US 5,858,655 AGrant
Method for Diagnosing Neoplasia by Detecting Expression of PRAD1 Cyclin
Issue Date:1999-01-12
•7 Claims
•18 Drawing Sheets
Abstract
A novel cyclin, termed prad1, is disclosed, along with the nucleic acid sequence that encodes human prad1. Antibodies that bind specifically to prad1 and cell lines and transgenic animals containing DNA that encodes prad1 are also disclosed. In addition, methods of using the antibodies or fragments of the nucleic acid sequence, for example, to diagnose a neoplastic condition by detecting expression of prad1 or to modulate cellular proliferation, are disclosed.
Metadata
Assignee
- The General Hospital Corporation
Inventor
- Andrew Arnold
Application Information
Application Number:US 4606949
Filing Date:1995-06-02
Priority Date:1991-03-11
Art Unit:187
Classifications
IPC:
C12Q 168
Field of Search:
435536935623.177;78
Patent Drawings (18 sheets)
Description
Background of the Invention
This invention relates to the field of cyclins.
The cyclins are a class of eukaryotic proteins that were originally identified by their cyclic accumulation and destruction at defined points in embryonic cell cycles (Evans et al., Cell 33:389-396, 1983). They bind to and are essential for activation of cdc2 protein kinase (reviewed in Murray et al., Science 246:614-621, 1989; Nurse, Nature 344:503-508, 1990; Draetta et al., Cell 56:829-838, 1989). At present, the cyclins can be divided into three families on the basis of their kinetics of oscillation across the cell cycle, their amino acid sequences, and, in some cases, genetic experiments in yeast that determine when their functions are needed (reviewed in Nurse, 1990; Nasmyth, Cell 63:1117-1120, 1990; Westendorf, J. Cell Biol. 108:1431-1444, 1989). The B-type "mitotic" cyclins drive cells into mitosis; their sequences are conserved from yeast to human (Nurse, 1990; Westencorf et al., 1989; and Pines et al., Cell 58:833-846, 1989). The A-type cyclins, which are less well understood, may act earlier in the cell cycle (Minshull et al., EMBO J. 9:2865-2875, 1990; Pines et al., Nature 346:760-763, 1990; Swenson et al., Cell 47:861-870, 1986). The recently described CLNs (or "G1 cyclins") of budding yeast are thought to perform analogous functions by interacting with cdc2 homologues at START, driving cells into S-phase (Nasmyth, 1990). A, B, and CLN cyclins may act as stage-specific regulators of progress across the cell cycle by conferring selective substrate specificity upon cdc2 kinase (Minshull et al., 1990) or by selectively targeting cdc2 to different intracellular compartments.
Summary of the Invention
The invention features a novel cyclin, prad1, and an isolated DNA (termed PRAD1) which encodes it. This DNA may e single-stranded or double-stranded, and may be genomic DNA, cDNA, or synthetic DNA. It may be identical to a naturally-occurring Prad1sequence (such as human PRAD1 CDNA, SEQ ID NO:1) or may differ from such sequence by the deletion, addition, or substitution of one or more nucleotides. By "isolated" is meant that the DNA is free of the coding sequences of genes that, in the naturally-occurring genome of the organism from which the DNA of the invention is derived, immediately flank the gene encoding prad1. Included within the term prad is human prad1and any homolog of human prad1(i.e., from another animal species, or a genetically altered version of a naturally-occurring prad1which exhibits a biological activity similar to that of the naturally-occurring protein) encoded by a DNA which is capable of hybridizing (1) under stringent hybridization conditions (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd edn., Cold Spring Harbor, N.Y., 1989: herein incorporated by reference) to a single-stranded probe consisting of a segment of at least eight (preferably 18-40) nucleotides of human Prad1cDNA (SEQ ID NO:1) or human Prad1genomic DNA, or (2) under less stringent conditions (e.g., washing at 2.times.SSC, at 40.degree.C.) to a probe consisting of a segment of at least 40 (preferably 200-5000) nucleotides of human Prad1cDNA (SEQ ID NO:1) or human Prad1genomic DNA. Also within the invention are peptide fragments of a naturally-occurring prad1, which fragments are at least six amino acids in length and preferably 10-50 amino acids; and single-stranded DNA or RNA probes (preferably radioactively labelled) containing at least 8 nucleotides of, but less than all of, human Prad1-encoding RNA, human Prad1cDNA (SEQ ID NO:1) or human PRAD1 genomic DNA, and preferably between 10 and 5000 bases. Such DNA or RNA probes may be used in a diagnostic method which includes the steps of obtaining a nucleic acid sample from an animal suspected of having a given neoplastic condition (or from a known tumor); contacting the nucleic acid sample with a single-stranded DNA or RNA probe capable of hybridizing to the Prad1homolog of the species to which the animal belongs; and detecting the level of hybridization of the probe with the nucleic acid sample, such level being diagnostic for the neoplastic condition. Two examples of neoplastic conditions that may be diagnosed by this method include centrocytic lymphomas, which appear to express abnormally high levels of Prad1mRNA, and those breast cancers which are characterized by a high degree of amplification of Prad1DNA.
The DNA sequence of the invention, which may be under the transcriptional control of a heterologous promoter (defined as a promoter sequence other than the naturally-occurring promoter of the gene encoding prad1), may be incorporated into a vector (such as a phage) and thereby introduced into a cell. Included within the invention is a eukaryotic or prokaryotic cell (or an essentially homogeneous population of such cells) containing (and preferably capable of expressing) a recombinant DNA molecule encoding prad1: that is, a cell into which (or into an ancestor of which) has been introduced, by means of genetic engineering, a DNA molecule encoding prad1, resulting in that DNA molecule's being positioned adjacent to a DNA sequence to which it is not naturally adjacent (e.g., the prad1-encoding sequence is integrated into the genome of such cell). The prad1protein of the invention may be produced by culturing such cells and recovering prad1from the cells, or from their medium. Alternatively, DNA or mRNA encoding prad1may be combined with a standard in vitro expression system to produce prad1. Prad1so produced can be utilized in combination with a pharmacologically-acceptable carrier to promote wound healing in an animal, or can be used to promote proliferation of an animal cell by treating the cell with a proliferation-inducing amount of the protein of the invention (for example, by transfecting the cell with DNA encoding prad1so that the cell itself produces such a proliferation-inducing amount of prad1). Alternatively, the prad1(or an antigenic fragment thereof, determined by standard methodology) can be used to raise polyclonal or monoclonal antibodies capable of forming immune complexes with prad1, and thus useful as a diagnostic for certain neoplastic conditions characterized by abnormally high levels of prad1expression. The method of using such an antibody as a diagnostic would include the steps of obtaining a sample of a tissue of an animal suspected of having a such a neoplastic condition (e.g., certain lymphomas or breast cancers); contacting the sample with the antibody; and detecting the level of immune complexes formed by the antibody, such level being diagnostic for the neoplastic condition.
Also within the invention is a transgenic non-human vertebrate animal (preferably a mammal such as a rodent, e.g., a mouse) bearing a transgene (i.e., a piece of DNA which is artificially inserted into an embryonic cell, and becomes a part of the genome of the animal which develops from that cell) which includes a DNA sequence encoding prad1, and any cells or cell lines derived from such an animal. A transgenic animal is an animal having cells that contain a transgene, which transgene was introduced into the animal, or an ancestor of the animal, at an embryonic stage. If the embryonic stage is a single-cell stage, then all nucleated cells of the animal will carry the transgene. The particular prad1encoded by the transgene may be endogenous to the species of the transgenic animal, or may be that of a different species (e.g., human). By using a Prad1together with an appropriate promoter, a transgenic animal which readily develops neoplasias in a selected organ or tissue type will result, making such animal useful as a model for studying cancer in that organ or tissue.
Other features and advantages of the invention will be apparent from the following detailed description, and from the claims.
Detailed Description
The Drawings Are First Described.
DRAWINGS
FIG. 1 is a Southern blot of Msp1-digested DNA probed with the 5' PTH gene probe (lanes 1, 2) and 3' PTH gene probe (lanes 3, 4).
FIGS. 2A and 2B are a diagrammatic representation of (2A) the normal PTH gene, and (2B) the two fragments resulting from the rearrangement in tumor M.
FIG. 3 is diagrammatic representation of the D11S287 region, indicating known restriction sites and the locations of the 500 bp fragment, the 1.6 kb XhoI fragment, and Probe B.
FIG. 4 is a Northern analysis of D11S287 expression in various cell types.
FIG. 5 is a diagrammatic representation of THD11S287 rearrangements in two parathyroid adenomas, and he relative locations of Probe B and a series of cloned cDNA segments.
FIGS. 6A-6G are a representation of the nucleotide sequence and predicted amino acid sequence of human PRAD1 (SEQ ID NO:1) cDNA.
FIG. 7 is an illustration of sequence homology between the "cyclin box" region of human prad1and the corresponding regions of some A-type, B-type, and G1 cyclins.
FIG. 8 is a Northern blot analysis of D11S287 human Prad1(SEQ ID NO:1)! expression in various cell types.
FIGS. 9A and 9B are (9A) a Northern blot analysis of HeLa cell RNA probed with a human Prad1cDNA (SEQ ID NO:1) probe, an H4 histone probe, and 28S rRNA; and (9B) b a graph depicting the results of the Northern blot.
FIGS. 10A-10D an analysis of the biological activity of recombinant human prad1.
dentification of Human PRAD1
Previous studies on DNA from cells of a benign parathyroid adenoma (reported in Arnold et al., J. Clin. Invest. 83:2034-2040, 1989) revealed evidence of a DNA rearrangement involving the parathyroid hormone (PTH) chromosomal locus (at chromosome 11, band p15) and a segment of DNA (identified as Human Genome Database assignment D11S287) which normally maps to chromosome 11, band q13. It is now known that (a) although a number of previously-identified oncogenes (including INT-2 and HST-1), as well as the translocation breakpoint marker BCL-1 and possibly the gene for multiple endocrine neoplasia type I (MEN-I), map to the 11q13 region, the so-called D11S287 locus rearranged in at least some parathyroid adenomas is distinct from these previously-described markers; (b) D11S287 mRNA, while detectable in all tissues analyzed, is significantly overexpressed in those parathyroid adenomas which have a 11q13/11p15 chromosomal rearrangement, and also in certain lymphomas (notably centrocytic lymphomas) characterized by rearrangement of the BCL-1 locus; and (c) the D11S287 locus is amplified and expressed in many squamous cell and mammary carcinomas. This evidence suggests that D11S287 (also referred to herein as human PRAD1, for parathyroid adenoma) is a newly-identified oncogene which figures in a variety of types of neoplasms.
Cloning Human Prad1CDNA (SEQ ID NO:1)
Human Prad1cDNA (SEQ ID NO: 1) has been cloned and sequenced by the methods described in detail below, yielding the sequence shown in FIG. 6. The longest open reading frame, starting at the first ATG codon, encodes a predicted protein of 295 amino acids (M.sub.r 33,729). Screening the Genbank peptide database with this sequence reveals significant homology only to members of the cyclin family, with greatest similarity in the region conserved among cyclins, ranging from 19.1% to 33.6% identity, and 44.1% to 59.2% similarity. The human Prad1(SEQ ID NO:1) protein (prad1) has significant sequence similarities to all three types of cyclins (A, B, and CLN cyclins), but cannot readily be assigned to any one type. This suggests that prad1may represent a new and different cyclin family member.
Prad1Expression
Prad1nRNA is expressed in many tissues and is highly conserved across species (FIG. 7). As with other cyclin mRNAs expressed in human cells (Pines et al., Cell 58:833-846, 1989; Pines et al., Nature 346:760-763, 1990), human Prad1MRNA levels vary across the cell cycle (FIG. 9), consistent with but not proving a role in cell cycle regulation. The peak in Prad1mRNA levels occurs late in the cell cycle or in G1.
Biological Activity of Recombinant Human Prad1Protein
Bacterially expressed recombinant human prad1, produced as described in detail below, was used to further investigate the link between human Prad1and the cyclins. Cyclins are known to form complexes with p.sub.34.sup.cdc2 protein kinase, leading to its activation which can be assayed using exogenous histone H1 as a substrate. In addition, cyclin/p34.sup.cdc2 complexes can be purified by exploiting the ability of beads linked to p13.sup.suc1, another cell cycle protein, to avidly bind p34.sup.cdc2 and, in turn, co-purify any proteins complexed with p34.sup.cdc2 (Draetta et al., Cell 56:829-838, 1989). When recombinant human prad1was added to clam embryo interphase cell lysates (which lack endogenous cyclins and contain inactive p34.sup.cdc2) , both p34.sup.cdc2 and prad1were bound by p13.sup.suc1 -beads (FIG. 10). As prad1does not bind to protein A-Sepharaose beads, its binding to p13.sup.suc1 -beads is most likely due to its interaction with p34.sup.cdc2 or a closely related protein. Furthermore, kinase activity was induced by the addition of the human Prad1(SEQ ID No:1) in vitro translation product to interphase lysates (FIG. 10). This kinase activity was lower than that seen with cyclin A. Cyclin B provided a negative control; for reasons not yet understood, our cyclin B translation product was not capable of activating p34.sup.cdc2 in this type of assay. The difference between the activities induced by cyclin A and human prad1may be specific to this clam assay system, or may reflect a genuine difference between the functions of, or the substrate specificities conferred by, cyclin A vs. human prad1.
Use
Both prad1and a nucleotide encoding prad1are useful for the preparation of diagnostic tools for the classification and/or prognosis of lymphomas, breast cancers, and squamous cell cancers, as well as other cancers characterized by a high level of expression and/or amplification of the Prad1gene. For example, prad1or an antigenic peptide fragment of prad1could be used in accordance with standard methods (see, e.g., Harlow et al., Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1988; Yanaihara et al., U.S. Pat. No. 4,855,406; and Slamon et al., U.S. Pat. No. 4,918,162; all of which are herein incorporated by reference) to raise polyclonal or monoclonal antibodies capable of forming immune complexes with prad1, and useful for detecting abnormally high levels of prad1in a given tissue sample. Similarly, a hybridization probe prepared from a segment of at least 8 (and preferably greater than 250) nucleotides of human Prad1-encoding RNA, human PRAD1 cDNA (SEQ ID NO:1) or human Prad1genomic DNA may be employed as a means for determining the number of copies of Prad1present in the genomic DNA of a given sample, or the level of Prad1mRNA expressed in cells of such sample.
The nucleic acids of the invention may also be used therapeutically. Oligonucleotides which are antisense to human Prad1mRNA (or which express RNA that is antisense to human Prad1mRNA) may be synthesized to serve as an anticancer therapy in those cases diagnosed as having a rearrangement or amplification of human PRAD1: such oligonucleotides would be introduced into tumor cells in vivo as a means to reduce production of prad1in such cells, and thereby to reduce neoplastic growth induced by an overabundance of prad1. (See, for example, Weinberg et al., U.S. Pat. No. 4,740,463, herein incorporated by reference.) By linking a Prad1sequence to a selected tissue-specific promoter or enhancer and introducing by standard methods (e.g., as described by Leder et al., U.S. Pat. No. 4,736,866, herein incorporated by reference) the resultant hybrid gene into an animal embryo at an early developmental stage (e.g., the fertilized oocyte stage), a transgenic animal which expresses elevated levels of prad1 in the selected tissue (e.g., breast, squamous cell, B-lymphoid cell, parathyroid, and others) can be produced. The form of Prad1utilized can be one which encodes a prad1 similar to that of the animal species used, or it can encode the prad1homolog of a different species (e.g., human). Such an animal would be useful as an in vivo model for neoplastic disease in the selected tissue. In addition, cells derived from. such a transgenic animal may be used to establish an immortal cell line that retains at least some of its differentiated characteristics while proliferating indefinitely in vitro. Alternatively, one could stably transfect primary cells (e.g., a type that has proven difficult to maintain in culture, such as pituitary cells) with a Prad1gene linked to an appropriate promoter (e.g., the metallothionin promoter) which ensures high levels of expression of the gene, and thereby establish an immortal cell line derived from such primary cells. Prad1sequences may be particularly useful in this regard because overexpression of Prad1(at least in parathyroid tissues) appears to trigger the proliferation of normally quiescent cells without causing them to completely lose their differentiated phenotype.
Experimental Data
The DNA abnormality in parathyroid tumor M was initially characterized by Southern analysis of MspI digests using probes specific for the 5' and 3' regions in the PTH gene (see below), which revealed a unique, tumor-specific band. FIG. 1 illustrates these Southern blots of tumor M (T) and peripheral blood leukocyte (L) DNA pairs. MspI-digested DNA was probed with the 51 PTH gene probe (lanes 1, 2) and 3' PTH gene probe (lanes 3, 4). Squares indicate the normal gene (6.3 kb); arrows indicate the rearranged allele (1.5 kb in lane 1, 5.4 kb in lane 3). There is an MspI site within the DNA to which the 31 probe hybridizes (see FIG. 2a); therefore, a smaller band (2.2 kb) representing the most 3' section of the normal PTH gene is present in lanes 3 and 4. The intensities of the bands representing the abnormal allele were approximately equal to those representing the normal allele. Thus, in tumor M, as in tumor Y (Arnold et al., 1989), a clonal rearrangement of the PTH gene has occurred: in every tumor cell, one of the two alleles of the PTH gene remains normal but the other is disrupted. FIG. 2(a) illustrates the normal PTH gene, with the positions of its three exons (Vasicek et al., Proc. Natl. Acad. Sci. USA 80:2127-2131, 1983), the 5' and 3' probes used in mapping and cloning, and the MspI sites indicated. In comparison, FIG. 2(b) shows the two fragments resulting from the rearrangement in tumor M: one consists of the 5' PTH gene sequences plus juxtaposed non-PTH DNA (stippled area), while the other consists of 3' PTH gene sequences plus juxtaposed non-PTH DNA (cross-hatched area). In each fragment, the location of the breakpoint is shown by a diagonal line. The locations of several restriction enzyme sites, determined by Southern blot analysis of tumor DNA, are indicated: EcoRI (R), BamHI (B), HindIII (H), XhoI (X), SstI (S), MspI (M). The locations and sizes of the 1.5 kb and 5.4 kb rearranged MspI fragments, (shown in FIG. 1) are indicated above each fragment. Below each fragment, lines ending in arrow tips depict the 1.5 kb and 16 kb cloned tumor DNA fragments. Analysis with multiple additional restriction enzymes indicated that the gene is separated into two parts, with the breakpoint located in the first intron (FIG. 2b). Consequently, upstream regulatory elements and the first, non-coding exon in the 5' fragment are separated from the coding sequences in the 3' fragment. Each PTH gene fragment remains internally intact (within the limits of sensitivity of restriction mapping), but has become juxtaposed to non-PTH DNA.
To identify the rearranged non-PTH DNA (shaded and cross-hatched areas in FIG. 2b), two DNA fragments containing PTH gene sequences plus breakpoint-adjacent DNA were cloned from tumor M DNA. One was a 16 kb BamHI fragment containing approximately 8 kb of non-PTH gene DNA adjacent to 8 kb of 3' PTH gene sequences (FIG. 2b). Genomic Southern blots of normal DNA probed with subclones spanning most of the 8 kb of non-PTH DNA showed diffuse smears that did not yield to attempts at competition with excess human DNA (Sealy et al., 1985). This indicated that the non-PTH DNA in the 16 kb fragment contained sequences highly repeated in the human genome, and precluded its chromosomal localization.
We also cloned a 1.5 kb EcoRI fragment containing approximately 1 kb of the PTH gene's 5' region plus 500 bp of juxtaposed non-PTH DNA (FIG. 2b). Probing normal human DNA blots with the subcloned 500 bp fragment demonstrated that it contained single-copy DNA; in situ hybridization and analysis of somatic cell hybrids revealed that the 500 bp fragment's normal chromosomal location is 11q13.
Hybridization of the 500 bp breakpoint-adjacent DNA fragment to an RNA blot of six parathyroid adenomas, including two with PTH gene rearrangements, was negative. To identify transcribed sequences near the breakpoint that could have been affected by the rearrangement, we walked along the chromosome by probing a normal human genomic library with the 500 bp subcloned fragment. We obtained a bacteriophage clone with a 14 kb insert, but Northern blot analyses revealed no hybridization of subclones spanning the entire insert. Mapping of the 14 kb insert showed that the 500 bp fragment was at one end, and demonstrated that the adjacent cloned DNA had a restriction map identical to that of the genomic DNA juxtaposed to tumor M's rearranged 5' PTH gene fragment. (Compare FIGS. 2b and 3). At the other end of the 14 kb insert was a 1.6 kb XhoI fragment (FIG. 3) identical in size to an XhoI fragment 1 kb from tumor Y's D11S287 breakpoint (Arnold et al., 1989). We subcloned these two independent 1.6 kb XhoI fragments (one from the above normal phage clone and one from a tumor Y-derived clone) and used them sequentially to probe blots of normal human genomic DNA digested with 7 restriction enzymes. With every enzyme, the two probes hybridized to precisely comigrating fragments. In addition, restriction maps of the two 1.6 kb fragments themselves were identical for all 6 enzymes used. Thus, the 1.6 kb XhoI fragment linked tumor M's breakpoint-adjacent DNA with that of tumor Y (D11S287), confirming that the 11q13 breakpoints in the two adenomas are both in the D11S287 region, separated by 15 kb. The composite restriction map of the unrearranged D11S287 region is shown in FIG. 3, in which restriction sites for the enzymes HindIII (H), BamHI (B), EcoRI (E), SacI (S), MspI (M) and XhoI (X) are indicated. The locations of the 500 bp fragment, the 1.6 kb XhoI fragment, and probe B are shown. This map is derived from the maps of the phage clones described above and by Arnold et al. (1989), and Southern blots of DNA from tumors M and Y.
The proximity of the 11q13 breakpoints suggested that the rearrangements could have similar functional consequences. Because none of the DNA between the two tumors' breakpoints is transcribed in parathyroid cells, we looked for transcribed sequences distal to tumor Y's breakpoint. We used fragment B (FIG. 3), a breakpoint-adjacent DNA fragment from tumor Y, to probe a blot containing total RNA from human placenta, several parathyroid adenomas lacking PTH gene rearrangements, and tumors M and Y. We also hybridized probe B to another blot containing total RNA from placenta and from another parathyroid adenoma (tumor F) that was found recently to contain a clonal rearrangement of the PTH and D11S287 loci (Friedman et al., 1990); Southern blotting indicated that tumor F's rearrangement closely resembled tumor Y's. FIG. 4 presents the results of the Northern blots, in which 10 micrograms of total RNA was probed with Probe B (top panels), and with a 28S rRNA probe (bottom panels). Size determination was based on the migration of 28S rRNA. Lanes contain the following samples: lanes 1, 7: placenta; lanes 2, 3, 4: parathyroid adenomas without PTH gene or D11S287 rearrangements; lanes 5, 6, 8: tumors Y, M, and F, respectively; lanes 7 and 8 are a separate Northern filter. The middle panel is a longer exposure of lanes 1-6 in the top panel. In lanes 5 and 8 (tumors Y and F) a faint band was visible, larger than the highly-overexpressed 4.5 kb band, which was not seen in lane 6 (tumor M) (data not shown). Exposure times: top row (probe B): lanes 1-6, 17h; lanes 7 and 8, 12h; Middle row (probe B): all lanes, 52h; Bottom row (28S rRNA): all lanes, 1.5h. An approximately 4.5 kb transcript (slightly smaller than the 28S rRNA band) was seen in all lanes of FIG. 4. However, the intensity of the 4.5 kb band in tumors M, Y and F was roughly 15-fold greater than that in any of the other specimens. We demonstrated that the 4.5 kb band represents polyadenylated RNA by finding its intensity amplified in poly A+ RNA (data not shown).
Parathyroid adenoma M initially was identified as having an abnormal PTH gene during studies of the monoclonality of parathyroid adenomas (tumor 1 in Arnold et al., N. Eng. J. Med. 318:658-662, 1988). All tumor specimens were frozen in liquid nitrogen shortly after surgical removal. Extraction of high molecular weight DNA, restriction enzyme digestion and Southern blotting were performed as previously described (Arnold et al., N. Eng. J. Med., 309:1593-1599, 1983). Total RNA was isolated by the guanidinium thiocyanate/cesium chloride method, electrophoresed on a denaturing formaldehyde-agarose gel, and transferred to nitrocellulose or nylon filters (Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 7.19-7.22, 7.37-7.39, 11.31-11.32, 1989). Hybridization conditions were similar to those used for Southern filters. Blots were washed at high stringency (0.1.times.SSC, 65.degree.).
PTH gene fragments used as hybridization probes were the 775 bp BglII fragment (5' PTH probe) and the 2.6 kb SstI-EcoRI fragment (3' PTH probe) from pPTHg108 (Igarashi et al., Mol. Cell. Biol. 6:1830-1833, 1986) (FIG. 2a). The 500 bp fragment and probe B (FIG. 3) were subcloned into pUC-18 from the breakpoint-adjacent DNA of the phage clones containing the rearranged PTH gene fragment plus juxtaposed DNA from tumor M (see above), and tumor Y (Arnold et al., 1989), respectively. The 1.6 kb XhoI fragment from the 14 kb insert cloned from the normal human genomic library was also sub-cloned into pUC-18. The 1.6 kb Xhol fragment from tumor Y was subcloned from a Xphage 2001 clone containing the 17 kb HindIII fragment of tumor Y's unrearranged D11S287 allele (Arnold et al., 1989). All the above probes were random-primed and labelled with .sup.32 P! dATP (Feinberg & Vogelstein, Anal. Biochem. 132:6-13, 1983). The 28S RNA oligonucleotide was end-labelled with .sup.32 P!dATP (Sambrook et al., 1989) and used to probe the Northern filters to control for the amount of high molecular weight RNA present in each lane.
To clone the rearranged 5' PTH gene fragment (FIG. 2b), an EcoRI library of tumor genomic DNA was constructed using the .lambda.ZapII vector (Stratagene). This library was screened with the 5' PTH gene probe, and the rearranged allele was distinguished from the normal allele by size, as DNA blots predicted that the rearranged EcoRI fragment would be 1.5 kb in size, and the normal fragment 3.5 kb. One clone containing the rearranged gene was identified in 1.times.10.sup.6 plaques that were screened.
To clone the rearranged 3' PTH gene fragment (FIG. 2b), a BamHI library of tumor genomic DNA was constructed in EMBL-3. Because restriction mapping indicated that both the normal and rearranged 3' PTH BamHI fragments were 16 kb in size, the library was screened with the 3' PTH probe (expected to hybridize to both the normal and rearranged PTH alleles) and then with the 5' PTH probe (expected to hybridize only to the normal allele). One clone containing the rearranged allele was identified in 6.5.times.10.sup.3 plaques screened. As predicted, it contained 8 kb of 3' PTH gene sequences and 8 kb of newly-juxtaposed DNA. Most of this 8 kb was sub-cloned in roughly 2 kb units into pUC-18, and used to probe Southern filters of normal genomic DNA.
Prereassociation was performed by sonicating 1 mg of human placental genomic DNA and incubating it for 10-60 min with 50-100 ng of labelled repeat-containing subcloned DNA. This mix was then hybridized to a Southern filter containing normal human DNA using standard conditions.
The genomic library used to obtain the 14 kb insert was a partial Sau-3a digest of normal human DNA cloned into an EMBL-3 like vector (Clontech).
Chromosomal mapping using human-mouse somatic cell hybrids (Shows et al., Adv. Hum. Genet. 12:341-452, 1982; Shows et al., Somatic Cell Mol. Genet. 10:315-318, 1984); Southern blotting (Naylor et al., J. Exp. Med. 57:1020-1027, 1983); and in situ hybridization (Zabel et al., Cytogenet. Cell Genet. 39:200-205, 1985; Nakai et al., Cytogenet. Cell Genet. 43:215-217, 1986) was performed as previously described.
A .lambda.gt11 placental cDNA library (Clontech) was screened with radiolabeled Probe B. A clone denominated XP1-4 and another similar phage clone were isolated. Probe B and the insert of XP1-4 were sequenced. The region of genomic and CDNA overlap was followed in Probe B by a GT splice donor sequence in only one orientation, confirming hybridization data which had suggested transcription in the left to right orientation, as shown in FIG. 5. The next probe was made by polymerase chain reaction amplification of the 3' region of the XP1-4 cDNA insert, and used to rescreen the same library. From 5.times.10.sup.5 pfu of this library, one of 16 positive clones, XP1-5, had an insert extending further downstream. The PstI/EcoRI fragment of .lambda.P1-5 was then used to rescreen the library, and 12 similar clones, the longest of which was .lambda.P2-3, were obtained. The sequence of the insert of .lambda.P2-3 revealed polyadenylation signals and a polyA stretch of 16 nucleotides in an appropriate position, consistent with the expected orientation. Standard methods for library screening and probe labeling were used (Davis et al., Basic Methods in Molecular Biology (Elsevier, N.Y., Amsterdam, London, 1986). These clones are illustrated in FIG. 5, together with a schematic representation of PTH/D11S287 rearrangements in two parathyroid adenomas. The 5' PTH region (11p15, thick lines) was juxtaposed to the D11S287 region (11q13, thin lines) in each of these adenomas. The breakpoints in the D11S287 region are 15 kb apart. Genomic Probe B is shown as a darkened box, whose open area represents the first exon of Prad1. Also shown are restriction maps of the inserts of representative overlapping Prad1cDNA clones, XP1-4, XP1-5, and XP2-3; and the deduced restriction map of the Prad1cDNA. The coding region is shown as a crosshatched box. Scale of 1 kb is shown as arrows. Symbols used for restriction sites are: B. BamHI; E, EcoRI; H, HindIII; P, PstI.
The inserts of the clones .lambda.P1-4, .lambda.P1-5, and .lambda.P2-3 shown in FIG. 5, and of other independent clones, were subcloned into pGEM7Zf(+) (Promega). Sequences were obtained using the double-stranded DNA sequencing technique (dideoxy method) with modified T7 DNa polymerase (Sequenase; U.S. Biochemical Corporation), as described by the manufacturer. Several oligonucleotides were synthesized as internal primers to facilitate sequencing. The coding region was sequenced in both orientations and in at least two independent clones. Set forth in FIG. 6 are the nucleotide sequence and predicted. amino acid sequence of human Prad1cDNA (SEQ ID NO:1). Nucleotide numbers are on the right. Nucleotide 3495, shown as W, indicates A or T because the sequences of two independent clones did not agree. Nucleotide 4017 is shown as R, meaning A or G, for the same reason.
FIG. 7 illustrates sequence homology between the "cyclin box" region of the predicted Prad1protein (prad1) and that of A-type cyclins (human and clam cyclin A) (Swenson et al., Cell 47:861-870, 1986, and Wang et al., Nature 343:555-557, 1990); B-type cyclins (human cyclin B and S. pombe cdc13) (Pines et al., Cell 58:833-846, 1989; and Booher et al., EMBO J. 7:2321-2327, 1988), and one S. cerevisiae G1 cyclin (cln3) (Nash et al., EMBO J. 7:43354346, 1988; Cross et al., Mol. Cell. Biol. 8:4675-4684, 1988) Clam cyclin A and S. pombe cdc13 homologies with prad1are representative of those found in their families; cln3 alignes with prad1more closely than does cln1 or 2. Identical amino acids are shown as .vertline.. Conservative substitutions are shown as *. Alignment was made with the assistance of the BESTFIT program (Devereux et al., Nucl. Acids Res. 12:387-395, 1984) and conservative amino acids are grouped as follows: D, E, N, Q; H, K, R; A, G, P, S, T; I, L, M, V; F, W, Y. Amino acid numbers are on the right in this Figure.
RNAs were prepared for Northern blot analysis from the indicated tissues by standard procedures (Davis et al., 1986). 10 .mu.g total RNA was loaded and separated on an agarose-formaldehyde gel, blotted onto nitrocellulose, and hybridized with Probe B or the 28S rRNA oligonucleotide. The filters were washed at high stringency (0.1.times.SSC, 60.degree.C.) and autoradiographed. FIG. 8 illustrates a Northern blot analysis of total RNA from human thyroid (lane 1), human placenta (lane 2), bovine parathyroid (lane 3), bovine thyroid (lane 4), bovine lymph node (lane 5), bovine skeletal muscle (lane 6), murine heart (lane 7), and murine liver (lane 8). Prad1RNA (shown in the upper panel) is approximately 4.5 kb in size, slightly smaller than the 28S rRNA; 28S rRNA hybridization is shown in the lower panel. FIG. 9(a) shows a Northern blot analysis of total RNA from HeLa S3 cells after release from G1/S block. Hela S3 cells (American Type Culture Collection), maintained in Dulbecco Modified Eagle Medium (DMEM, GIBCO) with 7% fetal bovine serum (FBS), were synchronized at the G1/S boundary by sequential thymidine-aphidicolin treatment (Heintz, et al., Mol. Cell. Biol. 3:539-550, 1983) with a slight modification. Log-phase cells were incubated in complete medium (DMEM with 7% FBS, penicillin G, and streptomycin) with addition of 2mM thymidine (Sigma) for 12 h. After release from thymidine block by 3 washes with PBS, the cells were incubated for 10 h with 24 .mu.M deoxycytidine (Sigma) and 24 .mu.M thymidine, recovered by trypsinization, counted, and aliquoted equally (5.0.times.10.sup.4 cells/cm.sup.2). Incubation with 5 .mu.g/ml aphidicolin (Sigma) for 14 h was followed by release from G1/S block with 4 DMEM washes and incubation in complete medium. .sup.3 H! Thymidine (NEN) was added to an aliquot 15 min before each indicated time point; a 30 min incubation and harvesting for trichloroacetic acid (TCA) precipitation followed. RNAs from parallel aliquots were extracted (Chomczynski et al., Anal. Biochem. 162:156-159, 1987) at the indicated times; time zero was just before release from aphidicolin. RNAs (5 .mu.g per lane) were blotted onto nitrocellulose and sequentially hybridized with the Prad1.lambda.p1-4 cDNA insert, human H4 histone pF0108X (Pauli et al., Science 236:1308-1311, 1987), and a 28S rRNA oligonucleotide as described above. Human Prad1TRNA is shown in the upper panel of FIG. 9(a); H4 histone mRNA in the middle panel shows the pattern expected in well-synchronized cells (Heintz et al., 1983); and 28S rRNA is shown in the lower panel as a control for RNA loading. In FIG. 9(b) are compared the relative amounts of human PRAD1 mRNA --.circle-solid.--, H4 histone mRNA --.smallcircle.--, and .sup.3 H! thymidine incorporation --.quadrature.--of HeLa S3 cells after release from G1/S block. The signals of the blot shown in FIG. 9(a) were measured by densitometry and normalized to the 28S rRNA to produce the graph of FIG. 9(b).
Clam embryo interphase cell lysates lacking endogenous cyclins were prepared by adding 100 .mu.M emetine during first mitosis, as described previously (Luca et al., J. Cell Biol. 109:1895-1909, 1989), followed by homogenization and centrifugation at 150,000.times.g. Aliquots of the supernatant were frozen in liquid nitrogen. .sup.35 S!methionine-labeled prad1was produced in a reticulocyte lysate in vitro translation system (Promega) according to manufacturer's instructions, by using a plasmid (denominated pP1-8) containing the XP1-4 insert in pGEM7Zf(+) (Promega). To produce prad1in E. coli, pT4R-1 was constructed by insertion of the XP1-4 insert into the NcoI and BamHI sites of pET-3d (Studier et al., Meth. Enzym. 108:60-89, 1990). BL21(DE3) cells were transformed with pT4R-1, cultured, and treated with 0.4 mM isopropylthio-beta-galactosidase (IPTG) for 3 h to induce prad1expression. The induced product was purified from cell culture as inclusion bodies (Gardella et al., J. Biol. Chem 265:15854-15859, 1990). On SDS-polyacrylamide gels, the apparent sizes of the in vitro translation product and the bacterially-expressed product were the same (M.sub.r 35 kD). Rabbit anti-prad1antisera were raised against a synthetic peptide corresponding to amino acids 9-37 of prad1. Antisera were assayed by immunoprecipitation of the in vitro translation product. Antisera specificity was shown by comparison with normal rabbit serum and by successful competition with the (9-37) peptide (data not shown).
Thawed clam embryo lysate (16.5 .mu.l) and bacterially-expressed prad1(5.5 .mu.l) were mixed and incubated at 18.degree. C. for 30 min before transfer to 4.degree. C., dilution with 4 volumes of buffer A (50 mM Tris pH 7.4, 150 mM NaCl, 5 mM EDTA, 5 mM EGTA, 1 mM ammonium molybdate) and addition of p13.sup.suc1 - or protein A-Sepharose, followed by mixing for 1 h. Beads were then pelleted and washed in buffer A+0.5% Tween-20; in buffer B (50 mM Tris pH 7.4, 1.0M NaCl, 5 mM EDTA, 5 mM EGTA, 1 mM molybdate, 0.5% Tween-20); and finally in buffer A without Tween-20, all at 4.degree.C. Washed beads were boiled in SDS sample buffer for 3 min and the supernatant split into three samples for electrophoresis. Gels were silver stained or blotted onto nitrocellulose filters and reacted with rabbit antibodies generated against bacterially-expressed, full-length S. pombe cdc2 protein or prad1peptide as above. Antibody binding was visualized by alkaline phosphatase-linked secondary antibodies, according to the manufacturer's directions (Promega). FIG. 10 demonstrates that prad1 protein added to clam embryo cell lysates binds to p13.sup.suc1 -Sepharose beads and activates histone H1 kinase activity. Bacterially expressed prad1was incubated with a clam embryo interphase lysate lacking endogenous cyclins A and B. The lysates were then mixed with p13.sup.suc1 -or protein A-Sepharose beads. The bound material was eluted, electrophoresed and either silver stained (a) or immunoblotted with anti-prad1 antiserum (b) or anti- cdc2 antiserum (c). Lane M shows molecular weight markers (from top to bottom) of 116, 94, 68, 56, 40, and 31 kD. Lane 1 shows whole clam embryo interphase lysate plus 18 ng prad1protein. Lanes 2, 3, 4, 5, and 6 represent clam embryo lysate to which 0, 18, 45, 225, or 18 ng of prad1, respectively, were added; these mixes were then assayed for material binding to p.sub.13.sup.suc1 -Sepharose (lanes 2-5) or protein A-Sepharose (lane 6) beads. Lane 7 shows bacterially-expressed prad1. Arrows indicate the positions of prad1and cdc2 marker proteins.
Equal volumes of clam embryo interphase lysate and reticulocyte lysate containing .sup.32 P!-labeled kinase products were then examined by SDS-PAGE, followed by autoradiography. Synthetic clam cyclins A and B (Westendorf et al., J. Cell Biol. 108:1431-1444; Swenson et al., Cell 47:861-870, 1986) and prad1mRNAs were transcribed and translated as described above. Translation product (3 .mu.l) and clam embryo lysate (3 .mu.l) were mixed. Samples were frozen immediately in liquid nitrogen. The remainder was incubated for 30 min at 18.degree. C. and then frozen. Samples were diluted with 1 volume of ice-cold buffer A, thawed on ice, and mixed with an equal volume of kinase mix (40 nM Hepes pH 7.3, 20mM MgCl.sub.2, 10 mM EGTA, 0.2 mg/ml histone H1, 10 .mu.M cAMP-dependent kinase inhibitor (Sigma), 0.5 mCi/ml .lambda.-.sup.32 P!ATP and incubated at 23.degree. C. for 10 min. Double-strength SDS sample buffer was then added and the entire mix was analyzed by SDS-PAGE followed by autoradiography, as shown in FIG. 10(d).
Claims
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What is claimed is:
1. A method for diagnosing neoplasia by detecting expression level of PRAD1 cyclin comprising: obtaining a nucleic acid sample from an animal suspected of having a neoplastic condition; contacting said nucleic acid sample with a single-stranded DNA comprising a segment of a PRAD 1 at least 8 nucleotides in length, said Prad1being the Prad1homolog of the species to which said animal belongs; and detecting the level of hybridization of said single-stranded DNA with said nucleic acid sample, said level being diagnostic for said neoplastic condition.
2. The method of claim 1, wherein said animal is a mammal.
3. The method of claim 2, wherein said mammal is a human.
4. The method of claim 1, wherein said neoplastic condition is breast cancer.
5. The method of claim 1, wherein said neoplastic condition is a lymphoma.
6. The method of claim 1, wherein said neoplastic condition is a squamous cell cancer.
7. The method of claim 1, wherein said neoplastic condition is parathyroid adenoma.
Patent Citations (5)
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