Abstract:
The DNA encoding human thyroid hormone receptor protein alpha-1 (hTR -1). This polynucleotide can be used as a probe to detect the presence of a third form of human thyroid hormone receptor protein.

Description:
The United States Government may have certain rights in the present invention pursuant to grant number USPHS DK 13377. 
    
    
     This application is a continuation, of application Ser. No. 07/405,342, filed Sep. 11, 1989, now abandoned. 
    
    
     BACKGROUND OF THE INVENTION 
     The present invention relates generally to DNA sequences encoding human thyroid hormone receptor proteins and more particularly to DNA sequences encoding human thyroid hormone receptor protein designated hTRα1, to the polypeptide products of recombinant expression of these DNA sequences, to peptides whose sequences are based on amino acid sequences deduced from these DNA sequences, to antibodies specific for such proteins and peptides, and to procedures for detection and quantification of such proteins and nucleic acids related thereto. 
     The physiological and developmental effects of thyroid hormone are mediated by a family of thyroid hormone receptors. The ligand-receptor complexes function as trans-acting transcriptional factors and exert their effects by binding to specific sequences in thyroid hormone responsive genes. (Larsen, P. R., et al., J. Biol. Chem., 261:14373-14376 (1986); Catanzaro, D. F., et al., Mol. Endocrinol., 1:90-96 (1987); Ye, Y. S., J. Biol. Chem., 262:6313-6317 (1986); Gustafson, T. A., et al., Proc. Nat&#39;l. Acad. Sci. (USA), 84:3122-3126 (1987)). In humans, two different types of thyroid hormone receptors (TR) have been described. One, designated human TRβ(hTRβ), is encoded by a gene on chromosome 3 and is expressed in placenta and several cell lines. (Weinberger, C., et al., Nature, 324:641-648 (1986)). The second, designated human TRα2 (hTRα2), is encoded by a gene on chromosome 17 and is expressed in several tissues including kidney, testis, liver, and brain, as well as placenta (Benbrook, D., et al., Science,  238-788-791 (1987); Nakai, A., et al., Proc. Nat&#39;l. Acad. Sci. USA, 85:2781-2785 (1988). cDNAs encoding other forms of thyroid hormone receptors have been isolated from a rat brain library (rTRα1) (Thompson, C. C., et al., Science, 237:1610-1614 (1987) and a chicken embryo library (cTRα). Sap, J., et al., Nature, 324:635-640 (1986). 
     Because of the possibility that additional forms of the thyroid hormone receptor might be expressed in human tissues, efforts have been directed towards isolating other putative receptors. The invention described herein relates, in part, to the results of these efforts. 
     Skeletal muscle is a thyroid hormone responsive tissue. Accordingly, a skeletal muscle cDNA library was screened for sequences that would cross-hybridize with the hTRα2 cDNA probe of the co-inventors herein. Nakai, A., et al., PNAS USA, 85:2781 (1988). A cDNA clone was isolated from this library and found to encode a unique form of the human thyroid hormone receptor that is closely related to the sequences of both hTRα2 and rTRα1. This third type of human thyroid hormone receptor, designated hTRα1, is expressed in many different tissues. Moreover, when expressed in vitro, a protein is produced which binds thyroid hormone with high affinity. A comparison of the sequences of hTRα1 and hTRα2 type thyroid hormone receptors suggests that they are likely encoded by the same gene and that alternative RNA splicing results in the synthesis of either hTRα1 or hTRα2. 
     BRIEF SUMMARY OF THE INVENTION 
     The present invention relates generally to hTRα1, to DNA sequences encoding hTRα1, to the polypeptide products of recombinant expression of these DNA sequences, to peptides whose sequences are based upon the amino acid sequences deduced from these DNA sequences, to antibodies specific for such proteins and peptides, to procedures for the detection and quantitation of such proteins and nucleic acids related thereto, as well as to procedures relating to the development of therapeutic agents. 
     In presently preferred forms, novel DNA sequences comprise cDNA sequences encoding hTRα1 protein. Specifically, this sequence is contained in the plasmid designated pMe21. Alternate DNA forms, such as genomic DNA, and DNA prepared by partial or total chemical synthesis from nucleotides, as well as DNA with deletions or mutations, is also within the contemplation of the invention. Also provided are novel messenger RNA (mRNA) sequences, specifically hTRα1 mRNA species. 
     Association of DNA sequences provided by the invention with homologous or heterologous species expression control DNA sequences, such as promoters, operators, regulators, and the like, allows for in vitro transcription to form mRNA which, in turn, is susceptible to translation to provide hTRα1 proteins, and related poly- and oligo-peptides in large quantities. 
     In a presently preferred in vitro DNA expression system of the invention, hTRα1 encoding DNA is inserted into the EcoR1 site of plasmid pGEM4Z and the resulting plasmid, designated pMe21 is linearized and used as a template for the SP6 polymerase catalyzed synthesis of RNA. Capped RNA is then translated in a rabbit reticulocyte system to provide two major forms of hTRα1 protein, including 55 and 50 kD species, capable of demonstrating functional characteristics of native hTRα1 including for example, control of transcription of T3 responsive genes in an in vitro cell assay system. 
     Incorporation of DNA sequences into procaryotic and eucaryotic host cells by standard transformation and transfection processes, potentially involving suitable viral and circular DNA plasmid vectors, is also within the contemplation of the invention and is expected to provide useful proteins in quantities heretofore unavailable from natural sources. Use of mammalian host cells is expected to provide for such post-translational modifications (e.g., truncation, glycosylation, and tyrosine, serine or threonine phosphorylation) as may be needed to confer optimal biological activity on recombinant expression products of the invention. 
     Novel protein products of the invention include polypeptides having the primary structural conformation (i.e., amino acid sequence) of hTRα1 protein, as set forth in FIG. 1A, FIG. 1B, and FIG. 1C, (therefor), as well as peptide fragments thereof and synthetic peptides assembled to be duplicative of amino acid sequences thereof. Proteins, protein fragments, and synthetic peptides of the invention are projected to have numerous uses including therapeutic uses and will provide the basis for preparation of monoclonal and polyclonal antibodies specifically immunoreactive with hTRα1. Preferred protein fragments and synthetic peptides include those duplicating regions of hTRα1 which are unique to hTRα1. The proteins of the invention are also expected to find utility in developing more effective tests of thyroid function. 
     Also provided by the present invention are polyclonal and monoclonal antibodies characterized by their ability to bind with high immunospecificity to hTRα1 proteins and to their fragments and peptides, recognizing unique epitopes which are not common to other proteins especially other human thryoid receptor proteins. The antibodies of the invention can be used for affinity purification of hTRα1 from other sources and cell types. 
     The present invention also provides novel procedures for the detection and/or quantification of normal, abnormal, or mutated forms, of hTRα1, as well as nucleic acids (e.g., DNA and mRNA) associated therewith. Illustratively, antibodies of the invention may be employed in known immunological procedures for quantitative detection of hTRα1 proteins in samples, and detection of DNA sequences of the invention (particularly those having sequences encoding hTRα1) that may be suitably labelled and employed for quantitative detection of mRNA encoding these proteins. 
     Among the multiple aspects of the present invention, therefore, is the provision of (a) novel hTRα1 encoding DNA sequence as set out in FIG. 1A, FIG. 1B, and FIG. 1C, (therefor), as well as (b) DNA sequences which hybridize thereto under hybridization conditions of the stringency equal to or greater than the conditions described herein and employed in the initial isolation of cDNAs of the invention, and (c) DNA sequences encoding the same allelic variant, or analog hTRα1 protein or polypeptide fragments, through use of, at least in part, degenerate codons. Correspondingly provided are vital or circular plasmid DNA vectors incorporating such DNA sequences in procaryotic and eucaryotic host cells transformed or transfected with such DNA sequences and vectors, as well as novel methods for the recombinant production of hTRα1 through cultured growth of such hosts and isolation of these proteins from the hosts or their culture media. 
     Other aspects and advantages of the present invention will be apparent upon consideration of the following detailed description thereof which includes numerous illustrative examples of the practice of the invention, reference being made to the drawing. 
    
    
     BRIEF DESCRIPTION OF FIGURES 
     FIG. 1A, FIG. 1B, and FIG. 1C, (therefor) is the nucleotide and deduced amino acid sequence of λMe2. 
    
    
     DETAILED DESCRIPTION 
     The following examples illustrate practice of the invention. Example 1 relates to complementary DNA cloning and sequencing. Example 2 relates to northern hybridization analysis. Example 3 relates to in vitro expression and hormone binding assay. Example 4 relates to use of hTRα1 DNA as a probe. 
     The examples which follow are for illustrative purposes only and are not intended in any way to limit the scope of the invention. 
     EXAMPLE 1 
     Complementary DNA Cloning and Sequencing: 
     Recombinant phage (˜10 8 ) from a human fetal muscle cDNA λgt10 library were screened using a nick-translated 1410 bp EcoR1 fragment from pke 711. Nakai, A., et al., Proc. Nat&#39;l. Acad. Sci. USA, 85:2781-2785 (1988). The hybridization mixture contained 25% formamide, 1× Denhardt&#39;s, 5× SSC, 0.1% SDS, 100 μg/ml denatured salmon sperm DNA, and 0.5×10 6  cpm/ml [ 32  p] labelled EcoR1 fragment (SA 1×10 8  cpm/μg). Nitrocellulose filters were hybridized at 37° C. for 18 h. washed in 2× SSC, 0.1% SDS at room temperature for 1 h, and then washed at 42° C. for 30 min. The EcoR1 insert of λMe2 was sequenced using the Sanger dideoxy chain termination procedure (Sanger, F., et al., Proc. Nat&#39;l. Acad. Sci. (USA), 74:5463-5467 (1977)) and Sequenase (U.S. Biochemical Corp., Cleveland, Ohio). The nucleotide sequence of the coding region was determined on both strands. 
     Two clones in a fetal skeletal muscle cDNA library (Koenig, M., Cell, 50:509-511 (1987)) hybridized with the 1400 bp EcoR1 fragment of the hTRα1 clone, λke12. The partial sequence of one, λMe1, indicated that it encoded hTRα2. The sequence of λMe2 was 1888 bp with an open reading frame of 1230 bp, encoding a different form of the human thyroid hormone receptor, having 410 amino acids, and having a predicted molecular mass of 47 kD. The protein is designated hTRα1. The nucleotide sequence and deduced amino acid sequence is given in FIG. 1A, FIG. 1B, and FIG. 1C, (therefor.) Initiation and termination codons of a short reading frame in the 5&#39;-untranslated region are underlined. The site of divergence of hTRα1 from hTRα2 is indicated by a triangle. Numbers above the translated sequence indicate amino acid residues. Nucleotides are numbered at the left of the sequence. The sequence from nucleotide 16 to 1183 of λMe2 is identical to that of the hTRα2 cDNA sequence (the sequence of hTRα2 corresponding to nucleotides 1-16 has not been determined). Correspondingly, the amino acid sequences of residues 1-370 of these two related human thyroid hormone receptors are identical; the COOH-terminal 40 residues of the hTRα1 sequence and 120 residues of hTRα2 are unique, as is the nucleotide sequence encoding this segment of each protein (the sequences of the 3&#39;-untranslated regions of each type of clone are also unique). Although the COOH-terminal sequence of hTRα1 has no homology with that of hTRα2, it has 100% identity with the sequence of the cognate rat TR receptor sequence, rTRα1, over a span of 120 nucleotides. Moreover, the nucleotide sequences of the human and rat clones are also identical in the COOH-terminal coding region. 
     EXAMPLE 2 
     Northern Hybridization Analysis: 
     Human tissues were obtained at surgery, with permission of the Committee on Human Investigation, and RNA was isolated using the guanidinium thiocyanate procedure (Chirgwin, J. M., et al., Biochemistry, 18:5294-5299 (1979)). Poly(A) RNA was prepared by oligo(dT) chromatography. Poly(A) RNAs were separated on a 1% agarose gel containing formaldehyde, transferred to nitrocellulose, and probed using an oligo-labeled 590 bp Xhol-EcoR1 fragment λMe2. Filters were hybridized overnight and washed with 0.2× SSC and 0.1% SDS at 60° C. 
     Hybridization of a 590 bp Xhol-EcoR1 fragment from the 3&#39;end of λMe2, which is specific for hTRα1, to a Northern blot containing RNA prepared from adult human kidney and spleen, adolescent tonsils, and term placenta revealed specific hybridization to a 3.2 kb transcript in each tissue, and hybridization to a larger, less abundant transcript of about 6 kb. The insert in λMe2 is 1888 bp. Although the clone terminates with a region of 17 As, it is not clear that this tract corresponds to the poly(A) tail of the mRNA since the sequence preceding it not typical for a pre-polyadenylation sequence. An hTRα2 mRNA specific probe also hybridized to 3.2 kb transcripts in each of these tissues. 
     EXAMPLE 3 
     In Vitro Expression and Hormone Binding Assay: 
     The EcoR1 insert of λMe2 was inserted in the EcoR1 site of pGEM4Z (Promega Biotec, Madison, Wis.) to yield pMe21. pMe21 was linearized with Hind III and used as a template. for SP6 polymerase catalyzed synthesis of RNA (Melton, D. A., et al., Nucleic Acids Res., 12:7035-7056 (1984)). Capped RNA was translated in a rabbit reticulocyte lysate (Promega Biotec). Thyroid hormone binding activity of the translated protein was assayed according to the method of Nakai, A., et al., Proc. Nat&#39;l. Acad. Sci. USA, 85:2781-2785 (1988). 
     Translation of in vitro expressed hTRα1 mRNA resulted in the synthesis of two major proteins having sizes of 55 and 50 kilodaltons (kDa) as determined by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. It is unknown why the protein displays a higher molecular weight than the predicted molecular mass of 47 kD on SDS-polyacrylamide gel electrophoresis. A similar discrepancy was observed during in vitro synthesis of rTRα1 (Thompson, C. C., et al., Science, 237:1610-1614 (1987). Moreover, the synthesis of two major proteins was unexpected. Possibly, the larger 55 kDa protein corresponds to the expected 410 amino acid protein and the 50 kDa protein may correspond to hTRα1 39-410 since initiation of translation at Met 39 would result in the synthesis of a protein having a mass of about 4 kDa less. 
     The translated hTRα1 protein(s) were assayed for their biological activity by their ability to bind thyroid hormone. For example, it was found that the proteins bound T 3  (triiodothyronine) with an association constant (K a ) of 1.8×10 9  liter/M; this is similar to the affinity of translated hTRα2 for this ligand. In competition experiments, the translated hTRα1 protein possessed affinities for T 4  and triiodothyroacetic acid (Triac) similar to those of hTRα2, and characteristic of thyroid hormone receptors from human and animal tissues. 
     The sequence at the site of divergence of hTRα1 and hTRα2, AAG/GTGACT, includes the consensus sequence for the donor site of an exon-intron junction Lewin, B., Cell, 22:324-326 (1980). Although gene duplication and partial gene conversion have not been totally excluded, it is possible that alternative splicing is responsible for generating TRα proteins having COOH-termini of different lengths as well as sequence. Alternative splicing has previously been reported for human glucocorticoid receptor (Hollenberg, S. M., et al., Nature, 318:635-641 (1985)). However, in that instance, one of the two proteins did not bind glucocorticoids in vitro, and its mRNA was not detected by Northern blot analysis of RNA from several tissues. In contrast, both hTRα1 and hTRα2 bind T 3  and are present in many human tissues. 
     EXAMPLE 4 
     Use of hTRα1 DNA as a Probe: 
     use of hTRα1 DNA as probes to study the expression of receptor protein in human tissue samples, e.g., the distribution of mRNA in all types of human tissue is contemplated by, i.e., in situ hybridization or Northern blot hybridization analysis. 
     For the analysis of mRNA for hTRα1, or for related proteins, dot hybridization and Northern hybridization analyses can be used to characterize mRNA and hTRα1 or hTRα1-like molecules quantitatively and qualitatively. From these studies valuable information about the number of different forms of hTRα1 genes and their expression in different human tissues can be obtained. 
     It is also possible to use appropriate oligonucleotide fragments of hTRα1 DNA as primers to amplify genomic DNA, isolated from, for example, human leucocytes, by specific DNA polymerases. The amplified genomic DNA can then be analyzed to identify sequence abnormality using the polymerase chain reaction (PCR) assay. Saiki, et al., Science, 230:1350 (1985). See also, Mullis, K. B., U.S. Pat. No. 4,683,202; Jul. 28, 1987; and Mullis, K. B., U.S. Pat. No. 4,683,195; Jul. 28, 1987. 
     The foregoing illustrative examples relate generally to DNA sequences encoding thyroid hormone receptor and more particularly to hTRα1 thyroid receptor, to DNA sequences encoding hTRα1, to the polypeptide products of recombinant expression of these DNA sequences, to peptides whose sequences are based upon the amino acid sequences deduced from these DNA sequences, to antibodies specific for such proteins and peptides, and to procedures for the detection and quantitation of such proteins and nucleic acids related thereto, as well as to procedures relating to the development of therapeutic agents. While the present invention has been described in terms of specific methods and compositions, it is understood that variations and modifications will occur to those skilled in the art upon consideration of the present invention. 
     Numerous modifications and variations in the invention as described in the above illustrative examples are expected to occur to those skilled in the art and consequently only such limitations as appear in the appended claims should be placed thereon. 
     Accordingly it is intended in the appended claims to cover all such equivalent variations which come within the scope of the invention as claimed.