Compositions for the diagnosis and treatment of chediak-higashi syndrome

Abstract

The present invention relates to the identification of novel nucleic acid molecules and proteins encoded by such nucleic acid molecules or degenerate variants thereof, that participate in the differentiation and/or function of intracellular vesicles. The nucleic acid molecules of the present invention represent the genes corresponding to the mammalian bg gene, a gene that, when mutated, is responsible for the human Chediak-Higashi syndrome.

Description

[0001] This application claims priority under 35 U.S.C. §119(e) to U.S. provisonal application Serial No. 60/021,064, filed Jul. 1, 1996, U.S. provisonal application Serial No. 60/015,673, filed Apr. 19, 1996 and U.S. provisonal application Serial No. 60/013,883, filed Mar. 22, 1996, each of which is incorporated herein by reference in its entirety.

1. INTRODUCTION

[0002] The present invention relates to the identification of novel nucleic acid molecules and proteins encoded by such nucleic acid molecules or degenerate, especially naturally occurring, variants thereof, that, when mutated, lead to disorders involving abnormal intracellular vesicles, especially abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, including Chediak-Higashi syndrome (CHS). The nucleic acid molecules of the present invention represent the genes corresponding to the mammalian bg gene, including the human bg gene, which are involved in the normal differentiation and/or function of such intracellular vesicles. Nucleic acid molecules representing loss-of-function alleles of the human bg gene bring about Chediak-Higashi syndrome (CHS), in individuals homozygous for such alleles.

[0003] In particular, the compositions of the present invention include nucleic acid molecules (e.g., bg gene), including recombinant DNA molecules, cloned genes or degenerate, especially naturally occurring, variants thereof, which encode novel bg gene products, and antibodies directed against such bg gene products or conserved variants or fragments thereof. The compositions of the present invention additionally include cloning vectors, including expression vectors, containing the nucleic acid molecules of the invention and hosts which have been transformed with such nucleic acid molecules.

[0004] In addition, this invention presents methods for the diagnostic evaluation and prognosis of disorders involving abnormal intracellular vesicles, especially abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, including CHS, and for the identification of subjects having a predisposition to such conditions. For example, nucleic acid molecules of the invention can be used as diagnostic hybridization probes or as primers for diagnostic PCR analysis for the identification of bg gene mutations, allelic variations and regulatory defects in the bg gene.

[0005] Further, methods and compositions are presented for the treatment of disorders involving abnormal intracellular vesicles, especially abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, including CHS. Such methods and compositions are capable of modulating the level of bg gene expression and/or the level of bg gene product activity.

[0006] Still further, the present invention relates to methods for the use of the bg gene, bg gene products and/or cells expressing wild type or mutant bg gene sequences for the identification of compounds which modulate bg gene expression and/or the activity of bg gene products. Such compounds can be used as agents to control disorders involving abnormal intracellular vesicles, especially abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, in particular, therapeutic agents in the treatment of CHS.

2. BACKGROUND OF THE INVENTION

[0007] Chediak-Higashi syndrome (CHS) is a lethal autosomal recessive disorder of humans mapping to 1q43. The clinical manifestations of this disorder include hypopigmentation, defective immune cell function, including severely impaired natural killer cell activity, and defective antibody-dependent, lymphocyte-mediated cytolysis against tumor cell targets. Further, neural degeneration is observed and, finally, the occurrence of a mononuclear cell lymphoma develops, which causes the death of afflicted individuals.

[0008] As mentioned above, the disease is accompanied by a marked susceptibility to infections. Young children have repeated infections, usually with gram-positive organisms of the staphylococcal and streptococcal type. Further, during the course of the disease, children may develop a progressive peripheral neuropathy. Children surviving the early infectious episodes (8-18 years of age), most frequently develop terminal lymphoreticular malignancy. Few patients survive beyond twenty years.

[0009] Pathological manifestation of the syndrome includes enlarged vesicles affecting lysosomes, melanosomes, platelet dense granules, cytolytic granules and Schwann cell granules. The abnormal size of these vesicles is thought to result from a malregulation of vesicle fusion or fission. Abnormal membrane-bound lysosomal-like organelles have been found in cells of the buccal mucosa, Schwann cells, pancreas, liver, gastric and duodenal mucosa, adrenal, pituitary, spleen, kidney, bone marrow, hair skin, iris and conjunctiva. The giant granules observed resemble the normal granules of the specific cell type in both fine structure and cytochemic reactions and result from the fusion of small primary granules.

[0010] Similar phenotypes are found in other species, most notably the beige mouse and the Aleutian mink, but are also found in such species as the Persian cat, cattle and even the killer whale. Somatic cell fusion studies have suggested that mutations within the same gene in mouse, mink, and man were responsible for the CHS-like phenotype in each of these species. In mice, the gene responsible for such a phenotype is the beige (bg) gene. Such studies, however, were not able to elucidate either the function or the identity of the bg gene product.

[0011] Over the past thirty years numerous theories have been evoked to explain the nature of these disorders. For example, it has been suggested that the defect might be caused by alterations in membrane fluidity, defects in microtubules or microtubule associated proteins, or changes in cyclic nucleotides levels. Upon further examination, though, each of these theories has been found to be inadequate, thus highlighting the fact that a great need remains for the discovery of the causative agent of the lethal Chediak-Higashi syndrome genetic disorder.

3. SUMMARY OF THE INVENTION

[0012] The present invention relates to the identification of novel nucleic acid molecules and proteins encoded by such nucleic acid molecules or degenerate, especially naturally occurring, variants thereof, that, when mutated, lead to disorders involving abnormal intracellular vesicles, especially abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, including Chediak-Higashi syndrome (CHS). The nucleic acid molecules of the present invention represent the genes corresponding to the mammalian bg gene, including the human bg gene, which are involved in the normal differentiation and/or function of such intracellular vesicles. Nucleic acid molecules representing loss-of-function alleles of the human bg gene bring about Chediak-Higashi syndrome (CHS), in individuals homozygous for such alleles.

[0013] In particular, the compositions of the present invention include nucleic acid molecules (e.g., bg gene), including recombinant DNA molecules, cloned genes or degenerate, especially naturally occurring, variants thereof, which encode novel bg gene products, and antibodies directed against such bg gene products or conserved variants or fragments thereof. The compositions of the present invention additionally include cloning vectors, including expression vectors, containing the nucleic acid molecules of the invention and hosts which have been transformed with such nucleic acid molecules.

[0014] Nucleic acid sequences of wild type and mutant forms of the murine bg gene are provided. Wild type murine bg gene produces a transcript of approximately 12-14 kb. The amino acid sequence of the predicted bg gene product indicates that the protein is novel.

[0015] Nucleic acid sequences of wild type forms of the human bg gene are also provided. The human bg gene produces alternatively spliced transcripts. The long, putatively full length bg transcript encodes a bg protein of 3801 amino acid residues, as shown in FIG. 7. A short form, alternatively spliced, human bg transcript encodes a bg protein of 3672 amino acid residues, as shown in FIG. 8. The amino acid sequence of the predicted human bg gene products indicates that the proteins are novel.

[0016] In addition, this invention presents methods for the diagnostic evaluation and prognosis of disorders involving abnormal intracellular vesicles, especially abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, including CHS, and for the identification of subjects having a predisposition to such conditions. For example, nucleic acid molecules of the invention can be used as diagnostic hybridization probes or as primers for diagnostic PCR analysis for the identification of bg gene mutations, allelic variations and regulatory defects in the bg gene.

[0017] Further, methods and compositions are presented for the treatment of disorders involving abnormal intracellular vesicles, especially abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, including CHS. Such methods and compositions are capable of modulating the level of bg gene expression and/or the level of bg gene product activity.

[0018] Still further, the present invention relates to methods for the use of the bg gene, bg gene products and/or cells expressing wild type or mutant bg gene sequences for the identification of compounds which modulate bg gene expression and/or the activity of bg gene products. Such compounds can be used as agents to control disorders involving abnormal intracellular vesicles, especially abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, in particular, therapeutic agents in the treatment of CHS.

[0019] This invention is based, in part, on a combination of in vitro complementation using yeast artificial chromosomes (YACs), positional cloning techniques and mutation detection which, together, were used to successfully identify and clone the murine bg gene, as described in the Examples, below, presented in Sections 6-9. Such analyses included the identification and sequencing of two independent bg mutations, one an insertion of 117 base pairs and the other a point mutation which results in an in-frame, premature stop codon. Both mutations result in the product of transcripts encoding truncated BG proteins.

4. DESCRIPTION OF THE FIGURES

[0020] FIG. 1. Genetic and physical map of mouse chromosome 13 region containing the bg gene interval.

[0021] FIGS. 2A-2B. Diagram depicting yeast artificial chromosomes (YACs) spanning the minimal bg interval. Ability of YACs to complement the bg mutation is noted.

[0022] FIG. 3A. Wild type and bg mouse fibroblasts plated together to demonstrate differences in phenotypes between the two cell types. The arrows denote two wild type cells. Two bg cells are just below the indicated wild type cells. Note the difference in lysosome size and distribution. Magnification was approximately 500×.

[0023] FIG. 3B. The initial mixed isolate of complemented colony 195-4, isolated from 400 &mgr;g/ml G418. This colony, as isolated from the plate contained complemented and uncomplemented bg cells. Magnification was approximately 500×.

[0024] FIG. 3C. Colony 195-4 after 10 days in 800 &mgr;g/ml G418. Note that the colony after this period of time was homogeneously complemented (i.e., all of the bg cells appeared wild type with respect to the lysosomal morphology.) Magnification was approximately 500×.

[0025] FIG. 3D. Colony 195-4 after culture i 800 &mgr;g/ml G418 for ten days, then cultured without G418 for thirty days. The result illustrated here demonstrates that the YAC was responsible for the complementation, in that, when the cells were cultured without G418, they lost the YAC and reverted back to the mutant bg morphology. Magnification was approximately 500×.

[0026] FIG. 4. Nucleotide sequence (bottom line; SEQ ID NO:1) and amino acid sequence (top line; SEQ ID NO:2) of the 22B/30B gene (the murine bg gene).

[0027] FIG. 5A-5D. Southern blot analysis of a chromosomal rearrangement associated with the bg allele. Southern blot analysis of a 510 bp fragment of 22B/30B hybridized to lane (1) C57BL/6J; (2) C57BL/6J-bg; (3) C57BL/6J-bgJ; (4) C57BL/6J-bg10J; (5) C57BL/6J-bg11J; (6) C3H/HeJ; (7) C3H/H3J-bg2J; (8) DBA/2J; and (9)DBA/2J-CO-bg8J DNAs digested with 5A: HindIII; 5B: PstI; 5C: BglII; and 5D: TaqI. Size markers are indicated.

[0028] FIG. 6. Diagram illustrating the location and structure of a Line 1 insertion representing mutation within the bg gene yielding truncated BG proteins which leads to a mutant bg phenotype.

[0029] FIG. 7. Human long form (putative full length) bg gene nucleotide (bottom line) and derived amino acid (top line) sequences.

[0030] FIG. 8. Human short form, alternatively spliced bg gene nucleotide (bottom line) and derived amino acid (top line) sequences.

5. DETAILED DESCRIPTION OF THE INVENTION

[0031] Described herein are novel mammalian genes, the beige (bg) genes, including the human bg gene. Such genes are involved in the normal differentiation and/or function of intracellular vesicles. When such sequences are mutated such that, for example, a functional beige gene product (BG) is no longer produced, disorders develop involving abnormal intracellular vesicles, especially abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, including Chediak-Higashi syndrome. Also described are recombinant mammalian, including human, bg DNA molecules, cloned genes, or degenerate variants thereof. The compositions of the present invention further include by gene products (e.g., proteins) that are encoded by the bg gene, and the modulation of bg gene expression and/or bg gene product activity in the treatment of disorders involving abnormal intracellular vesicles, including, but not limited to CHS. Also described herein are antibodies against bg gene products (e.g., proteins), or conserved variants or fragments thereof, and nucleic acid probes useful for the identification of bg gene mutations and the use of such nucleic acid probes in, for example, the identification of individuals predisposed to such disorders and/or individuals who carry mutant bg alleles. Further described are methods for the use of the bg gene and/or bg gene products in the identification of compounds which modulate the activity of the bg gene product.

[0032] Murine bg nucleic acid and amino acid compositions of the invention are demonstrated in the Examples presented, below, in Sections 6 through 9. A gene, referred to herein as the 22B/30B gene, representing a candidate for the murine bg gene was identified via a combination of genetic and physical mapping coupled with a yeast artificial chromosome (YAC) complementation assay by which complementation of the bg mutation was assessed via analysis of the morphological phenotype of YAC-transformed bg fibroblasts. Identification and sequencing of two independent bg mutations revealed that the mutations resided within the 22B/30B gene, representing compelling evidence that the 22B/30B gene was the bg gene. For clarity, it should, therefore, be noted that the murine bg gene is also referred to herein as the 22B/30B gene.

[0033] Human bg nucleic acid and amino acid compositions of the invention are demonstrated in Example 10, below.

5.1. The bg Gene

[0034] The bg gene, murine nucleic acid sequence of which is shown in FIG. 4 (SEQ ID NO:1) and human nucleic acid sequences of which are shown in FIGS. 7 and 8, is a novel gene involved in the normal differentiation and/or function of intracellular vesicles. Nucleic acid sequences of the bg gene are described herein. As used herein, “bg gene” refers to (a) a gene containing the DNA sequence shown in FIG. 4, FIG. 7 or FIG. 8; (b) any DNA sequence that encodes the amino acid sequence shown in FIG. 4 (SEQ ID NO:2), FIG. 7 or FIG. 8; (c) any DNA sequence that hybridizes to the complement of the DNA sequences that encode the amino acid sequence shown in FIG. 4, FIG. 7 or FIG. 8, under highly stringent conditions, e.g., hybridization to filter-bound DNA in 0.5 M NaHPO4, 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at 65° C., and washing in 0.1×SSC/0.1% SDS at 68° C. (Ausubel F. M. et al., eds., 1989, Current Protocols in Molecular Biology, Vol. I, Green Publishing Associates, Inc., and John Wiley & sons, Inc., New York, at p. 2.10.3); and/or (d) any DNA sequence that hybridizes to the complement of the DNA sequences that encode the amino acid sequence shown in FIG. 4, FIG. 7 or FIG. 8, under less stringent conditions, such as moderately stringent conditions, e.g., washing in 0.2×SSC/0.1% SDS at 42° C. (Ausubel et al., 1989, supra), yet which still encodes a functional bg gene product. As used herein, bg gene may also refer to degenerate variants of DNA sequences (a) through (d), including naturally occurring variants. The term “functional bg gene product,” as used herein, refers to a gene product encoded by a nucleic acid sequence capable of complementing a recessive, loss-of-function bg mutation.

[0035] The invention also includes nucleic acid molecules, preferably DNA molecules, that hybridize to, and are therefore the complements of, the DNA sequences (a) through (d), in the preceding paragraph, and to degenerate variants of the DNA sequences shown in (a) through (d) in the receding paragraph. Hybridization conditions may be highly stringent or less highly stringent, as described above. In instances wherein the nucleic acid molecules are deoxyoligonucleotides (“oligos”), highly stringent conditions may refer, e.g., to washing in 6×SSC/0.05% sodium pyrophosphate at 37° C. (for 14-base oligos), 48° C. (for 17-base oligos), 55° C. (for 20-base oligos), and 60° C. (for 23-base oligos). These nucleic acid molecules may encode or act as bg gene antisense molecules, useful, for example, in bg gene regulation, as antisense primers in amplification reactions of bg gene nucleic acid sequences and/or as hybridization probes for the identification of bg nucleic acid sequences. With respect to diagnostic procedures, such molecules may be used as components of methods whereby, for example, the presence of a particular bg allele responsible for causing a disorder, such as CHS, may be detected.

[0036] The invention also encompasses (a) DNA vectors that contain any of the foregoing bg coding sequences and/or their complements (i.e., antisense); (b) DNA expression vectors that contain any of the foregoing bg coding sequences operatively associated with a regulatory element that directs the expression of the coding sequences; and (c) genetically engineered host cells that contain any of the foregoing bg coding sequences operatively associated with a regulatory element that directs the expression of the coding sequences in the host cell. As used herein, regulatory elements include but are not limited to inducible and non-inducible promoters, enhancers, operators and other elements known to those skilled in the art that drive and regulate expression. Such regulatory elements include but are not limited to the cytomegalovirus hCMV immediate early gene, the early or late promoters of SV40 adenovirus, the lac system, the trp system, the TAC system, the TRC system, the major operator and promoter regions of phage A, the control regions of fd coat protein, the promoter for 3-phosphoglycerate kinase, the promoters of acid phosphatase, and the promoters of the yeast &agr;-mating factors. The invention includes fragments of any of the DNA sequences disclosed herein.

[0037] bg gene sequences include, for example, alleles and homologs of genes containing the sequence depicted in FIG. 4, FIG. 7 or FIG. 8, wherein such alleles are present at the same locus as the sequence depicted in FIG. 4, FIG. 7 or FIG. 8 and homologs are genes at other genetic loci within the genome that encode proteins which have extensive homology to one or more domains of the bg gene product. Such bg gene alleles and homologs can be identified and readily isolated, without undue experimentation, by molecular biological techniques well known in the art.

[0038] As an example, in order to clone a human bg gene sequence using isolated murine bg gene sequences as disclosed herein, such murine bg gene sequences may be labeled and used to screen a cDNA library constructed from mRNA obtained from appropriate cells or tissues of interest (e.g., a cell or tissue known to express the bg gene in mouse, and/or a cell or tissue known to be affected by CHS in humans, such as, for example, a retinal library). The hybridization washing conditions used should normally be of a lower stringency when the cDNA library is derived from an organism different from the type of organism from which the labeled sequence was derived, but appropriate stringency conditions for the specific sequence and library being utilized will be apparent to those of skill in the art.

[0039] Low stringency conditions, for example, are well known to those of skill in the art, and will vary predictably depending on the specific organisms from which the library and the labeled sequences are derived. For guidance regarding such conditions see, for example, Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Cold Springs Harbor Press, N.Y.; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y.

[0040] Alternatively, the labeled fragment may be used to screen a genomic library derived from the organism of interest, again, using appropriately stringent conditions. Such a screening procedure could be utilized, for example, to identify either bg alleles or bg homolog genes located in different portions of the genome containing sequences encoding one or more domains exhibiting extensive homology to one or more domains encoded by the bg gene.

[0041] Further, a bg gene sequence may be isolated from nucleic acid of the organism of interest by performing PCR using two degenerate oligonucleotide primer pools designed on the basis of amino acid sequences within the bg gene product disclosed herein. The template for the reaction may be cDNA obtained by reverse transcription of mRNA prepared from, for example, human or non-human cell lines or tissue known or suspected to express a bg gene allele.

[0042] The PCR product may be subcloned and sequenced to ensure that the amplified sequences represent the sequences of a bg gene nucleic acid sequence. The PCR fragment may then be used to isolate a full length cDNA clone by a variety of methods. For example, the amplified fragment may be labeled and used to screen a cDNA library, such as a bacteriophage cDNA library. Alternatively, the labeled fragment may be used to isolate genomic clones via the screening of a genomic library.

[0043] PCR technology may also be utilized to isolate full length cDNA sequences. For example, RNA may be isolated, following standard procedures, from an appropriate cellular or tissue source (i.e., one known, or suspected, to express the bg gene, and/or one known to be affected by disorders caused by bg mutations). A reverse transcription reaction may be performed on the RNA using an oligonucleotide primer specific for the most 5′ end of the amplified fragment for the priming of first strand synthesis. The resulting RNA/DNA hybrid may then be “tailed” with guanines using a standard terminal transferase reaction, the hybrid may be digested with RNAase H, and second strand synthesis may then be primed with a poly-C primer. Thus, cDNA sequences upstream of the amplified fragment may easily be isolated. For a review of cloning strategies which may be used, see e.g., Sambrook et al., 1989, supra.

[0044] bg gene sequences may additionally be used to isolate mutant bg gene alleles. Such mutant alleles may be isolated from individuals either known or proposed to have a genotype which contributes to the symptoms of intracellular vesicle disorders, including CHS. Mutant alleles and mutant allele products may then be utilized in the therapeutic and diagnostic systems described below. Additionally, such bg gene sequences can be used to detect bg gene regulatory (e.g., promoter) defects which can affect intracellular vesicle differentiation and/or function.

[0045] A cDNA of a mutant bg gene may be isolated, for example, by using PCR, a technique which is well known to those of skill in the art. In this case, the first cDNA strand may be synthesized by hybridizing an oligo-dT oligonucleotide to mRNA isolated from tissue known or suspected to be expressed in an individual putatively carrying the mutant bg allele, and by extending the new strand with reverse transcriptase. The second strand of the cDNA is then synthesized using an oligonucleotide that hybridizes specifically to the 5′ end of the normal gene. Using these two primers, the product is then amplified via PCR, cloned into a suitable vector, and subjected to DNA sequence analysis through methods well known to those of skill in the art. By comparing the DNA sequence of the mutant bg allele to that of the normal bg allele, the mutation(s) responsible for the loss or alteration of function of the mutant bg gene product can be ascertained.

[0046] Alternatively, a genomic library can be constructed using DNA obtained from an individual suspected of or known to carry the mutant bg allele, or a cDNA library can be constructed using RNA from a tissue known, or suspected, to express the mutant bg allele. The normal bg gene or any suitable fragment thereof may then be labeled and used as a probe to identify the corresponding mutant bg allele in such libraries. Clones containing the mutant bg gene sequences may then be purified and subjected to sequence analysis according to methods well known to those of skill in the art.

[0047] Additionally, an expression library can be constructed utilizing cDNA synthesized from, for example, RNA isolated from a tissue known, or suspected, to express a mutant bg allele in an individual suspected of or known to carry such a mutant allele. In this manner, gene products made by the putatively mutant tissue may be expressed and screened using standard antibody screening techniques in conjunction with antibodies raised against the normal bg gene product, as described, below, in Section 5.3. (For screening techniques, see, for example, Harlow, E. and Lane, eds., 1988, “Antibodies: A Laboratory Manual”, Cold Spring Harbor Press, Cold Spring Harbor.) In cases where a bg mutation results in an expressed gene product with altered function (e.g., as a result of a missense or a frameshift mutation), a polyclonal set of anti-bg gene product antibodies are likely to cross-react with the mutant bg gene product. Library clones detected via their reaction with such labeled antibodies can be purified and subjected to sequence analysis according to methods well known to those of skill in the art.

[0048] The Example presented in Section 9, below, demonstrates the successful isolation and sequencing of two bg mutations, each of which causes the production of truncated, non-functional BG proteins.

5.2. Protein Products of the bg GENE

[0049] bg gene products, peptide fragments thereof or fusion proeins, can be prepared for a variety of uses. For example, such gene products, peptide fragments thereof or fusion proteins, can be used for the generation of antibodies, in diagnostic assays, or for the identification of other cellular gene products involved in the differentiation and/or function of intracellular vesicles.

[0050] FIG. 4 depicts murine bg gene product amino acid sequence. FIG. 7 depicts the long form, putative full length, human bg gene product amino acid sequence. As shown in FIG. 7, the long form human bg gene product contains 3801 amino acid residues. FIG. 8 depicts the short form human bg gene product encoded by an alternatively spliced short form of bg transcript. As shown in FIG. 8, the human bg gene product encoded by this short form transcript contains 3672 amino acid residues. The bg gene product, sometimes referred to herein as “BG”, may additionally include those gene products encoded by the bg gene sequences described in Section 5.1, above.

[0051] In addition, bg gene products may include proteins that represent functionally equivalent bg gene products. The term “functionally equivalent bg gene product”, as used herein, refers to a gene product encoded by a nucleic acid sequence capable of complementing a bg mutation. Such an equivalent bg gene product may contain deletions, additions or substitutions of amino acid residues within the amino acid sequence encoded by the bg gene sequences described, above, in Section 5.1, but which result in a silent change, thus producing a functionally equivalent bg gene product. Amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues involved. For example, nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine; polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; positively charged (basic) amino acids include arginine, lysine, and histidine; and negatively charged (acidic) amino acids include-aspartic acid and glutamic acid.

[0052] The bg gene products, peptide fragments thereof or fusion proteins, may be produced by recombinant DNA technology using techniques well known in the art. Thus, methods for preparing the bg gene polypeptides, peptides and fusion proteins of the invention by expressing nucleic acid containing bg gene sequences are described herein. Methods which are well known to those skilled in the art can be used to construct expression vectors containing bg gene product coding sequences and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. See, for example, the techniques described in Sambrook et al., 1989, supra, and Ausubel et al., 1989, supra. Alternatively, RNA capable of encoding bg gene product sequences may be chemically synthesized using, for example, synthesizers. See, for example, the techniques described in “Oligonucleotide Synthesis”, 1984, Gait, M. J. ed., IRL Press, Oxford, which is incorporated by reference herein in its entirety.

[0053] A variety of host-expression vector systems may be utilized to express the bg gene coding sequences of the invention. Such host-expression systems represent vehicles by which the coding sequences of interest may be produced and subsequently purified, but also represent cells which may, when transformed or transfected with the appropriate nucleotide coding sequences, exhibit the bg gene product of the invention in situ. These include but are not limited to microorganisms such as bacteria (e.g., E. coli, B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing bg gene product coding sequences; yeast (e.g., Saccharomyces, Pichia) transformed with recombinant yeast expression vectors containing the bg gene product coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing the bg gene product coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing bg gene product coding sequences; or mammalian cell systems (e.g., COS, CHO, BHK, 293, 3T3) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter).

[0054] In bacterial systems, a number of expression vectors may be advantageously selected depending upon the use intended for the bg gene product being expressed. For example, when a large quantity of such a protein is to be produced, for the generation of pharmaceutical compositions of bg protein or for raising antibodies to bg protein, for example, vectors which direct the expression of high levels of fusion protein products that are readily purified may be desirable. Such vectors include, but are not limited, to the E. coli expression vector pUR278 (Ruther et al., 1983, EMBO J. 2:1791), in which the bg gene product coding sequence may be ligated individually into the vector in frame with the lac Z coding region so that a fusion protein is produced; pIN vectors (Inouye & Inouye, 1985, Nucleic Acids Res. 13:3101-3109; Van Heeke & Schuster, 1989, J. Biol. Chem. 264:5503-5509); and the like. pGEX vectors may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione. The pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene product can be released from the GST moiety.

[0055] In an insect system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The bg gene coding sequence may be cloned individually into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter). Successful insertion of bg gene coding sequence will result in inactivation of the polyhedrin gene and production of non-occluded recombinant virus (i.e., virus lacking the proteinaceous coat coded for by the polyhedrin gene). These recombinant viruses are then used to infect Spodoptera frugiperda cells in which the inserted gene is expressed. (E.g., see Smith et al., 1983, J. Virol. 46: 584; Smith, U.S. Pat. No. 4,215,051).

[0056] In mammalian host cells, a number of viral-based expression systems may be utilized. In cases where an adenovirus is used as an expression vector, the bg gene coding sequence of interest may be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and tripartite leader sequence. This chimeric gene may then be inserted in the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome (e.g., region E1 or E3) will result in a recombinant virus that is viable and capable of expressing bg gene product in infected hosts. (E.g., See Logan & Shenk, 1984, Proc. Natl. Acad. Sci. USA 81:3655-3659). Specific initiation signals may also be required for efficient translation of inserted bg gene product coding sequences. These signals include the ATG initiation codon and adjacent sequences. In cases where an entire bg gene, including its own initiation codon and adjacent sequences, is inserted into the appropriate expression vector, no additional translational control signals may be needed. However, in cases where only a portion of the bg gene coding sequence is inserted, exogenous translational control signals, including, perhaps, the ATG initiation codon, must be provided. Furthermore, the initiation codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert. These exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc. (see Bittner et al., 1987, Methods in Enzymol. 153:516-544).

[0057] In addition, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products may be important for the function of the protein. Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins and gene products. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed. To this end, eukaryotic host cells which possess the cellular machinery for proper processing of the primary transcript, glycosylation, and phosphorylation of the gene product may be used. Such mammalian host cells include but are not limited to CHO, VERO, BHK, HeLa, COS, MDCK, 293, 3T3 and WI38 cell lines.

[0058] For long-term, high-yield production of recombinant proteins, stable expression is preferred. For example, cell lines which stably express the bg gene product may be engineered. Rather than using expression vectors which contain viral origins of replication, host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker. Following the introduction of the foreign DNA, engineered cells may be allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media. The selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn can be cloned and expanded into cell lines. This method may advantageously be used to engineer cell lines which express the bg gene product. Such engineered cell lines may be particularly useful in screening and evaluation of compounds that affect the endogenous activity of the bg gene product.

[0059] A number of selection systems may be used, including but not limited to the herpes simplex virus thymidine kinase (Wigler, et al., 1977, Cell 11:223), hypoxanthine-guanine phosphoribosyltransferase (Szybalska & Szybalski, 1962, Proc. Natl. Acad. Sci. USA 48:2026), and adenine phosphoribosyltransferase (Lowy, et al., 1980, Cell 22:817) genes can be employed in tk−, bgprt− or aprt− cells, respectively. Also, antimetabolite resistance can be used as the basis of selection for the following genes: dhfr, which confers resistance to methotrexate (Wigler, et al., 1980, Natl. Acad. Sci. USA 77:3567; O'Hare, et al., 1981, Proc. Natl. Acad. Sci. USA 78:1527); gpt, which confers resistance to mycophenolic acid (Mulligan & Berg, 1981, Proc. Natl. Acad. Sci. USA 78:2072); neo, which confers resistance to the aminoglycoside G-418 (Colberre-Garapin, et al., 1981, J. Mol. Biol. 150:1); and hygro, which confers resistance to hygromycin (Santerre, et al., 1984, Gene 30:147).

[0060] Alternatively, any fusion protein may be readily purified by utilizing an antibody specific for the fusion protein being expressed. For example, a system described by Janknecht et al. allows for the ready purification of non-denatured fusion proteins expressed in human cell lines (Janknecht, et al., 1991, Proc. Natl. Acad. Sci. USA 88: 8972-8976). In this system, the gene of interest is subcloned into a vaccinia recombination plasmid such that the gene's open reading frame is translationally fused to an amino-terminal tag consisting of six histidine residues. Extracts from cells infected with recombinant vaccinia virus are loaded onto Ni2+·nitriloacetic acid-agarose columns and histidine-tagged proteins are selectively eluted with imidazole-containing buffers.

[0061] The bg gene products can also be expressed in transgenic animals. Animals of any species, including, but not limited to, mice, rats, rabbits, guinea pigs, pigs, micro-pigs, goats, and non-human primates, e.g., baboons, monkeys, and chimpanzees may be used to generate bg transgenic animals.

[0062] Any technique known in the art may be used to introduce the bg gene transgene into animals to produce the founder lines of transgenic animals. Such techniques include, but are not limited to pronuclear microinjection (Hoppe, P. C. and Wagner, T. E., 1989, U.S. Pat. No. 4,873,191); retrovirus mediated gene transfer into germ lines (Van der Putten et al., 1985, Proc. Natl. Acad. Sci., USA 82:6148-6152); gene targeting in embryonic stem cells (Thompson et al., 1989, Cell 56:313-321); electroporation of embryos (Lo, 1983, Mol Cell. Biol. 3:1803-1814); and sperm-mediated gene transfer (Lavitrano et al., 1989, Cell 57:717-723); etc. For a review of such techniques, see Gordon, 1989, Transgenic Animals, Intl. Rev. Cytol. 115:171-229, which is incorporated by reference herein in its entirety.

[0063] The present invention provides for transgenic animals that carry the bg transgene in all their cells, as well as animals which carry the transgene in some, but not all their cells, i.e., mosaic animals. The transgene may be integrated as a single transgene or in concatamers, e.g., head-to-head tandems or head-to-tail tandems. The transgene may also be selectively introduced into and activated in a particular cell type by following, for example, the teaching of Lasko et al. (Lasko, M. et al., 1992, Proc. Natl. Acad. Sci. USA 89: 6232-6236). The regulatory sequences required for such a cell-type specific activation will depend upon the particular cell type of interest, and will be apparent to those of skill in the art. When it is desired that the bg gene transgene be integrated into the chromosomal site of the endogenous bg gene, gene targeting is preferred. Briefly, when such a technique is to be utilized, vectors containing some nucleotide sequences homologous to the endogenous bg gene are designed for the purpose of integrating, via homologous recombination with chromosomal sequences, into and disrupting the function of the nucleotide sequence of the endogenous bg gene. The transgene may also be selectively introduced into a particular cell type, thus inactivating the endogenous bg gene in only that cell type, by following, for example, the teaching of Gu et al. (Gu, et al., 1994, Science 265: 103-106). The regulatory sequences required for such a cell-type specific inactivation will depend upon the particular cell type of interest, and will be apparent to those of skill in the art.

[0064] Once transgenic animals have been generated, the expression of the recombinant bg gene may be assayed utilizing standard techniques. Initial-screening may be accomplished by Southern blot analysis or PCR techniques to analyze animal tissues to assay whether integration of the transgene has taken place. The level of mRNA expression of the transgene in the tissues of the transgenic animals may also be assessed using techniques which include but are not limited to Northern blot analysis of tissue samples obtained from the animal, in situ hybridization analysis, and RT-PCR. Samples of bg gene-expressing tissue, may also be evaluated immunocytochemically using antibodies specific for the bg transgene product.

5.3. Antibodies to bg Gene Products

[0065] Described herein are methods for the production of antibodies capable of specifically recognizing one or more bg gene product epitopes or epitopes of conserved variants or peptide fragments of the bg gene products.

[0066] Such antibodies may include, but are not limited to, polyclonal antibodies, monoclonal antibodies (mAbs), humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab′)2 fragments, fragments produced by a Fab expression library, anti-idiotypic (anti-Id) antibodies, and epitope-binding fragments of any of the above. Such antibodies may be used, for example, in the detection of a bg gene product in an biological sample and may, therefore, be utilized as part of a diagnostic or prognostic technique whereby patients may be tested for abnormal levels of bg gene products, and/or for the presence of abnormal forms of the such gene products. Such antibodies may also be utilized in conjunction with, for example, compound screening schemes, as described, below, in Section 5.4.2, for the evaluation of the effect of test compounds on bg gene product levels and/or activity. Additionally, such antibodies can be used in conjunction with the gene therapy techniques described, below, in Section 5.4.3, to, for example, evaluate the normal and/or engineered bg-expressing cells prior to their introduction into the patient.

[0067] Anti-bg gene product antibodies may additionally be used as a method for the inhibition of abnormal bg gene product activity, in, for example, instances in which such abnormal activity is due to an increased level of bg gene product or to the presence of mutant, gain-of-function mutant bg gene products. Thus, such antibodies may, therefore, be utilized as part of methods for the treatment of disorders caused by such abnormal bg gene product activity, including, for example, disorders involving abnormal intracellular vesicle differentiation and/or function.

[0068] For the production of antibodies against a bg gene product, various host animals may be immunized by injection with a bg gene product, or a portion thereof. Such host animals may include but are not limited to rabbits, mice, and rats, to name but a few. Various adjuvants may be used to increase the immunological response, depending on the host species, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum.

[0069] Polyclonal antibodies are heterogeneous populations of antibody molecules derived from the sera of animals immunized with an antigen, such as a bg gene product, or an antigenic functional derivative thereof. For the production of polyclonal antibodies, host animals such as those described above, may be immunized by injection with bg gene product supplemented with adjuvants as also described above.

[0070] Monoclonal antibodies, which are homogeneous populations of antibodies to a particular antigen, may be obtained by any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique of Kohler and Milstein, (1975, Nature 256:495-497; and U.S. Pat. No. 4,376,110), the human B-cell hybridoma technique (Kosbor et al., 1983, Immunology Today 4:72; Cole et al., 1983, Proc. Natl. Acad. Sci. USA 80:2026-2030), and the EBV-hybridoma technique (Cole et al., 1985, Monoclonal Antibodies And Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). Such antibodies may be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD and any subclass thereof. The hybridoma producing the mAb of this invention may be cultivated in vitro or in vivo. Production of high titers of inAbs in vivo makes this the presently preferred method of production.

[0071] In addition, techniques developed for the production of “chimeric antibodies” (Morrison et al., 1984, Proc. Natl. Acad. Sci., 81:6851-6855; Neuberger et al., 1984, Nature, 312:604-608; Takeda et al., 1985, Nature, 314:452-454) by splicing the genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used. A chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine mAb and a human immunoglobulin constant region.

[0072] Alternatively, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778; Bird, 1988, Science 242:423-426; Huston et al., 1988, Proc. Natl. Acad. Sci. USA 85:5879-5883; and Ward et al., 1989, Nature 334:544-546) can be adapted to produce single chain antibodies against bg gene products. Single chain antibodies are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge, resulting in a single chain polypeptide.

[0073] Antibody fragments which recognize specific epitopes may be generated by known techniques. For example, such fragments include but are not limited to: the F(ab′)2 fragments which can be produced by pepsin digestion of the antibody molecule and the Fab fragments which can be generated by reducing the disulfide bridges of the F(ab′)2 fragments. Alternatively, Fab expression libraries may be constructed (Huse et al., 1989, Science, 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity.

5.4. Uses of the bg Gene, Gene Products, and Antibodies

[0074] Described herein are various applications of the bg gene, the bg gene product including peptide fragments thereof, and of antibodies directed against the bg gene product and peptide fragments thereof.

[0075] Such applications include, for example, prognostic and diagnostic evaluation of disorders involving abnormal intracellular vesicles, including, for example, abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, including, but not limited to Chediak-Higashi syndrome (CHS), and methods for the identification of subjects with a predisposition to such disorders and the identification of individuals carrying mutant bg alleles.

[0076] Such methods may, for example, utilize reagents such as the bg gene nucleotide sequences described in Sections 5.1, and antibodies directed against bg gene products, including peptide fragments thereof, as described, above, in Section 5.3. Specifically, such reagents may be used, for example, for: (1) nucleic acid-based techniques for the detection of the presence of bg gene mutations, or the detection of either over- or under-expression of bg gene mRNA relative levels known to be found in the normal state; and (2) peptide-based techniques for the detection of mutant BG proteins or either an over- or an under-abundance of BG relative levels known to be found in the normal state.

[0077] The methods described herein may be performed, for example, by utilizing pre-packaged diagnostic kits comprising at least one specific bg gene nucleic acid or anti-bg gene antibody reagent described herein, which may be conveniently used, e.g., in clinical settings, to diagnose patients exhibiting intracellular vesicle disorder abnormalities.

[0078] Nucleic acid-based detection techniques are described, below, in Section 5.4.1. Peptide detection techniques are described, below, in Section 5.4.2.

[0079] Additionally, such applications include methods for the treatment of disorders involving abnormal intracellular vesicles, including CHS, as described, below, in Section 5.4.4, and for the identification of compounds which modulate the expression of the bg gene and/or the activity of the bg gene product, as described below, in Section 5.4.3. Such compounds can include, for example, other cellular products which are involved in normal differentiation and/or function of intracellular vesicles.

5.4.1. Detection of bg Gene Nucleic Acid Molecules

[0080] Mutations within the bg gene can be detected by utilizing a number of techniques. Nucleic acid from any nucleated cell can be used as the starting point for such assay techniques, and may be isolated according to standard nucleic acid preparation procedures which are well known to those of skill in the art.

[0081] DNA may be used in hybridization or amplification assays of biological samples to detect abnormalities involving bg gene structure, including point mutations, insertions, deletions and chromosomal rearrangements. Such assays may include, but are not limited to, Southern analyses, single stranded conformational polymorphism analyses (SSCP), and PCR analyses.

[0082] Such diagnostic methods for the detection of bg gene-specific mutations can involve for example, contacting and incubating nucleic acids including recombinant DNA molecules, cloned genes or degenerate variants thereof, obtained from a sample, e.g., derived from a patient sample or other appropriate cellular source, with one or more labeled nucleic acid reagents including recombinant DNA molecules, cloned genes or degenerate variants thereof, as described in Section 5.1, under conditions favorable for the specific annealing of these reagents to their complementary sequences within the bg gene. Preferably, the lengths of these nucleic acid reagents are at least 15 to 30 nucleotides. After incubation, all non-annealed nucleic acids are removed from the nucleic acid:bg molecule hybrid. The presence of nucleic acids which have hybridized, if any such molecules exist, is then detected. Using such a detection scheme, the nucleic acid from the cell type or tissue of interest can be immobilized, for example, to a solid support such as a membrane, or a plastic surface such as that on a microtiter plate or polystyrene beads. In this case, after incubation, non-annealed, labeled nucleic acid reagents of the type described in Section 5.1 are easily removed. Detection of the remaining, annealed, labeled bg nucleic acid reagents is accomplished using standard techniques well-known to those in the art. The bg gene sequences to which the nucleic acid reagents have annealed can be compared to the annealing pattern expected from a normal bg gene sequence in order to determine whether a bg gene mutation is present.

[0083] Alternative diagnostic methods for the detection of bg gene specific nucleic acid molecules, in patient samples or other appropriate cell sources, may involve their amplification, e.g., by PCR (the experimental embodiment set forth in Mullis, K. B., 1987, U.S. Pat. No. 4,683,202), followed by the detection of the amplified molecules using techniques well known to those of skill in the art. The resulting amplified sequences can be compared to those which would be expected if the nucleic acid being-amplified contained only normal copies of the bg gene in order to determine whether a bg gene mutation exists.

[0084] Additionally, well-known genotyping techniques can be performed to identify individuals carrying bg gene mutations. Such techniques include, for example, the use of restriction fragment length polymorphisms (RFLPs), which involve sequence variations in one of the recognition sites for the specific restriction enzyme used.

[0085] Additionally, improved methods for analyzing DNA polymorphisms which can be utilized for the identification of bg gene mutations have been described which capitalize on the presence of variable numbers of short, tandemly repeated DNA sequences between the restriction enzyme sites. For example, Weber (U.S. Pat. No. 5,075,217, which is incorporated herein by reference in its entirety) describes a DNA marker based on length polymorphisms in blocks of (dC-dA)n-(dG-dT)n short tandem repeats. The average separation of (dC-dA)n-(dG-dT)n blocks is estimated to be 30,000-60,000 bp. Markers which are so closely spaced exhibit a high frequency co-inheritance, and are extremely useful in the identification of genetic mutations, such as, for example, mutations within the bg gene, and the diagnosis of diseases and disorders related to bg mutations.

[0086] Also, Caskey et al. (U.S. Pat. No. 5,364,759, which is incorporated herein by reference in its entirety) describe a DNA profiling assay for detecting short tri and tetra nucleotide repeat sequences. The process includes extracting the DNA of interest, such as the bg gene, amplifying the extracted DNA, and labelling the repeat sequences to form a genotypic map of the individual's DNA.

[0087] The level and/or type of bg gene expression can also be assayed. For example, RNA from a cell type or tissue known, or suspected, to express the bg gene, may be isolated and tested utilizing hybridization or PCR techniques such as are described, above. The isolated cells can be derived from cell culture or from a patient. The analysis of cells taken from culture may be a necessary step in the assessment of cells to be used as part of a cell-based gene therapy technique or, alternatively, to test the effect of compounds on the expression of the bg gene. Such analyses may reveal both quantitative and qualitative aspects of the expression pattern of the bg gene, including activation or inactivation of bg gene expression, as well as reveal the presence or absence of alternatively spliced forms of bg gene transcripts.

[0088] In one embodiment of such a detection scheme, a cDNA molecule is synthesized from an RNA molecule of interest (e.g., by reverse transcription of the RNA molecule into cDNA). A sequence within the cDNA is then used as the template for a nucleic acid amplification reaction, such as a PCR amplification reaction, or the like. The nucleic acid reagents used as synthesis initiation reagents (e.g., primers) in the reverse transcription and nucleic acid amplification steps of this method are chosen from among the bg gene nucleic acid reagents described in Section 5.1. The preferred lengths of such nucleic acid reagents are at least 9-30 nucleotides. For detection of the amplified product, the nucleic acid amplification may be performed using radioactively or non-radioactively labeled nucleotides. Alternatively, enough amplified product may be made such that the product may be visualized by standard ethidium bromide staining or by utilizing any other suitable nucleic acid staining method.

[0089] Additionally, it is possible to perform such bg gene expression assays “in situ”, i.e., directly upon tissue sections (fixed and/or frozen) of patient tissue obtained from biopsies or resections, such that no nucleic acid purification is necessary. Nucleic acid reagents such as those described in Section 5.1 may be used as probes and/or primers for such in situ procedures (see, for example, Nuovo, G. J., 1992, “PCR In Situ Hybridization: Protocols And Applications”, Raven Press, NY).

[0090] Alternatively, if a sufficient quantity of the appropriate cells can be obtained, standard Northern analysis can be performed to determine the level of mRNA expression of the bg gene.

5.4.2. Detection of bg Gene Products

[0091] Antibodies directed against wild type or mutant bg gene products or conserved variants or peptide fragments thereof, which are discussed, above, in Section 5.3, may also be used as intracellular vesicle, including, but not limited to CHS, disorder diagnostics and prognostics, as described herein. Such diagnostic methods, may be used to detect abnormalities in the level of bg gene expression, or abnormalities in the structure and/or temporal, tissue, cellular, or subcellular location of bg gene product. Further, such assays can be utilized to detect the presence or absence of bg gene products encoded by alternatively spliced bg gene transcripts. Given the intracellular vesicles affected by bg mutations, it is possible that the bg gene product is an intracellular gene product. The antibodies and immunoassay methods described below, therefore, have important in vitro applications in assessing the efficacy of treatments for such disorders. Antibodies, or fragments of antibodies, such as those described below, may be used to screen potentially therapeutic compounds in vitro to determine their effects on bg gene expression and bg peptide production. The compounds which have beneficial effects on intracellular vesicle disorders, such as for example, CHS, can be identified, and a therapeutically effective dose determined.

[0092] In vitro immunoassays may also be used, for example, to assess the efficacy of cell-based gene therapy for intracellular vesicle disorder, including, for example, CHS. Antibodies directed against bg peptides may be used in vitro to determine the level of bg gene expression achieved in cells genetically engineered to produce bg peptides. Given that the bg gene product may represent an intracellular gene product, such an assessment is, preferably, done using cell lysates or extracts. Such analysis will allow for a determination of the number of transformed cells necessary to. achieve therapeutic efficacy in vivo, as well as optimization of the gene replacement protocol.

[0093] The tissue or cell type to be analyzed will generally include those which are known, or suspected, to express the bg gene. The protein isolation methods employed herein may, for example, be such as those described in Harlow and Lane (Harlow, E. and Lane, D., 1988, “Antibodies: A Laboratory Manual”, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.), which is incorporated herein by reference in its entirety. The isolated cells can be derived from cell culture or from a patient. The analysis of cell taken from culture may be a necessary step in the assessment of cells to be used as part of a cell-based gene therapy technique or, alternatively, to test the effect of compounds on the expression of the bg gene.

[0094] Preferred diagnostic methods for the detection of bg gene products or conserved variants or peptide fragments thereof, may involve, for example, immunoassays wherein the bg gene products or conserved variants or peptide fragments are detected by their interaction with an anti-bg gene product-specific antibody.

[0095] For example, antibodies, or fragments of antibodies, such as those described, above, in Section 5.3, useful in the present invention may be used to quantitatively or qualitatively detect the presence of bg gene products or conserved variants or peptide fragments thereof. This can be accomplished, for example, by immunofluorescence techniques employing a fluorescently labeled antibody (see below, this Section) coupled with light microscopic, flow cytometric, or fluorimetric detection. Such techniques are especially preferred if such bg gene products are expressed on the cell surface.

[0096] The antibodies (or fragments thereof) useful in the present invention may, additionally, be employed histologically, as in immunofluorescence or immunoelectron microscopy, for in situ detection of bg gene products or conserved variants or peptide fragments thereof. In situ detection may be accomplished by removing a histological specimen from a patient, and applying thereto a labeled antibody of the present invention. The antibody (or fragment) is preferably applied by overlaying the labeled antibody (or fragment) onto a biological sample. Through the use of such a procedure, it is possible to determine not only the presence of the bg gene product, or conserved variants or peptide fragments, but also its distribution in the examined tissue. Using the present invention, those of ordinary skill will readily perceive that any of a wide variety of histological methods (such as staining procedures) can be modified in order to achieve such in situ detection.

[0097] Immunoassays for bg gene products or conserved variants or peptide fragments thereof will typically comprise incubating a sample, such as a biological fluid, a tissue extract, freshly harvested cells, or lysates of cells which have been incubated in cell culture, in the presence of a detectably labeled antibody capable of identifying bg gene products or conserved variants or peptide fragments thereof, and detecting the bound antibody by any of a number of techniques well-known in the art.

[0098] The biological sample may be brought in contact with and immobilized onto a solid phase support or carrier such as nitrocellulose, or other solid support which is capable of immobilizing cells, cell particles or soluble proteins. The support may then be washed with suitable buffers followed by treatment with the detectably labeled bg gene specific antibody. The solid phase support may then be washed with the buffer a second time to remove unbound antibody. The amount of bound label on solid support may then be detected by conventional means.

[0099] By “solid phase support or carrier” is intended any support capable of binding an antigen or an antibody. Well-known supports or carriers include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, gabbros, and magnetite. The nature of the carrier can be either soluble to some extent or insoluble for the purposes of the present invention. The support material may have virtually any possible structural configuration so long as the coupled molecule is capable of binding to an antigen or antibody. Thus, the support configuration may be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod. Alternatively, the surface may be flat such as a sheet, test strip, etc. Preferred supports include polystyrene beads. Those skilled in the art will know many other suitable carriers for binding antibody or antigen, or will be able to ascertain the same by use of routine experimentation.

[0100] The binding activity of a given lot of anti-bg gene product antibody may be determined according to well known methods. Those skilled in the art will be able to determine operative and optimal assay conditions for each determination by employing routine experimentation.

[0101] One of the ways in which the bg gene peptide-specific antibody can be detectably labeled is by linking the same to an enzyme and use in an enzyme immunoassay (EIA) (Voller, A., “The Enzyme Linked Immunosorbent Assay (ELISA)”, 1978, Diagnostic Horizons 2:1-7, Microbiological Associates Quarterly Publication, Walkersville, Md.); Voller, A. et al., 1978, J. Clin. Pathol. 31:507-520; Butler, J. E., 1981, Meth. Enzymol. 73:482-523; Maggio, E. (ed.), 1980, Enzyme Immunoassay, CRC Press, Boca Raton, Fla.,; Ishikawa, E. et al., (eds.), 1981, Enzyme Immunoassay, Kgaku Shoin, Tokyo). The enzyme which is bound to the antibody will react with an appropriate substrate, preferably a chromogenic substrate, in such a manner as to produce a chemical moiety which can be detected, for example, by spectrophotometric, fluorimetric or by visual means. Enzymes which can be used to detectably label the antibody include, but are not limited to, malate dehydrogenase, staphylococcal nuclease, delta-5-steroid isomerase, yeast alcohol dehydrogenase, alpha-glycerophosphate, dehydrogenase, triose phosphate isomerase, horseradish peroxidase, alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase, ribonuclease, urease, catalase, glucose-6-phosphate dehydrogenase, glucoamylase and acetylcholinesterase. The detection can be accomplished by colorimetric methods which employ a chromogenic substrate for the enzyme. Detection may also be accomplished by visual comparison of the extent of enzymatic reaction of a substrate in comparison with similarly prepared standards.

[0102] Detection may also be accomplished using any of a variety of other immunoassays. For example, by radioactively labeling the antibodies or antibody fragments, it is possible to detect bg gene peptides through the use of a radioimmunoassay (RIA) (see, for example, Weintraub, B., Principles of Radioimmunoassays, Seventh Training Course on Radioligand Assay Techniques, The Endocrine Society, March, 1986, which is incorporated by reference herein). The radioactive isotope can be detected by such means as the use of a gamma counter or a scintillation counter or by autoradiography.

[0103] It is also possible to label the antibody with a fluorescent compound. When the fluorescently labeled antibody is exposed to light of the proper wave length, its presence can then be detected due to fluorescence. Among the most commonly used fluorescent labeling compounds are fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine.

[0104] The antibody can also be detectably labeled using fluorescence emitting metals such as 152Eu, or others of the lanthanide series. These metals can be attached to the antibody using such metal chelating groups as diethylenetriaminepentacetic acid (DTPA) or ethylenediaminetetraacetic acid (EDTA).

[0105] The antibody also can be detectably labeled by coupling it to a chemiluminescent compound. The presence of the chemiluminescent-tagged antibody is then determined by detecting the presence of luminescence that arises during the course of a chemical reaction. Examples of particularly useful chemiluminescent labeling compounds are luminol, isoluminol, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester.

[0106] Likewise, a bioluminescent compound may be used to label the antibody of the present invention. Bioluminescence is a type of chemiluminescence found in biological systems in, which a catalytic protein increases the efficiency of the chemiluminescent reaction. The presence of a bioluminescent protein is determined by detecting the presence of luminescence. Important bioluminescent compounds for purposes of labeling are luciferin, luciferase and aequorin.

5.4.3. Screening Assays for Compounds that Modulate bg Activity

[0107] The following assays are designed to identify compounds that bind to bg gene products, bind to other intracellular proteins that interact with a bg gene product, to compounds that interfere with the interaction of the bg gene product with other intracellular proteins and to compounds which modulate the activity of bg gene (i.e., modulate the level of is gene expression and/or modulate the level of bg gene product activity). Assays may additionally be utilized which identify compounds which bind to bg gene regulatory sequences (e.g., promoter sequences). See e.g., Platt, K. A., 1994, J. Biol. Chem. 269:28558-28562, which is incorporated herein by reference in its entirety, which may modulate the level of bg gene expression. Compounds may include, but are not limited to, small organic molecules which are able to cross the blood-brain barrier, gain entry into an appropriate cell and affect expression of the bg gene or some other gene involved in the pathway or pathways regulating intracellular vesicle differentiation and/or function, or other intracellular proteins. Methods for the identification of such intracellular proteins are described, below, in Section 5.4.3.1. Such intracellular proteins may be involved in the differentiation and/or function of intracellular vesicles, including, but not limited to, lysosomes, melanosomes, platelet dense granules and cytolytic granules. Further, among these compounds are compounds which affect the level of bg gene expression and/or bg gene product activity and which can be used in the therapeutic treatment of disorders involving abnormal intracellular vesicles, including, but not limited to, abnormal lysosomes, melanosomes, platelet dense granules and cytolytic granules, including CHS, as described, below, in Section 5.4.4.

[0108] Compounds may include, but are not limited to, peptides such as, for example, soluble peptides, including but not limited to, Ig-tailed fusion peptides, and members of random peptide libraries; (see, e.g., Lam, K. S. et al., 1991, Nature 354:82-84; Houghten, R. et al., 1991, Nature 354:84-86), and combinatorial chemistry-derived molecular library made of D- and/or L-configuration amino acids, phosphopeptides (including, but not limited to members of random or partially degenerate, directed phosphopeptide libraries; see, e.g., Songyang, Z. et al., 1993, Cell 72:767-778), antibodies (including, but not limited to, polyclonal, monoclonal, humanized, anti-idiotypic, chimeric or single chain antibodies, and FAb, F(ab′)2 and FAb expression library fragments, and epitope-binding fragments thereof), and small organic or inorganic molecules.

[0109] Compounds identified via assays such as those described herein may be useful, for example, in elaborating the biological function of the bg gene product, and for ameliorating intracellular vesicle disorders such as, for example, CHS. Assays for testing the effectiveness of compounds, identified by, for example, techniques such as those described in Section 5.4.3.1-5.4.3.3, are discussed, below, in Section 5.4.3.4.

5.4.3.1. In vitro Screening Assays for Compounds that Bind to the Bg Gene Products

[0110] In vitro systems may be designed to identify compounds capable of binding the bg gene products of the invention. Compounds identified may be useful, for example, in modulating the activity of wild type and/or mutant bg gene products, may be useful in elaborating the biological function of the bg gene product, may be utilized in screens for identifying compounds that disrupt normal bg gene product interactions, or may in themselves disrupt such interactions.

[0111] The principle of the assays used to identify compounds that bind to the bg gene product involves preparing a reaction mixture of the bg gene product and the test compound under conditions and for a time sufficient to allow the two components to interact and bind, thus forming a complex which can be removed and/or detected in the reaction mixture. These assays can be conducted in a variety of ways. For example, one method to conduct such an assay would involve anchoring is gene product or the test substance onto a solid phase and detecting bg gene product/test compound complexes anchored on the solid phase at the end of the reaction. In one embodiment of such a method, the bg gene product may be anchored onto a solid surface, and the test compound, which is not anchored, may be labeled, either directly or indirectly.

[0112] In practice, microtiter plates may conveniently be utilized as the solid phase. The anchored component may be immobilized by non-covalent or covalent attachments. Non-covalent attachment may be accomplished by simply coating the solid surface with a solution of the protein and drying. Alternatively, an immobilized antibody, preferably a monoclonal antibody, specific for the protein to be immobilized may be used to anchor the protein to the solid surface. The surfaces may be prepared in advance and stored.

[0113] In order to conduct the assay, the nonimmobilized component is added to the coated surface containing the anchored component. After the reaction is complete, unreacted components are removed (e.g., by washing) under conditions such that any complexes formed will remain immobilized on the solid surface. The detection of complexes anchored on the solid surface can be accomplished in a number of ways. Where the previously nonimmobilized component is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the previously nonimmobilized component is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the previously nonimmobilized component (the antibody, in turn, may be directly labeled or indirectly labeled with a labeled anti-Ig antibody).

[0114] Alternatively, a reaction can be conducted in a liquid phase, the reaction products separated from unreacted components, and complexes detected; e.g., using an immobilized antibody specific for bg gene product or the test compound to anchor any complexes formed in solution, and a labeled antibody specific for the other component of the possible complex to detect anchored complexes.

5.4.3.2. Assays for Intracellular Proteins that Interact with the bg Gene Product

[0115] Any method suitable for detecting protein-protein interactions may be employed for identifying bg protein-intracellular protein interactions.

[0116] Among the traditional methods which may be employed are co-immunoprecipitation, crosslinking and co-purification through gradients or chromatographic columns. Utilizing procedures such as these allows for the identification of intracellular proteins which interact with bg gene products. Once isolated, such an intracellular protein can be identified and can, in turn, be used, in conjunction with standard techniques, to identify proteins it interacts with. For example, at least a portion of the amino acid sequence of the intracellular protein which interacts with the bg gene product can be ascertained using techniques well known to those of skill in the art, such as via the Edman degradation technique (see, e.g., Creighton, 1983, “Proteins: Structures and Molecular Principles”, W.H. Freeman & Co., N.Y., pp.34-49). The amino acid sequence obtained may be used as a guide for the generation of oligonucleotide mixtures that can be used to screen for gene sequences encoding such intracellular proteins. Screening made be accomplished, for example, by standard hybridization or PCR techniques. Techniques for the generation of oligonucleotide mixtures and the screening are well-known. (See, e.g., Ausubel, supra., and PCR Protocols: A Guide to Methods and Applications, 1990, Innis, M. et al., eds. Academic Press, Inc., New York).

[0117] Additionally, methods may be employed which result in the simultaneous identification of genes which encode the intracellular protein interacting with the bg protein. These methods include, for example, probing expression libraries with labeled bg protein, using bg protein in a manner similar to the well known technique of antibody probing of &lgr;gt11 libraries.

[0118] One method which detects protein interactions in vivo, the two-hybrid system, is described in detail for illustration only and not by way of limitation. One version of this system has been described (Chien et al., 1991, Proc. Natl. Acad. Sci. USA, 88:9578-9582) and is commercially available from Clontech (Palo Alto, Calif.).

[0119] Briefly, utilizing such a system, plasmids are constructed that encode two hybrid proteins: one consists of the DNA-binding domain of a transcription activator protein fused to the bg gene product and the other consists of the transcription activator protein's activation domain fused to an unknown protein that is encoded by a cDNA which has been recombined into this plasmid as part of a cDNA library. The DNA-binding domain fusion plasmid and the cDNA library are transformed into a strain of the yeast Saccharomyces cerevisiae that contains a reporter gene (e.g., HBS or lacZ) whose regulatory region contains the transcription activator's binding site. Either hybrid protein alone cannot activate transcription of the reporter gene: the DNA-binding domain hybrid cannot because it does not provide activation function and the activation domain hybrid cannot because it cannot localize to the activator's binding sites. Interaction of the two hybrid proteins reconstitutes the functional activator protein and results in expression of the reporter gene, which is detected by an assay for the reporter gene product.

[0120] The two-hybrid system or related methodology may be used to screen-activation domain libraries for proteins that interact with the “bait” gene product. By way of example, and not by way of limitation, bg gene products may be used as the bait gene product. Total genomic or cDNA sequences are fused to the DNA encoding an activation domain. This library and a plasmid encoding a hybrid of a bait bg gene product fused to the DNA-binding domain are cotransformed into a yeast reporter strain, and the resulting transformants are screened for those that express the reporter gene. For example, and not by way of limitation, a bait bg gene sequence, such as the bg open reading frame sequence in FIG. 4, can be cloned into a vector such that it is translationally fused to the DNA encoding the DNA-binding domain of the GAL4 protein. These colonies are purified and the library plasmids responsible for reporter gene expression are isolated. DNA sequencing is then used to identify the proteins encoded by the library plasmids.

[0121] A cDNA library of the cell line from which proteins that interact with bait bg gene product are to be detected can be made using methods routinely practiced in the art. According to the particular system described herein, for example, the cDNA fragments can be inserted into a vector such that they are translationally fused to the transcriptional activation domain of GAL4. This library can be co-transformed along with the bait bg gene-GAL4 fusion plasmid into a yeast strain which contains a lacZ gene driven by a promoter which contains GAL4 activation sequence. A cDNA encoded protein, fused to GAL4 transcriptional activation domain, that interacts with bait bg gene product will reconstitute an active GAL4 protein and thereby drive expression of the HIS3 gene. Colonies which express HIS3 can be detected by their growth on petri dishes containing semi-solid agar based media lacking histidine. The cDNA can then be purified from these strains, and used to produce and isolate the bait bg gene-interacting protein using techniques routinely practiced in the art.

5.4.3.3. Assays for Compounds that Interfere with bg Gene Product/Intracellular Macromolecule Interaction

[0122] The bg gene products of the invention may, in vivo, interact with one or more intracellular macromolecules, such as proteins. Such macromolecules may include, but are not limited to, nucleic acid molecules and those proteins identified via methods such as those described, above, in Section 5.4.3.2. For purposes of this discussion, such intracellular macromolecules are referred to herein as “binding partners”. Compounds that disrupt bg binding in this way may be useful in regulating the activity of the bg gene product, especially mutant bg gene products. Such compounds may include, but are not limited to molecules such as peptides, and the like, as described, for example, in Section 5.4.3.1. above, which would be capable of gaining access to the intracellular bg gene product.

[0123] The basic principle of the assay systems used to identify compounds that interfere with the interaction between the bg gene product and its intracellular binding partner or partners involves preparing a reaction mixture containing the bg gene product, and the binding partner under conditions and for a time sufficient to allow the two to interact and bind, thus forming a complex. In order to test a compound for inhibitory activity, the reaction mixture is prepared in the presence and absence of the test compound. The test compound may be initially included in the reaction mixture, or may be added at a time subsequent to the addition of bg gene product and its intracellular binding partner. Control reaction mixtures are incubated without the test compound or with a placebo. The formation of any complexes between the bg gene protein and the intracellular binding partner is then detected. The formation of a complex in the control reaction, but not in the reaction mixture containing the test compound, indicates that the compound interferes with the interaction of the bg gene protein and the interactive binding partner. Additionally, complex formation within reaction mixtures containing the test compound and normal bg gene protein may also be compared to complex formation within reaction mixtures containing the test compound and a mutant bg gene protein. This comparison may be important in those cases wherein it is desirable to identify compounds that disrupt interactions of mutant but not normal bg gene proteins.

[0124] The assay for compounds that interfere with the interaction of the bg gene products and binding partners can be conducted in a heterogeneous or homogeneous format. Heterogeneous assays involve anchoring either the bg gene product or the binding partner onto a solid phase and detecting complexes anchored on the solid phase at the end of the reaction. In homogeneous assays, the entire reaction is carried out in a liquid phase. In either approach, the order of addition of reactants can be varied to obtain different information about the-compounds being tested. For example, test compounds that interfere with the interaction between the bg gene products and the binding partners, e.g., by competition, can be identified by conducting the reaction in the presence of the test substance; i.e., by adding the test substance to the reaction mixture prior to or simultaneously with the bg gene protein and interactive intracellular binding partner. Alternatively, test compounds that disrupt preformed complexes, e.g. compounds with higher binding constants that displace one of the components from the complex, can be tested by adding the test compound to the reaction mixture after complexes have been formed. The various formats are described briefly below.

[0125] In a heterogeneous assay system, either the bg gene product or the interactive intracellular binding partner, is anchored onto a solid surface, while the non-anchored species is labeled, either directly or indirectly. In practice, microtiter plates are conveniently utilized. The anchored species may be immobilized by non-covalent or covalent attachments. Non-covalent attachment may be accomplished simply by coating the solid surface with a solution of the bg gene product or binding partner and drying. Alternatively, an immobilized antibody specific for the species to be anchored may be used to anchor the species to the solid surface. The surfaces may be prepared in advance and stored.

[0126] In order to conduct the assay, the partner of the immobilized species is exposed to the coated surface with or without the test compound. After the reaction is complete, unreacted components are removed (e.g., by washing) and any complexes formed will remain immobilized on the solid surface. The detection of complexes anchored on the solid surface can be accomplished in a number of ways. Where the non-immobilized species is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the non-immobilized species is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the initially non-immobilized species (the antibody, in turn, may be directly labeled or indirectly labeled with a labeled anti-Ig antibody). Depending upon the order of addition of reaction components, test compounds which inhibit complex formation or which disrupt preformed complexes can be detected.

[0127] Alternatively, the reaction can be conducted in a liquid phase in the presence or absence of the test compound, the reaction products separated from unreacted components, and complexes detected; e.g., using an immobilized antibody specific for one of the binding components to anchor any complexes formed in solution, and a labeled antibody specific for the other partner to detect anchored complexes. Again, depending upon the order of addition of reactants to the liquid phase, test compounds which inhibit complex or which disrupt preformed complexes can be identified.

[0128] In an alternate embodiment of the invention, a homogeneous assay can be used. In this approach, a preformed complex of the bg gene protein and the interactive intracellular binding partner is prepared in which either the bg gene product or its binding partners is labeled, but the signal generated by the label is quenched due to complex formation (see, e.g., U.S. Pat. No. 4,109,496 by Rubenstein which utilizes this approach for immunoassays). The addition of a test substance that competes with and displaces one of the species from the preformed complex will result in the generation of a signal above background. In this way, test substances which disrupt bg gene protein/intracellular binding partner interaction can be identified.

[0129] In a particular embodiment, the bg gene product can be prepared for immobilization using recombinant DNA techniques described in Section 5.2. above. For example, the bg coding region can be fused to a glutathione-S-transferase (GST) gene using a fusion vector, such as pGEX-5X-1, in such a manner that its binding activity is maintained in the resulting fusion protein. The interactive intracellular binding partner can be purified and used to raise a monoclonal antibody, using methods routinely practiced in the art and described above, in Section 5.3. This antibody can be labeled with the radioactive isotope 125I, for example, by methods routinely practiced in the art. In a heterogeneous assay, e.g., the GST-bg fusion protein can be anchored to glutathione-agarose beads. The interactive intracellular binding partner can then be added in the presence or absence of the test compound in a manner that allows interaction and binding to occur. At the end of the reaction period, unbound material can be washed away, and the labeled monoclonal antibody can be added to the system and allowed to bind to the complexed components. The interaction between the bg gene protein and the interactive intracellular binding partner can be detected by measuring the amount of radioactivity that remains associated with the glutathione-agarose beads. A successful inhibition of the interaction by the test compound will result in a decrease in measured radioactivity.

[0130] Alternatively, the GST-bg gene fusion protein and the interactive intracellular binding partner can be mixed together in liquid in the absence of the solid glutathione-agarose beads. The test compound can be added either during or after the species are allowed to interact. This mixture can then be added to the glutathione-agarose beads and unbound material is washed away. Again the extent of inhibition of the is gene product/binding partner interaction can be detected by adding the labeled antibody and measuring the radioactivity associated with the beads.

[0131] In another embodiment of the invention, these same techniques can be employed using peptide fragments that correspond to the binding domains of the bg protein and/or the interactive intracellular or binding partner (in cases where the binding partner is a protein), in place of one or both of the full length proteins. Any number of methods routinely practiced in the art can be used to identify and isolate the binding sites. These methods include, but are not limited to, mutagenesis of the gene encoding one of the proteins and screening for disruption of binding in a co-immunoprecipitation assay. Compensating mutations in the gene encoding the second species in the complex can then be selected. Sequence analysis of the genes encoding the respective proteins will reveal the mutations that correspond to the region of the protein involved in interactive binding. Alternatively, one protein can be anchored to a solid surface using methods described in this Section above, and allowed to interact with and bind to its labeled binding partner, which has been treated with a proteolytic enzyme, such as trypsin. After washing, a short, labeled peptide comprising the binding domain may remain associated with the solid material, which can be isolated and identified by amino acid sequencing. Also, once the gene coding for the intracellular binding partner is obtained, short gene segments can be engineered to express peptide fragments of the protein, which can then be tested for binding activity and purified or synthesized.

[0132] For-example, and not by way of limitation, a bg gene product can be anchored to a solid material as described, above, in this Section by making a GST-bg fusion protein and allowing it to bind to glutathione agarose beads. The interactive intracellular binding partner can be labeled with radioactive isotope, such as 35S, and cleaved with a proteolytic enzyme such as trypsin. Cleavage products can then be added to the anchored GST-bg fusion protein and allowed to bind. After washing away unbound peptides, labeled bound material, representing the intracellular binding partner binding domain, can be eluted, purified, and analyzed for amino acid sequence by well-known methods. Peptides so identified can be produced synthetically or fused to appropriate facilitative proteins using recombinant DNA technology.

5.4.3.4. Assays for Identification of Compounds that Ameliorate Intracellular Vesicle Disorders

[0133] Compounds, including but not limited to binding compounds identified via assay techniques such as those described, above, in Sections 5.4.3.1-5.4.3.3, can be tested for the ability to ameliorate intracellular vesicle disorder symptoms, including symptoms associated with CHS. It should be noted that although bg gene products may be intracellular molecules which are not secreted and have no transmembrane component, the assays described herein can identify compounds which affect bg gene activity by either affecting bg gene expression or by affecting the level of bg gene product activity. For example, compounds may be identified which are involved in another step in the pathway in which the bg gene and/or bg gene product is involved and, by affecting this same pathway may modulate the affect of bg on the development of intracellular vesicle disorders. Such compounds can be used as part of a therapeutic method for the treatment of intracellular vesicle disorders, including, for example, CHS.

[0134] Described below are cell-based and animal model-based assays for the identification of compounds exhibiting such an ability to intracellular vesicle disorder symptoms.

[0135] First, cell-based systems can be used to identify compounds which may act to ameliorate intracellular vesicle disorder symptoms. Such cell systems can include, for example, recombinant or non-recombinant cells, such as cell lines, which express the bg gene. Further, such cell systems can include, for example, recombinant or non-recombinant cell, such as cell lines, which express mutant forms of the bg gene and/or which exhibit elements of the bg phenotype. For example, bg fibroblast cells, Aleutian mink cells or human Chediak-Higashi cells, as described, below, in Sections 7 and 8, can be used.

[0136] In utilizing such cell systems, cells may be exposed to a compound, suspected of exhibiting an ability to ameliorate intracellular vesicle disorder symptoms, at a sufficient concentration and for a time sufficient to elicit such an amelioration in the exposed cells. After exposure, the cells can be assayed to measure alterations in the expression of the bg gene, e.g., by assaying cell lysates for bg mRNA transcripts (e.g., by Northern analysis) or for bg protein expressed in the cell; compounds which increase expression of the bg gene are good candidates as therapeutics. Alternatively, the cells are examined to determine whether one or more aspects of the bg cellular phenotype has been altered to resemble a more normal or more wild type, phenotype, or a phenotype more likely to produce a lower incidence or severity of intracellular disorder symptoms.

[0137] In addition, animal-based intracellular vesicle disorder systems, which may include, for example bg mice, may be used to identify compounds capable of ameliorating intracellular vesicle disorder-like symptoms (e.g., bg phenotype). Such animal models may be used as test substrates for the identification of drugs, pharmaceuticals, therapies and interventions which may be effective in treating such disorders. For example, animal models may be exposed to a compound, suspected of exhibiting an ability to ameliorate intracellular vesicle disorder symptoms, at a sufficient concentration and for a time sufficient to elicit such an amelioration of the symptoms in the exposed animals. The response of the animals to the exposure may be monitored by assessing the reversal of disorders associated with intracellular vesicle disorders such as CHS.

[0138] With regard to intervention, any treatments which reverse any aspect of the intracellular disorder-like symptoms should be considered as candidates for human intracellular disorder therapeutic intervention. Dosages of test agents may be determined by deriving dose-response curves, as discussed in Section 5.5.1, below.

15 5.4. Compounds and Methods for the Treatment of Intracellular Vesicle Disorders

[0139] Described below are methods and compositions whereby intracellular vesicle disorders, including, but not limited to, CHS may be treated. Loss of normal bg gene product function results in the development of a bg, or intracellular vesicle disorder, phenotype, an increase in bg gene product activity would facilitate progress towards a normal state in individuals exhibiting a deficient level of bg gene expression and/or bg gene product activity.

[0140] Alternatively, it is conceivable that symptoms of certain intracellular vesicle disorders may be ameliorated by decreasing the level of bg gene expression and/or in gene product activity. For example, bg gene sequences may be utilized-in conjunction with well-known antisense, gene “knock-out,” ribozyme and/or triple helix methods to decrease the level of bg gene expression.

[0141] With respect to an increase in the level of normal bg gene expression and/or bg gene product activity, bg gene nucleic acid sequences, described, above, in Section 5.1, can, for example, be utilized for the treatment of intracellular vesicle disorders, including CHS. Such treatment can be administered, for example, in the form of gene replacement therapy. Specifically, one or more copies of a normal bg gene or a portion of the bg gene that directs the production of a bg gene product exhibiting normal bg gene function, may be inserted into the appropriate cells within a patient, using vectors which include, but are not limited to adenovirus, adeno-associated virus, and retrovirus vectors, in addition to other particles that introduce DNA into cells, such as liposomes.

[0142] It is conceivable that it may be advantageous to achieve bg gene expression in the brain, given the large number of cell type affected by the bg and CHS phenotypes. As such, gene replacement therapy techniques may be utilized which are capable delivering bg gene sequences to these cell types within patients. Thus, the techniques for delivery of bg gene sequences should be able to readily cross the blood-brain barrier, which are well known to those of skill in the art (see, e.g., PCT application, publication No. WO89/10134, which is incorporated herein by reference in its entirety), or, alternatively, should involve direct administration of such bg gene sequences to the site of the cells in which the bg gene sequences are to be expressed. With respect to delivery which is capable of crossing the blood-brain barrier, viral vectors such as, for example, those described above, are preferable.

[0143] Additional methods which may be utilized to increase the overall level of bg gene expression and/or bg gene product activity include the introduction of appropriate bg-expressing cells, preferably autologous cells, into a patient at positions and in numbers which are sufficient to ameliorate the symptoms of intracellular vesicle disorders, including CHS. Such cells may be either recombinant or non-recombinant.

[0144] Alternatively, cells, preferably autologous cells, can be engineered to express bg gene sequences which may then be introduced into a patient in positions appropriate for the amelioration of intracellular vesicle disorder symptoms. Alternately, cells which express the bg gene in a wild type in MHC matched individuals, i.e., non-bg individual, and may include, for example, hypothalamic cells. The expression of the bg gene sequences is controlled by the appropriate gene regulatory sequences to allow such expression in the necessary cell types. Such gene regulatory sequences are well known to the skilled artisan. Such cell-based gene therapy techniques are well known to those skilled in the art, see, e.g., Anderson, F., U.S. Pat. No. 5,399,349.

[0145] When the cells to be administered are non-autologous cells, they can be administered using well known techniques which prevent a host immune response against the introduced cells from developing. For example, the cells may be introduced in an encapsulated form which, while allowing for an exchange of components with the immediate extracellular environment, does not allow the introduced cells to be recognized by the host immune system.

[0146] Additionally, compounds, such as those identified via techniques such as those described, above, in Section 5.4.3, which are capable of modulating bg gene product activity can be administered using standard techniques which are well known to those of skill in the art.

5.5. Pharmaceutical Preparations and Methods of Administration

[0147] The compounds that are determined to affect bg gene expression or gene product activity can be administered to a patient at therapeutically effective doses to treat or ameliorate intracellular vesicle disorders, including CHS. A therapeutically effective dose refers to that amount of the compound sufficient to result in amelioration of symptoms of intracellular vesicle disorders, including elements associated with the bg phenotype and/or the CHS phenotype.

5.5.1. Effective Dose

[0148] Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.

[0149] The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.

5.5.2. Formulations and Use

[0150] Pharmaceutical compositions for use in accordance with the present invention may be formulated in conventional manner using one or more physiologically acceptable carriers or excipients.

[0151] Thus, the compounds and their physiologically acceptable salts and solvates may be formulated for administration by inhalation or insufflation (either through the mouth or the nose) or oral, buccal, parenteral or rectal administration. For oral administration, the pharmaceutical compositions may take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulphate). The tablets may be coated by methods well known in the art. Liquid preparations for oral administration may take the form of, for example, solutions, syrups or suspensions, or they may be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., almond oil, oily esters, ethyl alcohol or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid). The preparations may also contain buffer salts, flavoring, coloring and sweetening agents as appropriate.

[0152] Preparations for oral administration may be suitably formulated to give controlled release of the active compound.

[0153] For buccal administration the compositions may take the form of tablets or lozenges formulated in conventional manner.

[0154] For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g. gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

[0155] The compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.

[0156] The compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides.

[0157] In addition to the formulations described previously, the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.

[0158] The compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may for example comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration.

6. EXAMPLE

Genetic and Physical Mapping of the bg Gene

[0159] The Example presented in this Section describes genetic mapping of the murine bg locus into a minimal genetic interval of 0.41 cM+/−0.1 cM on murine chromosome 13. Physical mapping of this minimal bg genetic interval is established herein to be approximately 1 Mb.

6.1 Material and Methods

[0160] Mouse crosses segregating beige. Multiple strain crosses were established to maximize inter strain variation in order to facilitate detection of polymorphisms of mapping markers. These included i) (C57BL/6J-bgJ X DBA/2J) X C57BL/6J-bgJ; ii) (DBA/2 Co-bg8J X C57BL/6J) X DBA/2 Co- bg8J; iii) (C3H/HeJ-bg2J X CAST/Ei) X C3H/HeJ-bg2J; iv) (C57BL/6J-bgJ X CAST/Ei) X C57BL/6J-bgJ; v) (DBA/2 Co- b8J X CAST/Ei) X DBA/2 Co- bg8J. The offspring of each of these backcrosses were analyzed, by coat color, for their bg genotype. Genomic DNA was made from a tail flip from each and analyzed for multiple simple sequence length repeat polymorphisms (SSLP). Not all strain combinations were polymorphic for all markers. Additional loci, Nidogen (Nid) and Ras like protein1 (Rasl1) were also genotyped in mice from crosses utilizing CAST/Ei. CAST/Ei vs inbred strain polymorphisms were detected using Single Stranded Conformational polymorphism (SSCP). The primers used for Nid were; forward 5′-CAGTGGAATGACCACCAGGCC-3′ and reverse 5′-GTTGCAGGCATGTACCACTAC-3′ (from mouse cDNA sequence, NCBI GenInfo ID: 53383) The Rasl1 primers were: forward 5′-TATGAACCTACCAAAGCAGAC-3′ and reverse 5′ACTTCGGAAGTAGTTGTCTC (from rat RALA cDNA sequence, GenBank Accession: L19698). The PCR amplification conditions were 94° C. for 2 minutes, 0.15 U of AmpliTaq was added for a hot start, followed by 30 cycles of 94° C. for 40 secs, 55° C. for 50 secs, 72° C. for 30 secs. The products were run on either a nondenaturing 8% acrylamide gel at 45 W, room temperature for 3 hours, for SSLP analysis or, for SSCP analysis, on a 10% acrylamide gel run at 20 W, 4° C. for 2.5 hours. Both types of gel were stained, post running, with SYBR Green I and scanned on an MD Fluorimager.

[0161] A linkage map of all loci, including bg was constructed, manually, for proximal MMU Chr 13 by minimizing double and multiple cross overs.

[0162] Interspecific backcross mapping. One hundred and eighty eight (C57BL/6J X Mus spretus) X C57BL/6J backcross mice were generated and genomic DNA was prepared to create a BSB mapping panel. A framework map was established using 80 previously mapped SSLP markers which encompassed each chromosome. The conditions used for SSLP analysis were as described above. Linkage maps were constructed using Map manager v2.6.5 (Manley, K. F., 1993, Mammalian Genome 4:303-313).

[0163] Additional loci, Nid, Rasl1, Ryanodine receptor 2, (Ryr2) and Neutrophil oxidase factor 2 -related sequence, (Ncf2-rs), were also placed on the Chr 13 map using SSCP as each gave a C57BL/6J vs Mus spretus polymorphism. Nid. Rasl, were typed as described above. Ryr2 was analyzed by SSCP using the following primers, (from mouse cDNA sequence, NCBI GenInfo ID: 516278): forward 5′-CAAAGAAAGCCCTCAGAAAC-3′ and reverse 5′-AAAGAGGAAAACCCAAGACT-3′. Ncf2-rs was also analyzed by SSCP using the following primers (designed from human cDNA sequence, GenBank Accession No. U00776): 1 forward 5′-CAAAAACAAGACACCCAAGT-3′ and 3 reverse 5′-TGTGGAATTGAGTGTTGTAG-3′.

[0164] Physical map of bg minimal interval. The Whitehead mouse YAC library (Research Genetics; Huntsville, Ala.) was screened using SSLP markers including D13Mit173, D13Mit44, D13Mit305 using the PCR conditions described above. The YAC end clones were isolated according to standard-methods. The YAC end clones were sequenced on an ABI sequencer. PCR primers from each unique end clone were designed, and used to map the end clone back to the mouse genome on the BSB map to check for chimeric YAC's. Those ends that mapped to the correct region of MMU Chr 13 were subsequently used in further rounds of YAC library screening. Cross addressing of the various SSLP markers and YAC end clones allowed a full YAC contig across the bg minimal genetic interval to be established. BACs were also isolated across the physical region using markers from the region.

[0165] In order to size the YACS, yeast genomic DNA was prepared according to the New England Biolabs Imbed procedure. Contour clamped homogeneous electric field (CHEF) electrophoresis was carried out using a CHEF MAPPER electrophoresis apparatus (Bio-Rad Laboratories, Inc., Hercules, Calif.) for 28 hours on a 1% agarose gel with an electric field gradient of 6V/cm at 14° C. and a pulse time of 12.55 sec.

6.2 Results

[0166] The mapping procedures described in Section 6.1, above, and depicted in FIG. 1, yielded a genetic map with gave a minimal genetic interval for the ha locus of 0.41±0.1 cM. The data giving this result are summarized herein.

[0167] The proximal interval, between bg and D13Mit173, was 2/690 recombinants which was 0.14±0.1 cM. The distal interval, between bg and D13Mit305, was 8/1496 recombinants which was 0.27±0.1 cM. The non-recombinant marker SSLP marker D13Mit44 was typed in 690 animals giving an upper genetic distance (at the 95% confidence limit) between bg and D13Mit44 of 0.4 cM.

[0168] The homologous genes Nid, which maps to human Chr 1q43, and Rasl, which maps to human Chr 7p, were also placed on the bg genetic map. Nid was non-recombinant in 690 mice putting it within (at the 95% confidence limit) 0.4 cM of bg. Rasl mapped 0.72 cM distal of bg. The homologous gene Ryr2, which maps to human Chr 1q43-q42, was not mapped in the bg segregating crosses as no polymorphism between any of the strains used was found but it was mapped in the BSB mapping panel. By inference from the BSB map, Ryr2 maps within 1.6 cM of Nid (95% confidence limit). The simplest interpretation of the mapping of homologous genes to the map of proximal mouse Chr 13 around the bg region was that bg is likely to fall within the 1q43 syntenic region on the human genetic map.

[0169] The mapping of the locus referred to herein as Ncf2-rs was done using primers designed to amplify human cDNA sequence. Ncf2 has been mapped to human Chr 1cen-q32 and to mouse chromosome 1 (Francke U., 1990, Am. J. Hum. Genet. 47:483-92). The primers designed produced a PCR fragment which mapped to the bg region of Chr13.

[0170] The YAC and BAC coverage across the minimal bg genetic interval gives an estimated physical distance of approximately 1 Mb.

7. EXAMPLE cl YAC Complementation of the Beige Mutation

[0171] The experiments presented in this Section describe results which have localized the murine bg gene to a specific interval on murine chromosome 13. Specifically, a complementation-based strategy was utilized to identify two overlapping murine yeast artificial chromosomes (YACs) capable of complementing the murine bg mutation. One of these YACs was tested, via cell fusion studies, and found to be capable of complementing Aleutian mink and human Chediak-Higashi syndrome (CHS) mutant phenotypes, thus strongly suggesting that the mouse, human and mink mutant phenotypes are caused by defects in homologous genes.

7.1. Materials and Methods

[0172] Isolation and Characterization of YACS. The primers F:5′-CCAGCCACAGAATACCATCC-3′ and R:5′-GGACATACTCTGCTGCCATC-3′ specific for Nidogen (Nid) amino terminal sequences were used to screen the Princeton and Whitehead mouse YAC libraries using the following conditions on an Idaho Technologies Thermal Cycler: 20 sec. 94° hot start, 94° 0 sec./50° 0 sec./72° 15 sec. for 35 cycles. To identify the positive pools, the PCR products were separated on 2% agarose gels, transferred to Nytran membranes and probed by standard hybridization techniques. This screen resulted in the isolation of YACs 195.A8, 151.H1, C9.E7, and C96.G11. YAC 113.G6 was isolated from the Whitehead library using the primers: F:5′-ACCCCAGAACTTGAGAAATAG-3′ and R:5′-TGCTGAGGTGATAGGTTTATG-3′ specific for the Sequence Tagged Site (STS) 195.A8-right end (R) using the above mentioned PCR conditions. Yeast plugs were prepared according to Gnirke et al. (Gnirke, A. et al., 1993, Genomics 15:659-667). YAC DNA was analyzed by Southern blots or PCR to determine STS and Nid content. The sizes of the YACs were determined using pulsed-field gel-electrophoresis on a Bio-Rad CHEF DRII, with a pulse time of 10 to 100 seconds.

[0173] YAC End Isolation. One or both end fragments of YACs C9.E7, 195.A8 and 151.H1 were isolated and used to create STS. The end fragments were isolated using inverse PCR according to Joslyn et al. (Joslyn, G., et al., 1991, Cell 66:601-613). Each inverse PCR product was either directly sequenced using the M13-UP and RP sites engineered into the primers, or cloned using Invitrogen's TA cloning kit, and then sequenced using the T7 and SP6 sequencing primers. PCR primers specific for each unique end were created and tested on mouse genomic DNA to determine whether they amplified the expected size product.

[0174] YAC End Analysis. Each YAC end was tested to determine whether it was derived from mouse chromosome 13. For YAC end analysis, all STS were tested against a panel of mouse/hamster somatic cell hybrids, some of which harbored mouse chromosome 13 (Kozak, C. A. et al., 1975, Som. Cell Gen. 1:371-382). Each hybrid was tested with the dinucleotide repeat markers D13MIT44 and 173 from Research Genetics specific for the bg/Nid region of mouse chromosome 13 before use to determine whether the relevant region of mouse chromosome 13 was present. Southern blots of these hybrids were then probed with YAC end STS to determine if these markers were present in the mouse chromosome 13 positive hybrids. In some instances, YAC end STS were assayed by PCR. The ends of YAC 195.A8 were further analyzed by genetic mapping onto a panel of interspecific backcrossed beige mice (Jenkins, N. A. et al., 1991, Genomics 9:401-403). Genomic DNA blots of mice from this panel were prepared and hybridized with the single copy STS 195.A8-R and 195.A8-left end (L). The map positions of these two markers was then determined using the program Map Manager v2.6.3 (Manley, K. F., 1993, Mammalian Genome 4:303-313). This analysis placed these two markers on the same genetic interval as bg and Nid.

[0175] Spheroplast fusion and YAC microinjection. All YACs were “retrofitted” with the neomycin resistance gene using the vector pRV1 and homologous recombination in yeast as described by Srivastava and Schlessinger (Srivastava, A. & Schlessinger, D., 1991, Gene 103:53-59). This protocol introduces the neomycin resistance gene and the LYS2 gene into the URA3 gene present in the YAC “right” arm. Spheroplast fusion using retrofitted YACs was performed according to Huxley et al. (Huxley, C. et al., 1991, Genomics 9:742-75D) with the following modifications. A 100 ml culture of yeast was grown to an OD600 of 3-4 in SD -Lys -Trp. Spheroplasts were prepared using Oxalyticase (Enzogenetics, Oregon) and resuspended in two milliliters of STC (1M Sorbitol, 10 mM CaCl2, 10 mM Tris pH8). bg mouse fibroblasts (3×106 MCHSF2) were fused to 0.5 ml of the spheroplast preparation in 0.4 mls of 50% PEG/10 mM CaCl2 (Boehringer Mannheim) for 100, 150 and 200 seconds. The fusion reaction, was diluted with 4.0 mls of serum-free Dulbecco's, incubated at room temperature for twenty minutes, centrifuged at long and plated into four 100 mm plates. Microinjections were performed according to Gnirke et al. (Gnirke, A. et al., 1993, Genomics 15:659-667). Twenty-four hours after fusion or microinjection, the cells were washed twice with PBS and incubated with Dulbecco's minimal essential media containing 10% FCS and 400-500 &mgr;g/ml G418 for three to four weeks. Individual colonies were isolated and expanded to at least 1×106 cells. Genomic DNA was isolated from these colonies using Qiagen Genomic DNA Tips and the DNA used for Southern or PCR analysis. YAC vector sequences which are immediately adjacent to the genomic insert were assayed using PCR primers specific for YAC “left” and “right” arms (Peterson, K. R. et al., 1993, Proc. Natl, Acad. Sci. U.S.A. 90:7593-7597), or by Southern blotting using the YAC vector as a probe. For Southern blotting, ten &mgr;g of fibroblast DNA or 2 &mgr;g of yeast DNA was cut with HindIII, run on a 0.8% agarose gel, and then transferred to a Nytran membrane. This membrane was then hybridized with the 9.5 kb gel purified HindIII fragment of the retrofitting vector pRV1.

[0176] Fluorescent-Microscopy. Cells were examined for lysosomal morphology using fluorescent labeling of lysosomes (Perou, C. M. & Kaplan, J., 1993, Som. Cell Mol. Gen. 19:459-468). Briefly, lysosomes were labeled by incubating cells overnight in Dulbecco's plus 10% FCS with 0.5 mg/ml Lucifer Yellow-CH, followed by two washes in culture medium, and a final 2-6 hour chase in medium alone. Lysosomes were visualized on live cells using standard fluorescent microscopy techniques.

[0177] Somatic Cell Fusions. Aleutian mink or Human CHS (GM02075A) fibroblast lysosomes were labeled with Lucifer Yellow-CH, while the complemented bg mouse fibroblast colony 195-4 lysosomes was separately labeled with dextran-Texas Red. The two cell populations were trypsinized, mixed together, and fused to one another using UV-inactivated Sendai virus (Perou, C. M. & Kaplan, J., 1993, Som. Cell Mol. Gen. 19:459-468; Schlegel, R. S. & Rechsteiner, M. C., 1975, Cell 5:371-379). The cells were plated and examined twenty-four hours later using fluorescent microscopy. Two photographs of the same field were taken, one to visualize the Lucifer Yellow fluorescence and a second to visualize the dextran-Texas Red. A heterokaryon could be identified by the presence of both dyes within ail lysosomes of one cell.

7.2. Results

[0178] The experiments reported herein describe, first, the isolation and characterization of murine YACs lying within the physical region in which the bg gene must reside. Further, a complementation-based strategy is utilized to identify which of the isolated YACs were able to complement the bg phenotype, thus significantly narrowing the region within which the bg gene must be located. Third, one of these murine YACs was tested, via cell fusion studies, and found to be capable of complementing the bg phenotype in cells of other species, namely those of Aleutian mink and human.

[0179] YAC Characterization. As discussed in Section 6, above, and in Jenkins et al. (Jenkins, N. A. et al., 1991, Genomics 9:401-403) the bg gene is located near Nid on chromosome 13. PCR primers specific for Nid were, therefore, utilized to isolate YACs from the bg/Nid region (FIG. 2A). The Princeton and Whitehead mouse YAC libraries were screened, yielding two YACs from each library. Inverse PCR was used to isolate YAC ends, which were sequenced and used to create STS. Each isolated YAC end was tested to determine if it was derived from mouse chromosome 13. Some of these STS were then used to develop a YAC contig across the bg interval of the four Nid positive YACs isolated, 151.H1 and C96.G11 were determined to be unstable and were not used. YACs C9.E7 and 195.A8 were both derived from chromosome 13, mapped to the bg interval, and remained stable with time. A fifth YAC, 113.G6, was isolated from the Whitehead Library using the STS 195.A8-R. It was determined that 113.G6 was chimeric, but had significant overlap (500 kb) with 195.A8. For all subsequent experiments, the retrofitted derivatives of YACs C9.E7, 195.A8, and 113.G6 were used.

[0180] Introduction of YACs into bg Mouse Fibroblasts. Retrofitted YACs were introduced by spheroplast fusion (Huxley, C. et al., 1991, Genomics 9:742-750) or microinjection (Gnirke, A. et al., 1993, Genomics 15:659-667) into fibroblasts derived from a C57BL/6J beige mouse (Perou, C. M. & Kaplan, J., 1993, Som. Cell Mol. Gen. 19:459-468). These cells retained the bg phenotype of abnormally large lysosomes with a clustered perinuclear distribution. This phenotype could be corrected by somatic cell fusion with normal cells (Perou, C. M. & Kaplan J., 1993, Som. Cell Mol. Gen. 19:459-468). Mutant cells containing YACs were selected for resistance to the neomycin analogue G418, and colonies were examined for lysosomal distribution and morphology by fluorescent microscopy using Lucifer Yellow labeling.

[0181] Seven G418 resistant colonies from several independent spheroplast fusions using YAC 195.A8 were obtained. The efficacy of YAC transfer using spheroplast fusion was extremely low as determined by G418-resistance. A frequency of colony formation of 10−7 was calculated. Southern and PCR analyses (Peterson, K. R. et al., 1993, Proc. Natl, Acad. Sci. U.S.A. 90:7593-7597) confirmed that all resistant colonies contained YAC “right” arm vector sequences. Only three of the seven colonies, however, contained YAC “left” arm vector sequences, indicating that the other four colonies contained only a fragment of the YAC. Of the seven colonies, five showed a complemented phenotype (FIG. 3B). These five colonies included the three complete YAC colonies and two of the fragmented YACs. Complemented cells showed dramatically smaller lysosomes than the parental bg cells (FIG. 3A and 3C). Other features indicating a corrected phenotype included lysosomes which were no longer clustered in the perinuclear region, and the-disappearance of tubular lysosomes. Tubular lysosomes are frequently seen in macrophages but are not observed in normal fibroblasts. Tubular lysosomes are seen, however, in bg mouse and Aleutian mink fibroblasts.

[0182] YAC 113.G6 was introduced into murine bg fibroblasts using spheroplast fusion and two independent colonies were obtained. One colony was complemented and contained sequences from both YAC arms. The other colony was not complemented and contained only a fragmented copy of the YAC. YAC C9.E7 was microinjected into the bg mouse cell line and thirty independent colonies were obtained, five of which contained both YAC vector arms as determined by PCR. All of these colonies retained the bg phenotype. Cells resistant to G418 due to YAC introduction, either uncomplemented cells carrying fragmented YACs or C9.E7 microinjected cells, showed no complemented features regardless of the concentration of G418 employed.

[0183] In the complemented colonies isolated using a G418 concentration of 400-500 &mgr;g/ml, it was observed that not all cells showed the complemented phenotype. Some colonies appeared to contain a mixture of bg and complemented cells (FIG. 3B). Two possibilities were considered. First, the colonies, as removed from the plate, might contain a mixture of G418-resistant complemented cells and G418-resistant bg cells. Second, the YAC might be unstable and, at the concentration of G418 employed, some cells may lose the YAC and revert to the bg phenotype. To distinguish between these possibilities, the cell line 195-4 was incubated in 800 &mgr;g/ml G418 and lysosomal morphology examined after 10 days. Examination of multiple fields and several hundred cells revealed-very few (<1%) bg appearing cells (FIG. 3C). When these complemented cells were incubated in the absence of G418 there was a time-dependent return to the bg phenotype. Seven days after the removal of G418, approximately 1.0% of the cells showed the mutant phenotype, but after thirty days greater than 30% of the cells showed the bg phenotype (FIG. 3D). These results demonstrate that complementation of the mutant phenotype was YAC-dependent.

[0184] The fact that not all YACs complement, and that not all spheroplast fusion generated colonies were complemented, suggests that the act of introducing these YACs along with yeast. DNA does not cause the reversion of the bg phenotype. Further, the fact that only certain fragmented YAC 195.A8 or 113.G6 YAC molecules failed to correct the phenotype, suggests that fragmented YACs can be utilized as part of a strategy to localize the relevant gene.

[0185] Complementation of the CHS Defect in Other Species by a Murine YAC. To analyze the nature of defective genes in different species exhibiting bg phenotypes, both complemented and uncomplemented 195.A8 YAC containing bg cells were fused with cultured Aleutian mink or human CHS derived cells (Perou, C. M. & Kaplan, J., 1993, Som. Cell Mol. Gen. 19:459-4682). When Aleutian mink cells were the recipient cell line, complementation occurred only when the complemented ha mouse cell lines were used. Identical results were obtained with the human CHS fibroblast cell line GM02075A. It was necessary to fuse complemented murine cells to mink and human cells as neither mink nor human cells will accept YACs using the spheroplast fusion or microinjection protocols. These results strongly support the hypothesis that a similar gene (or genes) is responsible for the Chediak phenotype.

[0186] It was found that the choice of cell lines was the most important parameter in determining the efficacy of YAC transfer. No G418-resistant colonies were ever obtained using primary human, mouse, or mink fibroblasts as the recipients. Colonies were obtained using the long term cultured bg mouse cell line MCHSF2. A ten to twenty fold increase in the frequency of transformants was obtained using mouse L-cells. These results suggest that increased chromosome instability resulting from long term culture may contribute to increased transformation efficiency.

8. EXAMPLE

Positional Cloning of a Candidate Beige Gene

[0187] The Example presented in this Section describes the cloning of a gene, referred to here as the 22B/30B gene, which represents a candidate murine beige (bg) gene. Extending the studies described in Sections 6 and 7, above, the 22B/30B gene was identified via a refinement of the YAC mapping data presented above, couple with a positional cloning strategy. Characterization of the 22B/30B gene indicated that the gene produces an approximately 12-14 kb mRNA that encodes a novel protein exhibiting strong nucleotide homology to multiple expressed sequence tags (ESTs), including human ESTS.

8.1. Material and Methods

[0188] YAC Characterization. The Princeton and Whitehead mouse YAC libraries were screened by PCR with primers specific for the right end sequence of YAC 195.A8, as described above. This screen resulted in the isolation of two additional YACS, 137.A10 and B27.F7. An additional YAC from this region was isolated from the Princeton library using primers from the end sequences of the cDNA clone 22B, described in Section 8, below. The F primer was 5′-ATTGGCTAGTGTGTGCAGAC-3′ and the R primer was 5′-GAAGCAGATGACTGAGCAGA-3′. PCR reactions were performed on an Idaho Technologies Thermal Cycler under the following conditions: 20 sec. 94° C. hot start, 94° C. 0 sec./55° C. 0 sec./72° C. 30 sec. for 30 cycles.

[0189] All other YAC techniques were as described, above, in Section 7.1.

[0190] Isolation of cDNAs and Preparation of Plugs. Agarose blocks containing yeast chromosomal and YAC 195.A8 DNA were prepared as described in Gnirke et al (Gnirke, A. et al., 1993, Genomics 15:659-667), loaded in a 1%, 0.5×TBE gel and electrophoresed in a Bio-Rad DRII clamped homogeneous electric field (CHEF) apparatus (Bio-Rad Laboratories, Inc., Hercules, Calif.) at 200 V with a constant pulse time of 60 sec. for 24 hrs. The YAC was excised and purified using the GeneClean II Kit according to manufacturers instructions (Bio 101, Inc., La Jolla, Calif.). Gel-purified YAC DNA was radiolabelled with 32P-dCTP by random priming. The hybridization probe was pre-competed with 100 &mgr;g of sonicated genomic mouse DNA, 50 &mgr;g of mouse COT-1 DNA (GIBCO BRL, Gaithersburg, Md.) and 20 &mgr;g of sonicated pYAC55 DNA (Sigma, St. Louis, Mo.) for 2 hrs at 65° C. Filters containing plaques from a C57BL/6J mouse E16.5 cDNA library (Stratagene, La Jolla, Calif.) were prehybridized at 65° C. for 6-8 hrs in RapidHyb buffer (Amersham, Arlington Heights, Ill.) containing 100 &mgr;g/ml sonicated mouse genomic DNA, 4 &mgr;g/ml COT-1 DNA and 2 &mgr;g/ml sonicated pYAC55 DNA. Hybridization proceeded overnight at 65° C. Filters were washed to 0.1×SSC at 65° C. Clones positive after a secondary screen were recovered as phagemids.

[0191] Genomic DNA Isolation and Southern Blots. High molecular weight mouse DNA for Southern Blots and PCR analysis was either purchased from the Jackson Labs (Bar Harbour, Me.) or isolated using a Qiagen tip 2500 (Qiagen, Inc., Chatsworth, Calif.). Southern blots were prepared and hybridized according to (Jenkins, N. A. et al., 1982, J. Virol. 43:26-36), exposed to Fuji Imaging Plates, Type BAS-IIIS and visualized using a Fujix Bas 1000 Phosphoimager (Fuji Film I & I, Fuji Medical Systems U.S.A., Inc., Stamford, Conn.).

[0192] RNA Isolation, Northern Blots. Total RNA was isolated from various mouse tissues and cultured mouse and human melanoma cells using the RNA STAT-60 reagent (Tel-Test “B”, Inc., Friendswood, Tex.) according to manufacturer's instructions. For Northern blot preparations, 25 &mgr;g of this RNA was run on a 1.5% denaturing gel and transferred overnight onto Zeta pore membrane (CUNO, Inc., Meriden, Conn.) in 10×SSC. Filters were hybridized with a gel purified 811 bp HindIII+Pst I fragment from the clone 30B that was radiolabeled with 32P-dCTP by random priming. Hybridization was performed at 65° C. overnight in QuikHybe Hybridization Solution (Stratagene, La Jolla, Calif.). Filters were washed to 0.1×SSC at 65° C. and visualized by X-ray film autoradiography.

8.2. Results

[0193] YAC characterization. The minimal bg interval was refined by further in vitro complementation of bg murine fibroblasts with additional YACS (FIG. 2B). First, it was demonstrated that YAC151.H1, which contains restriction fragments in common with YAC195.A8, as defined by fingerprinting with COT-1 DNA, was not capable of complementing bg. Furthermore, YAC137.A10 which is nearly identical to that of YAC 113.G6, also failed to complement the bg phenotype. These studies, therefore, demonstrate that the minimal bg region must lie-between the proximal end of YAC137.A10 and the distal end of YAC151.H1.

[0194] Isolation of candidate genes in the bg minimal region. The complementing YAC195.A8 (See Section 7, above) was gel purified, radiolabelled and used to isolate clones from an E16.5 day mouse embryo cDNA library. Forty five clones were isolated. Based on sequence analysis and mapping to the YAC-defined physical map, six genes were defined.

[0195] Of particular note was a gene, referred to herein as the 22B/30B gene, defined by two cDNA clones, 30B and 22B. These clones had 447 bp of overlap sequence, with 30B extending more 5′ than 22B, and were located within the region predicted to contain the bg gene. In order to determine whether the cDNA clones 22B and 30B mapped physically to the interval predicted to contain the bg gene, the clones were used as probes against restriction enzyme digested YAC DNA. The non-complementing YAC137.A10 lacked two HindIII 30B hybridizing bands that were present in complementing YAC113.G8. Likewise, YAC151H.1 lacked some HindIII bands hybridizing with 22B.

[0196] Based upon the complementation data, it was predicted that the complete bg gene would lie in the region of overlap between YACs 113.G6 and 195.A8, but would be disrupted or absent from the non-complementing YACs 137.A10 and 151.H1. This was the pattern observed for the 22B/30B gene, making it a candidate for the bg gene.

[0197] Sequence of 22B/30B gene. Sequencing of the two overlapping cDNA clones, 22B and 30B, of the putative bg gene totaled 6831 bp of contiguous sequence (FIG. 4; SEQ ID NO:1). 6559 bp of this was open reading frame followed by a stop codon at nucleotide 6560 and 269 bp of the 3′ untranslated region (with 30B present 5′ of this contiguous sequence relative to 22B).

[0198] The 22B/30B protein sequence predicted from the 22B/30B nucleotide sequence is 2186 amino acids and encodes a novel protein (FIG. 4; SEQ ID NO:2). A BLASTX (1993, Nature Genetics 3:266-272) search with the 22B/30B protein amino acid sequence did, however, identify significant homologies to several sequences. Such sequences included an anonymous S. cerievisiae protein, YCR032w, encoded by a 7 kb mRNA, two C. elegans novel proteins, T01H10.8 and F10F2.1 and a human gene, cell division control protein 4-related protein, CDC4L. Amino acid residues 1520-1807 of the 22B/30B protein sequence exhibited the highest level of amino acid conservation. Within this region, the S. cerievisiae and C. elegans proteins showed 50% identity and 75% similarity to murine 22B/30B. The homology to the human CDC4L protein spanned a shorter segment (22B/30B amino acid residues 1675-1806), but again showed 50% identity.

[0199] A known protein motif was found within the 22B/30B amino acid sequence. Specifically, a WD40 or G protein-beta subunit repeat motif (van der Voorn, L. & Ploegh, H. L., 1992, FEBS Lett. 307:131-134) was found to be located at amino acid residue 2016-2030. This motif was originally identified in the &bgr;-subunit of the G-protein transducin (Duronio, R. J. et a., 1992, Proteins 13:41-56), and is thought to be involved in mediating protein-protein interactions (Wang, D. S. et al., 1994, Biochem. Biophys. Res. Comm. 203:29-35). None of the proteins found to be homologous to the 22B/30B protein sequence contain such a motif.

[0200] Comparison of the 22B/30B DNA sequence to the dbEST database identified homologies to ESTs from two human cDNA libraries. Specifically, 22B/30B nucleotides 725-942 were 82% identical to human cDNA clone H51623 isolated from a fetal liver and spleen cDNA library, 22B/30B nucleotides 1530-1596 were 88% identical and 22B/30B nucleotides 1596-1842 were 74% identical to the human cDNA clone H50968 isolated from the same fetal cDNA library. 22B/30B nucleotides 1096-1269 were 89% identical to the cDNA clone Z21358 isolated from an adult human testis library. 22B/30B nucleotides 1092-1164 were 87% identical and nucleotides 1165-1302 were 91% identical to the human cDNA clone Z21296 isolated from the same testis cDNA library. In summary, the 22B/30B sequence from approximately nucleotide 725 to nucleotide 1842 appeared to be highly homologous at the nucleotide level to one or more human gene sequences.

[0201] Expression of the 22B/30B gene. PCR analysis from reverse transcribed murine mRNA was used for detecting expression of the 22B/30B gene. Such an analysis indicated that the 22B/30B message was expressed in each of the tissues tested, namely liver, spleen, kidney, thymus, muscle, fat, heart, lung, stomach, pancreas and cultured fibroblasts. Using an 811 bp probe from the most 51 end of the available cDNA 22B/30B sequence, a Northern blot of mRNA from two human melanoma cell lines, WM-115 and WM266-4 and from the mouse B16 melanoma cell line showed hybridization to an approximately 12-14 kb message. It should be noted that the 811 bp probe used overlapped with the portion of the 22B/30B sequence discussed above that exhibits 82% identity to a human EST.

9. EXAMPLE

Identification of the Beige Gene Via Beige Mutation Detection

[0202] The Example presented herein describes the successful identification of the bg gene, the homolog of the gene responsible for the human Chediak-Higashi syndrome (CHS), via the sequencing of two independent mutant bg alleles. The mutation detection analysis revealed that the bg gene corresponds to the 22B/30B gene described in Section 8, above.

9.1. Material and Methods

[0203] Southern blot/Genomic DNA isolation. The procedures utilized were as described in Section 8.1, above.

[0204] RT-PCR. RNA was isolated as described, above, in Section 8.1. Reverse transcription-polymerase chain reactions (RT-PCR) were carried out as follows: briefly, 0.5 &mgr;g of total RNA was reverse transcribed into cDNA using equal concentrations of random and oligo(dT)15 primers and AMV reverse transcriptase (Promega Corp., Madison, Wis.) in a final volume of 200 &mgr;l. One &mgr;l of each reaction was amplified with 0.25 &mgr;M of each of the appropriate primers. The primers were as follows: 22B-5F- 2 22B-5F-5′-TCTTCTTGTCCTGCCTGATGCT-3′; 22B-D11-5′-GTGCTTCACTTCCTCCAGATC-3′; 22B-D6-5′-GCCTCATTCCAGCGAAGC-3′; 22B-D10-5′-CTGGATAGCAGGTGATGGGTGGTTA-3′.

[0205] Amplifications were carried out in a final volume of 25 &mgr;l in 1×PCR buffer containing 1.5 mM MgCl2, 0.5 Units Ampli Taq polymerase (Perkin-Elmer-Cetus). After an initial denaturation step at 94° C. for 2 mins, samples were subjected to 35 cycles of 40 sec at 94° C., 50 sec at 57° C., and 2 mins at 72° C. Following a 10 mins final extension at 72° C., samples were stored at 4° C. PCR products were separated by electrophoresis through 2%, 1×TBE agarose gels.

[0206] PCR: Mouse genomic DNA (C57BL/6J, C57BL/6J-bg/bg, Satin/Beige-bg/bg DNA) was amplified using the following primers: 228F: 5′-TGCTGTGGATTATATGAACTC-3′ and 228R: 5′-GGTCTCTATTAGTCCGAGAAC-3′. Amplification parameters were as follows: 2 minutes hot start 94° C., 94° C. 30 seconds/52° C. 30 seconds/ 72° C. 4 minutes, for 30 cycles on a Perkin-Elmer DNA Thermal-Cycler.

9.2 Results

[0207] bg gene mutation detection. Described herein are bg gene mutation studies which reveal that the gene corresponding to the 22B/30B gene, described above, in Section 8, corresponds to the murine bg gene. Specifically, nucleotide defects within two bg mutant alleles are demonstrated to lie within the 22B/30B region and to result in the production of C terminally truncated proteins.

[0208] The original bg mutation arose in a radiation experiment at the Oak Ridge National Laboratory. Hence it was probably radiation induced and was either on a chromosome originating from the C3H/R1 or the 101/R1 inbred strains of mice. Because the original bg mutation was radiation-induced, it was possible that the mutation could be visible via Southern blot analysis. There have been many subsequent re-mutations of the mouse bg gene, all of which have arisen spontaneously. Some of these are extinct with no surviving tissues or DNA. For others, for example C57BL-bg10J and C57BL-bg11J although the mutation is extinct there is DNA available (Jackson Laboratories), and for others, the mutation is still available as a live mutant stock, e.g. SJL-bg, C57BL-bgJ, C3H/HeJ-bg2J, and DBA/2J-CO-bg8J. Southern blot analysis of these multiple bg alleles and their appropriate normal controls showed no polymorphic bands for probes from either the 5′ or 3′ regions of the 22B/30B gene sequence, although a probe, 22B/30B nucleotides 6489-6719, did make it possible to determine that the original bg allele arose on a C3H-like chromosome, not a 101/R1 derived chromosome. In contrast, when a 510 bp fragment, 22B/30B nucleotides 1618-2127, was used as a probe, the original mutant bg allele showed altered bands for 7 out of 9 enzymes (FIG. 5A-5D).

[0209] PCR primers, as described above, in Section 9.1, were designed which surrounded and spanned the 510 bp region and were used to amplify genomic DNA and cDNA. One primer set, designated 228F and R, amplified a 2 kb genomic fragment from C57BL/6J but amplified a 3 kb genomic fragment from the strain carrying the original bg allele. A similar set of primers, 22B-5F and 22B-11, was used to amplify cDNA prepared from the kidneys of C57BL/6J, C3H/HeJ and SJL/J-bg. A single band of 312 bp was detected in both C57BL/6J and C3H/HeJ. cDNA from the SJL/J-bg, mouse, however, produced two bands, 428 bp and 637 bp.

[0210] Both the RT-PCR products, as well as the genomic DNA PCR products were isolated and directly sequenced using standard procedures. Sequencing of the amplified products revealed that the bg mutation was located within the 22B/30B gene. Specifically, analysis of the amplified sequences revealed that the increased size of the genomic product from the bg allele was the result of an incomplete LINE 1 element (Burton, F. H. et al., 1986, J. Mol. Biol. 187:291-304) insertion into an intron contained within the 30B/22B gene's genomic DNA. As this element contained adventitious splice donor and acceptor sites, two aberrant mRNAs were created that each result in a frame shift. The 428 bp bg RT-PCR product had a 116 bp LINE 1 insertion between 22B/30B nucleotides 2235 and 2236, while analysis of the larger product demonstrated a 325 bp LINE 1 insertion at this same location. Both of these two LINE 1 insertions results in the introduction of stop codons and in a 22B/30B protein product that is truncated by 1442 amino acids. See FIG. 6 for a diagram depicting the location of these insertions.

[0211] Analysis of another bg allele, bg8J, by sequencing of an RT-PCR product produced using primers 22B-D6 and 22B-D10, identified a C to T base change creating a stop codon at 22B/30B bp 2027. The mutation resulted in the production of a truncated 22B/30B protein missing the last 1511 amino acids.

[0212] It should be noted that the truncated proteins produced by each of the bg (22B/30B) mutant alleles lack the amino acid sequence homologous to S. cerevisiae, C. elegans and human CDC4L genes and also delete the putative WD40 motif (described, above, in Section 8).

[0213] In summary, two independent bg gene mutations were revealed to lie within the sequence of the 22B/30B gene, thus presenting compelling evidence identifying the 22B/30B gene to, in fact, correspond the bg gene.

10. EXAMPLE

Identification and Characterization of the Human bg Gene

[0214] The Example presented herein describes the successful identification and characterization of cDNA molecules corresponding to the human beige (bg) gene. Characterization of the isolated cDNA molecules revealed that the human bg gene undergoes alternative splicing, yielding long (putative full length) and short forms of bg transcripts and bg gene products, as described below.

10.1. Materials and Methods

[0215] cDNA cloning. A human retina &lgr;gt10 library (Cat. No. HL1132a; Clontech, Palo Alto Calif.) was screened with a mixture of three DNA fragments isolated from mouse beige clones. They were, in order from 5′ to 3′, 30B (bp 82-921 of FIG. 4), 22B (bp 1650-2160 of FIG. 4), and K2+K5 (bp 6520-6750 of FIG. 4).

[0216] The three probes were labeled with 32P by random priming and hybridized with filters representing 106 clones overnight at 42° C. in Church's buffer (7% SDS, 250 mM NaHPO4, 2 &mgr;M EDTA, 1% BSA). The filters were washed in 2×SSC, 1% SDS at 42° C. Positive plaques were replated and treated in the same manner. Phage DNA was prepped by a standard plate lysate method. After digestion of the phage DNA with EcoRI, cDNA inserts were isolated and subcloned into pBluescript (Stratagene; La Jolla Calif.) for DNA sequencing. DNA sequencing was performed according to standard techniques.

[0217] cDNA identified in the above screening was used to probe a &lgr;gt10 human fetal liver library (Cat. No. HL3020a; Clontech, Palo Alto Calif.) and the human retina library described above. Filters representing 106 clones of each library were hybridized at 65° C. overnight with 32P labelled probe in Church's buffer and washed in 0.1×SSC, 0.1% SDS at 65° C. Positive plaques were replated and rescreened in the same manner. Phage DNA was prepared, and cDNA inserts were isolated and subcloned as described above.

10.2. Results

[0218] In order to identify the human bg gene, murine bg gene sequences were used to screen human cDNA libraries. Screening, phage isolation and details are presented in Section 10.1, above.

[0219] First, a murine bg sequences were used to probe a human retina cDNA library. This screen resulted in the identification of a phage containing a 2 kb cDNA insert (designated fvhx004). The cDNA insert was isolated and subcloned. The fvhx004 cDNA insert was then used to rescreen the human retina cDNA library and to screen a &lgr;gt10 human fetal liver library, as described in Section 10.1, above. This screen yielded two positive phage from the human fetal liver library. One phage contained a 4.4 kb cDNA insert (designated fvh1006) and the second contained a 6.3 kb cDNA insert (designated fvh1009). A 3 kb subclone of fvh1006 which overlapped the fvh1009 clone was designated fvh1006a. Additional subclones of fvh1006 were designated fvh1006b (a 1 kb sublcone) and fvh1006c (a 400 bp subclone). An additional positive phage was also isolated from the human retina library. This phage contained a 2 kb cDNA insert (designated fvhx003a). A 1.1 kb HindIII/EcoRV fragment from fvh1009 was used to rescreen the human retina library. This screen resulted in one positive phage containing a 1.6 kb insert, designated fvhx015.

[0220] The isolated clones were sequenced according to standard procedures. A database search using human bg nucleotide sequence revealed extensive homology to human cDNA clones H51623 (96% identity), Z21358 (99% identify) and Z21296 (97% identity), as indicated in parentheses. These clones were described in Section 9, above.

[0221] Comparison of the human bg sequence with that of mouse bg sequences revealed a 378 base pair region present in mouse sequence which was absent from the sequence obtained from the isolated human clones. PCR of both the retina and liver libraries with primers flanking this sequence, however, revealed that the sequence was present in both these libraries. Sequencing of the resultant PCR products, coupled with the sequence obtained from the isolated clones, produced what is referred to below as the “long” form of bg gene sequence, while the sequence of the isolated clones, alone, yielded what is referred to below as the “short” form of bg gene sequence.

[0222] FIG. 7 presents the long form (putative full length) human bg gene nucleic acid sequence. FIG. 7 further depicts the derived amino acid sequence encoded by the long form (putative full length) human bg gene nucleic acid sequence shown therein. As shown in FIG. 7, the predicted long form human bg gene product contains 3801 amino acid residues. As in the mouse bg gene product described in Section 8, above, the human bg gene product contains a WD40 or G protein-beta subunit repeat motif. In the long form human bg gene product this motif is present at amino acid residues 3694-4708.

[0223] FIG. 8 presents the short form human bg gene nucleic acid sequence. FIG. 8 further depicts the derived amino acid sequence encoded by the short form human bg gene nucleic acid sequence shown therein. As shown in FIG. 8, the predicted short form human bg gene product contains 3672 amino acid residues. It is missing base pairs 7544-7921 of the long form depicted in FIG. 7. The short form bg nucleic acid sequence retains the same frame as the long form throughout its length and encodes a bg gene product which is missing amino acid residues 2451-2577 of the long form depicted in FIG. 7. The WD40 sequence motif is present in the short form bg gene product at amino acid residues 3565-3579 depicted in FIG. 8.

[0224] The present invention is not to be limited in scope by the specific embodiments described herein, which are intended as single illustrations of individual aspects of the invention, and functionally equivalent methods and components are within the scope of the invention. Indeed, various modifications of the invention, in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and accompanying drawings. Such modifications are intended to fall within the scope of the appended claims.

Claims

1. An isolated nucleic acid molecule containing the nucleotide sequence of FIG. 4 (SEQ ID NO:1), FIG. 7 or FIG. 8.

2. An isolated nucleic acid molecule capable of complementing a bg mutation, having a nucleotide sequence that:

(a) encodes the amino acid sequence shown in FIG. 4, FIG. 7 or FIG. 8; or

(b) hybridizes under stringent conditions to the nucleotide sequence of (a) or to its complement.

3. A nucleotide vector containing the nucleotide sequence of claim 1 or 2.

4. An expression vector containing the nucleotide sequence of claim 1 or 2 in operative association with a nucleotide regulatory sequence that controls expression of the nucleotide sequence in a host cell.

5. The expression vector of claim 4, wherein said regulatory element is selected from the group consisting of the cytomegalovirus hCMV immediate early gene, the early or late promoters of SV40 adenovirus, the lac system, the trp system, the TAC system, the TRC system, the major operator and promoter regions of phage A, the control regions of fd coat protein, the promoter for 3-phosphoglycerate kinase, the promoters of acid phosphatase, and the promoters of the yeast &agr;-mating factors.

6. A genetically engineered host cell that contains the nucleotide sequence of claim 1 or 2.

7. A genetically engineered host cell that contains the nucleotide sequence of claim 1 or 2 in operative association with a nucleotide regulatory sequence that controls expression of the nucleotide sequence in the host cell.

8. An isolated bg protein.

9. The isolated bg protein of claim 8, wherein the protein has the amino acid sequence shown in FIG. 4, FIG. 7 or FIG. 8.

10. An antibody that immunospecifically binds the bg protein of claim 8.

11. A method for diagnosing intracellular vesicle disorders, in a mammal, comprising measuring bg gene expression in a patient sample.

12. The method of claim 11 in which expression is measured by detecting mRNA transcripts of the bg gene.

13. The method of claim 11 in which expression is measured by detecting the bg gene product.

14. A method for diagnosing intracellular vesicle disorders in a mammal, comprising detecting a bg gene mutation contained in the genome of the mammal.

15. The method of claim 14 in which the mutation is located in a splice site of the bg gene.

16. The method of claim 11 or 14 wherein the intracellular vesicle disorder is Chediak-Higashi syndrome.

17. A method for screening compounds useful for the treatment of intracellular vesicle disorders, comprising contacting a compound with a cultured cell that expresses the bg gene, and detecting a change in the expression of the bg gene by the cultured cell.

18. The method of claim 17 wherein the intracellular vesicle disorder is Chediak-Higashi syndrome.

19. A method for treating an intracellular vesicle disorder, in a mammal comprising administering a compound to the mammal that modulates the expression of the bg gene in the mammal.

20. The method of claim 19 in which the intracel lular vesicle disorder is Chediak-Higashi syndrome.