length and NMR Analysis in mDG770 Transgenic Mice
3 to 6 mice were housed per cage. Growth curves were generated by measuring the bodyweight of individual mDG770 transgenic mice and their wild-type littermates on a weekly basis using a normal balance. The body length was measured from nose to anus placing a ruler along the middle axis of the mouse. On selected time points the lean and fat body mass was measured using non-invasive NMR analysis: to do this individual mice were placed into a Bruker Minispec NMR machine (Bruker, USA) and the lean and body fat content was estimated.
Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in molecular biology or related fields are intended to be within the scope of the following claims.
1. Use of a nucleic acid molecule selected from DP119, DP444, DP810, DF685, WE474, DP160, RA977, or RA770 or a polypeptide encoded thereby or a fragment or variant of said nucleic acid molecule or said polypeptide or an effector/modulator of said nucleic acid or said polypeptide for the manufacture of a pharmaceutical agent.
2. The use of claim 1 wherein the nucleic acid molecule is a vertebrate nucleic acid, particularly a human nucleic acid, or a fragment thereof or variant thereof.
3. The use of claim 1, wherein said nucleic acid molecule
- (a) hybridizes under stringent conditions to the nucleic acid molecule of SEQ ID NO: 1, 3, 5, 7, 9, 11, 12, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43 and/or the complementary strand thereof,
- (b) it is degenerate with respect to the nucleic acid molecule of (a),
- (c) encodes a polypeptide which is at least 80% identical to SEQ ID NO:2, 4, 6, 8, 10, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44 or
- (d) differs from the nucleic acid molecule of (a) to (c) by mutation and wherein said mutation causes an alteration, deletion, duplication or premature stop in the encoded polypeptide.
4. The use of claim 1, wherein the nucleic acid molecule is a DNA molecule.
5. The use of claim 1, wherein the nucleic acid molecule encodes a protein of the invention specifically expressed in pancreatic tissues or other tissues.
6. The use of claim 1, wherein said nucleic acid molecule is a recombinant nucleic acid molecule.
7. The use of claim 6, wherein said recombinant nucleic acid molecule is a vector, particularly an expression vector.
8. The use of claim 1, wherein said polypeptide is a recombinant polypeptide.
9. The use of claim 8, wherein said polypeptide is a fusion polypeptide.
10. The use of claim 1, wherein said nucleic acid molecule is selected from hybridization probes, primers and anti-sense oligonucleotides and aptamers.
11. The use of claim 1 for diagnostic applications.
12. The use of claim 1 for therapeutic applications.
13. The use of claim 1 for the manufacture of an agent for diagnosis, monitoring, prevention or treatment of pancreatic disorders, such as diabetes and related disorders, as well as neurodegenerative disorders, and other diseases.
14. The use of claim 13 for detecting and/or verifying, for the treatment, alleviation and/or prevention of a pancreatic dysfunction (for example diabetes, hyperglycemia, and impaired glucose tolerance), and related disorders including obesity, and neurodegenerative disorders, and others, in cells, cell masses, organs and/or subjects.
15. The use of claim 13 for promoting the differentiation and/or function of beta-cells in vitro and/or in vivo.
16. The use of claim 13 for the regeneration of beta-cells in vitro and/or in vivo.
17. Use of a nucleic acid molecule selected from DP119, DP444, DP810, DP685, WE474, DPI 60, RA977, or RA770 or a polypeptide encoded thereby or a fragment or variant of said nucleic acid molecule or said polypeptide or an effector/modulator of said nucleic acid molecule or said polypeptide as defined in claim 1 for monitoring and/or controlling the function of a gene and/or a gene product which is influenced and/or modified by a DP119, DP444, DP81 0, DP685, WE474, DP160, RA977, or RA770 polypeptide.
18. Use of a nucleic acid molecule selected from DP119, DP444, DP810, DP685, WE474, or RA977 or a polypeptide encoded thereby or a fragment or variant of said nucleic acid molecule or said polypeptide or an effector/modulator of said nucleic acid molecule or said polypeptide as defined in claim 1 for identifying substances capable of interacting with a DP119, DP444, DP810, DP685, WE474, DP160, RA977, or RA770 polypeptide.
19. A non-human transgenic animal exhibiting a modified expression of a DP119, DP444, DP810, DP685, WE474, DP160, RA977, or RA770 polypeptide.
20. The animal of claim 19, wherein the expression of DP119, DP444, DP81 0, DP685, WE474, DP160, RA977, or RA770 polypeptide is increased and/or reduced.
21. A recombinant host cell exhibiting a modified expression of a DP119, DP444, DP81 0, DP685, WE474, DP160, RA977, or RA770 polypeptide.
22. The cell of claim 21 which is a human cell.
23. A method of identifying a (poly)peptide involved in a metabolic disorder or metabolic syndrome, particularly in pancreatic dysfunction, in a mammal comprising the steps of
- (a) contacting a collection of test (poly)peptides with a DP119, DP444, DP810, DP685, WE474, DP160, RA977, or RA770 polypeptide or a fragment thereof under conditions that allow binding of said test (poly)peptide;
- (b) removing test (poly)peptides which do not bind and
- (c) identifying test (poly)peptides that bind to said DP119, DP444, DP81 0, DP685, WE474, DP160, RA977, or RA770 polypeptide or the fragment thereof.
24. A method of screening for an agent which modulates the interaction of a DP1 19, DP444, DP81 0, DP685, WE474, DP160, RA977, or RA770 polypeptide or a fragment thereof with a binding target/agent, comprising the steps of
- (a) incubating a mixture comprising (aa) a DP119, DP444, DP810, DP685, WE474, DP160, RA977, or RA770 polypeptide or a fragment thereof; (ab) a binding target/agent of said DP119, DP444, DP81 0, DP685, WE474, DP160, RA977, or RA770 polypeptide or fragment thereof; and (ac) a candidate agent under conditions whereby said DP119, DP444, DP81 0, DP685, WE474, DP160, RA977, or RA770 polypeptide or fragment thereof specifically binds to said binding target/agent at a reference affinity;
- (b) detecting the binding affinity of said DP119, DP444, DP810, DP685, WE474, DP160, RA977, or RA770 polypeptide or fragment thereof to said binding target to determine an (candidate) agent-biased affinity; and
- (c) determining a difference between (candidate) agent-biased affinity and the reference affinity.
25. A method of screening for an agent which modulates the activity of a DP119, DP444, DP810, DP685, WE474, DP160, RA977, or 25 RA770 polypeptide, comprising the steps of
- (a) incubating a mixture comprising (aa) a DP119, DP444, DP81 0, DP685, WE474, DP160, RA977, or RA770 polypeptide or a fragment thereof; and (ab) a candidate agent
- b) a vector comprising the nucleic acid of (a);
- (c) a host cell comprising the nucleic acid molecule of (a) or the
26. A method of producing a composition comprising mixing a (poly)peptide identified by the method of claim 23 with a pharmaceutically acceptable carrier and/or diluent.
27. The method of claim 26 wherein said composition is a pharmaceutical composition is a pharmaceutical composition for preventing, alleviating or treating of a pancreatic dysfunction (for example diabetes, hyperglycemia, and impaired glucose tolerance), and related disorders including obesity, and neurodegenerative disorders, and others.
28. Use of a (poly)peptide as identified by the method of claim 23 for the preparation of a pharmaceutical composition for the treatment, alleviation and/or prevention of a pancreatic dysfunction (for example diabetes, hyperglycemia, and impaired glucose tolerance), and related disorders including obesity, and neurodegenerative disorders, and others.
29. Use of a nucleic acid molecule of the DP119, DP444, DP810, DP685, WE474, DP160, RA977 or RA770 gene family or of a fragment thereof for the preparation of a non-human animal which over- or underexpresses the DP119, DP444, DP810, DP685, WE474, DP160, RA977, RA770 gene product.
30. Kit comprising of at least one of
- (a) a DP119, DP444, DP810, DP685, WE474, DP160, RA977, or RA770 nucleic acid molecule or a fragment thereof;
- (b) a vector comprising the nucleic acid of (a);
- (c) a host cell comprising the nucleic acid molecule of (a) or the vector of (b);
- (d) a polypeptide encoded by the nucleic acid molecule of (a);
- (e) a fusion polypeptide encoded by the nucleic acid molecule of (a);
- (f) an antibody, an aptamer or another receptor the nucleic acid molecule of (a) or the polypeptide of (d) or (e) and
- (g) an anti-sense oligonucleotide of the nucleic acid molecule of (a).
31. A method of producing a composition comprising mixing an agent identified by the method of claim 24 with a pharmaceutically acceptable carrier and/or diluent.
32. Use of an agent as identified by the method of claim 24 for the preparation of a pharmaceutical composition for the treatment, alleviation and/or prevention of a pancreatic dysfunction (for example diabetes, hyperglycemia, and impaired glucose tolerance), and related disorders including obesity, and neurodegenerative disorders, and others.
Filed: Nov 29, 2004
Publication Date: Oct 6, 2005
Applicant: Develogen Aktiengesellschaft fuer Entwicklungsbiologische Forschung (Goettingen)
Inventors: Cord Dohrmann (Goettingen), Matthias Austen (Goettingen)
Application Number: 10/998,197