Patent Application
20150118158
This application incorporates by reference the Sequence Listing contained in the following ASCII text file being submitted concurrently herewith:
File name: 37861039003SEQLIST.txt; created Dec. 22, 2014, 133 KB in size.
Diabetes is a devastating disease that is caused by either the complete destruction of the pancreatic beta-cell (type I, or juvenile diabetes) or the deterioration of the function of such cells (Type II, or adult diabetes). Many people suffer from the diseases, with an estimated number in this country of app. 17.5 million diagnosed. As a percentage of the total population, this figure is rising. Associated health costs as outlined by the American Diabetes Association are estimated at $174 billion, of which one third is accredited to a loss of national productivity. The average cost for health care expenses for a diabetic person is 2.3 fold higher than in absence of diabetes, and is currently set at $11,744/year.
Temporal curing of diabetes has been achieved. Presently, a sparse supply of organ donor cadaveric human islets can be used to transplant a limited number of type I diabetic patients. Such recipients become insulin-independent, for periods now up to several years.
The etiology of the disease is related to the role of the pancreatic insulin-producing cell, the beta cell. The normal function of the pancreatic beta cell is to control blood glucose homeostasis, and in absence of such regulation several detrimental effects are observed in patients with the disease, even in the presence of intensive treatment. Such long-term complications affect the function of the kidneys (nephropathy), eye degeneration (retinopathy), loss of extremities by amputation (vascular complications) and diabetes is furthermore associated with increased cardiovascular risk, and results in a shortened lifespan.
In both type I and type II diabetes, focus is on the life and function of the pancreatic beta cell. This cell type is unique in multiple aspects, the most important being that it is the only cell type in the body capable of producing insulin. Consequently, a loss of such cells leads to insulin dependence. Type I or type II diabetes is diagnosed at a point where the function of such cells have decreased to a level not meeting initial demand for appropriate blood glucose lowering following a meal. It is generally believed, however, that if one could assess beta cell mass, and function prior to diagnosis, intervention strategies may be applied to circumvent the further demise of the failing cell population. For type I diabetes, current focus is on identifying the presence of circulating anti-islet auto-antigens, as such may help identify those children that are at-risk, or are overtly pre-diabetic due to an ongoing immune destruction. For type II diabetes, current focus is on establishing clinical testing, such as the use of oral glucose tolerance testing (OGTT), now suggested as a standard evaluation of males approaching 50 years of age. The result of an OGTT can help identify individuals that are at the pre-diabetic point, and interventions can be performed, mostly including counseling related to the benefits of lifestyle changes involving increased exercise, caloric intake, and balancing diets. In both cases, non-invasive imaging of the beta cell mass, if aided by reagents capable of marking the cell population, could substantially improve the diagnostic toolbox.
Presently, there is no method by which beta cell mass can be assessed in a non-biased manner non-invasively in human subjects. Accurate measurement of beta cell mass in pancreas is dependent on biopsy analysis followed by histological assessment of beta cell numbers and morphometric counting; in most cases obtained post-mortem through autopsy material. The amount of donor material reflecting on progressive disease development is therefore significantly limited, and kinetic studies on disease progression in an individual are impossible using this technology. Another important aspect related to a growing need for beta cell mass assessment is following islet transplantation. Although only performed in few individuals, this technology is becoming more widespread. It is carried out by isolating an islet-enriched cellular fraction from a human donor post-mortem, which is subsequently transplanted through portal vein injection into a HLA-matched type I diabetic recipient. Following transplantation, there is generally no means to assess the viability and health of the grafted islet cells, as these are inaccessible in the recipient's liver vascular system. A general assessment of graft function is determined by measurements of insulin-dependency, gradually lowering injected insulin as cells in the graft become capable of providing insulin. Often, multiple transplants are required, empirically defined based on outcome. There is no unbiased assessment of the actual viable islet cell mass that engrafts within the liver, and it cannot be followed. It should be mentioned that given the local production of insulin by such grafted islets, a local adipogenic effect occurs within the liver, and such changes may be measured non-invasively by MRI. However, in the best case, this only provides a read out of grafting efficiency; it is not able to accurately measure numbers/mass of viable grafted islet cells.
Thus, a need exists for methods of assessing beta cell mass and/or activity non-invasively.
The invention is based, in part, on the discovery that a polypeptide, referred to herein as Betacam, is selectively expressed on the surface of pancreatic islet cells. Thus, in one aspect, the invention is directed to compositions comprising Betacam or that can be used to detect Betacam. In another aspect, the invention provides methods of detecting (e.g., non-invasively) pancreatic beta cells from a mammalian cell source. Another aspect of the invention is directed to cellular purification of pancreatic beta cells from a heterogeneous cell source of multiple kinds. In another aspect, the invention provides methods of identifying agents that modulate activity of Betacam. In yet another aspect, the invention provides for improved treatment and diagnosis of diabetes.
Accordingly, in particular aspects, the invention is directed to an isolated nucleic acid that encodes an amino acid sequence of Betcam wherein the amino acid sequence comprises, consists essentially of, or consists of amino acids 31 through 462 of SEQ ID NO: 1, amino acids 19 through 450 of SEQ ID NO:2 or amino acids 30 through 463 of SEQ ID NO: 3. In other aspects the invention is directed to an isolated nucleic acid that encodes an amino acid sequence of an extracellular domain of Betacam, wherein the amino acid sequence comprises, consists essentially of, or consists of SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15. In a particular aspect, the invention is directed to an isolated nucleic acid comprising, consisting essentially of, or consisting of SEQ ID NO: 26.
In another aspect, the invention is directed to an isolated polypeptide that comprises, consists essentially of, or consists of amino acids 31 through 462 of SEQ ID NO: 1, amino acids 19 through 450 of SEQ ID NO:2 or amino acids 30 through 463 of SEQ ID NO: 3. In another aspect, the invention is directed to an isolated polypeptide that comprises, consists essentially of, or consists of SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15.
Also included in the invention are antibodies that have binding specificity for the Betacam polypeptide.
Another aspect of the invention is directed to a method of detecting beta cells in a mixture of pancreatic cells comprising detecting the presence of a polypeptide on the surface of the cells, wherein the polypeptide comprises SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15, and detection of expression of the polypeptide on the surface of the cells indicates that the cells are pancreatic beta cells. The method can further comprise isolating the pancreatic beta cells from the mixture of cells.
Another aspect of the invention is directed to a method of detecting pancreatic beta cells in an individual in need thereof, comprising administering to the individual an agent that detects the presence of a polypeptide on the surface of the pancreatic beta cells, wherein the polypeptide comprises SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15. This method can be used, for example, to determine whether an individual is at risk of developing diabetes, or to assess the beta cells of an individual that has diabetes (e.g., to determine the appropriate treatment needed for a diabetic patient or to assess the efficacy of a diabetic patient's existing treatment). In one embodiment, the individual has Type I diabetes, and in another embodiment, the individual has Type II diabetes. In yet another embodiment, the individual has had an islet cell transplantation.
In another aspect, the invention is directed to a method of isolating pancreatic beta cells from a mixture of pancreatic cells comprising contacting the mixture with a reagent that specifically binds to a polypeptide present on the surface of pancreatic beta cells, wherein the polypeptide comprises SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15, thereby producing a combination. The combination is maintained under conditions in which the reagent binds to the polypeptide present on the surface of the pancreatic beta cells, thereby producing a complex of pancreatic beta cells bound to the reagent; and the complex is separated from the combination, thereby isolating pancreatic beta cells from the mixture of pancreatic cells.
In yet another aspect, the invention is a method of identifying an agent that modulates (e.g., inhibits; enhances) the biological activity of betacam comprising contacting a composition comprising a polypeptide, wherein the polypeptide has an amino acid sequence comprising SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15 with an agent to be assessed. The biological activity of the polypeptide in the presence of the agent is measured and compared to a suitable control, wherein if the polypeptide modulates the activity of the polypeptide in the presence of the agent compared to the control, then the agent modulates the biological activity of betacam. In a particular embodiment, the composition is one or more pancreatic beta cells.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
The invention is based, in part, on the discovery that a polypeptide, referred to herein as Betacam, is selectively expressed on the surface of pancreatic islet cells. Specifically, as shown herein, expression of Betacam occurred in both normal and obese mouse pancreatic islet cells and was observed throughout the course of mouse pancreatic development. Expression of Betacam in human islets was validated through EST-sequencing, and the Betacam mRNA was detected 15 times through random sequencing of human islet cDNA.
The inventors named the gene locus in mouse, corresponding to Unigene Mm.206911,
The naming selected is one of convenience; none of the above genes/proteins are named based on previous knowledge of function, or expression in the liver. The arbitrary selection of gene/protein name Betacam is based on information provided within, where the inventors show that the protein is a member of a cell adhesion family group (-cam extension), and selectively expressed in pancreatic beta cells (beta-). It is believed that no other existing and described cell surface marker is known with a similar specificity of expression, as that displayed by the Betacam-encoded protein Betacam.
Betacam in humans exists in two alternative forms, isoform 1 (
Accordingly, particular aspects of the invention are directed to a composition (e.g., a cell adhesion modulating agent; pharmaceutical compositions) that comprises a select amino-acid sequence derived from proteins encoded by the group HomoloGene:18724, as shown in
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry, nucleic acid chemistry, and immunology, which are well known to those skilled in the art. Such techniques are explained fully in the literature, such as, Methods of Enzymology, Vol. 194, Guthrie et al., eds., Cold Spring Harbor Laboratory Press (1990); Molecular Cloning: A Laboratory Manual, second edition (Sambrook et al., 1989) and Molecular Cloning: A Laboratory Manual, third edition (Sambrook and Russel, 2001), (jointly referred to herein as “Sambrook”); Current Protocols in Molecular Biology (F. M. Ausubel et al., eds., 1987, including supplements through 2001); PCR: The Polymerase Chain Reaction, (Mullis et al., eds., 1994); Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York; Harlow and Lane (1999) Using Antibodies: A Laboratory Manual Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (jointly referred to herein as “Harlow and Lane”), Beaucage et al. eds., Current Protocols in Nucleic Acid Chemistry John Wiley & Sons, Inc., New York, 2000).
In accordance with the present invention, an isolated polynucleotide (also referred to as an isolated nucleic acid) is a nucleic acid molecule that has been removed from its natural milieu (e.g., that has been subject to human manipulation), its natural milieu being the genome or chromosome in which the nucleic acid molecule is found in nature. As such, “isolated” does not necessarily reflect the extent to which the nucleic acid molecule has been purified, but indicates that the molecule does not include an entire genome or an entire chromosome in which the nucleic acid molecule is found in nature. The polynucleotides useful in the present invention are typically a portion of a gene (sense or non-sense strand) of the present invention that is suitable for use as a hybridization probe or PCR primer for the identification of a full-length gene (or portion thereof) in a given sample, or that is suitable for encoding a Betacam protein or fragment thereof. An isolated nucleic acid molecule can include a gene or a portion of a gene (e.g., the regulatory region or promoter), for example, to produce a reporter construct or a recombinant protein. An isolated nucleic acid molecule that includes a gene is not a fragment of a chromosome that includes such gene, but rather includes the coding region and regulatory regions associated with the gene, but no additional genes naturally found on the same chromosome. An isolated nucleic acid molecule can also include a specified nucleic acid sequence flanked by (i.e., at the 5′ and/or the 3′ end of the sequence) additional nucleic acids that do not normally flank the specified nucleic acid sequence in nature (i.e., heterologous sequences). Isolated nucleic acid molecule can include DNA, RNA (e.g., mRNA), or derivatives of either DNA or RNA (e.g., cDNA). Although the phrase “nucleic acid molecule” primarily refers to the physical nucleic acid molecule and the phrase “nucleic acid sequence” primarily refers to the sequence of nucleotides on the nucleic acid molecule, the two phrases can be used interchangeably, especially with respect to a nucleic acid molecule, or a nucleic acid sequence, being capable of encoding a protein. In one embodiment, an isolated nucleic acid molecule of the present invention is produced using recombinant DNA technology (e.g., polymerase chain reaction (PCR) amplification, cloning) or chemical synthesis.
Another aspect of the invention are orthologous nucleic acids (e.g., orthologous gene). Orthologous nucleic acids (e.g., genes) are sequences or genes in different organisms that are direct evolutionary counterparts; that is, they are related by descent from a common ancestor. Orthologous nucleic acids normally have the same cellular function. Select members of the orthologous group of Betacam nucleic acids are displayed in
The minimum size of a nucleic acid molecule or polynucleotide of the present invention is a size sufficient to encode a protein having a desired biological activity, such as sufficient to form a probe or oligonucleotide primer that is capable of forming a stable hybrid with the complementary sequence of a nucleic acid molecule encoding the full length (e.g., natural) protein (e.g., under moderate, high or very high stringency conditions) or a biologically active fragment thereof, or to otherwise be used as a target or agent in an assay or in any therapeutic method discussed herein. If the polynucleotide is an oligonucleotide probe or primer, the size of the polynucleotide can be dependent on nucleic acid composition and percent homology or identity between the nucleic acid molecule and a complementary sequence as well as upon hybridization conditions per se (e.g., temperature, salt concentration, and formamide concentration). The minimum size of a polynucleotide that is used as an oligonucleotide probe or primer is at least about 5 nucleotides in length, and preferably ranges from about 5 to about 50 or about 500 nucleotides or greater (1000, 2000, etc.), including any length in between, in whole number increments (i.e., 5, 6, 7, 8, 9, 10, . . . 33, 34, . . . 256, 257, . . . 500 . . . 1000 . . . ), and more preferably from about 10 to about 40 nucleotides, and most preferably from about 15 to about 40 nucleotides in length. In one aspect, the oligonucleotide primer or probe is typically at least about 12 to about 15 nucleotides in length if the nucleic acid molecules are GC-rich and at least about 15 to about 18 bases in length if they are AT-rich. There is no limit, other than a practical limit, on the maximal size of a nucleic acid molecule of the present invention, in that the nucleic acid molecule can include a portion of a protein-encoding sequence or a nucleic acid sequence encoding a full-length protein. According to the present invention, an oligonucleotide probe (or simply, probe) is a nucleic acid molecule which most typically ranges in size from about 8 nucleotides to several hundred nucleotides in length. PCR primers are also nucleic acid sequences, although PCR primers are typically oligonucleotides of fairly short length that are used in polymerase chain reactions. PCR primers and hybridization probes can readily be developed and produced by those of skill in the art, using sequence information from the target sequence. (See, for example, Sambrook et al., supra or “Molecular Biotechnology,” Second Edition, by Glick and Pasternak, ASM Press, Washington D.C., 1998, pp. 555-590). Knowing the nucleic acid sequences of certain nucleic acid molecules of the present invention allows one skilled in the art to, for example, (a) make copies of those nucleic acid molecules and/or (b) obtain nucleic acid molecules including at least a portion of such nucleic acid molecules (e.g., nucleic acid molecules including full-length genes, full-length coding regions, regulatory control sequences, truncated coding regions). Such nucleic acid molecules can be obtained in a variety of ways including traditional cloning techniques using oligonucleotide probes to screen appropriate libraries or DNA and PCR amplification of appropriate libraries or DNA using oligonucleotide primers. Preferred libraries to screen or from which to amplify nucleic acid molecule include mammalian genomic DNA libraries. Techniques to clone and amplify genes are disclosed, for example, in Sambrook et al., ibid.
In particular aspects, the invention is directed to an isolated nucleic acid that encodes an amino acid sequence of Betcam wherein the amino acid sequence comprises, consists essentially of, or consists of amino acids 31 through 462 of SEQ ID NO: 1, amino acids 19 through 450 of SEQ ID NO: 2 or amino acids 30 through 463 of SEQ ID NO: 3. In other aspects the invention is directed to an isolated nucleic acid that encodes an amino acid sequence of an extracellular domain of Betacam, wherein the amino acid sequence comprises, consists essentially of, or consists of SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15. In a particular aspect, the invention is directed to an isolated nucleic acid comprising, consisting essentially of, or consisting of SEQ ID NO: 26.
Other aspects of the invention are directed to RNA molecules such as antisense and interfering RNA molecules specific for Betacam. As used herein, an anti-sense nucleic acid molecule is defined as an isolated nucleic acid molecule that reduces expression of a protein by hybridizing under high stringency conditions to a gene encoding the protein. Such a nucleic acid molecule is sufficiently similar to the gene encoding the protein that the molecule is capable of hybridizing under high stringency conditions to the coding or complementary strand of the gene or RNA encoding the natural protein. RNA interference (RNAi) is a process whereby double stranded RNA, and in mammalian systems, short interfering RNA (siRNA), is used to inhibit or silence expression of complementary genes. In the target cell, siRNA are unwound and associate with an RNA induced silencing complex (RISC), which is then guided to the mRNA sequences that are complementary to the siRNA, whereby the RISC cleaves the mRNA.
A recombinant nucleic acid molecule is a molecule that can include at least one of any nucleic acid sequence encoding a Betacam protein or other protein described herein. In one embodiment, a recombinant nucleic acid molecule is operatively linked to at least one expression control sequence capable of effectively regulating expression of the nucleic acid molecule(s) in a host cell. Preferably, a recombinant nucleic acid molecule is produced using recombinant DNA technology (e.g., polymerase chain reaction (PCR) amplification, cloning).
A recombinant nucleic acid molecule includes a recombinant vector, which is any nucleic acid sequence, typically a heterologous sequence, which is operatively linked to the isolated nucleic acid molecule encoding a protein (e.g., Betacam), which is capable of enabling recombinant production of the protein, or which is capable of delivering the nucleic acid molecule into a host cell in vitro, ex vivo or in vivo, according to the present invention. Such a vector can contain nucleic acid sequences that are not naturally found adjacent to the isolated nucleic acid molecules to be inserted into the vector. The vector can be either RNA or DNA, either prokaryotic or eukaryotic, and preferably in the present invention, is a virus or a plasmid. Recombinant vectors can be used in the cloning, sequencing, and/or otherwise manipulating of nucleic acid molecules. Recombinant vectors are preferably used in the expression of nucleic acid molecules, and can also be referred to as expression vectors. Preferred recombinant vectors are capable of being expressed in a transfected host cell, and particularly, in a transfected mammalian host cell in vivo.
In a recombinant molecule of the present invention, nucleic acid molecules are operatively linked to expression vectors containing regulatory sequences such as transcription control sequences, translation control sequences, origins of replication, and other regulatory sequences that are compatible with the host cell and that control the expression of nucleic acid molecules of the present invention. The phrase “operatively linked” refers to linking a nucleic acid molecule to an expression control sequence in a manner such that the molecule is expressed when transfected (i.e., transformed, transduced or transfected) into a host cell. Transcription control sequences are sequences that control the initiation, elongation, and termination of transcription. Particularly important transcription control sequences are those that control transcription initiation, such as promoter, enhancer, operator and repressor sequences. Suitable transcription control sequences include any transcription control sequence that can function in a host cell according to the present invention. A variety of suitable transcription control sequences are known to those skilled in the art. Particularly preferred transcription control sequences include inducible promoters, cell-specific promoters, tissue specific promoters (e.g., insulin or Pdx1 promoters) and enhancers. Transcription control sequences of the present invention can also include naturally occurring transcription control sequences naturally associated with the protein to be expressed prior to isolation. In one embodiment, a transcription control sequence includes an inducible promoter.
One type of recombinant vector useful in a recombinant nucleic acid molecule of the present invention is a recombinant viral vector. Such a vector includes a recombinant nucleic acid sequence encoding a Betacam protein of the present invention that is packaged in a viral coat that can be expressed in a host cell in an animal or ex vivo after administration. A number of recombinant viral vectors can be used, including, but not limited to, those based on alphaviruses, poxviruses, adenoviruses, herpesviruses, lentiviruses, adeno-associated viruses and retroviruses. Viral vectors suitable for gene delivery are well known in the art and can be selected by the skilled artisan for use in the present invention. A detailed discussion of current viral vectors is provided in “Molecular Biotechnology,” Second Edition, by Glick and Pasternak, ASM Press, Washington D.C., 1998, pp. 555-590, the entirety of which is incorporated herein by reference. Suitable host cells to transfect with a recombinant nucleic acid molecule according to the present invention include any microbial, insect, or animal cell that can be transfected. Host cells can be either untransfected cells or cells that are already transfected with at least one nucleic acid molecule.
According to the present invention, the term “transfection” is used to refer to any method by which an exogenous nucleic acid molecule (i.e., a recombinant nucleic acid molecule) can be inserted into the cell. The term “transformation” can be used interchangeably with the term “transfection” when such term is used to refer to the introduction of nucleic acid molecules into microbial cells, such as bacteria and yeast. In microbial systems, the term “transformation” is used to describe an inherited change due to the acquisition of exogenous nucleic acids by the microorganism and is essentially synonymous with the term “transfection”. However, in animal cells, transformation has acquired a second meaning which can refer to changes in the growth properties of cells in culture after they become cancerous, for example. Therefore, to avoid confusion, the term “transfection” is preferably used with regard to the introduction of exogenous nucleic acids into animal cells, and the term “transfection” will be used herein to generally encompass both transfection of animal cells and transformation of microbial cells, to the extent that the terms pertain to the introduction of exogenous nucleic acids into a cell. Therefore, transfection techniques include, but are not limited to, transformation, electroporation, microinjection, lipofection, adsorption, infection and protoplast fusion.
As used herein, reference to an isolated protein, also referred to herein an an isolated polypeptide, in the present invention, including a Betacam protein, is a protein that has been removed from its natural milieu (i.e., that has been subject to human manipulation), and includes full-length proteins, fusion or chimeric proteins, or any fragment or homologue of such a protein. Such a protein can include, but is not limited to, purified proteins, partially purified proteins, recombinantly produced proteins, synthetically produced proteins, membrane-bound proteins, proteins complexed with lipids, soluble proteins and isolated proteins associated with other proteins. As such, “isolated” does not reflect the extent to which the protein has been purified. Preferably, an isolated protein of the present invention is produced recombinantly. In addition, and again by way of example, a “human Betacam protein” or a protein “derived from” a human Betacam protein refers to a Betacam protein (generally including a homologue of a naturally occurring Betacam protein) from a human (Homo sapiens) or to a Betacam protein that has been otherwise produced from the knowledge of the structure (e.g., sequence) and perhaps the function of a naturally occurring Betacam protein from Homo sapiens. In other words, a human Betacam protein includes any Betacam protein that has substantially similar structure and function of a naturally occurring Betacam protein from Homo sapiens or that is a biologically active (i.e., has biological activity) homologue of a naturally occurring Betacam protein from Homo sapiens as described in detail herein. As such, a Betacam protein can include purified, partially purified, recombinant and synthetic proteins. Another aspect of the invention is directed to modified or mutated Betacam polypeptides. According to the present invention, the terms “modified”, “modification”, “mutated” and “mutation” can be used interchangeably, particularly with regard to the modifications/mutations to the amino acid sequence of protein (or nucleic acid sequences) described herein.
In particular aspects, the invention is directed to an isolated polypeptide that comprises, consists essentially of, or consists of amino acids 31 through 462 of SEQ ID NO: 1, amino acids 19 through 450 of SEQ ID NO: 2 or amino acids 30 through 463 of SEQ ID NO: 3. In another aspect, the invention is directed to an isolated polypeptide that comprises, consists essentially of, or consists of SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15.
Fusion proteins and chimeric proteins are also encompassed by the invention. A fusion protein is a protein produced by linking (typically recombinantly, although chemical and other types of linkage are encompassed by the invention) of a protein or peptide of the invention (e.g., Betacam or a variant or fragment thereof) to a fusion partner (fusion segment). Suitable fusion partners for use with the present invention include, but are not limited to, fusion partners that can: enhance a protein's stability; enhance or permit secretion of a protein from the host cell; provide other biological activity; and/or assist purification of a protein from a host cell (e.g., by affinity chromatography or affinity pull-down). A suitable fusion partner can be a protein or domain or fragment thereof of any size that has the desired function (e.g., imparts increased stability, solubility, action or activity; provides other activity; and/or simplifies purification of a protein). Fusion partners can be joined to amino and/or carboxyl termini of the protein of interest (e.g., Betacam), and can be susceptible to cleavage in order to enable straight-forward recovery of the expressed exogenous protein. A chimeric protein is similar to a fusion protein, and the terms may be used interchangeably, except that in the case of the chimeric protein, the fusion partner is most typically a second protein of interest (or a fragment thereof), such as a second protein with a desired biological activity. Accordingly, a chimeric protein may have the activity of each/both of the protein/peptide components, or a new activity resulting from the combination of protein domains.
In one preferred embodiment, proteins (including peptides and homologues) are produced using in vitro translation systems, such as systems based on reticulocyte lysate, wheat germ, yeast and bacteria. The systems preferably correctly post-translationally process the protein, e.g., by proteolysis and/or glycosylation. Products of in vitro translation systems are most typically used in the methods of the invention, although the invention is not limited to such products. As used herein, the term “homologue” or “variant” is used to refer to a protein or peptide which differs from a naturally occurring protein or peptide (i.e., the “prototype” or “wild-type” protein) by minor modifications to the naturally occurring protein or peptide, but which maintains the basic protein and side chain structure of the naturally occurring form. Such changes include, but are not limited to: changes in 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or a few more 30 amino acid side chains; changes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or a few more amino acids, including deletions (e.g., a truncated version of the protein or peptide) insertions and/or substitutions; changes in stereochemistry of one or a few atoms; and/or minor derivatizations, including but not limited to: methylation, glycosylation, phosphorylation, acetylation, myristoylation, prenylation, palmitation, amidation and/or addition of glycosylphosphatidyl inositol. A homologue can have enhanced, decreased, or substantially similar properties as compared to the naturally occurring protein or peptide. A homologue can include an agonist of a protein or an antagonist of a protein. Homologues can be the result of natural allelic variation or genetic polymorphism, or any natural mutation. A naturally occurring allelic variant or genetic polymorphism of a nucleic acid encoding a protein is a gene that occurs at essentially the same locus (or loci) in the genome as the gene which encodes such protein, but which, due to natural variations, has a similar but not identical sequence. Allelic variants typically encode proteins having similar activity to that of the protein encoded by the gene to which they are being compared. A single nucleotide polymorphism (SNP) is a DNA sequence variation occurring when a single nucleotide in the genome differs between members of a species, or between paired chromosomes in an individual. Due to variations between human populations, a SNP allele that is common in one geographical or ethnic group may be much rarer in another. In addition, variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens, chemicals, drugs, vaccines, and other agents.
One class of allelic variants can encode the same protein but have different nucleic acid sequences due to the degeneracy of the genetic code. Allelic variants can also comprise alterations in the 5′ or 3′ untranslated regions of the gene (e.g., in regulatory control regions). Allelic variants are well known to those skilled in the art.
Homologues can be produced using techniques known in the art for the production of proteins including, but not limited to, direct modifications to the isolated, naturally occurring protein, direct protein synthesis, or modifications to the nucleic acid sequence encoding the protein using, for example, classic or recombinant DNA techniques to effect random or targeted mutagenesis.
According to the present invention, an isolated protein, including a biologically active homologue or fragment thereof, has at least one characteristic of biological activity of activity the wild-type, or naturally occurring reference protein (which can vary depending on whether the homologue or fragment is an agonist or antagonist of the protein, or whether an agonist or antagonist mimetic of the protein is described). In general, the biological activity or biological action of a protein refers to any function(s) exhibited or performed by the protein that is ascribed to the naturally occurring form of the protein as measured or observed in vivo (i.e., in the natural physiological environment of the protein) or in vitro (i.e., under laboratory conditions).
The biological activity of a Betacam protein of the invention includes homotypic cell adhesion between Betacam-expressing cells, including pancreatic beta cells. More particularly, a biological activity of Betacam according to the invention includes the homotypic association of a Betacam protein expressed on one Betacam-expressing cell to another Betacam protein expressed on a neighboring cell. This includes cells of the islet. Such biological activities of Betacam useful in the present invention include the generation and use of molecular components designed to bind to, activate, or inhibit, or otherwise modulate the function of Betacam. Modifications, activities or interactions which result in a decrease in protein expression or a decrease in the activity of the protein (complete or partial), can be referred to as inactivation, down-regulation, inhibition, reduced action, or decreased action or activity of a protein. Similarly, modifications, activities or interactions that result in an increase in protein expression or an increase in the activity of the protein, can be referred to as amplification, overproduction, activation, enhancement, up-regulation or increased action of a protein. The biological activity of a protein according to the invention, and particularly a Betacam protein, can be measured or evaluated using any assay for the biological activity of the protein as known in the art. Such assays can include, but are not limited to, binding assays (including a variety of immunological assays), assays to determine internalization or localization of the protein and/or associated proteins, and/or assays for determining downstream cellular events that result from the activity of the protein.
As used herein, unless otherwise specified, reference to a percent (%) identity refers to an evaluation of homology which is performed using: (1) a BLAST 2.0 Basic BLAST homology search using blastp for amino acid searches and blastn for nucleic acid searches with standard default parameters, wherein the query sequence is filtered for low complexity regions by default (described in Altschul, S. F., Madden, T. L., Schääffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.” Nucleic Acids Res. 25:3389-3402, incorporated herein by reference in its entirety); (2) a BLAST 2 alignment (using the parameters described below); (3) and/or PSI30 BLAST with the standard default parameters (Position-Specific Iterated BLAST. It is noted that due to some differences in the standard parameters between BLAST 2.0 Basic BLAST and BLAST 2, two specific sequences might be recognized as having significant homology using the BLAST 2 program, whereas a search performed in BLAST 2.0 Basic BLAST using one of the sequences as the query sequence may not identify the second sequence in the top matches. In addition, PSI-BLAST provides an automated, easy-to-use version of a “profile” search, which is a sensitive way to look for sequence homologues. The program first performs a gapped BLAST database search. The PSI-BLAST program uses the information from any significant alignments returned to construct a position-specific score matrix, which replaces the query sequence for the next round of database searching. Therefore, it is to be understood that percent identity can be determined by using any one of these programs.
Two specific sequences can be aligned to one another using BLAST 2 sequence as described in Tatusova and Madden, (1999), “Blast 2 sequences—a new tool for comparing protein and nucleotide sequences”, FEMS Microbiol Lett. 174:247-250, incorporated herein by reference in its entirety. BLAST 2 sequence alignment is performed in blastp or blastn using the BLAST 2.0 algorithm to perform a Gapped BLAST search (BLAST 2.0) between the two sequences allowing for the introduction of gaps (deletions and insertions) in the resulting alignment. For purposes of clarity herein, a BLAST 2 sequence alignment is performed using, for example, the standard default parameters as follows.
As used herein, reference to an “agonist” of a given protein refers to any compound that is characterized by the ability to agonize (e.g., stimulate, induce, increase, enhance, or mimic) the biological activity of the naturally occurring protein, and includes any homologue, binding protein (e.g., an antibody), agent that interacts with a protein or receptor bound by the protein, or any suitable product of drug/compound/peptide design or selection which is characterized by its ability to agonize (e.g., stimulate, induce, increase, enhance) the biological activity of the naturally occurring protein in a manner similar to the natural agonist, which is the reference protein.
Similarly, reference to an “antagonist” refers to any compound which inhibits (e.g., antagonizes, reduces, decreases, blocks, reverses, or alters) the effect of a given agonist of a protein (including the protein itself) as described above. More particularly, an antagonist is capable of acting in a manner relative to the activity of the protein, such that the biological activity of the natural agonist or reference protein, is decreased in a manner that is antagonistic (e.g., against, a reversal of, contrary to) to the natural action of the protein. Such antagonists can include, but are not limited to, a protein, peptide, or nucleic acid (including ribozymes, RNAi, aptamers, and antisense), antibodies and antigen binding fragments thereof, or product of drug/compound/peptide design or selection that provides the antagonistic effect. Homologues of a given protein such as Betacam, including peptide and non-peptide agonists and antagonists (analogs), can be products of drug design or selection and can be produced using various methods known in the art. Such homologues can be referred to as mimetics. Various methods of drug design, useful to design or select mimetics or other therapeutic compounds useful in the present invention are disclosed in Maulik et al., 1997, Molecular Biotechnology: Therapeutic Applications and Strategies, Wiley-Liss, Inc., which is incorporated herein by reference in its entirety.
An isolated protein useful as an antagonist or agonist according to the present invention can be isolated from its natural source, produced recombinantly or produced synthetically.
As used herein, a mimetic refers to any peptide or non-peptide compound that is able to mimic the biological action of a naturally occurring peptide, often because the mimetic has a basic structure that mimics the basic structure of the naturally occurring peptide and/or has the salient biological properties of the naturally occurring peptide. Mimetics can include, but are not limited to: peptides that have substantial modifications from the prototype such as no side chain similarity with the naturally occurring peptide (such modifications, for example, may decrease its susceptibility to degradation); anti-idiotypic and/or catalytic antibodies, or fragments thereof; non-proteinaceous portions of an isolated protein (e.g., carbohydrate structures); or synthetic or natural organic molecules, including nucleic acids and drugs identified through combinatorial chemistry, for example. Such mimetics can be designed, selected and/or otherwise identified using a variety of methods known in the art. A mimetic can be obtained, for example, from molecular diversity strategies (a combination of related strategies allowing the rapid construction of large, chemically diverse molecule libraries), libraries of natural or synthetic compounds, in particular from chemical or combinatorial libraries (i.e., libraries of compounds that differ in sequence or size but that have the similar building blocks) or by rational, directed or random drug design. See for example, Maulik et al., supra.
In a molecular diversity strategy, large compound libraries are synthesized, for example, from peptides, oligonucleotides, carbohydrates and/or synthetic organic molecules, using biological, enzymatic and/or chemical approaches. The critical parameters in developing a molecular diversity strategy include subunit diversity, molecular size, and library diversity. The general goal of screening such libraries is to utilize sequential application of combinatorial selection to obtain high-affinity ligands for a desired target, and then to optimize the lead molecules by either random or directed design strategies. Methods of molecular diversity are described in detail in Maulik, et al., ibid.
In a rational drug design procedure, the three-dimensional structure of a regulatory compound can be analyzed by, for example, nuclear magnetic resonance (NMR) or X-ray crystallography. This three-dimensional structure can then be used to predict structures of potential compounds, such as potential regulatory agents by, for example, computer modeling. The predicted compound structure can be used to optimize lead compounds derived, for example, by molecular diversity methods. In addition, the predicted compound structure can be produced by, for example, chemical synthesis, recombinant DNA technology, or by isolating a mimetope from a natural source (e.g., plants, animals, bacteria and fungi). Maulik et al. also disclose, for example, methods of directed design, in which the user directs the process of creating novel molecules from a fragment library of appropriately selected fragments; random design, in which the user uses a genetic or other algorithm to randomly mutate fragments and their combinations while simultaneously applying a selection criterion to evaluate the fitness of candidate ligands; and a grid-based approach in which the user calculates the interaction energy between three dimensional receptor structures and small fragment probes, followed by linking together of favorable probe sites.
Also included in the present invention are antibodies and antigen binding fragments thereof that selectively bind to all or a portion (e.g., biologically active portion) Betacam, as well as the use of such antibodies and antigen binding fragments thereof in any of the methods described herein. Antibodies that selectively bind to a protein can be produced using the structural information available for the protein (e.g., the amino acid sequence of at least a portion of the protein). As used herein, the term “selectively binds to” refers to the specific binding of one protein to another (e.g., an antibody, fragment thereof, or binding partner to an antigen), wherein the level of binding, as measured by any standard assay (e.g., an immunoassay), is statistically significantly higher than the background control for the assay. For example, when performing an immunoassay, controls typically include a reaction well/tube that contain antibody or antigen binding fragment alone (i.e., in the absence of antigen), wherein an amount of reactivity (e.g., non-specific binding to the well) by the antibody or antigen binding fragment thereof in the absence of the antigen is considered to be background. Binding can be measured using a variety of methods standard in the art, including, but not limited to: Western blot, immunoblot, enzyme-linked immunosorbant assay (ELISA), radioimmunoassay (RIA), immunoprecipitation, surface plasmon resonance, chemiluminescence, fluorescent polarization, phosphorescence, immunohistochemical analysis, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, microcytometry, microarray, microscopy, fluorescence activated cell sorting (FACS), and flow cytometry.
According to the present invention, an “epitope” of a given protein or peptide or other molecule is generally defined, with regard to antibodies, as a part of or site on a larger molecule to which an antibody or antigen-binding fragment thereof will bind, and against which an antibody will be produced. The term epitope can be used interchangeably with the term “antigenic determinant”, “antibody binding site”, or “conserved binding surface” of a given protein or antigen. More specifically, an epitope can be defined by both the amino acid residues involved in antibody binding and also by their conformation in three dimensional space (e.g., a conformational epitope or the conserved binding surface). An epitope can be included in peptides as small as about 4-6 amino acid residues, or can be included in larger segments of a protein, and need not be comprised of contiguous amino acid residues when referring to a three dimensional structure of an epitope, particularly with regard to an antibody-binding epitope. Antibody-binding epitopes are frequently conformational epitopes rather than a sequential epitope (i.e., linear epitope), or in other words, an epitope defined by amino acid residues arrayed in three dimensions on the surface of a protein or polypeptide to which an antibody binds. As mentioned above, the conformational epitope is not comprised of a contiguous sequence of amino acid residues, but instead, the residues are perhaps widely separated in the primary protein sequence, and are brought together to form a binding surface by the way the protein folds in its native conformation in three dimensions. Accordingly, the present invention includes proteins or peptides comprising, consisting essentially of, or consisting of Betacam epitopes, as well as antibodies, antigen-binding fragments, or other binding partners (binding peptides) that bind to any epitope of a Betacam protein. An “isoepitope”, according to the invention, is an epitope that exists in variant forms or isoforms (naturally or by synthetic design), such as an epitope containing a polymorphic variant amino acid position. One of skill in the art can identify and/or assemble conformational epitopes and/or sequential epitopes using known techniques, including mutational analysis (e.g., site-directed mutagenesis); protection from proteolytic degradation (protein footprinting); mimotope analysis using, e.g., synthetic peptides and pepscan, BIACORE or ELISA; antibody competition mapping; combinatorial peptide library screening; matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry; or three-dimensional modeling. For example, one can use molecular replacement or other techniques and the known three-dimensional structure of a related protein to model the three-dimensional structure of Betacam and predict the conformational epitope of antibody binding to this structure. Indeed, one can use one or any combination of such techniques to define the antibody binding epitope.
Antibodies useful in the present invention can include polyclonal and monoclonal antibodies, divalent and monovalent antibodies, bi- or multi-specific antibodies, serum containing such antibodies, antibodies that have been purified to varying degrees, and any functional equivalents of whole antibodies. Isolated antibodies of the present invention can include serum containing such antibodies, or antibodies that have been purified to varying degrees. Alternatively, functional equivalents of whole antibodies, such as antigen binding fragments in which one or more antibody domains are truncated or absent (e.g., Fv, Fab, Fab′, or F(ab)2 fragments), as well as genetically-engineered antibodies or antigen binding fragments thereof, including single chain antibodies or antibodies that can bind to more than one epitope (e.g., bi-specific antibodies), or antibodies that can bind to one or more different antigens (e.g., bi- or multi-specific antibodies), may also be employed in the invention.
Genetically engineered antibodies include those produced by standard recombinant DNA techniques involving the manipulation and re-expression of DNA encoding antibody variable and/or constant regions. Particular examples include, chimeric antibodies, where the VH and/or VL domains of the antibody come from a different source to the remainder of the antibody, and CDR grafted antibodies (and antigen binding fragments thereof), in which at least one CDR sequence and optionally at least one variable region framework amino acid is (are) derived from one source and the remaining portions of the variable and the constant regions (as appropriate) are derived from a different source. Construction of chimeric and CDR-grafted antibodies are described, for example, in European Patent Applications: EP-A 0194276, EP-A 0239400, EP-A 0451216 and EP-A 0460617. Generally, in the production of an antibody, a suitable experimental animal, such as, for example, but not limited to, a rabbit, a sheep, a hamster, a guinea pig, a mouse, a rat, or a chicken, is exposed to an antigen against which an antibody is desired. Typically, an animal is immunized with an effective amount of antigen that is injected into the animal. An effective amount of antigen refers to an amount needed to induce antibody production by the animal. The animal's immune system is then allowed to respond over a pre-determined period of time. The immunization process can be repeated until the immune system is found to be producing antibodies to the antigen. In order to obtain polyclonal antibodies specific for the antigen, serum is collected from the animal that contains the desired antibodies (or in the case of a chicken, antibody can be collected from the eggs). Such serum is useful as a reagent. Polyclonal antibodies can be further purified from the serum (or eggs) by, for example, treating the serum with ammonium sulfate.
Monoclonal antibodies may be produced according to the methodology of Kohler and Milstein (Nature 256:495-497, 1975). For example, B lymphocytes are recovered from the spleen (or any suitable tissue) of an immunized animal and then fused with myeloma cells to obtain a population of hybridoma cells capable of continual growth in suitable culture medium. Hybridomas producing the desired antibody are selected by testing the ability of the antibody produced by the hybridoma to bind to the desired antigen.
In particular aspects, the invention is directed to an antibody that has binding specificity (e.g., epitopic specificity) for the Betacam polypeptide. In one embodiment, the invention is directed to an antibody that has binding specificity for a polypeptide that comprises, consists essentially of, or consists of amino acids 31 through 462 of SEQ ID NO: 1, amino acids 19 through 450 of SEQ ID NO: 2 or amino acids 30 through 463 of SEQ ID NO: 3. In another embodiment, the antibody has binding specificity for amino acids 31 through 462 of SEQ ID NO: 1, amino acids 19 through 450 of SEQ ID NO: 2 or amino acids 30 through 463 of SEQ ID NO: 3. In another embodiment, the antibody has binding specificity for a polypeptide that comprises, consists essentially of, consists of SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15. In yet another embodiment, the antibody has binding specificity for SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15.
Betacam proteins, homologues (including altered peptides), fragments, peptides, peptide and non-peptide mimetics, and antibodies and antigen-binding fragments thereof can be included in compositions and formulations. Such compositions, or formulations, can include a pharmaceutically acceptable carrier, which includes pharmaceutically acceptable excipients and/or delivery vehicles. As used herein, a pharmaceutically acceptable carrier refers to any substance suitable for delivering a composition, formulation or vaccine useful in the method of the present invention to a suitable in vivo or ex vivo site. Preferred pharmaceutically acceptable carriers are capable of maintaining the agent to be delivered (e.g., Betacam proteins, homologues (including altered peptides), fragments, peptides, peptide and non-peptide mimetics, and antibodies and antigen-binding fragments thereof) in a form that, upon arrival of the agent to a target cell or target site, the agent is capable of acting at that cell or site (e.g. capable of inducing an immune response). Suitable excipients of the present invention include excipients or formularies that transport or help transport, but do not specifically target an agent to a site (also referred to herein as non-targeting carriers). Examples of pharmaceutically acceptable excipients include, but are not limited to water, phosphate buffered saline, Ringer's solution, dextrose solution, serum-containing solutions, Hank's solution, other aqueous physiologically balanced solutions, oils, esters and glycols. Aqueous carriers can contain suitable auxiliary substances required to approximate the physiological conditions of the recipient, for example, by enhancing chemical stability and isotonicity. Suitable auxiliary substances include, for example, sodium acetate, sodium chloride, sodium lactate, potassium chloride, calcium chloride, and other substances used to produce phosphate buffer, Tris buffer, and bicarbonate buffer. Auxiliary substances can also include preservatives, such as thimerosal, m- or o-cresol, formalin and benzol alcohol. Compositions of the present invention can be sterilized by conventional methods and/or lyophilized. One type of pharmaceutically acceptable carrier includes a controlled release formulation that is capable of slowly releasing a composition of the present invention into an animal. As used herein, a controlled release formulation comprises an agent useful in the present invention in a controlled release vehicle. Suitable controlled release vehicles include, but are not limited to, biocompatible polymers, other polymeric matrices, capsules, microcapsules, microparticles, bolus preparations, osmotic pumps, diffusion devices, liposomes, lipospheres, and transdermal delivery systems. Suitable delivery vehicles also include, but are not limited to liposomes, viral vectors or other delivery vehicles, including ribozymes. Natural lipid-containing delivery vehicles include cells and cellular membranes. Artificial lipid-containing delivery vehicles include liposomes and micelles. A delivery vehicle of the present invention can be modified to target to a particular site in a patient, thereby targeting and making use of an agent at that site. Suitable modifications include manipulating the chemical formula of the lipid portion of the delivery vehicle and/or introducing into the vehicle a targeting agent capable of specifically targeting a delivery vehicle to a preferred site, for example, a preferred cell type.
The invention also extends to PET-tracer (positron emission tomography) methodology, related to the formulation of compounds derived from the Betacam sequence, which are traceable using PET methodology. A biomolecule that serves as a marker for some function can be labeled with an isotope that emits positrons—subatomic particles akin to positively charged electrons—such as 11C, 13N, and 15O, as well as 18F, which often replaces 1H. Upon tracer administration, emitted positrons interact with electrons from atoms in nearby tissues, usually within 1 mm. The collisions result in annihilation events that each simultaneously liberate two gamma rays at 180°. A scintillator (bismuth germanate is standard) and photomultipliers in the tomograph encircling the subject detect this energy pattern and extrapolate the approximate origin of the energy. About 500,000 annihilation events constitute a single slice or scan of body tissues. Scans allow visualization of the internal locations of the tracers, designed for measuring general body functions (e.g., glucose metabolism or blood flow in an organ) or highly specific functions (e.g., occupancy of a subtype of brain dopamine receptor). The intensity of emitted gamma radiation is proportional to the tracer concentration. Anatomical considerations and correlation of the range of radiation densities with colors of the spectrum provide quantitative and/or color representations of the magnitude of a physiological function. In humans, typical tissue resolution with PET is 4-7 mm—the width of a pencil. The potential for development of a PET system was realized in the 1950s, when interest in positron-emitting isotopes emerged. Invention of the PET scanner in the early 1970s is credited to Michael E. Phelps.
PET tracers can be divided into three broad categories based on what they measure, as described at http://pubs.acs.org/subscribe/journals/tcaw/10/i10/html/10mckenna.html. The first type of tracer provides general metabolic data, such as glucose uptake and protein synthesis, via labeled biomolecules (e.g., 11C-deoxyglucose and 11C-methionine, respectively) that leave the bloodstream and enter cells. The second type provides estimates for grosser physiological parameters, such as blood flow (e.g., 15O—H2O or 11CO2), and essentially remains in the bloodstream over the effective study duration. The third tracer type delineates and quantifies highly specific molecular targets, such as cellular receptors and transporters, for which tracers are either endogenous ligands or drugs (e.g., 11C-raclopride for the DA2 dopamine receptor). The high specific activity and sensitivity of PET tracers make them well suited for studying molecular targets present to low nanomolar concentrations. The design or selection of the optimal PET tracer integrates knowledge of cellular physiology and biochemistry, advances in radio- and synthetic chemistry, tracer pharmacology and kinetics, and refinements in cyclotron and PET technologies. Successful PET imaging requires consideration of the innate properties of both radioisotope and tracer molecule, and the route of tracer administration. Radioisotope selection criteria must include the ability to incorporate the isotope into the molecule of interest and the appropriateness of its radioactive half-life for the study design. Half-lives of positron emitters range from 20 min (11C) to 110 min (18F). All steps, from cyclotron generation to subject administration, must occur within the useful lifespan of the label—approximately 3 half-lives—to maximize the signal-to-noise ratio. Ideally, PET tracers have properties that accurately reflect what they are meant to measure and minimize radiolabeling effects on the parent molecule. Such properties include high target-site selectivity, specificity, sensitivity, minimal metabolism, and the attainment of equilibrium in the body during the study Inherent in tracer design is consideration of the tracer administration route. Intravenous tracers, by virtue of their rapid delivery, systemic distribution, and bypassing of gastrointestinal metabolism, are ideal and are most common. Inhalation, the second most prevalent administration route, suffers from complications related to swallowing, dispersal, physicochemical interactions between drug and vehicle, and patient-related issues. Ingested tracers are characterized by slower absorption, systemic distribution, and a greater chance of metabolites forming, making them much less attractive.
PET methodologies for detecting cells in-vivo: cancer. Early diagnosis and treatment of cancer are often crucial to a good prognosis. PET allows the detection of cancerous cells before tumors even form and can sometimes obviate the need for biopsies. PET's ability to detect tumors, determine malignancy and cancer progression, and ascertain cancer metastases stems from its capacity to assess the relatively higher energy needs of actively growing cancer cells. In particular for the present invention, the use of PET technology for detecting beta cells, is not dissimilar to that use of the PET technology of detecting cancerous cells. Glucose is in higher demand as an energy source by rapidly dividing cancer cells than by normal cells. Using a 11C- or 18F-labeled 2-deoxyglucose tracer (a non-metabolized glucose analogue), PET can detect cancer and establish a baseline tumor growth rate (the glucose utilization rate) in a patient. It can also assess antitumor activity during and after therapy. Successful therapy depends on eliminating tumor growth (metabolism), which is determined by decreased glucose uptake by tumor cells. Radiolabeled amino acids can be used in a similar way to deoxyglucose. Other indices of tumor growth, such as the extent and rate of tumor perfusion, and their projected decreases with treatment, can also be determined.
Cardiovascular Disease. PET has proved useful in the study and quantification of various aspects of heart and blood vessel function. As with cancer, clinical studies show an important role for PET in diagnosing patients, describing disease, and developing treatment strategies. PET has been applied in two major areas: assessment of coronary artery disease and impaired blood flow, and determination of the viability of heart tissue for revascularization. The latter helps physicians decide whether bypass surgery or heart transplant is a more viable option for a patient. Tracers that assess blood flow include 15O—H2O, 11CO2, and 13NH3, help establish the extent and progression of arterial blockage as well as the efficacy of drug therapy or surgery. They also are used to monitor the recovery and maintenance of a blockage-free state.
Central Nervous System. Conditions. PET can be used to diagnose functional brain disorders, such as Alzheimer's and Parkinson's diseases, childhood seizures, brain development disorders, and brain tumors. Cause and effect can also be investigated. In memory loss, PET can ascertain whether the loss is due to decreased blood flow, depression, or a molecular depletion, as in Alzheimer's disease. In addition, the appropriateness of therapies or interventions for these disorders can be monitored. PET even maps brain regions involved in specific activities, such as laughing, hearing, memory, and emotions, a useful function for planning neurosurgical procedures. PET also can measure the effects of drugs on region-specific brain functions. For a given drug, the capacity and occupancy of brain receptor molecules—the sites of action of antipsychotic drugs—and transporter molecules—associated with drug addiction and drugs of intervention—can be assessed. Tracers that bind to these molecules generate regional maps of receptors and transporters, estimate their occupancy by drugs of interest, and correlate drug occupancy with degrees of clinical efficacy. Examples of PET Radiocompounds include:
Particular aspects of the invention relate to a specific homologous gene group, referred to as the Betacam group of genes. Aspects of the present invention also include a variety of methods that make use of the identification of Betacam as a novel cell surface determinant of pancreatic beta cells.
A current focus on developing methods to measure beta cells in vitro and/or in vivo is highly prioritized by the juvenile diabetes foundation, as well as the NIH through particular funding mechanisms. However, such reagents and/or methods would not be limited to screening of pre-onset diabetes development in otherwise healthy subjects. The application extends to tracking pancreatic insulin cells in multiple scenarios, ranging from applications related to increasing the success of islet cell transplantation, the generation of novel beta cells from non-islet sources, and the purification of pancreatic beta cells from heterogeneous cell populations of various kinds Such considerations relate to finding cell surface determinants present on normal beta cells, simultaneously absent from most other cells, as this criterion of specificity is an absolute requirement for further successful development of both such a reagent type, and the methodology related to its application.
Some considerations as to the importance and significance of succeeding in the above ventures are as follows. Diabetes is presently incurable, and islet transplantation is only offered to very few individuals. Yet, envisioning the cure is simple: replenishment of the lost cell pool of insulin-producing cells (type I diabetes, juvenile form), or restoration of insulin producing cells in late-onset diabetes (type II diabetes), as their function has deteriorated to a level leading to incomplete control of glycaemia. The availability of a universal cell replacement source for insulin-producing cells would have significant impact on total people suffering from the disease, and lowering of health-care associated expenses. Likewise, if early diagnosis of pre-clinical symptoms of diabetes could be achieved, it would be expected that total numbers of patients would be reduced given early intervention.
One aspect of the invention is directed to a method of detecting beta cells in a mixture of pancreatic cells comprising detecting the presence of a polypeptide on the surface of the cells, wherein the polypeptide comprises SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15, and detection of expression of the polypeptide on the surface of the cells indicates that the cells are pancreatic beta cells. The method can further comprise isolating the pancreatic beta cells from the mixture of cells.
The mixture of pancreatic cells can be present in a variety of milieus. In one embodiment, the mixture of pancreatic cells are present in a biological sample. Examples of biological samples include pancreatic tissue (e.g., pancreatic donor tissue from, e.g., from a cadaver).
As will be appreciated by one of skill in the art, the Betacam polypeptide present on the surface of the beta cells can detected using a variety of reagents, and in particular labeled or tagged reagents, and methods for detecting such reagents. In one embodiment, an antibody that has binding affinity for the Betacam polypeptide is used. In another embodiment, since as shown herein homotypic interactions of Betacam/Betacam occur, a Betacam polypeptide can be used to detect the expression of Betacam on the surface of a pancreatic beta cell.
Particular aspects of the invention include the detection of pancreatic beta cells in pancreatic material obtained from a human cadaver. An application of the invention for this purpose could include contacting a labeled Betacam derived polypeptide, a Betacam reacting antibody, or a small engineered molecule (Betacam-derived reagent) designed to bind the Betacam protein surface, to a mixture of pancreatic beta cells (e.g., crude fractions of pancreatic cell suspensions, originating from donor pancreata).
It is known to those skilled in the art, that Betacam-derived molecules (i.e., nucleic acid, polypeptide) can be artificially labeled with multiple technologies, including fluorescent molecules, radioactive molecules (e.g., radioactive nucleide), enzymatic components (e.g., enzymes), select Tag sequence, PET-tracers, NMR tracers, or a drug for use in the methods described herein. Following contacting the cells with the molecule defined by the invention, measurements of labeling can be performed to assess islet cell purity as a function of total cell content based on the labeling component selected.
Crude isolated fractions of human islet preparations are often used for transplantation purpose for alleviating diabetic symptoms for extended periods (>1 year) in recipient individuals based on the more recent technology of islet cell transplantation as defined by the now commonly known “Edmonton protocol”. Enhancements of this particular protocol is envisioned as a particular application of the present invention. More specifically, an application of the invention would include tracking such islet cell preparations post-transplantation, as afforded by pre-contacting the islet cell preparation to a trackable Betacam-derived formulation, consequently labeling such and islet cell preparation. Considering that the trackable Betacam-derived reagent would facilitate non-invasive measurement of the transplanted cell population, methods for optimizing grafting methodology can be envisioned. Also, assessment of grafting, or transplantation, effectiveness, can be measured. This may be done very likely early following transplantation. Considering a certain stability of the Betacam-derived reagent, it may be possible to monitor the viability of the transplanted cells, which would be a benefit, as such measurements are not possible with existing technology.
Another aspect of the invention is directed to a method of detecting pancreatic beta cells in an individual in need thereof, comprising administering to the individual an agent that detects the presence of a polypeptide on the surface of the pancreatic beta cells, wherein the polypeptide comprises SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15. This method can be used, for example, to determine whether an individual is at risk of developing diabetes, or to assess the beta cells of an individual that has diabetes (e.g., to determine the appropriate treatment needed for a diabetic patient or to assess the efficacy of a diabetic patient's existing treatment). In one embodiment, the individual has Type I diabetes, and in another embodiment, the individual has Type II diabetes. In yet another embodiment, the individual has had an islet cell transplantation.
Another particular embodiment would apply a Betacam-derived formulation as described above for injection intravenously into the bloodstream after which contact to a beta cell surface would occur. Upon binding of said molecule to the surface to beta cells, and the emittance of a signal based on a trackable moiety, beta cell mass may be measured in a patient separately from the parameters of glucose dependent insulin secretion assays, and separate from oral glucose tolerance tests, which reflects on basal islet cell functionality, but not total beta cell mass. As such, the invention may be used to develop non-invasive assays for detecting various degrees of beta-cell loss in a human individual, which are of relevance for prognosis of disease. During the progression of type I diabetes, prior to diagnosis of the disease, an ongoing autoimmune attack is known to gradually eliminate the beta cell population. Similarly, the detection of a progressive deterioration of the beta-cell mass, as it gradually is lost in type II pre-diabetic individuals, is of clinical relevance. Consequently, for either consideration, detecting an ongoing beta cell loss may be of significant value in guiding decisions of prediction, and prevention, of type I and type II diabetes, based on earlier intervention.
In yet another method, the invention includes the development of a reagent capable of purification of pancreatic beta cells from human pancreatic donor material. More particularly, a Betacam-derived polypeptide, a Betacam reacting antibody, or a small engineered molecule, would be contacted to crude fractions of pancreatic cell suspensions, originating from donor pancreata. If said Betacam-derived polypeptide; Betacam reacting antibody; or a small engineered molecule was previously conjugated or otherwise stably connected to a ligand, affinity-Tag moiety, or fusion protein domain which allows binding to a support material (e.g., plastic dish, plastic tube, sutures, membranes, ultra thin films, bioreactors, microparticles) or suitable matrix (e.g., polymeric matrix), cellular fractional enrichment either through centrifugal spinning, gravitational force, magnetic bead cell adhesion, flow-sorting or other fluid-pressure methodologies, enrichment of the Betacam-expressing cell population, including pancreatic beta cells could be achieved. Such enrichment would be expected to favorably improve on current transplantation clinical outcomes.
In a particular aspect, the invention is directed to a method of isolating pancreatic beta cells from a mixture of pancreatic cells comprising contacting the mixture with a reagent that specifically binds to a polypeptide present on the surface of pancreatic beta cells, wherein the polypeptide comprises SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15, thereby producing a combination. The combination is maintained under conditions in which the reagent binds to the polypeptide present on the surface of the pancreatic beta cells, thereby producing a complex of pancreatic beta cells bound to the reagent; and the complex is separated from the combination, thereby isolating pancreatic beta cells from the mixture of pancreatic cells. The method can further comprise separating the pancreatic beta cells from the reagent.
In yet another method, the invention includes the development of technology leading to improved characterization of fraction enrichment of pancreatic beta cells from a heterogenous source of cells, including forward differentiated human embryonic stem cells. Current emphasis is presently on developing a universally available islet cell replacement cell resource, and particular efforts are directed on using human embryonic stem cells as a starting material. It is also known that such cells are pluripotent, and can adopt multiple cellular fates upon entering a differentiation process, which is controlled by an investigator. The promise of such cells is offset by the difficulties in specific directed differentiation method, which at present do not lead to a pure cell population of pancreatic beta cells. Other problems relate to the development of teratoma-type tumors upon transplantation to a live host. This particular problem is accredited to the co-transplantation of a limited set of undifferentiated, pluripotent, stem cells, existing along the more differentiated progeny. The consequence is detrimental, as such latent tumor forming capacity is posing a significant danger to a potential recipient. A solution to the problem would be to purify the insulin producing cell population to a level where such cells are not present. Therefore, in particular, one method of the invention would be to contact a Betacam-derived reagent to a forward-differentiated embryonic stem cell population, and purifying the insulin producing, Betacam expressing cells from contaminating non-endocrine cell types. Measures of purification capacity can be given in relative insulin expression per cell, or per DNA weight, as examples. Another measure of the purification can be given in the relative reduction o tumor forming capacity as events per million cells transplanted.
Accordingly, one, or more, embodiments of the invention relate to a method related to development of improved methods whereby the purification of pancreatic beta cells from any heterogenous source of cells can be achieved. It is known to those skilled in the arts that endocrine cells, including that of the pancreatic insulin-type, may possibly be derived from non embryonic stem cell sources. Regarding the emerging technologies of creating a universal cell source for diabetes treatment, these cover a wide area of investigative entries. Possible cell sources investigated as a means to this end includes in addition to human embryonic stem cells (hES), also hematopoietic stem cells (HSC), mesenchymal stem cell (MSC), multipotent adult progenitor cells (MPAC), pancreatic progenitor cells hPPCs), non-endocrine pancreatic epithelial cells (NEPECs), adult liver cells (Liver), adult GIP cells (K-cells), adult human duct cells (hDuct), adult human exocrine cells (hExocrine), genetically programmed transformed islet tumor cells, porcine embryonic pancreas (PEP), porcine islet cells (PIC), and ex-vivo expanded human islet cells. In all cases, the issue of initial clonal heterogeneity is a concern, and the end-point always defined by increasing the homogeneity of the end stage cell population. This invention relates to a method whereby purification of pancreatic beta cells from any such original heterogenous source of cells can be achieved.
Regarding the emerging technologies of creating a universal cell source for diabetes treatment, these cover a wide area of investigative entries, all having a similar end-point in common. The endpoint would be a glucose-responsive, insulin-producing cell, capable of being grafted into a human recipient. Possible cell sources investigated as a means to this end includes human embryonic stem cells (hES), hematopoietic stem cells (HSC), mesenchymal stem cell (MSC), multipotent adult progenitor cells (MPAC), pancreatic progenitor cells (PPCs), non-endocrine pancreatic epithelial cells (NEPECs), adult liver cells (Liver), adult GIP cells (K-cells), adult human duct cells (hDuct), adult human exocrine cells (hExocrine), genetically programmed transformed islet tumor cells, porcine embryonic pancreas (PEP), porcine islet cells (PIC), and ex-vivo expanded human islet cells. Other cell sources have been mentioned in literature, and the above list is not exhaustive, nor meant to be. For the remainder of the disclosure, all such cells are commonly referred to as a “progenitor cell source” (PCS), not requiring that such cells are defined as “progenitors” in the strict meaning of the word as employed by those skilled in the arts, but more generally applying the semantic use of “progenitor” as being a cell capable of change into another type, in this case pancreatic insulin-producing cells. Similarly, regarding the semantic use of “pancreatic beta cell” in this disclosure is not limited to the strict definition of a pancreatic beta cell by those skilled in the arts, but for the remainder of the disclosure encompasses any cell type capable of producing insulin, and secreting this hormonal product in response to extra-cellular glucose, which is hereby defined as the minimal set of requirements.
Another aspect of the invention is a method of identifying an agent that modulates (e.g., inhibits; enhances) the biological activity of betacam comprising contacting a composition comprising a polypeptide, wherein the polypeptide has an amino acid sequence comprising SEQ ID NO: 14, SEQ ID NO: 15, an amino acid sequence that has at least 50% identity to SEQ ID NO: 14 or an amino acid sequence that has at least 50% identity to SEQ ID NO: 15 with an agent to be assessed. The biological activity of the polypeptide in the presence of the agent is measured and compared to a suitable control, wherein if the polypeptide modulates the activity of the polypeptide in the presence of the agent compared to the control, then the agent modulates the biological activity of betacam. In a particular embodiment, the composition is one or more pancreatic beta cells. A any biological activity of betacam can be measured such as homotypic cell adhesion between betacam-expressing pancreatic beta cells. In addition, as will be appreciated by those of skill in the art, a variety of suitable controls are available for use in the method. In one embodiment, the control comprises pancreatic beta cells which have not been contacted with the agent to be assessed.
The following examples are provided for the purpose of illustration and are not intended to limit the scope of the present invention. Each publication or other reference disclosed below and elsewhere herein is incorporated herein by reference in its entirety.
In the following, a description of the amino acid sequence of the protein Betacam is provided. Homologous regions were easily detected for multiple species including human, pan troglodytes, canis familiaris, rat rattus, and gallus gallus, and several other species. Otherwise specified, the amino acid sequence numbering is in the following referring to that of mouse Betacam protein, isoform 1 [SEQ ID NO: 3], encoding a total of 463 amino acids.
In particular, the inventors named the gene locus in mouse, corresponding to Unigene Mm.206911,
These above mentioned Betacam genes are part of a homologous gene group, conserved during evolution, and NCBI refers to this group as HomoloGene 18724 (
The Betacam orthologous group contains multiple members in a large diversity of living species. The following sequence identities refer to individual members. SEQUENCE IDENTITY 1 [SEQ ID NO: 1] is human Betacam, isoform 1 (Homo Sapiens). [SEQ ID NO: 2] is human Betacam isoform 2 (Homo Sapiens). [SEQ ID NO: 3] is mouse Betacam isoform 1 (Mus Musculus). [SEQ ID NO: 4] is rat (rat rattus) Betacam. [SEQ ID NO: 5] is Bovine Betacam (Bos Taurus). [SEQ ID NO: 6] is dog Betacam (Canis familiaris). [SEQ ID NO: 7] is for Zebrafish Betacam (Danio Rerio). [SEQ ID NO: 8] is for horse Betacam (Equus caballus). [SEQ ID NO: 9] is for chicken Betacam (gallus gallus). [SEQ ID NO: 10] is for Chimpanzee Betacam (Pan troglodytes), [SEQ ID NO: 11] is for Macaque Monkey Betacam (Macaca Mulatta). [SEQ ID NO: 12] is for pufferfish Betacam (Tetraodon nigriviridis). [SEQ ID NO: 13] is for fruit fly (Drosophila Melanogaster) Lachesin.
The naming selected is one of convenience; none of the above genes/proteins are named based on previous knowledge of function, or expression in the liver. The arbitrary selection of gene/protein name Betacam is based on information provided within, where the inventors show that the protein is a member of a cell adhesion family group (-cam extension), and selectively expressed in pancreatic beta cells (beta-). The invention in particular is based on published knowledge that no other existing and described cell surface marker is known with a similar specificity of expression, as that displayed by the Betacam-encoded protein Betacam.
Betacam in humans exists in two alternative forms, isoform 1 (
In humans, Betacam resides on Chromosome 7, and is encoded on the reverse strand. It consists of 9 exons. (
A protein-Blast analysis of human Betacam protein sequence, isoform 1 against known human protein sequences was performed. This was done in order to assess which other protein share similarity to Betacam within the same species. A tree view is shown in
As shown herein, mouse Betacam contained a clearly detectable signal peptide (
As also shown herein, human Betacam isoform 1 contains a clearly detectable signal peptide (
Also shown herein, Betacam isoform 2 contained a clearly detectable signal peptide (
Also shown herein is that the long form of Betacam from macacca mulatta [SEQ ID NO: 11], does not contain a signal peptide (
Also shown herein is that Betacam contains a clearly detectable trans-membrane region, between amino acids proline 352 to tryptophan 373 (
Referring now to the invention in more detail, the inventors show that Betacam contains a series of high-probability N-linked glycosylation asparagines residues. A prediction analysis was carried out using the Net-N-glyc neural-network based prediction server a Center for Biological Sequence analysis (www.cbs.dtu.dk). The consensus sequence is Asn-X-Ser/Thr, and such sequences are detected at 9 positions in the extracellular domain of Betacam (
Initial assessment of expression of Betacam using genomics-type data was performed (
Oligonucleotide microarray experiments were performed on pancreatic-related samples using human U133 and mouse MOE430 Affymetrics chips that cover virtually the entire genome. Data was obtained from isolated islets from normal mice, diabetic models (NOD and ob/ob) and mice with deficiencies in the Ngn 3 as well as from mouse pancreatic tumor cell lines (aTC1-6 glucagonoma, βTC3 and Min6 insulinomas, and mPAC ductal tumor line). The data was analyzed to highlight transcripts that display islet cell-type-specific expression, and their segregation between pancreatic a- and β-cells.
Specifically, the advent of gene microarrays covering almost the complete spectrum of encoded mouse mRNAs (transcriptome) enabled the identification of the subsets of genes that are expressed in pancreatic islets. A number of published studies have documented genes that are expressed in pancreatic islet tissue, specific islet cell types and islet-derived cell lines (Shalev, 2002). In addition, studies have reported on the responses of islets to physiological and pathophysiological manipulation such as stimulation with glucose or inflammatory cytokines in vitro, and from mice carrying mutant genes that affect pancreatic function or development. The inventors performed more than 50 microarray experiments using both human U133 and mouse MOE430 oligonucleotide chips that report on virtually all transcripts from each species. This includes data from normal mice, diabetic models (NOD and ob/ob) and mice with deficiencies in Ngn3. Ngn3 null pancreas is completely devoid of pancreatic endocrine cells, and thus analysis at different gestational time points allowed the identification of transcripts that are highly expressed in the endocrine cells relative to exocrine and ductal tissue throughout development.
Further evaluation of tissue-specificity in-silico was made through queries against a larger series non-pancreatic type. Specifically, data were compared to array data obtained from a large non-pancreatic tissue pool of 45 tissue types (Novartis dataset and Unigene expression profiles). In addition, analysis of mouse pancreatic tumor cell lines (αTC1-6 glucagonoma, βTC3 and Min6 insulinomas, and mPAC ductal tumor line) further allowed the generation of predictive scores for select transcripts likely to display islet cell-type-specific expression, and their segregation between pancreatic α- and β-cells. These cell lines express genes related to the tumor cell phenotype and thus analyses were also performed on isolated pancreatic β-cell from a transgenic mouse expressing the autoantigen Phogrin linked to EGFP under the rat insulin 2 promoter. This resource was created by the inventors. The Table lists some of the genes for which transcripts were defined by ANOVA analysis, firstly as being differentially expressed in Ngn3 wild-type and knock-out mice at any embryological age (pancreatic endocrine and precursors) and secondly as being present in adult mouse islets. The list was then stratified on the basis of the relative expression in αTC and βTC cell lines. These approaches successfully predicted the islet cell specificity of the majority of the known transcriptional regulatory components involved in islet development, such as Ipf1, Arx, Pax4, Pax6, Brn4, NeuroD and known cell type specificity of several α- and β cell genes. Known neuroendocrine transcripts such as PTPRN (IA-2), prohormone convertases (Pcsk1, Pcsk2, Cpe) and the granins (Chga, Chgb Scg2, Sgne1) were in a pool of common αTC and βTC transcripts. Genes associated with other islet endocrine cells were, as predicted, not expressed in either (Ppy, Pyy, and ghrelin).
Referring now to the invention in more detail, the inventors describe in the following the discovery process of the Betacam gene. As an initial guide to the identification of pancreatic endocrine cell transcripts, E18.5 embryonic Ngn3 null pancreas was compared to WT littermate. This identified app. 180 individual transcripts that were absent in the endocrine-deficient pancreas, most of which correspond to known genes (the Table).
A limited number of transcript hits were previously uncharacterized, and further scrutinized by various prediction methods, results of which applying to AI987662/Betacam are shown in Example 1. Through this process, one particular gene, known as mouse gene AI987662 was discovered, which forms the basis of the particular aspects of the invention. Within the stratification method described in the Table, gene locus was observed within the pool of transcripts belonging to those >5-fold enriched in bTC cells versus aTC cells.
Foxa3
Frzb Gbp2 Gca
Ghrl H2-Ab1 Hba-a1
Gch
Gck
Gipr
Glp1r
Pcsk2 Pctk1 Pfdn1 Pitpnb
Ptprn
Pttg1 Rab6 Rad21
Insm1
Ipf1 Iqgap1 Krt2-8
Syt7
Syt7 Tmpo Tomm20-
Slc2a2 Slitl2 Stx3 Svil
Wbscr14.
Using the additionally available genomics datasets, it was found that expression of Betacam occurred in both normal, and obese mouse pancreatic islet cells (
It was also found that Betacam is expressed in the pituitary, small intestine and large intestine, but not elsewhere as judged from a genomics screen of multiple tissues (
It was also found that expression of Betacam as performed by GenePaint (www.genepaint.org), is observed in developing pancreas at E14.5, with a centrally regionalized expression pattern corresponding to that of developing endocrine cells (
The data on the predicted structural fold of the Betacam extracellular portion was based on a method known as “threading”, and provides to those skilled in the art, a confidence level basis for understanding an unknown 3-dimensional fold, as judged through comparisons to other similarly folding proteins. The resource that was applied to obtain these results is known as “Phyre”, provide by the imperial College, U. K. (http://www.sbg.bio.ic.ac.uk/phyre/). Uploading the amino acid sequence for mouse Betacam, the Phyre resource first performed a Psi-blast homology detection algorithm analysis using sequence identities for proteins for which a 3-dimensional structure has been solved, and is publicly available. Hits passing a minimal threshold were used for a “threading analysis” in which the novel protein sequence, in this case that of Betacam, was threaded through the fold libraries represented by the Psi-blast hit table. 3-dimensional “fits” were evaluated based on energy considerations, and if the unknown sequence is capable of adopting a fold structure similar to that of one, or more, of the library folds. The results were presented such that a 3D coordinate set for the unknown protein sequence, congruent to the library hit, was downloaded. A score, relating to the confidence of the particular prediction analysis was obtained. A detailed description of phyre is found within “Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. By Bennett-Lovsey R M, Herbert A D, Sternberg M J E, Kelley L A. Proteins: Structure, Function, Bioinformatics, vol 70(3) 611-625 (2008).”
Based on results of above, it was found that the extracellular domain consists of 3 Ig-type domains. Based on 3-dimensional modeling to distant relatives using the Phyre threading service, the structural fold of 95% of the extracellular domain, ranging from amino acid leu32 to Isoleucine 306 was predicted, and was fitted to the NCAM 3-dimensional fold, represented by the structure known in the Brookhaven protein data bank as structure c1qz1A.pdb.
Based on above results, a homotypic interaction method for Betacam/Betacam protein dimers was predicted. The homotypic interaction basis allows for the specific design of Betacam-derived single-molecules that are capable of interfering with Betacam/Betacam interactions, or binding to Betacam proteins localized on the beta cell surface.
Referring now to the invention in more detail, if one considers the capacity of D3-D3 homotypic interactions, the molecule will be capable of forming a multimeric structure between two Betacam-expressing cells. The iteration of the model described in
In a comparative perspective related to a predicted physiological involvement of Betacam,
Again, in a comparative perspective to the invention related to a predicted physiological involvement of Betacam,
Again in a comparative perspective to the invention, a magnified view of lachesin is shown in
Again in a comparative perspective to the invention, the charge-distribution of lachesin is shown in
Again, in a comparative perspective to the invention related to a predicted physiological involvement of Betacam,
Referring now to the invention in more detail,
The following plasmid backbones were applied to perform various functional assessments of Betacam.
Referring now to the invention in more detail,
Referring now to the invention in more detail,
Referring now to the invention in more detail,
Referring now to the invention in more detail,
Referring now to the invention in more detail,
Construction details for the generation of Fc-fusion construct plasmids is outlined in the following. Various Betacam domains (e. g. D1, D2, D3, D1/D2, D2/D3) were amplified by using appropriate primer pairs. The amplified fragments were purified and digested by using the corresponding restriction enzyme sites, and ligated into the vector pFUSE-hIgG1-Fc2. The primer pairs used for amplification are as following:
The following describes the methods applied by the inventors to prepare Fc-betacam fusion proteins using transient transfected Cos 7 cells. The calcium-phosphate transfection method was used for introduction of DNA into mammalian cells and was based on the formation of a calcium phosphate-DNA precipitate. The calcium phosphate facilitates the binding of the DNA to the cell surface. It is believed that the DNA then enters the cell by endocytosis. The procedure is routinely used to transfect a wide variety of cell types for either transient expression or for the production of stable transformants. The DNA is mixed directly with a concentrated solution of CaCl2. This is then added dropwise to a phosphate buffer to form a fine precipitate. Aeration of the phosphate buffer while adding the DNA-CaCl2 solution helps to ensure that the precipitate which forms is as fine as possible. This is important because clumped DNA will not adhere to or enter the cell as efficiently. Generally, a final CaCl2 concentration of 60 mM is used for calcium phosphate transfections. The final volume of DNA-CaCl2 should not exceed 1/10th of the volume of media in which the cells are plated. Cells should be seeded at a density such that on the day of transfection they are no more than 50% confluent. The optimal seeding density produces a nearly confluent dish of cells when they are harvested or split into selective media 48 hours after the transfection. This will vary for each cell line and is dependent upon their doubling time. Generally, cells are seeded at a density of 5×105/60 mm dish or 1-2×106/100 mm dish. Between 10 and 100 μg of DNA may be transfected.
Calcium Phosphate Transfection Procedure was performed as follows. Cos 7 cells were prepared for Transfection, by plating cells in 100 mm or 60 mm dishes at the required density. Generally, cells were seeded at a density of 1-2×106/100 mm dish or 5×107/150 mm dish. Cells were incubated overnight at 37° C. in a humidified CO2 incubator. On the following day, transfection was performed by 3-4 hours prior to transfection, the media was changed. At time of transfection, a transfection mixture was added to cells.
Specifically, as an example: For a 100 mm dish containing 10 ml of media, a transfection mix was made as in the following: To a 1.5 ml tube, add 62 μl of 2M CaCl2, adjust total Volume to 500 μl with sterile ddH2O, and mix gently. Add 10 μg DNA (Fc-betacam fusion constructs of various types), mix gently. On vortex, using a pasteur pipette, slowly add 500 μl 2×HBSS drop-wise. The transfection mix was hereafter incubated at room temperature for 15-20 minutes.
Subsequently, the precipitate was added dropwise to the media to the cells in dish. Cells were next incubated overnight at 37° C. in a humidified CO2 incubator.
Two days following Conditioned Media (CM) was isolated from the tissue culture dishes.
Fresh medium was added in a few cases for further production of Fc-betacam fusion protein.
Fc-fused Betacam Purification using HiTrap Protein A HP columns, GE Healthcare was done as follows, according to manufacturer's instructions:
1. Prepare working buffers:
5 ml
2. Fill up the 5 ml syringe with working Binding Buffer. Remove the stopper and connect the column to the syringe with the provided adaptor.
3. Wash the column with Binding Buffer at 1 ml/min. Wash two times. ‘drop to drop” to avoid introducing air into the column.
4. Apply the corresponding samples of Conditioned Fc-Betacam Cos 7 Media, using a new 5 ml syringe fitted to the adaptor by pumping it onto the column, at 1 ml/min.
5. Wash the column with Binding Buffer at 1 ml/min. Wash two times, until no material appears in the effluent.
6. Prepare a collection tube by adding 30 μl of Neutralizing Buffer. Elute with 400 ul of working Elution Buffer.
7. Re-load the flow-through onto the column for another elution, collect into the same collection tube.
Analysis of produced Betacam polypeptides by Western Blotting was done as follows. First, samples were prepared for SDS-PAGE analysis, by mixing 40 μl protein sample, 5 μl sample reducing reagent and 5 μl sample buffer (5× Sample Buffer: 10% w/v SDS, 10 mM beta-mercapto-ethanol, 20% w/v glycerol, 0.2 M Tris-HCl, pH 6.8, 0.05% w/v bromophenol blue). Samples were mixed gently, spun down, and subsequently boiled for 10 minutes to denature the protein. A cooling step on ice for 3-5 min was followed by spinning the sample down briefly. Samples were loaded onto NuPAGE® Novex® Bis-Tris Mini gels (Invitrogen). A protein molecular weight marker was added. Gel was run at 120 until loading dye began to exit gel. For Blotting, fiber pads, filter papers, and PVDF membrane were initially soaked in transfer buffer (25 mM Tris, 192 mM glycine, 20% methanol, pH8.3). Bubbles trapped in the filters or filter pads were removed. The PVDF membrane was activated in methanol prior to soaking in transfer buffer. The top and bottom of the gel were cut off. The gel was equilibrated in transfer buffer for a few minutes. Hereafter, the transfer cassette was assembled, and loaded in transfer apparatus. The transfer apparatus was filled with with transfer buffer prior to turning on the power supply. Proteins were transferred at 200 mA per transfer apparatus for 1 hr. After transfer, membranes were rinsed in ddH2O and placed in 5% milk solution (5% non-fat milk in 1×TBST) for 60 minutes at room temperature on a shaker to block non-specific binding. Following blocking, the membrane was soaked in primary antibody solution (example: goat anti-human IgG Fc specific, 1:500) on a shaker for overnight at 4° C. Hereafter the membrane was rinsed in ddH2O and washed 3 times for 10 min/wash. To detect the primary antibody binding, membranes were incubated in secondary antibody solution (donkey anti goat IgG-HRP, 1:5,000) for 60 min at room temperature on a shaker. Hereafter, the membrane was rinsed in ddH2O. Followed by three washes at 10 min/wash. Detection of signaling was performed using the ECL western blotting detection system (Amersham™ ECL™ Western Blotting Detection Reagents, GE Healthcare). 1 mL of solution A and 1 mL solution B was mixed. Membranes were incubated for various lengths of time, more preferably at 2 min. The reportable exposures differed, e.g. 30 sec, 1 min, 2 min, given optimal detection.
A result of production of Fc-Betacam proteins is shown in
Bead adhesion and recruitment assay. To detect Betacam-derived polypeptides directly binding to the cell surface of pancreatic insulin producing cells, a single-step binding assay was developed, referred to as the recruitment assay. The assay takes advantage of pre-binding Fc-Betacam fusion proteins to fluorescent beads which have been pre-coated by protein A by the vendor (Bangs Laboratories, Inc.). The beads were subsequently washed and added to Betacam-expressing cells and control cells. Imaging was done to assess adhesion of the fluorescent beads to the cell surface of the cells after exhaustive washing.
A specific experiment was done as follows. First, beads were coated with Fc-Betacam fusion proteins. Twenty microliters of Protein A coated microspheres (Dragon Green dyed) were washed three times in 200 μl of 50 mM sodium borate (pH 8.2), resuspended in 50 μl borate buffer 0.2 M pH 8.5, and incubated with 20 μg goat anti-human Fc fragment specific antibody with gentle mixing overnight at 4° C. Beads were washed three times by centrifugation at 9,000 rpm for 10 min with borate buffer containing 0.3% immunoglobulin-free BSA (Sigma), and hereafter incubated with 50 μl of purified various Fe-fused Betacam versions (e.g. Fc-D1, Fc-D2, Fc-D3, Fc-D1/D2, Fc-D2/D3) during 3 hr at room temperature with gentle mixing. The concentration of the Fc-betacam fusion proteins ranged typically from (0.05-0.09 ug/ul). Beads were finally washed three times in 0.3% BSA borate buffer and resuspended in 100 μl of this buffer. Immediately before loading on the cells, any possible bead aggregates were disrupted with a 1 s ultrasound pulse using a probe sonicator (Vibracell, Bioblock). The microsphere adhesion and recruitment assay was done as follows. βTC6 cells were cultured in a 12-well plate, and 10 μl of bead solution was added per well. After a 1 hr incubation time, three washes with PBS-BSA 0.3% were performed. Hereafter, the cells were photographed under the fluorescence microscopy.
Surface binding of Fc-Betacam to insulinoma cells. The inventors tested for direct binding of Fc-Betacam to the surface of pancreatic insulinoma cells, bTC6. The bTC6 cell line was found to express Betacam mRNA, as outlined in Example 2. The specific experimental conditions for the results shown in
Development and application of a fluorescent bead aggregation assay. Bead aggregation assays. The beads used in this assay were Protein A-conjugated polystyrene microspheres, fluorescent yellow-green (YG) (excitation maximum of 445 nm and emission maximum of 500 nm, the fluorescent emission is observed green) and fluorescent blue (excitation maximum of 475 nm and 600 nm & emission maximum of 663 nm, the fluorescent emission is observed red), 1.0 um (Polysciences, Inc.).
To coat fluorescent beads with Fc-Betacam proteins, the following procedure was applied by the inventors. 100 μl of Protein A-conjugated microspheres were added to a 1.5 ml microcentrifuge tube. The microspheres were washed once in sodium acetate 100 mM, pH3.9 (which is a pH at which any impurities coupled to protein A will be eluted) and twice in 10 mM Hepes, 50 mM NaCl, pH 7.2, by mixing the buffer, centrifuging in a micro-centrifuge for 5-6 min at 10,000×g, and then removing the supernatant. The Fc-Betacam proteins were bound to the beads at a ratio of 5 μg of protein per 40 μl of beads suspension in 10 mM Hepes, 50 mM NaCl, pH7.2, 1 mM CaCl2 for overnight at 4° C. on an Eppendorf shaker (1,400 rpm). Hereafter, the coated beads were pelleted, washed twice, and resuspended in 100 μl of 10 mM Hepes, 50 mM NaCl, pH 7.2. The suspension was briefly (˜30 sec) sonicated to obtain single beads, as determined by microscopy. Pictures were obtained recording the dissociation. The amount of protein coupled to the beads was determined by taking an aliquot and pelleting it and resuspending in 2×SDS sample buffer, boiling for 10 min. The beads were subsequently pelleted, and the supernatant was immunoblotted with the anti-human IgG (Fc specific)-HRP conjugate after SDS-PAGE.
An assay for establishing domain-specific interactions of Betacam-derived polypeptides was developed based on flow automated cell/bead sorting analysis. The detection of fluorescent beads allowed integer bead count assessment using fluorescence intensity as measured through FACS analysis. Such integer measurements therefore allowed the detection of bead aggregation as it may be mediated through conjugation of specific protein interaction domains. Beads were conjugated O/N. Prior to aggregation, sonication of the individual beads/mixtures was performed to achieve initial disaggregation. Hereafter, beads were incubated for 90 minutes, and subsequently analyzed by FACS analysis for multimer-formation. Following the FACS analysis, a spread of the bead mixture was performed on a microscope slide, and digital imaging using epifluorescence microscopy was done to assess visually the presence/absence of bead aggregates.
For the aggregation assay, Blue beads and YG beads were then mixed (equal volume of each) appropriately for a final volume of 100 μl and 1 mM CaCl2 was added to initiate aggregation. The samples were incubated at room temperature on an Eppendorf shaker (1,400 rpm), and at various time points, 10 μl aliquots were removed and diluted 30-fold with 10 mM Hepes, 50 mM NaCl, pH7.2, 1 mM CaCl2, and analyzed with the BD LSR II flow cytometer, or under the fluorescent microscopy for image acquisition.
The extent of aggregation, as determined by the aggregate size and aggregate composition, was quantified with a BD LSR II flow Cytometer. A 2D density plot of the intensity of red fluorescence versus green fluorescence in each aggregate revealed the size distribution and composition of the aggregates. The percentage of aggregates containing more than one red or green bead indicated the propensity for heterophilic binding.
The inventors first tested for intrinsic abilities of the fluorescent beads to bind as homodimers, or heterodimers. YG-beads (green fluorescent) showed no intrinsic capacity for aggregation (
The combined evidence of these interactions is strongly supportive of the proposed theoretical models of Betacam higher-order interactions as outlined in Example 2.
Referring now to the invention in more detail,
(Chinese hamster ovary) cells were transfected with pCMV-DsRED or pCMV-Betacam-DsRED. Selection of clones stably expressing the constructs was performed using G418 (neomycin). It was noted that loss of Betacam-DsRed colonies during the culture phase was prominent. Clonal homogeneity is apparent in both cases. DsRED distributes throughout the cell, whereas Betacam-DsRED becomes localized to strongly fluorescent aggregrates, predominantly in a perinuclear location. Such localization is commonly observed if proteins form intracellular aggregates, and generate “aggrosomes”, which a eukaryotic version of bacterial inclusion bodies. The formation of aggrosomes is a result of ER-stress. Often, apoptotic death is associated with this, and the cells are impaired in growth. The inventors subsequently produced stable clones expressing N-terminally truncated versions of Betacam-DsREd fusions. CHO-cells expressing Betacam-DsRed-ΔD1 and Betacam-DsRed-ΔD1/D2 were similarly selected by G418 treatment. Such cells revealed that Aggrosome formation was observed in cells expressing Betacam-DsRed-ΔD1, but not in cells expressing Betacam-DsRed-ΔD1/D2. The Betacam-DsRed-ΔD1/D2 fusion protein distributes over the entire cell, and seems incapable of aggregation in this assay.
Referring now to the invention in more detail,
Referring now to the invention in more detail,
Referring now to the invention in more detail,
Referring now to the invention in more detail, imaging of Att-20 clone 12E was performed using the V5 added tag to Betacam. Left image in
Another imaging result of Att20 clone 12E is shown in
HEK 293FT cells were grown on culture dishes and washed three times with phosphate-buffered saline (PBS) without Mg2+ or Ca2+, and collected after brief exposure (1 min at 37° C.) to trypsin-EDTA (Sigma). After centrifugation, a single-cell suspension was obtained by passing cells through a cell strainer (40-μm pore size). The cells were suspended into DMEM medium containing 10% FCS at a density of 1×106 cells/ml. The single-cell suspension was placed in 24-well plates pre-coated with 2% bovine serum albumin (BSA) and then rotated on a shaker at 37C for indicated periods (1 hr, 2 hr, 5 hr, overnight).
In a selected experiment, cells were suspended in normal Hanks' balanced salt solution (HBSS) containing Ca2+ and Mg2+ (Sigma), or Ca2+- and Mg2+-free HBSS (Sigma) containing 2 mM EDTA. Both HBSS solutions were supplemented with bovine serum albumin (BSA) at a final concentration of 2%.
In a selected experiment, two individual labeled Betacam forms (pBetacam-EGFP and pBetacam-DsRed) were transfected into HEK293FT cells; control transfections were performed using pEGFP-N1 and pDsRed-N1. The individual cells were subjected to the aggregation protocol as described earlier.
Referring now to the invention related to embodiments based on the Betacam peptide, an alternative method could be considered if a similar, but different gene as compared to Betacam exists which creates, upon its transcription and translation of its mRNA, a surface epitope present with high selectivity on the beta-cell surface. However, the inventors have reason to claim such a molecule is unlikely to exist. These claims are based on the following observations. 1. The genomics-based bioinformatics analysis was performed using the MOE-430v2 Affymetrix platform, which covers >90% of the transcribed genome (>40000 features are present on the platform). 2. The definition of tissue-specific expression towards pancreatic b-cells, also having selective expression of genes within the endocrine compartment of the pancreas was performed to lead to a much-reduced subset of genes (<200). 3. Within this list, all genes were manually curated for membrane localization, presumed function and novelty. 4. Only a single gene emerged, Betacam, consequently being the one exhibiting the highest degree of tissue-specificity for the pancreatic islet, beta-cells in particular, also being expressed on the surface of such cells, and representing a novel, uncharacterized gene. These criteria were fulfilled for both the mouse, and human Betacam genes and their translated products.
The embodiments of the invention are related to the utilization of Betacam as a novel, surface-expressed epitope, which normal pancreatic beta cells have. When combined with the predicted function of Betacam as a novel homotypic cell adhesion molecule, the various embodiments described are reagent definitions and formulations based on the advantageous features that such a unique component present on such cells provide.
The advantages of the present invention include, without limitation, the formulation of a reagent set capable of tracking a normal, as well as dysfunctional beta cells under several varying conditions. The advantage of the present invention is provided by our findings that a similar molecule is not known to exist. Our bioinformatics analysis suggests that an alternative molecule is unlikely to exist.
The advantages of the present invention lie in the recognition that there is no method to detect islet cells following transplantation in-vivo in a non-invasive manner.
The advantages of the present invention lies in the recognition that there is no specific purification step of the pancreatic beta cell type included current islet transplantation, as this is based on gradient purification of total islets, and results in quite crude cell populations.
The advantages of the present invention lie in the recognition that there is no non-invasive method to purify pancreatic beta cells from e.g. forward-differentiated human ES cells.
sapiens] (Human).
sapiens] (human)
The teachings of all patents, published applications and references cited herein are incorporated by reference in their entirety.
While this invention has been particularly shown and described with references to example embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention encompassed by the appended claims.
This application is a continuation of U.S. application Ser. No. 13/128,181 filed on Nov. 5, 2009 which is the U.S. National Stage of International Application No. PCT/US2009/063417, filed Nov. 5, 2009, which designates the U.S., published in English, and claims the benefit of U.S. Provisional Application No. 61/198,763, filed Nov. 7, 2008. The entire teachings of the above applications are incorporated herein by reference.
This invention was made with government support under Grant Numbers P30 DK057516 and U19 DK061248 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 61198763 | Nov 2008 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 13128181 | Nov 2011 | US |
| Child | 14579578 | US |
