# Patent

## Title
Compositions and methods for diagnosing autism

## Abstract

Mutations located within the gene encoding the homeobox transcription factor, ENGRAILED 2 (EN2), have now been identified as molecular markers associated with susceptibility for autism and related disorders. Thus, the present invention relates to compositions in the form of diagnostic kits, primers and target sequences, for use in methods for determining the predisposition, the onset or the presence of autism spectrum disorder in a mammal. Moreover, therapeutic methods for treating a person inflicted with, or predisposed to, an autism spectrum disorder based upon modulating the level or activity of EN2 are also provided.

## Background
INTRODUCTION
This application claims benefit of U.S. Provisional Patent Application Ser. No. 60/721,192, filed Sep. 28, 2005, and is a continuation-in-part of PCT/US2004/021301 filed Jul. 1, 2004, which claims benefit of U.S. Provisional Patent Application Ser. No. 60/484,633, filed Jul. 3, 2003, the contents of which are incorporated herein by reference in their entirety.


This invention was supported in part by funds from the U.S. government (National Institute of Mental Health, Grant No. R01 MH70366; National Institutes of Health, Grant No. P01 ES11256; and U.S. Environmental Protection Agency, Grant No. R829391). The U.S. government may therefore have certain rights in the invention.


BACKGROUND OF THE INVENTION
Autism spectrum disorder (AS) includes three separate diagnoses, which include autism, Asperger's syndrome and Pervasive Developmental Delay (PDD). PDD is characterized by developmental delays of sociability, communication and use of imagination. Asperger's syndrome is a more severe form of PDD but lacks the language and intelligence deficits normally associated with autism. Autism is exemplified by severe communication impairments, social interaction deficits and repetitive/stereotypic behaviors. Each of these disorders has specific diagnostic criteria as outlined by the American Psychiatric Association (APA) in its Diagnostic & Statistical Manual of Mental Disorders (DSM-IV-TR).
Autism impacts the normal development of the brain in the areas of social interaction and communication skills. Children and adults with autism typically have difficulties in verbal and non-verbal communication, social interactions, and leisure or play activities.
There is no known single cause for autism, but it is generally accepted that it is caused by abnormalities in brain structure or function. Brain scans show differences in the shape and structure of the brain in autistic versus non-autistic children. Links between heredity, genetics and medical problems have been analysed. In many families, there appears to be a pattern of autism or related disabilities, further supporting a genetic basis to the disorder. While no one gene has been identified as causing autism, it appears that some children are born with a susceptibility to autism.
It has also been suggested that under certain conditions, a number of genes with altered levels or functions may interfere with brain development resulting in autism. On the other hand, certain developmental genes may be associated with autism, including the Wnt2 and reelin genes (Wassink, et al. Am. J. Med. Genet. 105:406-413 (2001); Persico, et al. Mol. Psychiatry 6:150-159 (2001)). Pregnancy or delivery as well as environmental factors such as viral infections, metabolic imbalances, and exposure to environmental chemicals have also been implicated. Autism tends to occur more frequently than expected among individuals who have certain medical conditions, including Fragile X syndrome, tuberous sclerosis, congenital rubella syndrome, and untreated phenylketonuria (PKU). Some harmful substances ingested during pregnancy also have been associated with an increased risk of autism. In 2002, The Agency for Toxic Substances and Disease Registry (ATSDR) prepared a literature review of hazardous chemical exposures and autism and found no compelling evidence for an association; however, literature in this area was limited.
The question of a relationship between vaccines and autism continues has been debated. In a 2001 investigation by the Institute of Medicine, a committee concluded that the “evidence favors rejection of a causal relationship . . . between MMR vaccines and autistic spectrum disorders (ASD).” The committee acknowledged, however, that “they could not rule out” the possibility that the MMR vaccine could contribute to ASD in a small number of children. While other researchers agree the data does not support a link between the MMR and autism.
Whatever the cause, it is clear that children with autism and PDD are born with the disorder or born with the potential to develop it. Autism is not a mental illness. Children with autism are not unruly kids who choose not to behave. Furthermore, no known psychological factors in the development of the child have been shown to cause autism.
There are no medical tests for diagnosing autism. An accurate diagnosis must be based on observation of the individual's communication, behavior, and developmental levels. However, because many of the behaviors associated with autism are shared by other disorders, various medical tests may be ordered to rule out or identify other possible causes of the symptoms being exhibited.
A brief observation in a single setting cannot present a true picture of an individual's abilities and behaviors. Parental and other caregivers' input and developmental history are very important components of making an accurate diagnosis. At first glance, some persons with autism may appear to have mental retardation, a behavior disorder, problems with hearing, or even odd and eccentric behavior. To complicate matters further, these conditions can co-occur with autism. However, it is important to distinguish autism from other conditions, since an accurate diagnosis and early identification can provide the basis for building an appropriate and effective educational and treatment program.
Research indicates that early diagnosis is associated with dramatically better outcomes for individuals with autism. The earlier a child is diagnosed, the earlier the child can begin benefiting from one of the many specialized intervention approaches.
Accordingly, what is needed is a genetic marker to assess a subject's susceptibility to autism or a disease or disorder related thereto. Also needed is a genetic marker to diagnose autism, and the development of potential drugs or agents that have applications in treating autism or a disease or disorder related thereto, such as Asperger's Disorder or PDD.
The present invention addresses the unmet need for the identification of an autism susceptibility locus and the uses for early diagnostic and prognostic purposes.
SUMMARY OF THE INVENTION
There is provided, in accordance with the present invention, an isolated nucleic acid molecule which encodes human EN2, and the amino acid sequence of human EN2. Furthermore, there is provided, in accordance with the present invention, methods for determining a subject's susceptibility to autism or a disease or disorder related thereto, such as Asperger's Disorder or PDD using a variant allele of the Engrailed (EN2 [MIM131310]) gene, which maps to chromosome 7, in particular, to 7q36.3. Furthermore, transmission/disequilibrium tests (TDT), which were performed for two single nucleotide polymorphisms (Intron A/G and Intron C/T), revealed significant overtransmission of the A allele of Intron A/G and the C allele of Intron C/T (Intron A/G P=0.0009; Intron C/T P=0.0006). Haplotype analysis indicated that the A-C haplotype is specifically overtransmitted in autistic individuals (P=0.000062). Detection of such a variant allele in the genome of a subject is considered indicative of the subject's susceptibility to autism. Furthermore, a variant allele of the Engrailed gene is also useful to assay drugs and agents for potential use in treating autism or a disease or disorder related thereto, such as Asperger's Disorder or PDD.
Accordingly, a first aspect of the invention provides for an isolated variant allele of a human Engrailed gene (EN2), wherein the Engrailed gene comprises a DNA sequence of SEQ ID NO:1, and the variant allele comprises a DNA sequence having at least one single nucleotide polymorphism, wherein the at least one variation comprises a A to G transition at position 154556629; or a C to T transition at position 154556781 or a combination thereof, and wherein said variant allele correlates with the predisposition, the onset or the presence of autism spectrum disorder in a mammal.
A second aspect of the invention provides for a diagnostic method for determining the predisposition, the onset or the presence of autism spectrum disorder in a mammal, said method comprising detecting in said mammal the existence of a change in a segment of the genome, that segment located within the portion of chromosome 7 as set forth in SEQ ID NO:1. In one embodiment, the segment comprises the human EN2 gene and is located on chromosome 7 from about position 154552000 to about position 154560000. The autism spectrum disorder may be selected from the group consisting of autism, Asperger's disorder and Pervasive Development Delay (PDD). The segment of the genome may contain a mutation, and this mutation may be a deletion, an addition and a substitution of at least one nucleotide. Furthermore, the substitution may be a single nucleotide polymorphism (SNP) located at position 154556629. This substitution may comprise a G to A transition at position 154556629. Furthermore, the substitution may be a single nucleotide polymorphism (SNP) located at position 154556781. This substitution may comprise a T to C transition at position 154556781, or the substitution may be a combination of both SNPs.
In a third aspect, the present invention provides for a detectably labelled isolated variant allele of a human EN2 gene, wherein the EN2 gene comprises a DNA sequence of SEQ ID NO:1, and the variant allele comprises a DNA sequence having at least one variation in SEQ ID NO:1, wherein the at least one variation comprises a G to A transition at position 154556629; or a T to C transition at position 154556781 or a combination thereof.
Numerous detectable labels have applications in the present invention. For example the detectable label can be a radioactive element, such as the isotopes 3H, 14C, 32P, 35S, 36Cl, 51Cr, 57Co, 58Co, 59Fe, 90Y, 125I, 131I, and 186Re, to name only a few. Chemicals which fluoresce, or enzymes such as alkaline phosphatase or horseradish peroxidase, can also be used as detectable labels.
In a fourth aspect, the invention provides for a diagnostic method for determining that a person has a genetic abnormality that predisposes that person, or his or her offspring, to autism spectrum disorder, including autism, Asperger's disorder, or PDD, wherein said genetic abnormality is found on chromosome 7, said method comprising detecting, in that person, the existence of a change in a segment of the genome, that segment located within the portion of chromosome 7 as set forth in SEQ ID NO:1. The segment comprises the human EN2 gene which is located on chromosome 7 from about position 154552000 to about position 154560000, said segment having the sequence set forth is SEQ ID NO:1. The person diagnosed may not be autistic (i.e., may not exhibit any autistic symptoms or behaviors), however, if the person diagnosed has the genetic abnormality that predisposes that person to autism, then this diagnosis signifies that the person diagnosed could bear children who are predisposed to autism. The determination can be made before the person is born, as early as the blastocyst stage of embryonic development and throughout the fetal stage, or at any time after the person is born. It is sufficient that the abnormality occur in one chromosome of a person; i.e., the person can be heterozygous as regards the abnormality. In a specific embodiment, the invention provides for a method for determining whether a person has a genetic abnormality that predisposes such person to autism spectrum disorder, said method comprising examining chromosome 7 of said person, and detecting, where present, the existence of a change in a segment of the genome located in said chromosome 7, wherein said segment is set forth in SEQ ID NO:1.
The diagnostic method involves detecting changes in the Engrailed (EN2) gene. Changes (or mutations) are additions, deletions, or substitutions of at least one nucleotide. Thus, in one embodiment, the diagnostic method comprises detecting a change in a region of chromosome 7 spanning the EN2 gene. In the context of this application, the EN2 gene means the sequence necessary for transcription and translation such that normal levels of functional EN2 protein are generated. The substitution may be a single nucleotide polymorphism (SNP) located at position 154556629, and the substitution may consist of a guanine (G) to adenine (A) transition. Alternatively, the substitution may be a single nucleotide polymorphism (SNP) located at position 154556781 and may consist of a thymine (T) to cytosine (C) transition. In addition, since cis-regulatory regions needed for EN2 expression can be, for example, as far as 1000 kb away from the coding sequence of the gene, the EN2 gene also means a region on human Chromosome 7 of approximately 154010087-155102101 base pairs and encompasses the EN2 coding region (approximately 8000 base pairs) and flanking sequence.
In another embodiment, a diagnostic method useful for determining that a person has a genetic abnormality that predisposes that person to autism spectrum disorder is envisioned, said method comprising detecting in that person the existence of a mutation in the EN2 gene such that said mutation results in the deletion, addition, or substitution of at least one amino acid in the EN2 protein.
Another embodiment of the EN2 gene are the single nucleotide polymorphisms (SNPs) comprising a region amplifiable by polymerase chain reaction, wherein said region is amplified using a primer pair, wherein a primer is selected from the group consisting of the sequences set forth is SEQ ID NOs: 3, 4, 5, 6, 7, 8, 9 and 10. Accordingly, part of this invention is a diagnostic method for determining that a person has a genetic abnormality that predisposes that person to autism, said method comprising detecting, in that person, the existence of a change, i.e., a deletion, an addition or a substitution in a segment of the genome, that sequence located within the portion of chromosome 7 set forth in SEQ ID NO:1 (the EN2 gene), and amplifying portions of that sequence containing the SNPs identified herein, using primer pairs selected from the group consisting of the sequences set forth is SEQ ID NOs: 3, 4, 5, 6, 7, 8, 9 and 10.
Primer sequences that flank the EN2 transcript (i.e., the coding region) on chromosome 7 are:
Intron 1 A/G (rs1861972), Forward outer 5′-TGA AGC TGG GGC CAG ATG CTC CTA-3′ (SEQ ID NO:3), Reverse outer 5′-CAT GGG GAA AGG GCA GAG GGA GGA G-3′ (SEQ ID NO:4), Forward inner 5′-AGG CGA GGT CAC CAC TCC CTG CAA G-3′ (SEQ ID NO:5) and Reverse inner 5′-GGG GGA AGA AGG GGG CAA GGC AAT-3′ (SEQ ID NO:6), as well as those exemplified in Example 2;
Intron 2 C/T (rs1867973), Forward outer 5′-GCC AGG GGG TTG AGC CTC TTA T-3′ (SEQ ID NO:7), Reverse outer 5′-CAG GTC CAC TTC TGA CCC TC-3′ (SEQ ID NO:8), Forward inner 5′-GAA GCC TTA CAG CGA CCC GGT-3′ (SEQ ID NO:9) and Reverse inner 5′-GAC CTG CCC CAG GTT TTT GG-3′ (SEQ ID NO:10), as well as those exemplified in Example 2.
Within that region is the coding region of the EN2 gene. One or more single nucleotide polymorphisms (SNPs) in the EN2 gene are a preferred indicator of a predisposition to autism. Such SNPs may occur anywhere in the EN2 gene as defined above. Alternatively, a deletion in the coding region would affect the sequence of the expressed protein. A deletion in the 5′ or 3′ noncoding region would affect expression levels or RNA stability. A deletion 5′ or 3′ of the exons that encode EN2 mRNA would affect expression levels by perturbing the promoter or enhancers. Any of these deletions may have an impact on the expression product of the EN2 gene and consequently cause predisposition to autism.
Any deleted segment of one or more bases in size is diagnostically significant. Accordingly, a deletion of a single nucleotide is diagnostically significant, in particular this or any deletion that changes the function, activity, or expression levels of the EN2 protein. The deletion can be as large as a deletion of the entire en2 gene, or any portion of it.
In a fifth aspect, this invention comprises other changes (meaning in general mutations, but including any possible difference in the sequence of the gene from the wild-type) in the en2 gene as defined above. In addition to deletions as discussed above, these changes may involve additions or substitutions (by which is meant replacement of a given nucleotide or amino acid by another nucleotide or amino acid). The size or extent of the addition or substitution may be one nucleotide, to any size or extent which changes or disrupts EN2 expression as described above. Any one, two, or three of these changes, or mutations, may occur in one individual. Particular changes, or mutations, of interest are those that alter the function, activity, or expression levels of the EN2 protein. These additions or substitutions may be in the coding region, and thus would affect the expressed EN2 protein as described immediately below. The additions or substitutions may also be in the 5′ or 3′ noncoding region, in the introns, and accordingly would affect protein expression equivalently to the effect of deletions in these regions as described immediately above. Additions or substitutions in the areas spanned by the sequence pairs provided above are particularly of interest. Accordingly, part of this invention is a diagnostic method for determining that a person has a genetic abnormality that predisposes that person to autism said method comprising detecting, in that person, the existence of an addition or deletion of at least one nucleotide to a segment of the genome, that segment located within the portion of chromosome 7 as set forth is SEQ ID NO:1, or comprising detecting, in that person, the existence of a substitution of at least one nucleotide for another nucleotide in a segment of the genome, that segment located within the portion of chromosome 7 as set forth in SEQ ID NO:1. Such changes (i.e., deletions, additions, or substitutions) affect EN2 function, since they occur in some segment of the en2 gene.
Further, of particular interest are diagnostic methods where the changes (deletions, additions, or substitutions) are detected within the portion of chromosome 7, in an intron, or in a segment of an en2 gene, defined by the sequences selected from the group consisting of SEQ ID NOs:3, 4, 5, 6, 7, 8, 9, and 10, as well as those exemplified in Example 2.
In an alternative aspect, the invention comprises detecting a mutation in an exon, in any chromosome region or segment specified above providing the mutation results in a change in an amino acid in the protein coded for. Thus, the invention comprises detecting the existence of a mutation in the en2 gene such that the mutation results in the deletion, addition, or substitution of at least one amino acid in the EN2 protein.
In a related aspect, the invention comprises detecting deletions or mutations in the proteins coded for by the segments specified above, especially the EN2 protein (SEQ ID NO:2). Thus the invention comprises detecting a change with respect to at least one amino acid in, for example, the EN2 protein, which change can be one or more additions, deletions, or substitutions, or a combination thereof (the protein in question maintains its identity by virtue of being encoded by the locus which encodes that protein, for example even if there are multiple changes in the EN2 protein, it is still considered the EN2 protein in the context of this invention as it is encoded by the en2 gene).
In a sixth aspect, the invention provides for a diagnostic method for -determining a subject's susceptibility to autism or a related disorder, comprising measuring the presence or absence of the A allele of intron A/G and/or the presence or absence of the C allele of intron C/T.
In a seventh aspect, the invention provides for a diagnostic method comprising detecting, in tissue or cells from a person, an increase or a decrease in the level of normal RNA (mRNA and/or hnRNA) transcribed from a region of SEQ ID NO:1, for example those segments specified by the sequences set forth above. By normal RNA is meant RNA which encodes a protein which does not have an addition, deletion, or substitution, a wild-type protein, in particular which encodes such a protein which is an EN2 protein. Thus, in another aspect the diagnostic method comprises detecting abnormal RNA, which means RNA that is longer than normal RNA (i.e., has at least one addition), shorter than normal RNA (i.e., has at least one deletion), or is different than normal RNA (i.e., has at least one substitution, or has an equal number of deletions and additions).
One embodiment provides methods for diagnosing autism and/or Asperger's disorder and/or PDD and clinically related conditions. One embodiment includes the use of the genes or gene products identified by the methods described herein, including but not limited to those genes and gene products identified through use of a mammalian model of autism. In a particular embodiment, the gene useful for diagnosis of autism, Asperger's or PDD and other clinically related conditions includes the gene identified in the nucleic acid of SEQ ID NO:1 (EN2).
Another particular embodiment includes the use of the gene products, in particular, the protein identified by the methods described herein, including but not limited to the gene product identified as the protein of SEQ ID NO:2.
A further aspect of the invention provides a method of determining if a subject is at risk for developing autism and/or Asperger's and/or PDD, said method comprising:
(I) measuring an amount of an EN2 gene or gene product in a tissue sample derived from the subject, wherein said gene or gene product is:

    
    
        (a) a DNA corresponding to SEQ ID NO:1, or a nucleic acid derived therefrom;
        (b) a protein comprising SEQ ID NO:2;
        (c) a nucleic acid comprising a sequence hybridizable to SEQ ID NO:1, or its complement under conditions of high stringency, or a protein comprising a sequence encoded by said hybridizable sequence;
        (d) a nucleic acid at least 90% homologous to SEQ ID NO:1, or its complement as determined using the NBLAST algorithm; or a protein encoded thereby; and
    
    


(II) comparing the amount of said gene product in the subject with the amount of gene product present in a normal tissue sample (taken from a non-autistic individual) or predetermined standard for a normal tissue sample, wherein an elevated amount of said gene product in the subject compared to the amount in the normal tissue sample or pre-determined standard for a normal tissue sample indicates a risk of developing autism and/or Asperger's and/or PDD in the subject.
A further aspect of the invention provides a method for screening, diagnosis or prognosis of AS selected from the group consisting of autism, Asperger's and PDD, said method comprising:
(I) measuring an amount of an EN2 gene or gene product in a tissue sample derived from the subject, wherein said gene or gene product is:

    
    
        (a) a DNA corresponding to SEQ ID NO:1, or a nucleic acid derived therefrom;
        (b) a protein comprising SEQ ID NO:2;
        (c) a nucleic acid comprising a sequence hybridizable to SEQ ID NO:1, or its complement under conditions of high stringency, or a protein comprising a sequence encoded by said hybridizable sequence;
        (d) a nucleic acid at least 90% homologous to SEQ ID NO:1, or its complement as determined using the NBLAST algorithm; or a protein encoded thereby; and
    
    


(II) comparing the amount of said gene product in the subject with the amount of EN2 gene product present in a non-autistic tissue sample or predetermined standard for a non-autistic tissue sample, wherein an elevated amount of said EN2 gene product in the subject compared to the amount in the non-autistic tissue sample or pre-determined standard for a non-autistic tissue sample indicates a risk of developing autism and/or Asperger's and/or PDD in the subject.
In another embodiment, the diagnostic method comprises detecting, in tissue or cells from a person, an increase or a decrease in the level of normal EN2 protein, for example, protein coded for a by region of chromosome 7 set forth as SEQ ID NO:1, in particular a segment, or region specified above, for example those segments specified by the sequences set forth above. By normal protein is meant a protein which does not have an addition, deletion, or substitution, a wild-type protein, in particular an EN2 protein. Thus in another aspect the diagnostic method comprises detecting abnormal protein, which means a protein that is longer than the normal protein (i.e., has at least one addition), shorter than the normal protein (i.e., has at least one deletion), or different than the normal protein (i.e., has at least one substitution, or has an equal number of deletions and additions).
Overexpression of EN2 protein may also indicate autism or predisposition to autism. Accordingly, in yet another aspect, the diagnostic method comprises detecting, in tissues or cells from a person, an increased level of normal RNA transcribed from a region of chromosome 7 set forth is SEQ ID NO:1, in particular a segment, or region, for example those segments specified by the sequences set forth above.
In a related protein-based assay, the diagnostic method comprises detecting, in tissue or cells from a person, an increased level of normal EN2 protein, for example, protein coded for a by a region of chromosome 7 set forth in SEQ ID NO:1, in particular a segment, or region, for example, those segments specified by the sequences set forth above.
By increased or decreased levels of RNA or protein is meant levels that differ from levels found in a normal person with no predisposition to autism. Accordingly, the normal level of RNA or protein may be determined by measuring RNA or protein levels from a sufficiently large sample of the normal population (about N=100 or greater). Since there will be a certain amount of variability, conventional statistical analysis may be used to establish a mean for the normal level of RNA or protein. An increased level of RNA or protein is a level which is significantly higher than the mean normal level by statistical analysis. A decreased level of RNA or protein is a level which is significantly lower than the mean normal level by statistical analysis. For example, a level of 10% higher or lower than normal may be considered an increased or decreased level of RNA or protein.
In an eighth aspect, the invention provides for a diagnostic kit, comprising a nucleic acid hybridization probe specific for part or all of a region of the gene encoding en2, or a segment thereof. Alternatively, the kit comprises PCR primers that can be used to amplify part of a chromosome that falls within a region so specified (e.g., chromosome 7). In particular, such kits contain the PCR primers specified above, suitably paired. In another embodiment, the kit is a protein-based kit comprising an antibody probe specific for all or part of the EN2 protein.
In a ninth aspect, the invention extends to an antibody that recognizes and binds to the amino acid sequence of SEQ ID NO:2, encoded by the normal EN2 nucleic acid sequence and/or the nucleic acid sequence of SEQ ID NO:1, which contains the A allele of intron A/G located at position 154556629 and/or the C allele of intron C/T located at position 154556781 of chromosome 7, conservative variants thereof, fragments thereof, or analogs or derivatives thereof, as an immunogen. Such an antibody can be polyclonal, monoclonal, single chain, or chimeric. They may be human, mouse, rat, rabbit, goat, horse, sheep or may be obtained from other non-human animals. Further, an antibody of the invention having human EN2 as an immunogen can be detectably labelled. As explained above, examples of detectable labels having applications herein include, but certainly are not limited to radioactive isotopes, such as 3H, 14C, 32P, 35S, 36Cl, 51Cr, 57Co, 58Co, 59Fe, 90Y, 125I, 131I, and 186Re, to name only a few. Chemicals which fluoresce, or enzymes such as alkaline phosphatase or horseradish peroxidase, can also be used as detectable labels. These antibodies may be utilized for diagnostic or therapeutic purposes.
In a tenth aspect, the invention provides for a method of treating a subject with autism or an autism related disorder such as Asperger's or PDD, or a person predisposed to a developmental disorder (especially autism), the method comprising either administering a gene or a protein to the person. In one embodiment, the method of treating a subject comprises the step of introducing a DNA molecule coding for a polypeptide normally coded for (e.g., in non-autistic patients) by a gene located within the chromosome 7 region set forth is SEQ ID NO:1. In one embodiment, the polypeptide is the EN2 protein. In another embodiment, the disorder is autism.
In certain embodiments, the DNA molecule is introduced into a cell and the cell is administered to the person (postnatal or prenatal). The cell may, for example, be a stem cell. The stem cell into which a DNA molecule is introduced for therapeutic purposes is preferably a stem cell isolated from the person who will receive the stem cell containing the DNA molecule encoding the EN2 protein. The stem cell can, for example, be obtained from that person's bone marrow. Alternatively, the stem cell can be obtained from another person. An additional alternative is that the stem cell be obtained from an animal, especially a mammal.
In another embodiment, the therapeutic process comprises the step of introducing the EN2 protein into a person.
In another embodiment, the therapeutic process comprises the step of administering a drug to a person so as to normalize (i.e., increase or decrease to normal levels) the level of EN2 protein in a tissue in said person.
In another embodiment, the therapeutic process comprises the step of administering a drug so as to normalize (i.e., increase or decrease to normal levels) the level of genes that are activated by EN2 protein.
Any of these therapeutic processes may be used in particular to treat autism or a predisposition to autism or an autism related disorder such as Asperger's or PDD.
An eleventh aspect of the present invention provides pharmaceutical compositions comprising a therapeutically effective amount of the genes or gene products of the present invention including, but not limited to, the nucleic acid of SEQ ID NO:1 or the protein of SEQ ID NO:2, with a pharmaceutically acceptable carrier for delivery to an individual in need of such therapy. Included in this aspect of the invention are agonists or antagonists of the gene or gene products identified herein. Such agonists or antagonists may be small synthetic organic molecules, proteins, peptides, polypeptides or antibodies. A further embodiment comprises a therapeutically effective amount of an agent that modulates the expression and/or activity of the EN2 gene or gene product and a pharmaceutically acceptable carrier. The pharmaceutical compositions may be delivered orally, intravenously, intramuscularly, subcutaneously. intrathecally, intracranially. They may be in the form of tablets, capsules, suspensions, suppositories or in liquid form suitable for intravenous delivery.
Other objects and advantages will become apparent from a review of the ensuing detailed description and attendant claims. All references cited in the present application are incorporated herein in their entirety.


DETAILED DESCRIPTION OF THE INVENTION
As will be appreciated by one of skill in the art, the present invention is not to be limited to particular methods, and experimental conditions described, as such methods and conditions may vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only in the appended claims.
As used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, references to “the method” includes one or more methods, and/or steps of the type described herein and/or which will become apparent to those persons skilled in the art upon reading this disclosure and so forth.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the invention, the preferred methods and materials are now described.
The terms used herein have the meanings recognized and known to those of skill in the art, however, for convenience and completeness, particular terms and their meanings are set forth below.
“Treatment” refers to the administration of medicine or the performance of medical procedures with respect to a patient, for either prophylaxis (prevention) or to cure the infirmity or malady in the instance where the patient is afflicted.
A “therapeutically effective amount” is an amount sufficient to decrease or prevent the symptoms associated with autism associated with the presence of at least one of the SNPs identified in the presence invention.
The term “antibody” as used herein includes intact molecules as well as fragments thereof, such as Fab and F(ab′)2, which are capable of binding the epitopic determinant. Antibodies that bind EN2 can be prepared using intact polypeptides or fragments containing small peptides of interest as the immunizing antigen attached to a carrier molecule. Commonly used carriers that are chemically coupled to peptides include bovine serum albumin and thyroglobulin. The coupled peptide is then used to immunize the animal (e.g., a mouse, rat or rabbit).
“Gene Product” as used herein, unless otherwise indicated, is a protein or polypeptide encoded by the nucleic acid sequences identified by the methods of the present invention, including but not limited to SEQ ID NO:1; a nucleic acid comprising a sequence hybridizable to SEQ ID NO:1 or its complement under conditions of high stringency, or a protein comprising a sequence encoded by said hybridizable sequence; a nucleic acid at least 90% homologous to SEQ ID NO:1 or its complement as determined using the NBLAST algorithm; a nucleic acid at least 90% homologous to SEQ ID NO:1 or a fragment or derivative of any of the foregoing proteins or nucleic acids.
A “variant” (v) of polynucleotides or polypeptides, as the term is used herein, are polynucleotides or polypeptides that are different from a reference polynucleotide or polypeptide, respectively. Variant polynucleotides are generally limited so that the nucleotide sequence of the reference and the variant are closely related overall and, in many regions, identical. Changes in the nucleotide sequence of the variant may be silent. That is, they may not alter the amino acid sequence encoded by the polynucleotide. Where alterations are limited to silent changes of this type a variant will encode a polypeptide with the same amino acid sequence as the reference. However, silent variants can affect protein levels by codon use. Thus, in this particular situation, different tRNAs may vary in abundance so that even though the change is silent, it may still be functionally important. Alternatively, changes in the nucleotide sequence of the variant may alter the amino acid sequence of a polypeptide encoded by the reference polynucleotide. Such nucleotide changes may result in amino acid substitutions, additions, deletions, fusions, and truncations in the polypeptide encoded by the reference sequence. Variant polypeptides are generally limited so that the sequences of the reference and the variant are that are closely similar overall and, in many regions, identical. For example, a variant and reference polypeptide may differ in amino acid sequence by one or more substitutions, additions, deletions, fusions, and truncations, which may be present or absent in any combination. Such variants can differ in their amino acid composition (e.g., as a result of allelic or natural variation in the amino acid sequence, e.g., as a result of alternative mRNA or pre-mRNA processing, e.g. alternative splicing or limited proteolysis) and in addition, or in the alternative, may arise from differential post-translational modification (e.g., glycosylation, acylation, phosphorylation, isoprenylation, lipidation).
“Analog” as used herein, refers to a nucleotide, a protein, or a polypeptide that possesses similar or identical activity or function(s) as the nucleotide, protein or polypeptide having the desired activity and therapeutic effect of the present invention (e.g., diagnostic method for determining the predisposition, the onset or the presence of autism spectrum disorder in a mammal), but need not necessarily comprise a sequence that is similar or identical to the sequence of the preferred embodiment, such as that of SEQ ID NOs: 1 and 2, or possess a structure that is similar or identical to that of SEQ ID NOs: 1 and 2. As used herein, a nucleic acid or nucleotide sequence, or an amino acid sequence of a protein or polypeptide is “similar” to that of a nucleic acid, nucleotide or protein or polypeptide having the desired activity if it satisfies at least one of the following criteria: (a) the nucleic acid, nucleotide, protein or polypeptide has a sequence that is at least 30% (more preferably, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99%) identical to the nucleic acid, nucleotide, protein or polypeptide sequences having the desired activity as described herein (b) the polypeptide is encoded by a nucleotide sequence that hybridizes under stringent conditions to a nucleotide sequence encoding at least 5 amino acid residues (more preferably, at least 10 amino acid residues, at least 15 amino acid residues, at least 20 amino acid residues, at least 25 amino acid residues, at least 40 amino acid residues, at least 50 amino acid residues, at least 60 amino residues, at least 70 amino acid residues, at least 80 amino acid residues, at least 90 amino acid residues, at least 100 amino acid residues, at least 125 amino acid residues, or at least 150 amino acid residues) of the AAPI; or (c) the polypeptide is encoded by a nucleotide sequence that is at least 30% (more preferably, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99%) identical to the nucleotide sequence encoding the polypeptides of the present invention having the desired therapeutic effect. As used herein, a polypeptide with “similar structure” to that of the preferred embodiments of the invention refers to a polypeptide that has a similar secondary, tertiary or quarternary structure as that of the preferred embodiment (e.g., SEQ ID NO:2). The structure of a polypeptide can determined by methods known to those skilled in the art, including but not limited to, X-ray crystallography, nuclear magnetic resonance, and crystallographic electron microscopy.
“Derivative” refers to either a protein or polypeptide that comprises an amino acid sequence of a parent protein or polypeptide that has been altered by the introduction of amino acid residue substitutions, deletions or additions, or a nucleic acid or nucleotide that has been modified by either introduction of nucleotide substitutions or deletions, additions or mutations. The derivative nucleic acid, nucleotide, protein or polypeptide possesses a similar or identical function as the parent polypeptide.
“Fragment” refers to either a protein or polypeptide comprising an amino acid sequence of at least 5 amino acid residues (preferably, at least 10 amino acid residues, at least 15 amino acid residues, at least 20 amino acid residues, at least 25 amino acid residues, at least 40 amino acid residues, at least 50 amino acid residues, at least 60 amino residues, at least 70 amino acid residues, at least 80 amino acid residues, at least 90 amino acid residues, at least 100 amino acid residues, at least 125 amino acid residues, at least 150 amino acid residues, at least 175 amino acid residues, at least 200 amino acid residues, or at least 250 amino acid residues) of the amino acid sequence of a parent protein or polypeptide, or a nucleic acid comprising a nucleotide sequence of at least 10 base pairs (preferably at least 20 base pairs, at least 30 base pairs, at least 40 base pairs, at least 50 base pairs, at least 50 base pairs, at least 100 base pairs, at least 200 base pairs) of the nucleotide sequence of the parent nucleic acid. Any given fragment may or may not possess a functional activity of the parent nucleic acid or protein or polypeptide.
“Modulate” as used herein, refers to a compound or agent (including but not limited to proteins, polypeptides, or fragments thereof, nucleotides, nucleic acid fragments, synthetic organic compounds, antibodies) which are capable of increasing or decreasing the level and/or activity of a gene or gene product identified by the methods described herein, said genes or gene products having a beneficial effect in treating autism and/or Asperger's and/or PDD. Those skilled in the art, based on the present description, will understand that such modulation can be determined by assays and techniques known to those of skill in the art, including as described in more detail herein.
“Diagnosis” refers to diagnosis, prognosis, monitoring, characterizing, selecting patients, including participants in clinical trials, and identifying patients at risk for or having a particular disorder or clinical event or those most likely to respond to a particular therapeutic treatment, or for assessing or monitoring a patient's response to a particular therapeutic treatment.
As used herein, “detecting a target nucleic acid sequence” refers to determining the presence of a particular target nucleic acid sequence in a sample or determining the amount of a particular target nucleic acid sequence in a sample as an indication of the presence of a target nucleic acid sequence in a sample. The amount of a target nucleic acid sequence that can be measured or detected is preferably about 1 molecule to 1020 molecules, more preferably about 100 molecules to 1017 molecules and most preferably about 1000 molecules to 1014 molecules. Preferably there is a direct correlation between the amount of the target nucleic acid sequence and the signal generated by the detected nucleic acid.
As used herein, an “oligonucleotide primer” refers to a single stranded DNA or RNA molecule that is hybridizable (e.g., capable of annealing) to a nucleic acid template and is capable of priming enzymatic synthesis of a second nucleic acid strand. Alternatively, or in addition, oligonucleotide primers, when labeled directly or indirectly (e.g., bound by a labeled secondary probe which is specific for the oligonucleotide primer) may be used effectively as probes to detect the presence of a specific nucleic acid in a sample. Oligonucleotide primers useful according to the invention are between about 10 to 100 nucleotides in length, preferably about 17-50 nucleotides in length and more preferably about 17-40 nucleotides in length and more preferably about 17-30 nucleotides in length. Oligonucleotide probes useful for the formation of a cleavage structure according to the invention are between about 17-40 nucleotides in length, preferably about 17-30 nucleotides in length and more preferably about 17-25 nucleotides in length. The term “primer” can refer to more than one primer and generally refers to an oligonucleotide, whether occurring naturally, as in a purified restriction digest, or produced synthetically, which is capable of acting as a point of initiation of DNA synthesis when annealed to a nucleic acid template and placed under conditions in which synthesis of a primer extension product which is complementary to the template is catalyzed. Such conditions include the presence of four different deoxyribonucleoside triphosphates and a polymerization-inducing agent such as a DNA polymerase or reverse transcriptase, in a suitable buffer (“buffer” includes substituents which are cofactors, or which affect pH, ionic strength, etc.), and at a suitable temperature. The primer is preferably single-stranded for maximum efficiency in amplification.
As used herein, “amplifying” refers to the generation of additional copies of a nucleic acid sequence. A variety of methods have been developed to amplify nucleic acid sequences, including the polymerase chain reaction (PCR). PCR amplification of a nucleic acid sequence generally results in the exponential amplification of a nucleic acid sequence(s) and or fragments thereof. An “amplified” nucleic acid molecule (or portion thereof) refers to the fact that multiple copies of that molecule or a molecule of complementary base sequence have been made.
By “homologous” is meant a same sense nucleic acid which possesses a level of similarity with the target nucleic acid within reason and within standards known and accepted in the art. With regard to PCR, the term “homologous” may be used to refer to an amplicon that exhibits a high level of nucleic acid similarity to another nucleic acid, e.g., the template cDNA. As is understood in the art, enzymatic transcription has measurable and well known error rates (depending on the specific enzyme used), thus within the limits of transcriptional accuracy using the modes described herein, in that a skilled practitioner would understand that fidelity of enzymatic complementary strand synthesis is not absolute and that the amplified nucleic acid (i.e., amplicon) need not be completely identical in every nucleotide to the template nucleic acid.
“Complementary” is understood in its recognized meaning as identifying a nucleotide in one sequence that hybridizes (anneals) to a nucleotide in another sequence according to the rule A→T/U and C→G (and vice versa) and thus “matches” its partner for purposes of this definition. Enzymatic transcription has measurable and well known error rates (depending on the specific enzyme used), thus within the limits of transcriptional accuracy using the modes described herein, in that a skilled practitioner would understand that fidelity of enzymatic complementary strand synthesis is not absolute and that the amplicon need not be completely matched in every nucleotide to the target or template RNA.
As used herein, the terms “nucleic acid”, “polynucleotide” and “oligonucleotide” refer to primers, probes, and oligomer fragments to be detected, and shall be generic to polydeoxyribonucleotides (containing 2-deoxy-D-ribose), to polyribonucleotides (containing D-ribose), and to any other type of polynucleotide which is an N-glycoside of a purine or pyrimidine base, or modified purine or pyrimidine bases (including abasic sites). There is no intended distinction in length between the term “nucleic acid”, “polynucleotide” and “oligonucleotide”, and these terms will be used interchangeably. These terms refer only to the primary structure of the molecule. Thus, these terms include double- and single-stranded DNA, as well as double- and single-stranded RNA.
The “polymerase chain reaction (PCR)” technique, is disclosed in U.S. Pat. Nos. 4,683,202; 4,683,195 and 4,800,159. In its simplest form, PCR is an in vitro method for the enzymatic synthesis of specific DNA sequences, using two oligonucleotide primers that hybridize to opposite strands and flank the region of interest in the target DNA. A repetitive series of reaction steps involving template denaturation, primer annealing and the extension of the annealed primers by DNA polymerase results in the exponential accumulation of a specific fragment (i.e., an amplicon) whose termini are defined by the 5′ ends of the primers. PCR is reported to be capable of producing a selective enrichment of a specific DNA sequence by a factor of 109. The PCR method is also described in Saiki, et al. ((1985) Science 230:1350).
As used herein, “probe” refers to a labeled oligonucleotide primer, which forms a duplex structure with a sequence in the target nucleic acid, due to complementarity of at least one sequence in the probe with a sequence in the target region. Such probes are useful for identification of a target nucleic acid sequence for EN2 according to the invention. Pairs of single-stranded DNA primers can be annealed to sequences within a target nucleic acid sequence or can be used to prime DNA synthesis of a target nucleic acid sequence.
By “genetic abnormality” is meant any change in a nucleic acid sequence which may predispose a person to autism, or Asperger's or PDD. The change is determined using standard techniques in the art and a comparison is made to a known sequence obtained from a normal individual known to be free of autism, Asperger's or PDD. Such changes may include mutations and may be deletions, additions or substitutions in at least one base pair of the sequence.
“kD” stands for kilodalton.
Code-wise degenerate means that a base of a codon is changed without changing the amino acid that the codon codes for.
A “coding sequence” or a “coding region” of a nucleic acid for a designated protein refers to a region in an mRNA molecule that contains the base sequence which is translated into an amino acid sequence (i.e., that encodes that amino acid sequence), it covers any DNA or RNA sequence that is complementary in base sequence to such an mRNA sequence, it covers any DNA sequence that is the same as such an mRNA sequence (except that T is used in place of U) and, in the case of a DNA sequence that alternates introns with exons so that the sequence can be processed to make an mRNA molecule, “coding sequence” or “coding region” covers the populations of coding exons that determine the amino acid coding region of the mRNA molecule (i.e., that encode that amino acid sequence).
By way of example and not limitation, procedures using such conditions of low stringency are as follows (see also Shilo and Weinberg (1981) Proc. Natl. Acad. Sci. USA 78:6789-6792). Filters containing DNA are pretreated for 6 hours at 40° C. in a solution containing 35% formamide, 5×SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.1% polyvinylpyrrolidone (PVP), 0.1% FICOLLTM, 1% bovine serum albumin (BSA), and 500 μg/ml denatured salmon sperm DNA. Hybridizations are carried out in the same solution with the following modifications: 0.02% PVP, 0.02% FICOLLTM, 0.2% BSA, 100 μg/ml salmon sperm DNA, 10% (wt/vol) dextran sulfate, and 5-20×106 cpm 32P-labeled probe is used. Filters are incubated in hybridization mixture for 18-20 hours at 40° C., and then washed for 1.5 hours at 55° C. in a solution containing 2×SSC, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1% SDS. The wash solution is replaced with fresh solution and incubated an additional 1.5 hours at 60° C. Filters are blotted dry and exposed for autoradiography. If necessary, filters are washed for a third time at 65-68° C. and re-exposed to film. Other conditions of low stringency that may be used are well-known in the art (e.g., as employed for cross-species hybridizations).
Procedures using such conditions of moderate stringency are as follows: filters comprising immobilized DNA are pretreated for 6 hours at 55° C. in a solution containing 6×SSC, 5× Denhardt's solution, 0.5% SDS and 100 μg/ml denatured salmon sperm DNA. Hybridizations are carried out in the same solution with 5-20×106 cpm 32P-labeled probe. Filters are incubated in hybridization mixture for 18-20 hours at 55° C., and then washed twice for 30 minutes at 60° C. in a solution containing 1×SSC and 0.1% SDS. Filters are blotted dry and exposed for autoradiography. Washing of filters is done at 37° C. for 1 hour in a solution containing 2×SSC, 0.1% SDS. Other conditions of moderate stringency that may be used are well-known in the art. See, e.g., Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, 2d Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Ausubel et al., eds., in the Current Protocols in Molecular Biology series of laboratory technique manuals, 1987-1997 Current Protocols, © 1994-1997 John Wiley and Sons, Inc.
Procedures using such conditions of high stringency are as follows. Prehybridization of filters containing DNA is carried out for 8 hours to overnight at 65° C. in buffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% FICOLLTM, 0.02% BSA, and 500 μg/ml denatured salmon sperm DNA. Filters are hybridized for 48 hours at 65° C. in prehybridization mixture containing 100 μg/ml denatured salmon sperm DNA and 5-20×106 cpm of 32P-labeled probe. Washing of filters is done at 37° C. for 1 hour in a solution containing 2×SSC, 0.01% PVP, 0.01% FICOLLTM, and 0.01% BSA. This is followed by a wash in 0.1×SSC at 50° C. for 45 minutes before autoradiography. Other conditions of high stringency that may be used are well-known in the art.
An RNA base sequence (or molecule) is equivalent to a DNA base sequence (or molecule) if they are identical except that U in the RNA base sequence replaced T in the DNA base sequence.
The following one letter codes are used to represent amino acids: S-serine, T-threonine, N-asparagine, Q-glutamine, K-lysine, R-arginine, H-histidine, E-glutamic acid, D-aspartic acid, C-cystine, G-glycine, P-proline, A-alanine, I-isoleucine, L-leucine, M-methionine, F-phenylalanine, W-tryptophan, V-valine, Y-tyrosine, X-any amino acid.
The following one letter codes are used to represent nucleic acids: A-adenine, C-cytosine, G-guanine, T-thymidine, R represents A or G, Y represents T or C, N represents any nucleic acid.
An EN2 nucleic acid or protein referred to herein is a human one unless otherwise noted.
A chromosome region is spanned by two sequences if one sequence is at one end of the region and the other sequence is at the other end of the region.
An EN2 protein includes any protein or fragment encoded by the EN2 gene, including any segment, region, or exon.
Autism and allied autistic spectrum (AS) disorders present with a myriad of behavioral, clinical, and biochemical abnormalities. Several studies have demonstrated that AS has a genetic basis. Family studies have determined that there is a 75-fold greater chance of siblings inheriting the disorder than the general population if a brother or sister already has autism (Bolton, et al. (1994) J. Child Psychol. Psychiat. 35:877-900). Monozygotic twin studies display a 75% concordance in symptoms in comparison to only 10% in fraternal twins (Bailey, et al. (1998) Brain 121:889-905; Folstein and Rutter (1977) J. Child Psychol. Psychiat. 18:297-321; Ritvo, et al. (1985) Am. J. Psychiat. 142:74-77). This large difference suggests that multiple loci are involved, with some models predicting more than 15 genes contributing to the disorder (Folstein and Rosen-Sheidley (2001) Nat. Rev. Genet. 2:943-955; Lamb, et al. (2000) Hum. Mol. Genet. 9:861-868; Risch, et al. (1999) Am. J. Hum. Genet. 65:493-507).
Furthermore, the cerebellum is most often malformed in autistic individuals. 21/22 autopsy studies have revealed cerebellar abnormalities including Purkinje cell loss. These defects occur in the absence of any obvious sign of degeneration suggesting that autism is instead caused by developmental defects (Bailey, et al. (1998) Brain 121:889-905; Bauman and Kemper (1985) Neurology 35: 866-874; Bauman and Kemper (1986) Neurology 36(suppl. 1):190; Bauman and Kemper (1994) In The Neurobiology of Autism. Baltimore: John Hopkins University Press pp 119-145; Courchesne (1997) Learn Mem. 4:1-35; Kemper and Bauman (1993) Behav. Neuro. 11:175-187; Ritvo, et al. (1996) Am. J. Psychiatry 143:862-866). In addition, imaging studies have also demonstrated cerebellar hypoplasia (Courchesne, et al. (1988) New Eng. J. Med. 318:1349-1354; Courchesne (1997) Curr. Opin. Neurobiol. 7:269-278; Gaffney, et al. (1987) Br. J. Psychiatry 151:831-833; Hashimoto, et al. (1995) J. Autism Dev. Discord. 25:1-18; Kleiman, et al. (1992) Neurology 42:753-760; Murakami, et al. (1989) Arch. Neurol. 46:689-694). A recent imaging report has uncovered abnormal cerebellar growth patterns after birth. The growth is initially accelerated followed by a decrease after age six (Courchesne, et al. (2001) Neurology 57:245-254). These studies indicate that cerebellar development is perturbed in autism. Interestingly, recent fMRI studies indicate that the cerebellum is active during tasks that are defective in autism including language and attention (Akshoomoff, et al. (1997) Int. Rev. Neurobiol. 41:575-98; Allen, et al. (1997) Science 275:1940-1943; Allen and Courchesne (2003) Am. J. Psychiatry 160:262-73; Courchesne, et al. (1994) Behavioral Neuroscience 108:848-865; Courchesne and Allen (1997) Learn Mem. 4:1-35; Gao, et al. (1996) Science 272:545-547). Thus, these anatomical defects might directly contribute to the behavioral abnormalities associated with autism.
Mouse genetics have identified a large number of genes that function during cerebellar development (Hatten and Heintz (1995) Annu. Rev. Neurosci. 18:385-408; Hatten, et al. (1997) Curr. Opin. Neurobiol. 7(1):40-47). One such gene is Engrailed2, a homeobox transcription factor that is orthologous to Drosophila melanogaster engrailed. In the mouse, there are two Engrailed genes, En1 and En2. Knockout studies have demonstrated that En1 functions during early A-P patterning of neural tube while En2 is specifically required for normal postnatal cerebellar development (Millen, et al. (1994) Development 120:695-706; Hanks, et al. (1995) Science 269:679-682; Millen, et al. (1995) Development 121:3935-45; Liu and Joyner (2001) Annu. Rev. Neurosci. 24:869-896). The En2−/− mutant displays cerebellar hypoplasia that is due in part to a reduction in all the major cerebellar cell types including Purkinje cells (Millen, et al. (1994) Development 120:695-706; Millen, et al. (1995) Development 121:3935-45; Kuemerle, et al. (1997) J. Neurosci. 17:7881-9). Human EN2 maps to distal chromosome 7, a region that displays linkage to AS in two separate studies (Liu, et al. (2001) Annu. Rev. Neurosci. 24:869-896; Auranen, et al. (2002) Am. J. Hum. Genet. 71:777-790). Thus, EN2 was tested as a susceptibility locus for AS by performing family based association analysis.
Research suggests that early diagnosis of autism or autism related disorders such as Asperger's or PDD may be associated with dramatically better outcomes. The earlier a child is diagnosed, the earlier the child may begin benefiting from one of the many specialized intervention approaches.
There is provided, in accordance with the present invention, an isolated nucleic acid molecule (SEQ ID NO:1), which encodes human EN2, and the amino acid sequence of human EN2 (SEQ ID NO:2). SEQ ID NO:1 represents both exons of the EN2 locus, the single intron, as well as 1000 bp 5′ and 3′ of the coding sequence. The position of EN2 on chromosome 7 is between position 154552000 and position 154560000. More particularly, there is provided, in accordance with the present invention, methods for determining a subject's susceptibility to autism or a disease or disorder related thereto, such as Asperger's Disorder or PDD using a variant allele of the Engrailed (EN2) gene, which maps to chromosome 7, in particular, to 7q36.3. Furthermore, transmission/disequilibrium tests (TDT), which were performed for two single nucleotide polymorphisms (Intron 1: A/G and Intron 2: C/T), revealed significant overtransmission of the A allele of Intron 1: A/G and the C allele of Intron 2: C/T (Intron A/G P=0.0009; Intron C/T P=0.0006). Intron 1 (rs1861972), which is located at position 154556629 of human chromosome 7, results in a guanine to adenine transition, whereas Intron 2 (rs1867973), located at position 154556781 of human chromosome 7, results in a thymine to cytosine transition. Haplotype analysis indicated that the A-C haplotype is specifically overtransmitted in autistic individuals (P=0.000062). Thus, detection of such a variant allele in the genome of a subject is indicative of the subject's susceptibility to autism. Furthermore, a variant allele of the Engrailed gene can also be used to assay drugs and agents for potential use in treating autism or a disease or disorder related thereto, such as Asperger's Disorder or PDD.
The present invention relates to the identification of particular single nucleotide polymorphisms (SNPs), which show statistical relevance in terms of being markers of susceptibility to autism and autism related disorders. In particular, the two SNPs have been found on chromosome 7, in the gene that encodes for the transcription factor EN2.
In particular, the homeobox transcription factor, ENGRAILED 2 (EN2), was investigated for association with autism spectrum disorder (AS) by performing transmission/disequilibrium tests (TDT) for two SNPs (rs1861972 and rs1861973). Initially, TDT was performed using 137 triads of autistic individuals and their parents and significant overtransmission of the A allele of rs1861972 and the C allele of rs1861973 was observed (rs1861972 P=0.0009; rs1861973 P=0.0006; A-C haplotype P=0.000062). The analysis was then extended to include other affected and unaffected siblings as well as 29 additional families. Significant association was observed for both SNPs under both the broad and narrow diagnostic schemes (rs1861972: narrow P=0.0106, broad P=0.0050; rs1861973: narrow P=0.0033, broad P=0.0063; A-C Haplotype: narrow P=0.0007, broad P=0.0009). The procedures utilized for the analyses in these studies are known to those skilled in the art (see, e.g., Martin, et al. (2000) Am. J. Hum. Genet. 67:146-154; Terwilliger, (1995) Am. J. Hum. Genet. 56:777-787; Ye, et al. (2001) Nucleic Acids Res. 29:E88-8; Clayton, (1999) Am. J. Hum. Genet. 65:1170-1177; Strachan and Read, Human Molecular Genetics 2, Wiley Liss, New York, N.Y. (1999)). In summary, these results identify EN2 as a susceptibility locus for autism and related AS disorders. Accordingly, in certain embodiments, the EN2 locus set forth as SEQ ID NO:1 is employed to determine whether a person is predisposed to autism spectrum disorder. In particular embodiments nucleic acids corresponding to the intron of the EN2 locus are employed to determine whether a person is predisposed to autism spectrum disorder. The  ̃3.3 kb intron of the EN2 locus is set forth herein as SEQ ID NO:11.
The characteristic behaviors of autism spectrum disorders may or may not be apparent in infancy (18 to 24 months), but usually become obvious during early childhood (24 months to 6 years). While there is no one behavioral or communications test that can detect autism, several screening instruments have been developed that are now used in diagnosing autism. CARS rating system (Childhood Autism Rating Scale), developed in the early 1970s, is based on observed behavior. Using a 15-point scale, professionals evaluate a child's relationship to people, body use, adaptation to change, listening response, and verbal communication. The Checklist for Autism in Toddlers (CHAT) is used to screen for autism at 18 months of age. It was developed in the early 1990s to see if autism could be detected in children as young as 18 months. The screening tool uses a short questionnaire with two sections, one prepared by the parents, the other by the child's family doctor or pediatrician. The Autism Screening Questionnaire is a 40-item screening scale that has been used with children four and older to help evaluate communication skills and social functioning. The Screening Test for Autism in Two-Year Olds uses direct observations to study behavioral features in children under two. Three skills areas have been identified—play, motor imitation, and joint attention—that seem to indicate autism. The diagnostic criteria for Asperger's Disorder include 1) a qualitative impairment in social interaction, as manifested by at least two of the following: marked impairments in the use of multiple nonverbal behaviors such as eye-to-eye gaze, facial expression, body postures, and gestures to regulate social interaction; failure to develop peer relationships appropriate to developmental level; a lack of spontaneous seeking to share enjoyment, interests, or achievements with other people (e.g., by a lack of showing, bringing, or pointing out objects of interest to other people); or lack of social or emotional reciprocity, and 2) restricted repetitive and stereotyped patterns of behavior, interests, and activities, as manifested by at least one of the following: encompassing preoccupation with one or more stereotyped and restricted patterns of interest that is abnormal either in intensity or focus; apparently inflexible adherence to specific, nonfunctional routines or rituals; stereotyped and repetitive motor mannerisms (e.g., hand or finger flapping or twisting, or complex whole-body movements); or persistent preoccupation with parts of objects. Asperger's Disorder causes clinically significant impairment in social, occupational, or other important areas of functioning. There is no clinically significant general delay in language (e.g., single words used by age 2 years, communicative phrases used by age 3 years). There is no clinically significant delay in cognitive development or in the development of age-appropriate self-help skills, adaptive behavior (other than social interaction), and curiosity about the environment in childhood. Criteria are not met for another specific Pervasive Developmental Disorder or Schizophrenia.
Because a behaviour-based diagnosis of autism is difficult, especially in young patients, it is of value to have a genetic screening assay to assist in the diagnosis. Furthermore, such an assay can be used to advise potential parents of their chances of having autistic children. However, up until the disclosure in the present invention, there has been no genetic marker available which is indicative of a subject's susceptibility to autism, or a disease related thereto, such as Asperger's Disorder or PDD.
EN2 protein for use in this invention can be isolated and purified according to techniques known in the art. The protein may be made by known methods of chemical synthesis, or expressed. The description below provides examples of materials and methods for so doing, but is not intended to be either limiting or exclusive.
Expressed proteins are generally produced using the nucleotide sequence encoding the protein (provided herein) or antigenic fragment, derivative or analog thereof, or a functionally active derivative, including a chimeric protein, thereof. The nucleotide sequence can be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted protein-coding sequence. Such elements are termed herein a “promoter.” Thus, the nucleic acid encoding the EN2 protein of the protein of the present invention is operationally associated with a promoter in an expression vector of the invention. Both cDNA and genomic sequences can be cloned and expressed under control of such regulatory sequences. An expression vector also preferably includes a replication origin.
The necessary transcriptional and translational signals can be provided on a recombinant expression vector, or they may be supplied by the native gene encoding EN2 protein and/or its flanking regions. Chimeric proteins including EN2 protein may also be produced as described. Potential host-vector systems include but are not limited to mammalian cell systems infected with virus (e.g., vaccinia virus, adenovirus, etc.); insect cell systems infected with virus (e.g., baculovirus); microorganisms such as yeast containing yeast vectors; or bacteria transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA. The expression elements of vectors vary in their strengths and specificities. Depending on the host-vector system utilized, any one of a number of suitable transcription and translation elements may be used. In this regard, any of a number of amplification systems may be used to achieve high levels of stable gene expression.
The cell containing the recombinant expression vector is cultured in an appropriate cell culture medium under conditions that provide for expression of protein by the cell.
Any of the methods previously described for the insertion of DNA fragments into a cloning vector may be used to construct expression vectors containing a gene consisting of appropriate transcriptional/translational control signals and the protein coding sequences. These methods may include in vitro recombinant DNA and synthetic techniques and in vivo recombination (genetic recombination).
Expression may be controlled by any promoter/enhancer element known in the art, but these regulatory elements must be functional in the host selected for expression. Promoters which may be used to control EN2 gene expression include, but are not limited to, the SV40 early promoter region (Benoist and Chambon (19810 Nature 290:304-310), the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto, et al. (1980) Cell 22:787-797), the herpes thymidine kinase promoter (Wagner, et al. (1981) Proc. Natl. Acad. Sci. USA 78:1441-1445), the regulatory sequences of the metallothionein gene (Brinster, et al. (1982) Nature 296:39-42); prokaryotic expression vectors such as the β-lactamase promoter (Villa-Kamaroff, et al. (1978) Proc. Natl. Acad. Sci. USA 75:3727-3731), or the tac promoter (DeBoer, et al. (1983) Proc. Natl. Acad. Sci. USA 80:21-25); see also Scientific American (1980) 242:74-94; promoter elements from yeast or other fungi such as the Gal 4 promoter, the ADC (alcohol dehydrogenase) promoter, PGK (phosphoglycerol kinase) promoter, alkaline phosphatase promoter; and the animal transcriptional control regions, which exhibit tissue specificity and have been utilized in transgenic animals, e.g., elastase I gene control region which is active in pancreatic acinar cells (Swift, et al. (1984) Cell 38:639-646; Ornitz, et al. (1986) Cold Spring Harbor Symp. Quant. Biol. 50:399-409; MacDonald (1987) Hepatology 7:425-515); insulin gene control region which is active in pancreatic beta cells (Hanahan (1985) Nature 315:115-122); immunoglobulin gene control region which is active in lymphoid cells (Grosschedl, et al. (1984) Cell 38:647-658; (Adames, et al. (1985) Nature 318:533-538; Alexander, et al. (1987) Mol. Cell. Biol. 7:1436-1444); mouse mammary tumor virus control region which is active in testicular, breast, lymphoid and mast cells (Leder, et al. (1986) Cell 45:485-495); albumin gene control region which is active in liver (Pinkert, et al. (1987) Genes Dev. 1:268-276); alpha-fetoprotein gene control region which is active in liver (Krumlauf, et al. (1985) Mol. Cell. Biol. 5:1639-1648; Hammer, et al. (1987) Science 235:53-58); alpha 1-antitrypsin gene control region which is active in the liver (Kelsey, et al. (1987) Genes Dev. 1:161-171); beta-globin gene control region which is active in myeloid cells (Mogram, et al. (1985) Nature 315:338-340; Kollias, et al. (1986) Cell 46:89-94); myelin basic protein gene control region which is active in oligodendrocyte cells in the brain (Readhead, et al. (1987) Cell 48:703-712); myosin light chain-2 gene control region which is active in skeletal muscle (Sani (1985) Nature 314:283-286), and gonadotropic releasing hormone gene control region which is active in the hypothalamus (Mason, et al. (1986) Science 234:1372-1378).
Expression vectors containing a nucleic acid encoding an EN2 protein of the invention can be identified by four well-known approaches: (a) PCR amplification of the desired plasmid DNA or specific mRNA, (b) nucleic acid hybridization, (c) presence or absence of selection marker gene functions, and (d) expression of inserted sequences. A wide variety of host/expression vector combinations may be employed in expressing the EN2 gene or fragments of this invention. Useful expression vectors, for example, may include segments of chromosomal, non-chromosomal and synthetic DNA sequences. Suitable vectors include derivatives of SV40 and known bacterial plasmids, e.g., E. coli plasmids col E1, pCR1, pBR322, pMal-C2, pET, pGEX (Smith, et al. (1988) Gene 67:31-40), pMB9 and their derivatives, plasmids such as RP4; phage DNAS, e.g., the numerous derivatives of phage, e.g., NM989, and other phage DNA, e.g., M13 and filamentous single stranded phage DNA; yeast plasmids such as the 2μ plasmid or derivatives thereof; vectors useful in eukaryotic cells, such as vectors useful in insect or mammalian cells; vectors derived from combinations of plasmids and phage DNAs, such as plasmids that have been modified to employ phage DNA or other expression control sequences; and the like. For example, in a baculovirus expression systems, both non-fusion transfer vectors, such as but not limited to pVL941 (Summers), pVL1393 (INVITROGENTM), pVL1392 (Summers and INVITROGENTM), and pBlueBacIII (INVITROGENTM), and fusion transfer vectors, such as but not limited to pAc700 (Summers), pAc701 and pAc702, pAc360 (INVITROGENTM), and pBlueBacHisA, B, C (INVITROGENTM).
Mammalian expression vectors contemplated for use in the invention include vectors with inducible promoters, such as the dihydrofolate reductase (DHFR) promoter, e.g., any expression vector with a DHFR expression vector, or a DHFR/methotrexate co-amplification vector, such as pED (PstI, SalI, SbaI, SmaI, and EcoRI cloning site, with the vector expressing both the cloned gene and DHFR; see Kaufman, Current Protocols in Molecular Biology, 16.12 (1991). Alternatively, a glutamine synthetase/methionine sulfoximine co-amplification vector, such as pEE14 (Celltech). In another embodiment, a vector that directs episomal expression under control of Epstein Barr Virus (EBV) can be used, such as pREP4 (INVITROGENTM), pCEP4 (INVITROGENTM), pMEP4 (INVITROGENTM), pREP8 (INVITROGENTM), pREP9 (INVITROGENTM), and pEBVHis (INVITROGENTM). Selectable mammalian expression vectors for use in the invention include pRc/CMV (INVITROGENTM), pRc/RSV (INVITROGENTM), and others. Vaccinia virus mammalian expression vectors (see, Kaufman (1991) supra) for use according to the invention include but are not limited to pSC11 and pMJ601. Yeast expression systems can also be used according to the invention. For example, the non-fusion pYEN2 vector (INVITROGENTM) or the fusion pYESHisA, B, C (INVITROGENTM), to mention just two, can be employed according to the invention.
Once a particular recombinant DNA molecule is identified and isolated, several methods known in the art may be used to propagate it. Once a suitable host system and growth conditions are established, recombinant expression vectors can be propagated and prepared in quantity. As previously explained, the expression vectors which can be used include, but are not limited to, the following vectors or their derivatives: human or animal viruses such as vaccinia virus or adenovirus; insect viruses such as baculovirus; yeast vectors; bacteriophage vectors (e.g., lambda), and plasmid and cosmid DNA vectors, to name but a few.
In addition, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Different host cells have characteristic and specific mechanisms for the translational and post-translational processing and modification (e.g., glycosylation, cleavage of signal sequence) of proteins. Appropriate cell lines or host systems can be chosen to ensure the desired modification and processing of the foreign protein expressed. For example, expression in a bacterial system can be used to produce a non-glycosylated core protein product.
Vectors are introduced into the desired host cells by methods known in the art, e.g., transfection, electroporation, micro injection, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, lipofection (lysosome fusion), use of a gene gun, or a DNA vector transporter (see, e.g., Wu, et al. (1992) J. Biol. Chem. 267:963-967; Wu and Wu (1988) J. Biol. Chem. 263:14621-14624; Canadian Patent Application No. 2,012,311).
The purification of EN2 Protein can be accomplished by any number of procedures that encompass a wide variety of known purification steps. Those with skill in the art would know to refer to references, such as the Methods of Enzymology series, for greater detail and breadth. Initial steps for purifying the proteins of the present invention include salting in or salting out, such as in ammonium sulfate fractionations; solvent exclusion fractionations, e.g., an ethanol precipitation; detergent extractions to free membrane bound proteins using such detergents as TRITONTM X-100, TWEENTM-20 etc.; or high salt extractions. Solubilization of proteins may also be achieved using aprotic solvents such as dimethyl sulfoxide and hexamethylphosphoramide. In addition, high speed ultracentrifugation may be used either alone or in conjunction with other extraction techniques. A useful method is tagging the protein with hexa-histidine via Ni+ chromatography (Coligan, et al. (1995) Current Protocols in Protein Science, vol. 1, John Wiley and Sons, New York; Methods in Enzymology (1990) M. P. Deutscher, ed., vol. 185 Guide to Protein Purification, Academic Press, San Diego, Calif.; Crowe, et al. (1994) Methods Mol. Biol. 31:371-387; Schmitt, et al. (1993) Mol. Biol. Rep. 18:223-230).
Generally good secondary isolation or purification steps include solid phase absorption using calcium phosphate gel or hydroxyapatite, or solid phase binding. Solid phase binding may be performed through ionic bonding, with either an anion exchanger, such as diethylaminoethyl (DEAE), or diethyl [2-hydroxy propyl] amino ethyl (QAE) SEPHADEX® or cellulose; or with a cation exchanger such as carboxymethyl (CM) or sulfo propyl (SP) SEPHADEX® or cellulose. Alternative means of solid phase binding includes the exploitation of hydrophobic interactions, e.g., the using of a solid support such as phenyl-SEPHAROSE® and a high salt buffer; affinity-binding, bound to an activated support; immuno-binding, using, e.g., an antibody to the EN2 protein bound to an activated support; as well as other solid phase supports including those that contain specific dyes or lectins etc. A further solid phase support technique that is often used at the end of the purification procedure relies on size exclusion, such as SEPHADEX® and SEPHAROSE® gels, or pressurized or centrifugal membrane techniques, using size exclusion membrane filters.
Solid phase support separations are generally performed batch-wise with low-speed centrifugations or by column chromatography. High performance liquid chromatography (HPLC), including such related techniques as FPLC, is presently the most common means of performing liquid chromatography. Size exclusion techniques may also be accomplished with the aid of low speed centrifugation.
In addition size permeation techniques such as gel electrophoretic techniques may be employed. These techniques are generally performed in tubes, slabs or by capillary electrophoresis.
Almost all steps involving protein purification employ a biological buffer at a pH close to the pKa of that buffer. Typical buffers can be purchased from most biochemical catalogues and include the classical buffers such as Tris, pyrophosphate, monophosphate, and diphosphate, or the Good buffers (Good, et al. (1966) Biochemistry 5:467; Good and Izawa (1972) Meth. Enzymol. 24(Part B):53; Fergunson and Good (1980) Anal. Biochem. 104:300) such as MES, HEPES, MOPS, tricine and CHES.
Materials to perform all of these techniques are available from a variety of sources such as Sigma Chemical Company in St. Louis, Mo.
Antibodies for use in this invention can be produced according to techniques known in the art. The description below provides examples of materials and methods for so doing, but is not intended to be either limiting or exclusive.
According to the invention, EN2 protein may produced recombinantly or by chemical synthesis as described above, and fragments or other derivatives or analogs thereof, including fusion proteins, may be used as an immunogen to generate antibodies that recognize the protein. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, Fab fragments, and an Fab expression library. The anti-EN2 Protein antibodies of the invention may be cross-reactive, e.g., they may recognize EN2 protein from different species. Polyclonal antibodies have greater likelihood of cross-reactivity. Alternatively, an antibody of the invention may be specific for a single form of EN2 protein, such as murine EN2 protein. Preferably, such an antibody is specific for human EN2 protein.
Various procedures known in the art may be used for the production of polyclonal antibodies to EN2 protein. For the production of antibody, various host animals can be immunized by injection with the EN2 protein, including but not limited to rabbits, mice, rats, sheep, goats, etc. In one embodiment, the EN2 protein thereof can be conjugated to an immunogenic carrier, e.g., BSA or keyhole limpet hemocyanin (KLH). Various adjuvants may be used to increase the immunological response, depending on the host species, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface-active substances such as lysolecithin, PLURONICTM polyols, polyanions, peptides, oil emulsions, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum. 
For preparation of monoclonal antibodies directed toward the EN2 protein, any technique that provides for the production of antibody molecules by continuous cell lines in culture may be used. These include, but are not limited to, the hybridoma technique originally developed by Kohler and Milstein ((1975) Nature 256:495-497), as well as the trioma technique, the human B-cell hybridoma technique (Kozbor, et al. (1983) Immunol. Today 4:72; Cote, et al. (1983) Proc. Natl. Acad. Sci. USA 80:2026-2030), 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). In an additional embodiment of the invention, monoclonal antibodies can be produced in germ-free animals. In fact, according to the invention, techniques developed for the production of “chimeric antibodies” (Morrison, et al. (1984) J. Bacteriol. 159:870; Neuberger, et al. (1984) Nature 312:604-608; Takeda, et al. (1985) Nature 314:452-454) by splicing the genes from a mouse antibody molecule specific for an EN2 protein together with genes from a human antibody molecule of appropriate biological activity can be used; such antibodies are within the scope of this invention. Such human or humanized chimeric antibodies are preferred for use in therapy of human diseases or disorders (described infra), since the human or humanized antibodies are much less likely than xenogenic antibodies to induce an immune response, in particular an allergic response, themselves.
According to the invention, techniques described for the production of single chain antibodies (U.S. Pat. Nos. 5,476,786 and 5,132,405; U.S. Pat. No. 4,946,778) can be adapted to produce EN2 protein-specific single chain antibodies. An additional embodiment of the invention utilizes the techniques described for the construction of Fab expression libraries (Huse, et al. (1989) Science 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity for an EN2 protein. Antibody fragments which contain the idiotype of the antibody molecule can be generated by known techniques. For example, such fragments include but are not limited to: the F(ab′)2 fragment which can be produced by pepsin digestion of the antibody molecule; the Fab′ fragments which can be generated by reducing the disulfide bridges of the F(ab′)2 fragment, and the Fab fragments which can be generated by treating the antibody molecule with papain and a reducing agent.
In the production of antibodies, screening for the desired antibody can be accomplished by techniques known in the art, e.g., radioimmunoassay, ELISA (enzyme-linked immunosorbant assay), “sandwich” immunoassays, immunoradiometric assays, gel diffusion precipitin reactions, immunodiffusion assays, in situ immunoassays (using colloidal gold, enzyme or radioisotope labels, for example), western blots, precipitation reactions, agglutination assays (e.g., gel agglutination assays, hemagglutination assays), complement fixation assays, immunofluorescence assays, protein A assays, and immunoelectrophoresis assays, etc. In one embodiment, antibody binding is detected by detecting a label on the primary antibody. In another embodiment, the primary antibody is detected by detecting binding of a secondary antibody or reagent to the primary antibody. In a further embodiment, the secondary antibody is labeled. Many means are known in the art for detecting binding in an immunoassay and are within the scope of the present invention. For example, to select antibodies which recognize a specific epitope of an EN2 protein, one may assay generated hybridomas for a product which binds to an EN2 protein fragment containing such epitope. For selection of an antibody specific to an EN2 protein from a particular species of animal, one can select on the basis of positive binding with EN2 protein expressed by or isolated from cells of that species of animal.
The foregoing antibodies can be used in methods known in the art relating to the localization and activity of the EN2 protein, e.g., for western blot analysis, imaging EN2 protein in situ, measuring levels thereof in appropriate physiological samples, etc. using any of the detection techniques mentioned above or known in the art.
In a specific embodiment, antibodies that agonize or antagonize the activity of EN2 protein can be generated. Such antibodies can be tested using the assays described infra for identifying ligands.
In an immunoassay, a control quantity of the antagonists or antibodies thereto, or the like may be prepared and labeled with an enzyme, a specific binding partner and/or a radioactive element, and may then be introduced into a cellular sample. After the labeled material or its binding partner(s) has had an opportunity to react with sites within the sample, the resulting mass may be examined by known techniques, which may vary with the nature of the label attached.
In the instance where a radioactive label, such as the isotopes 3H, 14C, 32P , 35S, 36Cl, 51Cr, 57Co, 58Co, 59Fe, 90Y, 125I, 131I, and 186Re are used, known currently available counting procedures may be utilized. In the instance where the label is an enzyme, detection may be accomplished by any of the presently utilized calorimetric, spectrophotometric, fluorospectrophotometric, amperometric or gasometric techniques known in the art.
The present invention includes an assay system which may be prepared in the form of a test kit for the quantitative analysis of the extent of the presence of the EN2 protein, or to identify drugs or other agents that may mimic or block its activity. Alternatively, the presence of the single nucleotide polymorphisms of the present invention can be monitored using standard techniques known in the art. The system or test kit may comprise a labeled component prepared by one of the radioactive and/or enzymatic techniques discussed herein, coupling a label to the antibody or an agonist and/or antagonist, and one or more additional immunochemical reagents, at least one of which is a free or immobilized ligand, capable either of binding with the labeled component, its binding partner, one of the components to be determined or their binding partner(s).
In the context of treatment, administration of cells, genes, and proteins to a person can be carried by a variety of methods. For example, in gene therapy, the EN2 gene or appropriate fragments of the gene (for example corresponding to a deleted region in an individual patient) can be used in methods known in the art. In such methods, the gene is introduced in vivo in a viral vector. Such vectors include an attenuated or defective DNA virus, such as but not limited to herpes simplex virus (HSV), papillomavirus, Epstein Barr virus (EBV), adenovirus, adeno-associated virus (AAV), and the like. Defective viruses, which entirely or almost entirely lack viral genes, are preferred. Defective virus is not infective after introduction into a cell. Use of defective viral vectors allows for administration to cells in a specific, localized area, without concern that the vector can infect other cells. Examples of particular vectors include, but are not limited to, a defective herpes virus 1 (HSV1) vector (Kaplitt, et al. (1991) Mol. Cell. Neurosci. 2:320-330), an attenuated adenovirus vector (Stratford-Perricaudet, et al. (1992) J. Clin. Invest. 90: 626-630), and a defective adeno-associated virus vector (Samulski, et al. (1987) J. Virol. 61:3096-3101; Samulski, et al. (1989) J. Virol. 63:3822-3828).
Preferably, for in vitro administration, an appropriate immunosuppressive treatment is employed in conjunction with the viral vector, e.g., adenovirus vector, to avoid immuno-deactivation of the viral vector and transfected cells. For example, immunosuppressive cytokines, such as interleukin-12, interferon, or anti-CD4 antibody, can be administered to block humoral or cellular immune responses to the viral vectors (see, e.g., Yang, et al. (1995) Nat. Med. 1(9):890-3). In addition, it is advantageous to employ a viral vector that is engineered to express a minimal number of antigens.
In another embodiment the gene can be introduced in a retroviral vector, e.g., as described in U.S. Pat. No. 5,399,346; Mann, et al. ((1983) Cell 33:153); U.S. Pat. No. 4,650,764; U.S. Pat. No. 4,980,289; Markowitz, et al. (1988) J. Virol. 62:1120; U.S. Pat. No. 5,124,263; WO 95/07358; and Kuo, et al. ((1993) Blood 82:845). Targeted gene delivery is described in WO 95/28494.
Alternatively, the vector can be introduced in vivo by lipofection. Synthetic cationic lipids can be used to prepare liposomes for in vivo transfection of a gene encoding a marker (Felgner, et. al. (1987) Proc. Natl. Acad. Sci. USA 84:7413-7417; Mackey, et al. (1988) Proc. Natl. Acad. Sci. USA 85:8027-8031). The use of cationic lipids can promote encapsulation of negatively charged nucleic acids, and also promote fusion with negatively charged cell membranes (Felgner and Ringold (1989) Science 337:387-388). Lipids can be chemically coupled to other molecules for the purpose of targeting (see Mackey, et. al. (1988) supra). Targeted peptides, e.g., hormones or neurotransmitters, and proteins such as antibodies, or non-peptide molecules could be coupled to liposomes chemically.
It is also possible to introduce the vector in vivo as a naked DNA plasmid. Naked DNA vectors for gene therapy can be introduced into the desired host cells by methods known in the art, e.g., transfection, electroporation, microinjection, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, use of a gene gun, or use of a DNA vector transporter (see, e.g., Wu, et al. (1992) J. Biol. Chem. 267:963-967; Wu and Wu (1988) J. Biol. Chem. 263:14621-14624).
A regulatable expression vector is particularly useful to regulate expression of a therapeutic EN2 gene. In one embodiment, the present invention contemplates constitutive expression of the EN2 gene, even if at low levels. Various therapeutic heterologous genes can be inserted in a gene therapy vector of the invention such as but not limited to adenosine deaminase (ADA) to treat severe combined immunodeficiency (SCID); marker genes or lymphokine genes into tumor infiltrating (TIL) T cells (Kasis, et al. (1990) Proc. Natl. Acad. Sci. USA 87:473; Culver, et al. (1991) ibid. 88:3155); genes for clotting factors such as Factor VIII and Factor IX for treating hemophilia (Dwarki, et al. (1995) Proc. Natl. Acad. Sci. USA 92:1023-1027); Thompson (1991) Thromb. Haemostatis 66:119-122); and various other well known therapeutic genes such as, but not limited to, dystrophin, insulin, erythropoietin, growth hormone, glucocerebrosidase, glucuronidase, antitrypsin, phenylalanine hydroxylase, tyrosine hydroxylase, ornithine transcarbamylase, apolipoproteins, and the like. In general, see U.S. Pat. No. 5,399,346.
In a further embodiment, the present invention provides for co-expression of EN2 and a therapeutic heterologous gene under control of a specific DNA recognition sequence by providing a gene therapy expression vector comprising both an EN2 coding gene and a gene under control of, inter alia, the EN2 regulatory sequence. The most effective use of this mode of treatment is to administer the gene therapy expression vector by known methods to a pregnant woman at risk of carrying an affected fetus. In this context the EN2 regulatory sequence would target the vector to cells types which are affected in autism. Thus if the gene targeting vector is provided during gestation of a fetus, then the therapeutic gene and/or the EN2 gene itself would be targeted, for example, to neurons which might otherwise fail to develop normally or at all in the fetus. In one embodiment, these elements are provided on separate vectors, e.g., as exemplified infra. These elements may be provided in a single expression vector.
An EN2 protein or nucleic acid of this invention can be a therapeutic compound. A therapeutic compound of the present invention also embraces a drug which increases or decreases, i.e., normalizes (brings to normal levels as described above) the level of EN2 protein. A drug which normalizes any deleterious downstream effects caused by the presence of SNPS in the EN2 gene are also contemplated by the present invention. Such drugs can be obtained by assays which detect increase or decrease of EN2 protein or its expression or which normalize the expression of genes which are downstream of the EN2 gene. Such assays are part of this invention. A cell-based assay where compounds are tested for the ability to increase EN2 in cultured cells is one such assay. Accordingly, a drug which increases the amount of EN2 protein produced by cultured cells is part of this invention.
Pharmaceutical compositions including compounds of this invention, preferably EN2 protein, antibodies, or polynucleotides are also part of the invention. Such pharmaceutical compositions are formulated for administration by any standard means, such as injection, oral, pulmonary, nasal, rectal, etc.
In general, comprehended by the invention are pharmaceutical compositions comprising effective amounts of a compound, nucleic acid, antibody or protein of the invention together with pharmaceutically acceptable diluents, preservatives, solubilizers, emulsifiers, adjuvants and/or carriers. Such compositions include diluents of various buffer content (e.g., Tris-HCl, acetate, phosphate), pH and ionic strength; additives such as detergents and solubilizing agents (e.g., TWEENTM 80, Polysorbate 80); anti-oxidants (e.g., ascorbic acid, sodium metabisulfite); preservatives (e.g., THIMERSOLTM, benzyl alcohol) and bulking substances (e.g., lactose, mannitol); incorporation of the material into particulate preparations of polymeric compounds such as polylactic acid, polyglycolic acid, etc. or into liposomes. Hylauronic acid can also be used.
Such compositions can influence the physical state, stability, rate of in vivo release, and rate of in vivo clearance of the present proteins and derivatives. See, e.g., Remington's Pharmaceutical Sciences, 18th Ed., 1990, Mack Publishing Co., Easton, Pa., pages 1435-1712.
The compositions of the present invention can be prepared in liquid form, or may be in dried powder, such as lyophilized form. Oral solid dosage forms are described generally in Remington's Pharmaceutical Sciences, 18th Ed., 1990, Mack Publishing Co., Easton, Pa. at Chapter 89. Solid dosage forms include tablets, capsules, pills, troches or lozenges, cachets or pellets. Formulations for rectal delivery include suppository formulations, which may be similar to those prepared for oral delivery. Also, liposomal or proteinoid encapsulation may be used to formulate the present compositions (as, for example, proteinoid microspheres reported in U.S. Pat. No. 4,925,673). Liposomal encapsulation can be used and the liposomes can be derivatized with various polymers (e.g., U.S. Pat. No. 5,013,556). A description of possible solid dosage forms for the therapeutic is given by Marshall (1979) In: Modern Pharmaceutics, Banker and Rhodes, ed., Chapter 10.
In general, the formulation will include the component or components (or chemically modified forms thereof) and inert ingredients which allow for protection against the stomach environment, and release of the biologically active material in the intestine. The active compounds can be chemically modified so that oral delivery is efficacious. Generally, the chemical modification contemplated is the attachment of at least one moiety to the component molecule itself, where said moiety permits (a) inhibition of proteolysis; and (b) uptake into the blood stream from the stomach or intestine. Also desired is the increase in overall stability of the component or components and increase in circulation time in the body. Examples of such moieties include: polyethylene glycol, copolymers of ethylene glycol and propylene glycol, carboxymethyl cellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone and polyproline.
One can dilute or increase the volume of the therapeutic with an inert material such as carbohydrates, especially mannitol, a-lactose, anhydrous lactose, cellulose, sucrose, modified dextrans and starch. Certain inorganic salts may be also be used as fillers including calcium triphosphate, magnesium carbonate and sodium chloride. Materials used as disintegrates include, but are not limited to, starch including sodium starch glycolate, AMBERLITETM, sodium carboxymethylcellulose, ultramylopectin, sodium alginate, gelatin, orange peel, acid carboxymethyl cellulose, natural sponge and bentonite, and insoluble cationic exchange resins. Powdered gums as disintegrants and as binders can include powdered gums such as agar, Karaya or tragacanth. Alginic acid and its sodium salt are also useful as disintegrants.
Binders may be used to hold the therapeutic agent together to form a hard tablet and include materials from natural products such as acacia, tragacanth, starch and gelatin. Others include methyl cellulose (MC), ethyl cellulose (EC) and carboxymethyl cellulose (CMC). Polyvinyl pyrrolidone (PVP) and hydroxypropylmethyl cellulose (HPMC) could both be used in alcoholic solutions to granulate the therapeutic. An antifrictional agent can also be included.
Lubricants such as stearic acid including its magnesium and calcium salts, polytetrafluoroethylene (PTFE), liquid paraffin, vegetable oils and waxes, sodium lauryl sulfate, magnesium lauryl sulfate, polyethylene glycol of various molecular weights, CARBOWAX® 4000 and 6000 can be used. Glidants may include starch, talc, pyrogenic silica and hydrated silicoaluminate. A surfactant can be added as a wetting agent. Surfactants can include anionic detergents such as sodium lauryl sulfate, dioctyl sodium sulfosuccinate and dioctyl sodium sulfonate. Cationic detergents might be used and could include benzalkonium chloride or benzethomium chloride. Anionic detergents that could be included are lauromacrogol 400, polyoxyl 40 stearate, polyoxyethylene hydrogenated castor oil 10, 50 and 60, glycerol monostearate, polysorbate 40, 60, 65 and 80, sucrose fatty acid ester, methyl cellulose and carboxymethyl cellulose. Additives which potentially enhance uptake of the protein are for instance the fatty acids oleic acid, linoleic acid and linolenic acid.
Controlled release oral formulation may be desirable. Pulmonary delivery by known methods, for example as described in U.S. Pat. No. 5,451,569, is also contemplated. Vehicles include but are not limited to nebulizers, metered dose inhalers, and powder inhalers. All such devices require the use of suitable formulations. Typically, each formulation is specific to the type of device employed and may involve the use of an appropriate propellant material, in addition to the usual diluents, adjuvants and/or carriers useful in therapy. Also, the use of liposomes, microcapsules or microspheres, inclusion complexes, or other types of carriers is contemplated.
Chemically modified protein may also be prepared in different formulations depending on the type of chemical modification or the type of device employed. Formulations for nasal delivery include those with dextran or cyclodextran. For injectable compositions, various standard aqueous formulations are suitable.
In accordance with the above, the therapeutic compounds of the present invention can be delivered by standard means including intravenous, intraarterial, intraperitoneal, intramuscular, intracerebral, intraventricular, intrathecal or subcutaneous routes of administration. Alternatively, these compounds, properly formulated, can be administered by nasal, oral, or rectal administration. A constant supply of these therapeutic compounds can be ensured by providing a therapeutically effective dose, i.e., a dose effective to induce normalized (i.e., increased or decreased) levels of EN2 protein in a subject at the necessary intervals, e.g., daily, every 12 hours, etc. These parameters will depend on the severity of the disease condition being treated, other actions, such as diet modification, that are implemented, the weight, age, and sex of the subject, and other criteria, which can be readily determined according to standard good medical practice by those of skill in the art. Normal levels of EN2 protein can be determined as described above. The subject can be tested to determine whether levels are normalized by, for example, determining the amount of EN2 protein in the cells or tissues of the subject. Similarly dosage can be titrated during treatment by determining whether levels of EN2 protein are increasing or decreasing compared to the subject's levels of EN2 before treatment.
The therapeutic compound can be delivered in a vesicle, in particular a liposome (see Langer (1990) Science 249:1527-1533; Treat, et al. (1989) In: Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss: New York, pp. 353-365; Lopez-Berestein, ibid., pp. 317-327). The therapeutic compound can be delivered in a controlled release system, may be administered using intravenous infusion, an implantable osmotic pump, a transdermal patch, liposomes, or other modes of administration. In one embodiment, a pump can be used (see Langer, supra; Sefton (1987) CRC Crit. Ref. Biomed. Eng. 14:201; Buchwald, et al. (1980) Surgery 88:507; Saudek, et al. (1989) N. Engl. J. Med. 321:574). In another embodiment, polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise, eds. (1974) CRC Press: Boca Raton, Fla.; Controlled Drug Bioavailability, Drug Product Design and Performance (1984) Smolen and Ball (eds.), Wiley: New York; Ranger and Peppas (1983) J. Macromol. Sci. Rev. Macromol. Chem. 23:61; Levy, et al. (1985) Science 228:190; During, et al. (1989) Ann. Neurol. 25:351; Howard, et al. (1989) J. Neurosurg. 71:105). In yet another embodiment, a controlled release system can be placed in proximity of the therapeutic target, i.e., the brain, thus requiring only a fraction of the systemic dose (see, e.g., Goodson (1984) In: Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138).
A subject in whom administration of these therapeutic agents is an effective therapeutic regimen is preferably a human, but can be any animal. The amount administered is an amount effective to normalize the amount of EN2 protein in the subject, whether by increasing or decreasing the amount of protein or the expression of the protein. Thus, as can be readily appreciated by one of ordinary skill in the art, the methods and pharmaceutical compositions of the present invention are particularly suited to administration to any animal, i.e., for veterinary medical use.
Detection of deletions, additions, substitutions and any other mutations can be carried out according to standard methods. In general, the identification of a mutation that involves as little as one nucleotide can be achieved by observing the mutation through nucleotide sequence analysis or a change in an amino acid through amino acid sequence analysis, using techniques known in the art. For example using probes developed from the EN2 sequence provided herein, or PCR primers provided herein, a suspected mutant gene can be obtained from cells or tissue using known techniques. The gene can then be sequenced by standard methods, and the mutation observed by comparing sequences. Alternatively, the gene can be expressed in an expression vector, again using standard protocols, and the resulting protein isolated and sequenced to provide a sequence comparison. An example of a mutant analysis method is single-strand polymorphism mutation screening (SSCP), which employs a PCR-based protocol to accomplish mutation screening. As discussed above, a mutation can comprise one or more deletions, additions, or substitutions of nucleotides. The mutation can be in a coding region, which would affect the sequence of the resulting protein. The mutation can also be in the 5′ or 3′ noncoding region, which would affect expression of protein, by for example affecting the promoter or enhancer, or by affecting the 3′-UTR (affecting RNA stability). A mutation can be as small as one nucleotide, or as large as the entire gene.
Suitable hybridization probes for use in accordance with the methods of the present invention include SEQ ID NO:1, which encompasses the coding sequence of EN2 and SEQ ID NO:11, which encompasses the intron of the EN2 locus. SEQ ID NO:2, is the complete sequence of the human EN2 protein. DNA sequences encoding the EN2 protein, segments thereof, and sequences complementary in base sequence to said sequences and segments, are preferred hybridization probes in assays for RNA levels. Probes against EN2 intron sequences, obtainable from the results of the Human Genome Project, can also be used as EN2 gene-specific probes. In particular embodiments, the probe hybridizes to a nucleic acid sequence at or near SNPs rs1861972, rs1861973 or rs2361688. Probes for segments of the EN2 gene or mRNA can be isolated, for example, by cloning the EN2 gene or cDNA and using PCR to amplify desired regions of the cloned nucleic acid to create a probe population.
Hybridization assays are done under conditions where a probe complementary to a segment of EN2 nucleic acid will preferentially bind to that nucleic acid, as compared to other nucleic acid. An extensive volume of literature exists on various appropriate hybridization conditions for achieving such specificity.
Hybridization can be done by a variety of methods. The optimal solvent composition, probe size, and temperature, will depend on whether the target nucleic acid is for example, in solution, on a solid support (e.g., a nitrocellulose filter) in solution, and or in a cell. Conditions will also depend on whether the probe is in solution or in a solid support (e.g., in a gene chip experiment). The hybridization conditions described for the northern blot experiments below are illustrative of possible hybridization conditions. Persons in the art will appreciate which conditions are optimal for the various types of possible hybridization experiments.
Single base mutations can, for example, be detected by nucleic acid sequencing, by SSCP, or by hybridization with small probes that require a perfectly complementary target sequence in order to hybridize. In particular embodiments, a single-base mutation indicative of a person inflicted with, or predisposed to, an autism spectrum disorder is a A to G transition at position 2236 of SEQ ID NO:11 (rs1861972); a C to T transition at position 2388 of SEQ ID NO:11 (rs1861973); a A to G transition at position 1921 of SEQ ID NO:11 (rs2361688); or a combination thereof.
The results of the various assays can be analyzed to determine whether one or both genes have the deletion. For example, if Southern electrophoretic gel analysis of restriction digests of cell DNA reveals the presence of half as much intact EN2 gene DNA as a normal person (as regards the EN2 gene) has, that will indicate that only one of the two gene copies is missing. Also hybridization to chromosomes in situ or in chromosomal preparations, using fluorescent in situ hybridization or other hybridization techniques, can show if the deletion of a gene is in one or both chromosomes of a chromosome pair. A gel analysis may also reveal an alteration in the pattern of bands from a normal DNA sample. For example, a deletion will move its two flanking regions containing restriction sites closer to each other, resulting in different sized fragments than normal DNA when exposed to the same restriction enzyme.
In certain embodiments of the diagnostic methods and kits, EN2 defects are determined by protein analysis, wherein the protein is isolated from a patient for purposes of determining subnormal levels of protein, especially EN2 protein. Protein may be isolated from cell, tissue, or blood samples using known methods of protein isolation from these materials. In particular, a given protein such as EN2 can be isolated using antibodies. Once isolated, the protein can be sequenced by known methods to determine whether it is a mutant protein. See, for example, Vladimirov, et al. (1996) Eur. J. Biochem. 239:144-149; Wang and Chait (1997) Methods Mol. Biol. 64:175-182; Hines, et al. (1998) J. Protein Chemistry 17:525-526).
In particular embodiments of the diagnostic methods and kits, an antibody probe is used in an assay for purposes of demonstrating the subnormal levels of protein, especially the EN2 protein. Antibodies can be obtained as described above. Also, antibodies that react with EN2 protein have been reported (Ericson, et al. (1992) Science 256:1555-1560; Ericson, et al. (1997) Cell 90:169-180). EN2 size and amount can be determined by western blot analysis.
As used in the context of the present invention, autism includes any form of autism. Such diseases are currently denoted as autism or an autistic spectrum disorder which includes Asperger's Syndrome and Pervasive Developmental Disorder (PDD).
The “DSM-IV” criteria for autistic disorder are those set forth in the American Psychiatric Association's Diagnostic and Statistical Manual of Mental Disorders, 4th edition, Washington, D.C., 199 pp 70-71. The diagnosis is based on the presence of 6 or more diagnostic criteria from three possible Groups 1, 2, and 3 with at least two of the criteria being from Group 1, at least one from Group 2, and at least one from Group 3. The three groups correspond to three core symptoms:
Group 1—Qualitative impairment in social interaction.
Group 2—Qualitative impairment in communication.
Group 3—Restricted repetitive and stereotyped patterns of behavior, interests and activities.
The four diagnostic criteria in Group 1 are: (i) marked impairment in multiple nonverbal behaviors (e.g., eye to eye gaze, facial expression, body postures, and gestures to regulate social interaction); (ii) failure to develop peer relationships appropriate to developmental level; (iii) absence of spontaneous seeking to share enjoyment, interests, or achievements with others (e.g., lack of showing, bringing, or pointing out objects of interest); and (iv) absence of social or emotional reciprocity.
The four diagnostic criteria in Group 2 are: (i) delay in, or total absence of spoken language development (without an attempt to compensate through alternative modes of communication, such as gesture or mime); (ii) adequate speech but marked impairment in ability to initiate or sustain a conversation with others; (c) stereotyped and repetitive use of language or idiosyncratic language; and (iv) absence of varied, spontaneous make-believe play or social imitative play appropriate to developmental level.
The four diagnostic criteria in Group 3 are: (i) encompassing preoccupation with one or more stereotyped and restricted patterns of interest that is abnormal either in intensity or focus; (ii) inflexible adherence to specific nonfunctional routines or rituals, stereotyped and repetitive motor mannerisms (e.g., hand or finger flapping or twisting, or complex whole-body movements); and (iv) persistent preoccupation with parts of objects.
Diagnosis of autism using the DSM-IV criteria, followed by confirmation of the diagnosis by the Autism Diagnostic Interview-Revised (ADI-R), provides good results. The ADI-R is a well-known review process for establishing autism (see, for example, Lord, et al. (1994) J. Autism Dev. Disord. 2:659-85; Le Couteur, et al. (1989) J. Autism Dev. Disord. 19:363-87).
In the Examples described here, the clinical diagnosis was determined by the DSM-IV criteria and then each individual was then subjected to the Autism Diagnostic Interview-Revised (ADI-R). The autistic individuals were identified by having at least six of the items described above.
Genes that are directly regulated by EN2 are also part of this invention. Mutations in EN2 may result in increase or decrease of the expression of these genes. Such downstream genes may be expressed at increased or decreased levels when EN2 is downregulated, and this is one means of isolating such genes using known methods. For example, cerebellar anlage (e10.5) could be dissected from EN2−/− knockout mice and wild-type littermates and their mRNA isolated to determine which are expressed at lower levels. For example, the mRNA could be hybridized against microarrays containing all the genes from the mouse genome. Genes directly regulated by EN2 such as PCP2 (L7) (Sanlioglu, et al. (1998) J. Neurobiol. 36:559-71) may be expressed at higher or lower levels than the others.
The invention is described in greater detail by the following non-limiting examples.
EXAMPLE 1
Transmission Disequilibrium Analysis—Study 1
Families recruited to the Autism Genetic Resource Exchange (AGRE) were used for these studies. AGRE is a central repository of family DNA samples created by The Cure Autism Now (CAN) Foundation and the Human Biological Data Interchange. The selection criteria required was that at least two family members had been diagnosed with autism, Asperger's Syndrome or PDD. The diagnosis and characteristics of these families are described in detail elsewhere (Geschwind, et al. (2001) Am. J. Hum. Genet. 69:463-6; Liu, et al. (2001) Annu. Rev. Neurosci. 24:869-896). For the analysis disclosed herein, a narrow diagnosis was defined as only autism while a broad diagnostic included individuals affected with either autism, Asperger's Syndrome or PDD. In this study, 137 triads (parent-offspring trios) under the narrow diagnostic were initially evaluated. This was then extended to a total of 166 pedigrees that included 310 triads and 168 phenotypic discordant sib pairs (DSP) under the broad diagnosis (740 total subjects). For the narrow diagnostic, 163 pedigrees with 250 triads and 134 DSP were analyzed (n=672).
EN2 spans 8kb of the genome and is encoded by two exons separated by a single intron. SNPs within the EN2 gene were initially identified through genome browsers. Two SNPs (rs1861972 and rs1861973) located 152 bp apart in the intron were initially verified by DNA sequence analysis of 24 individuals.














TABLE 1





dbSNP
Poly-








No.
morphisma
Frequencyb
Tc
Uc
P-valued
GRRe
PARf







rs1867972
A/G
0.297
77
41
0.0009
1.88
62%


rs1861973
C/T
0.292
70
35
0.0006
2.00
66%





aSecond allele is rare allele.


bFrequency of rare allele.


cT = number of times frequent allele transmitted and U = number of times frequent allele not transmitted from heterozygous parents.


dTwo-sided P-value (1 df) corresponding to χ2 generated by TRANSMIT.


eGenotype relative risk estimated by transmission ratio (T/U) assuming a multiplicative model.


fPopulation attributable risk calculated as PAR = (X − 1)/X; where X = (1 − f)2 + 2f(1 − f)Υ + f2Υ2 and Υ = GRR.






The tetra-primer ARMS-PCR strategy was then used to genotype family members (Ye, et al. (2001) Nucl. Acids Res. 29:E88-8). Primers were selected using a web-based software program and PCR conditions were determined that allowed the specific amplification of all possible genotypes. Genotypes for both SNPs were determined for the initial 137 triads that displayed just the narrow diagnostic and were verified to be in Hardy Weinberg equilibrium. The frequencies for the A and G alleles of rs1861972 were 70.3 and 29.7, respectively (Table 1). Similar values were observed for rs1861973 (C=70.8 and T=29.2) (Table 1). There was a significant positive linkage disequilibrium (LD) between the alleles of these markers (delta=0.82, delta-χ2=227.96, df=1, P<0.00001) (Hill and Weir (1994) Am. J. Hum. Genet. 54: 705-714).
Allelic transmission distortions were assessed for each SNP by the transmission disequilibrium test (TDT) (Spielman, et al. (1993) Am. J. Hum. Genet. 52:506-516), using the TRANSMIT program (Clayton (1999) Am. J. Hum. Genet. 65:1170-1177). Excess transmission of the rs1861972 A-allele to affected offspring was observed, with 77 of 118 heterozygous parents (65%) transmitting the A-allele and only 41 transmitting the G allele (McNemar's χ2=10.98, df=1, P=0.0009) (Table 1). Under a multiplicative model, the transmission ratio Transmitted/Untransmitted (T/U) is an estimator of genotype relative risk (GRR) (Altshuler, et al. (2000) Nat. Genet. 26:76-80). The GRR attributable to the A allele of the rs1861972 SNP was estimated to be 1.88 which in turn corresponded to a population attributable risk (PAR) (Altshuler, et al. (2000) Nat. Genet. 26:76-80) of approximately 62%. In other words, these data indicated that if the population were monomorphic for the G (protective) allele the prevalence of autism would be 62% lower. Since the GRR and PAR were calculated from a sample population ascertained for multiple affected siblings, the actual risk estimates may be different in the general AS population.
A similar distortion of transmissions was observed for the rs1861973 SNP with 70 of 105 heterozygous parents (67%) preferentially transmitting the C allele to their Autistic offspring (McNemar's χ2=11.67, df=1, P=0.0006) (Table 1). The C allele of the rs1861973 SNP provided a GRR of 2.00 with a corresponding PAR of 66%.
Haplotype transmission/disequilibrium tests were then performed again using TRANSMIT software. In the population tested, the A-C haplotype had an observed frequency of 67.6%. This haplotype was specifically overtransmitted (80 transmitted vs. 36 untransmitted) to affected individuals (χ2=16.07, df=1, P=0.000062) (Table 2). The G-T, A-T, and G-C haplotypes were all undertransmitted (Table 2). The global χ2 test based upon the common haplotypes A-C and G-T (frequency>5%) was then calculated to be χ2=18.90 (df=2), with a corresponding P-value of 0.000079 (Table 2). These tests were then reiterated 50000 times by a bootstrap simulation procedure to control for ambiguous haplotypes. Similar empirical P-values as before were obtained (P=0.00012) (Table 2). The GRR attributable to the A-C haplotype was found to be 2.19 with a corresponding PAR of 69%. Together this analysis demonstrates that the EN2 A-C haplotype is overtransmitted and is a high risk haplotype in autistic individuals.













TABLE 2







Haplotype
Frequency
T
U
P-valuea






















A-Cb
0.676
79
36
0.000062



A-T
0.032
4
12
0.0455



G-C
0.028
3
10
0.0525



G-T
0.262
39
67
0.0065



Globalc



0.000079



Globald



0.00012







aTwo-sided P-value corresponding to χ2 generated by TRANSMIT.



bGRR = 2.19, PAR = 69%.



cGlobal χ2 test based on combined common haplotypes, frequency greater than 5% (2 df).



dBootstrap simulation of global χ2 test (50000 reiterations).






To determine whether these findings could be extended to a larger sample, affected and unaffected siblings from the original 137 triads and 29 additional families were examined. The inheritance of each SNP was then assessed in these extended pedigrees using the Pedigree Disequilibrium Test (PDT) (Martin, et al. (2000) Am. J. Hum. Genet. 67:146-154). This program was used in place of TRANSMIT for the analysis of the extended pedigrees since the inevitable non-independence of affected siblings would render analysis conducted using TRANSMIT and other similar programs as invalid tests of association though they remain appropriate for linkage analysis. PDT has been specifically designed to overcome this limitation by allowing the use of data from related triads and discordant sibships from extended families when testing for LD.
For rs1861972, the A allele was again overtransmitted from heterozygous parents when individuals under a broad or narrow diagnostic were included in the analysis (narrow: 120 transmitted vs. 82 untransmitted; and broad: 150 transmitted vs. 107 untransmitted). The A allele was also over-represented in affected siblings of DSPs (defined by both genotypic and phenotypic discordance) under both diagnostics (narrow: 67 alleles in affected and 50 in unaffected siblings of 44 genotypic DSPs; broad: 89 in affected and 63 in unaffected of 57 genotypic DSPs). These results were significant when analyzed by PDT (narrow P=0.0106, broad P=0.0050) (Table 3).











TABLE 3









Parental





Transmissions
DSPa














dbSNP No.
Diagnostic
T
U
A
UA
Total
P-valueb

















rs1867972
narrow
120
82
67
50
44
0.0106


rs1867972
broad
150
107
89
63
57
0.0050


rs1867973
narrow
108
68
59
40
37
0.0033


rs1867973
broad
129
90
73
50
46
0.0063





aDiscordant sibpair counts: A = total number of the common allele in affected siblings and UA = total number of the common allele in unaffected siblings of genotypic discordant DSPs; Total = total number of genotypic discordant DSPs.


bP-value generated by PDT.






Analysis for the rs1861973 SNP revealed a similar pattern. The C allele was again overtransmitted to affected individuals (narrow: 108 transmitted vs. 68 untransmitted, broad: 129 transmitted vs. 90 untransmitted) and over-represented in affected siblings of DSPs (narrow: 59 in affected and 40 in unaffected of 37 genotypic DSPs; broad: 73 vs. 50 in affected and unaffected siblings respectively of 46 genotypic DSPs). This inheritance pattern was significant under the broad and narrow diagnosis when analyzed by PDT (narrow P=0.0033, broad P=0.0063) (Table 3). Thus, rs1861972 and rs1861973 demonstrate significant association to both autism and related AS disorders.
Haplotype analysis on the extended pedigrees was then performed. Since the two SNPs were in tight LD and were only 152 bp apart from each other, a recombination event likely occurred between them in a sample of this size. In the absence of recombination, unambiguous haplotypes could be assigned to all individuals in 160 of the 166 pedigrees. In only 6 families the parental haplotype phase could not be distinguished. These pedigrees were omitted for further analysis. Each haplotype was recoded as a single allele. By recoding the haplotypes as a single locus, the transmissions could be analyzed by PDT. The A-C haplotype was again overtransmitted under both diagnostic classifications (narrow: 120 transmitted vs. 66 untransmitted, broad: 143 transmitted vs. 86 untransmitted) and over-represented in affected siblings of DSPs (narrow: 64 vs. 45 from 44 genotypic DSPs; broad: 76 vs. 53 from 52 genotypic DSPs) at significant levels (narrow P=0.0007, broad P=0.0009) (Table 4). Conversely, the A-T, G-C, and G-T haplotypes were all undertransmitted. Global χ2 tests for all haplotypes also yielded significant P-values (narrow P=0.0003, broad P=0.0005) (Table 4). These results demonstrate significant association between EN2 and autism spectrum disorders.











TABLE 4









Parental





Transmissions
DSP














Haplotypea
Diagnostic
T
U
A
UA
Total
P-valueb

















A-C
narrow
120
66
64
45
44
0.0007


A-T
narrow
7
21
1
3
4
0.0136


G-C
narrow
7
20
3
5
8
0.0997


G-T
narrow
69
96
17
30
35
0.0299


Global
narrow





0.0003


A-C
broad
143
86
76
53
52
0.0009


A-T
broad
10
25
1
3
4
0.0195


G-C
broad
9
26
4
5
9
0.0587


G-T
broad
92
117
20
40
43
0.0634


Global
broad





0.0005





aHaplotypes recoded as alleles prior to PDT analysis.


bP-value generated by PDT.






The haplotype transmissions were also investigated for parent of origin and sex differences using ETDT (Sham and Curtis (1995) Ann. Hum. Genet. 59:323-336) and TRANSMIT software, respectively. When maternal and paternal transmissions were investigated separately, no parental differences in transmission ratios was observed. Male and female affected individuals are also equally likely to inherit the A-C haplotype. Thus, these data do not support a significant parent of origin or sex bias effects.
Computer prediction programs indicated that these polymorphisms did not introduce new splice acceptor or donor sites. Similar analysis was used to demonstrate that the A and G alleles of rs1861972 did not alter any putative transcription factor binding sites in the intron. However, the C allele for rs1861973 generated a consensus binding site for the general transcription factor, Sp1. This difference in transcription factor binding could alter the transcriptional regulation of EN2 and confer risk to autism.
These data represent the most significant genetic association reported for AS disorders. The overtransmission of the A and C alleles of both SNPs indicate risk or these SNPs are in linkage disequilibrium with other polymorphisms that contribute to autism.
The results of this association study together with the similarities in the cerebellar phenotype observed in the mouse knockout and autistic individuals make EN2 an excellent candidate for an autism susceptibility locus. Using the transmission data observed in the sample population disclosed herein, a genotype relative risk was estimated at 2.19 and a population attributable risk of 69% for the A-C predisposing haplotype. In other words, these data indicate that if the population were monomorphic for the G and T (protective) alleles, the prevalence of autism would be 69% lower. These data indicate a highly significant role for variation at this locus in the etiology of AS. Since the GRR and PAR were calculated from a sample population ascertained for multiple affected siblings, the actual risk estimates could be different in the general AS population. Estimates of GRR in multiplex sibships compared with singleton families were thought to be distorted depending on the background heritability (multilocus model of the disorder). The GRR was in fact expected to be deflated at a rate that was proportional to an increase in background heritability and more accurately estimated in situations of low background heritability (Risch (2001) Theor. Popul. Biol. 60:215-220). Given the complex polygenic model of inheritance with anywhere between 3-15 interacting loci that have been proposed for AS, other loci may contribute to the phenotype.
En2 functions in cerebellar patterning during development. Although En2 is expressed as early as embryonic day 9.5 during mouse cerebellar development, it is believed to be redundant to En1 in anterior-posterior patterning of the neural tube necessary to form the cerebellum (Hanks, et al. (1995) Science 269:679-682; Liu and Joyner (2001) Annu. Rev. Neurosci. 24:869-896). The knockout has demonstrated that En2 is essential for normal postnatal cerebellar development (Millen, et al. (1994) Development 120:695-706; Millen, et al. (1995) Development 121:3935-45; Kuemerle, et al. (1997) J. Neurosci. 17:7881-9). Although the cerebellum is often noted for its uniform structure, anatomical and biochemical studies have determined that the cerebellum is highly patterned. A number of genes including En2 are expressed in stripes in the postnatal cerebellum. These genes are believed to coordinate both the differential proliferation that is potentially responsible for proper cerebellar foliation as well as the topographic mapping of spinocerebellar and olivocerebellar afferents (Hawkes and Eisenmann (1997) Perspect. Dev. Neurobiol. 5:95-105). In the En2 knockout, this postnatal patterning is disrupted as evidenced by abnormal gene expression, foliation and misrouting of afferents (Vogel, et al. (1996) Brain Res. Dev. Brain Res. 96:210-218; Kuemerle, et al. (1997) J. Neurosci. 17:7881-9). This abnormal patterning could either directly affect cerebellar function or indirectly perturb interacting forebrain structures that mediate altered social, language and cognitive abilities observed in autism.
EXAMPLE 2
Transmission Disequilibrium Analysis—Study 2
The analysis presented in Example 1 demonstrated that the A allele of rs1861972 and the C allele of rs1861973 were significantly associated with ASD individually and as a haplotype under both narrow and broad diagnostic criteria. Replication of these association results is now observed in both another 222 AGRE families (AGRE II) and 129 National Institute of Mental Health (NIMH) families.
Subjects. Families recruited to the AGRE and to the NIMH Center for Collaborative Genetic Studies were used for this study (Risch, et al. (1999) Am. J. Hum. Genet. 65:493-507; Geschwind, et al. (2001) Am. J. Hum. Genet. 69:463-466).
The AGRE I dataset included 167 families, while the AGRE II dataset included 222 additional families. Family selection criteria have been described (Liu, et al. (2001) Am. J. Hum. Genet. 69:327-340; Geschwind, et al. (2001) supra). Families recruited by AGRE included at least two affected siblings (diagnosed with either autism, Asperger's Syndrome or Pervasive Development Disorder-Not Otherwise Specified (PDD-NOS)), one or both parents and additional affected and unaffected siblings when available. Although unaffected siblings had not undergone an Autism Diagnostic Interview-Revised (ADI-R) evaluation, in the combined AGRE sample extensive neurological, psychological and medical evaluations were available for 69 of the 277 unaffected siblings. None of the unaffected siblings displayed characteristics of a broad autism phenotype. Fragile X information was available for 381 of the 399 AGRE families considered for use in this study. Ten families were removed because at least one individual per family displayed a pre, intermediate or full Fragile X mutation state. Karyotypic data was available for 109 AGRE families used in this study. Five karyotypically abnormal families with a duplication of SNRPN on chromosome 15q12 (a marker for cytogenic abnormality at the chromosome 15 autism critical region) were also removed.
The NIMH dataset included 143 families. 14 of these families were also included in the AGRE datasets so were removed from this analysis. Selection criteria have been described previously (Risch, et al. (1999) supra) and anonymous data on family structure, age, sex, diagnostic interview data and status were available. Families in the NIMH dataset had at least 2 affected siblings or more distantly related individuals (e.g., cousins) with a diagnosis of autism or another pervasive developmental disorder, without any associated primary disorder such as Fragile X syndrome. The majority of the families included in the collection were affected sib multiplex families. 46 of the 53 unaffected children have undergone ADI-R evaluation and these individuals did not meet criteria for any ASD (Risch, et al. (1999) supra). The diagnosis for six individuals was uncertain and one individual did not meet ASD criteria by the ADI-R but exhibited behavioral and developmental abnormalities. These seven individuals were excluded from the analysis. No karyotype data was available for the NIMH dataset. For this analysis, individuals were considered affected under a narrow diagnostic definition if they were diagnosed with autism, while they were considered affected under a broad diagnostic definition if they were diagnosed with autism, Asperger's syndrome, or PDD-NOS.
Thirty-two of the families in the AGRE II sample and 20 in the NIMH sample included multiple births. In the AGRE II sample there were 19 families with MZ multiple births (16 MZ twins were autism:autism concordant, 2 were autism:PDD discordant, and 1 was MZ autism:autism concordant quadruplets), 11 families with DZ multiple births (9 twins and two triplets), and two additional families with twins of unknown zygosity. In the NIMH sample, 10 families had MZ twins (9 MZ twins were autism:autism concordant and 1 was autism:PDD discordant), 9 families had DZ twins, and one family had a triplet with a MZ pair and a third DZ sibling (all were autism:autism concordant). DNA was available for all twins in both datasets and all siblings were genotyped. All DZ were included in the data analysis, but for MZ siblings only the first MZ cotwin was selected for analysis.
DNA Analysis. Samples in the AGRE II and NIMH dataset were genotyped for the SNPs rs1861972 and rs1861973 using simplex PYROSEQUENCINGTM assays and the automated PSQ HS 96A platform according to established methods (Ronaghi, et al. (1998) Science 281:363-365; Ahmadian, et al. (2000) Anal. Biochem. 280:103-110). Fourteen additional polymorphisms (rs6150410, rs1345514, rs3735653, rs3735652, rs6460013, rs7794177, rs3824068, rs2361688, rs3824067, rs3808332, rs3808331, rs4717034, rs2361689, rs3808329) were genotyped in the AGRE I dataset, 12 were identified by dbSNP. The PvuII RFLP, suggested to be associated with autism (Petit, et al. (1995) J. Med. Genet. 32: 269-274), was identified as a −/CG insertion/deletion polymorphism by sequence analysis and comparisons to published RFLP reports (Logan and Joyner (1989) Nucleic Acids Res. 17(7):2879). For PvuII and rs2361688, a PvuII and HinfI RFLP assay was used respectively. An additional intronic SNP (ss38341503) was identified by sequence analysis. Each dbSNP polymorphism was sequence verified using 24 unrelated individuals (23 Caucasian and 1 of Hispanic/Latino descent) prior to the design of genotyping assays. A standard PCR amplification followed by allele separation on a 10% polyacrylamide gel electrophoresis assay was used to genotype the rs6150410 insertion/deletion polymorphism. Genotypes were called based upon band size differences of 263-bp (insertion allele) and 254-bp (deletion allele). Primers were designed using publicly available software (see Table 5). For rs6460013, rs7794177, rs1264067, rs3808332, rs3808331 and rs4717034, a tetra-primer ARMS-PCR strategy was used to genotype individuals (Ye, et al. (2001) Nucleic Acids Res. 29:E88-8). Primers were designed using the publicly available software (see Table 5). For rs3735652, ss38341503, and rs3808329, a ligase detection reaction (LDR) and the LUMINEXTM 100 flow cytometry platform was used (Iannone, et al. (2000) Cytometry 39(2):131-40).










TABLE 5







SEQ



SNP

ID


Primers
Sequence
NO:







rs6150410





Forward
CTAGAGGGAAAACGGGGTTC
12


Reverse
AACTCCGCAAGGTGTTTCAG
13


 


PvuII


Forward
TGGCAGATGTGTGCCTAG
14


Reverse
CCAGACCGGTCATCTCGTTTTC
15


 


rs1345514


Forward
AGAGCTGCCCTATCGGATGTT
16


Reverse
AAACTAATTTTGCCGGAGAGC
17


PYROSEQUENCING TM
CCCACCAAACACCC
18


 


rs3735652


Forward
CTGTCGGTGAGCTCGGACT
19


Reverse
TGGAAGACAGAGAGGGGAGA
20


LUMINEX TM G
GCGACATTGTGTGAAGCTGACG
21


LUMINEX TM C
GCGACATTGTGTGAAGCTGACC
22


LUMINEX TM common
CCGGCCCGGGCAGCGGC
23


 


rs6460013


Forward outer
CGCATCTCTTCCCAGCCCCTAGC
24


Reverse outer
TGCATCCTCCTGAGTCCCACCG
25


Forward inner
CCTTCCCTACGATCTTCCAACTCGGG
26


Reverse inner
GCATGCGTCCCCGGCCTAGA
27


 


rs7794177


Forward outer
CACAGGGAAGGAGGAAAATAAA
28


Reverse outer
TCATCAGAAATATGCACGCATA
29


Forward inner
AGATCTGCGATTTTAAAAAACTAACT
30


Reverse inner
TTGATGATTTCTACAAGGACAAGG
31


 


rs3824068


Forward
CATTAACAAGAGCCCCAGGA
32


Reverse
CCATGAGAGCACACACCCTA
33


PYROSEQUENCING TM
CAGTGCCTGTCTTGC
34


 


rs2361688


Forward
TGCACCTACCCCTACCAAAGCCA
35


Reverse
TGTGGATCTCCTTGGAGGCCCT
36


 


rs3824067


Forward outer
CTCCAAGGAGATCCACATTCCTCTT
37


Reverse outer
GGGTCGCTGTAAGGCTTCTAGGAC
38


Forward inner
CGAGATGCTCCCTAAAGCCCAA
39


Reverse inner
GGTTTCAATTTGTGCGGTGATTCAA
40


 


rs1861972


Forward
CATACACCGCACAAATTGAAAC
41


Reverse
GATTCAGACTTATGAACCTGACCTG
42


PYROSEQUENCING TM
CACCACTCCCTGCCA
43


 


rs1861973


Forward
CATACACCGCACAAATTGAAAC
41


Reverse
GATTCAGACTTATGAACCTGACCTG
42


PYROSEQUENCING TM
CCTTACAGCGACCCT
44


 


ss38341503


Forward
CCTTCTGCTCTCCTCCCTCT
45


Reverse
GGCCTGGTTTTTCCTAGTCC
46


LUMINEX TM C
CCCTCCTGTCCTCAGGGCC
47


LUMINEX TM T
CCCTCCTGTCCTCAGGGCT
48


LUMINEX TM common
CACCTGCCCCTGATTCCCAC
49


 


rs3808332


Forward outer
GCCCTTGGCTGGGAGTCATAGA
50


Reverse outer
GGGACTATGGGGCAGGCCTAGT
51


Forward inner
TTTCCCAGTCTTCTCTCCTCCACC
52


Reverse inner
GCGGTAGGTGCTGAGAGCGA
53


 


rs3808331


Forward outer
AGTCTTCTCTCCTCCCCTCTCT
54


Reverse outer
GAGGACTGCGTGTGATGTAAGT
55


Forward inner
GAAAGTGTGGGGAGTTTTGATT
56


Reverse inner
TCTAGATAAAAGTAAAACTCCTGGAT
57


 


rs4717034


Forward outer
CCGCCATCCCTGTTCCTGAACA
58


Reverse outer
GTGTGCCACCCAATAGGCACCG
59


Forward inner
CCCTCACCAAGTGGTGGAGGTCAGT
60


Reverse inner
GACTGGGCATGGGCTCACCG
61


 


rs3808329


Forward
GTTTGTGTTGGCTTGGTGAG
62


Reverse
CCCTCTACAGAGCCTTCTGC
63


LUMINEX TM G
CCTCTCCTCACCCTCCTGCG
64


LUMINEX TM A
CCTCTCCTCACCCTCCTGCA
65


LUMINEX TM common
CTAACTCCCTCCTCCTTCTCC
66









For rs6460013, rs7794177, rs1264067, rs3808332, rs3808331, rs4717034, tetra-primer ARMS-PCR was conducted in a 10 μl reaction using 1 pmol for each of the inner primers and 0.1 pmol for each of the outer primers, 0.2 5 mM dNTP, 1.5 mM MgCl2, 25 mM KCl, 10 mM Tris-HCl (pH 8.3 for rs6460013, rs7794177, rs1264067; pH 8.8 for rs3808332, rs4717034 and pH 9.2 for rs3808331). For rs1264067, the same conditions were used except for 3.5 mM MgCl2. For rs6150410, the same conditions were used as for rs1264067 with the following exceptions: 0.4 μM of each primer and 10 mM Tris-HCl (pH 8.8). Standard cycling conditions were used: 1 cycle of 94° C. for 4 minutes; 35 cycles of 94° C. for 30 seconds, Tm ° C. for 30 seconds, 74° C. for 30 seconds; and 1 cycle of 74° C. for 10 minutes (Tm 50° C. for rs1264067, Tm 55° C. for rs6460013, rs7794177, Tm 56° C. for rs3808331, Tm 59° C. for rs6150410; Tm 62° C. for rs3808332, rs4717034).
Rs1345514, rs3824068, rs1861972 and rs1861973 were genotyped using a PYROSEQUENCINGTM assay. PCR was conducted in a 20 μl reaction using 0.25 mM dNTP, 1.875 mM MgCl2, 6.25 mM KCl, 1.25 mM Tris-HCl (pH 9.0), 0.1% TRITONTM X-100, 0.05 μM of each primer for rs1861972, rs1861973 and 0.075 μM of each primer for rs3824068. For rs1345514, the same PCR conditions as rs1861972 were used except 0.025 μM of each primer, 0.01 mM dATP, dCTP, dTTP, 2.5 μM dGTP and 7.5 μM 7-deaza-2′-deoxyguanosine triphosphate, 1.25 mM MgCl2. Standard cycling conditions were as follows: 1 cycle of 94° C. for 4 minutes; 40 cycles of 94° C. for 30 seconds, Tm ° C. for 30 seconds, 74° C. for 30 seconds; and 1 cycle of 74° C. for 10 minutes (Tm 60° C. for rs3824068, rs1861972 and rs1861973; Tm 62° C. for rs3808332 and rs4717034).
For SNPs genotyped using LUMINEXTM 100 flow cytometry platform (rs3808329, rs3735652, and ss38341503), PCR was conducted in a 20 μl reaction using 0.4 μM of each primer. 0.125 mM dNTP, 1.875 mM MgCl2, 31.25 mM KCl and 12.5 mM Tris-HCl (pH 8.8 for rs3808329 and 8.3 for ss38341503) were used for rs3808329 and ss38341503. For rs3735652, 1.25 mM MgCl2, 1.25 mM Tris-HCl (pH 9.0), 6.25 mM KCl, 0.1% TRITONTM X-100, 0.01 mM dATP, dCTP, dTTP, 2.5 μM dGTP and 7.5 μM 7-deaza-2′-deoxyguanosine triphosphate were used. Standard cycling conditions were used: 1 cycle at 94° C. for 4 minutes; 35 cycles of 94° C. for 30 seconds, Tm ° C. for 30 seconds, 74° C. for 40 seconds; and 1 cycle of 74° C. for 10 minutes (Tm 66.3° C. for rs3808329, Tm 58° C. for rs3735652, Tm 57° C. for ss38341503).
Rs2361688 and PvuII were genotyped using an RFLP assay. PCR was conducted in 10 μl reaction using 0.1 μM of each primer, 0.25 mM dNTP. For rs2361688, 10 mM Tris-HCl (pH 9.2), 1.5 mM MgCl2, 25 mM KCl were used. For PvuII, 1 mM Tris-HCl (pH 9.2), 5 mM KCl, 0.1% TRITONTMTM X-100, 1.25 mM MgCl2 were used. Cycling conditions were as follows: 1 cycle of 94° C. for 4 minutes; 35 cycles of 94° C. for 30 seconds, Tm ° C. for 30 seconds, 74° C. for 30 seconds; and 1 cycle of 74° C. for 10 minutes (Tm 64° C. for rs2361688, Tm 61° C. for PvuII.
Statistical analysis. Prior to data analysis, each polymorphism was assessed for deviations from Hardy-Weinberg equilibrium using genotype data from all parents and standard formulae. The DNA from the MZ twins was used as a genotyping internal control, with complete genotypic concordance observed for all MZ cotwins. Genotypes were checked for Mendelian inconsistencies using the PEDCHECK program version 1.1 (O'Connell and Weeks (1998) Am. J. Hum. Genet. 63: 259-266) and all identified Mendelian errors were corrected by re-genotyping individual samples. In the AGRE I dataset, missing genotyping data was present for 9 individuals for four markers. Since recombination events were not expected at a high frequency given the small (<8kb) inter-marker distances, haplotype inconsistencies were identified by the SIMWALK program version 2.86 (Weeks and Lathrop (1995) Trends Genet. 11: 513-519). For each of the 14 polymorphisms genotyped in the AGRE I dataset, three marker haplotype analysis with rs1861972 and rs1861973 was performed. Regenotyping of flagged polymorphisms identified only 155 of the 10360 genotypes (1.5%) that could not be resolved. These genotypes were distributed between the 14 polymorphisms, ranging from 45 genotypes for rs1345514 to 7 genotypes for rs3824068. For rs1861972 and rs1861973 genotyped in the AGRE II and NIMH datasets, two SNP haplotype analyses identified only 12 of the 1741 genotypes (0.7%) that could not be resolved upon re-genotyping. The linkage disequilibrium (LD) coefficient (D′) for the 18 different polymorphisms was calculated in the AGRE I dataset using the parental genotypes and the GOLD (version 1.0) program (Abecasis and Cookson (2000) Bioinformatics 16:182-3).
All single and multi-locus association analyses were performed using the program PDTPHASE (version 2.404) which also calculates the corresponding P-values. Both haplotype-specific P-values and global P-values (with adjustments for all possible common haplotypes with a frequency greater than 5%) were calculated by the PDTPHASE program. PDTPHASE is a component of the UNPHASED package of association analysis programs (Dudbridge (2003) Genetic Epidim. 25:115-121). PDTPHASE is a modification of the pedigree-based transmission disequilibrium test PDT (Martin, et al. (2000) Am. J. Hum. Genet. 67: 146-154). PDTPHASE like PDT was designed to allow the use of data from related triads and disease discordant sibships from extended pedigrees when testing for transmission disequilibrium. It determines the presence of association by testing for unequal transmission of either allele from parents to affected offspring and/or unequal sharing of either allele between discordant sibships. Informative extended pedigrees contain at least one informative triad (i.e., an affected child with at least one parent heterozygous at the marker) and/or discordant sibship (i.e., at least one affected and one unaffected sibling with different marker genotypes). PDTPHASE has a number of advantages over PDT that increase the statistical power of the analysis. It can handle missing parental data, is able to perform multilocus analysis and includes an EM algorithm that calculates maximum-likelihood gametic frequencies under the null hypothesis, allowing the inclusion of phase uncertain haplotypes.
The total number of families, triads and Discordant Sib Pairs (DSPs) used for the rs1861972 and rs1861973 replication analyses in the AGRE II and NIMH datasets as well as the extension of the LD map in the original AGRE I dataset is listed in Table 6.












TABLE 6





Dataset
Diagnosis
Familiesc
Triadsc
DSPsc
Subjects




















AGRE Ia
Narrow
166
262
134
689



Broad
167
322
168
750


AGRE IIb
Narrow
211
342
225
1033



Broad
222
434
269
1071


NIMH
Narrow
127
228
71
501



Broad
129
237
73
515





aThe 167 AGRE I families of Example 1.


b222 additional AGRE families.


cNumber of families, Triads and discordant sibpairs (DSPs) as calculated by PDT (Martin, et al. (2000) supra).






In all the haplotype analyses, haplotypes with a frequency <5% were pooled for analysis. PDTPHASE, like PDT, can calculate two global scores: the PDTsum (which sums the level of significance from all families) and the PDTave (which gives equal weight to all families in a data set). Since most families in this study had similar size and structure, and it was observed that the χ2 distribution and P-values were similar for both PDT scores, only PDTsum were reported herein.
Using a multiplicative model, haplotype relative risk for the rs1861972-rs1861973 A-C haplotype was estimated as the transmission ratio (Transmitted/Untransmitted—T/U) (Altshuler, et al. (2000) Nat. Genet. 26:76-80) from heterozygous parents to a single affected offspring that was selected randomly from each of the 532 families. TRANSMIT (version 2.5.4) was used for this analysis because it is capable of selecting at random a single affected offspring per family for association analysis. From the output, the number of informative transmissions (i.e., from heterozygous parents) may be derived (see Example 1) and the transmission ratio estimated. This analysis was repeated 20 times each for the narrow and broad diagnosis and mean relative risk was estimated under each diagnosis. The relative risk and haplotype frequency for the A-C haplotype were then used to estimate the population attributable risk (PAR) using the following standard formula: PAR=(X−1)/X; where X=(1−f)2+2f(1−f)γ+f2γ2 and γ=haplotype relative risk.
Sequence Analysis. Four overlapping PCR products of the EN2 intron were PCR amplified from 20 ASD-affected individuals who inherited the rs1861972-rs1861973 A-C haplotype from heterozygous parents. Each PCR product was then purified (QIAGEN®-QLAQUICK® PCR Purification Kit) and sequenced on an ABI 3730 DNA analyzer. The sequence was then analyzed for DNA alterations using CODONCODE ALIGNER®. The primer sequences are listed in Table 7 and PCR conditions employed are as follows.
PCR for amplification of PCR product 1 was conducted in a 50 μl reaction using 2 mM MgCl2, 5 mM KCl, 1 mM Tris-HCl (pH 9.2), 0.1% TRITONTM X-100, 2 μl of GC melt (BD Biosciences), 5% Dimethyl Sulfoxide (Sigma), 0.4 μM of each primer, 8 μM dATP, dCTP, dTTP, 2 μM dGTP and 6 μM 7-deaza-2′-deoxyguanosine triphosphate. Standard cycling conditions were used: 1 cycle of 94° C. for 1 minute; 35 cycles of 94° C. for 40 seconds, 59° C. for 30 seconds, 68° C. for 3 minutes 30 seconds; and 1 cycle of 68° C. for 3 minutes. For PCR products 2, 3, and 4, PCR was conducted in a 20 μl reaction using 0.625 mM MgCl2, 5 mM KCl, 1 mM Tris-HCl (pH 9.2), 0.1% TRITONTM X-100, 0.25 mM dNTPs, 0.5 ng/μl of each primer. Standard cycling conditions for PCR products 2, 3, and 4 were used: 1 cycle of 94° C. for 5 minutes; 35 cycles of 94° C. for 30 seconds, Tm ° C. for 30 seconds, 74° C. for 60 seconds; and 1 cycle of 74° C. for 10 minutes (where Tm 60° C. for PCR product 2 and 4, Tm 62° C. for PCR product 3).










TABLE 7







SEQ





ID


Primer
Sequence
NO:







PCR Product 1





Forward
CTG TCG GTG AGC TCG GAC TCG G
67


Reverse
GCC CTG CAG AGA TGC TGG ATA TAT
68


 


PCR Product 2


Forward
TAG AAA GGA CCT TCT CTC AGG G
69


Reverse
GTG GTT GGA AAC CCA GAC AGA GAT
70


 


PCR Product 3


Forward
CAT TAA CAA GAG CCC CAG GAC CAG AAG
71


Reverse
GAC AAG GTC AGC TGG GCT AC
72


 


PCR Product 4


Forward
TTC CCC ATG GAT AGC AGG TCC TAG
73


Reverse
GGT CTC GAA AAC CAA AGA AGA AGA ACC CGA
74









En2 Expression Constructs. To misexpress the En2 protein, total RNA was isolated from adult C57BL6/J mouse cerebellum, a 1012-bp PCR product that included the En2 protein coding sequence was amplified by RT-PCR (SUPERSCRIPTTM RT) and subcloned 3′ of a CMV protein/enhancer. PCR was conducted in a 25 μl reaction of 0.4 μM of each primer, 0.25 mM dNTP, 1.5 mM MgCl2, 25 mM KCl, 10 mM Tris-HCl pH 8.3 and cycling conditions of 1 cycle of 94° C. for 4 minutes; 35 cycles of 94° C. for 45 seconds, 61° C. for 1 minute, 74° C. for 2 minutes; and 1 cycle of 74° C. for 10 minutes were used. The primer sequences were: Forward, 5′-GTG AAG TAT GGA GGA GAA GG-3′ (SEQ ID NO:75); Reverse, 5′-CTA AAC AGT CCC CTT TGC AG-3′ (SEQ ID NO:76). The PCR product was isolated by 0.8% agarose gel electrophoresis, purified and cloned into the pCR2.1® vector (INVITROGENTM). EcoRI restriction enzyme digestion was used to clone the En2 cDNA into the PCMS-EGFP expression vector (CLONTECHTM).
Cell Culture and cDNA Transfections. Time-mated pregnant Sprague Dawley rats were obtained from Hilltop Labs (Philadelphia, Pa.). At embryonic day 14.5 (E14.5), embryonic skull and meninges were removed and dorsolateral cerebral cortex was dissected, mechanically dissociated, and plated at 4×105 cells on poly-D-lysine (0.1 mg/mL) and laminin (20 μg/mL)-coated 25-mm glass coverslips (VWR) in defined medium according to established methods (Nicot and DiCicco-Bloom (2001) Proc. Natl. Acad. Sci. USA 98(8): 4758-63). Culture medium consisted of NEUROBASALTM (GIBCO-BRL®) supplemented with 2% B27, and contained glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 μg/ml), bovine serum albumin (1 mg/ml), and basic fibroblast growth factor (10 ng/ml). Unless stated otherwise, components were obtained from Sigma (St. Louis, Mo.). Cultures were maintained in a humidified 5% CO2/air incubator at 37° C.
After 24 hours in culture, cells were transfected using LIPOFECTAMINETM Plus Reagent (GIBCO-BRL®) for 5 hours containing one of the following: 1) the mouse En2 EGFP-expression plasmid which codes for a full-length En2 protein with 93% nucleotide identity with rat En2, 2) pCMS-EGFP with En2 cloned in the non-protein coding, reverse orientation (REn2), or 3) pCMS-EGFP alone. After an additional day of incubation, cells were fixed with 4% paraformaldehyde and assessed using phase and fluorescence microscopy.
En2 RT-PCR Expression Analysis. Total RNA was isolated from freshly dissected E14.5 rat cortices and hindbrains, and the expression of En2 was determined by PCR amplification of a 220-bp 3′-UTR PCR product in a 25 μl reaction, using 0.4 μM of each primer, 0.25 mM dNTP, 1.5 mM MgCl2, 25 mM KCl, 10 mM Tris-HCl pH 8.3 and cycling conditions of 1 cycle of 94° C. for 4 minutes; 35 cycles of 94° C. for 45 seconds, 56° C. for 1 minute, 74° C. for 90 seconds; and 1 cycle of 74° C. for 10 minutes. The primer sequences were: Forward, 5′-AAC CGT GAA CAA AAG GCC AGT G-3′ (SEQ ID NO:77), Reverse: 5′-CTA AAC AGT CCC CTT TGC AG-3′ (SEQ ID NO:76).
Immunocytochemistry. Immunocytochemistry was performed according to established methods (Nicot and DiCicco-Bloom (2001) supra). The following dilutions of primary and secondary antibodies were used: polyclonal chicken anti-GFP (1:8000; Chemicon), polyclonal goat anti-En2 (1:500; Santa Cruz), mouse TuJ1 (1:1500; COVANCE®), ALEXA FLUOR® 488-conjugated rabbit anti-chicken IgG (1:800; Chemicon) and ALEXA FLUOR® 594-conjugated rabbit anti-goat or goat anti-mouse IgG (1:1000; Vector).
Results. For the AGRE II dataset, significant (P<0.05) evidence of association for the A allele of rs1861972 was observed under the broad diagnosis while a trend towards association was observed under the narrow diagnosis (Table 8). For rs1861973, significant association of the C allele was observed under both diagnostic criteria (Table 8). Analysis of rs1861972-rs1861973 haplotypes demonstrated that the A-C haplotype was significantly over-transmitted to affected offspring under both diagnostic criteria (Table 9) while the A-T, G-C and G-T haplotypes were all under-transmitted. Global χ2 tests for all haplotypes yielded significant P-values (narrow: P=0.0048; broad: P=0.0016) (Table 9) that were similar to those of the AGRE I dataset presented in Example 1. Thus, replication of the association results for the same alleles of rs1861972 and rs1861973 with ASD was observed in this second AGRE dataset.











TABLE 8









Parental





Transmissionsd
DSPse















Dataset
SNPc
Diagnosis
T
U
A
UA
χ2f
P-valueg


















AGRE Ia
rs1861972
narrow
383
354
202
185
4.991
0.0255




broad
467
436
253
226
5.861
0.0155



rs1861973
narrow
373
338
199
183
6.936
0.0084




broad
449
415
242
220
6.297
0.0121


AGRE IIb
rs1861972
narrow
438
408
314
297
2.997
0.0834




broad
555
513
381
359
4.73
0.0296



rs1861973
narrow
433
395
308
285
4.903
0.0268




broad
546
500
375
346
6.299
0.0121


NIMH
rs1861972
narrow
222
200
113
107
4.000
0.0455




broad
228
206
115
109
3.843
0.0500



rs1861973
narrow
227
203
111
104
5.139
0.0234




broad
234
209
113
105
5.585
0.0181





aThe 167 AGRE families of Example 1.


bThe additional 222 AGRE families.


cThe MAF for rs1861972 was 0.269 and 0.317 in the AGRE II and NIMH datasets, respectively. For rs1861973, the MAF was 0.279 and 0.295, respectively.


dT = number of times common allele transmitted; U = number of times common allele not transmitted from parents to affected offspring.


eDiscordant sibpair counts: A = total number of the common allele in affected siblings; UA = total number of the common allele in unaffected siblings of DSPs.


fGlobal χ2 values calculated by PDTPHASEsum (Dudbridge (2003) supra).


gP-value generated by PDTPHASEsum (1 df). Bolded P-values represent significant (P < 0.05) association.






Since identical criteria have been used to obtain all the AGRE pedigrees, the AGRE I and AGRE II datasets were combined and association of rs1816972 and rs1861973 with ASD was re-analyzed. Smaller P-values were observed than in either dataset alone (haplotype—narrow: P=0.0000067; broad: P=0.0000033), indicating that the same alleles are associated with ASD in both datasets.
Association of rs1861972 and rs1861973 was then tested in the NIMH dataset. Statistically significant association was obtained for both SNPs individually (Table 8) and as a haplotype (Table 9).











TABLE 9









Parental





Transmissionsd
DSPse
















Dataset
Haplotypec
Diagnosis
T
U
A
UA
Freq.
χ2f
P-valueg



















AGRE Ia
A-C
narrow
369
323
195
179
0.732

0.0024



A-T

8
25
5
4
0.014

—



G-C

4
15
4
4
0.006

—



G-T

111
129
52
69
0.247

0.0714



global






14
0.0009



A-C
broad
444
399
238
216
0.734

0.0039



A-T

11
28
5
4
0.016

—



G-C

5
16
4
4
0.007

—



G-T

140
157
69
92
0.243

0.0765



global






13
0.0017


AGRE
A-C
narrow
429
386
308
285
0.713

0.0168


IIb
A-T

4
16
2
5
0.017

—



G-C

2
8
0
0
0.007

—



G-T

161
186
128
148
0.263

0.0928



global






11
0.0048



A-C
broad
540
487
375
346
0.721

0.0061



A-T

6
18
2
6
0.014

—



G-C

2
11
0
0
0.006

—



G-T

210
242
149
174
0.259

0.0493



global






13
0.0016


NIMH
A-C
narrow
221
198
111
104
0.676

0.0321



A-T

1
2
0
1
0.007

—



G-C

6
5
0
0
0.025

—



G-T

78
101
27
34
0.292

0.0329



global






6.1
0.0463



A-C
broad
227
204
113
105
0.672

0.0312



A-T

1
2
0
2
0.008

—



G-C

7
5
0
0
0.023

—



G-T

81
105
29
35
0.296

0.0295



global






6.3
0.0431





aThe 167 initial AGRE families of Example 1.


bThe additional 222 AGRE II families.


cThe frequency of the A-C haplotype was 0.715 and 0.680 in the AGRE II and NIMH datasets, respectively.


dT = number of times test haplotype transmitted; U = number of times test haplotype not transmitted from parents to affected offspring.


eDiscordant sibpair counts: A = total number of the test haplotype in affected siblings; UA = total number of the test haplotype in unaffected siblings of DSPs.


fGlobal χ2 values calculated by PDTPHASEsum (Dudbridge (2003) supra), restricted to common haplotypes with frequency greater than 5%.


gP-value generated by PDTPHASEsum (1 df for single haplotype and 2 df for the global tests). Bolded P-values represent significant (P < 0.05) association.






When the NIMH dataset was combined with both AGRE datasets and re-analyzed for association, further reduction of the P-values was obtained (rs1861972-rs1861973 haplotype—narrow: P=0.00000065; broad: P=0.00000035). These data represent one of the most significant associations for any gene with ASD. Given the large sample size (518 families), these results indicate an inherited variation in EN2 in susceptibility to ASD.
Since a P-value is not a measure of effect size, this large combined sample of 518 families was used to estimate the relative risk and the associated population attributable risk (PAR) under a multiplicative model for the A-C haplotype. The haplotype relative risk was estimated as approximately 1.42 and 1.40 under the narrow and broad diagnosis, respectively. Although this represents a relatively modest increase in individual risk, given the high frequency of this common haplotype ( ̃67% in the combined sample), a relative risk of 1.42 and 1.40 corresponds to a large PAR of approximately 39.5% and 38% for the narrow and broad diagnosis of ASD, respectively. These data indicate that as many as 40% of the ASD cases in the population were influenced by variation in EN2 gene.
The data presented in Example 1 demonstrated that rs1861972 and rs1861973 were in strong LD with each other. Similar results were obtained in both the AGRE II an NIMH datasets (AGRE II: D′=0.967; NIMH: D′=0.977). In addition, the allele frequencies for rs1861972 and rs1861973 in both the AGRE II an NIMH datasets were almost identical to each other and to what was found for the AGRE I dataset of Example 1 (Table 10). This together with the association results obtained in the AGRE II and NIMH samples indicates that they are likely to be derived from the same population and therefore share a similar LD relationship with the etiological variant.











TABLE 10





SNP
Location
Polymorphisma
Freq.b
Assay Typec







rs6150410
Promoter
CGCATCCCC/— (SEQ 
0.334
PCR/gel electrophor.




ID NO: 78)



PvuII
Promoter
GC/—
0.469
RFLP


rs1345514
Promoter
C/T
0.340
Pyrosequencing TM


rs3735653
Exon 1
C/T
0.486
Pyrosequencing TM


rs3735652
Intron
G/C
0.402
Luminex TM


rs6460013
Intron
G/T
0.054
Tetra-Primer ARMS


rs7794177
Intron
C/G
0.077
Tetra-Primer ARMS


rs3824068
Intron
C/T
0.386
Pyrosequencing TM


rs2361688
Intron
A/G
0.271
RFLP


rs3824067
Intron
T/A
0.181
Tetra-Primer ARMS


rs1861972
Intron
A/G
0.281
Pyrosequencing TM


rs1861973
Intron
C/T
0.287
Pyrosequencing TM


ss38341503
Intron
C/T
0.010
Luminex TM


rs3808332
Intron
T/C
0.192
Tetra-Primer ARMS


rs3808331
Intron
T/C
0.063
Tetra-Primer ARMS


rs4717034
Intron
C/T
0.175
Tetra-Primer ARMS


rs2361689
Exon 2
T/C
0.322
Pyrosequencing TM


rs3808329
3′ UTR
A/T
0.130
Luminex TM





aSecond allele is rare allele.


bFrequency of rare allele in AGRE I dataset.


cPyrosequencing TM (Ronaghi, et al. (1998) supra; Ahmadian, et al. (2000) supra), Tetra-primer ARMS (Ye, et al. (2001) supra), Luminex TM (Iannone, et al. (2000) supra).






Analysis of the AGRE I dataset indicated that rs1861972 and rs1861973 were non-functional polymorphisms in LD with a risk allele(s) located elsewhere in the gene. To identify this risk allele, the LD map was extended in the original AGRE I dataset. This dataset was selected for LD mapping because it displayed the most significant association for rs1861972 and rs1861973, both individually and as a haplotype, and therefore represented a minimal cost-effective sample set with sufficient power to detect the putative risk allele. Fourteen additional polymorphisms (3 in the promoter, 10 in the intron and 1 in the 3′ UTR) were tested for association with ASD, giving a total of 18 markers typed across the entire gene. Thirteen of these newly typed polymorphisms were identified through dbSNP, while one, ss38341503, was identified by resequencing the entire intron in 20 individuals with ASD who inherited the rs1861972-rs1861973 A-C haplotype from heterozygous parents. The location, DNA change and minor allele frequency (MAF) of each polymorphism are presented in Table 10.
In the absence of knowledge about the exact mode of inheritance at this locus, a risk allele(s) responsible for rs1861972 and rs1861973 association was expected to exhibit the following inheritance pattern. The polymorphism(s) should display strong LD (D′>0.70) with both rs1861972 and rs1861973 and therefore, was expected to have a similar frequency as the A-C haplotype. Further, individually the polymorphism(s) should also be associated with ASD. If a single polymorphism was responsible for the association of rs1861972 and rs1861973, then this polymorphism should demonstrate at least as significant association as the A-C haplotype under both the narrow and broad diagnosis. However, if multiple alleles were working in concert and a simple additive model is assumed, then each of these polymorphisms should display association with ASD individually because they will be in strong LD with rs1861972 and rs1861973 but their statistical significance might not be as great as when they are analyzed as a haplotype. Moreover, in multi-SNP haplotype analysis for a single locus model, the associated allele in conjunction with the A-C haplotype should display at least as significant association as the A-C haplotype alone. In a multi-locus model, only the haplotypes with all or most of the risk alleles would display the greatest statistical significance.
When the 14 additional polymorphisms were tested for association in the AGRE I dataset, 12 displayed no evidence for association under both the narrow and broad diagnosis (Table 11).











TABLE 11








Parental





Poly-
Transmissionsa
DSPsb

P-














morphism
Diagnosis
T
U
A
UA
χ2c
valued

















rs6150410
narrow
317
317
183
189
0.081
0.776



broad
394
384
234
239
0.043
0.835


PvuII
narrow
253
249
127
131
0.000
1.000



broad
306
303
163
162
0.025
0.875


rs1345514
narrow
271
278
165
168
0.220
0.639



broad
332
331
211
215
0.015
0.902


rs3735652
narrow
274
291
156
168
1.532
0.216



broad
350
357
203
220
0.867
0.352


rs6460013
narrow
467
466
249
246
0.364
0.546



broad
568
569
314
309
0.381
0.537


rs7794177
narrow
425
414
239
237
1.374
0.241



broad
519
509
295
299
0.237
0.626


rs3824068
narrow
280
316
156
166
4.372
0.036



broad
355
384
205
215
2.664
0.103


rs2361688
narrow
347
328
193
183
2.317
0.128



broad
423
394
243
224
4.208
0.040


rs3824067
narrow
370
357
213
214
0.581
0.446



broad
443
438
263
267
0.003
0.959


ss38341503
narrow
464
458
266
265
1.581
0.209



broad
565
559
334
332
1.684
0.194


rs3808332
narrow
361
361
208
208
0.000
1.000



broad
433
440
260
261
0.173
0.677


rs3808331
narrow
421
417
243
245
0.040
0.841



broad
519
510
309
310
0.525
0.469


rs4717034
narrow
365
362
205
212
0.056
0.812



broad
436
444
257
267
0.802
0.37


rs3808329
narrow
424
405
229
243
0.108
0.742



broad
516
491
289
303
0.434
0.510





aT = number of times common allele transmitted; U = number of times common allele not transmitted from parents to affected offspring.


bDiscordant sibpair counts: A = total number of the common allele in affected siblings; UA = total number of the common allele in unaffected siblings of DSPs.


cGlobal χ2 values calculated by PDTPHASEsum (Dudbridge (2003) supra).


dBolded P-values represent significant (P < 0.05) association.






Two intronic SNPs, rs3824068 and rs2361688, displayed minimally significant association but only under one diagnosis (Table 11). To investigate whether rs3824068 and rs2361688 could be functioning in a multi-locus manner, 3 and 4 marker haplotype analysis with the rs1861972-rs1861973 A-C haplotype was performed. For the rs3824068-rs2361688-rs1861972-rs1861973 and the rs3824068-rs1861972-rs1816973 haplotype analysis, all common core A-C haplotypes (frequency>5%) displayed no association with the exception of the T-A-C rs3824068-rs1861972-rs1816973 haplotype that displayed minimal association under one diagnosis (Tables 6 and 8).
For the rs2361688-rs1861972-rs1861973 analysis, the G-A-C haplotype displayed similar statistical significance as the A-C haplotype under the broad diagnosis but under the narrow diagnosis the effect was diluted. Four other common 3 marker A-C haplotypes (G-A-C rs6460013-rs1861972-rs1861973, C-A-C rs7794177-rs1861972-rs1861973, A-C-C rs1861972-rs1861973-ss38341503 and A-C-A rs1861972-rs1861973-rs3808329) displayed similar statistically significant association as the A-C haplotype under at least one diagnosis. However, rs6460013, rs7794177, ss38341503 and rs3808329 were not associated individually with ASD, indicating that these polymorphisms were not functioning as risk alleles according to the criteria herein.
The inter-marker LD relationships for these 14 polymorphisms plus the 4 previously tested SNPs were then examined. All promoter, exonic and 3′-UTR polymorphisms displayed weak or intermediate LD (D′: 0.024-0.632) respectively with both rs1861972 and rs1861973, providing an explanation why they were not associated with ASD (Table 12). However, all new intronic SNPs displayed strong LD (D′:0.720-1.00) with both rs1861972 and rs1861973 (Table 12). The lack of association with ASD observed for 8 of the intronic SNPs indicates that these intronic variants were in weaker LD with the risk allele than rs1861872 or rs1861973. This reduced power to detect LD may be due to differences in allele frequencies and may reflect the genetic history of when these intronic alleles arose in relation to the risk allele. Evidence for some association of rs2361688 and rs3824068 with ASD indicates that these variants are in stronger LD with the risk allele(s) than the other newly genotyped intronic SNPs.







TABLE 12













 








 








 




















Data represent pairwise linkage disequilibrium (D′) in the AGRE I dataset. The LD relationship of each polymorphism with rs1861972 and rs1861973 are outlined with number of lines corresponding to the strength of LD (three lines-strong LD: D′>0.72; two lines-intermediate/weak LD: D′: 0.024–0.632).






One interpretation of the strong LD observed between the intronic SNPs and rs1861972 and rs1861973 as well as the decay of LD for flanking polymorphisms is that the risk allele is situated approximately 3.0 kb in the intron. Sequence analysis of the intron in 20 individuals affected with ASD who inherited the rs1861972-rs1861973 A-C haplotype from heterozygous parents has identified only one novel SNP (ss383341503) with a MAF of 1%, indicating that additional common intronic polymorphisms are unlikely. All intronic SNPs were tested and only rs1861972 and rs1861973 were consistently associated both individually and as a haplotype under both diagnostic criteria. Together this analysis indicates that the A allele of rs1861972 and the C allele of rs1861973 function as risk alleles in cis and the lack of association of some of the core A-C haplotypes identified in the multi-SNP haplotype analysis was due to other unidentified epistatic genetic or environmental interactions. Comparative genomic studies of human, chimp, mouse, rat and dog sequences do not place either SNP within conserved regions. However, computer prediction programs determined that the associated alleles of rs1861972 and rs1861973 were situated within consensus binding sites for the CBP and LvC transcription factors, respectively. For the associated alleles, the match ratio for each transcription factor was 100%. The non-associated alleles alter a conserved nucleotide in the consensus binding site so when the sequence was re-analyzed, the non-associated alleles were predicted to abolish binding of both transcription factors.
Risk alleles of human EN2 associated with ASD may alter the spatial and/or temporal expression of the gene during brain development. To examine the consequences of gene misexpression, En2 EGFP vectors were transfected into cultures of primary neuronal precursors obtained from rat E14.5 cerebral cortex. The expression plasmid alone (PCMS-EGFP) or with En2 cloned in the reverse orientation (REn2) was used as controls. This well-characterized model system has been used to define the effects of extracellular signals and transfected genes on cortical neurogenesis (Lu and DiCicco-Bloom (1997) Proc. Natl. Acad. Sci. USA 94(7):3357-62; Nicot and DiCicco-Bloom (2001) supra; Carey, et al. (2002) J. Neurosci. 22(5) :1583-91). En2 was not expressed in E14.5 rat cortical cells as assessed by RT-PCR, thereby defining the effects of En2 misexpression in a naive cell population. Twenty-four hours after transfection, all three vectors generated similar numbers of EGFP-expressing cells (pCMS-EGFP: 174.5±45.1; REn2: 201±20.4; En2: 163.3±11.9; GFP+ Cells±SEM: P>0.05), as detected by EGFP autofluorescence and immunocytochemistry, indicating that vector expression per se was not deleterious. En2 protein immunoreactivity was detected only in EGFP-positive, En2-transfected cells, but not in REn2- or EGFP-transfected cells.
The effects of vector expression were examined on cortical cell morphology, assessing undifferentiated precursors and mature neurons. Undifferentiated neural precursors appeared as flat cells that sometimes extended processes of variable diameter and length with distal filopodia. Precursors did not express the early marker of neuronal differentiation, cytoskeletal protein βIII-tubulin (TuJ1). Differentiated neurons exhibited a round or pyramidal cell body, extended thin, uniform processes and expressed βIII-tubulin. In cultures transfected with control vectors, approximately equal proportions of cells exhibited morphologies of precursors and neurons, reproducing ratios obtained previously in this model (Nicot and DiCicco-Bloom (2001) supra). In contrast, following En2 transfection, the proportion of undifferentiated precursors increased from 55% in controls to 71% in En2-transfected cells. As overall numbers of cells were similar across conditions, the increase in precursors occurred at the expense of cells exhibiting neuronal morphology: neurons decreased from 45% in controls to only 29% following En2 transfection. The reduction in neuronal differentiation was further verified by assessing βIII-tubulin-expressing cells, which was decreased by 55% in En2 transfected cells (100% in controls, 45% following En2 transfection), indicating that altered cytoskeletal protein expression may underlie changes observed in cellular morphology elicited by En2. These data demonstrate that En2 ectopic expression disrupts neuronal differentiation, indicating that the gene is an important regulator of neuronal development.
In summary, these data indicate that EN2 is involved in ASD susceptibility. Evidence for association was presented for rs1861972 and rs1861973 in the AGRE II and NIMH datasets. PAR estimations using the entire sample of 518 families indicated that the risk allele responsible for rs1861972-rs1861973 association contributed to approximately 40% of ASD cases in the general population. In addition, LD mapping using 18 SNPs distributed across the gene localized the associated genomic region to the intron. Analysis of this region identified associated intronic alleles that could be characterized for functional differences. Further, single and multi-SNP association data indicated that rs1861972, rs1861973 and rs2361688 were candidate risk alleles that function together in cis to increase risk for ASD. Moreover, it was demonstrated that ectopic misexpression of En2 disrupts neuronal development. Together these data indicate that variation within the EN2 gene plays an important role in ASD etiology and a risk allele(s) which causes altered expression of EN2 to perturb neuronal development and contribute to the pathology associated with ASD.

## Claims

1. A method for diagnosing the predisposition for developing autism spectrum disorder in a human comprising,
obtaining a sample from a human subject, said sample comprising nucleic acids; and
detecting in said nucleic acids the presence of
(i) an A at position 2236 of SEQ ID NO:11;
(ii) a C at position 2388 of SEQ ID NO:11; or
(iii) a combination of (i) and (ii),

wherein the presence of (i), (ii) or (iii) is indicative of the predisposition for developing autism spectrum disorder in the human.