AU2001269712A2 - Regulating lipid levels via the ZMAXI or HBM gene - Google Patents

Description

REGULATING LIPID LEVELS VIA THE ZMAX1 OR HBM GENE INVENTORS: John P. Carulli, Randall D. Little, Robert R. Recker and Mark L. Johnson RELATED APPLICATIONS This application is a continuation-in-part of Application No. 09/543,771 filed April 2000 and Application No. 09/544,398 filed April 5, 2000, which are continuation-in-part applications of Application No. 09/229,319, filed January 13, 1999, which claims benefit of U.S. Provisional Application No. 60/071,449, filed January 13, 1998, and U.S. Provisional Application No. 60/105,511, filed October 23, 1998, all of which are herein incorporated by reference in their entirety.

FIELD OF THE INVENTION The present invention relates generally to the field of genetics, genomics and molecular biology. More particularly, the invention relates to methods and materials used to isolate, detect and sequence a high bone mass gene and corresponding wild-type gene, and mutants thereof that may be involved with modulating lipid levels. The present invention also relates to the high bone mass gene, the corresponding wild-type gene, and mutants thereof. The genes identified in the present invention are implicated in the ontology and physiology of atherosclerosis, arteriosclerosis and associated diseases and conditions related thereto. The invention also provides nucleic acids, proteins, cloning vectors, expression vectors, transformed hosts, methods of developing pharmaceutical compositions, methods of identifying molecules involved in arteriosclerosis and associated conditions, and methods of treating or preventing diseases associated with abnormal lipid levels. In preferred embodiments, the present invention is directed to methods for treating, diagnosing, WO 01/92891 PCT/US01/16946 preventing and screening for normal and abnormal lipid-associated conditions, including arteriosclerosis, cardiovascular disease and stroke.

BACKGROUND OF THE INVENTION Cardiovascular disease is the number one killer in the United States, and atherosclerosis is the major cause of heart disease and stroke. It is widely appreciated that cholesterol plays an important role in atherogenesis. Normally, most cholesterol serves as a structural element in the walls of cells, whereas much of the rest is in transit through the blood or functions as the starting material for the synthesis of bile acids in the liver, steroid hormones in endocrine cells and vitamin D in skin. The transport of cholesterol and other lipids through the circulatory system is facilitated by their packaging into lipoprotein carriers.

These spherical particles comprise protein and phospholipid shells surrounding a core of neutral lipid, including unesterified ("free") or esterified cholesterol and triglycerides. Risk for atherosclerosis increases with increasing concentrations of low density lipoprotein (LDL) cholesterol, whereas risk is inversely proportional to the levels of high density lipoprotein (HDL) cholesterol. The receptor-mediated control of plasma LDL levels has been welldefined, and recent studies have now provided new insights into HDL metabolism..

The elucidation of LDL metabolism began in 1974 by Michael Brown and Joseph Goldstein. In brief, the liver synthesizes a precursor lipoprotein (very low density lipoprotein, VLDL) that is converted during circulation to intermediate density lipoprotein (IDL) and then to LDL. The majority of the LDL receptors expressed in the body are on the surfaces of liver cells, although virtually all other tissues ("peripheral tissues") express some LDL receptors. After binding, the receptor-lipoprotein complex is internalized by the cells via coated pits and vesicles, and the entire LDL particle is delivered to lysosomes, wherein it -2- WO 01/92891 PCT/US01/16946 is disassembled by enzymatic hydrolysis, releasing cholesterol for subsequent cellular metabolism. This whole-particle uptake pathway is called "receptor-mediated endocytosis." Cholesterol-mediated feedback regulation of both the levels of LDL receptors and cellular cholesterol biosynthesis help ensure cellular cholesterol homeostasis. Genetic defects in the LDL receptor in humans results in familial hypercholesterolemia, a disease characterized by elevated plasma LDL cholesterol and premature atherosclerosis and heart attacks. One hypothesis for the deleterious effects of excess plasma LDL cholesterol is that LDL enters the artery wall, is chemically modified, and then is recognized by a special class of receptors called macrophage scavenger receptors, that mediate the cellular accumulation of the LDL cholesterol in the artery, eventually leading to the formation of an atherosclerotic lesion.

The major lipoprotein classes include intestinally derived chylomicrons that transport dietary fats and cholesterol, hepatic-derived VLDL, IDL and LDL that can be atherogenic, and hepatic- and intestinally-derived HDL that are antiatherogenic. Apoprotein B (ApoB) is necessary for the secretion of chylomicrons (Apo B48) and VLDL, IDL and LDL (Apo B 100). Plasma levels of VLDL triglycerides are determined mainly by rates of secretion in LPL lipolytic activity. Plasma levels of LDL cholesterol are determined mainly by the secretion ofApo B100 into plasma, the efficacy with which VLDL are converted to LDL and by LDL receptor-mediated clearance. Regulation of HDL cholesterol levels is complex and is affected by rates of synthesis of its Apo proteins, rates of esterfication of free cholesterol to cholesterol ester by LCAT, levels of triglyceride-rich lipoproteins and CETP-mediated transfer of cholesterol esters from HDL, and clearance from plasma of HDL lipids and Apo proteins.

Normal lipoprotein transport is associated with low levels of triglycerides and LDL cholesterol and high levels of HDL cholesterol. When lipoprotein transport is abnormal, WO 01/92891 PCT/US01/16946 lipoprotein levels can change in ways that predispose individuals to atherosclerosis and arteriosclerosis (see Ginsberg, Endocrinol. Metab. Clin. North Am., 27: 503-19 (1998)).

Several lipoprotein receptors may be involved in cellular lipid uptake. These receptors include: scavenger receptors; LDL receptor-related protein/a2-macroglobulin receptor (LRP); LDL receptor; and VLDL receptor. With the exception of the LDL receptor, all of these receptors are expressed in atherosclerotic lesions while scavenger receptors are mostly expressed in macrophages, the LRP and VLDL receptors may play an important role in mediating lipid uptake in smooth muscle cells (Hiltunen et al., Atherosclerosis, 137 suppl.: S81-8 (1998)).

A major breakthrough in the pharmacologic treatment of hypercholesterolemia has been the development of the "statin" class of 3-hydroxy-3-methylglutaryl-CoA reductase (HMG CoA reductase) inhibitory drugs. 3-Hydroxy-3-methylglutaryl-CoA reductase is the rate controlling enzyme in cholesterol biosynthesis, and its inhibition in the liver stimulates LDL receptor expression. As a consequence, both plasma LDL cholesterol levels and the risk for atherosclerosis decrease. The discovery and analysis of the LDL receptor system has had a profound impact on cell biology, physiology, and medicine.

HDL is thought to remove unesterified, or "free" cholesterol (FC) from peripheral tissues, after which most of the cholesterol is converted to cholesteryl ester (CE) by enzymes in the plasma. Subsequently, HDL cholesterol is efficiently delivered directly to the liver and steroidogenic tissues via a selective uptake pathway and the HDL receptor, SR-BI (class B type I scavenger receptor) or, in some species, transferred to other lypoproteins for additional transport in metabolism. For additional discussion on HDL and LDL metabolism see Krieger, Proc. Natl. Acad. Sci. USA, 95:4077-4080, 1998.

-4- WO 01/92891 PCT/US01/16946 Recently, a strong interest in the genetic control of peak bone mass has developed in the field ofosteoporosis. The interest has focused mainly on candidate genes with suitable polymorphisms to test for association with variation in bone mass within the normal range, or has focused on examination of genes and gene loci associated with low bone mass in the range found in patients with osteoporosis. The vitamin D receptor locus (VDR) (Morrison et al., Nature, 367:284-287 (1994)), PTH gene (Howard et al., J Clin. Endocrinol. Metab., 80:2800-2805 (1995); Johnson et al.,J. Bone Miner. Res., 8:11-17 (1995); Gong et al., J.

Bone Miner. Res., 10:S462 (1995)) and the estrogen receptor gene (Hosoi et al., J Bone Miner. Res., 10:S170 (1995); Morrison et al., Nature, 367:284-287 (1994)) have figured most prominently in this work. These studies are difficult because bone mass (the phenotype) is a continuous, quantitative, polygenic trait, and is confounded by environmental factors such as nutrition, co-morbid disease, age, physical activity, and other factors. Also, this type of study design requires large numbers of subjects. In particular, the results of VDR studies to date have been confusing and contradictory (Garnero et J. Bone Miner. Res., 10:1283-1288 (1995); Eisman et al., J. Bone. Miner. Res., 10:1289-1293 (1995); Peacock, J. Bone Miner.

Res., 10:1294-1297 (1995)). Furthermore, the work thus far has not shed much light on the mechanism(s) whereby the genetic influences might exert their effect on bone mass.

While it is well known that peak bone mass is largely determined by genetic rather than environmental factors, studies to determine the gene loci (and ultimately the genes) linked to variation in bone mass are difficult and expensive. Study designs which utilize the power of linkage analysis, sib-pair or extended family, are generally more informative than simple association studies, although the latter do have value. However, genetic linkage studies involving bone mass are hampered by two major problems. The first problem is the phenotype, as discussed briefly above. Bone mass is a continuous, quantitative trait, and WO 01/92891 PCT/US01/16946 establishing a discrete phenotype is difficult. Each anatomical site for measurement may be influenced by several genes, many of which may be different from site to site. The second problem is the age component of the phenotype. By the time an individual can be identified as having low bone mass, there is a high probability that their parents or other members of prior generations will be deceased and therefore unavailable for study, and younger generations may not have even reached peak bone mass, making their phenotyping uncertain for genetic analysis.

Regardless, linkage analysis can be used to find the location.ofa gene causing a hereditary "disorder" and does not require any knowledge of the biochemical nature of the disorder, a mutated protein that is believed to cause the disorder does not need to be known. Traditional approaches depend on assumptions concerning the disease process that might implicate a known protein as a candidate to be evaluated. The genetic localization approach using linkage analysis can be used to first find the general chromosomal region in which the defective gene is located and then to gradually reduce-the size of the region in order to determine the location of the specific mutated gene as precisely as possible. After the gene itself is discovered within the candidate region, the messenger RNA and the protein are identified and, along with the DNA, are checked for mutations.

The genetic localization approach has practical implications since the location of the disease can be used for prenatal diagnosis even before the altered gene that causes the disease is found. Linkage analysis can enable families, even many of those that do not have a sick child, to know whether they are carriers of a disease gene and to evaluate the condition of an unborn child through molecular diagnosis. The transmission of a disease within families, then, can be used to find the defective gene. As used herein, reference to "high bone mass" WO 01/92891 PCT/US01/16946 (HBM) is analogous to reference to a disease state, although from a practical standpoint high bone mass can actually help a subject avoid the disease known as osteoporosis.

Linkage analysis is possible because of the nature of inheritance of chromosomes from parents to offspring. During meiosis, the two parental homologues pair to guide their proper separation to daughter cells. While they are lined up and paired, the two homologues exchange pieces of the chromosomes, in an event called "crossing over" or "recombination." The resulting chromosomes are chimeric, that is, they contain parts that originate from both parental homologues. The closer together two sequences are on the chromosome, the less likely that a recombination event will occur between them, and the more closely linked they are. In a linkage analysis experiment, two positions on the chromosomes are followed from one generation to the next to determine the frequency of recombination between them. In a study of an inherited disease, one of the chromosomal positions is marked by the disease gene or its normal counterpart, the inheritance of the chromosomal region can be determined by examining whether the individual displays symptoms of the disorder or not. The other position is marked by a DNA sequence that shows natural variation in the population such that the two homologues can be distinguished based on the copy of the "marker" sequence that they possess. In every family, the inheritance of the genetic marker sequence is compared to the inheritance of the disease state. If, within a family carrying an autosomal dominant disorder such as high bone mass, every affected individual carries the same form of the marker and all the unaffected individuals carry at least one different form of the marker, there is a great probability that the disease gene and the marker are located close to each other. In this way, chromosomes may be systematically checked with known markers and compared to the disease state. The data obtained from the different families is combined, and analyzed together by a computer using statistical-methods. The result is information WO 01/92891 PCT/US01/16946 indicating the probability of linkage between the genetic marker and the disease allowing different distances between them. A positive result can mean that the disease is very close to the marker, while a negative result indicates that it is far away on that chromosome, or on an entirely different chromosome.

Linkage analysis is performed by typing all members of the affected family at a given marker locus and evaluating the co-inheritance of a particular disease state with the marker probe, thereby determining how often the two of them are co-inherited. The recombination frequency can be used as a measure of the genetic distance between two gene loci. A recombination frequency of 1% is equivalent to 1 map unit, or 1 centiMorgan which is roughly equivalent to 1,000 kb of DNA. This relationship holds up to frequencies of about or 20 cM.

The entire human genome is 3,300 cM long. In order to find an unknown disease gene within 5-10 cM of a marker locus, the whole human genome can be searched with roughly 330 informative marker loci spaced at approximately 10 cM intervals (Botstein et al., Am. J. Hum. Genet., 32:314-331 (1980)). The reliability of linkage results is established by using a number of statisticalmethods. The method most commonly used for the analysis of linkage in humans is the LOD score method (Morton, Prog, Clin. Biol. Res., 147:245-265 (1984), Morton'et al., Am. J. Hum. Genet., 38:868-883 (1986)) which was incorporated into the computer program LIPED by Ott, Am. J. Hum. Genet., 28:528-529 (1976). LOD scores are the logarithm of the ratio of the likelihood that two loci are linked at a given distance to that they are not linked (>50 cM apart). The advantage of using logarithmic values is that they can be summed among families with the same disease. This becomes necessary given the relatively small size of human families.

WO 01/92891 PCT/US01/16946 By convention, a total LOD score greater than 3.0 (that is, odds of linkage at the specified recombination frequency being 1000 times greater than odds of no linkage) is considered to be significant evidence for linkage at that particular recombination frequency.

A total LOD score of less than 2.0 (that is, odds of no linkage being 100 times greater than odds of linkage at the specified frequency) is considered to be strong evidence that the two loci uinder consideration are not linked at that particular recombination frequency. Until recently, most linkage analyses have been performed on the basis of two-point data, which is the relationship between the disorder under consideration and a particular genetic marker.

However, as a result of the rapid advances in mapping the human genome over the last few years, and concomitant improvements in computer methodology, it has become feasible to carry out linkage analyses using multi-point data. Multi-point analysis provide a simultaneous analysis of linkage between the disease and several linked genetic markers, when the recombination distance among the markers is known.

Multi-point analysis is advantageous for two reasons. First, the informativeness of the pedigree is usually increased. Each pedigree has a certain amount of potential information, dependent on the number of parents heterozygous for the marker loci and the number of affected individuals in the family. However, few markers are sufficiently polymorphic as to be informative in all those individuals. If multiple markers are considered simultaneously, then the probability of an individual being heterozygous for at least one of the markers is greatly increased. Second, an indication of the position of the disease gene among the markers may be determined. This allows identification of flanking markers, and thus eventually allows isolation of a small region in which the disease gene resides. Lathrop et al., Proc. Natl. Acad. Sci. USA, 81:3443-3446 (1984) have written the most widely used computer package, LINKAGE, for multi-point analysis.

WO 01/92891 PCT/US01/16946 There is a need in the art for identifying the gene associated with a high bone mass phenotype. The present invention is directed to this, as well as other, important ends.

SUMMARY OF THE INVENTION The present invention describes the Zmaxl gene and the HBM gene on chromosome 1 lq13.3 by genetic linkage and mutation analysis. The use of additional genetic markers linked to the genes has aided this discovery. By using linkage analysis and mutation analysis, persons predisposed to lipid associated disorders may be readily identified. Cloning methods using Bacterial Artificial Chromosomes have enabled the inventors to focus on the chromosome region of 1 lql3.3 and to accelerate the sequencing of the autosomal dominant gene. In addition, the invention identifies the Zmaxl gene and the HBM gene, and identifies the guanine-to-thymine polymorphism mutation at position 582 in the Zmaxl gene that produces the HBM gene and the HBM phenotype as well as altered lipid levels.

The present invention identifies the Zmaxl gene and the HBM gene, which can be used to determine if people are predisposed to abnormal lipid levels and, therefore, susceptible to diseases mediated by lipids, including, for example, atherosclerosis, arteriosclerosis and associated conditions. Individuals with the HBM gene have lower LDL, triglyceride and VLDL levels and higher HDL levels. In other words, the HBM gene is a suppressor of atherosclerosis, arteriosclerosis and associated conditions. This in vivo observation is a strong evidence that treatment of normal individuals with the HBM gene or protein, or fragments thereof, will ameliorate atherosclerosis, arteriosclerosis and conditions related thereto.

Moreover, such treatment will be indicated in the treatment of lipid-mediated diseases, particularly arteriosclerosis and conditions related thereto. For example, persons predisposed to elevated lipid levels diabetes, hypercholesteremia and other genetic diseases, obesity, male gender, and individuals who smoke) may be identified and/or treated by means of the invention. Moreover, the methods and compositions of the invention will be of use in the treatment or prevention of diabetic atherosclerotic disease, neurovascular conditions caused by plaque build-up stroke), cardiovascular disease, poor circulation due to plaque build-up ad associated poor would healing.

In various embodiments, the present invention is directed to nucleic acids, proteins, vectors, and transformed hosts of HBM and Zmaxl.

Additionally, the present invention is directed to applications of the above embodiments of the invention including, for example, gene therapy, pharmaceutical development, and diagnostic assays for bone development disorders. In preferred embodiments, the present invention is directed to methods for treating, diagnosing, preventing and screening for osteoporosis.

These and other aspects of the present invention are described in more detail below.

BRIEF DESCRIPTION OF THE FIGURES Figs. 1A and 1B show the pedigree of the individuals used in the genetic linkage studies. Under each individual is an ID number, the z-score for spinal BMD, and the allele calls for the critical markers on chromosome 11. Solid symbols represent "affected" individuals. Symbols containing are "unaffected" individuals. DNA from 37 individuals was genotyped. Question marks denote unknown genotypes or individuals who were not genotyped.

Figs. 2A and 2B depict the BAC/STS content physical map of the HBM region in 1 lq13.3. STS markers derived from genes, ESTs, microsatellites, random sequences, and

BAC

EPO DG 1 S2. 12 2001 -11- SUBSTITUTE SHEET AMENDED SHEET WO 01/92891 PCT/US01/16946 endsequences are denoted above the long horizontal line. For markers that are present in GDB the same nomenclature has been used. Locus names are listed in parentheses after the primary name if available. STSs derived from BAC endsequences are listed with the BAC name first followed by L or R for the left and right end of the clone, respectively. The two large arrows indicate the genetic markers that define the HBM critical region. The horizontal lines below the STSs indicate BAC clones identified by PCR-based screening of a nine-fold coverage BAC library. Open circles indicate that the marker did not amplify the corresponding BAC library address during library screening. Clone names use the following convention: B for BAC, the plate, row and column address, followed by -H indicating the HBM project B36F16-H).

Figs. 3A-3F show the genomic structure ofZmaxl with flanking intron sequences.

Translation is initiated by the underlined "ATG" in exon 1. The site of the polymorphism in the HBM gene is in exon 3 and is represented by the underlined whereby this nucleotide is a in the HBM gene. The 3' untranslated region of the mRNA is underlined within exon 23 (exon 1, SEQ ID NO:40; exon 2, SEQ ID NO:41; exon 3, SEQ ID NO:42; exon 4, SEQ ID NO:43; exon 5, SEQ ID NO:44; exon 6, SEQ ID NO:45; exon 7, SEQ ID NO:46; exon 8, SEQ ID NO:47; exon 9, SEQ ID NO:48; exon 10, SEQ ID NO:49; exon 11, SEQ ID exon 12, SEQ ID NO:51; exon 13, SEQ ID NO:52; exon 14, SEQ ID NO:53; exon 15, SEQ ID NO:54; exon 16, SEQ ID NO:55; exon 17, SEQ ID NO:56; exon 18, SEQ ID NO:57; exon 19, SEQ ID NO:58; exon 20, SEQ ID NO:59; exon 21, SEQ ID NO:60; exon 22, SEQ ID NO:61; and exon 23; SEQ ID NO:62).

Fig. 4 shows the domain organization of Zmaxl, including the YWTD spacers, the extracellular attachment site, the binding site for LDL and calcium, the cysteine-rich growth factor repeats, the transmembrane region, the ideal PEST region with the CK-II -12phosphorylation site and the internalization domain. Fig. 4 also shows the site of the glycine to valine change that occurs in the HBM protein. The signal peptide is located at amino acids 1-22, the extracellular domain is located at amino acids 23-1385, the transmembrane segment is located at amino acids 1386-1413, and the cytoplasmic domain is located at amino acids 1414-1615.

Fig. 5 shows a schematic illustration of the BAC contigs B527D12 and B200E21 in relation to the HBM gene.

Figs. 6A-6J show the nucleotide and amino acid sequences of the wild-type gene, Zmaxl. The location for the base pair substitution at nucleotide 582, a guanine to thymine, is underlined. This allelic variant is the HBM gene. The HBM gene encodes for a protein with an amino acid substitution of glycine to valine at position 171. The untranslated region (UTR) consists of bases 1 to 70, and the 3' UTR consists of bases 4916-5120.

Figs. 7A and 7B show northern blot analyses showing the expression of Zmaxl in various tissues.

Fig. 8 shows a PCR product analysis.

Fig. 9 shows allele specific oligonucleotide detection of the Zmaxl exon 3 mutation.

Figs. 10A and 10B show the cellular localization of mouse Zmaxl by in situ hybridization at 100X magnification using sense and antisense probes.

Figs. 11A and 11B show the cellular localization of mouse Zmaxl by in situ hybridization at 400X magnification using sense and antisense probes.

Figs. 12A and 12B show the cellular localization of mouse Zmaxl by in situ hybridization of osteoblasts in the endosteum at 400X magnification using sense and antisense probes.

Fig. 13 shows antisense inhibition of Zmaxl expression in MC-3T3 cells.

-13- SUBSTITUTE SHEET '2 AMENDED SHEET WO 01/92891 PCT/US01/16946 DETAILED DESCRIPTION OF THE INVENTION To aid in the understanding of the specification and claims, the following definitions are provided.

"Gene" refers to a DNA sequence that encodes through its template or messenger RNA a sequence of amino acids characteristic of a specific peptide. The term "gene" includes intervening, non-coding regions, as well as regulatory regions, and can include and 3' ends.

"Gene sequence" refers to a DNA molecule, including both a DNA molecule which contains a non-transcribed or non-translated sequence. The term is also intended to include any combination of gene(s), gene fragment(s), non-transcribed sequence(s) or non-translated sequence(s) which are present on the same DNA molecule.

The sequences of the present invention may be derived from a variety of sources including DNA, cDNA, synthetic DNA, synthetic RNA or combinations thereof. Such sequences may comprise genomic DNA which may or may not include naturally occurring introns. Moreover, such genomic DNA may be obtained in association with promoter regions or poly sequences. The sequences, genomic DNA or cDNA may be obtained in any of several ways. Genomic DNA can be extracted and purified from suitable cells by means well known in the art. Alternatively, mRNA can be isolated from a cell and used to produce cDNA by reverse transcription or other means.

"cDNA" refers to complementary or copy DNA produced from an RNA template by the action ofRNA-dependent DNA polymerase (reverse transcriptase). Thus, a "cDNA clone" means a duplex DNA sequence complementary to an RNA molecule of interest, carried in a cloning vector or PCR amplified. This term includes genes from which the intervening sequences have been removed.

-14- WO 01/92891 PCT/US01/16946 "Recombinant DNA" means a molecule that has been recombined by in vitro splicing cDNA or a genomic DNA sequence.

"Cloning" refers to the use of in vitro recombination techniques to insert a particular gene or other DNA sequence into a vector molecule. In order to successfully clone a desired gene, it is necessary to use methods for generating DNA fragments, for joining the fragments to vector molecules, for introducing the composite DNA molecule into a host cell in which it can replicate, and for selecting the clone having the target gene from amongst the recipient host cells.

"cDNA library" refers to a collection of recombinant DNA molecules containing cDNA inserts which together comprise the entire genome of an organism. Such a cDNA library can be prepared by methods known to one skilled in the art and described by, for example, Cowell and Austin, "cDNA Library Protocols," Methods in Molecular Biology (1997). Generally, RNA is first isolated from the cells of an organism from whose genome it is desired to clone a particular gene.

"Cloning vehicle" refers to a plasmid or phage DNA or other DNA sequence which is able to replicate in a host cell. The cloning vehicle is characterized by one or more endonuclease recognition sites at which such DNA sequences may be cut in a determinable fashion without loss of an essential biological function of the DNA, which may contain a marker suitable for use in the identification of transformed cells.

"Expression control sequence" refers to a sequence ofnucleotides that control or regulate expression of structural genes when operably linked to those genes. These include, for example, the lac systems, the trp system, major operator and promoter regions of the phage lambda, the control region of fd coat protein and other.sequences known to control the expression of genes in prokaryotic or eukaryotic cells. Expression control sequences will WO 01/92891 PCT/US01/16946 vary depending on whether the vector is designed to express the operably linked gene in a prokaryotic or eukaryotic host, and may contain transcriptional elements such as enhancer elements, termination sequences, tissue-specificity elements and/or translational initiation and termination sites.

"Expression vehicle" refers to a vehicle or vector similar to a cloning vehicle but which is capable of expressing a gene which has been cloned into it, after transformation into a host. The cloned gene is usually placed under the control of(i.e., operably linked to) an expression control sequence.

"Operator" refers to a DNA sequence capable of interacting with the specific repressor, thereby controlling the transcription of adjacent gene(s).

"Promoter" refers to a DNA sequence that can be recognized by an RNA polymerase.

The presence of such a sequence permits the RNA polymerase to bind and initiate transcription of operably linked gene sequences.

"Promoter region" is intended to include the promoter as well as other gene sequences which may be necessary for the initiation of transcription. The presence of a promoter region is sufficient to cause the expression of an operably linked gene sequence.

"Operably linked" means that the promoter controls the initiation of expression of the gene. A promoter is operably linked to a sequence of proximal DNA if upon introduction into a host cell the promoter determines the transcription of the proximal DNA sequence(s) into one or more species of RNA. A promoter is operably linked to a DNA sequence if the promoter is capable of initiating transcription of that DNA sequence.

"Prokaryote" refers to all organisms without a true nucleus, including bacteria.

"Eukaryote" refers to organisms and cells that have a true nucleus, including mammalian cells.

-16- WO 01/92891 PCT/US01/16946 "Host" includes prokaryotes and eukaryotes, such as yeast and filamentous fungi, as well as plant and animal cells. The term includes an organism or cell that is the recipient of a replicable expression vehicle.

By "animal" is meant to include vertebrates. Preferred vertebrates include mammals and birds, but also include fish, reptiles and amphibians. Preferred mammals include: humans, primates, rodents, canines, felines and livestock.

"Fragment" of a gene refers to any variant of the gene that possesses the biological activity of that gene.

"Variant" refers to a gene that is substantially similar in structure and biological activity or immunological characteristics to either the entire gene or to a fragment of the gene. Provided that the two genes possess a similar activity, they are considered variant as that term is used herein even if the sequence of amino acid residues is not identical.

"Amplification of nucleic acids" refers to methods such as polymerase chain reaction (PCR), ligation amplification (or ligase chain reaction, LCR) and amplification methods based on the use of Q-beta replicase. These methods are well known in the art and described, for example, in U.S. Patent Nos. 4,683,195 and 4,683,202. Reagents and hardware for conducting PCR are commercially available. Primers useful for amplifying sequences from the HBM region are preferably complementary to, and hybridize specifically to sequences in the HBM region or in regions that flank a target region therein. HBM sequences generated by amplification may be sequenced directly. Alternatively, the amplified sequence(s) may be cloned prior to sequence analysis.

"Antibodies" may refer to polyclonal and/or monoclonal antibodies and fragments thereof, and immunologic binding equivalents thereof, that can bind to the HBM and Zmaxl proteins and fragments thereof or to nucleic acid sequences from the HBM or Zmaxl region, -17- WO 01/92891 PCT/US01/16946 particularly from the HBM locus or a portion thereof. The term antibody is used both to refer to a homogeneous molecular entity, or a mixture such as a serum product made up of a plurality of different molecular entities. Proteins may be prepared synthetically in a protein synthesizer and coupled to a carrier molecule and injected over several months into rabbits.

Rabbit sera is tested for immunoreactivity to the HBM protein or fragment. Monoclonal antibodies may be made by injecting mice with the proteins, or fragments thereof.

Monoclonal antibodies will be screened by ELISA and tested for specific immunoreactivity with HBM protein or fragments thereof. Harlow et al., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1988). These antibodies will be useful in assays as well as pharmaceuticals. Antibodies can include antibody fragments scFv, Fab, F(ab') 2 etc.) as well as human antibodies, humanized antibodies and primatized antibodies.

"HBM" refers to high bone mass, but polymorphisms associated with HBM gene, which can also be involved in lipid modulation.

"HBM protein" refers to a protein that is identical to a Zmaxl protein except that it contains an alteration of glycine 171 to valine. An HBM protein is defined for any organism that encodes a Zmaxl true homologue. For example, a mouse HBM protein refers to the mouse Zmaxl protein having the glycine 170 to valine substitution.

"HBM gene" refers to the genomic DNA sequence found in individuals showing the HBM characteristic or phenotype, where the sequence encodes the protein indicated by SEQ ID NO: 4. The HBM gene and the Zmaxl gene are allelic. The protein encoded by the HBM gene has the property of causing elevated bone mass and also altering physiologic lipid levels, while the protein encoded by the Zmaxl gene does not. The HBM gene and the Zmaxl gene differ in that the HBM gene has a thymine at position 582, while the Zmaxl gene has a 18- WO 01/92891 PCT/US01/16946 guanine at position 582. The HBM gene comprises the nucleic acid sequence shown as SEQ ID NO: 2. The HBM gene may also be referred to as an "HBM polymorphism." "Normal," "wild-type," "unaffected" and "Zmaxl" all refer to the genomic DNA sequence that encodes the protein indicated by SEQ ID NO: 3. The Zmaxl gene has a guanine at position 582. The ZmaxI gene comprises the nucleic acid sequence shown as SEQ ID NO: 1. "Normal," "wild-type," "unaffected" and "Zmaxl" also refer to allelic variants of the genomic sequence that encodes proteins that do not contribute to elevated bone mass.

The Zmaxl gene is common in the human population, while the HBM gene is rare.

refers to a repeat unit found in the Zmaxi protein, consisting of five YWT repeats followed by an EGF repeat.

"Bone development" generally refers to any process involved in the change of bone over time, including, for example, normal development, changes that occur during disease states, and changes that occur during aging. "Bone development disorder" particularly refers to any disorders in bone development including, for example, changes that occur during disease states and changes that occur during aging. Bone development may be progressive or cyclical in nature. Aspects of bone that may change during development include, for example, mineralization, formation of specific anatomical features, and relative or absolute numbers of various cell types.

"Bone modulation" or "modulation of bone formation" refers to the ability to affect any of the physiological processes involved in bone remodeling, as will be appreciated by one skilled in the art, including, for example, bone resorption and appositional bone growth, by, inter alia, osteoclastic and osteoblastic activity, and may comprise some or all of bone formation and development as used herein.

-19- WO 01/92891 PCT/US01/16946 "Normal bone density" refers to a bone density withun two stanaara aeviatons oi a z score of 0.

By "lipid regulation" or "lipid modulation" is meant the ability to alter by modulating the HBMor Zmaxl genes, mRNA or protein encoded thereby the levels of a lipid. Altered levels of lipid include very low density lipoproteins (VLDL), low density lipoproteins (LDL), high density lipoprotein (HDL) and triglycerides. The regulation or modulation can be an increase or decrease in the lipid level by an agent, which when administered to a subject modulates HBM or Zmaxl activity. By "lipid metabolism" is meant the physiological cycle through which the various triglycerides and lipoproteins proceed. Agents of the invention can also be said to modulate the metabolism of various lipids.

"Lipid" preferably includes very low density lipoproteins (VLDL), low density lipoproteins (LDL), intermediate density lipoprotein (IDL), high density lipoprotein (HDL) and triglycerides. Lipids can also include apolipoproteins, such as apolipoprotein A-1 (APO apolipoprotein B (APO apoliprotein E (APO E) and lipoproteins such as lipoprotein a (LIPOa).

By "lipid-mediated disease or condition" is meant to include arteriosclerosis and related conditions, hypercholesteremia, hyperlipidemia, atherosclerosis, and conditions or lifestyles associated with elevated lipid levels diabetes mellitus, smoking and obesity) such as those discussed herein.

By "arteriosclerosis" is meant to include hypertrophy of the media and subintimal fibrosis with hyaline degeneration which can result in ectasia, aneurysm, increased systolic pressure, thrombus formation and embolism. Disorders associated with arteriosclerosis include, but are not limited to, nonatheromatous arteriosclerosis conditions such as: diabetes mellitus, chronic renal insufficiency, chronic vitamin D intoxication, pseudoxanthoma WO 01/92891 PCT/US01/16946 elasticum, idiopathic arterial calcification in infancy, aortic valvular calcification in the elderly, and Werer's syndrome. Additional disorders associated with arteriosclerosis and atherosclerosis include: diabetes mellitus, hypertension, familial hypercholesterolemia, familial combined hyperlipidemia, familial dysbetalipoproteinemia, familial hypoalphalipoproteinemia, hypothyroidism, cholesterol ester storage disease, systemic lupus erythematosus and homocysteinemia.

By "atherosclerosis" is meant patchy intramural thickening of the subintima that encroaches on the arterial lumen and can cause obstruction. Atherosclerotic plaque consists of the accumulation of lipids, cells, annective tissue and glycosaminoglycans. It can cause the following conditions: stenosis, thrombosis, aneurysm, or embolus supervenes, as well as angina as well as the conditions listed above.

A "Zmaxl system" refers to a purified protein, cell extract, cell, animal, human or any other composition of matter in which Zmaxl is present in a normal or mutant form.

A "surrogate marker" refers to a diagnostic indication, symptom, sign or other feature that can be observed in a cell, tissue, human or animal that is correlated with the HBM gene or elevated bone mass or both, but that is easier to measure than bone density. The general concept of a surrogate marker is well accepted in diagnostic medicine.

The present invention encompasses the Zmaxl gene and Zmaxl protein in the forms indicated by SEQ ID NOS: 1 and 3, respectively, and other closely related variants, as well as the adjacent chromosomal regions of Zmaxl necessary for its accurate expression. In a preferred embodiment, the present invention is directed to at least 15 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 1.

The present invention also encompasses the HBM gene and HBM protein in the forms indicated by SEQ ID NO: 2 and 4, respectively, and other closely related variants, as well as -21- WO 01/92891 PCT/US01/16946 the adjacent chromosomal regions of the HBM gene necessary for its accurate expression. In a preferred embodiment, the present invention is directed to at least 15 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 2. More preferably, the present invention is directed to at least 15 contiguous nucleotides of the nucleic acid sequence of SEQ ID NO: 2, wherein one of the 15 contiguous nucleotides is the thymine at nucleotide 582.

The invention also relates to the nucleotide sequence of the Zmaxl gene region, as well as the nucleotide sequence of the HBM gene region. More particularly, a preferred embodiment are the BAC clones containing segments of the Zmaxl gene region B200E21-H and B527D12-H. A preferred embodiment is the nucleotide sequence of the BAC clones consisting of SEQ ID NOS: 5-12.

The invention also concerns the use of the nucleotide sequence to identify DNA probes for the Zmaxl gene and the HBM gene, PCR primers to amplify the Zmaxl gene and the HBM gene, nucleotide polymorphisms in the Zmaxl gene and the HBM gene, and regulatory elements of the Zmaxl gene and the HBM gene.

This invention describes the further localization of the chromosomal location of the Zmaxl gene and HBM gene on chromosome 1 ql3.3 between genetic markers D11S987 and SNP_CONTIG033-6, as well as the DNA sequences of the Zmaxl gene and the HBM gene.

The chromosomal location was refined by the addition of more genetic markers to the mapping panel used to map the gene, and by the extension of the pedigree to include more individuals. The pedigree extension was critical because the new individuals that have been genotyped harbor critical recombination events that narrow the region. To identify genes in the region on 1 lq13.3, a set of BAC clones containing this chromosomal region was identified. The BAC clones served as a template for genomic DNA sequencing, and also as a -22- WO 01/92891 PCT/US01/16946 reagent for identifying coding sequences by direct cDNA selection. Genomic sequencing and direct cDNA selection were used to characterize more than 1.5 million base pairs of DNA from 11q13.3. The Zmaxl gene was identified within this region and the HBM gene was then discovered after mutational analysis of affected and unaffected individuals.

When a gene has been genetically localized to a specific chromosomal region, the genes in this region can be characterized at the molecular level by a series of steps that include: cloning of the entire region of DNA in a set of overlapping clones (physical mapping), characterization of genes encoded by these clones by a combination of direct cDNA selection, exon trapping and DNA sequencing (gene identification), and identification of mutations in these genes by comparative DNA sequencing of affected and unaffected members of the HBM kindred (mutation analysis).

Physical mapping is accomplished by screening libraries of human DNA cloned in vectors that are propagated in E. coli or S. cereviseae using PCR assays designed to amplify unique molecular landmarks in the chromosomal region of interest. To generate a physical map of the HBM candidate region, a library of human DNA cloned in Bacterial Artificial Chromosomes (BACs) was screened with a set of Sequence Tagged Site (STS) markers that had been previously mapped to chromosome 1 lql2-ql3 by.the efforts of the Human Genome Project.

STSs are unique molecular landmarks in the human genome that can be assayed by PCR. Through the combined efforts of the Human Genome Project, the location of thousands of STSs on the twenty-two autosomes and two sex chromosomes has been determined. For a positional cloning effort, the physical map is tied to the genetic map because the markers used for genetic mapping can also be used as STSs for physical mapping. By screening a BAC library with a combination of STSs derived from genetic markers, genes, and random -23- WO 01/92891 PCT/US01/16946 DNA fragments, a physical map comprised of overlapping clones representing all of the DNA in a chromosomal region of interest can be assembled.

BACs are cloning vectors for large (80 kilobase to 200 kilobase) segments of human or other DNA that are propagated in E. coli. To construct a physical map using BACs, a library of BAC clones is screened so that individual clones harboring the DNA sequence corresponding to a given STS or set of STSs are identified. Throughout most of the human genome, the STS markers are spaced approximately 20 to 50 kilobases apart, so that an individual BAC clone typically contains at least two STS markers. In addition, the BAC libraries that were screened contain enough cloned DNA to cover the human genome six times over. Therefore, an individual STS typically identifies more than one BAC clone. By screening a six-fold coverage BAC library with a series of STS markers spaced approximately 50 kilobases apart, a physical map consisting of a series of overlapping BAC clones, i.e. BAC contigs, can be assembled for any region of the human genome. This map is closely tied to the genetic map because many of the STS markers used to prepare the physical map are also genetic markers.

When constructing a physical map, it often happens that there are gaps in the STS map of the genome that result in the inability to identify BAC clones that are overlapping in a given location. Typically, the physical map is first constructed from a set of STSs that have been identified through the publicly available literature and World Wide Web resources. The initial map consists of several separate BAC contigs that are separated by gaps of unknown molecular distance. To identify BAC clones that fill these gaps, it is necessary to develop new STS markers from the ends of the clones on either side of the gap. This is done by sequencing the terminal 200 to 300 base pairs of the BACs flanking the gap, and developing a PCR assay to amplify a sequence of 100 or more base pairs. If the terminal sequences are -24- WO 01/92891 PCT/US01/16946 demonstrated to be unique within the human genome, then the new STS can be used to screen the BAC library to identify additional BACs that contain the DNA from the gap in the physical map. To assemble a BAC contig that covers a region the size of the HBM candidate region (2,000,000 or more base pairs), it is often necessary to develop new STS markers from the ends of several clones.

After building a BAC contig, this set of overlapping clones serves as a template for identifying the genes encoded in the chromosomal region. Gene identification can be accomplished by many methods. Three methods are commonly used: a set of BACs selected from the BAC contig to represent the entire chromosomal region can be sequenced, and computational methods can be used to identify all of the genes, the BACs from the BAC contig can be used as a reagent to clone cDNAs corresponding to the genes encoded in the region by a method termed direct cDNA selection, or the BACs from the BAC contig can be used to identify coding sequences by selecting for specific DNA sequence motifs in a procedure called exon trapping. The present invention includes genes identified by the first two methods.

To sequence the entire BAC contig representing the HBM candidate region, a set of BACs was chosen for subcloning into plasmid vectors and subsequent DNA sequencing of these subclones. Since the DNA cloned in the BACs represents genomic DNA, this sequencing is referred to as genomic sequencing to distinguish it from cDNA sequencing. To initiate the genomic sequencing for a chromosomal region of interest, several nonoverlapping BAC clones are chosen. DNA for each BAC clone is prepared, and the clones are sheared into random small fragments which are subsequently cloned into standard plasmid vectors such as pUC18. The plasmid clones are then grown to propagate the smaller fragments, and these are the templates for sequencing. To ensure adequate coverage and WO 01/92891 PCT/US01/16946 sequence quality for the BAC DNA sequence, sufficient plasmid clones are sequenced to yield six-fold coverage of the BAC clone. For example, if the BAC is 100 kilobases long, then phagemids are sequenced to yield 600 kilobases of sequence. Since the BAC DNA was randomly sheared prior to cloning in the phagemid vector, the 600 kilobases of raw DNA sequence can be assembled by computational methods into overlapping DNA sequences termed sequence contigs. For the purposes of initial gene identification by computational methods, six-fold coverage of each BAC is sufficient to yield ten to twenty sequence contigs of 1000 base pairs to 20,000 base pairs.

The sequencing strategy employed in this invention was to initially sequence "seed" BACs from the BAC contig in the HBM candidate region. The sequence of the "seed" BACs was then used to identify minimally overlapping BACs from the contig, and these were subsequently sequenced. In this manner, the entire candidate region was sequenced, with several small sequence gaps left in each BAC. This sequence served as the template for computational gene identification. One method for computational gene identification is to compare the sequence of BAC contig to publicly available databases of cDNA and genomic sequences, e.g. unigene, dbEST, genbank. These comparisons are typically done using the BLAST family of computer algorithms and programs (Altschul et al., J Mol. Biol., 215:403- 410 (1990)). The BAC sequence can also be translated into protein sequence, and the protein sequence can be used to search publicly available protein databases, using a version of BLAST designed to analyze protein sequences (Altschul et al., Nucl. Acids Res., 25:3389- 3402 (1997)). Another method is to use computer algorithms such as MZEF (Zhang, Proc.

Natl. Acad. Sci., 94:565-568 (1997)) and GRAIL (Uberbacher et al., Methods Enzymol., 266:259-281 (1996)), which predict the location of exons in the sequence based on the -26- WO 01/92891 PCT/US01/16946 presence of specific DNA sequence motifs that are common to all exons, as well as the presence of codon usage typical of human protein encoding sequences.

In addition to identifying genes by computational methods, genes were also identified by direct cDNA selection (Del Mastro et al., Genome Res. 185-194 (1995)). In direct cDNA selection, cDNA pools from tissues of interest are prepared, and the BACs from the candidate region are used in a liquid hybridization assay to capture the cDNAs which base pair to coding regions in the BAC. In the methods described herein, the cDNA pools were created from several different tissues by random priming the first strand cDNA from polyA RNA, synthesizing the second strand cDNA by standard methods, and adding linkers to the ends of the cDNA fragments. The linkers are used to amplify the cDNA pools. The BAC clones are used as a template for in vitro DNA synthesis to create a biotin labelled copy of the BAC DNA. The biotin labelled copy of the BAC DNA is then denatured and incubated with an excess of the PCR amplified, linkered cDNA pools which have also been denatured. The BAC DNA and cDNA are allowed to anneal in solution, and heteroduplexes between the BAC and the cDNA are isolated using streptavidin coated magnetic beads. The cDNAs that are captured by the BAC are then amplified using primers complimentary to the linker sequences, and the hybridization/selection process is repeated for a second round. After two rounds of direct cDNA selection, the cDNA fragments are cloned, and a library of these direct selected fragments is created.

The cDNA clones isolated by direct selection are analyzed by two methods. Since a pool of BACs from the HBM candidate region is used to provide the genomic DNA sequence, the cDNAs must be mapped to individual BACs. This is accomplished by arraying the BACs in microtiter dishes, and replicating their DNA in high density grids. Individual cDNA clones are then hybridized to the grid to confirm that they have sequence identity to an -27- WO 01/92891 PCT/US01/16946 individual BAC from the set used for direct selection, and to determine the specific identity of that BAC. cDNA clones that are confirmed to correspond to individual BACs are sequenced. To determine whether the cDNA clones isolated by direct selection share sequence identity or similarity to previously identified genes, the DNA and protein coding sequences are compared to publicly available databases using the BLAST family of programs.

The combination of genomic DNA sequence and cDNA sequence provided by BAC sequencing and by direct cDNA selection yields an initial list of putative genes in the region.

The genes in the region were all candidates for the HBM locus. To further characterize each gene, Northern blots were performed to determine the size of the transcript corresponding to each gene, and to determine which putative exons were transcribed together to make an individual gene. For Northern blot analysis of each gene, probes were prepared from direct selected cDNA clones or by PCR amplifying specific fragments from genomic DNA or from the BAC encoding the putative gene of interest. The Northern blots gave information on the size of the transcript and the tissues in which it was expressed. For transcripts which were not highly expressed, it was sometimes necessary to perform a reverse transcription PCR assay using RNA from the tissues of interest as a template for the reaction.

Gene identification by computational methods and by direct cDNA selection provides unique information about the genes in a region of a chromosome. When genes are identified, then it is possible to examine different individuals for mutations in each gene.

I. Phenotyping using DXA Measurements Spinal bone mineral content (BMC) and bone mineral density (BMD) measurements performed at Creighton University (Omaha, Nebraska) were made by DXA using a Norland 28 WO 01/92891 PCT/US01/16946 Instruments densitometer (Norland XR2600 Densitometer, Dual Energy X-ray Absorptiometry, DXA). Spinal BMC and BMD at other locations used the machinery available. There are estimated to be 800 DXA machines currently operating in the U.S. Most larger cities have offices or imaging centers which have DXA capabilities, usually a Lunar or Hologic machine. Each location that provided spine BMC and BMD data included copies of the printouts from their machines to provide verification that the regions of interest for measurement of BMD have been chosen appropriately. Complete clinical histories and skeletal radiographs were obtained.

The HBM phenotype is defined by the following criteria: very high spinal BMD; a clinical history devoid of any known high bone mass syndrome; and skeletal radiographs showing a normal shape of the appendicular skeleton.

II. Genotyping of Microsatellite Markers To narrow the genetic interval to a region smaller than that originally reported by Johnson et al., Am. J. Hum. Genet., 60:1326-1332 (1997), additional microsatellite markers on chromosome 11ql2-1 3 were typed. The new markers included: D11S4191, D11S1883, D11S1785, D11S4113, D11S4136, D11S4139, (Dib, et al.,Nature, 380:152-154 (1996), FGF3 (Polymeropolous, et al., Nucl. Acid Res., 18:7468 (1990)), as well as GTC_HBM_Marker 1, GTC_HBM_Marker_2, GTC_HBM_Marker_3, GTCHBM_Marker_4, GTC_HBMMarker_5, GTC HBMMarker_6, and GTCHBM_Marker_7 (See Fig. 2).

Blood (20 ml) was drawn into lavender cap (EDTA containing) tubes by a certified phlebotomist. The blood was stored refrigerated until DNA extraction. DNA has been extracted from blood stored for up to 7 days in the refrigerator without reduction in the -29- WO 01/92891 PCT/US01/16946 quality or quantity of yield. For those subjects that have blood drawn at distant sites, a shipping protocol was successfully used on more than a dozen occasions. Blood samples were shipped by overnight express in a styrofoam container with freezer packs to provide cooling. Lavender cap tubes were placed on individual plastic shipping tubes and then into "zip-lock" biohazard bags. When the samples arrived the next day, they were immediately processed to extract DNA.

The DNA extraction procedure used a kit purchased from Gentra Systems, Inc.

(Minneapolis, Minnesota). Briefly, the procedure involved adding 3 volumes of a red blood cell lysis buffer to the whole blood. After incubations for 10 minutes at room temperature, the solution was centrifuged in a Beckman tabletop centrifuge at 2,000 X g for 10 minutes.

The white blood cell pellet was resuspended in Cell Lysis Buffer. Once the pellet was completely resuspended and free of cell clumps, the solution was digested with RNase A for minutes at 37 C. Proteins were precipitated by addition of the provided Protein Precipitation Solution and removed by centrifugation. The DNA was precipitated out of the supernatant by addition of isopropanol. This method was simple and fast, requiring only 1-2 hours, and allowed for the processing of dozens of samples simultaneously. The yield of DNA was routinely >8 mg for a 20 ml sample of whole blood and had a MW of>50 kb.

DNA was archived by storing coded 50 gg aliquots at -80°C as an ethanol precipitate.

DNA was genotyped using one fluorescently labeled oligonucleotide primer and one unlabeled oligonucleotide primer. Labeled and unlabeled oligonucleotides were obtained from Integrated DNA Technologies, Inc. (Coralville, Iowa). All other reagents for microsatellite genotyping were purchased from Perkin Elmer-Applied Biosystems, Inc. ("PE- ABI") (Norwalk, Connecticut). Individual PCR reactions were performed for each marker, as described by PE-ABI using AmpliTag DNA Polymerase. The reactions were added to 3.5 yl WO 01/92891 PCT/US01/16946 of loading buffer containing deionized formamide, blue dextran and TAMRA 350 size standards (PE-ABI). After heating at 95 C for 5 minutes to denature the DNA, the samples were loaded and electrophoresed as described in the operator's manual for the Model 377 DNA Sequencer (PE-ABI, Foster City, California). After gel electrophoresis, the data was analyzed using PE-ABI GENESCAN T M and GENOTYPER TM software. First, within the GENESCANTM software, the lane tracking was manually optimized prior to the first step of analysis. After the gel lane data was extracted, the standard curve profiles of each lane were examined and verified for linearity and size calling. Lanes, which had problems with either of these parameters, were re-tracked and verified. Once all lanes were tracked and the size standards were correctly identified, the data were imported into GENOTYPER TM for allele identification To expedite allele calling (binning), the program Linkage Designer from the Internet web-site of Dr. Guy Van Camp (http://alt.www.uia.ac.be/u/dnalab/ld.html) was used.

This program greatly facilitates the importing of data generated by GENOTYPER T M into the pedigree drawing program Cyrillic (Version 2.0, Cherwell Scientific Publishing Limited, Oxford, Great Britain) and subsequent linkage analysis using the program LINKAGE (Lathrop et al., Am. J Hum. Genet., 37:482-498 (1985)).

III. Linkage Analysis Fig. 1 demonstrates the pedigree of the individuals used in the genetic linkage studies for this invention. Specifically, two-point linkage analysis was performed using the MLINK and LINKMAP components of the program LINKAGE (Lathrop et al., Am. J. Hum. Genet., 37:482-498 (1985)). Pedigree/marker data was exported from Cyrillic as a pre-file into the Makeped program and converted into a suitable ped-file for linkage analysis.

-31- WO 01/92891 PCT/US01/16946 The original linkage analysis was performed using three models: an autosomal dominant, fully penetrant model, (ii) an autosomal dominant model with reduced penetrance, and (iii) a quantitative trait model. The HBM locus was mapped to chromosome 1 lq12-13 by analyzing DNA for linked markers from 22 members of a large, extended kindred. A highly automated technology was used with a panel of 345 fluorescent markers which spanned the 22 autosomes at a spacing interval ranging from 6-22 cM. Only markers from this region of chromosome 11 showed evidence of linkage (LOD score The highest LOD score (5.74) obtained by two-point and multipoint analysis was D 1S987 (map position in Fig. The 95% confidence interval placed the HBM locus between markers D11S905 and D 1 S937 (map position 41-71 in Fig. Haplotype analysis also places the Zmaxl gene in this same region. Further descriptions of the markers D 11S987, D11S905, and D 1S937 can be found in Gyapay et al., Nature Genetics, Vol. 7, (1994).

In this invention, the inventors report the narrowing of the HBM interval to the region between markers Dl11S987 and GTC_HBM_Marker_5. These two markers lie between the delimiting markers from the original analysis (D11S11S905 and D11S937) and are approximately 3 cM from one another. The narrowing of the interval was accomplished using genotypic data from the markers D11S4191, D11S1883, D11S1785, D11S4113, D11S4136, D11S4139, (Dib et al., Nature, 380:152-154 (1996)), FGF3 (Polymeropolous et al., Nucl, Acid Res., 18:7468 (1990)) (information about the genetic markers can be found at the internet site of the Genome Database, http://gdbwww.gdb.org/), as well as the markers GTCHBMMarker_l, GTC_HBMMarker_2, GTC_HBMMarker_3, GTC_HBM_Marker_4, GTC_HBM Marker_5, GTC_HBMMarker_6, and GTCHBM Marker 7.

-32- WO 01/92891 PCT/US01/16946 As shown in Fig. 1, haplotype analysis with the above genetic markers identifies recombination events (crossovers) in individuals 9019 and 9020 that significantly refine the interval of chromosome 11 to which the Zmaxl gene is localized. Individual 9019 is an HBM-affected individual that inherits a portion of chromosome 11 from the maternal chromosome with the HBM gene, and a portion from the chromosome 11 homologue. The portion inherited from the HBM gene-carrying chromosome includes markers D11S935, D11S1313, GTC_HBM_Marker_4, D11S987, D11S1296, GTC_HBMMarker_6, GTC_HBM_Marker_2, D11S970, GTCHBMMarker_3, D11S4113, GTC_HBM_Marker l, GTC_HBM_Marker_7 and GTCHBMMarker_5. The portion from D11S4136 and continuing in the telomeric direction is derived from the non-HBM chromosome. This data places the Zmaxl gene in a location centromeric to the marker GTC HBM Marker_5. Individual 9020 is an unaffected individual who also exhibits a critical recombination event. This individual inherits a recombinant paternal chromosome 11 that includes markers D11S935, D11S1313, GTCHBM_Marker_4, D11S987, D11S1296 and GTCHBM_Marker_6 from her father's (individual 0115) chromosome 11 homologue that carries the HBM gene, and markers GTCHBMMarker_2, D11 S970, GTCHBMMarker_3, GTCHBM_Marker_1, GTC_HBMMarker_7, D11S4136, D11S4139, D11S1314, and D11S937 from her father's chromosome 11 that does not carry the HBM gene. Marker D11 S4113 is uninformative due to its homozygous nature in individual 0115. This recombination event places the centromeric boundary of the HBM region between markers D1 IS 1296 and D 1 S987.

Two-point linkage analysis was also used to confirm the location of the Zmaxl gene on chromosome 11. The linkage results for two point linkage analysis under a model of full penetrance are presented in Table 1 below. This table lists the genetic markers in the first -33- WO 01/92891 PCT/US01/16946 column and the recombination fractions across the top of the table. Each cell of the column shows the LOD score for an individual marker tested for linkage to the Zmaxi gene at the recombination fraction shown in the first row. For example, the peak LOD score of 7.66 occurs at marker D11 S970, which is within the interval defined by haplotype analysis.

TABLE 1 Marker 0.0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 D11S935 infinity 0.39 0.49 0.47 0.41 0.33 0.25 0.17 1 0.10 D11S1313 infinity 2.64 2.86 2.80 2.59 2.30 1.93 1.49_ 1.00 1 D11S987 infinity 5.49 5.18 4.70 4.13 3.49 79 2.03 1.26 D11S4113 4.35 3.99 3.62 3.24 2.83 2.40 1.94 1.46 0.97 D11S1337 2.29 2.06 1.81 1.55 1.27 0.99 0.70 0.42 0.18 D11S970 7.66 6.99 6.29 5.56 4.79 3.99 3.15 2.30 1.44 D11S4136 6.34 5.79 5.22 4.61 3.98 3.30 2.59 1.85 1.11 D11S4139 6.80 6.28 5.73 5.13 4.50 3.84 3.13 1 2.38 1.59 FGF3 0.59 3.23 3.15 2.91 2.61 2.25 1.84 11.40 0.92 D11S1314 6.96 6.49 5.94 5.34 4.69 4.01 3.27 2.49 1.67 D11S937 -infinity 4.98 4.86 4.52 4.06 3.51 2.88 2.20 1.47 A single nucleotide polymorphism (SNP) further defines the HBM region. This SNP is termed SNP Contig033-6 and is located 25 kb centromeric to the genetic marker GTC_HBM_Marker_5. This SNP is telomeric to the genetic marker GTCHBM_Marker_7.

SNP_Contig033-6 is present in HBM-affected individual 0113.. However, the HBM-affected individual 9019, who is the son of 0113, does not carry this SNP. Therefore, this indicates that the'crossover is centromeric to this SNP. The primer sequence for the genetic markers and GTC_HBM_Marker 7 is shown in Table 2 below.

-34 WO 01/92891 PCT/US01/16946 TABLE 2 Marker Primer (Forward) Primer (Reverse) GTC HBM Marker 5 TTTTGGGTACACAATTCAGTCG AAAACTGTGGGTGCTTCTGG GTC HBM Marker 7 GTGATTGAGCCAATCCTGAGA TGAGCCAAATAAACCCCTTCT The kindred described have several features of great interest, the most important being that their bones, while very dense, have an absolutely normal shape. The outer dimensions of the skeletons of the HBM-affected individuals are normal, and, while medullary cavities are present, there is no interference with hematopoiesis. The HBM-affected members seem to be resistant to fracture, and there are no neurologic symptoms, and no symptoms of impairment of any'organ or system function in the members examined. HBM-affected members of the kindred live to advanced age without undue illness or disability. Furthermore, the HBM phenotype matches no other bone disorders such as osteoporosis, osteoporosis pseudoglioma, Engelmann's disease, Ribbing's disease, hyperphosphatasemia, Van Buchem's disease, melorheostosis, osteopetrosis, pycnodysostosis, sclerostenosis, osteopoikilosis, acromegaly, Paget's disease, fibrous dysplasia, tubular stenosis, osteogenesis imperfecta,hypoparathyroidism, pseudohypoparathyroidism, pseudopseudohypoparathyroidism, primary and secondary hyperparathyroidism and associated syndromes, hypercalciuria, medullary carcinoma of the thyroid gland, osteomnalacia and other diseases. Clearly, the HBM locus in this family has a very powerful and substantial role in regulating bone density, and its identification is an important step in understanding the pathway(s) that regulate bone density and the pathogenesis of diseases such as osteoporosis.

In addition, older individuals carrying the HBM gene, and therefore expression of the HBM protein, do not show loss of bone mass characteristic of normal individuals. Moreover, individuals carrying the HBM gene have lower triglycerides, VLDLs, and LDLs and/or WO 01/92891 PCT/US01/16946 increased HDLs. In other words, the HBM gene is a suppressor of osteoporosis and may lessen cardiovascular risk arteriosclerotic and/or atherosclerotic associated conditions. In essence, individuals carrying the HBM gene are dosed with the HBM protein, and, as a result, lower levels of detrimental lipids VLDL, LDL and triglycerides). This in vivo observation is strong evidence that treatment of normal individuals with the HBM gene or protein, or a fragment thereof, will ameliorate osteoporosis and arterio- or atherosclerotic conditions or diseases.

IV. Physical Mapping To provide reagents for the cloning and characterization of the HBM locus, the genetic mapping data described above were used to construct a physical map of the region containing Zmaxl on chromosome 11q13.3. The physical map consists of an ordered set of molecular landmarks, and a set of BAC clones that contain the Zmaxl gene region from chromosome 11q13.3.

Various publicly available mapping resources were utilized to identify existing STS markers (Olson et al., Science, 245:1434-1435 (1989)) in the HBM region. Resources included the GDB, the Whitehead Institute Genome Center,.dbSTS and dbEST (NCBI), 1 Idb, the University of Texas Southwestern GESTEC, the Stanford Human Genome Center, and several,literature references (Courseaux et al., Genomics, 40:13-23 (1997), Courseaux et al., Genomics, 37:354-365 (1996), Guru et al., Genomics, 42:436-445 (1997), Hosoda et al., Genes Cells, 2:345-357 (1997), James et al., Nat. Genet., 8:70-76 (1994), Kitamura et al., DNA Research, 4:281-289 (1997), Lemmens et al., Genomics, 44:94-100 (1997), Smith et al., Genome Res., 7:835-842 (1997)). Maps were integrated manually to identify markers mapping to the region containing Zmaxl.

-36- WO 01/92891 PCT/US01/16946 Primers for existing STSs were obtained from the GDB or literature references are listed in Table 3 below. Thus, Table 3 shows the STS markers used to prepare the physical map of the Zmaxl gene region.

-37- TABLE 3: HBM STS Table STS Name Locus Horn Type GOB Access. Size (kb Forward Primer Reverse PrimerGeeNm ACTN3 Gene GD13:1976 0.1164 CTGGACTAC0 rGGCCTTCT( 1TCAGAAGCACTGGCTGG AcItoin alpha 3skeletal mnuscle PC-BIPC-Y Gene GDB:197884 0.125 CTCAGTGCCATGAAGATGGJ CAAGATCACTCGATCTCCAGG Fyruvate CaiboxyLase 21132181 Gena.e 0,322 GMCtAGGAG AG1CAGAOTO TTC1GCAGGTTGCTG1TGAG Adenosina Receptcc (A2 Gene ADR8KI Gene 000:4590179 0.117 TATGTGAfl fCCCGIGGC ___GCCCTCTGTCCTGACTTCALGG Beta-adfLegic receptor Ideasa PSANKa GENE 0.250 GAGAAAGAAATAAGGGGACU 1GCnTGTAAAGCACTGAGA sim, to Human andopenousttrovirus mRNA long terminal repeat PI(U2/PIIW2 Gone 0131:1197M6 0.208 CAAGTACGGGCAG1FTCAGTGGtCCT ATACACCAAGGTCCATG1TCCCCGT Pmalain nheSnhatasa 1, Catalytic subunit, ateha isaforro GSTPI.PCR1 Gene GDDB:270056 0.19 AGCCTGGGCCACAGCGTGA 3ACTAC TCCCGGAGCYTGOACACCC( CTrCA Glutaltone S-trnansferase pi NDUFVI ____Gene 1(521 CATGTGCCCACCTCA1TCAT CAAGATTC1GTAGCTCTGG ____IAOl dehydranase (ubiquinons) flavoprotein 1 (SIMI) PSANK2 GENE (0157 CAGAGAAGTCAAGGGAC1T ATCCTCTCACATCCCACACT N'dehyde, Dehydrogenase 8 (AtLlHS) PSANKI 51_ 0.3 CAAGGGTAAMAGACGAAAAI___ TOAGGAOCA11TCATcTT Human ribsooear prolain L37 (PSANK1l pseudogona.

UT5620 1 w811917 MAT GDO:3146211 0.211 AAGTCGAGGCTOCAAGGAC GCCCTGTGTICCTTrCACTA AFMV289 ,ag 01131337 msAT' am:19980 0w 297GGIGTOAGGATCACTGG___ AGCTCATGGGGGCTATT Gana D.322 GCTTCTCCGAGTGTATCM( ATGGCAGAGGAC1[TAGAACA repareoslanin (GALl) 2465 027 V0WR .308:17750 GATCAGCGAACTrCCTCTCGGCTC TCCACATrGAGGACTGTGGf-AACG BCL-1 I BCLI Gene 0.205 GGTAATCACAGICTAACCGA TGCACTGTCflTGGATGCA -cell CjLeAYMphoma 1 Croin D21 (PRAD1 gene) CHN Gene G00BA590141 I 4aGGACAGCTGTAGTGGGGTT iTAGGG CAGGCGCAAAGGATGA ACG eeiD FGF4 Gena IGOB 4593113 5491CACCGATGAGTGCACGTTC tAGGAG CAGACAGAGATGCTCCACGCCIATAC Firbatgohfco FGFa-PCRI Gena IGOB18627 0. 161 ITCTGGGTGTGTCTGAAT ACACAG7TGCTCTAIGGT Fi__ brolast orath factor3 AFIAI64Zi12 13115913 MSAT 005.18151 0 f.22 CATTTGGGAAMTCCAGAAGA TAGGTGTCTTATTTTrGTFGCYrO AFcMA190YI16 MAT GOB:1222329 0.275 GACATACCATGAACACTATA AGAGG CAACCCATACCAGGGATAAG SHOC-1 5295 D11S46SS STS G05:740600 0,It147 GAACPAGAGOGGGIAAGTh GO TGAGGACACAGATACTGATG.GG SHOC-3084 D1184540 STS GOB:74D102 -0.167 GAAGTGTTCCCTTAAAT.CTTTG GAA TTTGTAGTTAG.TGAGGAG SHGC6-14407 O11s4sr4 sIB GD00740516 0159B CCTOTAACCCCCAGTCCC____ TCTrGCTrCCTAAGTrrCTCGG SH-GC-101946 011S4327 Gene GOB 674522 0.311 ACTCCATCCACCTCATCACTG TGOTGM1GCCTCATCTGAC LCheline Matss 5515 1S703 -STS GOB 196260 0MISS GTGGAC 3GC TCGAG G TGTTCACTCTTCTGCCTGCAG AFM147XOiO 0II11883 MSA. GOB 337595 0.183 AGCTGGACTCTCACAGAA1 3 CAAG.AGGCIGGTAGAAGGTG AFMA131' DIISS87 -MSAT GOB 195002 Cl )82 GACTCCAGTCTGGGCAATA AAAGC GGTGGCAGCATGACCTCTA AAG AI-Mb358a D11S4178 MSAT 0D13:6111922 0.2371CAGGCCCAGTOCCTG CGTGTCCAGAT2AAAGTG AieMa272yb5 D11S4113 MSATIGD608115 0.213 ACCTCACGGTGTAATCOG CTIGAAGCCCATCTITGC VW1-17803 ST GOB:4531644 O15 IAITrGCAAAGCTTGAGACTTCT AATCACTGTGCTrrGTGCC SGC31923 ST- GODB-45?86 01325 ACTTATrGTcAGCGTGGG.2 ACTCCO CGATGGCT1)CC WI-7741 iS4354 GENE 1310:677652 0.124 GAGCAGGGGAGAGAAGGC CCCAAGTGGCTGTrAlTO Yanstermaticn-sensitsiva protein IEF SSP 3521 SGC35223 EST GOB:4532598 0.iB AGCCAGTTA1TGTTATITI BATGC AAGAGTGAACAAAAGCAAACATACC Z~NF162 splicing factor I UIJI.57&4 EKI -005477 015 GTGGAGTGTGGGATFGGG ___TACTGTVTTGATMAGTArTCG1000 I-6315 01S44l8 EST GD1B:678804 0.224 ATOCTITCATGATTCTAATTAIT TCCCCCAAMAGMTGTAMAGG- 55 G131:4155 0.125 CTGGTC1-rcCTrGTGTGcIC ATCACCCAGGCOAGGGA1 itogen inducile nee MG-21 60U0201 551 0.128 TOAGAAGCAGAACTGTI1TTAACA CCTGCTrGAAAGTTCTAGAGCC W61 006:4592461 -0126 CAAGCCGGGT1TATGAAA___ GATGCCAGGACCATGGAC____ V61-6233 Gena GD1B:1222237 10 -IBGCATATAGAAACAATrrATrGCCG rTOTGAAGCAGGGACCA( AG Human0 tat interactive Podain (TIPSO) SGC31583_7__ Gene GDB3:'ro714321 0.207ICTACCAGACCACCAGGC CAAGCGAAAGCTGCCTTC Calcium activated neutral prateasa large subunit, muCANP. calpain 56020656 551 008:45840371 A0.1 GrTGTC1TGACTTCAGOiTCTOT ro ITICCTI'CACAATCAC7

T

ACTCC

S0034599) EST1 0.13 GCGTGGGG.ATATAGAGr.TCA ___TACGTGGCCAAGMAGCTASGG 36033927 EST OBA42382 0.15 UATATAICCCCAOTOTAAGG 0A hGOTTOCAGATGACC WI-Bel 6 0:11222236 0.124 TOOTITTTAAACCTTTAATGACAAAA TOTGOATOTATAC2CTGTTTCOG.

IM-12334 851 005:1222257- 0.127 AATrATTTAAAAGAGAGGAAA GCGA 1GGCTGTGAACTTCCTC1GA IM-18402 Gr~AAA~c7TAAGTTAcrrGr~c~TT WM-18671 55T 008:48554947 -0.131 ITGAAAAACCAT7TTCACCG TCTGCGGC1GTTGGATTT M-lark I/s-1285 851 008457680 0.209 TTGAAAAMCCA1 T/sn TCACCG TGTTOCTGTCCPAGCAGG .HMrk SGC33767 EST 008:4581106 0.5 CTTrATIGAAAACATTGAGTG)A- 1TGTCAAATCCCCCCAAAA .AtFtA42YU5 MSAT G08:.1222332- 0.181 AAACCACGArCNCCAA CCCTGGAAAGGTAAGATGCT SGC3374_______ 851T 005:4575826 -0.15 CTrGGTAGAGACAAGGT( TO/ TATCTGTGTGTAGTGCTTCA/sATGT SGC32272_______ EST 008:4581592 -0.135 G/sCCA/GGIGATTCAGGGO AGTGA/sGAAC1CTGCCT 56034145 5S1 G08:4583094 0,1 C/sGATAAAAGAGTCACTATGGCTCA CACTCTCCCACTrGTCC0 W-856ES :GD4974598 -0.133 TAITG/sT/AGC/sITAOTGA SOCCC TGGCAGTTAGGCACAGTOA Htuman 1. 1 kb1 meRNA upregulated in retiesie acid treatad H-L-60 noutrnpdlin ells SGC3II05 EST GD11:4567265 al 1TATGCCCAGAG.ATGACAGG 6 CCACTAMGGGCTATGTCE C SGC3002't Gene G0D:4580505 0.128 GCCAr.CTI.rT-rGAGTAAAC TrCC ICACTGGAG3CTACAAGTGGTIGG Human pyruvat carboeylase precursor W4-2876 1S4407 515S 008:57B54 1 0.125 CATCCCAACCATCACTCAG1 ____GGGGAOT/sGCTACGAr.TTGA SGC36985____ Gen 00:4571821 023 AGAGTACAU1TTGGAAGCAGT160 TGAAAGGAIAsTT1ATAGCC TiGA *./sl-lnjrtaratt protein Itb GCGT1607 11S4270 STS G13B:62624M 0137 !GA/GGfTrG*SCCCTCGAT(- ITGAGGGTTGGGAAGATCA r Wt-504 I1153974 551T GDO:5831142 I 0.1741CCTTCATAGC ACACCCG ICAOCTAACTGTG(ACATGC C ISGC31049 I ESFT G0B:45e0099 0f1TCT7TACTGTGCTTACAC7ITTCOT C IPA01GC-AGTCGGTAT CG TABLE 3:1-IBM STS Table TIGR-A002S117 EST 008:1222119 0.199 AGATCAGCAAGCAGATAG ATTCCACATGGATAGAC NDU7V1 VO5996 01192092 EST 008:4803 __0A CATArrTATGAGGTG7GCTACA(3G GGAlTI CTI :ATCTOcTG amoaxin EIVS11) Vv.199 ST G08:45758413 0.16 TTACAGCCACCAA 76117cc ATOTTGG ,T f CGqO Nuclear mlcleapparatus proleirf, NUM SC2319I2 EST 600:4587895 101 CACTGT ATCTCAITAAC F rGAGG YiTGATFlITG( TfTCTCCCAAA 81l-13b00 EST 8457793 0 .15 CCCCAC fCCCACT ITFAl I CCAGT CACCTrTAGTAGTCCTUFl CH-LO.GAATI 1101.1 7933 0il ss71 MSAT G131:6114255 0.103 AGGACI CAGCCTGCATCTAG ACCAC GCAT rGCACTAA.AAG §-G-C3661- Gen~e GDB:467719'1 0.134 GATGGGTCACACTAACCTGTGA, ACAll rATAl rrGGACATGCAACC LA~trcigprti amN WI-i 1974 EST G131:1222255 -0.108 AGCATG [UAATGTGTCAG0.A ATGTGGTGGGCTGGAAAG Carnillne palmitny teaneferase 1 WII-1,524 Gene 608:4574740 0.10a TCACATTCAAAAATCGGCMA CTGCCTOTGT0O.TGTCGC 2 ~-deegeeetreraeI 09 95148EST 008:40983336 0.131 TGT0T1rTCTCAGAAAPC;G GACCTCCTGTGACACCACG 95-9159 D)11S4381 EST 608:678M144 1 0.111 CCACC A TA AAGTr( roco GTAAGATTC~cACZTTGf6Cr FIF4 95-4232 STS 000:1222250 -0.175 CCTATAATGGGCTGACCA.__

ACTCCTCATGTGAAGTCACC

SHOC0-4167 EST 008:4689 0.161 CAGTGTGGCcGiiiTCATV -A C-~CACCTACC Humen DNA helicase gn 8P2 VVI-14303 TC TGA WI-16597 EST 600:4570938 0.15 CTGCAMTTATGAGAATC ACAG M TGTGG CTC___ VA-16__ EST G08:4585666 0.13 CAGGGOACTGAGATACACf A.CC RC2551CATTFORiI~c29S1CAfl- 111970 USI-T 608191094- 0.15 AAATCUTCTGOCCCC TGAACCOTGGAGCAGAG UT978 S111298 MSAT .1 6:198525 .382 CATTCCCCAGMTECAGAC GTGCTGGGATTACAGGTGT U281/1292 fllSGOSS EST 60:335218' 0.07 GCAGAGAAGTCCTGTTAGCC

CCATGCTAGAGAAGCACAA(

0118I 0118,168 STS 0.009 AGTGTGGOGCAGGACOTCr CAGACAGATAGCCTGGGfl 031108 IlS668 STS 608:119349 -ff.143 TCCCTCATC CCCITGTCTGT ___AGOCCCC CTG rGA-TAATC RH18048 ena 000-4572903 -M0.88 GA-TGCTTACCTAc;CACGGC; G_ AG AT T CCTATCfG G G CTAT 0 Akdehyde dehydrogenes aL0 NUHMAP Gon 0:90097 -0.899 TGGCAGACCATGCTCCGCCT ____GAGAAG(3CCGGGAGUGCTC1 H iuman DNA helicase non (SMBP2) KRI4I Gene 608:4590244 d.-277 C-CCATOACAAOOAGAITTGAGGr.T G6TGTGATCTCTAAG Nuclear miic apparatus protein 1. IU&8A KRI41Gans 608:490232 0.1229 AGTGGGAAACC-tCAGGTAGC TCCCG CAGITTGGCTCAGArATATG OGG6C Iligh -aphur keraIIA KEN OdaiffD6 DI1IS2302 EST 00D:A45887 U.091 CA I AAGTAGTGGGGG0Go, S CAAAGCGACAGTGAGTTAG( RHI0753 Gone 008:459358a '3194 42GAGTAGAC ~GArrACTG CATGGTCTATfATTCTCG Proeainhesphatase 2A,*P2 EMSI e 008:545901 -50.94 eGecCTGGATCCTCACACTA CA GGGGATCAGGGGATGGGT AGA Aenplai SHIGC4108 DXS9736 Gene 008:737974 0 .137 GCT;CCTATCTGTGTTrrOAA GG CCGTGGCATAAGAMTA.AG drgneeto INPPLI -Goe G00:459009fl 0.382 CTTGGAG3CGCTATGAGGAGGC ATGGCAACTGACCTTCCGTCT iCytennoolpyphosph ate phosehes-like 1 RH18051 EST GD0:4572858 i0.195 TTGGAOTCACAGGGGC CA GTATCCTTGGGG NUFM Cdalcoll D11182297 ST 008:445969 _0.1 AACAJA0CTOOTTACCACCjTO GATOGQACCAACTOGT TAO 124911250 .31151957 EST IG00:335210 0.247 TMlCCAAATGTACTT cAATccc:AAccaT-AAcA( O NOULFVI D1IS2245 EST 008:445695 CTTGA1r-TCGCCCAGGAAC___ GCTCgCIrGAGGATGAAGAC NOUFVl AFMb32z D113,4138 MAT 608:809549 0.19 GAATCGCTTGAACCCAG. CCAGGTG M1TACOG AE!10150,ra0 03118,4198 MSAT 00B:1514025 0.2 GAAGVTfTTATGTAGGCC T TAATGGTCGCTGTCCC C1.17.l2 01182288 657T 608:445842 0.156 AGOGAAAATGGTATGTOGG. TAG OCAGTGTGTGAAGGCAGG SIHGC -1364 2118!991E EST 008:4082785 -0.137 AGTGGACAAAATGAGGAAA CAGG CCAACACAGMTGCTCAC/ TGCO Ri-7410 EST 00D:4571597 -0.128 TGCT1FC1ATG GITCCCArrTGATACC 6 RF117414 EST 600:5710595 0.121 AGCTCTTGCTTCTCAGTCCA AA GTTTCTGTGMTT rr RI117270 EST 60:47201 0267 GOCTCTCAAAGTAGTTGGAACC TGTACTAGCA CA SEA ST GD6849019 D13 CTCAAGGCCAGGCATCACT GACTCTTCCATGCCAGTT 81 ava ~tbatssocnn ooo RHI0689 EST l08:488349 0.107 AATGAT6ATCTGAACICTG

ACTGAAGAACTCTTTOO

TIGR-A007015 EST 609:4587592 -0.236 GACATCTGTFA-GTCTCArAkT-rC GGTAACAGTGTC1-TGCT TIRA0D5Gone 008:458B398 0.24 CTATGTACAAAACAGGAAC.AG ATCCTAG1TICCTOTCCI enln gene (EI TIGRI-ADOUB14 EST 008:45988682 10.141 dT-AAATGAGAAACAGACA( ATGA CTATTGG ATGT0ATATGTT 1.TGG TIGR-AG09K1 1 EST 000:4589894 .203 AAGTAGiAAACAAAATGAGGiGAC CTACCCCAAGGTAACAG TIGR-ACDBPiS EST 000:409892 0.192 ACITCCTATAAATrGAGGJ 3AG GA6GAGCTTCAAGAGGAA 1108-A005T1 EST G01:4589278 0.108 CATACTCCTAGACTCAAG1 ATC OJTGATQTA CATGOAA1TCMfIG 1168-Afto81ulS EST 008:4059394 £1107 GTGTTGAGGAGAAAAGCACT CTCCA TAGTCACATTCC I16GR-AOX45 EST GOB:46938 0.242 CAAGTACAAATACTrMIAoCC CAAGACCCTATCTCTAcAAoA SH-GC-l 7839 D1184611 Gans IGOB740339 U.151i i IIAI rAGAAGTGACTCT-UGDCO GACTACCTGCGCTCAGCTTO F olata receptor 2 (FBP2) NIE81242 01S920 ST 00aB388276 0.149 1TCTCATGTACAAAGC6GTC CCACTGGCTTCTTCTflr rGMP-sfimulated3O,8 1 ccl nclaeod Plluephociestarase PDE2A3 (POE2AI !116-C3599 D2291663 Gene 008:737599 0.14? CACCAGAAuMGGTGTo ACTAITACGACA I AARGC OG Maecrapnaga Migratio "f3bit factor S§HGC-1 1867- 011S43 oe 00:974984 0-14 (TOATGCTGGATGACCCC TTUCCTFTrGAAACTTAATCC E'21. Purimeceptor SHIGC-15349 D12S212 4 EST 008:7408189 0.1141 1TCACAGCCTECAGTCA-GG I ACATGrTGTGGCACCkA 15 B&e84450 )11S235 SOT 00:445882 095 C OTGAGCTACTGCCACAG CCCTGA1TrGGACAG1 7CC Bda99j07 DIIS2238 EST 00:484-(.09 TCAGAGTCACTCCTOCCC CAAATTCAAGCTCATCC AGACO foin Genet A 708:197 C19G0ATFCATCCAGGAC 3GTOTACGAGGTGCGI CAAT Frtt rcilor2 tFBP2)__ NIB01738 31154284 EST 008:529260 11.15 TCCAT ATTGAGCAC T CITMAGCCACTGTGm ITOG M5-7351 631184433- Gene 008:879143 l)34CCTCCTACACCTGCAAAAGC TC CAAG/ ACCCCAGAO 3AC Fotate receptoG (FOP3) 95-14320 EST 000:4*.578017, 0.31AGAA 61GGC GCCATATG [W5-15192 EST G0:50 0.1jGGACCrOC A J ACAATCT 7ATCACAGG TABLE 3: HBM STS Table M~-17872 GDW.45742 0.141 AAMMPGGACAG-IGTGTAAANTGA AATTGiTrGTmTTGrMAGT S"GC-30732 ESiT G0004567830 0.1 6 GATfAGCGAGTACAAGTGCGC GGGGACAAATATACTTATTCAGG stSG42Sf FST GDtBASESW5 DA1 3 CCATCATrATArFlGGTGACC TGGCTGCCOAAGAAGAAG VVI-13814 (208:4579290 0.1 TTAAGATGCCATrAAACTCATGAC CCAAGGAGATGACCAAGTGG DRES9 VVI-14122 Gens GOB:4576114 01T26 CCATCTCTIMATCAGGGTTGG CTCTGTGCAAGTAAGCATCTYACA HurnenVEGF related ftoir Isefrm VIFiss procursor eJRFI 2729/273D D)11S4057 EST (20:596609 0.118 CGACTGTGIATITCCACAG AGAAGCCCATArCAATGCAC SHGC-31329 EST Gtia:4567386 0115 AGC1TFAAGTAGGACAACCATGG GGATGCITCACTCCAGAAAG SGCS3858 EST -G131:467600 0.27 TGTTA11TCCACOTGCC AGA(2TGGCTGCAGGCCAG VVI-12191 EST IGOB1222208 0.16 TTrr1TMACACGAA.TTTGAGG TGAGGAA.GTAAAAACAGGI DATC 161-13701 EST IGOA574892 0.15jATGAA.ATCTTAAGCA63AATCCCA CACAGAGTCCCAGGGTCTGT VVI-14069 EST -GOBA4584373 0.15 AAAGGCCMTATITATCTOTCTCTG VVI1-4272 EST GD13:578525 0.125 GCTrCTAAGTCTrAGAGTCAGGTGG- Wdi-17347 EST GOB3:4676623 0.127 TTIGTA-AA*CGATGCCCAGA. GTC/CC0TC s[SGI551 EST (206:4564415 0.215 ACACAGCATGCAGGGAGAG ATCCCTGGTGCTTAGGTGG siS~li93 EST (208:4564568 0.137 GATGAAGTAGCTCCTCTCC-G GGAAGGCCAGCAAGTACTACG sLS02769 EST (20:4566137 0.141 CCGGTCCTTGC2AGAATG ____GAAGTGTCTCTGrrGGGG11 RH97 GDOB:4559690 -0.17 TTACAGGCATGAGTCACTA GC ACCACTCTCACAGCCCTTAC A slSG4794 EST (205:4573113 -0.141 CCCTCCCTCCACACACAC GCTCACTGAAC1TrCAGGGL.

e54957 EST GDB:4569051 0.171,AGATACGGOCAAAACACT0O3 GTTflAATATAGA(CAGGGCC s[SG4974 EST (206:466903 O.168 flCTGAGGTCAGGGOTGTC r AGiflTG2AAAATCTCGTr.TCA~ stEGE1144 (20:4573137 -0.17 ACTCA(2TCCCTCCCACCC ____TCCTGTCACTCC1TCCCAGA st506275 ESTI GDB:4569999 0.19 GTGATCAGGGCTCAACCTG BHGC-10667 111S4583 Gene GOB:740246T -W0.277 CTGGAGCTCTCAGTfC TCAAMAGTGCTGGTOACAGC Human protein kinaea (MLK-3) SHGC-11930 GOS1:1231223 0. 121 ATITCCAGAGCCAGCTCAAA C1TAATG1TrGTGATGACACAAAGC FGF SIAGC-32786 EST Gog-:456671012 GATCA.TGCAcTGTTGAccAC. TACAITTGAAMCATTAPAACCTGA FKBP2 Gene 0.064 ZZCTGAGCTGTAACCAGACTSGGA TGGAACAGTCTGGTCCTGATGO "466-Binding Preti Procursaor(FI{BP-13) I-13116 GOB3:4585099 0.202 TACTTAGTCCCTO TOGTCACCTGTATrATTCTAGG MOUI ____Gene (206:4560084 0.859 TC1TCAACCTCT3CAGTAC CTCATCTCCAMCCTGTGTAACC 4F2 CelL-Surface Antigen Heavy Chain (4F2HCI S453 0116519 STS GOB3:195276 0.108,GTGI3CTGCAGTAATGTAACZ A2CAAGACAT2GCGTAMGT0C STSI-e6RL-1112al1 011133136 6T8 (203:647681 0.135 CTGA1TGAGAACCAGAACAG TAAAGCCCTATAACCTCTCO STS1-cSRL-44a3 C11S3830 STS GTC:547609 .0.1181TAGTAAI2GGACCTTCACCAG AGATGMTGGTATG.AC1TGG STSI-cSilL-3lb12 DIIS 12439 STS GDBA459728 111231GATGA7TAAACTCTCrTGGC GAGACAGCTAAGGACTCATG cSRL-419 D1161t3 STS G08:197824 0.1961GAGGTGGTGGGCACCTGTX AGAGGGGAGGAACACACOTT Folats FeceptpQ (FH?2) SH-GC.1 0323 Dl 1S4351 Gene (203:676135 141 IGACCAGAGTCTGCCCAGAAG TCCCCAGCTCTATCCCAC Conllagen binding protein 2, coligin-2 gene (CBP2) M6-9219 Gene (208:678176 0.1 IGGAGGGATGGACAAGTCTGA GTCCAGCTCGCTGACTATCC Rlinal outer segmenti membrane protein 1. ROMI (210 2NF ____Gene 0.172 TCAAAAOACAOTCATCTCOA GCAAAGGCT7ACCATATTO ZNF126 AFNMI52VI 0V18S4057 WAX GDR*:6037G7 0.198 GCTCAGCACCCCCA1T TCCCTGCTCGGGAAkC AFMbn33zh5 DII IS4162 ]VSATIG 1:611241 11263 GTTCTCCAGAGAGACAGCAG GAGAGCAAI2ACTATTGCC AFMbO3Byb9 01164139 USA,' (2.1:609821 0.151 TrATAGACTTCAGCCCTGCTSC CCTCT(2TAGGATGCAGTTG AS'M212xe3 D1161314 USA G'D:199202 0.209 1TGCTACGCACTCCTCTACT GTGAAGGCAGGAAATGTGAC 'A4-8813 EST 0.13 ATCCTAGACCAGAGGAGCCC CTCCCCOTGGTCCAGTrAT Safineftwronine tdneae M5-19649 0.252 AACTUUCATTTGCCAAGGGA AGCAGATCTGCTCTFGCGAT 'M-20154 0.25 ACACTTGTCATCGdT-AGGCA AAAA.GTATOAATGGGATGGC M8-22293 (203:4583384 0.142 GTGCAOGTGGCGTTTA1TT1" CCCTATATCTCCGTGTGCTC C DRES9 MI-75117 EST GDR81223732 0.274 GCTCTAGTG(GPACCTCAGG GAATI'CCAGGCTCTFTGT-__ Ultra inli-sulpluwrarin Prolein IKRNI) EST45557S EST 0.273 GGmOTGGTcTAAAGGCAAA CAGTACATGTGGTCACC,, VVI-21134 EST 0.293 GOTOCCTTGGAAflTCTG1T GTGCTGTGGTGGGGAA.AG Fas-associaing death dezaain-oontaining protein FADD 58-21695 EST_ 9 0.25 ATrCAAGUCCATC.CAGACCC IGAQTGI3C(f.TTTGAAACTC SHGC13-7373 01164567 ST6 GD08:740192 0.225 ATATITGACCGTGCACAAATACG AGACCTGGGAMAAGTGGAGAA SHGC-35533 07 0126 ATrGGCAGTGGMAATGCTT TTAATCFTrGTCAACTFCCTGAT ARIX Gene 0,242 tle cInetaca ago (natasaaaaad dc ci In jgfa Arix homeodomin podain, neturcendacrine specific txfactor CLCIFOCR Gerr GD1:5262M1 TCAGGGCCTG3TGTTGccorACTrTG AGCGATGTAAAGGOTACCAG1GCCG Chloride chennel currnt inducer, ICLN gene 31 96N21-HiL STS IAGGCAT~cAAGCrCl-A CCGGGAGGAGACATCTAT IS234C17-FIR. STS TOGTAAGCACAGAAAATGC AATGGATGGi3GGATrATT B236G10-HR

AAGCCGCAAA

247F23+iR STS ATCACTCTGAACTGCCACT CCCTTCTGTITrCTG1TT 1B337124-HL T______AGQAAG

TGGGTTATOGA

B337LS-IIL STS_ GCTCTGCAGTGGGTAAAA ACTCTCCAAOGACTGTGCG 8382610-HR CCCTITCTGAGGCAAGAT B1211-HR STS__57 C(2CTATGAGTCCCATCTG GATFCAGCTGCAATGAAGG 180017-HR67 TTGAGTACAO(2GGGTGAC 823696-HR ISTS ACCTGTCTCCTCTCCTGG TGCITrCTCTGTGr.GA 0 TABLE 3: HBM STS Table 2(bE22-1K 2312F21-HR !3373124-HR SS8SHR 1146418-HIL 11721412-HL 0172Hi2-HR 1215J11-HR 1223E54IR 131203.HR 1328GIO-HL 132BG1 5-HR 1329110-HL 1329110-HR Mo0901-IlL 3368G15-HR 336F16-HL 32501(11-HR 133501 -HR 3268123-IlL 3268123-H-R 1371E1 5-HR 3312F21-HL 33BD17-HL 336S931-HL 359H1 3444M1 I-HR 126SL23-HL 125OK11-HL 1269L23-HR 1334314.H-L 3364314-HR 347303-HR IISOD17-HL 120CE21 -HL 00

ITCTAP

GGAATCOCT1TcmCCA

GATGGGTGTGAATGAACAA

GCTGTGAGTGTCTTGGCT

GCCACCAAMGGAAAGAIT

TCACTTAGCAGGAGGCAG

GTGCAAAATGAGCAGCOU

TCCTCPAAACTGGGAATGA

ATCTCCCCZACYCAGAAG

TGAGCATA1TTCA1TAGC

GGTGOACAGAATTGTTCAT

GTAACACCAOCAGGGACA

GGOGGTGAGAAGTAGOAA

AGCTAGCATfOGGCTC1T C33CCTfACAAGGCAAGTA CACAAGT33TCTGGAAGOC

ACTTAS

0.1IS7IGAGGAGAAGATCCACAAGCG UWr I_ B444M1 1-HL B543019-HR B117N118-HR B543015-HL B442PS-HL 9357314-HR- B25DE21-HR 132SOE21,-HL B24BC16-HR 624aG16-IlL B16ODS-HR 853DL7-HR r3AACCACATCGTCACCAG TABLE 3: HBM STS Table ARRB1 2) ST _AkGCAGAGTC ACCACTTCG ARRBI(I 1T AG______CGGAG CTTTACT____CT P102F3S STS- G'B;O054145 GAGCGTGAGAGG1TGAGGA 3 AAACAAACTCCAGACriCACC N172A S TS GO:6054146' 0.208 CTGAACCACTACCTGTATGA ICTG CTAACTACTTAGTCCTACAGGGCCC NSQA S§TS DB:SGS4147 0.23 GAAGCATTHCAATACMfAACTG CCACTCCAGTGCACCCAATc cC1l1-44A STS GOB:605414 0.239 CTTCTCCTGGCCACTCTGAC OGTTTACCTTTGAATCCCAGi CN1677-2A STS 'IOB:6054149 0.271 TGAGGATGAATGAGCACATAGG fTGTGGTCCATGAGTAGC I cCIIl-524B G08:605415' 0.221 AGGGGAAGGAATGGrGG TCGGCTGAGEGGGCArnG P1171'3T STS 00:6054151. 0.18 ATTGMAGGTCCTCCAAAAGA AfGCTG AGAACr.TCAACATATCT11 r GGGG GAC ARRBI(3) C~am FGTATTGAGGAC1TrGCTUG CGGTACCATCCTCCTCTTuC B215J1I-HL 0.122 TTT(SGCCTCATCTATGCCC GGGTGACAGAGCAAGACTCC 11317G1-HR TS TTGCTCAAGTTCTCCTG.G ACCTFGTTGACGGGGAG B317G1I-HL STS CTTGGCTA1TIGGACAGC GGGCATTrACTCACTTGC B292JIS-HR ___STS CTTIGT AGTGTrAGGG TGrATGTGTrCTGO O10A18-HL STS CCAGTTCCACTGGATGTT ATGGGCTGTG1TTCTCAA 810MBS-HR STS__ BI CTGCCTATCCCTGGAGT AGTTTGTCCCTAGTGCCC S527D12-HL- STS CAACACGTCTGACATCCAT. GGATAGTGCACACCCA 0572J14-fI STS TGGGTOGTACTATTGTTCCOAT AG1TCCAGCCCCCTTACCAS B372JI-HL STS GCCACTATCATCCCTGTGT 1TICACATGGCAAGAACACG B37E17-HR(GSB STS AGAGTSGACACTAGGGXCGGG TGCCAGGATGr.AGATAAcAA 837Ei7-HL( CS STS i CCTGTGGCACACATATCAGC ACAACCAAGAAIGGAGCCAC B34F22-HiR GS) BTS .TGCTGTGTAACAAGTCCCCA TGAACGGAGGAccTACCAAG 834F22-HL(GB) TS GCAGGGTCCGACTCAGTAAG GCTfGTUAGTICCC1TTACGC B648P22-HRI ACAGTGGGGACAAAGACAG ____ACAGGGCACCTCCCAGTAG 8B2A4.HR2 TCTTCTGTAGGMCCCCL___ TGTCTCAAACCTCCCTCTC B640P22-HL SYS__ sI AACATATCCTCCCCAGCC ___CAGTCCrAGCCAATGACAAC BB2L11-HL(GB___ SIB CTCCTCTGCATGGGAGAATC AGACCTGGGACCAGTCTGTG 885J1-HL GB TB GGGAGAGGACGTCACAG GTTGGAAGATGGTGA 144A24-HL TS CAGOCATCTrCTATGTGCCA GGa( GACAG "CCA 882111-HR(G STS ACTTCGTGCAOTGAGTGTr, cC1TrCTACGGATGA CcA S8J3H G) ST___BI GGCTGCTGAGCTCMTTGAT TG-GGTCICTCTGCGTGAOCTT 88Lm-L G STS TCACCTAC7TCCAOCTCCG AGACCTGGGACCAGTCTGTG 8B8212 1-fIL3GS)___ STS CTCCTCTGCATGGGAG.AATC AICCAACTG3C WO 01/92891 PCT/US01/16946 Novel STSs were developed either from publicly available genomic sequence or from sequence-derived BAC insert ends. Primers were chosen using a script which automatically performs vector and repetitive sequence masking using Cross_match Green, U. of Washington) and subsequent primer picking using Primer3 (Rozen, Skaletsky (1996, 1997).

Primer3 is available at www.genome.wi.mit. edu/genome_software/other/primer3.html.

Polymerase chain reaction (PCR) conditions for each primer pair were initially optimized with respect to MgC1 2 concentration. The standard buffer was 10 mM Tris-HC1 (pH 50 mM KC1, MgC1 2 0.2 mM each dNTP, 0.2 gM each primer, 2.7 ng/pl human DNA, 0.25 U ofAmpliTaq (Perkin Elmer) and MgC1, concentrations of 1.0 mM, 1.5 mM, 2.0 mM or 2.4 mM. Cycling conditions included an initial denaturation at 94 0 C for 2 minutes followed by 40 cycles at 94°C for 15 seconds, 55°C for 25 seconds, and 72 0 C for seconds followed by a final extension at 72 C for 3 minutes. Depending on the results from the initial round of optimization the conditions were further optimized if necessary.

Variables included increasing the annealing temperature to 58 0 C or 60°C, increasing the cycle number to 42 and the annealing and extension times to 30 seconds, and using AmpliTaqGold (Perkin Elmer).

BAC clones (Kim et al., Genomics, 32:213-218 (1996), Shizuya et al., Proc. Natl.

Acad. Sci. USA, 89:8794-8797 (1992)) containing STS markers of interest were obtained by PCR-based screening of DNA pools from a total human BAC library purchased from Research Genetics. DNA pools derived from library plates 1-596 were used corresponding to nine genomic equivalents of human DNA. The initial screening process involved PCR reactions of individual markers against superpools, a mixture of DNA derived from all BAC clones from eight 384-well library plates. For each positive superpool, plate row (16) and column (24) pools were screened to identify a unique library address. PCR products -43- WO 01/92891 PCT/US01/16946 were electrophoresed m 2% agarose gels (Sigma) containing U.S Ig/ml etmhdlum bromide in IX TBE at 150 volts for 45 min. The electrophoresis units used were the Model A3-1 systems from Owl Scientific Products. Typically, gels contained 10 tiers of lanes with wells/tier. Molecular weight markers (100 bp ladder, Life Technologies, Bethesda, MD) were loaded at both ends of the gel. Images of the gels were captured with a Kodak CCD camera and processed with Kodak 1D software.' The gel data were exported as tab delimited text files; names of the files included information about the library screened, the gel image files and the marker screened. These data were automatically imported using a customized Perl script into FilemakerTM PRO (Claris Corp.) databases for data storage and analysis. In cases where incomplete or ambiguous clone address information was obtained, additional experiments were performed to recover a unique, complete library address.

Recovery of clonal BAC cultures from the library involved streaking out a sample from the library well onto LB agar (Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1982)) containing 12.5 gg/ml chloramphenicol (Sigma). Two individual colonies and a portion of the initial streak quadrant were tested with appropriate STS markers by colony PCR for verification. Positive clones were stored in LB broth containing 12.5 jgg/ml chloramphenicol and 15% glycerol at Several different types of DNA preparation methods were used for isolation of BAC DNA. The manual alkaline lysis miniprep protocol listed below (Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1982)) was successfully used for most applications, restriction mapping, CHEF gel analysis, FISH mapping, but was not successfully reproducible in endsequencing. The 44- WO 01/92891 PCT/US01/16946 Autogen and Qiagen protocols were used specilically for BAC DNA preparation tor endsequencing purposes.

Bacteria were grown in 15 ml Terrific Broth containing 12.5 gg/ml chloramphenicol in a 50 ml conical tube at 37 0 C for 20 hrs with shaking at 300 rpm. The cultures were centrifuged in a Sorvall RT 6000 D at 3000 rpm (~1800 g) at 4°C for 15 min. The supernatant was then aspirated as completely as possible. In some cases cell pellets were frozen at -200C at this step for up to 2 weeks. The pellet was then vortexed to homogenize the cells and minimize clumping. 250 tl of P1 solution (50 mM glucose, 15 mM Tris-HC1, pH 8, 10 mM EDTA, and 100 ug/ml RNase A) was added and the mixture pipetted up and down to mix. The mixture was then transferred to a 2 ml Eppendorf tube. 350 gl of P2 solution (0.2 N NaOH, 1% SDS) was then added, the mixture mixed gently and incubated for min. at room temperature. 350 1l of P3 solution (3M KOAc, pH 5.5) was added and the mixture mixed gently until a white precipitate formed. The solution was incubated on ice for min. and then centrifuged at 40C in a microfuge for 10 min. The supematant was transferred carefully (avoiding the white precipitate) to a fresh 2 ml Eppendorf tube, and 0.9 ml ofisopropanol was. added, the solution mixed and left on ice for 5 min. The samples were centrifuged for 10 min., and the supernatant removed carefully. Pellets were washed in ethanol and air dried for 5 min. Pellets were resuspended in 200 l. of TE8 (10 mM Tris-HC1, pH 8.0, 1.0 mM EDTA), and RNase A (Boehringer Mannheim) added to 100 pig/ml.

Samples were incubated at 37 0 C for 30 min., then precipitated by addition of CzH3ONa-3HO to 0.5 M and 2 volumes of ethanol. Samples were centrifuged for 10 min., and the pellets washed with 70% ethanol followed by air drying and dissolving in 50 Al TE8.

Typical yields for this DNA prep were 3-5 gig/15 ml bacterial culture. Ten to 15 ul were used WO 01/92891 PCT/US01/16946 for HindIII restriction analysis; 5 pl was used for NotI digestion and clone insert sizing by CHEF gel electrophoresis.

BACs were inoculated into 15 ml of2X LB Broth containing 12.5 ig/ml chloramphenicol in a 50 ml conical tube. 4 tubes were inoculated for each clone. Cultures were grown overnight (-16 hr) at 37 0 C with vigorous shaking (>300 rpm). Standard conditions for BAC DNA isolation were followed as recommended by the Autogen 740 manufacturer. 3 ml samples of culture were placed into Autogen tubes for a total of 60 ml or tubes per clone. Samples were dissolved finally in 100 pl TE8 with 15 seconds of shaking as part of the Autogen protocol. After the Autogen protocol was finished DNA solutions were transferred from each individual tube and pooled into a 2 ml Eppendorftube. Tubes with large amounts of debris (carry over from the pelleting debris step) were avoided. The tubes were then rinsed with 0.5 ml of TE8 successively and this solution added to the pooled material. DNA solutions were stored at 4 0 C; clumping tended to occur upon freezing at 0 C. This DNA was either used directly for restriction mapping, CHEF gel.analysis or FISH mapping or was further purified as described below for use in endsequencing reactions.

The volume of DNA solutions was adjusted to 2 ml with TE8, samples were then mixed gently and heated at 65 0 C for 10 min. The DNA solutions were then centrifuged at 4°C for 5 min. and the supernatants transferred to a 15 ml conical tube. The NaCi concentration was then adjusted to 0.75 M ml of 5 M NaCI to the 2 ml sample). The total volume was then adjusted to 6 ml with Qiagen column equilibration buffer (Buffer QBT). The supernatant containing the DNA was then applied to the column and allowed to enter by gravity flow. Columns were washed twice with 10 ml of Qiagen Buffer QC. Bound DNA was then eluted with four separate 1 ml aliquots of Buffer QF kept at 65 0 C. DNA was precipitated with 0.7 volumes ofisopropanol ml). Each sample was then transferred to -46- WO 01/92891 PCT/US01/16946 4 individual 2.2 ml Eppendorf tubes and incubated at room temperature for 2 hr or overnight.

Samples were centrifuged in a microfuge for 10 min. at 4 0 C. The supernatant was removed carefully and 1 ml of 70% ethanol was added. Samples were centrifuged again and because the DNA pellets were often loose at this stage, the supernatant removed carefully. Samples were centrifuged again to concentrate remaining liquid which was removed with a micropipet tip. DNA pellets were then dried in a desiccator for 10 min. 20 lA of sterile distilled and deionized HzO was added to each tube which was then placed at 4°C overnight. The four M1 samples for each clone were pooled and the tubes rinsed with another 20 /l of sterile distilled and deionized H20 for a final volume of 100 Al. Samples were then heated at 65 C for 5 min. and then mixed gently. Typical yields were 2-5 ug/60 ml culture as assessed by NotI digestion and comparison with uncut lambda DNA.

3 ml of LB Broth containing 12.5 yg/ml of chloramphenicol was dispensed into autoclaved Autogen tubes. A single tube was used for each clone. For inoculation, glycerol stocks were removed from -70 0 C storage and placed on dry ice. A small portion of the glycerol stock was removed from the original tube with a sterile toothpick and transferred into the Autogen tube; the toothpick was left in the Autogen tube for at least two minutes before discarding. After inoculation the tubes were covered.with tape making sure the seal was tight. When all samples were inoculated, the tube units were transferred into an Autogen rack holder and placed into a rotary shaker at 37 C for 16-17 hours at 250 rpm. Following growth, standard conditions for BAC DNA preparation, as defined by the manufacturer, were used to program the Autogen. Samples were not dissolved in TE8 as part of the program and DNA pellets were left dry. When the program was complete, the tubes were removed from the output tray and 30 pl of sterile distilled and deionized H20 was added directly to the bottom of the tube. The tubes were then gently shaken for 2-5 seconds and then covered with -47- WO 01/92891 PCT/US01/16946 parafilm and incubated at room temperature for 1-3 hours. DNA samples were then transferred to an Eppendorftube and used either directly for sequencing or stored at 4°C for later use.

V. BAC Clone Characterization for Physical Mapping DNA samples prepared either by manual alkaline lysis or the Autogen protocol were digested with HindIII for analysis of restriction fragment sizes. This data were used to compare the extent of overlap among clones. Typically 1-2 gg were used for each reaction.

Reaction mixtures included: 1X Buffer 2 (New England Biolabs), 0.1 mg/ml bovine serum albumin (New England Biolabs), 50 g/ml RNase A (Boehringer Mannheim), and 20 units of HindIII (New England Biolabs) in a final volume of 25 tl. Digestions were incubated at 37 0 C for 4-6 hours. BAC DNA was also digested with NotI for estimation of insert size by CHEF gel analysis (see below). Reaction conditions were identical to those for HindIII except that 20 units of NotI were used. Six ul of6X Ficoll loading buffer containing bromphenol blue and xylene cyanol was added prior to electrophoresis.

HindII digests were analyzed on 0.6% agarose (Seakem, FMC Bioproducts) in 1X TBE containing 0.5 tg/ml ethidium bromide. Gels (20 cm X 25 cm) were electrophoresed in a Model A4 electrophoresis unit (Owl Scientific) at 50 volts for 20-24 hrs. Molecular weight size markers included undigested lambda DNA, HindIII digested lambda DNA, and Haem digested X174 DNA. Molecular weight markers were heated at 65°C for 2 min. prior to .loading the gel. Images were captured with a Kodak DC40 CCD camera and analyzed with Kodak 1D software.

NotI digests were analyzed on a CHEF DRII (BioRad) electrophoresis unit according to the manufacturer's recommendations. Briefly, 1% agarose gels (BioRad pulsed field -48- WO 01/92891 PCT/US01/16946 grade) were prepared in 0.5X TBE, equilibrated for 30 minutes in the electrophoresis unit at 14 0 C, and electrophoresed at 6 volts/cm for 14 hrs with circulation. Switching times were ramped from 10 sec to 20 sec. Gels were stained after electrophoresis in 0.5 ug/ml ethidium bromide. Molecular weight markers included undigested lambda DNA, HindIII digested lambda DNA, lambda ladder PFG ladder, and low range PFG marker (all from New England Biolabs).

BAC DNA prepared either by the manual alkaline lysis or Autogen protocols were labeled for FISH analysis using a Bioprime labeling kit (BioRad) according to the manufacturer's recommendation with minor modifications. Approximately 200 ng of DNA was used for each 50 pl reaction. 3 gl were analyzed on a 2% agarose gel to determine the extent of labeling. Reactions were purified using a Sephadex G50 spin column prior to in situ hybridization. Metaphase FISH was performed as described (Ma et al., Cytogenet. Cell Genet., 74:266-271 (1996)).

VI. BAC Endsequencing The sequencing of BAC insert ends utilized DNA prepared by either of the two methods described above. The DYEnamic energy transfer primers and Dynamic Direct cycle sequencing kits from Amersham were used for sequencing reactions. Ready made sequencing mix including theM13 -40 forward sequencing primer was used (Catalog US79730) for the T7 BAC vector terminus; ready made sequencing mix (Catalog US79530) was mixed with the M13 -28 reverse sequencing primer (Catalog US79339) for the SP6 BAC vector terminus. The sequencing reaction mixes included one of the four fluorescently labeled dye-primers, one of the four dideoxy termination mixes, dNTPs, reaction buffer, and Thermosequenase. For each BAC DNA sample, 3 jl of the BAC DNA -49- WO 01/92891 PCT/US01/16946 sample was aliquoted to 4 PCR strip tubes. 2 pl of one of the four dye primer/termination mix combinations was then added to each of the four tubes. The tubes were then sealed and centrifuged briefly prior to PCR. Thermocycling conditions involved a 1 minute denaturation at 95 0 C, 15 second annealing at 45°C, and extension for 1 minute at 70 0 C for 35 total cycles.

After cycling the plates were centrifuged briefly to collect all the liquid to the bottom of the tubes. 5 p/ of sterile distilled and deionized HO 2 was then added into each tube, the plates sealed and centrifuged briefly again. The four samples for each BAC were then pooled together. DNA was then precipitated by adding 1.5 gl of 7.5 M NH 4 OAc and 100 1 of 0 C 100% ethanol to each tube. Samples were mixed by pipetting up and down once. The plates were then sealed and incubated on ice for 10 minutes. Plates were centrifuged in a table top Haraeus centrifuge at 4000 rpm (3,290 xg) for 30 minutes at 4 0 C to recover the DNA. The supernatant was removed and excess liquid blotted onto paper towels. Pellets were washed by adding 100 d of-20'C 70% ethanol into each tube and recentrifuging at 4000 rpm (3,290 xg) for 10 minutes at 4°C. The supernatant was removed and excess liquid again removed by blotting on a paper towel. Remaining traces of liquid were removed by placing the plates upside down over a paper towel and centrifuging only until the centrifuge reached 800 rpm. Samples were then air dried at room temperature for 30 min. Tubes were capped and stored dry at -20 0 C until electrophoresis. Immediately prior to electrophoresis the DNA was dissolved in 1.5 pl of Amersham loading dye. Plates were then sealed and centrifuged at 2000 rpm (825 xg). The plates were then vortexed on a plate shaker for 1-2 minutes. Samples were then recentrifuged at 2000 rpm (825 xg) briefly. Samples were then heated at 65 °C for 2 min. and immediately placed on ice. Standard gel electrophoresis was performed on ABI 377 fluorescent sequencers according to the manufacturer's recommendation.

WO 01/92891 PCT/US01/16946 VII. Sub-cloning and Sequencing of IBM BAC DNA The physical map of the Zmaxl gene region provides a set of BAC clones that contain within them the Zmax gene and the HBMI gene. DNA sequencing of several of the BACs from the region has been completed. The DNA sequence data is a unique reagent that includes data that one skilled in the art can use to identify the Zmaxl gene and the HBM gene, or to prepare probes to identify the gene(s), or to identify DNA sequence polymorphisms that identify the gene(s).

BAC DNA was isolated according to one of two protocols, either a Qiagen purification ofBAC DNA (Qiagen, Inc. as described in the product literature) or a manual purification which is a modification of the standard alkaline lysis/Cesium Chloride preparation of plasmid DNA (see Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons (1997)). Briefly for the manual protocol, cells were pelleted, resuspended in GTE (50 mM glucose, 25 mM Tris-Cl (pH 10 mM EDTA) and lysozyme mg/ml solution), followed by NaOH/SDS SDS/0.2N NaOH) and then an ice-cold solution of 3 M KOAc (pH RnaseA was added to the filtered supernatant, followed by Proteinase K and 20% SDS. The DNA was then precipitated with isopropanol, dried and resuspended in TE (10 mM Tris, 1 mM EDTA (pH The BAC DNA was further purified by Cesium Chloride density gradient centrifugation (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons (1997)).

Following isolation, the BAC DNA was sheared hydrodynamically using an HPLC (Hengen, Trends in Biochem. Sci., 22:273-274 (1997)) to an insert size of 2000-3000 bp.

After shearing, the DNA was concentrated and separated on a standard 1% agarose gel. A single fraction, corresponding to the approximate size, was excised from the gel and purified -51- WO 01/92891 PCT/US01/16946 by electroelution (Sambrook et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring, NY (1989)).

The purified DNA fragments were then blunt-ended using T4 DNA polymerase. The blunt-ended DNA was then ligated to unique BstXI-linker adapters GTCTTCACCACGGGG and 5' GTGGTGAAGAC in 100-1000 fold molar excess). These linkers were complimentary to the BstXI-cut pMPX vectors (constructed by the inventors), while the overhang was not self-complimentary. Therefore, the linkers would not concatemerize nor would the cut-vector religate itself easily. The linker-adapted inserts were separated from the unincorporated linkers on a 1% agarose gel and purified using GeneClean (BIO 101, Inc.). The linker-adapted insert was then ligated to a modified pBlueScript vector to construct a "shotgun" subclone library. The vector contained an out-of-frame lacZ gene at the cloning site which became in-frame in the event that an adapter-dimer is cloned, allowing these to be avoided by their blue-color.

All subsequent steps were based on sequencing by ABI377 automated DNA sequencing methods. Only major modifications to the protocols are highlighted. Briefly, the library was then transformed into DH5a competent cells (Life Technologies, Bethesda, MD, transformation protocol). It was assessed by plating onto antibiotic plates containing ampicillin and IPTG/Xgal. The plates were incubated overnight at 37 Successful transformants were then used for plating of clones and picking for sequencing. The cultures were grown overnight at 37 C. DNA was purified using a silica bead DNA preparation (Ng et al., Nucl. Acids Res., 24:5045-5047 (1996)) method. In this manner, 25 /2g of DNA was obtained per clone.

These purified DNA samples were then sequenced using ABI dye-terminator chemistry. The ABI dye terminator sequence reads were run on ABI377 machines and the -52- WO 01/92891 PCT/US01/16946 data was directly transferred to UNIX machines following lane tracking of the gels. All reads were assembled using PHRAP Green, Abstracts of DOE Human Genome Program Contractor-Grantee Workshop V, Jan. 1996, p.157) with default parameters and quality scores. The initial assembly was done at 6-fold coverage and yielded an average of 8-15 contigs. Following the initial assembly, missing mates (sequences from clones that only gave one strand reads) were identified and sequenced with ABI technology to allow the identification of additional overlapping contigs. Primers for walking were selected using a Genome Therapeutics program Pick_primer near the ends of the clones to facilitate gap closure. These walks were sequenced using the selected clones and primers. Data were reassembled with PHRAP into sequence contigs.

VIII. Gene Identification by Computational Methods Following assembly of the BAC sequences into contigs, the contigs were subjected to computational analyses to identify coding regions and regions bearing DNA sequence similarity to known genes. This protocol included the following steps.

1. Degap the contigs: the sequence contigs often contain symbols (denoted by a period symbol) that represent locations where the individual ABI sequence reads have insertions or deletions. Prior to automated computational analysis of the contigs, the periods were removed. The original data was maintained for future reference.

2. BAC vector sequences were "masked" within the sequence by using the program cross match (Phil Green, http:\\chimera.biotech.washington.edu\UWGC). Since the shotgun libraries construction detailed above leaves some BAC vector in the shotgun libraries, this program was used to compare the sequence of the BAC contigs to the BAC -53- WO 01/92891 PCT/US01/16946 vector and to mask any vector sequence prior to subsequent steps. Masked sequences were marked by an in the sequence files, and remained inert during subsequent analyses.

3. E. coli sequences contaminating the BAC sequences were masked by comparing the BAC contigs to the entire E. coli DNA sequence.

4. Repetitive elements known to be common in the human genome were masked using cross match. In this implementation of crossmatch, the BAC sequence was compared to a database of human repetitive elements (Jerzy Jerka, Genetic Information Research Institute, Palo Alto, CA). The masked repeats were marked by X and remained inert during subsequent analyses.

5. The location of exons within the sequence was predicted using the MZEF computer program (Zhang, Proc. Natl. Acad. Sci., 94:565-568 (1997)).

6. The sequence was compared to the publicly available unigene database (National Center for Biotechnology Information, National Library of Medicine, 38A, 8N905, 8600 Rockville Pike, Bethesda, MD 20894; www.ncbi.nlm.nih.gov) using the blastn2 algorithm (Altschul et al, Nucl. Acids Res., 25:3389-3402 (1997)). The parameters for this search were: E=0.05, v=50, B=50 (where E is the expected probability score cutoff, V is the number of database entries returned in the reporting of the results, and B is the number of sequence alignments returned in the reporting of the results (Altschul et al., J Mol. Biol., 215:403-410 (1990)).

7. The sequence was translated into protein for all six reading frames, and the protein sequences were compared to a non-redundant protein database compiled from Genpept Swissprot PIR (National Center for Biotechnology Information, National Library of Medicine, 38A, 8N905, 8600 Rockville Pike, Bethesda, MD 20894; www.ncbi.nlm.nih.gov).

54 WO 01/92891 PCT/US01/16946 The parameters for this search were E=0.05, V=50, B= 50, where E, V, and B are defined as above.

8. The BAC DNA sequence was compared to the database of the cDNA clones derived from direct selection experiments (described below) using blastn2 (Altschul et al., Nucl. Acids. Res., 25:3389-3402 (1997)). The parameters for this search were E-0.05, V=250, B=250, where E, V, and B are defined as above.

9. The BAC sequence was compared to the sequences of all other BACs from the HBM region on chromosome 11q12-13 using blastn2 (Altschul et al., Nucl. Acids. Res., 25:3389-3402 (1997)). The parameters for this search were E=0.05, V=50, B=50, where E, V, and B are defined as above.

The BAC sequence was compared to the sequences derived from the ends of BACs from the HBM region on chromosome 11q12-13 using blastn2 (Altschul et al., Nucl.

Acids. Res.,-25:3389-3 4 0 2 (1997)). The parameters for this search were E=0.05, V=50, where E, V, and B are defined as above.

11. The BAC sequence was compared to the Genbank database (National Center for Biotechnology Information, National Library of Medicine, 38A, 8N905, 8600 Rockville Pike, Bethesda, MD 20894; www.ncbi.nlm.nih.gov) using blastn2 (Altschul et al., Nucl.

Acids. Res., 25:3389-3402 (1997)). The parameters for this search were E=0.05, V=50, where E, V, and B are defined as above.

12. The BAC sequence was compared to the STS division of Genbank database (National Center for Biotechnology Information, National Library of Medicine, 38A, 8N905, 8600 Rockville Pike, Bethesda, MD 20894; www.ncbi.nlm.nih.gov) using blastn2 (Altschul et al., 1997). The parameters for this search were E=0.05, V=50, B= 50, where E, V, and B are defined as above.

WO 01/92891 PCT/US01/16946 13. The BAC sequence was compared to the Expressed Sequence (EST) Tag Genbank database (National Center for Biotechnology Information, National Library of Medicine, 38A, 8N905, 8600 Rockville Pike, Bethesda, MD 20894; www.ncbi.nlm.nih.gov) using blastn2 (Altschul et al., Nucl. Acids. Res., 25:3389-3402 (1997)). The parameters for this search were E=0.05, V=250, B=250, where E, V, and B are defined as above.

IX. Gene Identification by Direct cDNA Selection Primary linkered cDNA pools were prepared from bone marrow, calvarial bone, femoral bone, kidney, skeletal muscle, testis and total brain. Poly RNA was prepared from calvarial and femoral bone tissue (Chomczynski et al., Anal. Biochem., 162:156-159 (1987); D'Alessio et al., Focus, 9:1-4 (1987)) and the remainder of the mRNA was purchased from Clontech (Palo Alto, California). In order to generate oligo(dT) and random primed cDNA pools from the same tissue, 2.5 jig mRNA was mixed with oligo(dT) primer in one reaction and 2.5 tg mRNA was mixed with random hexamers in another reaction, and both were converted to first and second strand cDNA according to manufacturers recommendations (Life Technologies, Bethesda, MD). Paired phosphorylated cDNA linkers (see sequence below) were annealed together by mixing in a 1:1 ratio (10 og each) incubated at 65 C for five minutes and allowed to cool to room temperature.

Paired linkers oligol/2 OLIGO 1: 5'CTG AGC GGA ATT CGT GAG ACC3' (SEQ ID NO:12) OLIGO 2: 5'TTG GTC TCA CGT ATT CCG CTC GA3' (SEQ ID NO:13) Paired linkers oligo3/4 OLIGO 3: 5'CTC GAG AAT TCT GGA TCC TC3' (SEQ ID NO:14) -56- WO 01/92891 PCT/US01/16946 OLIGO 4: 5'TTG AGG ATC CAG AAT TCT CGA G3' (SEQ Paired linkers oligo5/6 OLIGO 5: 5'TGT ATG CGA ATT CGC TGC GCG3' (SEQ ID NO:16) OLIGO 6: 5'TTC GCG CAG CGA ATT CGC ATA CA3' (SEQ ID NO:17) Paired linkers oligo7/8 OLIGO 7: 5'GTC CAC TGA ATT CTC AGT GAG3' (SEQ ID NO:18) OLIGO 8: 5'TTG TCA CTG AGA ATT CAG TGG AC3' (SEQ ID NO:19) Paired linkers oligol 1/12 OLIGO 11: 5'GAA TCC GAA TTC CTG GTC AGC3' (SEQ ID OLIGO 12: 5'TTG CTG ACC AGG AAT TCG GAT TC3' (SEQ ID NO:21) Linkers were ligated to all oligo(dT) and random primed cDNA pools (see below) according to manufacturers instructions (Life Technologies, Bethesda, MD).

Oligo 1/2 was ligated to oligo(dT) and random primed cDNA pools prepared from bone marrow. Oligo 3/4 was ligated to oligo(dT) and random primed cDNA pools prepared from calvarial bone. Oligo 5/6 was ligated to oligo(dT) and random primed cDNA pools prepared from brain and skeletal muscle. Oligo 7/8 was ligated to oligo(dT) and random primed cDNA pools prepared from kidney. Oligo 11/12 was ligated to oligo(dT) and random primed cDNA pools prepared from femoral bone.

The cDNA pools were evaluated for length distribution by PCR amplification using 1 p1 of a 1:1, 1:10, and 1:100 dilution of the ligation reaction, respectively. PCR reactions were performed in a Perkin Elmer 9600, each 25 p1 volume reaction contained 1 pl of DNA, mrM Tris-HCI (pH 50 mM KCl, 1.5 mM MgCl2, 0.001% gelatin, 200 mM each -57- WO 01/92891 PCT/US01/16946 dNTPs, 10 gM primer and 1 unit Taq DNA polymerase (Perkin Elmer) and was amplified under the following conditions: 30 seconds at 940C, 30 seconds at 60 0 C and 2 minutes at 72 C for 30 cycles. The length distribution of the amplified cDNA pools were evaluated by electrophoresis on a 1% agarose gel. The PCR reaction that gave the best representation of the random primed and oligo(dT) primed cDNA pools was scaled up so that -2-3 gg of each cDNA pool was produced. The starting cDNA for the direct selection reaction comprised of gg of random primed cDNAs mixed with 0.5 gg of oligo(dT) primed cDNAs.

The DNA from the 54 BACs that were used in the direct cDNA selection procedure was isolated using Nucleobond AX columns as described by the manufacturer (The Nest Group, Inc.).

The BACs were pooled in equimolar amounts and 1 pg of the isolated genomic DNA was labelled with biotin 16-UTP by nick translation in accordance with the manufacturers instructions (Boehringer Mannheim). The incorporation of the biotin was monitored by methods that could be practiced by one skilled in the art (Del Mastro and Lovett, Methods in Molecular Biology, Humana Press Inc., NJ (1996)).

Direct cDNA selection was performed using methods that could be practiced by one skilled in the art (Del Mastro and Lovett, Methods in Molecular Biology, Humana Press Inc., NJ (1996)). Briefly, the cDNA pools were multiplexed in two separate reactions: In one reaction cDNA pools from bone marrow, calvarial bone, brain and testis were mixed, and in the other cDNA pools from skeletal muscle, kidney and femoral bone were mixed.

Suppression of the repeats, yeast sequences and plasmid in the cDNA pools was performed to a Cot of 20. 100 ng ofbiotinylated BAC DNA was mixed with the suppressed cDNAs and hybridized in solution to a Cot of 200. The biotinylated DNA and the cognate cDNAs was captured on streptavidin-coated paramagnetic beads. The beads were washed and the primary -58- WO 01/92891 PCT/US01/16946 selected cDNAs were eluted. These cDNAs were PCR amplified and a second round of direct selection was performed. The product of the second round of direct selection is referred to as the secondary selected material. A Galanin cDNA clone, previously shown to map to 11lq2-13 (Evans, Genomics, 18:473-477 (1993)), was used to monitor enrichment during the two rounds of selection.

The secondary selected material from bone marrow, calvarial bone, femoral bone, kidney, skeletal muscle, testis and total brain was PCR amplified using modified primers of oligos 1, 3, 5, 7 and 11, shown below, and cloned into the UDG vector pAMPIO (Life Technologies, Bethesda, MD), in accordance with the manufacturer's recommendations.

Modified primer sequences: Oligol-CUA: 5'CUA CUA CUA CUA CTG AGC GGA ATT CGT GAG ACC3' (SEQ ID NO:22) Oligo3-CUA: 5'CUA CUA CUA CUA CTC GAG AAT TCT GGA TCC TC3' (SEQ ID NO:23) Oligo5-CUA: 5'CUA CUA CUA CUA TGT ATG CGA ATT CGC TGC GCG3' (SEQ ID NO:24) Oligo7-CUA: 5'CUA CUA CUA CUA GTC CAC TGA ATT CTC AGT GAG3' (SEQ ID Oligol l-CUA: 5'CUA CUA CUA CUA GAA TCC GAA TTC CTG GTC AGC3' (SEQ ID NO:26) The cloned secondary selected material, from each tissue source, was transformed into MAX Efficiency DH5a Competent Cells (Life Technologies, Bethesda, MD) as recommended by the manufacturer. 384 colonies were picked from each transformed source and arrayed into four 96 well microtiter plates.

-59- WO 01/92891 PCT/US01/16946 All secondarily selected cDNA clones were sequenced using M13 dye primer terminator cycle sequencing kit (Applied Biosystems), and the data collected by the ABI 377 automated fluorescence sequencer (Applied Biosystems).

All sequences were analyzed using the BLASTN, BLASTX and FASTA programs (Altschul et al.,J. Mol. Biol., 215:403-410 (1990), Altschul et al., Nucl. Acids. Res., 25:3389- 3402 (1997)). The cDNA sequences were compared to a database containing sequences derived from human repeats, mitochondrial DNA, ribosomal RNA, E. coli DNA to remove background clones from the dataset using the program cross_match. A further round of comparison was also performed using the program BLASTN2 against known genes (Genbank) and the BAC sequences from the HBM region. Those cDNAs that were homologous to these sequences were filed according to the result and the data stored in a database for further analysis. cDNA sequences that were identified but did not have significant similarity to the BAC sequences from the HBM region or were eliminated by cross_match were hybridized to nylon membranes which contained the BACs from the HBM region, to ascertain whether they hybridized to the target.

Hybridization analysis was used to map the cDNA clones to the BAC target that selected them. The BACs that were identified from the HBM region were arrayed and grown into a 96 well microtiter plate. LB agar containing 25 tg/ml kanamycin was poured into 96 well microtiter plate lids. Once the agar had solidified, pre-cut Hybond N+ nylon membranes (Amersham) were laid on top of the agar and the BACs were stamped onto the membranes in duplicate using a hand held 96 well replica plater (V&P Scientific, Inc.). The plates were incubated overnight at 37°C. The membranes were processed according to the manufacturers recommendations.

WO 01/92891 PCT/US01/16946 The cDNAs that needed to be mapped by hybridization were PCR amplified using the relevant primer (oligos 1, 3, 5, 7 and 11) that would amplify that clone. For this PCR amplification, the primers were modified to contain a linkered digoxigenin molecule at the of the oligonucleotide. The PCR amplification was performed under the same conditions as described in Preparation of cDNA Pools (above). The PCR products were evaluated for quality and quantity by electrophoresis on a 1% agarose gel by loading 5 gl of the PCR reaction. The nylon membranes containing the stamped BACs were individually prehybridized in 50 ml conical tubes containing 10 ml of hybridization solution (5x SSPE, Blotto, 2.5% SDS and 1 mM EDTA (pH The 50 ml conical tubes were placed in a rotisserie oven (Robbins Scientific) for 2 hours at 65 C. 25 ng of each cDNA probe was denatured and added into individual 50 ml conical tubes containing the nylon membrane and hybridization solution. The hybridization was performed overnight at 65 The filters were washed for 20 minutes at 65 0 C in each of the following solutions: 3x SSPE, 0.1% SDS; Ix SSPE, 0.1% SDS and 0.1x SSPE, 0.1% SDS.

The membranes were removed from the 50 ml conical tubes and placed in a dish.

Acetate sheets were placed between each membrane to prevent them from sticking to each other. The incubation of the membranes with the Anti-DIG-AP and CDP-Star was performed according to manufacturers recommendations (Boehringer Mannheim). The membranes were wrapped in Saran wrap and exposed to Kodak Bio-Max X-ray film for 1 hour.

X. cDNA Cloning and Expression Analysis To characterize the expression of the genes identified by direct cDNA selection and genomic DNA sequencing in comparison to the publicly available databases, a series of experiments were performed to further characterize the genes in the HBM region. First, -61- WO 01/92891 PCT/US01/16946 oligonucleotide primers were designed for use in the polymerase chain reaction (PCR) so that portions of a cDNA, EST, or genomic DNA could be amplified from a pool of DNA molecules (a cDNA library) or RNA population (RT-PCR and RACE). The PCR primers were used in a reaction containing genomic DNA to verify that they generated a product of the size predicted based on the genomic (BAC) sequence. A number of cDNA libraries were then examined for the presence of the specific cDNA or EST. The presence of a fragment of a transcription unit in a particular cDNA library indicates a high probability that additional portions of the same transcription unit will be present as well.

A critical piece of data that is required when characterizing novel genes is the length, in nucleotides, of the processed transcript or messenger RNA (mRNA). One skilled in the art primarily determines the length of an mRNA by Northern blot hybridization (Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor NY (1989)). Groups of ESTs and direct-selected cDNA clones that displayed significant sequence similarity to sequenced BACs in the critical region were grouped for convenience into approximately 30 kilobase units. Within each 30 kilobase unit there were from one up to fifty ESTs and direct-selected cDNA clones which comprised one or more independent transcription units. One or more ESTs or direct-selected cDNAs were used as hybridization probes to determine the length of the mRNA in a variety of tissues, using commercially available reagents (Multiple Tissue Northern blot; Clontech, Palo Alto, California) under conditions recommended by the manufacturer.

Directionally cloned cDNA libraries from femoral bone, and calvarial bone tissue were constructed by methods familiar to one skilled in the art (for example, Soares in Automated DNA Sequencing and Analysis, Adams, Fields and Venter, Eds., Academic Press, NY, pages 110-114 (1994)). Bones were initially broken into fragments with a hammer, and -62- WO 01/92891 PCT/US01/16946 the small pieces were frozen in liquid nitrogen and reduced to a powder in a tissue pulverizer (Spectrum Laboratory Products). RNA was extracted from the powdered bone by homogenizing the powdered bone with a standard Acid Guanidinium Thiocyanate-Phenol-Chloroform extraction buffer Chomczynski and Sacchi, Anal.

Biochem., 162:156-159 (1987)) using a polytron homogenizer (Brinkman Instruments).

Additionally, human brain and lung total RNA was purchased from Clontech. PolyA RNA was isolated from total RNA using dynabeads-dT according to the manufacturer's recommendations (Dynal, Inc.).

First strand cDNA synthesis was initiated using an oligonucleotide primer with the sequence: 5'-AACTGGAAGAATTCGCGGCCGCAGGAATTTTTTTTTTTTTTTTTT-3' (SEQ ID NO:27). This primer introduces a NotI restriction site (underlined) at the 3' end of the cDNA. First and second strand synthesis were performed using the "one-tube" cDNA synthesis kit as described by the anufacturer (Life Technologies, Bethesda, MD). Double stranded cDNAs were treated with T4 polynucleotide kinase to ensure that the ends of the molecules were blunt (Soares, in Automated DNA Sequencing and Analysis, Adams, Fields and Venter, Eds., Academic Press, NY, pages 110-114 (1994)), and the blunt ended cDNAs were then size selected by a Biogel column (Huynh et al.. ii-DNA Cloning, Vol. 1, Glover, Ed., IRL Press, Oxford, pages 49-78 (1985)) or with a size-sep 400 sepharose column (Pharmacia, catalog 27-5105-01). Only cDNAs of 400 base pairs or longer were used in subsequent steps. EcoRI adapters (sequence: 5' OH-AATTCGGCACGAG-OH 3' (SEQ ID NO:28), and 5' p-CTCGTGCCG-OH 3' (SEQ ID NO:29)) were then ligated to the double stranded cDNAs by methods familiar to one skilled in the art (Soares, 1994). The EcoRI adapters were then removed from the 3' end of the cDNA by digestion with NotI (Soares, 1994). The cDNA was then ligated into the plasmid vector pBluescript II KS+ (Stratagene, -63- WO 01/92891 PCT/US01/16946 La Jolla, California), and the ligated material was transformed into E. coli host DH1 0B or DH12S by electroporation methods familiar to one skilled in the art (Soares, 1994). After growth overnight at 37 0 C, DNA was recovered from the E. coli colonies after scraping the plates by processing as directed for the Mega-prep kit (Qiagen, Chatsworth, California). The quality of the'cDNA libraries was estimated by counting a portion of the total numbers of primary transformants and determining the average insert size and the percentage of plasmids with no cDNA insert. Additional cDNA libraries (human total brain, heart, kidney, leukocyte, and fetal brain) were purchased from Life Technologies, Bethesda, MD.

cDNA libraries, both oligo (dT) and random hexamer (N 6 primed, were used for isolating cDNA clones transcribed within the HBM region: human bone, human brain, human kidney and human skeletal muscle (all cDNA libraries were made by the inventors, except for skeletal muscle (dT) and kidney (dT) cDNA libraries). Four 10 x 10 arrays of each of the cDNA libraries were prepared as follows: the cDNA libraries were titered to 2.5 x 10 6 using primary transformants. The appropriate volume of frozen stock was used to inoculate 2 L of LB/ampicillin (100 mg/ml). This inoculated liquid culture was aliquotted into 400 tubes of 4 ml each. Each tube contained approximately 5000 cfu. The tubes were incubated at 30 0

C

overnight with gentle agitation. The cultures were grown to an OD of 0.7-0.9. Frozen stocks were prepared for each of the cultures by aliquotting 100 [l of culture and 300 gl of glycerol. Stocks were frozen in a dry ice/ethanol bath and stored at -70 C. The remaining culture was DNA prepared using the Qiagen (Chatsworth, CA) spin miniprep kit according to the manufacturer's instructions. The DNAs from the 400 cultures were pooled to make column and row pools. The cDNA libraries were determined to contain HBM cDNA clones of interest by PCR. Markers were designed to amplify putative exons. Once a standard PCR optimization was performed and specific cDNA libraries were determined to contain cDNA -64 WO 01/92891 PCT/US01/16946 clones of interest, the markers were used to screen the arrayed library. Positive addresses indicating the presence ofcDNA clones were confirmed by a second PCR using the same markers.

Once a cDNA library was identified as likely to contain cDNA clones corresponding to a specific transcript of interest from the HBM region, it was manipulated to isolate the clone or clones containing cDNA inserts identical to the EST or direct-selected cDNA of interest. This was accomplished by a modification of the standard "colony screening" method (Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor NY (1989)). Specifically, twenty 150 mm LB+ampicillin agar plates were spread with 20,000 colony forming units (cfu) of cDNA library and the colonies allowed to grow overnight at 37 0 C. Colonies were transferred to nylon filters (Hybond from Amersham, or equivalent) and duplicates prepared by pressing two filters together essentially as described (Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor NY (1989)). The "master" plate was then incubated an additional 6-8 hours to allow the colonies to grow back. The DNA from the bacterial colonies was then affixed to the nylon filters by treating the filters sequentially with denaturing solution (0.5 N NaOH, 1.5 M NaC1) for two minutes, neutralization solution M Tris-C1 pH 8.0, 1.5 M NaC1) for two minutes (twice). The bacterial colonies were removed from the filters by washing in a solution of2X SSC/0.1% SDS for one minute while rubbing with tissue paper. The filters were air dried and baked under vacuum at 80 0 C for 1-2 hours.

A cDNA hybridization probe was prepared by random hexamer labeling (Fineberg and Vogelstein, Anal. Biochem., 132:6-13 (1983)) or by including gene-specific primers and no random hexamers in the reaction (for small fragments). Specific activity was calculated WO 01/92891 PCT/US01/16946 and was >5X10 8 cpm/108 uig of cDNA. The colony membranes were then prewashed in mM Tris-Cl pH 8.0, 1 M NaC1, 1 mM EDTA, 0.1% SDS for 30 minutes at 55 Following the prewash, the filters were prehybridized in 2 ml/filter of 6X SSC, 50 deionized formamide, 2% SDS, 5X Denhardt's solution, and 100 mg/ml denatured salmon sperm DNA, at 42 °C for 30 minutes. The filters were then transferred to hybridization solution (6X SSC, 2% SDS, 5X Denhardt's, 100 mg/ml denatured salmon sperm DNA) containing denatured a 3 P-dCTP-labelled cDNA probe and incubated at 42 C for 16-18 hours.

After the 16-18 hour incubation, the filters were washed under constant agitation in 2X SSC, 2% SDS at room temperature for 20 minutes, followed by two washes at 65°C for 15 minutes each. A second wash was performed in 0.5 X SSC, 0.5% SDS for 15 minutes at 0 C. Filters were then wrapped in plastic wrap and exposed to radiographic film for several hours to overnight. After film development, individual colonies on plates were aligned with the autoradiograph so that they could be picked into a 1 ml solution of LB Broth containing ampicillin. After shaking at 37 0 C for 1-2 hours, aliquots of the solution were plated on 150 mm plates for secondary screening. Secondary screening was identical to primary screening (above) except that it was performed on plates containing -250 colonies so that individual colonies could be clearly identified for picking.

After colony screening with radiolabeled probes yielded cDNA clones, the clones were characterized by restriction endonuclease cleavage, PCR, and direct sequencing to confirm the sequence identity between the original probe and the isolated clone. To obtain the full-length cDNA, the novel sequence from the end of the clone identified was used to probe the library again. This process was repeated until the length of the cDNA cloned matches that estimated to be full-length by the northern blot analysis.

-66- WO 01/92891 PCT/US01/16946 RT-PCR was used as another method to isolate full length clones. The cDNA was synthesized and amplified using a "Superscript One Step RT-PCR" kit (Life Technologies, Gaithersburg, MD). The procedure involved adding 1.5 gg of RNA to the following: 25 gl of reaction mix provided which is a proprietary buffer mix with MgSO 4 and dNTP's, 1 gL sense primer (10 pM) and 1 gl anti-sense primer (10 giM), 1 pl reverse transcriptase and Taq DNA polymerase mix provided and autoclaved water to a total reaction mix of 50 pl. The reaction was then placed in a thermocycler for 1 cycle at 50 0 C for 15 to 30 minutes, then 94°C for seconds, 55-60 °C for 30 seconds and 68-72 C for 1 minute per kilobase of anticipated product and finally 1 cycle of 72°C for 5-10 minutes. The sample was analyzed on an agarose gel. The product was excised from the gel and purified from the gel (GeneClean, Bio 101). The purified product was cloned in pCTNR (General Contractor DNA Cloning System, 5 Prime 3 Prime, Inc.) and sequenced to verify that the clone was specific to the gene of interest.

Rapid Amplification of cDNA ends (RACE) was performed following the manufacturer's instructions using a Marathon cDNA Amplification Kit (Clontech, Palo Alto, CA) as a method for cloning the 5' and 3' ends of candidate genes. cDNA pools were prepared from total RNA by performing first strand synthesis, where a sample of total RNA sample was mixed with a modified oligo (dT) primer, heated to 70C, cooled on ice and followed by the addition of: 5x first strand buffer, 10 mM dNTP mix, and AMV Reverse Transcriptase (20 U/gl). The tube was incubated at 42 0 C for one hour and then the reaction tube was placed on ice. For second strand synthesis, the following components were added directly to the reaction tube: 5x second strand buffer, 10 mM dNTP mix, sterile water, second strand enzyme cocktail and the reaction tube was incubated at 160C for 1.5 hours. T4 DNA Polymerase was added to the reaction tube and incubated at 16°C for 45 minutes. The -67- WO 01/92891 PCT/US01/16946 second-strand synthesis was terminated with the addition of an EDTA/Glycogen mix. The sample was subjected to a phenol/chloroform extraction and an ammonium acetate precipitation. The cDNA pools were checked for quality by analyzing on an agarose gel for size distribution. Marathon cDNA adapters (Clontech) were then ligated onto the cDNA ends. The specific adapters contained priming sites that allowed for amplification of either or 3' ends, depending on the orientation of the gene specific primer (GSP) that was chosen.

An aliquot of the double stranded cDNA was added to the following reagents: 10 mM Marathon cDNA adapter, 5x DNA ligation buffer, T4 DNA ligase. The reaction was incubated at 16 C overnight. The reaction was heat inactivated to terminate the reaction.

PCR was performed by the addition of the following to the diluted double stranded cDNA pool: 1Ox cDNA PCR reaction buffer, 10 ,M dNTP mix, 10 uM GSP, 10 puM AP1 primer (kit), 50x Advantage cDNA Polymerase Mix. Thermal Cycling conditions were 94 0 C for seconds, 5 cycles of 94°C for 5 seconds, 72 0 C for 4 minutes, 5 cycles of 94°C for 5 seconds, 0 C for 4 minutes, 23 cycles of 94 0 C for 5 seconds, 68 0 C for 4 minutes. After the first round of PCR was performed using the GSP.to extend to the end of the adapter to create the adapter primer binding site, exponential amplification of the specific cDNA of interest was observed. Usually a second nested PCR is performed to confirm the specific cDNA. The RACE product was analyzed on an agarose gel and then excised and purified from the gel (GeneClean, BIO 101). The RACE product was then cloned into pCTNR (General Contractor DNA Cloning System, 5' Inc.) and the DNA sequence determined to verify that the clone is specific to the gene of interest.

-68- WO 01/92891 PCT/US01/16946 XI. Mutation Analysis Comparative genes were identified using the above procedures and the exons from each gene were subjected to mutation detection analysis. Comparative DNA sequencing was used to identify polymorphisms in HBM candidate genes from chromosome 1lq12-13. DNA sequences for candidate genes were amplified from patient lymphoblastoid cell lines.

The inventors developed a method based on analysis of direct DNA sequencing of PCR products amplified from candidate regions to search for the causative polymorphism.

The procedure consisted of three stages that used different subsets of HBM family to find segregating polymorphisms and a population panel to assess the frequency of the polymorphisms. The family resources result from a single founder leading to the assumption that all affected individuals will share the same causative polymorphism.

Candidate regions were first screened in a subset of the HBM family consisting of the proband, daughter, and her mother, father and brother. Monochromosomal reference sequences were produced concurrently and used for comparison. The mother and daughter carried the HBM polymorphism in this nuclear family, providing the ability to monitor polymorphism transmission. The net result is that two HBM chromosomes and six non- HBM chromosomes were screened. This allowed exclusion of numerous frequent alleles.

Only alleles exclusively present in the affected individuals passed to the next level of analysis.

Polymorphisms that segregated exclusively with the HBM phenotype in this original family were then re-examined in an extended portion of the HBM pedigree consisting of two additional nuclear families. These families consisted of five HBM and three unaffected individuals. The HBM individuals in this group included the two critical crossover individuals, providing the centromeric and telomeric boundaries of the critical region.

-69- WO 01/92891 PCT/US01/16946 Tracking the heredity of polymorphisms between these individuals and their affected parents allowed for further refining of the critical region. This group brought the total of HBM chromosomes screened to seven and the total of non-HBM chromosomes to seventeen.

When a given polymorphism continued to segregate exclusively with the HBM phenotype in the extended group, a population panel was then examined. This panel of 84 persons consisted of 42 individuals known to have normal bone mineral density and 42 individuals known to be unrelated but with untyped bone mineral density. Normal bone mineral density is within two standard deviations ofBMD Z score 0. The second group was from the widely used CEPH panel of individuals. Any segregating polymorphisms found to be rare in this population were subsequently examined on the entire HBM pedigree and a larger population.

Polymerase chain reaction (PCR) was used to generate sequencing templates from the HIBM family's DNA and monochromosomal controls. Enzymatic amplification of genes within the HBM region on 1 lq12-13 was accomplished using the PCR with oligonucleotides flanking each exon as well as the putative 5' regulatory elements of each gene. The primers were chosen to amplify each exon as well as 15 or more base pairs within each intron on either side of the splice. All PCR primers were made as chimeras to facilitate dye primer sequencing. The M13-21F GTA A CGA CGG CCA GT (SEQ ID NO:30) and 28REV AAC AGC TAT GAC CAT G (SEQ ID NO:31) primer binding sites were built on to the 5' end of each forward and reverse PCR primer, respectively, during synthesis.

150 ng of genomic DNA was used in a 50 1l PCR with 2UAmpliTaq, 500 nM primer and 125 pM dNTP. Buffer and cycling conditions were specific to each primer set. TaqStart antibody (Clontech) was used for hot start PCR to minimize primer dimer formation. 10% of WO 01/92891 PCT/US01/16946 the product was examined on an agarose gel. The appropriate samples were diluted 1:25 with deionized water before sequencing.

Each PCR product was sequenced according to the standard Energy Transfer primer (Amersham) protocol. All reactions took place in 96 well trays. 4 separate reactions, one each for A, C, G and T were performed for each template. Each reaction included 2 l of the sequencing reaction mix and 3 ul of diluted template. The plates were then heat sealed with foil tape and placed in a thermal cycler and cycled according to the manufacturer's recommendation. After cycling, the 4 reactions were pooled. 3 l1 of the pooled product was transferred to a new 96 well plate and 1 Il of the manufacturer's loading dye was added to each well. All 96 well pipetting procedures occurred on a Hydra 96 pipetting station (Robbins Scientific, USA). 1 gl of pooled material was directly loaded onto a 48 lane gel running on an ABI 377 DNA sequencer for a 10 hour, 2.4 kV run.

Polyphred (University of Washington) was used to assemble sequence sets for viewing with Consed (University of Washington). Sequences were assembled in groups representing all relevant family members and controls for a specified target region. This was done separately for each of the three stages. Forward and reverse reads were included for each individual along with reads from the monochromosomal templates and a color annotated reference sequence. Polyphred indicated potential polymorphic sites with a purple flag. Two readers independently viewed each assembly and assessed the validity of the purple-flagged sites.

A total of 23 exons present in the mature mRNA and several other portions of the primary transcript were evaluated for heterozygosity in the nuclear family of two HBMaffected and two unaffected individuals. Twenty-five single nucleotide polymorphisms (SNPs) were identified, as shown in the table below.

-71- WO 01/92891 WO 0192891PCT/US01/16946 TABLE 4: Single Nucleotide Polymorphisms in the Zinaxi gene and Environs Exon Name Location Base Change b200e2l-h-Contigl l.nt 69169 (309G) C/A b200e2-h-Conig4 _12.nt 27402 (3090) AIG b200e2l-h-Contig4_13.nt 27841 (309G) T/C b200e2l-h-Config4_16.nt 35600 (309G) A/G b200e2l-h Cotig4_21.nt 45619 (309G) 0/A b200e2 1 -h Contig4 _22.nt-a 46018 (3090) T/G b200e2 1 -h Contig4 _22.nt-b 46093 (3090) TIG b200e2l-h Contig4 _22.nt-c 46190 (3090) A/G b200e2l-h-Contig4_24.nt-a 50993 (309G) TIC b200e2l-h-Contig4_24.nt-b 51124 (3090) CIT b200e2l-h Contig4 _25.nt 55461 (3090) C/T b200e2l1-h-Contig4 _33 .nt-a 63645 (3090) C/A b200e2l-h Contig4_33.nt-b 63646 (309G) A/C b200e21-h Contig46lint 24809 (3090) TIG b200e21-h Contig462.nt 27837 (3090) TIC b200e21-h-Config4_63.nt-a 31485 (3090) C/T b200e21-h Contig4_63.nt-b 31683 (3090) AIG b200e2 1-hConig4 _9.nt 24808(309G)

T/G

b527d12-h Contig3Ogl.nt-a 31340(308G)

TIC

b527d12-h ConfiSg30gl.nt-b 32538 (308G) A/G b527d1-h ConigO8OC 2.nt 13224 (3080) AIG b527d12-h ConigO87C I.nt 21119 (3080) C/A b527d12-h ContigO87C 4.nt 30497 (3080) 0/A b527d12-h. ContigO88C 4.nt 24811(3090)

A/C

b527d1-hContigO89 1BP.nt 68280 (309G) 0/A -72 WO 01/92891 PCT/US01/16946 In addition to the polymorplusms presented m 'Table 4, two adcitional polymorphisms can also be present in SEQ ID NO:2. These is a change at position 2002 of SEQ ID NO:2. Either a guanine or an adenine can appear at this position. This polymorphism is silent and is not associated with any change in the amino acid sequence.

The second change is at position 4059 of SEQ ID NO:2 corresponding in a cytosine to thymine change. This polymorphism results in a corresponding amino acid change from a valine to an alanine Other polymorphisms were found in the candidate gene exons and adjacent intron sequences. Any one or combination of the polymorphisms listed in Table 4 or the two discussed above could also have a minor effect on bone mass or lipid levels when present in SEQ ID NO:2.

The present invention encompasses the nucleic acid sequences having the nucleic acid sequence of SEQ ID NO: 1 with the above-identified point mutations.

Preferably, the present invention encompasses the nucleic acid of SEQ ID NO: 2.

Specifically, a base-pair substitution changing G to T at position 582 in the coding sequence of Zmaxl (the HBM gene) was identified as heterozygous in all HBM individuals, and not found in the unaffected individuals b527dl2-h_Contig087C_l.nt). Fig. 5 shows the order of the contigs in B527D12. The direction of transcription for the HBM gene is from left to right. The sequence of contig308G of B527D12 is the reverse complement of the coding region to the HBM gene. Therefore, the relative polymorphism in contig 308G shown in Table 4 as a base change substitution of C to A is the complement to the G to T substitution in the HBM gene. This mutation causes a substitution of glycine 171 with valine (G171V).

The HBM polymorphism was confirmed by examining the DNA sequence of different groups of individuals. In all members of the HBM pedigree (38 individuals), the HBM polymorphism was observed in the heterozygous form in affected elevated bone mass) -73- WO 01/92891 PCT/US01/16946 individuals only In unaffected relatives (N=20) (BMDZ<2.0) the HBM polymorphism was never observed. To determine whether this gene was ever observed in individuals outside of the HBM pedigree, 297 phenotyped individuals were characterized at the site of the HBM gene. None were heterozygous at the site of the HBM polymorphism. In an unphenotyped control group, 1 of 42 individuals was observed to be heterozygous at position 582. Since this individual is deceased, their bone mineral density could not be obtained. Taken together, these data prove that the polymorphism observed in the kindred displaying the high bone mass phenotype is strongly correlated with the G-IT polymorphism at position 582 of Zmaxl. Taken together, these results establish that the HBM polymorphism genetically segregates with the HBM phenotype, and that both the HBM polymorphism and phenotype are rare in the general population.

XII. Allele Specific Oligonucleotide (ASO) Analysis The amplicon containing the HBM1 polymorphism was PCR amplified using primers specific for the exon of interest. The appropriate population of individuals was PCR amplified in 96 well microtiter plates as follows. PCR reactions (20 jl) containing 1X Promega PCR buffer (Cat. M1883 containing 1.5 mM MgCl1), 100mM dNTP, 200 nM PCR primers (1863F: CCAAGTTCTGAGAAGTCC and 1864R: AATACCTGAAACCAT ACCTG), 1 U Amplitaq, and 20 ng of genomic DNA were prepared and amplified under the following PCR conditions: 94 0 C, 1 minute, (94°C, 30 sec.; 58 0 C, 30 sec.; 72 0 C, 1 min.) cycles), 72C, 4 0 C, hold. Loading dye was then added and 10 pl of the products was electrophoresed on 1.5% agarose gels containing 1 p g/ml ethidium bromide at 100-150 V for 5-10 minutes. Gels were treated 20 minutes in denaturing solution (1.5 M NaC1, 0.5 N NaOH), and rinsed briefly with water. Gels were then neutralized in 1 M Tris-HC1, pH -74- WO 01/92891 PCT/US01/16946 M NaCI, for 20 minutes and rinsed with water. Gels were soaked in 1 X SCU tor 2U minutes and blotted onto nylon transfer membrane (Hybond Amersham) in 10X SSC overnight. Filters were the rinsed in 6X SSC for 10 minutes and UV crosslinked.

The allele specific oligonucleotides (ASO) were designed with the polymorphism approximately in the middle. Oligonucleotides were phosphate free at the 5'end and were purchased from Gibco BRL. Sequences of the oligonucleotides are: 2326 Zmaxl.ASO.g: AGACTGGGGTGAGACGC 2327 Zmaxl.ASO.t: CAGACTGGGTTGAGACGCC The polymorphic nucleotides are underlined. To label the oligos, 1.5 ptl of 1 p[g/pl ASO oligo (2326.Zmaxl.ASO.g or 2327.Zmaxl.ASO.t), 11 py ddH0O, 2 C 1 10X kinase forward buffer, 5 pl y- 32 P-ATP (6000 Ci/mMole), and 1 pl T4 polynucleotide kinase (10 U/pl) were mixed, and the reaction incubated at 37 0 C for 30-60 minutes. Reactions were then placed at 0 C for 2 minutes and 30 ml H20 was added. The probes were purified using a microspin column (Pharmacia).

Blots were prehybridized in 10 ml 5X SSPE, 5X Denhardt's, 2% SDS, and 100 pg/ml, denatured, sonicated salmon sperm DNA at 40 0 C for 2 hr. The entire reaction mix ofkinased oligo was then added to 10 ml fresh hybridization buffer (5X SSPE, 5X Denhardts, 2% SDS) and hybridized at 40 0 C for at least 4 hours to overnight.

All washes done in 5X SSPE, 0.1 SDS. The first wash was at 45 0 C for 15 minutes; the solution was then changed and the filters washed 50 0 C for 15 minutes. Filters were then exposed to Kodak biomax film with 2 intensifying screens at -70 0 C for 15 minutes to 1 hr. If necessary the filters were washed at 55C for 15 minutes and exposed to film again. Filters were stripped by washing in boiling 0.1X SSC, 0.1% SDS for 10 minutes at least 3 times.

WO 01/92891 PCT/US01/16946 The two films that best captured the allele specific assay with the 2 ASOs were converted into digital images by scanning them into Adobe PhotoShop. These images were overlaid against each other in Graphic Converter and then scored and stored in FileMaker Pro 4.0 (see Fig. 9).

XIII. Cellular Localization of Zmaxl A. Gene Expression in Rat tibia by non isotopic In Situ Hybridization In situ hybridization was conducted by Pathology Associates International (PAI), Frederick, MD. This study was undertaken to determine the specific cell types that express the Zmaxl gene in rat bone with particular emphasis on areas of bone growth and remodeling.

Zmaxl probes used in this study were generated from both human (HuZmaxl) and mouse (MsZmaxl) cDNAs, which share an 87% sequence identity. The homology of human and mouse Zmaxl with rat Zmaxl is unknown.

For example, gene expression by non-isotopic in situ hybridization was performed as follows, but other methods would be known to the skilled artisan. Tibias were collected from two 6 to 8 week old female Sprague Dawley rats euthanized by carbon dioxide asphyxiation.

Distal ends were removed and proximal tibias were snap frozen in OCT embedding medium with liquid nitrogen immediately following death. Tissues were stored in a -80'C freezer.

Probes for amplifying PCR products from cDNA were prepared as follows. The primers to amplify PCR products from a cDNA clone were chosen using published sequences of both human LRP5 (Genbank Accession No. ABO17498) and mouse LRP5 (Genbank Accession No. AF064984). In order to minimize cross reactivity with other genes in the LDL receptor family, the PCR products were derived from an intracellular portion of the protein coding region. PCR was performed in a 50 g1 reaction volume using cDNA clone as -76- WO 01/92891 WO 0192891PCT/US01/16946 template. FUR reactions contained LI .mxn.V MgCI 2 1 unit Amplitaq, 200 .tM dNT11s and 2 j iM each primer. PCR cycling conditions were 94'C for 1 min., followed by 3 5 cycles of 94'C for 30 seconds, 55'C for 30 seconds, 72'C for 30 seconds; followed by a 5 minute extension at 72'C. The reactions were then ran on a 1.5 agarose Tris-Acetate gel. DNA was eluted from the agaro se, ethanol precipitated and resuspended in 10 mM Tris, pH Gel purified PCR products were prepared for both mouse and human cDXAs and supplied to Pathology Associates International for in situ hybridizations.

The sequence of the human and mouse PCR primers and products were as follows: Human ZmaxlI sense primer MM 3125 3)

CCCGTGTGCTCCGCCOCCCAOTTC

Human Zmaxl antisense primer MHM145)

GGCTCACGGAGCTCATCATGGACTT

Human ZmaxlI PCR p2roduct

CCCGTGTGCTCCOCCGCCCAGTTCCCCTGCGCGCGGGGTCAGTGTGTGGACCTGCGCCTGCGCTGCGACGGCGAG

GCAGACTGTCAGGACCGCTCAGACGAGGTGGACTGTGACGCCATCTGCCTGCCCAACCAGTTCCGGTGTGCGAGC

GGCCAGTGTGTCCTCATCAAACAGC;LGTGCGACTCCTTCCCCGACTGTATCGACGGCTCCGACGAGCTCATGTGT

GAAATCACCAAGCCGCCCTCAGACGACAGCCCGOCCCAcAGCAGTGCCATCGGGCCCGTCATTGGCATc-ATCCTC

TCTCTCTTCGTCATGGGTGGTGTCTATTTTGTGTGCCAGCGCGTGGTGTGCCAGCGCTAGCGGGGGCCAACGGG

CTTCCC~CACGAGTATGTCAGCGOGACCCCGCACGTGCCCCTCAATTTCATAGCCCCGGGCGGTTCCCAGCAT

GGCCCCTTCACAGGCATCGCATGCGGAAAGTCCATGATGAGCTCCGTGAGCC

Mouse Zmaxl Sense primer (HBM1655)

AGCGAGGCCACCATCCACAGG

Mouse Zmaxl antisense primer (FiM 656)

TCGCTGGTCGGCATAATCAAT

-77 WO 01/92891 WO 0192891PCT/USOI/16946 Mouse Zmaxl PCR nrod-Lct

AGAACACTCCGACCCGAATACAACAGGCACCCCCGTT-A

CAGCCGATG-TTAGrTCAATAACATGCGTTACTAGCACG

CGAGCCTTCATGAAGGGAGCTCAGTGGAGCACGTGATTGAGTTTGGCCTCGACTACCCTGAGGAATGGCTGTG

GACTGGATGGOAGAACCTCTATTGGGCGGACACAGGGACCACGGATTGAGTGGCCCGrCTGGATGGGCAG

TTCCGGCAGGTGCTTGTGTGGAGAGACCTTGACAACCCCAGGTCTCGGCTCTGGATCCTACTAAGGCTACATC

TACTGGACTGAGTGGGGTGGCAAGCCAAGGATTGTGCGGGCCTTCATGGATGGGACCATTGTATGACACTGGTA

GACAAGGTGGGCCGGGCCAACGACCTCACCATTGATTATGCCGACCAGCGA

Riboprobes were synthesized as follows. The POR products were reamplified with chimeric primers designed to incorporate either a T3 promoter upstream, or a T7 promoter downstream of the reamnplification products. The resulting PCR products were used as template to synthesize digoxigenin-labeled riboprobes by in vitro transcription (IVT).

Antisense and sense riboprobes were synthesized using T7 and T3 RNA polymerases, respectively, in the presence of digoxigenin-1 l-UTP (Boebringer-Mannheiui) using a MAXlscript IVT kit (Ambion)'according to the manufacturer. The DNA was then degraded with Dnase-l, and unincorporated digoxigenin was removed by ultrdfhltration. Riboprobe integrity was assessed by electrophoresis through a denaturing polyacrylamide gel.

Molecular size was compared with the electrophoretic mobility of a lOO-100.) base pair (bp) RNA ladder (Ambion). Probe yield and labeling was evaluated by blot inirunochemistry.

Riboprobes were stored in 5 jLd aliquois at The in situ hybridization was performed as follows. Frozen rat bone was cut into jiM sections on a Jung CM3000 cryostat (Leica) and mounted on adhesive slides (Instrumedics). Sections were kept in the cryostat at -20'C until all the slides were prepared in order to prevent niRNA degradation prior to post-fixation for 15 minutes in 4% paraformaldehyde. Following post-fixation, sections were incubated with 1 ng/jd of either -78 WO 01/92891 PCT/US01/16946 antisense or sense riboprobe in Pathology Associates International (PAI) customized hybridization buffer for approximately 40 hours at 58'C. Following hybridization, slides were subjected to a series of post-hybridization stringency washes to reduce nonspecific probe binding. Hybridization was visualized by immunohistochemistry with an antidigoxigenin antibody (FAB fragment) conjugated to alkaline phosphatase. Nitroblue tetrazolium chloride/bromochloroindolyl phosphate (Boehringer-Mannheim), a precipitating alkaline phosphatase substrate, was used as the chromogen to stain hybridizing cells purple to nearly black, depending on the degree of staining. Tissue sections were counter-stained with nuclear fast red. Assay controls included omission of the probe, omission of probe and antidigoxigenin antibody.

Specific cell types were assessed for demonstration of hybridization with antisense probes by visualizing a purple to black cytoplasmic and/or peri-nuclear staining indicating a positive hybridization signal for mRNA. Each cell type was compared to the replicate sections, which were hybridized with the respective sense probe. Results were considered positive if staining was observed with the antisense probe and no staining or weak background with the sense probe.

The cellular localization of the hybridization signal for each of the study probes is summarized in Table 5. Hybridization for Zmaxl was primarily detected in areas of bone involved in remodeling, including the endosteum and trabecular bone within the metaphysis.

Hybridization in selected bone lining cells of the periosteum and epiphysis were also observed. Positive signal was also noted in chondrocytes within the growth plate, particularly in the proliferating chondrocytes. See Figs. 10, 11 and 12 for representative photomicrographs of in situ hybridization results.

-79- WO 01/92891 WO 0192891PCT/US01/16946 TABLE Summary of Zmaxl in situ hybridization in rat tibia PROBE SITE ISIT SIGNAL Hu ZmaxlI E ihysis Osteoblasts Osteoclast.

Growth Plate resting chondrocytes_______ proliferating chondrocytes hypertrophic chondrocytes Metgphysis osteoblasts osteoclasts Diaphysis_______ Endosteum osteoblasts osteoclasts Periosteum_______ MsZmaxl Epiphysis Osteoblasts Osteoclasts Growth Plate chondrocytes ________proliferating chondrocytes _______hypertrophic; chondrocytes Metaphysis________ osteoblasts osteoclasts -Endosteuni osteolasts+ osteoclasts IPero~steum Legend: hybridization signal detected hybridizatiosinldtce "ISH" In situ hybridization WO 01/92891 PCT/US01/16946 These studies confirm the positional expression of Zmaxl in cells involved in bone remodeling and bone formation. Zmaxl expression in the zone of proliferation and in the osteoblasts and osteoclasts of the proximal metaphysis, suggests that the Zmaxl gene is involved in the process of bone growth and mineralization. The activity and differentiation of osteoblasts and osteoclasts are closely coordinated during development as bone is formed and during growth as well as in adult life as bone undergoes continuous remodeling. The formation of internal bone structures and bone remodeling result from the coupling of bone resorption by activated osteoclasts with subsequent deposition of new material by osteoblasts.

Zmax1 is related to the LDL receptor gene, and thus may be a receptor involved in mechanosensation and subsequent signaling in the process of bone remodeling. Therefore, changes in the level of expression of this gene could impact on the rate of remodeling and degree of mineralization of bone. Similar studies can be designed for in situ analysis of HBM or Zmaxl in other cells or tissues.

XIV. Antisense Antisense oligonucleotides are short synthetic nucleic acids that contain complementary base sequences to a targeted RNA. Hybridization of the RNA in.living cells with the antisense oligonucleotide interferes with RNA function and ultimately blocks protein expression. Therefore, any gene for which the partial sequence is known can be targeted by an antisense oligonucleotide.

Antisense technology is becoming a widely used research tool and will play an increasingly important role in the validation and elucidation of therapeutic targets identified by genomic sequencing efforts.

-81- WO 01/92891 PCT/US01/16946 Antisense technology was developed to inhibit gene expression by utilizmg an oligonucleotide complementary to the mRNA that encodes the target gene. There are several possible mechanisms for the inhibitory effects of antisense oligonucleotides. Among them, degradation of mRNA by RNase H is considered to be the major mechanism of inhibition of protein function. This technique was originally used to elucidate the function of a target gene, but may also have therapeutic applications, provided it is designed carefully and properly.

An example of materials and methods for preparing antisense oligonucleotides can be performed as follows. Preliminary studies have been undertaken in collaboration with Sequiter (Natick, MA) using the antisense technology in the osteoblast-like murine cell line, MC3T3. These cells canbe triggered to develop along the bone differentiation sequence. An initial proliferation period is characterized by minimal expression of differentiation markers and initial synthesis of collagenous extracellular matrix. Collagen matrix synthesis is required for subsequent induction of differentiation markers. Once the matrix synthesis begins, osteoblast marker genes are activated in a clear temporal sequence: alkaline phosphatase is induced at early times while bone sialoprotien and osteocalcin appear later in the differentiation process. This temporal sequence of gene expression is useful in monitoring the maturation and mineralization process. Matrix mineralization, which does not begin until several days after maturation has started, involves deposition of mineral on and within collagen fibrils deep within the matrix near the cell layer-culture plate interface. The collagen fibril-associated mineral formed by cultured osteoblasts resembles that found in woven bone in vivo and therefore is used frequently as a study reagent.

MC3T3 cells were transfected with antisense oligonucleotides for the first week of the differentiation, according to the manufacturer's specifications Patent No. 5,849,902).

-82- WO 01/92891 PCT/US01/16946 The oligonucleotides designed for Zmaxl are given below: 10875: AGUACAGCUUCUUGCCAACCCAGUC 10876: UCCUCCAGGUCGAUGGUCAGCCCAU 10877: GUCUGAGUCCGAGUUCAAAUCCAGG Figure 13 shows the results ofantisense inhibition ofZmaxl in MC3T3 cells. The three oligonucleotides shown above were transfected into MC3T3 and RNA was isolated according to standard procedures. Northern analysis clearly shows markedly lower steady state levels of the Zmaxl transcript while the control gene GAPDH remained unchanged. Thus, antisense technology using the primers described above allows for the study of the role of Zmaxl expression on bone biology. Similar primers can be used to study Zmaxl expression and its ability to regulate lipid levels in an animal.

The protein encoded by Zmaxl is related to the Low Density Lipoprotein receptor (LDL receptor). See, Goldstein etal., Ann. Rev. Cell Biology, 1:1-39 (1985); Brown etal., Science, 232:34-47 (1986). The LDL receptor is responsible for uptake of low density lipoprotein, a lipid-protein aggregate that includes cholesterol. Individuals with a defect in the LDL receptor are deficient in cholesterol removal and tend to develop artherosclerosis. In addition, cells with a defective LDL receptor show increased production of cholesterol, in part because of altered feedback regulation of cholesterol synthetic enzymes and in part because of increased transcription of the genes for these enzymes. In some cell types, cholesterol is a precursor for the formation of steroid hormones.

Thus, the LDL receptor may, directly or indirectly, function as a signal transduction protein and may regulate gene expression. Because Zmaxl is related to the LDL receptor, this protein may also be involved in signaling between cells in a way that affects bone remodeling as well as regulate lipid levels and therefore lipid-mediated diseases.

-83- The glycine 171 amino acid is likely to be important for the function of Zmax1 because this amino acid is also found in the mouse homologue ofZmaxl. The closely related LRP6 protein also contains glycine at the corresponding position (Brown et al., Biochemical and Biophysical Research Comm., 248:879-888 (1988)). Amino acids that are important in a protein's structure or function tend to be conserved between species, because natural selection prevents mutations with altered amino acids at important positions from arising.

In addition, the extracellular domain of Zmaxl contains four repeats consisting of five YWT motifs followed by an EFG motif. This 5YWT+EGF repeat is likely to form a distinct folded protein domain, as this repeat is also found in the LDL receptor and other LDL receptor-related proteins. The first three 5YWT+EGF repeats are very similar in their structure, while the fourth is highly divergent. Glycine 171 occurs in the central YWT motif of the first 5YWT+EGF repeat in Zmaxl. The other two similar repeats of Zmaxl also contain glycine at the corresponding position, as does the 5YWT+EGF repeat in the LDL receptor protein. However, only 17.6% of the amino acids are identical among the first three 5YWT+EGF repeats in Zmaxl and the single repeat in the LDL receptor. These observations indicate that glycine 171 is essential to the function of this repeat, and mutation of glycine 171 causes a functional alteration of Zmaxl. The cDNA and peptide sequences are shown in Figs. 6A-6J. The critical base at nucleotide position 582 is indicated in bold and is underlined.

Northern blot analysis (Figs. 7A-B) reveals that Zmaxl is expressed in human bone tissue as well as numerous other tissues. A multiple-tissue Northern blot (Clontech, Palo Alto, CA) was probed with exons from Zmaxl. As shown in Fig. 7A, the 5.5 kb Zmaxl transcript was highly expressed in heart, kidney, lung, liver and pancreas and is expressed at lower levels in skeletal muscle and brain. A second northern blot, shown in Fig. 7B, -84- SUBSTITUTE SHEET 3 AMENDED SHEET WO 01/92891 PCT/US01/16946 confirmed the transcript size at 5.5 kb, and indicated that Zmaxl is expressed m bone, bone marrow, calvaria and human osteoblastic cell lines.

Taken together, these results indicate that the HBM polymorphism in the Zmaxl gene is responsible for the HBM phenotype, and that the Zmaxl gene is important in bone development. In addition, because mutation of Zmaxl can alter bone mineralization and development as well as lipid levels, it is likely that molecules that bind to Zmaxi may usefully alter bone development and lipid levels. Such molecules may include, for example, small molecules, proteins, RNA aptamers, peptide aptamers, and the like.

XV. Preparation of Nucleic Acids, Vectors, Transformations and Host Cells Large amounts of the nucleic acids of the present invention may be produced by replication in a suitable host cell. Natural or synthetic nucleic acid fragments coding for a desired fragment will be incorporated into recombinant nucleic acid constructs, usually DNA constructs, capable of introduction into and replication in a prokaryotic or eukaryotic cell.

Usually the nucleic acid constructs will be suitable for replication in a unicellular host, such as yeast or bacteria, but may also be intended for introduction to (with and without integration within the genome) cultured mammalian or plant or other eukaryotic cell lines.

The purification of nucleic acids produced by the methods of the present invention is described, for example, in Sambrook et al., Molecular Cloning. A Laboratory Manual, 2nd Ed. (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1989) or Ausubel et al., Current Protocols in Molecular Biology, J. Wiley and Sons, NY (1992).

The nucleic acids of the present invention may also be produced by chemical synthesis, by the phosphoramidite method described by Beaucage et al., Tetra. Letts., 22:1859-1862 (1981) or the triester method according to Matteucci, et al., J. Am. Chem. Soc., WO 01/92891 PCT/US01/16946 103:3185 (1981), and may be performed on commercial, automated oligonucleotide synthesizers. A double-stranded fragment may be obtained from the single-stranded product of chemical synthesis either by synthesizing the complementary strand and annealing the strands together under appropriate conditions or by adding the complementary strand using DNA polymerase with an appropriate primer sequence.

Nucleic acid constructs prepared for introduction into a prokaryotic or eukaryotic host may comprise a replication system recognized by the host, including the intended nucleic acid fragment encoding the desired protein, and will preferably also include transcription and translational initiation regulatory sequences operably linked to the protein encoding segment.

Expression vectors may include, for example, an origin of replication or autonomously replicating sequence (ARS) and expression control sequences, a promoter, an enhancer and necessary processing information sites, such as ribosome-binding sites, RNA splice sites, polyadenylation sites, transcriptional terminator sequences, and mRNA stabilizing sequences.

Secretion signals may also be included where appropriate, whether from a native HBM or Zmaxl protein or from other receptors or from secreted proteins of the same or related species, which allow the protein to cross and/or lodge in cell membranes, and thus attain its functional topology, or be secreted from the cell. Such vectors may be prepared by means of standard recombinant techniques well known in the art and discussed, for example, in Sambrook et al., Molecular Cloning. A Laboratory Manual, 2nd Ed. (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1989) or Ausubel et al., Current Protocols in Molecular Biology, J. Wiley and Sons, NY (1992).

An appropriate promoter and other necessary vector sequences will be selected so as to be functional in the host, and may include, when appropriate, those naturally associated with Zmaxl or HBM genes. Examples of workable combinations of cell lines and expression -86- WO 01/92891 PCT/US01/16946 vectors are described in Sambrook et al., Molecular Cloning. A Laboratory Manual, 2nd Ed.

(Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (1989) or Ausubel et al., Current Protocols in Molecular Biology, J. Wiley and Sons, NY (1992). Many useful vectors are known in the art and may be obtained from such vendors as Stratagene, New England BioLabs, Promega Biotech, and others. Promoters such as the trp, lac and phage promoters, tRNA promoters and glycolytic enzyme promoters may be used in prokaryotic hosts. Useful yeast promoters include promoter regions for metallothionein, 3-phosphoglycerate kinase or other glycolytic enzymes such as enolase or glyceraldehyde-3-phosphate dehydrogenase, enzymes responsible for maltose and galactose utilization, and others. Vectors and promoters suitable for use in yeast expression are further described in EP 73,675A. Appropriate nonnative mammalian promoters might include the early and late promoters from SV40 (Fiers et al., Nature, 273:113 (1978)) or promoters derived from murine Moloney leukemia virus, mouse tumor virus, avian sarcoma viruses, adenovirus II, bovine papilloma virus or polyoma.

In addition, the construct may bejoined to an amplifiable gene DHFR) so that multiple copies of the gene may be made. For appropriate enhancer and other expression control sequences, see also Enhancers and Eukaryotic Gene Expression, Cold Spring Harbor Press, Cold Spring Harbor, NY (1983).

While such expression vectors may replicate autonomously, they may also replicate by being inserted into the genome of the host cell, by methods well known in the art.

Expression and cloning vectors will likely contain a selectable marker, a gene encoding a protein necessary for survival or growth of a host cell transformed with the vector.

The presence of this gene ensures growth of only those host cells which express the inserts.

Typical selection genes encode proteins that a) confer resistance to antibiotics or other toxic substances, e.g. ampicillin, neomycin, methotrexate, etc.; b) complement auxotrophic -87- WO 01/92891 PCT/US01/16946 aenciencies, or c) supply cnrcal nunents not avanace rrom complex mecna, me gene encoding D-alanine racemase for Bacilli. The choice of the proper selectable marker will depend on the host cell, and appropriate markers for different hosts are well known in the art.

The vectors containing the nucleic acids of interest can be transcribed in vitro, and the resulting RNA introduced into the host cell by well-known methods, by injection (see, Kubo et al., FEBS Letts. 241:119 (1988)), or the vectors can be introduced directly into host cells by methods well known in the art, which vary depending on the type of cellular host, including electroporation; transfection employing calcium chloride, rubidium chloride, calcium phosphate, DEAE-dextran, or other substances; microprojectile bombardment; lipofection; infection (where the vector is an infectious agent, such as a retroviral genome); and other methods. See generally, Sambrook et al., 1989 and Ausubel et al., 1992. The introduction of the nucleic acids into the host cell by any method known in the art, including those described above, will be referred to herein as "transformation." The cells into which have been introduced nucleic acids described above are meant to also include the progeny of such cells.

Large quantities of the nucleic acids and proteins of the present invention may be prepared by expressing the Zmaxl or HBM nucleic acids or portions thereof in vectors or other expression vehicles in compatible prokaryotic or eukaryotic host cells. The most commonly used prokaryotic hosts are strains ofEscherichia coli, although other prokaryotes, such as Bacillus subtilis or Pseudomonas may also be used.

Mammalian or other eukaryotic host cells, such as those of yeast, filamentous fungi, plant, insect, or amphibian or avian species, may also be useful for production of the proteins of the present invention. Propagation of mammalian cells in culture is per se well known.

See, Jakoby and Pastan Cell Culture. Methods in Enzymology, volume 58, Academic 88 WO 01/92891 PCT/US01/16946 Press, Inc., Harcourt Brace Jovanovich, NY, (1979)). Examples of commonly used mammalian host cell lines are VERO and HeLa cells, Chinese hamster ovary (CHO) cells, and WI38, BHK, and COS cell lines, although it will be appreciated by the skilled practitioner that other cell lines may be appropriate, to provide higher expression desirable glycosylation patterns, or other features.

Clones are selected by using markers depending on the mode of the vector construction. The marker may be on the same or a different DNA molecule, preferably the same DNA molecule. In prokaryotic hosts, the transformant may be selected, by resistance to ampicillin, tetracycline or other antibiotics. Production of a particular product based on temperature sensitivity may also serve as an appropriate marker.

Prokaryotic or eukaryotic cells transformed with the nucleic acids of the present invention will be useful not only for the production of the nucleic acids and proteins of the present invention, but also, for example, in studying the characteristics of Zmaxl or HBM proteins.

Antisense nucleic acid sequences arc useful in preventing or diminishing the expression of Zmaxl or HBM, as will be appreciated by one skilled in the art. For example, nucleic acid vectors containing all or a portion of the Zmaxl or HBM gene or other sequences from the Zmaxl or HBM region may be placed under the control of a promoter in an antisense orientation and introduced into a cell. Expression of such an antisense construct within a cell will interfere with Zmaxl or HBM transcription and/or translation and/or replication.

The probes and primers based on the Zmaxl and HBM gene sequences disclosed herein are used to identify homologous Zmaxl and HBM gene sequences and proteins in other species. These Zmaxl and HBM gene sequences and proteins are used in the -89- WO 01/92891 PCT/US01/16946 Sdiagnostic/prognostic, therapeutic and drug screening methods described herein for the species from which they have been isolated.

XVI. Protein Expression and Purification Expression and purification of the HBM protein of the invention can be performed essentially as outlined below. To facilitate the cloning, expression and purification of membrane and secreted protein from the HBM gene, a gene expression system, such as the pET System (Novagen), for cloning and expression of recombinant proteins in E. coli was selected. Also, a DNA sequence encoding a peptide tag, the His-Tap, was fused to the 3' end of DNA sequences of interest to facilitate purification of the recombinant protein products.

The 3' end was selected for fusion to avoid alteration of any 5' terminal signal sequence.

Nucleic acids chosen, for example, from the nucleic acids set forth in SEQ ID NOS: 1, 3 and 5-12 for cloning HBM were prepared by polymerase chain reaction (PCR).

Synthetic oligonucleotide primers specific for the 5' and 3' ends of the HBM nucleotide sequence were designed and purchased from Life Technologies (Gaithersburg, MD). All forward primers (specific for the 5' end of the sequence) were designed to include an NcoI cloning site at the 5' terminus. These primers were designed to permit initiation of protein translation at the methionine residue encoded within the Ncol site followed by a valine residue and the protein encoded by the HBM DNA sequence. All reverse primers (specific for the 3' end of the sequence) included an EcoRI site at the 5' terminus to permit cloning of the HBM sequence into the reading frame of the pET-28b. The pET-28b vector provided a sequence encoding an additional 20 carboxyl-terminal amino acids including six histidine residues (at the C-terminus), which comprised the histidine affinity tag.

WO 01/92891 PCT/US01/16946 Uenomic DNA prepared trom the nhM gene was used as the source 0o template UNA for PCR amplification (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons (1994)). To amplify a DNA sequence containing the HBM nucleotide sequence, genomic DNA (50 ng) was introduced into a reaction vial containing 2 mM MgC12, 1 M synthetic oligonucleotide primers (forward and reverse primers) complementary to and flanking a defined HBM, 0.2 mM of each of deoxynucleotide triphosphate, dATP, dGTP, dCTP, dTTP and 2.5 units of heat stable DNA polymerase (Amplitaq, Roche Molecular Systems, Inc., Branchburg, NJ) in a final volume of 100 pl.

Upon completion of thermal cycling reactions, each sample of amplified DNA was purified using the Qiaquick Spin PCR purification kit (Qiagen, Gaithersburg, MD). All amplified DNA samples were subjected to digestion with the restriction endonucleases, e.g., NcoI and EcoRI (New England BioLabs, Beverly, MA) (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons, Inc. (1994)). DNA samples were then subjected to electrophoresis on 1.0% NuSeive (FMC BioProducts, Rockland, ME) agarose gels. DNA was visualized by exposure to ethidium bromide and long wave UV irradiation. DNA contained in slices isolated from the agarose gel was purified using the Bio 101 GeneClean Kit protocol (Bio 101, Vista, CA).

The pET-28b vector was prepared for cloning by digestion with restriction endonucleases, Ncol and EcoRI (New England BioLabs, Beverly, MA) (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons, Inc. (1994)). The pET-28a vector, which encodes the histidine affinity tag that can be fused to the 5' end of an inserted gene, was prepared by digestion with appropriate restriction endonucleases.

Following digestion, DNA inserts were cloned (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons, Inc. (1994)) into the previously digested pET-28b -91- WO 01/92891 PCT/US01/16946 expression vector. Products of the ligation reaction were then used to transform the BL21 strain of E. coli (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons, Inc. (1994)) as described below.

Competent bacteria, E. coli strain BL21 or E. coli strain BL21 (DE3), were transformed with recombinant pET expression plasmids carrying the cloned HBM sequence according to standard methods (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons, Inc. (1994)). Briefly, 1 pl of ligation reaction was mixed with 50 il of electrocompetent cells and subjected to a high voltage pulse, after which samples were incubated in 0.45 ml SOC medium yeast extract, 2.0% tryptone, 10 mM NaCI, 2.5 mM KC1, 10 mM MgClz, 10 mM MgSO 4 and 20 mM glucose) at 37 0 C with shaking for 1 hour.

Samples were then spread on LB agar plates containing 25 Ig/ml kanamycin sulfate for growth overnight. Transformed colonies of BL21 were then picked and analyzed to evaluate cloned inserts, as described below.

Individual BL21 clones transformed with recombinant pET-28b HBM nucleotide sequences were analyzed by PCR amplification of the cloned inserts using the same forward and reverse primers specific for the HBM sequences that were used in the original PCR amplification cloning reactions. Successful amplification verifies the integration of the HBM sequence in the expression vector (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons, Inc. (1994)).

Individual clones of recombinant pET-28b vectors carrying properly cloned HBM nucleotide sequences were picked and incubated in 5 ml of LB broth plus 25 Ag/ml kanamycin sulfate overnight. The following day plasmid DNA was isolated and purified using the Qiagen plasmid purification protocol (Qiagen Inc., Chatsworth, CA).

-92- WO 01/92891 PCT/US01/16946 The pET vector can be propagated in any E. coli K-12 strain, HIMS174, HB 101, JM109, DH5 and the like, for purposes of cloning or plasmid preparation. Hosts for expression include E. coli strains containing a chromosomal copy of the gene for T7 RNA, polymerase. These hosts were lysogens of bacteriophage DE3, a lambda derivative that carries the lad gene, the lacUV5 promoter and the gene for T7 RNA polymerase. T7 RNA polymerase was induced by addition of isopropyl-P-D-thiogalactoside (IPTG), and the T7 RNA polymerase transcribes any target plasmid containing a functional T7 promoter, such as pET-28b, carrying its gene of interest. Strains include, for example, BL21(DE3) (Studier. et al., Meth. Enzymol., 185:60-89 (1990)).

To express the recombinant HBM sequence, 50 ng of plasmid DNA are isolated as described above to transform competent BL21(DE3) bacteria as described above (provided by Novagen as part of the pET expression kit). The lacZ gene (p-galactosidase) is expressed in the pET-System as described for the HBM recombinant constructions. Transformed cells were cultured in SOC medium for 1 hour, and the culture was then plated on LB plates containing 25 gg/ml kanamycin sulfate. The following day, the bacterial colonies were pooled and grown in LB medium containing kanamycin sulfate (25 p.g/ml) to an optical density at 600 nM of 0.5 to 1.0 O.D. units, at which point 1 mM IPTG was added to the culture for 3 hours to induce gene expression of the HBM recombinant DNA constructions.

After induction of gene expression with IPTG, bacteria were collected by centrifugation in a Sorvall RC-3B centrifuge at 3500 x g for 15 minutes at 4'C. Pellets were resuspended in 50 ml of cold mM Tris-HC1, pH 8.0, 0.1 M NaC1 and 0.1 mM EDTA (STE buffer). Cells were then centrifuged at 2000 x g for 20 minutes at 4 0 C. Wet pellets were weighed and frozen at -80 C until ready for protein purification.

-93- WO 01/92891 PCT/US01/16946 A variety of methodologies known in the art can be used to purify the isolated proteins (Coligan et al., Current Protocols in Protein Science, John Wiley Sons (1995)).

For example, the frozen cells can be thawed, resuspended in buffer and ruptured by several passages through a small volume microfluidizer (Model M-110S, Microfluidics International Corp., Newton, MA). The resultant homogenate is centrifuged to yield a clear supernatant (crude extract) and, following filtration, the crude extract is fractioned over columns.

Fractions are monitored by absorbance at OD, 2 0 nm and peak fractions may be analyzed by

SDS-PAGE.

The concentrations of purified protein preparations are quantified spectrophotometrically using absorbance coefficients calculated from amino acid content (Perkins, Eur. J. Biochem., 157:169-180 (1986)). Protein concentrations are also measured by the method of Bradford, Anal. Biochem., 72:248-254 (1976) and Lowry et al., J. Biol.

Chem., 193:265-275 (1951) using bovine serum albumin as a standard.

SDS-polyacrylamide gels of various concentrations were purchased from BioRad (Hercules, CA), and stained with Coomassie blue. Molecular weight markers may include rabbit skeletal muscle myosin (200 kDa), E. coli P-galactosidase (116 kDa), rabbit muscle phosphorylase B (97.4 kDa), bovine serum albumin (66.2 kDa), ovalbumin (45 kDa), bovine carbonic anyhdrase (31 kDa), soybean trypsin inhibitor (21.5 kDa), egg white lysozyme (14.4 kDa) and bovine aprotinin (6.5 kDa).

Once a sufficient quantity of the desired protein has been obtained, it may be used for Various purposes. A typical use is the production of antibodies specific for binding. These antibodies may be either polyclonal or monoclonal, and may be produced by in vitro or in vivo techniques well known in the art. Monoclonal antibodies to epitopes of any of the peptides identified and isolated as described can be prepared from murine hybridomas -94- WO 01/92891 PCT/US01/16946 (Kohler, Nature, 256:495 (1975)). In summary, a mouse is inoculated with a few micrograms of HBM protein over a period of two weeks. The mouse is then sacrificed. The cells that produce antibodies are then removed from the mouse's spleen. The spleen cells are then fused with polyethylene glycol with mouse myeloma cells. The successfully fused cells are diluted in a microtiter plate and growth of the culture is continued. The amount of antibody per well is measured by immunoassay methods such as ELISA (Engvall, Meth. Enzymol., 70:419 (1980)). Clones producing antibody can be expanded and further propagated to produce HBM antibodies. Other suitable techniques involve in vitro exposure of lymphocytes to the antigenic polypeptides, or alternatively, to selection of libraries of antibodies in phage or similar vectors. See Huse et al., Science, 246:1275-1281 (1989). For additional information on antibody production see Davis et al., Basic Methods in Molecular Biology, Elsevier, NY, Section 21-2 (1989).

Standard protocols for assessing the influence of an agent antibody, HBM protein, protein polymorphism or Zmaxl protein or compound) to alter lipid levels in a cell or the physiological levels in a subject are known. For example, see F.W. HEMMING, LIPID ANALYSIS (Bios Scientific Pub. 1996) and J. M. ORDOVAS, LIPOPROTEIN PROTOCOLS (Humana Press Inc. 1997). More specifically, cholesterol and triglyceride analysis can be performed using the Olympus AU5000 Cholesterol method. This method of measuring cholesterol combines the use of the enzymes with a modification of the peroxidase-pheol-4aminoantipyrine system, substituting 2-hydroxy-3,5-dichlorobenzene sulfonic acid (2-OH DCBSA) for the phenolic group for the measurement of total cholesterol in the subject serum.

The assay is based on a series of coupled enzymatic reactions. Cholesterol esters present in serum are hydrolyzed to free cholesterol and fatty acids by cholesterol esterase. The cholesterol is in turn oxidized by cholesterol oxidase to cholest-4-en-3-one with the WO 01/92891 PCT/US01/16946 simultaneous proauction ot nydrogen peroxidase. The hydrogen peroxidase reacts with 4aminoantipyrine in the presence of 2-OH-3,5-DCBSA to produce a chromophore that absorbs at 570 nm. The absorbance of the reaction mixture is measured biochromatically at 570/750 nm and is proportional to the cholesterol concentration of the sample.

For serum triglyceride analysis, the Olympus AU5000 triglyceride procedure can also be used. Briefly, it is based on a series of coupled enzymatic reactions. Triglycerides in the serum are hydrolyzed to free fatty acids and glycerol by lipoprotein lipase. Glycerol is phosphorylated enzymatically and then oxidized with glycerol phosphate oxidase. The hydrogen peroxidase reacts with the chromogen 4-amino-antipyrine in the presence of DCB Sulfonic Acid to give a chromophore with absorption which is measured bichromatically at 520/660 nm. The increase in absorbance of the reaction mixture is proportional to the triglyceride concentration of the sample.

XVII. Methods of Use: Gene Therapy In recent years, significant technological advances have been made in the area of gene therapy for both genetic and acquired diseases. (Kay et al., Proc. Natl. Acad. Sci. USA, 94:12744-12746 (1997)) Gene therapy can be defined as the deliberate transfer of DNA for therapeutic purposes. Improvement in gene transfer methods has allowed for development of gene therapy protocols for the treatment of diverse types of diseases. Gene therapy has also taken advantage of recent advances in the identification of new therapeutic genes, improvement in both viral and nonviral gene delivery systems, better understanding of gene regulation, and improvement in cell isolation and transplantation.

The experiments below identify the HBM gene as a dominant mutation conferring elevated bone mass and that alters lipid levels. The fact that this mutation is dominant -96- WO 01/92891 PCT/US01/16946 indicates that expression of the HBM protein causes elevated bone mass and perhaps changes in lipid levels. Older individuals carrying the HBM gene, and, therefore expressing the HBM protein, do not suffer from osteoporosis. These individuals are equivalent to individuals being treated with the HBM protein. These observations are a strong experimental indication that therapeutic treatment with the HBM protein prevents osteoporosis. The bone mass elevating activity of the HBMgene is termed "HBM function." Therefore, according to the present invention, a method is also provided of supplying HBM function to mesenchymal stem cells (Onyia et al., J. Bone Miner. Res., 13:20-30 (1998); Ko et al., Cancer Res., 56:4614-4619 (1996)). Supplying such a function provides protection against osteoporosis. For regulating lipid levels, HBM function can be supplied to liver cells, as well as other cells involved in lipid metabolism and lipid regulation muscle cells, lesion cells, lipid laiden foam cells and megakaryoblasts). The HBM gene or a part of the gene may be introduced into the cell in a vector such that the gene remains extrachromosomal. In such a situation, the gene will be expressed by the cell from the extrachromosomal location.

Vectors for introduction of genes both for recombination and for extrachromosomal maintenance are known in the art, and any suitable vector may be used. Methods for introducing DNA into cells such as electroporation, calcium phosphate co-precipitation, and viral transduction are known in the art, and the choice of method is within the competence of one skilled in the art (Robbins, Ed., Gene Therapy Protocols, Human Press, NJ (1997)).

Cells transformed with the HBM gene can be used as model systems to study osteoporosis and drug treatments that promote bone growth as well as to study lipid-mediated diseases.

As generally discussed above, the HBM gene or fragment, where applicable, may be used in gene therapy methods in order to increase the amount of the expression products of -97- WO 01/92891 PCT/US01/16946 such genes in mesenchymal stem cells or in other cells. It may be useful also to increase the level of expression of a given HBM protein, or a fragment thereof, even in those cells in which the wild type gene is expressed normally. Gene therapy would be carried out according to generally accepted methods as described by, for example, Friedman, Therapy for Genetic Diseases, Friedman, Ed., Oxford University Press, pages 105-121 (1991).

A virus or plasmid vector containing a copy of the HBM gene linked to expression control elements and capable of replicating inside mesenchymal stem cells or liver cells, is prepared. Suitable vectors are known and described, for example, in U.S. Patent No.

5,252,479 and WO 93/07282, the disclosures of which are incorporated by reference herein in their entirety. The vector is then injected into the patient, either locally into the bone marrow or liver, or systemically (in order to reach any mesenchymal stem cells located at other sites, in the blood). If the transfected gene is not permanently incorporated into the genome of each of the targeted cells, the treatment may have to be repeated periodically.

Gene transfer systems known in the art may be useful in the practice of the gene therapy methods of the present invention. These include viral and non-viral transfer methods.

A number of viruses have been used as gene transfer vectors, including polyoma, (Madzak et al., J. Gen. Virol., 73:1533-1536 (1992)), adenovirus (Berkner, Curr. Top.

Microbiol. Immunol., 158:39-61 (1992); Berkner et al., Bio Techniques, 6:616-629 (1988); Gorziglia et al., J Virol., 66:4407-4412 (1992); Quantin et al., Proc. Natl. Acad. Sci. USA, 89:2581-2584 (1992); Rosenfeld et al., Cell, 68:143-155 (1992); Wilkinson et al., Nucl.

Acids Res., 20:2233-2239 (1992); Stratford-Perricaudet et al., Hum. Gene Ther., 1:241-256 (1990)), vaccinia virus (Mackett et al., Biotechnology, 24:495-499 (1992)), adeno-associated virus (Muzyczka, Curr. Top. Microbiol. Immunol., 158:91-123 (1992); Ohi et al., Gene, 89:279-282 (1990)), herpes viruses including HSV and EBV (Margolskee, Curr. Top.

-98- WO 01/92891 WO 0192891PCT/USOI/16946 Microbial. Immunol., I (1992); Johnson et al., J. ViroL, 66:2952-2965 (1992); Finic et al.,I-Hum. Gene Ther., 3:11-19 (1992); Breakfield et al,Mol. Neurobiol., 1:337-371 (1987;) Fresse et aL, Biochem. PharmacoL, 40:2189-2199 (1990)), and retroviruses of avian (B3randyopadhyay et Mo?. Cell Bio., 4:749-754 (1984); Petropouplos et al., J1 Virol, 66:3391-3397 (1992)), murine (Miller, Curr. Top. Microbiol. Immuno?., 158:1-24 (1992); Miller et al., Mo?. Cell Bio., 5:431-437 (1985); Sorge et al., Mo?. Cell Biol., 4:1730-1737 (1984); Mann et al., J Virol., 54:401-407 (1985)), and human origin (Page et al., J Virol., 64:5370-5276 (1990); Buchschalcher et al., J~ Viral., 66:273 1-2739 (1992)). Most human gene therapy protocols have been based on disabled murine retroviruses.

Non-viral gene transfer methods known in the art include chemical techniques such as calcium phosphate coprecipitation (Graham et Virology, 52:456-467 (1973); Pellicer et al., Science, 209:1414-1422 (1980)), mechanical techniques, for example microinjection (Anderson et al., Proc. Nat?. Acad Sci. USA, 77:5399-5403 (1980); Gordon et Proc. Nat.

Acad. Sci. USA, 77:7380-7384 (1980); Brinster et Cell, 27:223-23 1 (1981); Constantini et Nature, 294:92-94 (1981)), membrane fasion-mediated transfer via liposomes (Feigner et al, Proc. Nat?. Acad Sci. USA, 84:7413-7417 (1987); Wang et al., Biochemistry, 28:9508- 9514 (1989); Kaneda et J Bid. Chem., 264: 12 126-12129 (1989); Stewart eta?., Hum.

Gene Ther., 3:267-275 (1992); Nabel et Science, 249:1285-1288 (1990); Lim et Circulation, 83:2007-2011 (1992)), and direct DNA uptake and receptor-mediated DNA transfer (Wolff et Science, 247:1465-1468 (1990); Wu et BioTechniques, 11:474-485 (1991); Zenke et al, Proc. Nat. Acad. Sci. USA, 87:3655-3659 (1990); Wu et J Biol.

Chem., 264:16985-16987 (1989); Wolff et RioTechniques, 11:474-485 (1991); Wagner eta?., 1990; Wagner et Proc. Nat?. Acad. Sci. USA4, 88:4255-4259 (1991); Cotten et al., Proc. Nat?. Acad. Sci. USA, 87:4033-4037 (1990); Curiel et Proc. Nat?. Acad. Sd. USA, 99 WO 01/92891 PCT/US01/16946 88:8850-8854 (1991); Curiel et al., Hum. Gene Ther., 3:147-154 (1991)). Viral-mediated gene transfer can be combined with direct in vivo vectors to the mesenchymal stem cells and not into the surrounding cells (Romano et In Vivo, 12(1):59-67 (1998); Gonez et al., Hum. Mol. Genetics, 7(12):1913-9 (1998)). Alternatively, the retroviral vector producer cell line can be injected into the bone marrow (Culver et al., Science, 256:1550-1552 (1992)).

Injection of producer cells would then provide a continuous source of vector particles. This technique has been approved for use in humans with inoperable brain tumors.

In an approach which combines biological and physical gene transfer methods, plasmid DNA of any size is combined with a polylysine-conjugated antibody specific to the adenovirus hexon protein, and the resulting complex is bound to an adenovirus vector. The trimolecular complex is then used to infect cells. The adenovirus vector permits efficient binding, internalization, and degradation of the endosome before the coupled DNA is damaged.

Liposome/DNA complexes have been shown to be capable of mediating direct in vivo gene transfer. While in standard liposome preparations the gene transfer process is nonspecific, localized in vivo uptake and expression have been reported in tumor deposits, for example, following direct in situ administration (Nabel, Hum. Gene Ther., 3:399-410 (1992))..

XVIII. Methods of Use: Transformed Hosts, Development of Pharmaceuticals and Research Tools Cells and animals that carry the HBM gene can be used as model systems to study and test for substances that have potential as therapeutic agents (Onyia et al., J. Bone Miner. Res., 13:20-30 (1998); Broder et al., Bone, 21:225-235 (1997)). The cells are typically cultured mesenchymal stem cells or liver cells. These may be isolated from individuals with somatic -100- WO 01/92891 PCT/US01/16946 or germline HBM genes. Alternatively, the cell line can be engineered to carry the HBM gene, as described above. After a test substance is applied to the cells, the transformed phenotype of the cell is determined. Any trait of transformed cells can be assessed, including formation of bone matrix in culture (Broder et al., Bone, 21:225-235 (1997)), mechanical properties (Kizer et al., Proc. Natl. Acad. Sci. USA, 94:1013-1018 (1997)), and response to application of putative therapeutic agents.

Animals for testing therapeutic agents can be selected after treatment of germline cells or zygotes. Such treatments include insertion of the Zmaxl gene, as well as insertion of the HBM gene and disrupted homologous genes. Alternatively, the inserted Zmaxl gene(s) and/or HBM gene(s) of the animals may be disrupted by insertion or deletion mutation of other genetic alterations using conventional techniques, such as those described by, for example, Capechi, Science, 244:1288 (1989); Valancuis et al., Mol. Cell Biol., 11:1402 (1991); Hasty et al., Nature, 350:243 (1991); Shinkai et al., Cell, 68:855 (1992); Mombaerts et al., Cell, 68:869 (1992); Philpott et al., Science, 256:1448 (1992); Snouwaert et al., Science, 257:1083 (1992); Donehower et al., Nature, 356:215 (1992). After test substances have been administered to the animals, the growth of bone or modulation of lipids must be assessed. If the test substance enhances the growth of bone or regulates lipid levels, then the test substance is a candidate therapeutic agent. These animal models provide an extremely important vehicle for potential therapeutic products. Preferred models for studying lipid modulation include mice (Smith et al., J Intern. Med., 242: 99-109 (1997)) and guinea pigs.

Individuals carrying the HBM gene have elevated bone mass and altered lipid levels as discussed in the example below. The HBM gene causes this phenotype by altering the activities, levels, expression patterns, and modification states of other molecules involved in bone development. Using a variety of established techniques, it is possible to identify 101- WO 01/92891 PCT/US01/16946 molecules, preferably proteins or mRNAs, whose activities, levels, expression patterns, and modification states are different between systems containing the Zmax 1 gene and systems containing the HBM gene. Such systems can be, for example, cell-free extracts, cells, tissues or living organisms, such as mice or humans. For a mutant form of Zmaxl, a complete deletion of Zmax mutations lacking the extracellular or intracellular portion of the protein, or any other mutation in the Zmnax gene may be used. It is also possible to use expression of antisense Zmaxl RNA or oligonucleotides to inhibit production of the Zmaxl protein. For a mutant form of HBM, a complete deletion of HBM, mutations lacking the extracellular or intracellular portion of the HBM protein, or any other mutation in the HBM gene may be used. It is also possible to use expression of antisense HBM RNA or oligonucleotides to inhibit production of the HBM protein.

Molecules identified by comparison ofZmaxl systems and HBM systems can be used as surrogate markers in pharmaceutical development or in diagnosis of human or animal bone disease. Alternatively, such molecules may be used in treatment of bone disease. See, Schena et al., Science, 270:467-470 (1995).

For example, a transgenic mouse carrying the HBM gene in the mouse homologue is constructed. A mouse of the genotype HBM/+ is viable, healthy and has elevated bone mass.

To identify surrogate markers for elevated bone mass, HBM-/+ heterozygous) and isogenic wild-type) mice are sacrificed. Bone tissue mRNA is extracted from each animal, and a "gene chip" corresponding to mRNAs expressed in the individual is constructed. mRNA from different tissues is isolated from animals of each genotype, reverse-transcribed, fluorescently labeled, and then hybridized to gene fragments affixed to a solid support. The ratio of fluorescent intensity between the two populations is indicative of the relative abundance of the specific mRNAs in the and HBM/+ animals. Genes -102- WO 01/92891 PCT/US01/16946 encoding mRNAs over- and under-expressed relative to the wild-type control are candidates for genes coordinately regulated by the HBM gene. This strategy can be similarly used to study lipid regulation.

Mice also serve as the most common experimental animal model for atherosclerosis research. There are at least three ways of inducing atherosclerosis in mice: diet induced, apoE deficiency-induced and LDL receptor-deficiency induced. The methods for using a mouse model for testing agents which modulate lipid levels in vivo can be performed as described in Smith et al., J Intern. Med. 242: 99-109 (1997).

One standard procedure for identification of new proteins that are part of the same signaling cascade as an already-discovered protein is as follows. Cells are treated with radioactive phosphorous, and the already-discovered protein is manipulated to be more or less active. The phosphorylation state of other proteins in the cell is then monitored by polyacrylamide gel electrophoresis and autoradiography, or similar techniques. Levels of activity of the known protein may be manipulated by many methods, including, for example, comparing wild-type mutant proteins using specific inhibitors such as drugs or antibodies, simply adding or not adding a known extracellular protein, or using antisense inhibition of the expression of the known protein (Tamura et al., Science, 280(5369):1614-7 (1998); Meng, EMBO J, 17(15):4391-403 (1998); Cooper et al., Cell, 1:263-73 (1982)).

In another example, proteins with different levels of phosphorylation are identified in TE85 osteosarcoma cells expressing either a sense or antisense cDNA for Zmaxl. TE85 cells normally express high levels of Zmaxl (Dong et al., Biochem. Biophys. Res. Comm., 251:784-790 (1998)). Cells containing the sense construct express even higher levels of Zmaxl, while cells expressing the antisense construct express lower levels. Cells are grown in the presence of 32 P, harvested, lysed, and the lysates run on SDS polyacrylamide gels to -103- WO 01/92891 PCT/US01/16946 separate proteins, and the gels subjected to autoradiography (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons (1997)). Bands that differ in intensity between the sense and antisense cell lines represent phosphoproteins whose phosphorylation state or absolute level varies in response to levels of Zmaxl. As an alternative to the 32 p_ labeling, unlabeled proteins may be separated by SDS-PAGE and subjected to immunoblotting, using the commercially available anti-phosphotyrosine antibody as a probe (Thomas et al., Nature, 376(6537):267-71 (1995)). As an alternative to the expression of antisense RNA, transfection with chemically modified antisense oligonucleotides can be used (Woolf et al., Nucleic Acids Res., 18(7):1763-9 (1990)).

Many bone disorders, such as osteoporosis, have a slow onset and a slow response to treatment. It is therefore useful to develop surrogate markers for bone development and mineralization. Such markers can be useful in developing treatments for bone disorders, and for diagnosing patients who may be at risk for later development of bone disorders.

Examples of preferred markers are N- and C-terminal telopeptide markers described, for example, in U.S. Patent Nos. 5,455,179, 5,641,837 and 5,652,112, the disclosures of which are incorporated by reference herein in their entirety. In the area of HIV disease, CD4 counts and viral load are useful surrogate markers for disease progression (Vlahov et al., JAMA, 279(1):35-40 (1998)). There is a need for analogous surrogate markers in the area of bone disease.

A surrogate marker can be any characteristic that is easily tested and relatively insensitive to non-specific influences. For example, a surrogate marker can be a molecule such as a protein or mRNA in a tissue or in blood serum. Alternatively, a surrogate marker may be a diagnostic sign such as sensitivity to pain, a reflex response or the like.

104- WO 01/92891 PCT/US01/16946 In yet another example, surrogate markers for elevated bone mass are identified using a pedigree of humans carrying the HBM gene. Blood samples are withdrawn from three individuals that carry the HBM gene, and from three closely related individuals that do not.

Proteins in the serum from these individuals are electrophoresed on a two dimensional gel system, in which one dimension separates proteins by size, and another dimension separates proteins by isoelectric point (Epstein et al., Electrophoresis, 17(11):1655-70 (1996)). Spots corresponding to proteins are identified. A few spots are expected to be present in different amounts or in slightly different positions for the HBM individuals compared to their normal relatives. These spots correspond to proteins that are candidate surrogate markers. The identities of the proteins are determined by microsequencing, and antibodies to the proteins can be produced by standard methods for use in diagnostic testing procedures. Diagnostic assays for HBM proteins or other candidate surrogate markers include using antibodies described in this invention and a reporter molecule to detect HBM in human body fluids, membranes, bones, cells, tissues or extracts thereof. The antibodies can be labeled by joining them covalently or noncovalently with a substance that provides a detectable signal. In many scientific and patent literature, a variety of reporter molecules or labels are described including radionuclides, enzymes, fluorescent, chemi-luminescent or chromogenic agents Patent Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241).

Using these antibodies, the levels of candidate surrogate markers are measured in normal individuals and in patients suffering from a bone disorder, such as osteoporosis, osteoporosis pseudoglioma, Engelmann's disease, Ribbing's disease, hyperphosphatasemia, Van Buchem's disease, melorheostosis, osteopetrosis, pychodysostosis, sclerosteosis, osteopoikilosis, acromegaly, Paget's disease, fibrous dysplasia, tubular stenosis, osteogenesis -105- WO 01/92891 PCT/US01/16946 imperfecta, hypoparathyroidism, pseudohypoparathyroidism, pseudopseudohypoparathyroidism, primary and secondary hyperparathyroidism and associated syndromes, hypercalciuria, medullary carcinoma of the thyroid gland, osteomalacia and other diseases including lipid-mediated diseases. Techniques for measuring levels of protein in serum in a clinical setting using antibodies are well established. A protein that is consistently present in higher or lower levels in individuals carrying a particular disease or type of disease is a useful surrogate marker.

A surrogate marker can be used in diagnosis of a bone disorder. For example, consider a child that present to a physician with a high frequency of bone fracture. The underlying cause may be child abuse, inappropriate behavior by the child, or a bone disorder.

To rapidly test for a bone disorder, the levels of the surrogate marker protein are measured using the antibody described above.

Levels of modification states of surrogate markers can be measured as indicators of the likely effectiveness of a drug that is being developed. It is especially convenient to use surrogate markers in creating treatments for bone disorders, because alterations in bone development or mineralization may require a long time to be observed. For example, a set of bone mRNAs, termed the "HBM-inducible mRNA set" is found to be overexpressed in HBM/+ mice as compared to mice, as described above. Expression of this set can be used as a surrogate marker. Specifically, if treatment mice with a compound results in overexpression of the HBM-inducible mRNA set, then that compound is considered a promising candidate for further development.

This invention is particularly useful for screening compounds by using the Zmaxl or HEM protein or binding fragment thereof in any of a variety of drug screening techniques.

-106- WO 01/92891 PCT/US01/16946 The Zmaxl or HBM protein or fragment employed in such a test may either be free in solution, affixed to a solid support, or borne on a cell surface. One method of drug screening utilizes eukaryotic or prokaryotic host cells which are stably transformed with recombinant nucleic acids expressing the protein or fragment, preferably in competitive binding assays.

Such cells, either in viable or fixed form, can be used for standard binding assays. One may measure, for example, for the formation of complexes between a Zmaxl or HBM protein or fragment and the agent being tested, or examine the degree to which the formation of a complex between a Zmaxl or HBM protein or fragment and a known ligand is interfered with by the agent being tested.

Thus, the present invention provides methods of screening for drugs comprising contacting such an agent with a Zmaxl or HBM protein, or fragment thereof, and assaying (i) for the presence of a complex between the agent and the Zmaxl or HBM protein or fragment, or (ii) for the presence of a complex between the Zmaxl or HBM protein or fragment and a ligand, by methods well known in the art. In such competitive binding assays the Zmaxl or HBM protein or fragment is typically labeled. Free Zmaxl or HBM protein or fragment is separated from that present in a protein:protein complex, and the amount of free uncomplexed) label is a measure of the binding of the agent being tested to Zmaxl or HBM or its interference with Zmaxl or HBM: ligand binding, respectively.

Another technique for drug screening provides high throughput screening for compounds having suitable binding affinity to the Zmaxl or HBM proteins and is described in detail in WO 84/03564. Briefly stated, large numbers of different small peptide test compounds are synthesized on a solid substrate, such as plastic pins or some other surface.

The peptide test compounds are reacted with Zmaxl or HBM proteins and washed. Bound Zmaxl or HBM protein is then detected by methods well known in the art. Purified Zmaxl -107- WO 01/92891 PCT/US01/16946 or HBM can be coated directly onto plates for use in the aforementioned drug screening techniques. However, non-neutralizing antibodies to the protein can be used to capture antibodies to immobilize the Zmaxl or HBM protein on the solid phase.

This invention also contemplates the use of competitive drug screening assays in which neutralizing antibodies capable of specifically binding the Zmaxl or HBM protein compete with a test compound for binding to the Zmaxl or HBM protein or fragments thereof. In this manner, the antibodies can be used to detect the presence of any peptide that shares one or more antigenic determinants of the Zmaxl or HBM protein.

A further technique for drug screening involves the use of host eukaryotic cell lines or cells (such as described above) that have a nonfunctional Zmaxl or HBM gene. These host cell lines or cells are defective at the Zmax or HBM protein level. The host cell lines or cells are grown in the presence of drug compound. The rate of growth of the host cells or impact on lipid metabolism is measured to determine if the compound is capable of regulating the growth or lipid metabolism of Zmaxl or HBM defective cells.

The goal of rational drug design is to produce structural analogs of biologically active proteins of interest or of small molecules with which they interact agonists, antagonists, inhibitors) in order to fashion drugs which are, for example, more active or stable forms of the protein, or which, enhance or interfere with the function of a protein in vivo. See, Hodgson, Bio/Technology, 9:19-21 (1991). In one approach, one first determines the three-dimensional structure of a protein of interest Zmaxl or HBM protein) or, for example, of the Zmaxl- or HBM-receptor or ligand complex, by X-ray crystallography, by computer modeling or most typically, by a combination of approaches. Less often, useful information regarding the structure of a protein may be gained by modeling based on the structure of homologous proteins. An example of rational drug design is the development of -108- WO 01/92891 PCT/US01/16946 HIV protease inhibitors (Erickson et al., Science, 249:527-533 (1990)). In addition, peptides Zmaxl or HBM protein) are analyzed by an alanine scan (Wells, Methods in Enzymol., 202:390-411 (1991)). In this technique, an amino acid residue is replaced by Ala, and its effect on the peptide's activity is determined. Each of the amino acid residues of the peptide is analyzed in this manner to determine the important regions of the peptide.

It is also possible to isolate a target-specific antibody, selected by a functional assay, and then to solve its crystal structure. In principle, this approach yields a pharmacore upon which subsequent drug design can be based. It is possible to bypass protein crystallography altogether by generating anti-idiotypic antibodies (anti-ids) to a functional, pharmacologically active antibody. As a mirror image of a mirror image, the binding site of the anti-ids would be expected to be an analog of the original receptor. The anti-id could then be used to identify and isolate peptides from banks of chemically or biologically produced banks of peptides. Selected peptides would then act as the pharmacore.

Thus, one may design drugs which have, improved Zmaxl or HBM protein activity or stability or which act as inhibitors, agonists, antagonists, etc. of Zmaxl or HBM protein activity. By virtue of the availability of cloned Zmaxl or HBM sequences, sufficient amounts of the Zmaxl or HBM protein may be made available to perform such analytical studies as X-ray crystallography. In addition, the knowledge of the Zmaxl or HBM protein sequence provided herein will guide those employing computer modeling techniques in place of, or in addition to x-ray crystallography.

XIX. Methods of Use: Avian and Mammalian Animal Husbandry The Zmaxl DNA and Zmaxl protein and/or the HBM DNA and HBM protein can be used for vertebrate and preferably human therapeutic agents and for avian and mammalian -109- WO 01/92891 PCT/US01/16946 veterinary agents, including for livestock breeding. Animals contemplated as subjects include livestock cattle, pigs, sheep, goats, horses, buffalo, etc.), primates, canines, felines, rodents, birds, as well as reptiles, fish, and amphibians. Birds, including, for example, chickens, roosters, hens, turkeys, ostriches, ducks, pheasants and quails, can benefit from the identification of the gene and pathway for high bone mass. In many examples cited in literature (for example, McCoy et al., Res. Vet. Sci., 60(2):185-186 (1996)), weakened bones due to husbandry conditions cause cage layer fatigue, osteoporosis and high mortality rates. Additional therapeutic agents to treat osteoporosis or other bone disorders in birds can have considerable beneficial effects on avian welfare and the economic conditions of the livestock industry, including, for example, meat and egg production.

XX. Methods of use: Diagnostic assays using Zmaxl-specific oligonucleotides for detection of genetic alterations affecting bone development and lipid regulation.

In cases where an alteration or disease of bone development or lipid metabolism is suspected to involve an alteration of the Zmaxl gene or the HBM gene, specific oligonucleotides may be constructed and used to assess the level of Zmaxl mRNA or HBM mRNA, respectively, in bone tissue or in another tissue that affects bone development.

For example, to test whether a person has the HBM gene, which affects bone density and lipid regulation, polymerase chain reaction can be used. Two oligonucleotides are synthesized by standard methods or are obtained from a commercial supplier of custom-made oligonucleotides. The length and base composition are determined by standard criteria using the Oligo 4.0 primer Picking program (Wojchich Rychlik, 1992). One of the oligonucleotides is designed so that it will hybridize only to HBM DNA under the PCR conditions used. The other oligonucleotide is designed to hybridize a segment of Zmaxl -110- WO 01/92891 PCT/US01/16946 genomic DNA, such that amplification ofDNA using these oligonucleotide primers produces a conveniently identified DNA fragment. For example, the pair of primers CCAAGTTCTGAGAAGTCC (SEQ ID NO:32) and AATACCTGAAACCA TACCTG (SEQ ID NO:33) will amplify a 530 base pair DNA fragment from a DNA sample when the following conditions are used: step 1 at 95°C for 120 seconds; step 2 at 95°C for 30 seconds; step 3 at 58 0 C for 30 seconds; step 4 at 72 0 C for 120 seconds; where steps 2-4 are repeated times. Tissue samples may be obtained from hair follicles, whole blood, or the buccal cavity.

The fragment generated by the above procedure is sequenced by standard techniques.

Individuals heterozygous for the HBM gene will show an equal amount of G and T at the second position in the codon for glycine 171. Normal or homozygous wild-type individuals will show only G at this position.

Other amplification techniques besides PCR may be used as alternatives, such as ligation-mediated PCR or techniques involving Q-beta replicase (Cahill et al., Clin. Chem., 37(9):1482-5 (1991)). For example, the oligonucleotides AGCTGCTCGTAGCTGTCTCT CCCTGGATCACGGGTACATGTACTGGACAGACTGGGT (SEQ ID NO:34) and

TGAGACGCCCCGGATTGAGCGGGCAGGGATAGCTTATTCCCTGTGCCGCATTACG

GC (SEQ ID NO:35) can be hybridized to a denatured human DNA sample, treated with a DNA ligase, and then subjected to PCR amplification using the primer oligonucleotides AGCTGCTCGTAG CTGTCTCTCCCTGGA (SEQ ID NO:36) and GCCGTAATGCGGCACAGGGAATAAGCT (SEQ ID NO:37). In the first two oligonucleotides, the outer 27 bases are random sequence corresponding to primer binding sites, and the inner 30 bases correspond to sequences in the Zmaxl gene. The T at the end of the first oligonucleotide corresponds to the HBM gene. The first two oligonucleotides are -111- WO 01/92891 PCT/US01/16946 ligated only when hybridized to human DNA carrying the HBM gene, which results in the formation of an amplifiable 114 bp DNA fragment.

Products of amplification can be detected by agarose gel electrophoresis, quantitative hybridization, or equivalent techniques for nucleic acid detection known to one skilled in the art of molecular biology (Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring, NY (1989)).

Other alterations in the Zmaxl gene or the HBM gene may be diagnosed by the same type of amplification-detection procedures, by using oligonucleotides designed to identify those alterations. These procedures can be used in animals as well as humans to identify alterations in Zmaxl or HBM that affect bone development and/or lipid metabolism or levels.

Expression of Zmaxl or HBM in bone tissue may be accomplished by fusing the cDNA of Zmaxl or HBM, respectively, to a bone-specific promoter in the context of a vector for genetically engineering vertebrate cells. DNA constructs are introduced into cells by packaging the DNA into virus capsids, by the use of cationic liposomes, electroporation, or by calcium phosphate transfection. Transfected cells, preferably osteoblasts, may be studied in culture or may be introduced into bone tissue in animals by direct injection into bone or by intravenous injection of osteoblasts, followed by incorporation into bone tissue (Ko et al., Cancer Research, 56(20):4614-9 (1996)). For example, the osteocalcin promoter, which is specifically active in osteoblasts, may be used to direct transcription of the Zmaxl gene or the HBM gene. Any of several vectors and transfection methods may be used, such as retroviral vectors, adenovirus vectors, or vectors that are maintained after transfection using cationic liposomes, or other methods and vectors described herein.

Similarly Zmaxl, or HBM can be expressed in liver tissue or in other lipidmetabolism or lipid-regulating cells, such as lipid laden foam cells or lesion cells. This can -112- WO 01/92891 PCT/US01/16946 be accomplished by fusing the cDNA ofZmaxl or HBM respectively to, for example, a liver specific promoter or other suitable promoter in the context of a vector for genetically engineering vertebrate cells. DNA constructs are introduced into cells by packaging the DNA into, for example,' virus capsids, by the use of cationic liposomes, electroporation, or calcium phosphate transfection. The transfected cells, preferably liver cells, may be studied in culture or can be introduced into animals by direct injection into the liver or other cell involved in lipid regulation or metabolism. The vectors and transfection methods to be used are similar to those described herein.

Alteration of the level of functional Zmaxl protein or HBM protein affects the level of bone mineralization and lipid levels. By manipulating levels of functional Zmaxl protein or HBM protein, it is possible to affect bone development and to increase or decrease levels of bone mineralization as well as lipid levels. For example, it may be useful to increase bone mineralization in patients with osteoporosis. Alternatively, it may be useful to decrease bone mineralization in patients with osteopetrosis or Paget's disease. Alteration of Zmaxl levels or HBM levels can also be used as a research tool. Specifically, it is possible to identify proteins, mRNA and other molecules whose level or modification status is altered in response to changes in functional levels of Zmaxl or HBM. The pathology and pathogenesis of bone disorders is known and described, for example, in Rubin and Farber Pathology, 2nd Ed., S.B. Lippincott Co., Philadelphia, PA (1994).

Zmaxl or HBM protein levels can be altered to regulate lipid levels in a cell or a subject. The pathology and pathogenesis of atherosclerosis and arteriosclerosis is known and described, for example, in Edwin L. Bierman, "Atherosclerosis and Other Forms of Arteriosclerosis," in Harrison's Principles ofInternal Medicine, 1106-1116 (13th Ed., 1994).

Modulation of lipid levels may be useful to lower certain levels of lipids LDL) in 113- WO 01/92891 PCT/US01/16946 patients with arteriosclerosis and/or atherosclerosis, as well as conditions and diseases affiliated with atherosclerosis and arteriosclerosis, as described by Bierman (1994).

A variety of techniques can be used to alter the levels of functional Zmaxl or HBM.

For example, intravenous or intraosseous injection of the extracellular portion of Zmaxl or mutations thereof, or HBM or mutations thereof, will alter the level of Zmaxl activity or HBM activity, respectively, in the body of the treated human, animal or bird. Truncated versions of the Zmaxl protein or HBM protein can also be injected to alter the levels of functional Zmax1 protein or HBM protein, respectively. Certain forms of Zmaxl or HBM enhance the activity of endogenous protein, while other forms are inhibitory.

In a preferred embodiment, the HBM protein is used to treat osteoporosis or arteriosclerosis. In a further preferred embodiment, the extracellular portion of the HBM protein is used. This HBM protein may be optionally modified by the addition of a moiety that causes the protein to adhere to the surface of cells. The protein is prepared in a pharmaceutically acceptable solution and is administered by injection or another method that achieves acceptable pharmacokinetics and distribution.

In a second embodiment of this method, Zmaxl or HBM levels are increased or decreased by gene therapy techniques. To increase Zmaxl or HBM levels, osteoblasts or another useful cell type are genetically engineered to express high levels of Zmaxl or HBM as described above. Alternatively, to decrease Zmaxl or HBM levels, antisense constructs that specifically reduce the level of translatable Zmaxl or HBM mRNA can be used. In general, a tissue-nonspecific promoter may be used, such as the CMV promoter or another commercially available promoter found in expression vectors (Wu et al., Toxicol. Appl.

Pharmacol., 141(1):330-9 (1996)). In a preferred embodiment, a Zmaxl cDNA or its antisense is transcribed by a bone-specific promoter, such as the osteocalcin or another -114- WO 01/92891 PCT/US01/16946 promoter, to achieve specific expression in bone tissue. In this way, if a Zmaxl-expressing DNA construct or HBM-expressing construct is introduced into non-bone tissue, it will not be expressed. Similarly, if a liver-specific promoter is used to express the HBM or Zmaxl proteins in liver or other cell involved in lipid regulation or metabolism, the DNA construct with, for example, a liver-specific promoter will not be expressed in other non-liver tissues.

In a third embodiment of this method, antibodies against Zmaxl or HBM are used to inhibit its function. Such antibodies are identified herein.

In a fourth embodiment of this method, drugs that inhibit Zmaxl function or HBM function are used. Such drugs are described herein and optimized according to techniques of medicinal chemistry well known to one skilled in the art of pharmaceutical development, Zmaxl and HBM interact with several proteins, such as ApoE. Molecules that inhibit the interaction between Zmaxl or HBM and ApoE or another binding partner are expected to alter bone development and mineralization. Such inhibitors may be useful as drugs in the treatment of osteoporosis, osteopetrosis, or other diseases of bone mineralization. Such inhibitors may be low molecular weight compounds, proteins or other types of molecules.

See, Kim et al., J. Biochem. (Tokyo), 124(6):1072-1076 (1998).

Inhibitors of the interaction between Zmaxl or HBM and interacting proteins may be isolated by standard drug-screening techniques. For example, Zmaxl protein, (or a fragment thereof) or HBM protein (or a fragment thereof) can be immobilized on a solid support such as the base of microtiter well. A second protein or protein fragment, such as ApoE is derivatized to aid in detection, for example with fluorescein. Iodine, or biotin, then added to the Zmaxl or HBM in the presence of candidate compounds that may specifically inhibit this protein-protein domain of Zmax1 or HBM, respectively, and thus avoid problems associated -115- WO 01/92891 PCT/US01/16946 with its transmembrane segment. Drug screens of this type are well known to one skilled in the art of pharmaceutical development.

Because Zmaxl and HBM are involved in bone development and lipid regulation, proteins that bind to Zmaxl and HBM are also expected to be involved in bone development and lipid regulation. Such binding proteins can be identified by standard methods, such as co-immunoprecipitation, co-fractionation, or the two-hybrid screen (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons (1997)). For example, to identify Zmaxl-interacting proteins or HBM-interacting proteins using the two-hybrid system, the extracellular domain of Zmaxl or HBM is fused to LexA and expressed for the yeast vector pEG202 (the "bait") and expressed in the yeast strain EGY48. The yeast strain is transformed with a "prey" library in the appropriate vector, which encodes a galactose-inducible transcription-activation sequence fused to candidate interacting proteins. The techniques for initially selecting and subsequently verifying interacting proteins by this method are well known to one skilled in the art of molecular biology (Ausubel et al., Current Protocols in Molecular Biology, John Wiley Sons (1997)).

In a preferred embodiment, proteins that interact with HBM, but not Zmax 1, are identified using a variation of the above procedure (Xu et al., Proc. Natl. Acad. Sci. USA, 94(23):12473-8 (Nov. 1997)). This variation of the two-hybrid system uses two baits, and Zmaxl and HBM are each fused to LexA and TetR, respectively. Alternatively, proteins that interact with the HBM but not Zmaxl are also isolated. These procedures are well known to one skilled in the art of molecular biology, and are a simple variation of standard two-hybrid procedures.

As an alternative method of isolating Zmaxl or HBM interacting proteins, a biochemical approach is used. The Zmaxl protein or a fragment thereof, such as the -116- WO 01/92891 PCT/US01/16946 extracellular domain, or the HBM protein or a fragment thereof, such as the extracellular domain, is chemically coupled to Sepharose beads. The Zmaxl- or HBM-coupled beads are poured into a column. An extract of proteins, such as serum proteins, proteins in the supernatant of a bone biopsy, or intracellular proteins from gently lysed TE85 osteoblastic cells, is added to the column. Non-specifically bound proteins are eluted, the column is washed several times with a low-salt buffer, and then tightly binding proteins are eluted with a high-salt buffer. These,are candidate proteins that bind to Zmaxl or HBM, and can be tested for specific binding by standard tests and control experiments. Sepharose beads used for coupling proteins and the methods for performing the coupling are commercially available (Sigma), and the procedures described here are well known to one skilled in the art of protein biochemistry.

As a variation of the above procedure, proteins that are eluted by high salt from the Zmaxl- or HBM-Sepharose column are then added to an HBM-Zmaxl-sepharose column.

Proteins that flow through without sticking are proteins that bind to Zmaxl but not to HBM.

Alternatively, proteins that bind to the HBM protein and not to the Zmaxl protein can be isolated by reversing the order in which the columns are used. Similar columns can be prepared for use in assessing lipid regulation in liver and other tissues and cells involved in lipid regulation and or metabolism.

XXI. Method of Use: Transformation-Associated Recombination (TAR) Cloning Essential for the identification of novel allelic variants of Zmax is the ability to examine the sequence of both copies of the gene in an individual. To accomplish this, two "hooks," or regions of significant similarity, are identified within the genomic sequence such that they flank the portion of DNA that is to be cloned. Most preferably, the first of these -117- WO 01/92891 PCT/US01/16946 hooks is derived from sequences 5' to the first exon of interest and the second is derived from sequences 3' to the last exon of interest. These two "hooks" are cloned into a bacterial/yeast shuttle vector such as that described by Larionov et al., Proc. Natl. Acad. Sci. USA, 94:7384- 7387 (1997). Other similar vector systems may also be used. To recover the entire genomic copy of the Zmaxl gene, the plasmid containing the two "hooks" is linearized with a restriction endonuclease or is produced by another method such as PCR. This linear DNA fragment is introduced into yeast cells along with human genomic DNA. Typically, the yeast Saccharomyces cerevisiae is used as a host cell, although chicken host cells can be used as well (Larionov et al., Genet. Eng. 21:37-55 (1999). During and after the process of transformation, the endogenous host cell converts the linear plasmid to a circle by a recombination event whereby the region of the human genomic DNA homologous to the "hooks" is inserted into the plasmid. This plasmid can be recovered and analyzed by methods well known to one skilled in the art. Obviously, the specificity for this reaction requires the host cell machinery to recognize sequences similar to the "hooks" present in the linear fragment. However, 100% sequence identity is not required, as shown by Kouprina et al., Genomics, 53(1):21-28 (October 1998), where the author describes using degenerate repeated sequences common in the human genome to recover fragments of human DNA from a rodent/human hybrid cell line.

In another example, only one "hook" is required, as described by Larionov et al., Proc. Natl. Acad. Sci. USA, 95(8):4469-74 (April 1998). For this type of experiment, termed "radial TAR cloning," the other region of sequence similarity to drive the recombination is derived from a repeated sequence from the genome. In this way, regions of DNA adjacent to the Zmaxl gene coding region can be recovered and examined for alterations that may affect function.

118 WO 01/92891 PCT/US01/16946 XXII. Methods of Use: Genomic Screening The use of polymorphic genetic markers linked to the HBMgene or to Zmaxl is very useful in predicting susceptibility to osteoporosis or other bone diseases. Polymorphic genetic markers linked to the HBM gene or the Zmaxl gene also can be used to predict susceptibility to arteriosclerosis or atherosclerosis and conditions related thereto. Koller et al., Amer. J Bone Min. Res., 13:1903-1908 (1998) have demonstrated that the use of polymorphic genetic markers is useful for linkage analysis. Similarly, the identification of polymorphic genetic markers within the HBM gene will allow the identification of specific allelic variants that are in linkage disequilibrium with other genetic lesions that affect bone development. Using the DNA sequence from the BACs, a dinucleotide CAn repeat was identified and two unique PCR primers that will amplify the genomic DNA containing this repeat were designed, as shown below: B200E21C16 L: GAGAGGCTATATCCCTGGGC (SEQ ID NO:38) B200E21C16 R: ACAGCACGTGTTTAAAGGGG (SEQ ID NO:39) and used in the genetic mapping study.

This method has been used successfully by others skilled in the art Sheffield et al., Genet., 4:1837-1844 (1995); LeBlanc-Straceski et al., Genomics, 19:341-9 (1994); Chen et al., Genomics, 25:1-8 (1995)). Use of these reagents with populations or individuals will predict their risk for osteoporosis. Similarly, single nucleotide polymorphisms (SNPs), such as those shown in Table 4 above, can be used as well to predict risk for developing bone diseases or resistance to osteoporosis in the case of the HBM gene. It is also contemplated that single nucleotide polymorphisms (SNPs) such as those described above, may be used to predict the risk in a subject for developing arteriosclerosis and atherosclerosis and related conditions.

-119- WO 01/92891 PCT/US01/16946 XXIII. Methods of Use: Modulators of Tissue Calcification The calcification of tissues in the human body is well documented. Towler et al., J Biol. Chem., 273:30427-34 (1998) demonstrated that several proteins known to regulate calcification of the developing skull in a model system are expressed in calcified aorta. The expression of Msx2, a gene transcribed in osteoprogenitor cells, in calcified vascular tissue indicates that genes which are important in bone development are involved in calcification of other tissues. Treatment with HBM protein, agonists or antagonists is likely to ameliorate calcification (such as the vasculature, dentin and bone of the skull visera) due to its demonstrated effect on bone mineral density. In experimental systems where tissue calcification is demonstrated, the over-expression or repression of Zmaxl activity permits the identification of molecules that are directly regulated by the Zmaxl gene. These genes are potential targets for therapeutics aimed at modulating tissue calcification. For example, an animal, such as the LDLR mouse is fed a high fat diet and is observed to demonstrate expression of markers of tissue calcification, including Zmaxl. These animals are then treated with antibodies to Zmaxl or HBM protein, antisense oligonucleotides directed against Zmaxl or HBM cDNA, or with compounds known to bind the Zmaxl or HBM protein or its binding partner or ligand. RNA or proteins are extracted from the vascular tissue and the relative expression levels of the genes expressed in the tissue are determined by methods well known in the art. Genes that are regulated in the tissue are potential therapeutic targets for pharmaceutical development as modulators of tissue calcification.

The nucleic acids, proteins, peptides, amino acids, small molecules or other pharmaceutically useful compounds of the present invention that are to be given to an individual may be administered in the form of a composition with a pharmaceutically acceptable carrier, excipient or diluent, which are well known in the art. The individual may -120- WO 01/92891 PCT/US01/16946 be a mammal or a bird, preferably a human, a rat, a mouse or bird. Such compositions may be administered to an individual in a pharmaceutically effective amount. The amount administered will vary depending on the condition being treated and the patient being treated.

The compositions may be administered alone or in combination with other treatments.

XXIV. Pharmaceutical Compositions The invention also contemplates pharmaceutical compositions comprising a lipid mediating agent which modulates HBM and/or Zmaxl activity in combination with a lipoprotein modulating agent blofibrate, gemfibrozil, nicotinic acid, cholestyramine, cholestipol, lovastatin, simvastatin, pravastain, probucol, premarin or estradiol.). Liprotein modulating agents can include compounds or compositions which modulate up-regulate or down-regulate) LDL, VLDL, HDL or IDL levels.

The lipid mediating agent, which modulates HBM and/or Zmaxl activity, can include proteins, monoclonal antibodies or fragments thereof, chemicals, and mimetics. One contemplated pharmaceutical composition can comprise the monoclonal antibody and a pharmaceutically acceptable carrier. For the purposes of the present invention, a "pharmaceutically acceptable carrier" can be any of the standard carriers well known in the art.. For example, suitable carriers can include phosphate buffered saline solutions, emulsions such as oil/water emulsions, and various types of wetting agents. Other carriers can also include sterile solutions, tablets, coated tablets, and capsules. Typically, such carriers can also contain excipients such as starch, milk, sugar, types of clay, gelatin, stearic acid, or salts thereof, magnesium or calcium sterate, talc, vegetable fats or oils, gums, glycerols, or other known excipients. Such carriers can also include flavors and color additives, preservatives, -121- WO 01/92891 PCT/US01/16946 or other ingredients. Compositions comprising such carriers are formulated by well known conventional means. See REMINGTON'S PHARMACEUTICAL SCIENCE (15th ed. 1980).

For diagnostic purposes, the antibodies and recombinant binding proteins can be either labeled or unlabeled. Typically, diagnostic assays entail detecting the formation of a complex through the binding of the monoclonal antibody or recombinant binding protein to a HBM protein or Zmaxl protein. When unlabeled, the antibodies and recombinant binding proteins find use in agglutination assays. In addition, unlabeled antibodies can be used in combination with other labeled antibodies (second antibodies) that are specifically reactive with the monoclonal antibody or recombinant binding protein, such as antibodies specific for immunoglobulin. Alternatively, the monoclonal antibodies and recombinant binding proteins can be directly labeled. A wide variety of labels can be employed, such as radionuclides 99 Tc, I'In, 123I and 131I), fluorescers, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, ligands (particularly haptens), etc. Numerous types of immunoassays are well known in the art.

Commonly, the monoclonal antibodies and recombinant binding proteins of the present invention are used in fluorescent assays, where the subject antibodies or recombinant binding proteins are conjugated to a fluorescent molecule, such as fluorescein isothiocyanate

(FITC).

The examples provided below are not meant to limit the invention in any way, but serve to provide preferred embodiments for the invention.

EXAMPLES

The present invention is described by reference to the following Examples, which are offered by way of illustration and are not intended to limit the invention in any manner.

-122- WO 01/92891 PCT/US01/16946 Standard techniques well known in the art or the techniques specifically described below were utilized.

Example 1 The propositus was referred by her physicians to the Creighton Osteoporosis Center for evaluation of what appeared to be unusually dense bones. She was 18 years old and came to medical attention two years previous because of back pain, which was precipitated by an auto accident in which the car in which she was riding as a passenger was struck from behind.

Her only injury was soft tissue injury to her lower back that was manifested by pain and muscle tenderness. There was no evidence of fracture or subluxation on radiographs. The pain lasted for two years, although she was able to attend school full time. By the time she was seen in the Center, the pain was nearly resolved and she was back to her usual activities as a high school student. Physical exam revealed a normal healthy young woman standing 66 inches and weighing 128 pounds. Radiographs of the entire skeleton revealed dense looking bones with thick cortices. All bones of the skeleton were involved. Most importantly, the shapes of all the bones were entirely normal. The spinal BMC was 94.48 grams in L1-4, and the spinal BMD was 1.667 gm/cm 2 in L1-4. BMD was 5.62 standard deviations (SD) above peak skeletal mass for women. These were measured by DXA using a Hologic 2000~. Her mother was then scanned and a lumbar spinal BMC of 58.05 grams and BMD of 1.500 gm/cm 2 were found. Her mother's values place her 4.12 SD above peak mass and 4.98 SD above her peers. Her mother was 51 years old, stood 65 inches and weighed 140 pounds.

Her mother was in excellent health with no history of musculoskeletal or other symptoms.

Her father's lumbar BMC was 75.33 grams and his BMD was 1.118 gm/cm 2 These values -123place him 0.25 SD above peak bone mass for males. He was in good health, stood 72 inches tall, and weighed 187 pounds.

These clinical data suggested that the propositus inherited a trait from her mother, which resulted in very high bone mass, but an otherwise normal skeleton, and attention was focused on the maternal klndred. In U.S. Patent No. 5,691,153, twenty- two of these members had measurement of bone mass by DXA. In one case, the maternal grandfather of the propositus, was deceased, however, medical records, antemortem skeletal radiographs and a gall bladder specimen embedded in paraffin for DNA genotyping were obtained. His radiographs showed obvious extreme density of all of the bones available for examination including the femur and the spine, and he was included among the affected members. In this invention, the pedigree has been expanded to include 37 informative individuals. These additions are a significant improvement over the original kinship (Johnson et al., Am. J. Hum.

Genet., 60:1326-1332 (1997)) because, among the fourteen individuals added since the original study, two individuals harbor key crossovers. X-linkage is ruled out by the presence of male-to-male transmission from individual 12 to 14 and Example 2 The present invention describes DNA sequences derived from two BAC clones from the HBM gene region, as evident in Table 6 below, which is an assembly of these clones.

Clone b200e21-h (ATCC No. 98628; SEQ ID NOS: 10-11) was deposited at the American Type Culture Collection (ATCC), 10801 University Blvd, Manassas, VA 20110-2209 on December 30, 1997. Clone b527d12-h (ATCC No. 98907; SEQ ID NOS: 5-9) was deposited at the American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, VA 20110-2209 on October 2, 1998. These sequences are unique reagents -124that can be used by one skilled in the art to identify DNA probes for the Zmarl gene, PCR primers to amplify the gene, nucleotide polymorphisms in the Zmaxl gene, or regulatory elements of the Zmaxl gene.

TABLE 6 Contig ATCC No. SEQ ID NO. Length b527dl2-h_contig302G 98907 5 3096 b527d12-h_contig306G 98907 6 26928 b527dl2-h contig307G 98907 7 29430 b527d12-hcontig308G 98907 8 33769 b527d12-h contig309G 98907 9 72049 b200e12-h_contig1 98628 10 8705 b200e21-hcontig4 98628 11 66933 The disclosure of each of the patents, patent applications and publications cited in the specification is hereby incorporated by reference herein in its entirety.

i 15 Although the invention has been set forth in detail, one skilled in the art will recognize that numerous changes and modifications can be made, and that such changes and modifications may be made without departing from the spirit and scope of the invention.

Example 3 Since Zmaxl has similarity to the LDL receptor family of genes, it may be involved in lipid metabolism. However, others have reported that lipid profile variables did not show significant association with bone mass and could not be used as indicators for bone mineral density (Zabaglia et al., "An exploratory study of association between lipid profile and bone mineral density in menopausal women in a Campinas reference hospital," Cad. Saude Publica 14: 779-86 (1998)). Zmaxl may be normally involved in regulating bone density by -125- WO 01/92891 PCT/US01/16946 depositing calcium during bone remodeling. The HBM mutation may result in increased deposition thus conferring denser bone structure. Interestingly, atherosclerotic plaques contain calcified material and express a variety of genes involved in bone differentiation.

To test whether the HBM gene was involved in lipid regulation, biochemical tests were performed to measure serum level of various lipid containing molecules or precursors in affected and unaffected HBM family members to test whether the HBM mutation in the Zmaxl gene effects lipid metabolism. Table 7 shows the results of testing eight HBM individuals and seven unaffected individuals. Wilcoxon rank-sum tests (non-parametric equivalent of a T-test) were performed to assess whether levels of biochemical markers from affected HBM individuals deviated from unaffected individuals. The data obtained were analyzed separately by gender, as well as by combining values from males and females, when appropriate.

Standard diagnostic protocols were used to determine the concentration (mg/dL) with triglycerides, cholesterol, high density lipoprotein (HDL), low density lipoprotein (LDL), very low density lipoprotein (VLDL), apolipoprotein A-1 (APO apolipoprotein B (APO and lipoprotein a (LIPOa). For such procedures, see for example, F. W. HEMMING, LIPID ANALYSIS (Bios Scientific Pub. 1996) and J. M. ORDOVAS, LIPOPROTEIN PROTOCOLS (Humana Press Inc., 1997). The genotype for apolipoprotein E (APO E) was also reported.

There are three common alleles E2, E3 and E4). The affected and unaffected HBM family members are heterozygous or homozygous for the alleles.

The results obtained were statistically significant: Triglyceride levels were generally lower in affected individuals than in unaffected individuals, and very low density lipoprotein (VLDL) levels were generally lower in affected individuals than in unaffected individuals. Additionally, the following comparisons approached statistical significance (p=0.0 6 high density lipoprotein (HDL) levels were higher in affected males than in unaffected males, and the ratio of low density lipoprotein (LDL) to high density lipoprotein (HDL) was generally higher in affected males than in unaffected males.

In Table 7, "ARUP" is ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108 where one of the studies was performed. "SJH" refers to the second center which -126- WO 01/92891 PCT/US01/16946 performed these studies, Creighton Medical Laboratories, 28th Burt, Dental-Rm 306, Omaha, NE 68178. APO-A1, APO-B and LIPO-a are reported in mg.dL. Total serum levels also are in mg/dL.

All cited patents and publications referred to in this application are herein incorporated by reference in their entirety.

-127- Lipid Studies in HBM Kindred ID Numbem 2-score Gender TRIGLYC. CHOLESTEROL, erel(di HDL. mgstdl VLDL, rgs/di LOL, mgsdl TC:HDL LDL:HDL APO A-1 APO B LIPO a APO E mgsidl ARJP SJH ARUP SJH ARUP SJH ARUP SJ-I ARUP SJH ARUP SJH ARUP sJHI SJ I Sil ARUP HBM-OR1-9019 2.36 m A 105 105 111 117 48 47 21 21 42 49 2.31 2.50 0.88 1.00 133 57 6 214 1166.ORI-1044 6.05 F A 125 129 208 207 57 58 25 26 126 123 3.65 -3.60 2.21 2.10 179 125 15 314 M1M-ORI-1041 6.21 F A as 88 175 175 86 82 16 18 71 75 2.03 2.10 0.63 0.90 220 74 8 1 213 HBM-ORl-1031 3.42 m A 99 76 159 167 49 47 14 15 96 105 3.24 3.60 1.66 220 142 se 4 213 HUM-ORI-0115 6.47 m A 113 112 229 219 70 60 23 23 136 127 3-27 3.20 1.94 1680 192 122 10 313 HBM.ORlO11.4 3.31 NI A 373 370 240 241 54 55 1 76 74 11l 112 4.44 4.40 2.06 2.00 167 134 4 273 HBM-ORI-0113 3.70 F A 107 104 134 139 72 68 21 21 41, 50 1.86 2.00 0.57 0.70 179 65 6 213 HBM.OR100l 5.92 F A 09 113 152' 155 44 44 22 23 66 88 3.45 3.50 1.95 2.00 150 95 9 313 HBM-OR.1042 1.85 M U 125 120 163 163 44 40 25 24 94 99 3.70 4.10 2.14 2.50 130 106 17 3/4

C

Ic.

HaM-OR1-1033 1 0.99 I 258 43 46 521 56 123 1 4.93 4.901 2.72 1 2.70 119-oRI-1030 U 1 363 361 231 244 40 38 1 73 72 118 134 5.78 6.40 2.95 3.50 139 139 6 2/3 HBM-ORI-1029 1.05 F U 186 217 169 182 51 55 37 43 80 84 3.29 3.30 1.57 1.50 189 112 6 3/3 HBM-OR1-1026 -0.21 F U 160 175 244 256 38 38 32 35 174 183 6.42 670 4.58 4.60 129 161 14 313 H6M-oR1-1629 -0.57 F UJ 216 240 197 207 57 68 44 46 ee 101 3.46 3.50 1 69 1.70 189 11l 8 213 HMORI0149 0.45 MI J 166 169 188 193 42 44 38 36 108 111 4.48 440 2.57 2.50 140 120 2 3/4 Mean A 59 1 271 28 891 911 3.03 3.11, 1.551 1.591 170 954 StDevA 97 95 46 42 1i 13 20 19 36 31 0.89 0.84 0.67 0.131 29 31 3.74 Mean U 214 226 200 210 45 46 43 45 112 119 4.55 4.77 2.60 2.14 154 125 9.865 6tDevU 76 76 311 S41 7 8 16 16 30 33 1.20 1.32 1.01 1.12 20 19 5.30 P 0.11 0.07 0.25 0.13 0.03 0.041 0.12 0.06 0.19 0.11 1 0.01 001 1 003 0.03 0.27 0.04 0,36 C'eightn GTC Analyis P-value P-value P-value eer e c r \e p Comb/ned Female Male 0.02 0.32 0.09 DA88 0.11 1.00 0.63 0.86

Claims (38)

1. A method of identifying a molecule involved in lipid regulation comprising identifying a molecule that binds to, or that inhibits binding of a molecule to, HBM or Zmaxl.

2. The method of claim 2, wherein said molecule is a protein.

3. The method of claim 2, further comprising producing an antibody to the protein.

4. A method for identifying a protein involved in lipid regulation comprising identifying a protein that has an expression level that is different in a first host comprising the Zmraxl gene when compared to a second host comprising the HBM gene. The method of claim 4, wherein the host is an animal.

6. A method for identification of a candidate molecule involved in lipid regulation comprising: identifying a molecule that binds to, or that inhibits binding of a molecule to, the nucleic acid sequence of SEQ ID NO: 1 or a Zmaxl nucleic acid comprising a polymorphism of Table 4; identifying a molecule that binds to, or that inhibits binding of a molecule to, the nucleic acid sequence of SEQ ID NO: 2; and comparing the extent of binding, or the extent of inhibition of binding, of the molecule to each nucleic acid sequence, wherein the molecule that binds, or inhibits binding, more or less to the nucleic acid sequence of SEQ ID NO: 2 or the nucleic acid sequence of -129- WO 01/92891 PCT/US01/16946 SEQ ID NO: 1 or a Zmaxl nucleic acid comprising a polymorphism of Table 4 is the candidate molecule.

7. The method of claim 6, wherein the candidate molecule is a protein, an mRNA or an antisense nucleic acid.

8. A method for testing a substance as a therapeutic agent for modulating lipid levels comprising administering a nucleic acid comprising SEQ ID NO: 2 or a nucleic acid sequence with an HBM polymorphism to a subject, and assessing whether lipid levels are modulated.

9. The method of claim 8, wherein the subject is an animal and the animal is selected from the group consisting of: livestock, primates, humans, canines, felines, rodents, birds, reptiles, fish, and amphibians. A method for testing a substance as a therapeutic agent for modulating lipid levels comprising administering a protein comprising SEQ ID NO: 4 or a Zmaxl protein comprising a polymorphism of Table 4 to a subject, and assessing whether lipid levels are modulated.

11. -A method of pharmaceutical development for treating lipid-mediated disorders comprising identifying a molecule that binds to the amino acid sequence of SEQ ID NO: 4 or to a Zmaxl protein comprising a polymorphism of Table 4.

12. The method of claim 11, wherein the molecule inhibits or enhances the function of the amino acid.

13. A method of pharmaceutical development for treatment of lipid-mediated disorders comprising: -130- WO 01/92891 PCT/US01/16946 constructing a first host that contains the Zmaxl gene or protein; constructing a second host that contains the HBM gene or protein; analyzing a difference between the first host and the second host; and identifying a molecule that, when added to the first host, causes the first host to exhibit a characteristic feature of the second host.

14. The method of claim 13, wherein the host is a cell-free extract, a cell or an animal. The method of claim 13, wherein the difference is a surrogate marker.

16. A method of regulating lipid levels in a host comprising, administering the amino acid sequence comprising SEQ ID NO: 4 to a somatic cell or to a germ-line cell of a host suffering from a lipid-mediated disorder.

17. The method of claim 16, wherein the host is livestock, primates, humans, canines, felines, rodents, birds, reptiles, fish, or amphibians.

19. A method for treating or preventing a lipid-mediated disorder in an animal comprising transferring a nucleic acid sequence comprising SEQ ID NO: 2 or a Zmaxl nucleic acid comprising a polymorphism of Table 4 into a somatic cell or a germ-line cell of an animal suffering from a lipid-mediated disorder. The method of claim 19, wherein the animal is livestock, primates, humans, canines, felines, rodents, birds, reptiles, fish, or amphibians.

21. A method of treating or preventing arteriosclerosis or an arteriosclerosis- associated condition comprising administering an amino acid sequence comprising SEQ ID NO: 4 to a patient in need thereof. -131- WO 01/92891 PCT/US01/16946

22. The method of claim 21, wherein the patient is livestock, primates, humans, canines, felines, rodents, birds, reptiles, fish, or amphibians.

23. The method of claim 21, wherein the amino acid sequence administered to a patient in need thereof comprises the extracellular domain of the amino acid sequence comprising SEQ ID NO: 4.

24. The method of claim 21, wherein the amino acid sequence administered to a patient in need thereof comprises the intracellular domain of the amino acid sequence comprising SEQ ID NO:. 4. A method for treating or preventing a lipid-mediated disorders comprising administering a molecule that binds to a nucleic acid sequence comprising SEQ ID NO: 2 or a Zmaxl nucleic acid comprising a polymorphism of Table 4 to a patient in need thereof.

26. The method of claim 25, wherein the patient is livestock, primates, humans, canines, felines, rodents, birds, reptiles, fish, or amphibians.

27. A method for treating or preventing lipid-mediated disorders comprising administering an antibody to a patient in need thereof, wherein the antibody is to the amino acid sequence comprising SEQ ID NO: 4.

28. A method for diagnostic screening for agenetic predisposition to arteriosclerosis or an arteriosclerosis associated condition or a lipid-mediated disorder comprising screening a sample from a patient with a nucleotide sequence derived from the genomic or cDNA nucleic acid sequence of HBM. -132- WO 01/92891 PCT/US01/16946

29. The method of claim 28, wherein the screening involves, performing a haplotype analysis using the nucleic acid sequence comprising SEQ ID NO: 2 and determining whether the subject contains the Zmaxl gene or lacks an HBM polymorphism. A diagnostic assay for determining a predisposition for a lipid-mediated disorders comprising an antibody to the HBM protein and an antibody to the Zmaxl protein.

31. A method of expressing the HBM protein in tissue comprising constructing an expression vector comprising a promoter that directs expression in tissue operably linked to SEQ ID NO:2 and the tissue in which the HBM protein is expressed is a lipid regulating cell or a cell involved in lipid metabolism.

32. The method of claim 31, wherein the tissue is liver.

33. The method of claim 31, wherein the promoter that directs expression in tissue is an osteocalcin promoter or an AML-3 promoter.

34. A method of modulating lipid levels in a subject by administering an HBM protein or a Zmaxl protein comprising a polymorphism of Table 4. The method of claim 34, wherein the HBM protein comprises SEQ ID NO: 4.

36. The method of claim34, wherein the lipid modulated is selected from the group consisting of: VLDL, LDL, IDL, HDL, LIPOa, APO A-I, APO B and APO E.

37. A method of modulating lipid levels in a subject by administering an agent which regulates HBM or Zmaxl activity. -133- WO 01/92891 PCT/US01/16946

38. The method of claim 37, wherein the lipid modulated is selected from the group consisting of: VLDL, LDL, IDL, HDL, LIPOa, APO A-i, APO B and APO E.

39. The method of claim 37, wherein the regulation of HBM or Zmaxl activity is modulates gene transcription, protein translation or Zmaxl or HBM protein binding to its cognate target thereby regulating lipid levels. A composition for treating a lipid-mediated condition comprising an agent that modulates lipid levels by regulating Zmaxl or HBM activity and a lipoprotein modulating agent with a pharmaceutically acceptable carrier.

41. The composition of claim 40, wherein the lipoprotein modulating agent is blofibrate, gemfibrozil, nicotinic acid, cholestyramine, cholestipol, lovastatin, simvastatin, pravastatin, probucol, premarin or estradiol.

42. The composition of claim 40, wherein the lipoprotein modulating agent modulates LDL levels.

43. The composition of claim 42, wherein the lipoprotein modulating agent is selected from the group consisting of bile acid binding resins, HMG-CoA reductase inhibitors and estrogens.

44. A method of treating a subject suffering from a lipid-mediated condition comprising the step of administering the composition of claim The method of claim 44, wherein the lipid-mediated condition is atherosclerosis, arteriosclerosis, or a disease associated with atherosclerosis or arteriosclerosis. -134- WO 01/92891 PCT/US01/16946

46. A combination therapy for treating a subject suffering from a lipid-mediated disease or condition comprising administering to a subject an agent which regulates HBM or Zmaxl and an agent which regulates a lipoprotein.

47. The combination therapy of claim 46, wherein the agent regulating lipoprotein concentrations is blofibrate, gemfibrozil, nicotinic acid, cholestyramine, cholestipol, lovastatin, simvastatin, pravastain, probucol, premarin or estradiol.

48. The method of claim 46, wherein the lipid-mediated disease is atherosclerosis, arteriosclerosis, an atherosclerosis associated condition or an arteriosclerosis associated condition. -135-