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Title:  Gene functionally related to dyslexia
United States Patent: 
7,355,022
Issued: 
April 8, 2008

Inventors:
 Kere; Juha (Stockholm, SE), Taipale; Mikko (Heidelberg, DE), Nopola-Hemmi; Jaana (Helsinki, FI), Kaminen; Nina (Helsinki, FI)
Assignee:
  Licentia Ltd. (Helsinki, FI)
Appl. No.:
 10/681,199
Filed:
 October 9, 2003


 

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Abstract

The present invention describes a novel human gene, DYXC1, which is functionally related to dyslexia. DYXC1 gene encodes a 420-amino acid residue protein. DYXC1 is expressed in several tissues, including the brain, and is localized in the nucleus. In addition, four single nucleotide polymorphisms (SNPs) in DYXC1 mRNA have been characterized in this invention. The invention provides diagnostic methods and materials for analysing allelic variation in DYXC1 gene. This invention also provides polypeptides encoded by DYXC1 gene and antibodies binding to said polypeptides.

Description of the Invention

SUMMARY OF THE INVENTION

The present invention describes a novel human gene, DYXC1, which is causally correlated with dyslexia. The coding sequence of DYXC1 is 1260 bp in length (SEQ ID NO: 1), and it encodes a predicted protein of 420 amino acids (SEQ ID NO: 3). DYXC1 is expressed in several tissues, most abundantly in brain, lung, kidney and testis. DYXC1 protein resides in cell nuclei, and in brain, it localizes to a subset of cortical neurons and glial cells. DYXC1 protein appears rapidly upregulated and translocated after brain ischemia. The predicted 420 amino-acid protein contains three C-terminal tetratricopeptide repeat (TPR) domains, thought to mediate protein-protein interactions. Besides these domains, it bears no similarity to known proteins. Transfection and immunofluorescence studies indicate that DYXC1 is a nuclear protein.

The coding sequence of DYXC1 was predicted from the genomic sequence of BAC clones RP11-178D12 and CTD-2137J4. The length of DYXC1 mRNA is 1993 bp (SEQ ID NO: 2), and it encodes a predicted protein of 420 amino acids. DYXC1 consists of 10 exons spanning approximately 78 kb of genomic DNA (FIG. 1D, see Original Patent). The start codon (AUG) of DYXC1 is located 369 bp from the predicted transcription initiation site in exon 2. Putative promoter of DYXC1 has a TATA box (TATAAAT) at position -31.

In one aspect, the invention features isolated DYXC1 nucleic acid molecules having the sequence of SEQ ID NO:1 or a complement thereof; homologs and variants thereof as well as fragments thereof. In a preferred embodiment the isolated DYXC1 nucleic acid is mammalian. In an even more preferred embodiment the isolated DYXC1 nucleic acid is from a primate, most preferably the DYXC1 nucleic acid is human. The invention features also vectors comprising the disclosed nucleic acid as well as host cells for the expression or amplification of such vectors.

In addition, we have characterized in this invention five single nucleotide polymorphisms (SNPs) in DYXC1 mRNA. One sequence variant (1249G.fwdarw.T) introduces a premature stop codon and is inherited with dyslexia in a three-generation family. The frequency of the polymorphism is significantly (p=0.0278) elevated in dyslexic subjects, compared to control samples. The polymorphism truncates the predicted DYXC1 protein by four amino acids, suggesting that it is a functional SNP. Thus, in another aspect, the invention features nucleic acids comprising at least one single nucleotide polymorphism in any one of the following positions as defined by SEQ ID NO: 1: position 4 (C preferably to T), 572 (G preferably to A), 1249 (G preferably to T), 1259 (C preferably to G); and SEQ ID NO:2: position 205 (C preferably to T).

The invention further provides polypeptides encoded by DYXC1 gene or allelic variants thereof and antibodies binding to said polypeptides. The invention also relates to diagnostic methods, kits and materials for analysing allelic variation in DYXC1 gene and its cellular function.

DETAILED DESCRIPTION OF THE INVENTION

This invention is based on the discovery and characterization of a novel human gene termed DYXC1. The human DYXC1 gene is 1260 bp in length (SEQ ID NO: 1) and it encodes a 420-amino acid residue protein (SEQ ID NO: 3). The cDNA of total DYXC1 mRNA (SEQ ID NO:2) has been deposited in GenBank with accession number AF337549. DYXC1 maps to human chromosome 15q21. The present invention shows that previously reported balanced translocation breakpoint t(2;15)(q11;q21) segregating coincidentally with developmental dyslexia is located in DYXC1 thus indicating that DYXC1 is linked to dyslexia. In addition, it was unexpectedly discovered in the present invention that point mutations, i.e. SNPs, in DYXC1 segregate with the susceptibility to develop dyslexia.

The present invention provides DYXC1 nucleic acids, homologs thereof and fragments thereof. The human DYXC1 cDNA sequence is disclosed in SEQ ID NO: 1. Preferred homologs, such as chimpanzee (SEQ ID NO:13), pygmy chimpanzee (SEQ ID NO:19), gorilla (SEQ ID NO:15), orangutan (SEQ ID NO:17) and mouse dyxc1 (SEQ ID NO: 4), have a sequence at least about 79% homologous with a nucleotide sequence of SEQ ID NO: 1. In a preferred embodiment, the DYXC1 nucleic acid is from a mammal, e.g. a mouse, primate or human. In another preferred embodiment the nucleic acid has the sequence of SEQ ID NO: 1 a complement thereof or a fragment thereof. In one embodiment of the invention the fragment disclosed can be a primer or probe, which is capable to hybridise specifically to the DYXC1 nucleic acids described herein. The preparation and modification of primers and probes capable of binding to a known nucleic acid are well-established techniques in the art (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al, John Wiley & Sons: 1992). Generally, a primer or a probe is a substantially purified oligonucleotide being 12 to 60 nucleotides long, preferably 16 to 40 nucleotides. A primer or probe need not reflect the exact sequence of a template, i.e. a target nucleic acid, but must be sufficiently complementary to hybridise with the template under stringent conditions.

The invention also involves nucleotide sequence variants capable of encoding DYXC1 polypeptides. Such variants include sequences that differ from the disclosed DYXC1 nucleic acids by one or more nucleotide substitutions, additions or deletions, such as allelic variants. Said nucleotide substitutions may also arise due to the degeneracy of the genetic code. The nucleic acids of the invention can also be described as capable of hybridising under stringent conditions to the nucleic acid sequence of SEQ ID NO: 1 or 2 or a complement thereof. Such stringent DNA hybridisation conditions are well-known in the art, e.g. 6.times.NaCl/sodium citrate (SSC) at about 45.degree. C. is applied for a hybridisation step, followed by a wash of 2.times.SSC at 50.degree. C. or, e.g., alternatively hybridization at 42.degree. C. in 5.times.SSC, 20 mM NaPO4, pH 6.8, 50% formamide; and washing at 42.degree. C. in 0.2.times.SSC. Those skilled in the art understand that it is desirable to vary these conditions empirically based on the length and the GC nucleotide base content of the sequences to be hybridised, and that formulas for determining such variation exist (See, for example, Sambrook et al, "Molecular Cloning: A Laboratory Manual", Second Edition, pages 9.47-9.51, Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press (1989)). Nucleic acids of the invention, fragments thereof and variants thereof with sufficient similarity to the non-coding strand of said nucleic acids to hybridise thereto under stringent conditions are useful for identifying, purifying, and isolating nucleic acids encoding other, non-human, mammalian forms of DYXC1. Thus, such polynucleotide fragments and variants are intended as aspects of the invention.

The present invention also provides plasmids and vectors encoding an DYXC1 polypeptide, which constructs can be used in the expression of said DYXC1 polypeptide in or from a host cell. The selecting of a suitable plasmid or vector for a certain use is within the abilities of a skilled artisan. As the host cell may be any prokaryotic or eukaryotic cell, a plasmid or vector encoding an DYXC1 polypeptide can be used to the production of said DYXC1 polypeptide as a recombinant protein via microbial or eukaryotic cellular processes. Typically, said plasmids and vectors comprises a ligated nucleic acid encoding a recombinant protein, said nucleic acid operably linked to at least one transcriptional regulatory sequence (See, for example, Sambrook et al, "Molecular Cloning: A Laboratory Manual", Second Edition, Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press (1989)).

The present invention further describes the characterization of single nucleotide polymorphisms (SNPs) in human DYXC1 gene. SNPs can be used in mapping the human genome and, when a SNP is linked with a disease or condition, to clarify genetic basis of the disease or condition, in this particular case, at least of dyslexia. In this invention we have characterized five single nucleotide polymorphisms (SNPs) in DYXC1 mRNA (SEQ ID NOS:1 and 2). Accordingly, the present invention provides an DYXC1 nucleic acid comprising a SNP in any one of the following positions in the nucleic acid sequence of SEQ ID NO:1: position 4; 572; 1249 or 1259. Allelic variation at position 4 consists of a single base substitution from C preferably to T. Allelic variation at position 572 consists of a single base substitution from G preferably to A. Allelic variation at position 1249 consists of a single base substitution from G preferably to T. Allelic variation at position 1259 consists of a single base substitution from C preferably to G. The present invention also describes a SNP in DYXC1 mRNA at position-164 outside the coding sequence of DYXC1. This position corresponds to position 205 set forth in SEQ ID NO:2. Allelic variation at position -164 consists of a single base substitution from C preferably to T.

The SNP variant of DYXC1, wherein the single base substitution is at position 1249 (G.fwdarw.T), introduces a premature stop codon and is inherited with dyslexia in a three-generation family. The frequency of the polymorphism is significantly (p=0.0278) elevated in dyslexic subjects, compared to control samples as shown in Examples. The polymorphism truncates the predicted DYXC1 protein by four amino acids, suggesting that it is a functional SNP.

Further, new polymorphic gene regions in DYXC1 nucleic acids can be identified by determining the DYXC1 nucleic acid sequences in population of inviduals. If new polymorphic region (e.g. SNP) is found, then the link with a specific disease can be determined by studying specific populations of individuals, such as dyslexics. A polymorphic site or region may be located in any part of a gene, e.g., exons, introns and promoter region.

The present invention makes available DYXC1 polypeptides. Such polypeptides can be recombinant proteins produced by, e.g., the host cells described hereinabove, said recombinant proteins being isolated from other cellular proteins. Preferably, said polypeptides have an amino acid which is at least about 78% identical or homologous to human DYXC1 protein of sequence set forth in SEQ ID NO: 3. In a preferred embodiment, an DYXC1 polypeptide of the present invention is mammalian, e.g. murine or human, DYXC1 protein. In addition, the present invention provides splice variants of DYXC1 protein.

An DYXC1 polypeptide of the invention can also be used as an antigen to produce antibodies. Techniques of preparing antisera, poly- or monoclonal antibodies are well-known protocols in the art (see, for example, Antibodies: A laboratory Manual, eds. Harlow and Lane, Cold Spring Harbor Laboratory Press: 1988). Thus, the present invention makes available DYXC1 specific antibodies. Especially, the antibodies of the invention can be labeled with a detectable label and used in the determination of the presence of DYXC1 polypeptides in a sample, e.g. for diagnosis of dyslexia.

The present invention further provides means for prognostic or diagnostic assays for determining if a subject has or is likely to develop dyslexia, which is associated with the variation or dysfunction of DYXC1. Basically, such assays comprise a detection step, wherein the presence or absence of a genetic alteration or defect in DYXC1 is determined in a biological sample from the subject. Said detection step can be performed, e.g., by methods involving sequence analysis, nucleic acid hybridisation, primer extension, restriction enzyme site mapping or antibody binding. These methods are well-known in the art (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al, John Wiley & Sons:1992).

In particular, the present invention is directed to a method of determining the presence or absence of an DYXC1 SNP of the invention in a biological sample from a human for diagnostics of dyslexia or for assessing the predisposition of an individual to dyslexia. Said method comprises determining the sequence of the nucleic acid of a human at one or more positions 4, 572, 1249 and 1259 in the DYXC1 gene or mRNA as defined in SEQ ID NO:1 and position 205 as defined by SEQ ID NO:2 and determining the status of the human by reference to polymorphism in DYXC1 gene. In a preferred embodiment the sample is contacted with oligonucleotide primers so that the nucleic acid region containing the potential single nucleotide polymorphism is amplified by polymerase chain reaction prior to determining the sequence. The final results can be obtained by using a method selected from, e.g., allele specific nucleic acid amplification, allele specific nucleic acid hybridisation, oligonucleotide ligation assay or restriction fragment length polymorphism (RFLP). These methods are well-known for a skilled person of the art (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al, John Wiley & Sons: 1992, or Landegren et al, "Reading Bits of Genetic Information: Methods for Single-Nucleotide Polymorphism Analysis", Genome Research 8:769-776).

The invention also features diagnostic or prognostic kits for use in detecting the presence of DYXC1 SNP in a biological sample. The kit provides means for the diagnostics of dyslexia or for assessing the predisposition of an individual to dyslexia mediated by variation or dysfunction of DYXC1. The kit can comprise a labeled compound capable of detecting DYXC1 polypeptide or nucleic acid (e.g. mRNA) in a biological sample. The kit can also comprise nucleic acid primers or probes capable of hybridising specifically to at least of portion of an DYXC1 gene or allelic variant thereof. The kit can be packaged in a suitable container and preferably it contains instructions for using the kit.

It is also realised in the present invention that transgenic non-human animals, such as transgenic mice, which include a heterologous form of an DYXC1 gene, can be designed and produced utilising the disclosure presented herein (see, for example, Manipulating the Mouse Embryo: A laboratory Manual, eds. Hogan et al, Cold Spring Harbor Laboratory Press, 1986). Such transgenic animals can be useful as animal models for studying, e.g., the function of DYXC1 gene and alleles thereof, or for expressing recombinant DYXC1 polypeptides.

A further embodiment of the present invention is a method for identifying a mutant DYXC1 nucleotide sequence in a suspected mutant DYXC1 allele which comprises comparing the nucleotide sequence of the suspected mutant DYXC1 allele with a wild-type DYXC1 nucleotide sequence or a part thereof, wherein a difference between the suspected mutant and the wild-type sequence identifies a mutant DYXC1 nucleotide sequence. In said method the sequence of said suspected mutant DYXC1 allele can be compared with the sequence of one or more wild-type DYXC1 gene sequences selected from the sequences set forth in SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10 and wild-type allelic variants thereof. For the screening of new point mutations, deletion mutations and insertion mutations in DYXC1 a plentiful of techniques well-known for a skilled artisan can be utilised, such as methods involving sequence analysis, nucleic acid hybridisation, primer extension, restriction enzyme site mapping and particularly methods described below in Experimental Section and Materials and Methods.

Screening Assays

The subject methods include screens for agents which modulate the activity of DYXC1 gene or protein. The methods are amenable to automated, cost-effective high throughput screening of chemical libraries for lead compounds. Identified reagents find use in the pharmaceutical industries for animal and human trials; for example, the reagents may be derivatized and rescreened in vitro and in vivo assays to optimize activity and minimize toxicity for pharmaceutical development. More specifically, identified reagents may find use in the treatment of dyslexia or brain ischemia.

The invention further provides methods (also referred to herein as "screening assays") for identifying modulators, i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, peptoids, small molecules or other drugs) which bind to DYXC1 protein, have a stimulatory or inhibitory effect on, for example, DYXC1 expression or DYXC1 activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of a DYXC1 substrate. Compounds thus identified can be used to modulate the activity of DYXC1 in a therapeutic protocol, to elaborate the biological function of the DYXC1, or to identify compounds that disrupt normal DYXC1 activity. The preferred DYXC1 used in this embodiment are human, primate or mouse DYXC1 of the present invention.

In one embodiment, the invention provides assays for screening candidate or test compounds which are substrates of a DYXC1 protein or polypeptide or biologically active portion thereof. In another embodiment, the invention provides assays for screening candidate or test compounds which bind to or modulate the activity of a DYXC1 protein or polypeptide or biologically active portion thereof.

The test compounds of the present invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; peptoid libraries [libraries of molecules having the functionalities of peptides, but with a novel, non-peptide backbone which are resistant to enzymatic degradation but which nevertheless remain bioactive] (see, e.g., Zuckermann, R. N. et al. J. Med. Chem. 1994, 37: 2678-85); spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the `one-bead one-compound` library method; and synthetic library methods using affinity chromatography selection. The biological library and peptoid library approaches are limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, K. S. (1997) Anticancer Drug Des. 12:145).

In one embodiment, an assay is a cell-based assay in which a cell which undergoes a simulated ischaemia is contacted with a test compound and the ability of the test compound to modulate DYXC1 activity is determined. Determining the ability of the test compound to modulate DYXC1 activity can be accomplished by monitoring, for example, cell death, cell growth, cell attachment, and cell chemotaxis. The cell, for example, can be of mammalian origin, e.g., a neuronal cell or a non-neuronal cell. In preferred embodiment, the ability of the test compound to modulate DYXC1 activity is accomplished by monitoring DYXC1 activation with Western blot, immunohistochemical staining using anti DYXC1 antibodies, or fluorometric assays.

Determining the ability of DYXC1 protein or a biologically active fragment thereof, to bind to or interact with an agent can be accomplished by one of the methods described above for determining direct binding. In a preferred embodiment, determining the ability of DYXC1 protein to bind to or interact with an agent can be accomplished by determining the activity of DYXC1 protein. For example, the activity of DYXC1 can be determined by detecting the induction of a reporter gene (recombinant DYXC1 gene products labelled with detectable marker), or detecting a target-regulated cellular response (i.e., cell attachment, cell adhesion, cell growth, cell death, neurite outgrowth or cell migration).

In yet another embodiment, an assay of the present invention is a cell-free assay in which DYXC1 protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to DYXC1 protein or biologically active portion thereof is determined.

Assays for the Detection of the Ability of a Test Compound to Modulate Expression of DYXC1

In another embodiment, modulators of DYXC1 expression are identified in a method wherein a cell is contacted with a candidate compound/agent and the expression of DYXC1 mRNA or protein in the cell is determined. The level of expression of DYXC1 mRNA or protein in the presence of the candidate compound is compared to the level of expression of DYXC1 mRNA or protein in the absence of the candidate compound. The candidate compound can then be identified as a modulator of DYXC1 expression based on this comparison. For example, when the expression of DYXC1 mRNA or protein is higher (i.e. statistically significantly higher) in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of DYXC1 mRNA or protein expression. Alternatively, when expression of DYXC1 mRNA or protein is lower (i.e. statistically significantly lower) in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of DYXC1 mRNA or protein expression. The level of DYXC1 mRNA or protein expression in the cells can be determined by methods described herein for detecting DYXC1 mRNA or protein or by methods which a skilled artisan can readily adapt for use in the present invention.

Combination Assays

In another aspect, the invention pertains to a combination of two or more of the assays described herein. For example, a modulating agent can be identified using a cell-based or a cell free assay, and the ability of the agent to modulate the activity of DYXC1 protein can be confirmed in vivo, e.g., in an animal such as an animal model for brain ischemia.

This invention further pertains to novel agents identified by the above-described screening assays. Accordingly, it is within the scope of this invention to further use an agent identified as described herein in an appropriate animal model. For example, an agent identified as described herein (e.g., a DYXC1 modulating agent, an antisense DYXC1 nucleic acid molecule, a DYXC1-specific antibody, or a DYXC1-binding partner) can be used in an animal model to determine the efficacy, toxicity, or side effects of treatment with such an agent. Alternatively, an agent identified as described herein can be used in an animal model to determine the mechanism of action of such an agent. Furthermore, this invention pertains to uses of novel agents identified by the above-described screening assays for treatments as described herein.

The choice of assay format will be based primarily on the nature and type of sensitivity/resistance protein being assayed. A skilled artisan can readily adapt protein activity assays for use in the present invention with the genes identified herein.

One preferred embodiment of the invention is a screening method, wherein a compound that modulates the expression of DYXC1 is identified, the method comprising: (a) incubating a cell that can express DYXC1 gene with a compound under conditions and for a time sufficient required for the cell to express DYXC1 gene, when the compound is not present; (b) incubating a control cell under the same conditions and for the same time without the compound; (c) measuring expression of DYXC1 gene in the cell in the presence of the compound; (d) measuring expression of DYXC1 gene in the control cell; and (e) comparing the amount of expression of DYXC1 gene in the presence and absence of the compound, wherein a difference in the level of expression indicates that the compound modulates the expression of DYXC1 gene

Another preferred embodiment of the invention is a method of identifying a compound that modulates DYXC1 activity, the method comprising: (a) incubating a cell that has said activity with a compound under conditions and for a time sufficient required for the cell to express said activity, when the compound is not present; (b) incubating a control cell under the same conditions and for the same time without the compound; (c) measuring said activity in the cell in the presence of the compound; (d) measuring said activity in the control cell; and (e) comparing the amount of said acitivity in the presence and absence of the compound, wherein a difference in the level of activity indicates that the compound modulates the activity of said gene

Another preferred emdiment of the invention is a method for affinity purification of a substance that binds to the DYXC1, comprising the following steps: a) contacting a source suspected to contain said substance with an immobilized DYXC1 under conditions whereby said substance to be purified is selectively adsorbed onto the immobilized DYXC1; (b) washing the immobilized DYXC1 and its support to remove non-adsorbed material; and (c) eluting said substance from the immobilized DYXC1 to which they are adsorbed with an elution buffer.
 

Claim 1 of 7 Claims

1. An isolated, purified DYXC1 nucleic acid selected from the group consisting of: SEQ ID NO:1 or the complement of SEQ ID NO:1.

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