Abstract:
The human tryptophan oxygenase gene sequence and chromosomal location are described. Procedures for the diagnosis of genetic Tourette syndrome and many psychiatric and behavioral disorders by genetic tests to identify deletions or defective alleles in the human tryptophan oxygenase (TO) gene and cDNA probes for use in such tests are also described.

Description:
This application is a continuation-in-part of each of application Ser. No. 125,577, filed Nov. 25, 1987, abandoned, application Ser. No. 271,653, filed Nov. 16, 1988, abandoned, and application Ser. No. 410,831, filed Sep. 22, 1989, abandoned. Each of these applications is incorporated into this application by reference. 
    
    
     BACKGROUND 
     Tourette syndrome (TS) is a common, hereditary, neuro-behavioral disorder characterized by motor and vocal tics. Autism is a trait of three sets of symptoms: (1) a profound failure to develop social relationships; (2) defective speech and language; and (3) ritualistic or compulsive behavior. 
     The symptoms of TS and its related disorders fit a model in which the frontal lobe and limbic system in the brain are disinhibited by a relative deficiency in brain serotonin and tryptophan. 
     Like TS, autism and MR are neurological disorders. The areas of the brain involved in autism and MR, the frontal lobe and limbic system, are often the same as those involved in TS. Unlike TS where both brain serotonin and tryptophan levels tend to be low, in autism and MR each is often significantly elevated. 
     Tryptophan-2,3 dioxygenase (tryptophan oxygenase, tryptophan pyrrolase) is considered primarily to be a liver enzyme. However, the same or a very similar enzyme, indoleamine 2,3 dioxygenase is also present in the brain, intestines and other organs. See Gal, E. M. and Sherman, A. D., &#34;L-kynurenine: its synthesis and possible regulatory function in brain&#34;, Neurochem. Res. 5:223-239 (1980). 
     Table 1 depicts several apparent differences between the functions of these enzymes. See Hayaishi, O., &#34;Properties and function of indoleamine 2,3-dioxygenase&#34;, J. Biochem 79:13p-21p (1976); Gal, E. M., &#34;Cerebral tryptophan-2,3-dioxygenase (pyrrolase) and its induction in rat brain&#34; J. Neurochem 22:861-863 (1974); and Gal, E. M. and Sherman, A. D., &#34;L-kynurenine: its synthesis and possible regulatory function in brain&#34;, Neurochem. Res. 5:223-239 (1980). 
     
                       TABLE 1______________________________________        Tryptophan Indoleamine        2,3-dioxygenase                   2,3-dioxygenase______________________________________SimilaritiesSubstrate      L-tryptophan L-tryptophanProduct        N-formyl     N-formyl          kynurenine   kynurenineType of protein          heme         hemeInducible by tryptophan          yes          yesDifferencesLocation       liver        brain and many                       other organsType of oxygen used          O.sub.2      O--O.sup.-Other substrates          none         D-tryptophan                       5-hydroxy-                       tryptophan                       serotonin                       melantoinInducible by cortisol          yes          no______________________________________ 
    
     It is not known whether these differences are due to the presence of the enzyme in a different form in different tissues or to the fact that the enzymes are produced by different genes. For the purposes of this invention, it is unnecessary to determine whether one or two genes is implicated. A reasonable possibility is that the two forms of TO (liver and intestine-brain) represent alternate modes of transcription or mRNA processing of the human TO gene. Unless separately identified, the liver and brain-intestine enzymes are referenced collectively herein as tryptophan oxygenase or TO. 
     If TO were present only in the liver, then the level of tryptophan in the brain would be almost completely dependent on the blood level of tryptophan and of the compounds that compete for its transport across the blood brain barrier. However, as FIG. 1 shows, tryptophan oxygenase activity is also present in the brain where it is effective to siphon off some of the tryptophan after brain entry and before it is converted to serotonin. 
     In rats, under normal conditions 70% of the brain tryptophan is converted to serotonin and 30% to brain kynurenine. Gal, E. M. and Sherman, A. D., &#34;L-kynurenine: its synthesis and possible regulatory function in brain&#34;, Neurochem. Res. 5:223-239 (1980). Even a moderate increase in brain tryptophan oxygenase could markedly change this ratio and lower the level of brain serotonin. Significant changes in the breakdown of tryptophan in the brain may thus occur concurrently with only moderate changes in the blood tryptophan and serotonin. 
     In humans, serotonin and tryptophan levels are apparently interdependent, serotonin level abnormalities being a consequence of tryptophan level abnormalities. As FIG. 2 shows, human brain tryptophan can take two major metabolic pathways, i.e., 90% conversion to kynurenine and 10% conversion to serotonin. TO activity is the rate limiting step in the degradation of tryptophan to kynurenine. 
     Because TO is implicated in both TS and autism, fairly subtle changes in the level of the enzyme would be expected to significantly affect serotonin production. The TO level may be increased in TS and decreased in autism. However, since some autistic children have low levels of serotonin and some TS patients have high levels, the basic defect in both may be a dysregulation (too high or too low) of serotonin. 
     More particularly, FIG. 3 indicates that the genetic defect in TS related disorders may be either a duplication or a mutation of the TO gene resulting in high levels of hyperinducability, whereas in autism and some forms of MR the TO gene is either defective or deleted. 
     Since the serotonin levels in some severe mental retardation are even higher than those in autism, it is likely that the genetic defect causing the elevated serotonin is also more severe and may represent a deletion of the TO gene. By contrast, in TS, the TO genes are duplicated or otherwise mutated so the amount of enzyme is increased. 
     In genetic terms the most detrimental thing that can be done to a gene is to delete it. A single base change mutation within the gene may have no effect, a mild effect or a significant effect on the function of the enzyme that gene makes. Table 2 presents some possible genotypes and phenotypes as a guide to the basic idea. A deletion of a TO gene is termed TO 0, a base pair substitution mutation causing decreased function of TO is termed TO -, a normal gene will be termed TO + and a duplicated gene, or a gene with a mutation causing increased levels or increased efficiency of the tryptophan oxygenase enzyme, is termed TO ++. 
     
                       TABLE 2______________________________________                   Effect onType of                 BloodDefect     Genotype     Serotonin Result______________________________________None       TO +/TO +    Normal    Normal                   LevelsDeleted/   TO 0/TO 0    Extremely Severe M.R.Deleted                 High      ± AutismDeleted/   TO 0/TO -    Very High Autism withMutant                            M.R.Mutant/    TO -/TO -    High      AutismMutant                            Some TSMutant     TO 0/TO +    Moderately                             Normal oror Deleted/      TO -/TO +    High      Mild AutismNormal                            Some TSMutant or  TO ++/TO +   Low       TSDup/Normal              Serotonin Some AutismNormalMutant or Dup/      TO ++/TO ++  Low       HomozygousMutant or Dup           Serotonin Grade 3 TS                             Some Autism______________________________________ 
    
     Hence, mutations of the human TO gene which result in decreased activity of the TO gene are likely to be involved in some cases of the autism or autism with mental retardation. These mutations would be various heterozygous or homozygous combinations of deletions or base pair mutations affecting activity or function of the human TO gene or genes. 
     In contrast, mutations of the human TO gene which result in increased activity, or increased inducability or increased efficiency of the TO gene are likely to be involved in Tourette syndrome and many of the wide range of behaviors associated with the TS spectrum of behaviors. These mutations include various heterozygous or homozygous combinations of gene duplications, or mutations of the regulatory or structural sequences of the human TO gene or genes. 
     Because the defects are enzyme deficiencies, the autism and MR disorders are autosomal recessive. By contrast, for TS because the enzyme level is apparently increased, the trait is autosomal dominant or semi-dominant. 
     These examples are meant to be an approximation. An abnormal serotonin level (too high or too low) may cause either autism or TS or autism and TS. Many cases of both occurring in the same patient have been described. 
     SUMMARY OF THE INVENTION 
     This invention relates to the diagnosis of genetic Tourette syndrome and related psychiatric and behavioral disorders by genetic tests to identify deletions, duplications or defective alleles in the human tryptophan oxygenase (TO) gene and to probes for use in such tests. More particularly, the invention relates to certain cDNA tryptophan oxygenase clones derived from mRNA and to the use of such clones as probes to identify genomic clones from a human genomic library and to identify the chromosomal location of the human TO gene. The invention also relates to the identification, chromosomal location, isolation, nucleotide sequence and synthesis of the human TO gene and of peptides encoded by the TO gene. 
     Diagnostic tests are provided for, among other things, Tourette syndrome (TS) chronic motor and vocal tics, attention deficit disorder (ADD) with or without hyperactivity, obsessive-compulsive behavior, unipolar or bipolar affective disorder, phobias, panic attacks, significant premenstrual tension, generalized anxiety disorder, autism, pervasive developmental disorder, dyslexia, learning disabilities, dysgraphia, borderline personality disorder, migraine headaches, exhibitionism, stuttering, delayed speech, schizophreniform disorder, schizoid disorder, drug or alcohol addiction or abuse, bulimia, compulsive eating with obesity, physical or sexual abuse of spouse or children, and severe mental retardation (MR). The fact that TS is a wide-based, generalized behavioral disorder associated with the above list of abnormalities is documented in Comings, D. E. and Comings, B. G., &#34;A controlled study of Tourette syndrome. I. Attention deficient disorder, learning disorders and school problems&#34;, Amer. J. Human Genetics 41:701-741 (1987); Comings, D. E. and Comings, B. G., &#34;A controlled study of Tourette syndrome II. Conduct disorder&#34;, Amer. J. Human Genetics 41:742-760 (1987); Comings, D. E. and Comings, B. G., &#34;A controlled study of Tourette syndrome. III. Phobias and panic attacks&#34;, Amer. J. Human Genetics 41:761-781 (1987); Comings, D. E. and Comings, B. G., &#34;A controlled study of Tourette syndrome IV. Obsessive compulsive and schizoid behavior&#34;, Amer. J. Human Genetics 41:782-803 (1987); Comings, D. E. and Comings, B. G., &#34;A controlled study of Tourette syndrome. V. Depression and mania&#34;, Amer. J. Human Genetics 41:804-821 (1987); Comings, D. E. and Comings, B. G., &#34;A controlled study of Tourette syndrome. VI. Early development, sleep problems, allergies and handedness&#34;, Amer. J. Human Genetics 41:822-838 (1987); Comings, D. E., Tourette Syndrome and Human Behavior, Hope Press, Duarte, Calif. 91009-0188, 830 pages (1990). Hereinafter these abnormalities are collectively referenced as &#34;TS related disorders&#34;. 
    
    
     BRIEF DESCRIPTION OF THE FIGURES 
     FIG. 1 is a schematic illustration of TDO2-IDO2 activity present in the brain. 
     FIG. 2 is a schematic illustration of two metabolic pathways available to peripheral tryptophan. 
     FIG. 3 indicates genetic defects in TDO2-IDO2 that may occur in TS, TS related disorders and autism. 
     FIG. 4 depicts autoradiograms of duplicate filter lifts from a human liver cDNA library in gtill hybridized with rat liver superimposed and turned slightly to reveal human cDNA clones of human tryptophan oxygenase. 
     FIG. 5 and 5A depict the sequence of the human HTO3 (TDO2) clone and the translation into the open reading frame. 
     FIG. 6 depicts the sequence of rat pcTO1 and rat TDO2. 
     FIG. 7 shows the region of homology between the sequences depicted by FIGS. 5 and 5A and FIG. 6. 
     FIG. 8 depicts the results of hybridization studies to identify the chromosomal location of the human TDO gene. 
     FIG. 9 depicts the chromosomal location of the human tDO2 gene to 4q31. 
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     This invention provides genetic tests for TS, autism and the related disorders listed in the &#34;Summary of The Invention&#34;. These tests entail the identification of deletions, duplications and other defective alleles of the TO gene. 
     These genetic tests, per se, may be of conventional nature and involve, for example: 
     (a) Obtaining DNA from subjects to be tested (blood, skin, hair follicles or any other source). 
     (b) Identifying mutations in this DNA by hybridization of specific DNA or RNA probes to various parts of the tryptophan oxygenase gene, or DNA surrounding the tryptophan oxygenase gene. The mutations may be partial or complete gene duplications, double or multiple gene duplications, partial or complete gene deletions, single nucleotide substitutions, or frame shift mutations. The probes may, for example, be oligonucleotide probes including allele specific synthetic oligonucleotides, cloned cDNA, genomic DNA fragments, or RNA. The test may include hybridization of DNA electrophoresed in gels, or spotted on a support media, or amplified by DNA polymerases. 
     The invention includes a cloned cDNA and a genomic DNA probe for the human TO gene useful to conduct such genetic tests. The invention also includes an isolated or synthetic DNA sequence comprising at least a portion of the TO gene sequence, and isolated or synthetic proteins encoded by the TO gene sequence in whole or in part. 
     Cloning of The Human TO Gene 
     Schmidt, et al. report the isolation of the rat liver tryptophan oxygenase gene. See EMBO Journal 1:1287 (1982). Two cDNA probes, pcTO1 and pcT02 covering parts of the entire rat TO gene are described. 
     To provide an appropriate human cDNA probe, the rat pcTO1 570 base pair clone was labelled with  32  p and hybridized to a Clonetech human liver cDNA library (Clonetech Laboratories, Inc., Human Liver cDNA, Library Catalogue No. HL 10lB, Lot No. 2102). 
     The Clonetech cDNA library to human liver messenger RNA, in λGT11, was plated on LB plates at a density of 30,000 pfu, using LE192 host E. coli. Plaques were lifted in duplicate on BA85 circles, washed in 0.5N NaOH, 1.5M NaCl, then 0.5M Tris, pH 8, 1.5M NaCl, then baked 2 hours at 80° C. The filters were then prehybridized 2 hours in 6× SSC, 1× Denhardts, 100 ug/ml salmon sperm DNA at 65° C., 0.2 ml/sq.cm. 
     The 565 base pair pcTO1 insert DNA was labelled with  32  P by nick translation and hybridized overnight in 6× SSC, 1× Denhardts, 0.1% SDS, 65° C., then washed in 2× SSC, 1× Denhardts at room temperature for 30 min, then twice in 0.3× SSC, 0.5% SDS, 65° C. for 1 hour. Seventeen of the plaques that were positive on both duplicate plaque lifts were identified and replated at low density, about 100 plaques per disk, and final single plaques grown up of each positive clone. 
     Non-specific artifacts were ruled out if a positive signal (dark spot on the autoradiogram) was obtained in the same position on each duplicate lift as determined by superimposing the two autoradiograms in a slightly shifted position and examination for double spots. 
     FIG. 4, from just one of nine different dishes, depicts autoradiograms of duplicate filter lifts superimposed and turned slightly. Double spots (duplicate hybridizations) each represent presumptive human cDNA clones of human tryptophan oxygenase. The +&#39;s are orientation markers. 
     To ascertain if these presumptive clones truly represent human TO, the rat pcTO1 cDNA and one of the human cDNA clones (HTO 3 ) were sequenced, using the Sanger method. 
     The sequence of human HTO 3  clone and the translation into protein to the open reading frame are shown in FIGS. 5 and 5A, the sequence of the rat pcTO1 is shown in FIG. 6, and the region of analogy between the two is shown in FIG. 7. The fact that all 565 base pairs of the rat pcTO1 were 80% homologous with a comparable portion of the human HTO 3  sequence and that the protein sequence of the human and the rat cDNA match indicates that the human TO cDNA was isolated. The DNA sequence corresponding to that shown in FIG. 5 or any portion thereof or other regions of the gene and its surrounding DNA sequences may be synthesized in a known manner by commercially available DNA synthesis instruments. 
     The invention also includes a diagnostic technique for determining the presence or absence of defective human TO genes. Specifically, a probe having a sequence complementary to all or a unique portion of the DNA illustrated by FIG. 5 or to other portions of the TO gene and its surrounding DNA is used to determine the presence or absence of the normal human TO gene in a patient specimen such as a peripheral blood sample. The sequence presented in FIG. 5 represents the 5&#39; end of the transcribed sequences. It is likely that the most important regions for mutations causing an increased level of TO will be in the sequence immediately 5&#39; to this sequence. 
     Chromosal Location of the Human TO Gene 
     To identify the location of the human TO gene, DNA from a set of 16 Chinese hamster cell hybrids containing varying amounts of different human chromosomes was obtained from Dr. Mohandas, the Department of Medical Genetics of the University of California at Los Angeles (UCLA). These 16 samples of DNA were cut with a Puv II restriction endonuclease, electrophoresed and Southern blotted on a nylon filter. The DNA restriction fragments were then hybridized with  32  p labelled pHT03. FIG. 8 shows the results. The column labelled A.R. shows the results of the hybridization to the human DNA where ++ to ± indicates positive hybridization and--represents no hybridization. No discrepancies were observed for chromosome #4, thus indicating that the pHTO3 sequences were on chromosome #4. 
     A different set of DNA from hybrid Chinese hamster cells containing varying amounts of human chromosome #4 was obtained from Dr. John Wasmuth of the University of California at Irvine. A similar series of cutting with the restriction endonuclease Puv II, electrophoresis, Southern blotting and hybridization was performed. The results of the hybridization are depicted by FIG. 9. In the figure, the numbers 416, 582, 693, 842, 848 and 882 indicate hybrids of rodent cells with parts of human chromosome #4 shown. Inasmuch as 693, which contained only the tip of the short arm of chromosome #4 was negative, the gene for pHTO3 was not on this part of the chromosome. Since all the other hybridizations were positive but varying amounts of chromosome #4 were missing from several of these cell hybrids, FIG. 9 shows the gene to pHT03 to be on 4q between band q25 and q31. 
     To further identify the location of the human TO gene, radioactivity labelled HTO 3  was hybridized to human metaphase chromosomes by the technique of in situ hybridization. This indicated the HTO 3  gene was on chromosome band 4q 31-32. See FIG. 9.