US20030129701A1

US20030129701A1 - Retinoic Acid Receptor Epsilon

Info

Publication number: US20030129701A1
Application number: US10/278,945
Authority: US
Inventors: Liang Cao; Jian Ni; Robert Fleischmann
Original assignee: Human Genome Sciences Inc
Current assignee: Human Genome Sciences Inc
Priority date: 1994-06-24
Filing date: 2002-10-24
Publication date: 2003-07-10
Also published as: WO1996000242A1; US5869284A

Abstract

Disclosed is an RARε polypeptide and DNA (RNA) encoding the polypeptide. Also provided is a procedure for producing such polypeptide by recombinant techniques and utilizing such polypeptide for therapeutic purposes, for example, tissue regeneration and stimulation of the immune and hematopoietic system. Also disclosed are methods of identifying ligands which stimulate the RARε. Also disclosed are diagnostic methods for detecting a mutation in the RARε receptor nucleic acid sequences and detecting a level of the soluble form of the receptors in a sample derived from a host.

Description

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of and claims priority under 35 U.S.C. § 120 to U.S. application Ser. No. 09/022,789, filed Feb. 12, 1998, which is a divisional of and claims priority under 35 U.S.C. § 120 to U.S. application Ser. No. 08/466,120, filed Jun. 6, 1995 (now U.S. Pat. No. 5,869,284, issued Feb. 9, 1999), which is a continuation of and claims priority under 35 U.S.C. § 120 to International Application No. PCT/US94/07266, filed Jun. 24, 1994.[0001]

FIELD OF THE INVENTION

This invention relates to newly identified polynucleotides, polypeptides encoded by such polynucleotides, the use of such polynucleotides and polypeptides, as well as the production of such polynucleotides and polypeptides. More particularly, the polypeptide of the present invention is Retinoic Acid Receptor Epsilon (RARε). The invention also relates to inhibiting the action of such polypeptides.

BACKGROUND OF THE INVENTION

Retinoids (Vitamin A derivatives) are crucial for normal growth, vision, maintenance of numerous tissues, reproduction and overall survival (Wolbach, S. B., J. Exp Med, 42:753-777 (1925)). In addition, offspring of Vitamin A deficient (VAD) dams exhibit a number of developmental defects, indicating that retinoids are also important during embryogenesis (Wilson, J. G., et al., Am. J. Anat., 92:189-217 (1953)). The effects of Vitamin A deficiency in fetuses and young and adult animals can be prevented and/or reversed by retinoic acid (RA) administration (Wilson, J. G., et al., Am. J. Anat., 92:189-217 (1953)). The dramatic teratogenic effects of maternal RA administration on mammalian embryos and the spectacular effects of topical administration of retinoids on embryonic development of vertebrates and limb-regeneration in amphibians have markedly contributed to the belief that RA could, in fact, be a morphogen (conferring positional information during development) and may also play a critical role during organogenesis (Tabin, C. J., Cell, 66:199-217 (1991)).

Retinoids are also crucial for normal growth, vision, maintenance of numerous tissues, reproduction and overall survival (Wolbach, S. B. and Howe, P. R., J. Exp. Med., 42:753-777 (1925)).

It is thought that the effects of the RA signal are mediated through two families of receptors that belong to the superfamily of ligand-inducible transcriptional regulatory factors, which includes steroid-thyroid hormone and vitamin D3 receptors (Evans, R. M., Science, 240:889-895 (1988)).

The retinoic acid receptor genes belong to the superfamily of genes known as the steroid hormone receptor family. All genes in this family can be divided into discrete regions or domains that are sometimes referred to as regions A/B, C, D, E, and F. The C region encodes the DNA-binding domain, the E region encodes the ligand-binding domain and the F region encodes the carboxy-terminus domain. The D region is believed to function as a “hinge”. The function of the A/B (or N-terminus) region is not entirely clear but it may be involved with enhancement and repression of receptor transcription activity. (Hollenberg et al., Cell, 55:899-906 (1988)).

The RA receptor (RAR) family (RARα, β and γ and their isoforms) are activated by both all-trans and non-cis RA. RARδ has also been cloned (Mech. Dev., 40:99-112 (1993)). Within a given species, the DNA-binding region and the ligand-binding region domains of the three RAR types are highly similar, whereas the C-terminal region and the middle region exhibit no or little similarity. The amino acid sequences of the three RAR types are also notably different in their B regions, and their main isoforms (α1 and α2, β1 to β4, γ1 and γ2 and δ1 and δ2) further differ in their N-terminal A regions (Leid, M. et al., Trends Biochem. Sci. 17:427-433 (1992)).

RARγ mutant mice exhibit growth deficiency, early lethality, and male sterility due to squamous metaplasia of the seminal vesicles and prostate (Lohnes, D. et al., Cell, 73:643-658 (1993)).

RARγ transcripts are found in precartilaginous condensations, with subsequent restriction to cartilage and differentiating squamous keratinizing epithelia, regardless of their embryonic origin (Dolle, P. et al., Nature, 342:702-705 (1989)). These observations suggest a role for RARγ in morphogenesis and chondrogenesis (Dolle et al., Development, 100:1133-1151 (1990)).

BRIEF SUMMARY OF THE INVENTION

The DNA sequence and polypeptide encoded by such DNA sequence of the present invention belongs to the retinoic acid receptor family and is most homologous to retinoic acid receptor gamma. Both modulator and the DNA binding domains share the highest homology with the corresponding parts of the ecdysone receptor of Drosophila. The ecdysone receptor plays an important role during development.

In accordance with one aspect of the present invention, there is provided a novel mature polypeptide, as well as biologically active and diagnostically or therapeutically useful fragments, analogs and derivatives thereof. The polypeptide of the present invention is of human origin.

In accordance with another aspect of the present invention, there are provided isolated nucleic acid molecules encoding a polypeptide of the present invention including mRNAs, DNAs, cDNAs, genomic DNAs as well as analogs and biologically active and diagnostically or therapeutically useful fragments thereof.

In accordance with yet a further aspect of the present invention, there is provided a process for producing such polypeptide by recombinant techniques comprising culturing recombinant prokaryotic and/or eukaryotic host cells, containing a nucleic acid sequence encoding a polypeptide of the present invention, under conditions promoting expression of said protein and subsequent recovery of said protein.

In accordance with yet a further aspect of the present invention, there is provided a process for utilizing such polypeptide, or polynucleotide encoding such polypeptide for therapeutic purposes, for example, to identify its novel hormone, DNA binding sites, gene targets and tissue specificity, which provide therapeutic targets for stimulating development, differentiation, tissue regeneration, reproduction and stimulation of immune and hematopoietic systems.

In accordance with yet a further aspect of the present invention, there is also provided nucleic acid probes comprising nucleic acid molecules of sufficient length to specifically hybridize to a nucleic acid sequence of the present invention.

In accordance with yet a further aspect of the present invention, there are provided antibodies against such polypeptides.

In accordance with still another aspect of the present invention, there are provided diagnostic assays for detecting diseases or susceptibility to diseases related to mutations in the nucleic acid sequences encoding a polypeptide of the present invention.

In accordance with yet a further aspect of the present invention, there is provided a process for utilizing such polypeptides, or polynucleotides encoding such polypeptides, for in vitro purposes related to scientific research, for example, synthesis of DNA and manufacture of DNA vectors.

These and other aspects of the present invention should be apparent to those skilled in the art from the teachings herein.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings are illustrative of embodiments of the invention and are not meant to limit the scope of the invention as encompassed by the claims. [0020]
FIGS. [0021] 1A-1D depict the polynucleotide sequence (SEQ ID NO: 1) which encodes the retinoic acid receptor polypeptide, and the corresponding amino acid sequence (SEQ ID NO: 2). The standard one letter abbreviation for amino acids is used. Sequencing was performed using a 373 automated DNA sequencer (Applied Biosystems, Inc.).
FIGS. [0022] 2A-2B illustrate the high homology between the polypeptide of the present invention (SEQ ID NO: 2) and RARγ (SEQ ID NO: 5) at the DNA binding region and ligand binding region.
FIG. 3 depicts the results of a Northern blot analysis of the gene of the present invention in human adult tissues. [0023]
FIG. 4 shows the results of electrophoresing RARε on a gel after in vitro transcription/translation. [0024]
FIG. 5 illustrates the baculovirus transfer plasmid pA2 used for expression of the polypeptide of the present invention.[0025]

DETAILED DESCRIPTION

In accordance with an aspect of the present invention, there is provided an isolated nucleic acid (polynucleotide) which encodes for the mature polypeptide having the deduced amino acid sequence of FIGS. [0026] 1A-1D (SEQ ID NO: 2) or for the mature polypeptide encoded by the cDNA of the clone deposited on Apr. 25, 1994 with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209 (present address), as ATCC Deposit No. 75754. The deposit is being maintained under the terms of the Budapest Treaty and will be made available to a patent office signatory to the Budapest Treaty.
A polynucleotide encoding a polypeptide of the present invention may be obtained from testes, spleen and thymus. The polynucleotide of this invention was discovered in a cDNA library derived from human adult lung. It is structurally related to the retinoic acid receptor family. It contains an open reading frame encoding a protein of approximately 433 amino acid residues. The protein exhibits the highest degree of homology to retinoic acid receptor gamma (SEQ ID NO: 5) with 48% identity and 58% similarity over a 70 amino acid stretch of the modulator region. Similarly, the DNA binding region and ligand binding region are also highly homologous to retinoid acid receptor gamma (SEQ ID NO: 5). [0027]
The polynucleotide of the present invention may be in the form of RNA or in the form of DNA, which DNA includes cDNA, genomic DNA, and synthetic DNA. The DNA may be double-stranded or single-stranded, and if single stranded may be the coding strand or non-coding (anti-sense) strand. The coding sequence which encodes the mature polypeptide may be identical to the coding sequence shown in FIGS. [0028] 1A-1D (SEQ ID NO: 1) or that of the deposited clone or may be a different coding sequence which coding sequence, as a result of the redundancy or degeneracy of the genetic code, encodes the same mature polypeptide as the DNA of FIGS. 1A-1D (SEQ ID NO: 1) or the deposited cDNA.
The polynucleotide which encodes for the mature polypeptide of FIGS. [0029] 1A-1D (SEQ ID NO: 2) or for the mature polypeptide encoded by the deposited cDNA may include: only the coding sequence for the mature polypeptide; the coding sequence for the mature polypeptide and additional coding sequence; the coding sequence for the mature polypeptide (and optionally additional coding sequence) and non-coding sequence, such as introns or non-coding sequence 5′ and/or 3′ of the coding sequence for the mature polypeptide.
Thus, the term “polynucleotide encoding a polypeptide” encompasses a polynucleotide which includes only coding sequence for the polypeptide as well as a polynucleotide which includes additional coding and/or non-coding sequence. [0030]
The present invention further relates to variants of the hereinabove described polynucleotides which encode for fragments, analogs and derivatives of the polypeptide having the deduced amino acid sequence of FIGS. [0031] 1A-1D (SEQ ID NO: 2) or the polypeptide encoded by the cDNA of the deposited clone. The variant of the polynucleotide may be a naturally occurring allelic variant of the polynucleotide or a non-naturally occurring variant of the polynucleotide.
Thus, the present invention includes polynucleotides encoding the same mature polypeptide as shown in FIGS. [0032] 1A-1D (SEQ ID NO: 2) or the same mature polypeptide encoded by the cDNA of the deposited clone as well as variants of such polynucleotides which variants encode for a fragment, derivative or analog of the polypeptide of FIGS. 1A-1D (SEQ ID NO: 2) or the polypeptide encoded by the cDNA of the deposited clone. Such nucleotide variants include deletion variants, substitution variants and addition or insertion variants.
As hereinabove indicated, the polynucleotide may have a coding sequence which is a naturally occurring allelic variant of the coding sequence shown in FIGS. [0033] 1A-1D (SEQ ID NO: 1) or of the coding sequence of the deposited clone. As known in the art, an allelic variant is an alternate form of a polynucleotide sequence which may have a substitution, deletion or addition of one or more nucleotides, which does not substantially alter the function of the encoded polypeptide.
The polynucleotides may also encode for a soluble form of the receptor polypeptide of the present invention which is the extracellular portion of the polypeptide which has been cleaved from the TM and intracellular domain of the full-length polypeptide of the present invention. [0034]
The polynucleotides of the present invention may also have the coding sequence fused in frame to a marker sequence which allows for purification of the polypeptide of the present invention. The marker sequence may be a hexa-histidine tag supplied by a pQE-9 vector to provide for purification of the mature polypeptide fused to the marker in the case of a bacterial host, or, for example, the marker sequence may be a hemagglutinin (HA) tag when a mammalian host, e.g. COS-7 cells, is used. The HA tag corresponds to an epitope derived from the influenza hemagglutinin protein (Wilson, I., et al., Cell, 37:767 (1984)). [0035]
The present invention further relates to polynucleotides which hybridize to the herinabove-described sequences if there is at least 70%, preferably at least 90%, and more preferably at least 95% identity between the sequences. The present invention particularly relates to polynucleotides which hybridize under stringent conditions to the hereinabove-described polynucleotides. As herein used, the term “stringent conditions” means hybridization will occur only if there is at least 95% and preferably at least 97% identity between the sequences. The polynucleotides which hybridize to the hereinabove described polynucleotides in a preferred embodiment encode polypeptides which either retain substantially the same biological function or activity as the mature polypeptide encoded by the cDNAs of FIGS. [0036] 1A-1D (SEQ ID NO: 1) or the deposited cDNA(s), i.e. function as a soluble receptor by retaining the ability to bind the ligands for the receptor even though the polypeptide does not function as a membrane bound receptor, for example, by eliciting a second messenger response.
Alternatively, the polynucleotides may have at least 20 bases, preferably 30 bases and more preferably at least 50 bases which hybridize to a polynucleotide of the present invention and which have an identity thereto, as hereinabove described, and which may or may not retain activity. For example, such polynucleotides may be employed as probes for the polynucleotide of SEQ ID NO: 1, or for variants thereof, for example, for recovery of the polynucleotide or as a diagnostic probe or as a PCR primer. [0037]
Thus, the present invention is directed to polynucleotides having at least a 70% identity, preferably at least 90% and more preferably at least a 95% identity to a polynucleotide which encodes the polypeptide of SEQ ID NO: 2 as well as fragments thereof, which fragments have at least 30 bases and preferably at least 50 bases and to polypeptides encoded by such polynucleotides. [0038]
The term “gene” means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region “leader and trailer” as well as intervening sequences (introns) between individual coding segments (exons). [0039]
Fragments of the genes may be employed as a hybridization probe for a cDNA library to isolate other genes which have a high sequence similarity to the genes of the present invention, or which have similar biological activity. Probes of this type are at least 20 bases, preferably at least 30 bases and most preferably at least 50 bases or more. The probe may also be used to identify a cDNA clone corresponding to a full length transcript and a genomic clone or clones that contain the complete gene of the present invention including regulatory and promoter regions, exons and introns. An example of a screen of this type comprises isolating the coding region of the gene by using the known DNA sequence to synthesize an oligonucleotide probe. Labeled oligonucleotides having a sequence complementary to that of the genes of the present invention are used to screen a library of human cDNA, genomic DNA or mRNA to determine which members of the library the probe hybridizes to. [0040]
The deposit(s) referred to herein will be maintained under the terms of the Budapest Treaty on the International Recognition of the Deposit of Micro-organisms for purposes of Patent Procedure. These deposits are provided merely as convenience to those of skill in the art and are not an admission that a deposit is required under 35 U.S.C. §112. The sequence of the polynucleotides contained in the deposited materials, as well as the amino acid sequence of the polypeptides encoded thereby, are incorporated herein by reference and are controlling in the event of any conflict with any description of sequences herein. A license may be required to make, use or sell the deposited materials, and no such license is hereby granted. [0041]
The present invention further relates to a receptor polypeptide which has the deduced amino acid sequence of FIGS. [0042] 1A-1D (SEQ ID NO: 2) or which has the amino acid sequence encoded by the deposited cDNA, as well as fragments, analogs and derivatives of such polypeptide.
The terms “fragment,” “derivative” and “analog” when referring to the polypeptide of FIGS. [0043] 1A-1D (SEQ ID NO: 2) or that encoded by the deposited cDNA, means a polypeptide which either retains substantially the same biological function or activity as such polypeptide, i.e. functions as a receptor, or retains the ability to bind the ligand for the receptor even though the polypeptide does not function as an RARε receptor, for example, a soluble form of the receptor.
The polypeptide of the present invention may be a recombinant polypeptide, a natural polypeptide or a synthetic polypeptide, preferably a recombinant polypeptide. [0044]
The fragment, derivative or analog of the polypeptide of FIGS. [0045] 1A-1D (SEQ ID NO: 2) or that encoded by the deposited cDNA may be (i) one in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue (preferably a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code, or (ii) one in which one or more of the amino acid residues includes a substituent group, or (iii) one in which the mature polypeptide is fused with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol), or (iv) one in which the additional amino acids are fused to the mature polypeptide which are employed for purification of the mature polypeptide or a proprotein sequence or (v) one in which a fragment of the polypeptide is soluble, i.e. not membrane bound, yet still binds ligands to the membrane bound receptor. Such fragments, derivatives and analogs are deemed to be within the scope of those skilled in the art from the teachings herein.
The polypeptides and polynucleotides of the present invention are preferably provided in an isolated form, and preferably are purified to homogeneity. [0046]
The polypeptides of the present invention include the polypeptide of SEQ ID NO: 2 (in particular the mature polypeptide) as well as polypeptides which have at least 70% similarity (preferably at least a 70% identity) to the polypeptide of SEQ ID NO: 2 and more preferably at least a 90% similarity (more preferably at least a 90% identity) to the polypeptide of SEQ ID NO: 2 and still more preferably at least a 95% similarity (still more preferably at least a 95% identity) to the polypeptide of SEQ ID NO: 2 and also includes portions of such polypeptides with such portion of the polypeptide generally containing at least 30 amino acids and more preferably at least 50 amino acids. [0047]
As known in the art “similarity” between two polypeptides is determined by comparing the amino acid sequence and its conserved amino acid substitutes of one polypeptide to the sequence of a second polypeptide. [0048]
Fragments or portions of the polypeptides of the present invention may be employed for producing the corresponding full-length polypeptide by peptide synthesis, therefore, the fragments may be employed as intermediates for producing the full-length polypeptides. Fragments or portions of the polynucleotides of the present invention may be used to synthesize full-length polynucleotides of the present invention. [0049]
The term “isolated” means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring). For example, a naturally-occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide, separated from some or all of the coexisting materials in the natural system, is isolated. Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition, and still be isolated in that such vector or composition is not part of its natural environment. [0050]
The present invention also relates to vectors which include polynucleotides of the present invention, host cells which are genetically engineered with vectors of the invention and the production of polypeptides of the invention by recombinant techniques. [0051]
Host cells are genetically engineered (transduced or transformed or transfected) with the vectors of this invention which may be, for example, a cloning vector or an expression vector. The vector may be, for example, in the form of a plasmid, a viral particle, a phage, etc. The engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying the RARε genes. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan. [0052]
The polynucleotides of the present invention may be employed for producing polypeptides by recombinant techniques. Thus, for example, the polynucleotide may be included in any one of a variety of expression vectors for expressing a polypeptide. Such vectors include chromosomal, nonchromosomal and synthetic DNA sequences, e.g., derivatives of SV40; bacterial plasmids; phage DNA; baculovirus; yeast plasmids; vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus, and pseudorabies. However, any other vector may be used as long as it is replicable and viable in the host. [0053]
The appropriate DNA sequence may be inserted into the vector by a variety of procedures. In general, the DNA sequence is inserted into an appropriate restriction endonuclease site(s) by procedures known in the art. Such procedures and others are deemed to be within the scope of those skilled in the art. [0054]
The DNA sequence in the expression vector is operatively linked to an appropriate expression control sequence(s) (promoter) to direct mRNA synthesis. As representative examples of such promoters, there may be mentioned: LTR or SV40 promoter, the [0055] E. coli lac or trp, the phage lambda P_Lpromoter and other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses. The expression vector also contains a ribosome binding site for translation initiation and a transcription terminator. The vector may also include appropriate sequences for amplifying expression.
In addition, the expression vectors preferably contain one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in [0056] E. coli.
The vector containing the appropriate DNA sequence as hereinabove described, as well as an appropriate promoter or control sequence, may be employed to transform an appropriate host to permit the host to express the protein. [0057]
As representative examples of appropriate hosts, there may be mentioned: bacterial cells, such as [0058] E. coli, Streptomyces, Salmonella typhimlirilim; fungal cells, such as yeast; insect cells such as Drosophila and Spondoptera Sf9; animal cells such as CHO, COS or Bowes melanoma; plant cells, etc. The selection of an appropriate host is deemed to be within the scope of those skilled in the art from the teachings herein.
More particularly, the present invention also includes recombinant constructs comprising one or more of the sequences as broadly described above. The constructs comprise a vector, such as a plasmid or viral vector, into which a sequence of the invention has been inserted, in a forward or reverse orientation. In a preferred aspect of this embodiment, the construct further comprises regulatory sequences, including, for example, a promoter, operably linked to the sequence. Large numbers of suitable vectors and promoters are known to those of skill in the art, and are commercially available. The following vectors are provided by way of example. Bacterial: pQE70, pQE60, pQE-9 (Qiagen), pbs, pD10, phagescript, psiX174, pbluescript SK, pbsks, pNH8A, pNH16a, pNH18A, pNH46A (Stratagene); ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 (Pharmacia), pRS and pGEM. Eukaryotic: pWLNEO, pSV2CAT, pOG44, pXT1, pSG (Stratagene) pSVK3, pBPV, pMSG, pSVL (Pharmacia). However, any other plasmid or vector may be used as long as they are replicable and viable in the host. [0059]
Promoter regions can be selected from any desired gene using CAT (chloramphenicol transferase) vectors or other vectors with selectable markers. Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lacI, lacZ, T3, T7, gpt, lambda PR, PL and trp. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art. [0060]
In a further embodiment, the present invention relates to host cells containing the above-described constructs. The host cell can be a higher eukaryotic cell, such as a mammalian cell, or a lower eukaryotic cell, such as a yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-Dextran mediated transfection, or electroporation. (Davis, L., Dibner, M., Battey, I., Basic Methods in Molecular Biology, (1986)). [0061]
The constructs in host cells can be used in a conventional manner to produce the gene product encoded by the recombinant sequence. Alternatively, the polypeptides of the invention can be synthetically produced by conventional peptide synthesizers. [0062]
Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989), the disclosure of which is hereby incorporated by reference. [0063]
Transcription of the DNA encoding the polypeptides of the present invention by higher eukaryotes is increased by inserting an enhancer sequence into the vector. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp that act on a promoter to increase its transcription. Examples including the SV40 enhancer on the late side of the [0064] replication origin bp 100 to 270, a cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of [0065] E. coli and S. cerevisiae TRP1 gene, and a promoter derived from a highly-expressed gene to direct transcription of a downstream structural sequence. Such promoters can be derived from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), α-factor, acid phosphatase, or heat shock proteins, among others. The heterologous structural sequence is assembled in appropriate phase with translation initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated protein into the periplasmic space or extracellular medium. Optionally, the heterologous sequence can encode a fusion protein including an N-terminal identification peptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed recombinant product.
Useful expression vectors for bacterial use are constructed by inserting a structural DNA sequence encoding a desired protein together with suitable translation initiation and termination signals in operable reading phase with a functional promoter. The vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and to, if desirable, provide amplification within the host. Suitable prokaryotic hosts for transformation include [0066] E. coli, Bacillus subtilis, Salmonella typhimurium and various species within the genera Pseudomonas, Streptomyces, and Staphylococcus, although others may also be employed as a matter of choice.
As a representative but nonlimiting example, useful expression vectors for bacterial use can comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3 (Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM1 (Promega Biotec, Madison, Wis., USA). These pBR322 “backbone” sections are combined with an appropriate promoter and the structural sequence to be expressed. [0067]
Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter is induced by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period. [0068]
Cells are typically harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification. [0069]
Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents, such methods are well know to those skilled in the art. [0070]
Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described by Gluzman, Cell, 23:175 (1981), and other cell lines capable of expressing a compatible vector, for example, the C127, 3T3, CHO, HeLa and BHK cell lines. Mammalian expression vectors will comprise an origin of replication, a suitable promoter and enhancer, and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5′ flanking nontranscribed sequences. DNA sequences derived from the SV40 splice, and polyadenylation sites may be used to provide the required nontranscribed genetic elements. [0071]
The RARε polypeptides can be recovered and purified from recombinant cell cultures by methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography hydroxylapatite chromatography and lectin chromatography. It is preferred to have low concentrations (approximately 0.15-5 mM) of calcium ion present during purification. (Price et al., J. Biol. Chem., 244:917 (1969)). Protein refolding steps can be used, as necessary, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed for final purification steps. [0072]
The polypeptides of the present invention may be a naturally purified product, or a product of chemical synthetic procedures, or produced by recombinant techniques from a prokaryotic or eukaryotic host (for example, by bacterial, yeast, higher plant, insect and mammalian cells in culture). Depending upon the host employed in a recombinant production procedure, the polypeptides of the present invention may be glycosylated or may be non-glycosylated. Polypeptides of the invention may also include an initial methionine amino acid residue. [0073]
The RARε receptor may be employed for the identification of its novel hormones, DNA binding sites, gene targets and tissue specificity. The RARε polypeptide may also be employed as a therapeutic target for tissue regeneration, reproduction, stimulation of the immune and hematopoietic system, and for the treatment of male sterility. This is particularly important since RAR mutant mice exhibited the previously stated abnormalities. Accordingly, the RARε receptor may be employed to treat these disorders. [0074]
The RARε polypeptide may also be employed for screening of putative hormone molecules, such as steroid agonists that can modulate the hormone response mediated through this receptor. To assay for these and other ligands for the RARε, for example, the gene encoding RARε binding sites is cloned in the pRS eukaryotic expression vector (Giguere et al., Cell, 46:645 (1986)) producing pRShRARε. The plasmid is then introduced into monkey kidney CV-1 cells via calcium-phosphate transfection together with a reporter plasmid DELTA MTV-TRE sub p-CAT. TRE means thyroid receptor response element and TRE sub p is a TRE that has been engineered to maximize the palindorminicity of this element. As a control, pRSerbA sup-1 (encodes no protein, stands as a negative control), is also examined. The transfected cells are incubated in the presence or absence of 100 nM retinoic acid, or other potential ligands, for 36 hours, and the induced CAT activities were analyzed by chromatography. The results will indicate which ligands bind to RARε. [0075]
This invention further provides a method of screening compounds to identify those which enhance (agonists) interaction of ligands to the RARε. As an example, a reporter plasmid and pRShRARε are introduced into monkey cells as discussed above. The transfected cells are then incubated with a candidate compound under conditions favoring binding of known ligands, for example, retinoic acid. The reporter gene can be a CAT or luciferase gene whose activities with respect to the interaction of ligand and receptor are capable of being measured (Promega Technical Bulletin No. 126, July, 1993). Transfection systems are useful as living cell cultures for competitive binding assays between known or candidate drugs and ligands which bind to the receptor and which are labeled by radioactive, spectroscopic or other reagents. A transfection system constitutes a “drug discovery system” useful for the identification of natural or synthetic compounds with potential for drug development that can be further modified or used directly as therapeutic compounds to activate or inhibit the natural functions of the human RARε. The transfection system is also useful for determining the affinity and efficacy of known drugs at the human RARε sites. [0076]
The agonist compounds and soluble form of the receptor may be employed in combination with a suitable pharmaceutical carrier. Such compositions comprise a therapeutically effective amount of the compound, and a pharmaceutically acceptable carrier or excipient. Such a carrier includes but is not limited to saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof. The formulation should suit the mode of administration. [0077]
The invention also provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention. Associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration. In addition, the pharmaceutical compositions of the present invention may be employed in conjunction with other therapeutic compounds. [0078]
The pharmaceutical compositions may be administered in a convenient manner such as by the topical, intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal or intradermal routes. The pharmaceutical compositions are administered in an amount which is effective for treating and/or prophylaxis of the specific indication. In general, the pharmaceutical compositions will be administered in an amount of at least about 10 μg/kg body weight and in most cases they will be administered in an amount not in excess of about 8 mg/Kg body weight per day. In most cases, the dosage is from about 10 μg/kg to about 1 mg/kg body weight daily, taking into account the routes of administration, symptoms, etc. [0079]
The soluble form of the receptor and agonists which are polypeptides may also be employed in accordance with the present invention by expression of such polypeptides in vivo, which is often refeffed to as “gene therapy.” Thus, for example, cells from a patient may be engineered with a polynucleotide (DNA or RNA) encoding a polypeptide ex vivo, with the engineered cells then being provided to a patient to be treated with the polypeptide. Such methods are well-known in the art. For example, cells may be engineered by procedures known in the art by use of a retroviral particle containing RNA encoding a polypeptide of the present invention. [0080]
Similarly, cells may be engineered in vivo for expression of a polypeptide in vivo by, for example, procedures known in the art. As known in the art, a producer cell for producing a retroviral particle containing RNA encoding the polypeptide of the present invention may be administered to a patient for engineering cells in vivo and expression of the polypeptide in vivo. These and other methods for administering a polypeptide of the present invention by such method should be apparent to those skilled in the art from the teachings of the present invention. For example, the expression vehicle for engineering cells may be other than a retrovirus, for example, an adenovirus which may be used to engineer cells in vivo after combination with a suitable delivery vehicle. [0081]
Retroviruses from which the retroviral plasmid vectors hereinabove mentioned may be derived include, but are not limited to, Moloney Murine Leukemia Virus, spleen necrosis virus, retroviruses such as Rous Sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, gibbon ape leukemia virus, human immunodeficiency virus, adenovirus, Myeloproliferative Sarcoma Virus, and mammary tumor virus. In one embodiment, the retroviral plasmid vector is derived from Moloney Murine Leukemia Virus. [0082]
The vector includes one or more promoters. Suitable promoters which may be employed include, but are not limited to, the retroviral LTR; the SV40 promoter; and the human cytomegalovirus (CMV) promoter described in Miller, et al., [0083] Biotechniques, Vol. 7, No. 9, 980-990 (1989), or any other promoter (e.g., cellular promoters such as eukaryotic cellular promoters including, but not limited to, the histone, pol III, and β-actin promoters). Other viral promoters which may be employed include, but are not limited to, adenovirus promoters, thymidine kinase (TK) promoters, and B19 parvovirus promoters. The selection of a suitable promoter will be apparent to those skilled in the art from the teachings contained herein.
The nucleic acid sequence encoding the polypeptide of the present invention is under the control of a suitable promoter. Suitable promoters which may be employed include, but are not limited to, adenoviral promoters, such as the adenoviral major late promoter; or heterologous promoters, such as the cytomegalovirus (CMV) promoter; the respiratory syncytial virus (RSV) promoter; inducible promoters, such as the MMT promoter, the metallothionein promoter; heat shock promoters; the albumin promoter; the ApoAI promoter; human globin promoters; viral thymidine kinase promoters, such as the Herpes Simplex thymidine kinase promoter; retroviral LTRs (including the modified retroviral LTRs hereinabove described); the β-actin promoter; and human growth hormone promoters. The promoter also may be the native promoter which controls the genes encoding the polypeptides. [0084]
The retroviral plasmid vector is employed to transduce packaging cell lines to form producer cell lines. Examples of packaging cells which may be transfected include, but are not limited to, the PE501, PA317, ψ-2, ψ-AM, PA12, T19-14X, VT-19-17-H2, ψCRE, ψCRIP, GP+E-86, GP+envAm12, and DAN cell lines as described in Miller, [0085] Human Gene Therapy, Vol. 1, pgs. 5-14 (1990), which is incorporated herein by reference in its entirety. The vector may transduce the packaging cells through any means known in the art. Such means include, but are not limited to, electroporation, the use of liposomes, and CaPO₄precipitation. In one alternative, the retroviral plasmid vector may be encapsulated into a liposome, or coupled to a lipid, and then administered to a host.
The producer cell line generates infectious retroviral vector particles which include the nucleic acid sequence(s) encoding the polypeptides. Such retroviral vector particles then may be employed, to transduce eukaryotic cells, either in vitro or in vivo. The transduced eukaryotic cells will express the nucleic acid sequence(s) encoding the polypeptide. Eukaryotic cells which may be transduced include, but are not limited to, embryonic stem cells, embryonic carcinoma cells, as well as hematopoietic stem cells, hepatocytes, fibroblasts, myoblasts, keratinocytes, endothelial cells, and bronchial epithelial cells. [0086]
This invention also provides a method of detecting expression of an RARε receptor polypeptide of the present invention on the surface of a cell by detecting the presence of mRNA coding for the receptor which comprises obtaining total mRNA from the cell and contacting the mRNA so obtained with a nucleic acid probe comprising a nucleic acid molecule of at least 10 nucleotides capable of specifically hybridizing with a sequence included within the sequence of a nucleic acid molecule encoding the receptor under hybridizing conditions, detecting the presence of mRNA hybridized to the probe, and thereby detecting the expression of the receptor by the cell. [0087]
The present invention also provides a method for identifying receptors related to the receptor polypeptides of the present invention. These related receptors may be identified by homology to a receptor polypeptide of the present invention, by low stringency cross hybridization, or by identifying receptors that interact with related natural or synthetic ligands and or elicit similar behaviors after genetic or pharmacological blockade of the receptor polypeptides of the present invention. [0088]
The present invention also contemplates the use of the genes of the present invention as a diagnostic, for example, some diseases result from inherited defective genes. These genes can be detected by comparing the sequences of the defective gene with that of a normal one. Subsequently, one can verify that a “mutant” gene is associated with abnormal receptor activity. In addition, one can insert mutant receptor genes into a suitable vector for expression in a functional assay system (e.g., calorimetric assay, expression on MacConkey plates, complementation experiments, in a receptor deficient strain of HEK293 cells) as yet another means to verify or identify mutations. Once “mutant” genes have been identified, one can then screen population for carriers of the “mutant” receptor gene. [0089]
Individuals carrying mutations in the gene of the present invention may be detected at the DNA level by a variety of techniques. Nucleic acids used for diagnosis may be obtained from a patient's cells, including but not limited to such as from blood, urine, saliva, tissue biopsy and autopsy material. The genomic DNA may be used directly for detection or may be amplified enzymatically by using PCR (Saiki, et al., [0090] Nature, 324:163-166 1986) prior to analysis. RNA or cDNA may also be used for the same purpose. As an example, PCR primers complimentary to the nucleic acid of the instant invention can be used to identify and analyze mutations in the gene of the present invention. For example, deletions and insertions can be detected by a change in size of the amplified product in comparison to the normal genotype. Point mutations can be identified by hybridizing amplified DNA to radio labeled RNA of the invention or alternatively, radio labeled antisense DNA sequences of the invention. Perfectly matched sequences can be distinguished from mismatched duplexes by RNase A digestion or by differences in melting temperatures. Such a diagnostic would be particularly useful for prenatal or even neonatal testing. Sequence differences between the reference gene and “mutants” may be revealed by the direct DNA sequencing method. In addition, cloned DNA segments may be used as probes to detect specific DNA segments. The sensitivity of this method is greatly enhanced when combined with PCR. For example, a sequence primer is used with double stranded PCR product or a single stranded template molecule generated by a modified PCR. The sequence determination is performed by conventional procedures with radio labeled nucleotide or by an automatic sequencing procedure with fluorescent-tags.
Genetic testing based on DNA sequence differences may be achieved by detection of alterations in the electrophoretic mobility of DNA fragments in gels with or without denaturing agents. Sequences changes at specific locations may also be revealed by nucleus protection assays, such RNase and S1 protection or the chemical cleavage method (e.g. Cotton, et al., [0091] PNAS, USA, 85:4397-4401 1985).
In addition, some diseases are a result of, or are characterized by changes in gene expression which can be detected by changes in the mRNA. Alternatively, the genes of the present invention can be used as a reference to identify individuals expressing a decrease of functions associated with receptors of this type. [0092]
The present invention also relates to a diagnostic assay for detecting altered levels of soluble forms of the receptor polypeptides of the present invention in various tissues. Assays used to detect levels of the soluble receptor polypeptides in a sample derived from a host are well known to those of skill in the art and include radioimmunoassays, competitive-binding assays, Western blot analysis and preferably as ELISA assay. [0093]
An ELISA assay initially comprises preparing an antibody specific to antigens of the receptor polypeptides, preferably a monoclonal antibody. In addition a reporter antibody is prepared against the monoclonal antibody. To the reporter antibody is attached a detectable reagent such as radioactivity, fluorescence or in this example a horseradish peroxidase enzyme. A sample is now removed from a host and incubated on a solid support, e.g. a polystyrene dish, that binds the proteins in the sample. Any free protein binding sites on the dish are then covered by incubating with a non-specific protein such as bovine serum albumin. Next, the monoclonal antibody is incubated in the dish during which time the monoclonal antibodies attach to any RARε receptor proteins attached to the polystyrene dish. All unbound monoclonal antibody is washed out with buffer. The reporter antibody linked to horseradish peroxidase is now placed in the dish resulting in binding of the reporter antibody to any monoclonal antibody bound to RARε receptor proteins. Unattached reporter antibody is then washed out. Peroxidase substrates are then added to the dish and the amount of color developed in a given time period is a measurement of the amount of RARε receptor proteins present in a given volume of patient sample when compared against a standard curve. [0094]
The sequences of the present invention are also valuable for chromosome identification. The sequence is specifically targeted to and can hybridize with a particular location on an individual human chromosome. Moreover, there is a current need for identifying particular sites on the chromosome. Few chromosome marking reagents based on actual sequence data (repeat polymorphisms) are presently available for marking chromosomal location. The mapping of DNAs to chromosomes according to the present invention is an important first step in correlating those sequences with genes associated with disease. [0095]
Briefly, sequences can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp) from the cDNA. Computer analysis of the cDNA is used to rapidly select primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process. These primers are then used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the primer will yield an amplified fragment. [0096]
PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular DNA to a particular chromosome. Using the present invention with the same oligonucleotide primers, sublocalization can be achieved with panels of fragments from specific chromosomes or pools of large genomic clones in an analogous manner. Other mapping strategies that can similarly be used to map to its chromosome include in situ hybridization, prescreening with labeled flow-sorted chromosomes and preselection by hybridization to construct chromosome specific-cDNA libraries. [0097]
Fluorescence in situ hybridization (FISH) of a cDNA clone to a metaphase chromosomal spread can be used to provide a precise chromosomal location in one step. This technique can be used with cDNA as short as 50 or 60 bases. For a review of this technique, see Verma et al., Human Chromosomes: a Manual of Basic Techniques, Pergamon Press, New York (1988). [0098]
Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. Such data are found, for example, in V. McKusick, Mendelian Inheritance in Man (available on line through Johns Hopkins University Welch Medical Library). The relationship between genes and diseases that have been mapped to the same chromosomal region are then identified through linkage analysis (coinheritance of physically adjacent genes). [0099]
Next, it is necessary to determine the differences in the cDNA or genomic sequence between affected and unaffected individuals. If a mutation is observed in some or all of the affected individuals but not in any normal individuals, then the mutation is likely to be the causative agent of the disease. [0100]
With current resolution of physical mapping and genetic mapping techniques, a cDNA precisely localized to a chromosomal region associated with the disease could be one of between 50 and 500 potential causative genes. (This assumes 1 megabase mapping resolution and one gene per 20 kb). [0101]
The polypeptides, their fragments or other derivatives, or analogs thereof, or cells expressing them can be used as an immunogen to produce antibodies thereto. These antibodies can be, for example, polyclonal or monoclonal antibodies. The present invention also includes chimeric, single chain, and humanized antibodies, as well as Fab fragments, or the product of an Fab expression library. Various procedures known in the art may be used for the production of such antibodies and fragments. [0102]
Antibodies generated against the polypeptides corresponding to a sequence of the present invention can be obtained by direct injection of the polypeptides into an animal or by administering the polypeptides to an animal, preferably a nonhuman. The antibody so obtained will then bind the polypeptides itself. In this manner, even a sequence encoding only a fragment of the polypeptides can be used to generate antibodies binding the whole native polypeptides. Such antibodies can then be used to isolate the polypeptide from tissue expressing that polypeptide. [0103]
For preparation of monoclonal antibodies, any technique which provides antibodies produced by continuous cell line cultures can be used. Examples include the hybridoma technique (Kohler and Milstein, 1975, Nature, 256:495-497), the trioma technique, the human B-cell hybridoma technique (Kozbor et al., 1983, Immunology Today 4:72), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole, et al., 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). [0104]
Techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce single chain antibodies to immunogenic polypeptide products of this invention. Also, transgenic mice may be used to express humanized antibodies to immunogenic polypeptide products of this invention. [0105]
The present invention will be further described with reference to the following examples; however, it is to be understood that the present invention is not limited to such examples. All parts or amounts, unless otherwise specified, are by weight. [0106]
In order to facilitate understanding of the following examples certain frequently occurring methods and/or terms will be described. [0107]
“Plasmids” are designated by a lower case p preceded and/or followed by capital letters and/or numbers. The starting plasmids herein are either commercially available, publicly available on an unrestricted basis, or can be constructed from available plasmids in accord with published procedures. In addition, equivalent plasmids to those described are known in the art and will be apparent to the ordinarily skilled artisan. [0108]
“Digestion” of DNA refers to catalytic cleavage of the DNA with a restriction enzyme that acts only at certain sequences in the DNA. The various restriction enzymes used herein are commercially available and their reaction conditions, cofactors and other requirements were used as would be known to the ordinarily skilled artisan. For analytical purposes, typically 1 μg of plasmid or DNA fragment is used with about 2 units of enzyme in about 20 μl of buffer solution. For the purpose of isolating DNA fragments for plasmid construction, typically 5 to 50 μg of DNA are digested with 20 to 250 units of enzyme in a larger volume. Appropriate buffers and substrate amounts for particular restriction enzymes are specified by the manufacturer. Incubation times of about 1 hour at 37° C. are ordinarily used, but may vary in accordance with the supplier's instructions. After digestion the reaction is electrophoresed directly on a polyacrylamide gel to isolate the desired fragment. [0109]
Size separation of the cleaved fragments is performed using 8 percent polyacrylamide gel described by Goeddel, D. et al., Nucleic Acids Res., 8:4057 (1980). [0110]
“Oligonucleotides” refers to either a single stranded polydeoxynucleotide or two complementary polydeoxynucleotide strands which may be chemically synthesized. Such synthetic oligonucleotides have no 5′ phosphate and thus will not ligate to another oligonucleotide without adding a phosphate with an ATP in the presence of a kinase. A synthetic oligonucleotide will ligate to a fragment that has not been dephosphorylated. [0111]
“Ligation” refers to the process of forming phosphodiester bonds between two double stranded nucleic acid fragments (Maniatis, T., et al., Id., p. 146). Unless otherwise provided, ligation may be accomplished using known buffers and conditions with 10 units to T4 DNA ligase (“ligase”) per 0.5 μg of approximately equimolar amounts of the DNA fragments to be ligated. [0112]
Unless otherwise stated, transformation was performed as described in the method of Graham, F. and Van der Eb, A., Virology, 52:456-457 (1973). [0113]

EXAMPLE 1

Expression of RARε by in vitro Transcription and Translation [0114]
The in vitro transcription and translation of RARε was carried out using the TNT Coupled Reticulocyte Lysate System (Promega, 2800 Woods Hollow Road, Madison, Wis. 53771-5399). The cDNA encoding for RARε, ATCC # 75754, was cloned directionally EcoRI to XhoI with the EcoRI site defining the 5′ end of the gene and the XhoI site defining the 3′ end of the gene. The gene was inserted in the T3 direction. T3 defines a bacteriophage RNA polymerase which recognizes a specific promoter, and transcribes the DNA into a mRNA. A rabbit reticulocyte lysate is supplemented with T3 RNA polymerase and directs the expression of proteins with a T3 promoter utilizing the T3 RNA polymerase to transcribe the message, and the reticulocyte lysate to translate the nascent RNA. 1 μg of circular (or linear) plasmid containing the RARε DNA was added directly to TNT™ lysate and incubated in a 50 μl reaction volume at 30° C. for 1 hour with T3 RNA polymerase and [[0115] ³⁵S]-Methionine. After incubation, the translation product was separated by 10% SDS-PAGE gel electrophoresis. The gel was fixed in 10% acetic acid, 15% methanol for 30 minutes followed by drying on a Bio-Rad gel dryer for one hour. Autoradiography was carried out with Kodak XAR film. The film was exposed at −80° C. with intensifying screen. A prominent translation product is visible at 49 kd (FIG. 4)

EXAMPLE 2

Expression and Purification of RARε, in Baculoviris-Insect Cell System [0116]
Sf9 insect cells are maintained in culture using Grace's Insect medium (Gibco) supplemented with 10% FBS at 270C. The baculovirus transfer plasmid pA2 was constructed by Gentz et al (unpublished results) (FIG. 5). The entire human RARε cDNA including the BamH1 site at 5′ end and Asp 718 site at 3′ end were amplified using PCR. The PCR oligonucleotide primers used for the amplification of the human RARε are:5′-GCGCGGATCCACCATGTCCTTGTGGCTGGGG-3′ (SEQ ID NO: 3) 5′-GCGCGGTA CCTCATTCGTGCACATCCCAGAT-3′ (SEQ ID NO: 4). [0117]
The amplified fragment containing human RARε cDNA, and plasmid pA2 were digested by BamHI and Asp 718 and purified by Geneclean kit. The amplified fragment containing human RARε cDNA was inserted into vector pA2 to generate the recombinant transfer vector pA2RARε. The accuracy of the construct was verified using restriction—endonuclease, PCR and DNA sequencing. Transfer of the human RARε cDNA from and pA2RAR to an AcNPV genome can be achieved by co-transfection using Lipofectin (Gibco). AcNPV is a wild-type virus available from Pharmagene (San Diego, Calif.). Techniques for manipulation of baculovirus and insect cell culture such as cultivation, co-transfection, virus infection, isolation, screening and purification of putative recombinant plaques and virus titer determination was described by O'Reilly D. R. et al [Baculovirus expression vectors: A Laboratory Manual (1992), W. H. Freeman and Company]. The plaques will be screened for recombinant baculovirus by using the blue-white selection. The visually screened plaques are to be analyzed and confirmed by PCR screening. Once the recombinant virus is obtained, Sf9 cells (2×10[0118] ⁶cells/ml) can be infected with recombinant RAR virus (10⁸plaque-forming units/ml) for 2 hr at room temperature. After transfection, the viral inoculum is replaced with fresh medium. The supernatant and cells are harvested after 60-72 hr. The extra cellular and intracellular fractions are then analyzed for the expression of RARε by SDS-PAGE. The receptor can be partially purified by sequential anion-exchange, gel-filtration and DNA affinity chromatography.

EXAMPLE 3

Expression Pattern of RARε in Human Tissue [0119]
Northern blot analysis was carried out to examine the levels of expression of RARε in human tissues. Total cellular RNA samples were isolated with RNAzol™ B system (Biotecx Laboratories, Inc. 6023 South Loop East, Houston, Tex. 77033). About 10 μg of total RNA isolated from each human tissue specified was separated on 1% agarose gel and blotted onto a nylon filter. (Sambrook, Fritsch, and Maniatis, Molecular Cloning, Cold Spring Harbor Press, (1989)). The labeling reaction was done according to the Stratagene Prime-It kit with 50 ng DNA fragment. The labeled DNA was purified with a Select-G-50 column. (5 Prime-3 Prime, Inc. 5603 Arapahoe Road, Boulder, Colo. 80303). The filter was then hybridized with radioactive labeled full length RARε gene at 1,000,000 cpm/ml in 0.5 M NaPO[0120] ₄, pH 7.4 and 7% SDS overnight at 65° C. After wash twice at room temperature and twice at 60° C. with 0.5×SSC, 0.1% SDS, the filter was then exposed at −70° C. overnight with an intensifying screen. The message RNA for RARε is abundant in testes, placenta, spleen, thymus and lung. (FIG. 3).

EXAMPLE 4

Expression via Gene Therapy [0121]
Fibroblasts are obtained from a subject by skin biopsy. The resulting tissue is placed in tissue-culture medium and separated into small pieces. Small chunks of the tissue are placed on a wet surface of a tissue culture flask, approximately ten pieces are placed in each flask. The flask is turned upside down, closed tight and left at room temperature over night. After 24 hours at room temperature, the flask is inverted and the chunks of tissue remain fixed to the bottom of the flask and fresh media (e.g., Ham's F12 media, with 10% FBS, penicillin and streptomycin, is added. This is then incubated at 37° C. for approximately one week. At this time, fresh media is added and subsequently changed every several days. After an additional two weeks in culture, a monolayer of fibroblasts emerge. The monolayer is trypsinized and scaled into larger flasks. [0122]
pMV-7 (Kirschmeier, P. T. et al, DNA, 7:219-25 (1988) flanked by the long terminal repeats of the Moloney murine sarcoma virus, is digested with EcoRI and HindIII and subsequently treated with calf intestinal phosphatase. The linear vector is fractionated on agarose gel and purified, using glass beads. [0123]
The cDNA encoding a polypeptide of the present invention is amplified using PCR primers which correspond to the 5′ and 3′ end sequences respectively. The 5′ primer containing an EcoRI site and the 3′ primer having contains a HindIII site. Equal quantities of the Moloney murine sarcoma virus linear backbone and the EcoRI and HindIII fragment are added together, in the presence of T4 DNA ligase. The resulting mixture is maintained under conditions appropriate for ligation of the two fragments. The ligation mixture is used to transform bacteria HB101, which are then plated onto agar-containing kanamycin for the purpose of confirming that the vector had the gene of interest properly inserted. [0124]
The amphotropic pA317 or GP+am12 packaging cells are grown in tissue culture to confluent density in Dulbecco's Modified Eagles Medium (DMEM) with 10% calf serum (CS), penicillin and streptomycin. The MSV vector containing the gene is then added to the media and the packaging cells are transduced with the vector. The packaging cells now produce infectious viral particles containing the gene (the packaging cells are now referred to as producer cells). [0125]
Fresh media is added to the transduced producer cells, and subsequently, the media is harvested from a 10 cm plate of confluent producer cells. The spent media, containing the infectious viral particles, is filtered through a millipore filter to remove detached producer cells and this media is then used to infect fibroblast cells. Media is removed from a sub-confluent plate of fibroblasts and quickly replaced with the media from the producer cells. This media is removed and replaced with fresh media. If the titer of virus is high, then virtually all fibroblasts will be infected and no selection is required. If the titer is very low, then it is necessary to use a retroviral vector that has a selectable marker, such as neo or his. [0126]
The engineered fibroblasts are then injected into the host, either alone or after having been grown to confluence on [0127] cytodex 3 microcarrier beads. The fibroblasts now produce the protein product.
Numerous modifications and variations of the present invention are possible in light of the above teachings and, therefore, within the scope of the appended claims, the invention may be practiced otherwise than as particularly described. [0128]
1 5 1 1649 DNA Homo sapiens CDS (180)..(1481) 1 agtccaggtc ctgcttgtgc tcagctccag ctcactggct ggccaccgaa acttctggac 60 aggaaactgc accatcctct tctcccagca agggggctcc agagaactgc ccacccagga 120 agtctggtgg cctggggatt tggacagtgc cttggtaatg accagggctc caggaagag 179 atg tcc ttg tgg ctg ggg gcc cct gtg cct gac att cct cct gac tct 227 Met Ser Leu Trp Leu Gly Ala Pro Val Pro Asp Ile Pro Pro Asp Ser 1 5 10 15 gcg gtg gag ctg tgg aag cca ggc gca cag gat gca ggc agc cag gcc 275 Ala Val Glu Leu Trp Lys Pro Gly Ala Gln Asp Ala Gly Ser Gln Ala 20 25 30 cag gga ggc agc agc tgc atc ctc aga gag gaa gcc agg atg ccc cac 323 Gln Gly Gly Ser Ser Cys Ile Leu Arg Glu Glu Ala Arg Met Pro His 35 40 45 tct gct ggg ggt act gca ggg gtg ggg ctg gag gct gca gag ccc aca 371 Ser Ala Gly Gly Thr Ala Gly Val Gly Leu Glu Ala Ala Glu Pro Thr 50 55 60 gcc ctg ctc acc agg gca gag ccc cct tca gaa ccc aca gag atc cgt 419 Ala Leu Leu Thr Arg Ala Glu Pro Pro Ser Glu Pro Thr Glu Ile Arg 65 70 75 80 cca cca aag cgg aaa aag ggg cca gcc ccc aaa atg ctg ggg aac gag 467 Pro Pro Lys Arg Lys Lys Gly Pro Ala Pro Lys Met Leu Gly Asn Glu 85 90 95 cta tgc agc gtg tgt ggg gac aag gcc tcg ggc ttc cac tac aat gtt 515 Leu Cys Ser Val Cys Gly Asp Lys Ala Ser Gly Phe His Tyr Asn Val 100 105 110 ctg agc tgc gag ggc tgc aag gaa ttc ttc cgc cgc agc gtc atc aag 563 Leu Ser Cys Glu Gly Cys Lys Glu Phe Phe Arg Arg Ser Val Ile Lys 115 120 125 gga gcg cac tac atc tgc cac agt ggc ggc cac tgc cca tgg aac acc 611 Gly Ala His Tyr Ile Cys His Ser Gly Gly His Cys Pro Trp Asn Thr 130 135 140 tac atg cgt cgc aag tgc cag gag tgt gtc ctg tca gaa gaa cag atc 659 Tyr Met Arg Arg Lys Cys Gln Glu Cys Val Leu Ser Glu Glu Gln Ile 145 150 155 160 cgc ctg aag aaa ctg aag cgg caa gag gag gaa cag gtt cat gcc aca 707 Arg Leu Lys Lys Leu Lys Arg Gln Glu Glu Glu Gln Val His Ala Thr 165 170 175 tcc ttg ccc ccc agg gct tcc tca ccc ccc caa atc ctg ccc cag ctc 755 Ser Leu Pro Pro Arg Ala Ser Ser Pro Pro Gln Ile Leu Pro Gln Leu 180 185 190 aac ccg gaa caa ctg ggc atg atc gag aag ctc gtc cct gcc cag caa 803 Asn Pro Glu Gln Leu Gly Met Ile Glu Lys Leu Val Pro Ala Gln Gln 195 200 205 cag tgt aac cgg cgc tcc ttt tct gac cgg ctt cga gtc acg cct tgg 851 Gln Cys Asn Arg Arg Ser Phe Ser Asp Arg Leu Arg Val Thr Pro Trp 210 215 220 ccc atg gca cca gat ccc cat agc cgg gag gcc cgt cag cag cgc ttt 899 Pro Met Ala Pro Asp Pro His Ser Arg Glu Ala Arg Gln Gln Arg Phe 225 230 235 240 gcc cac ttc act gag ctg gcc atc gtc tct gtg cag gag ata gtt gac 947 Ala His Phe Thr Glu Leu Ala Ile Val Ser Val Gln Glu Ile Val Asp 245 250 255 ttt gct aaa cag cta ccc ggc ttc ctg cag ctc agc cgg gag gac cag 995 Phe Ala Lys Gln Leu Pro Gly Phe Leu Gln Leu Ser Arg Glu Asp Gln 260 265 270 att gcc ctg ctg aag acc tct gcg atc gag gtg atg ctt gtg gag aca 1043 Ile Ala Leu Leu Lys Thr Ser Ala Ile Glu Val Met Leu Val Glu Thr 275 280 285 tct cgg agg tac aac cct ggg agt gag agt atc acc ttc ctc aag gat 1091 Ser Arg Arg Tyr Asn Pro Gly Ser Glu Ser Ile Thr Phe Leu Lys Asp 290 295 300 ttc agt tat aac cgg gaa gac ttt gcc aaa gca ggg ctg caa gtg gaa 1139 Phe Ser Tyr Asn Arg Glu Asp Phe Ala Lys Ala Gly Leu Gln Val Glu 305 310 315 320 ttc atc aac ccc atc ttc gag ttc tcc agg gcc atg aat gag ctg caa 1187 Phe Ile Asn Pro Ile Phe Glu Phe Ser Arg Ala Met Asn Glu Leu Gln 325 330 335 ctc aat gat ccc gag ttt gcc ttg ctc att gct atc agc atc ttc tct 1235 Leu Asn Asp Pro Glu Phe Ala Leu Leu Ile Ala Ile Ser Ile Phe Ser 340 345 350 gca gac cgg ccc aac gtg cag gac cag ctc cag gta gag agg ctg cag 1283 Ala Asp Arg Pro Asn Val Gln Asp Gln Leu Gln Val Glu Arg Leu Gln 355 360 365 cac aca tat gtg gaa gcc ctg cat gcc tac gtc tcc atc cac cat ccc 1331 His Thr Tyr Val Glu Ala Leu His Ala Tyr Val Ser Ile His His Pro 370 375 380 cat gac cga ctg atg ttc cca cgg atg cta atg aaa ctg gtg agc ctc 1379 His Asp Arg Leu Met Phe Pro Arg Met Leu Met Lys Leu Val Ser Leu 385 390 395 400 cgg acc ctg agc agc gtc cac tca gag caa gtg ttt gca ctg cgt ctg 1427 Arg Thr Leu Ser Ser Val His Ser Glu Gln Val Phe Ala Leu Arg Leu 405 410 415 cag gac aaa aag ctc cca ccg ctg ctc tct gag atc tgg gat gtg cac 1475 Gln Asp Lys Lys Leu Pro Pro Leu Leu Ser Glu Ile Trp Asp Val His 420 425 430 gaa tga ctgttctgtc cccatatttt ctgttttctt ggccggatgg ctgaggcctg 1531 Glu gtggctgcct cctagaagtg gaacagactg agaagggcaa acattcctgg gagctgggaa 1591 aggagatcct cccgtggcat taaaagagag tcaaagggta aaaaaaaaaa aaaaaaaa 1649 2 433 PRT Homo sapiens 2 Met Ser Leu Trp Leu Gly Ala Pro Val Pro Asp Ile Pro Pro Asp Ser 1 5 10 15 Ala Val Glu Leu Trp Lys Pro Gly Ala Gln Asp Ala Gly Ser Gln Ala 20 25 30 Gln Gly Gly Ser Ser Cys Ile Leu Arg Glu Glu Ala Arg Met Pro His 35 40 45 Ser Ala Gly Gly Thr Ala Gly Val Gly Leu Glu Ala Ala Glu Pro Thr 50 55 60 Ala Leu Leu Thr Arg Ala Glu Pro Pro Ser Glu Pro Thr Glu Ile Arg 65 70 75 80 Pro Pro Lys Arg Lys Lys Gly Pro Ala Pro Lys Met Leu Gly Asn Glu 85 90 95 Leu Cys Ser Val Cys Gly Asp Lys Ala Ser Gly Phe His Tyr Asn Val 100 105 110 Leu Ser Cys Glu Gly Cys Lys Glu Phe Phe Arg Arg Ser Val Ile Lys 115 120 125 Gly Ala His Tyr Ile Cys His Ser Gly Gly His Cys Pro Trp Asn Thr 130 135 140 Tyr Met Arg Arg Lys Cys Gln Glu Cys Val Leu Ser Glu Glu Gln Ile 145 150 155 160 Arg Leu Lys Lys Leu Lys Arg Gln Glu Glu Glu Gln Val His Ala Thr 165 170 175 Ser Leu Pro Pro Arg Ala Ser Ser Pro Pro Gln Ile Leu Pro Gln Leu 180 185 190 Asn Pro Glu Gln Leu Gly Met Ile Glu Lys Leu Val Pro Ala Gln Gln 195 200 205 Gln Cys Asn Arg Arg Ser Phe Ser Asp Arg Leu Arg Val Thr Pro Trp 210 215 220 Pro Met Ala Pro Asp Pro His Ser Arg Glu Ala Arg Gln Gln Arg Phe 225 230 235 240 Ala His Phe Thr Glu Leu Ala Ile Val Ser Val Gln Glu Ile Val Asp 245 250 255 Phe Ala Lys Gln Leu Pro Gly Phe Leu Gln Leu Ser Arg Glu Asp Gln 260 265 270 Ile Ala Leu Leu Lys Thr Ser Ala Ile Glu Val Met Leu Val Glu Thr 275 280 285 Ser Arg Arg Tyr Asn Pro Gly Ser Glu Ser Ile Thr Phe Leu Lys Asp 290 295 300 Phe Ser Tyr Asn Arg Glu Asp Phe Ala Lys Ala Gly Leu Gln Val Glu 305 310 315 320 Phe Ile Asn Pro Ile Phe Glu Phe Ser Arg Ala Met Asn Glu Leu Gln 325 330 335 Leu Asn Asp Pro Glu Phe Ala Leu Leu Ile Ala Ile Ser Ile Phe Ser 340 345 350 Ala Asp Arg Pro Asn Val Gln Asp Gln Leu Gln Val Glu Arg Leu Gln 355 360 365 His Thr Tyr Val Glu Ala Leu His Ala Tyr Val Ser Ile His His Pro 370 375 380 His Asp Arg Leu Met Phe Pro Arg Met Leu Met Lys Leu Val Ser Leu 385 390 395 400 Arg Thr Leu Ser Ser Val His Ser Glu Gln Val Phe Ala Leu Arg Leu 405 410 415 Gln Asp Lys Lys Leu Pro Pro Leu Leu Ser Glu Ile Trp Asp Val His 420 425 430 Glu 3 31 DNA Artificial sequence PCR oligonucleotide primer used for the amplification of the human RARe 3 gcgcggatcc accatgtcct tgtggctggg g 31 4 30 DNA Artificial sequence PCR oligonucleotide primer used for the amplification of the human RARe 4 gcgcggtacc tcattcgtgc acatcccaga 30 5 443 PRT Homo sapiens 5 Met Tyr Asp Cys Met Glu Thr Phe Ala Pro Gly Pro Arg Arg Leu Tyr 1 5 10 15 Gly Ala Ala Gly Pro Gly Ala Gly Leu Leu Arg Arg Ala Thr Gly Gly 20 25 30 Ser Cys Phe Ala Gly Leu Glu Ser Phe Ala Trp Pro Gln Pro Ala Ser 35 40 45 Leu Gln Ser Val Glu Thr Gln Ser Thr Ser Ser Glu Glu Met Val Pro 50 55 60 Ser Ser Pro Ser Pro Pro Pro Pro Pro Arg Val Tyr Lys Pro Cys Phe 65 70 75 80 Val Cys Asn Asp Lys Ser Ser Gly Tyr His Tyr Gly Val Ser Ser Cys 85 90 95 Glu Gly Cys Lys Gly Phe Phe Arg Arg Ser Ile Gln Lys Asn Met Val 100 105 110 Tyr Thr Cys His Arg Asp Lys Asn Cys Ile Ile Asn Lys Val Thr Arg 115 120 125 Asn Arg Cys Gln Tyr Cys Arg Leu Gln Lys Cys Phe Glu Val Gly Met 130 135 140 Ser Lys Glu Ala Val Arg Asn Asp Arg Asn Lys Lys Lys Lys Glu Val 145 150 155 160 Lys Glu Glu Gly Ser Pro Asp Ser Tyr Glu Leu Ser Pro Gln Leu Glu 165 170 175 Glu Leu Ile Thr Lys Val Ser Lys Ala His Gln Glu Thr Phe Pro Ser 180 185 190 Leu Cys Gln Leu Gly Lys Tyr Thr Thr Asn Ser Ser Ala Asp His Arg 195 200 205 Val Gln Leu Asp Leu Gly Leu Trp Asp Lys Phe Ser Glu Leu Ala Thr 210 215 220 Lys Cys Ile Ile Lys Ile Val Glu Phe Ala Lys Arg Leu Pro Gly Phe 225 230 235 240 Thr Gly Leu Ser Ile Ala Asp Gln Ile Thr Leu Leu Lys Ala Ala Cys 245 250 255 Leu Asp Ile Leu Met Leu Arg Ile Cys Thr Arg Tyr Thr Pro Glu Gln 260 265 270 Asp Thr Met Thr Phe Ser Asp Gly Leu Thr Leu Asn Arg Thr Gln Met 275 280 285 His Asn Ala Gly Phe Gly Pro Leu Thr Asp Leu Val Phe Ala Phe Ala 290 295 300 Gly Gln Leu Leu Pro Leu Glu Met Asp Asp Thr Glu Thr Gly Leu Leu 305 310 315 320 Ser Ala Ile Cys Leu Ile Cys Gly Asp Arg Met Asp Leu Glu Glu Pro 325 330 335 Glu Lys Val Asp Lys Leu Gln Glu Pro Leu Leu Glu Ala Leu Arg Leu 340 345 350 Tyr Ala Arg Arg Arg Arg Pro Ser Gln Pro Tyr Met Phe Pro Arg Met 355 360 365 Leu Met Lys Ile Thr Asp Leu Arg Gly Ile Ser Thr Lys Gly Ala Glu 370 375 380 Arg Ala Ile Thr Leu Lys Met Glu Ile Pro Gly Pro Met Pro Pro Leu 385 390 395 400 Ile Arg Glu Met Leu Glu Asn Pro Glu Met Phe Glu Asp Asp Ser Ser 405 410 415 Gln Pro Gly Pro His Pro Asn Ala Ser Ser Glu Asp Glu Val Pro Gly 420 425 430 Gly Gln Gly Lys Gly Gly Leu Lys Ser Pro Ala 435 440

Claims

What is claimed is:

1. An isolated polynucleotide comprising a member selected from the group consisting of:

(a) a polynucleotide encoding the polypeptide as set forth in SEQ ID NO: 2;

(b) a polynucleotide capable of hybridizing to and which is at least 70% identical to the polynucleotide of (a); and

(c) a polynucleotide fragment of the polynucleotide of (a) or (b).

2. The polynucleotide of claim 1 encoding the polypeptide as set forth in SEQ ID NO: 2.

3. The polynucleotide of claim 1 wherein the polynucleotide is DNA.

4. The polynucleotide of claim 1 wherein said polynucleotide is RNA.

5. The polynucleotide of claim 1 wherein the polynucleotide is genomic DNA.

6. The polynucleotide of claim 1 encoding a soluble form of the polypeptide of SEQ ID NO: 2.

7. An isolated polynucleotide comprising a member selected from the group consisting of:

(a) a polynucleotide encoding a mature polypeptide encoded by the DNA contained in ATCC Deposit No. 75754;

(b) a polynucleotide encoding the polypeptide expressed by the DNA contained in ATCC Deposit No. 75754;

(c) a polynucleotide capable of hybridizing to and which is at least 70% identical to the polynucleotide of (a) or (b); and

(d) a polynucleotide fragment of the polynucleotide of (a), (b) or (c).

8. A vector containing the DNA of claim 2.

9. A host cell transformed or transfected with the vector of claim 8.

10. A process for producing a polypeptide comprising: expressing from the host cell of claim 9 the polypeptide encoded by said DNA.

11. A process for producing cells capable of expressing a polypeptide comprising transforming or transfecting the cells with the vector of claim 8.

12. A receptor polypeptide selected from the group consisting of:

(a) a polypeptide having the deduced amino acid sequence of SEQ ID NO: 2 and fragments, analogs and derivatives thereof; and

(b) a polypeptide encoded by the cDNA of ATCC Deposit No. 75754 and fragments, analogs and derivatives of said polypeptide.

13. An antibody against the polypeptide of claim 12.

14. A compound which activates the polypeptide of claim 12.

15. A method for the treatment of a patient having need to activate an RARε receptor comprising administering to the patient a therapeutically effective amount of the compound of claim 14.

16. The method of claim 15 wherein said compound is a polypeptide and a therapeutically effective amount of the compound is administered by providing to the patient DNA encoding said agonist and expressing said agonist in vivo.

17. A process for diagnosing a disease or a susceptibility to a disease related to an under-expression of the polypeptide of claim 12 comprising determining a mutation in the nucleic acid sequence encoding said polypeptide.

18. The polypeptide of claim 12 wherein the polypeptide is a soluble fragment of the polypeptide and is capable of binding a ligand for the receptor.

19. A diagnostic process comprising analyzing for the presence of the polypeptide of claim 12 in a sample derived from a host.

20. A method of identifying compounds which interact with the polypeptide of claim 12 comprising:

(a) contacting a cell containing an RARε gene and a reporter gene with a compound; and

(b) determining whether the compound interacts with the RARε.