Patent Application
20070218068
The present invention relates generally to the fields of genetics and medicine.
Autism is a neuropsychiatric developmental disorder characterized by impairments in reciprocal social interaction and verbal and non-verbal communication, restricted and stereotyped patterns of interests and activities, and the presence of developmental abnormalities by 3 years of age (Bailey et al., 1996). In his pioneer description of infantile autism, Kanner (1943) included the following symptoms: impaired language, lack of eye contact, lack of social interaction, repetitive behavior, and a rigid need for routine. He noted that in most cases the child's behavior was abnormal from early infancy. On this basis, he suggested the presence of an inborn, presumably genetic, defect. One year later, Hans Asperger in Germany described similar patients and termed the condition “autistic psychopathy”.
Autism is defined using behavioral criteria because, so far, no specific biological markers are known for diagnosing the disease. The clinical picture of autism varies in severity and is modified by many factors, including education, ability and temperament. Furthermore, the clinical picture changes over the course of the development within an individual. In addition, autism is frequently associated with other disorders such as attention deficit disorder, motor in coordination and psychiatric symptoms such as anxiety and depression. There is some evidence that autism may also encompass epileptic, metabolic and immune disorder. In line with the clinical recognition of the variability, there is now general agreement that there is a spectrum of autistic disorders, which includes individuals at all levels of intelligence and language ability and spanning all degrees of severity.
Part of the autism spectrum, but considered a special subgroup, is Asperger syndrome (AS). AS is distinguished from autistic disorder by the lack of a clinically significant delay in language development in the presence of the impaired social interaction and restricted repetitive behaviors, interests, and activities that characterize the autism spectrum disorders (ASDs).
ASDs are types of pervasive developmental disorders (PPD). PPD, “not otherwise specified” (PPD-NOS) is used to categorize children who do not meet the strict criteria for autism but who come close, either by manifesting atypical autism or by nearly meeting the diagnostic criteria in two or three of the key areas.
To standardize the diagnosis of autism, diagnostic criteria have been defined by the World Health Organisation (International Classification of Diseases, 10th Revision (ICD-10), 1992) and the American Psychiatric Association (Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV), 1994). An Autism Diagnostic Interview (ADI) has been developed (Le Couteur et al., 1989; Lord et al., 1994). The ADI is the only diagnostic tool available to diagnose ASD that has been standardized, rigorously tested and is universally recognized. The ADI is a scored, semi-structured interview of parents that is based on ICD-10 and DSM-IV criteria for the diagnosis of autism. It focuses on behavior in three main areas: qualities of reciprocal social interaction; communication and language; and restricted and repetitive, stereotyped interests and behaviors. Using these criteria, autism is no longer considered a rare disorder. Higher rates of 10-12 cases per 10,000 individuals have been reported in more recent studies (Gillberg and Wing, 1999) compared to the previously reported prevalence rate of 4-5 patients per 10,000 individuals based on Kanner's criteria (Folstein and Rosen-Sheidley, 2001). Estimates for the prevalence rate of the full spectrum of autistic disorders are 1.5 to 2.5 times higher. Reports of a four times higher occurrence in males compared to females are consistent. Mental retardation is present in between 25% and 40% of cases with ASD (Baird et al. 2000; Chakrabarti and Fombonne, 2001). Additional medical conditions involving the brain are seen in ca. 10% of the population (Gillberg and Coleman, 2000).
The mechanisms underlying the increase in reported cases of autism are unknown. It is highly debated whether this difference reflects an increase in the prevalence of autism, a gradual change in diagnostic criteria, a recognition of greater variability of disease expression, or an increased awareness of the disorder. In addition, there is a widespread public perception that the apparent increase is due primarily to environmentally factors (Nelson, 1991; Rodier and Hyman, 1998). However, it seems likely that most of the increased prevalence can be explained by a broadening of the diagnostic criteria, in combination with a broader application of these criteria.
Although there are effective treatments for ameliorating the disease, there are no cures available and benefits of treatment tend to be modest. Promising results have been obtained for several programs utilizing various behavioral and developmental strategies. Among the most promising are programs based on applied behavior analysis (ABA). Several medications appeared to improve various symptoms associated with autism, thereby increasing individuals's ability to benefit from educational and behavioral interventions. The most extensively studied agents are the dopamine antagonists. Several studies suggest the usefulness of various selective serotonin reuptake inhibitors.
Three twin studies have been performed to estimate heritability of autism (Folstein and Rutter, 1977; Bailey et al., 1995; Steffenburg et al., 1989). All twins who lived in a geographically defined population were sought out. In the combined data 36 monozygotic (MZ) and 30 dizygotic (DZ) twins were studied. The average MZ concordance rate is 70% compared to a DZ rate of 0%. A heritability of more than 90% was calculated from the MZ to DZ concordance ratio and the sibling recurrence risk that has been estimated to be ca 2%-4% (Jorde et al., 1991 Szatmari et al., 1998). Studies of non-autistic relatives have clearly shown that several characteristics of the ASDs are found more often in the parents of autistic children than the parents of controls including social reticence, communication difficulties, preference for routines and difficulty with change (Folstein and Rutter, 1977). Delayed onset of speech and difficulty with reading are also more common in family members of individuals with autism, as are recurrent depression, anxiety disorders, elevated platelet serotonin and increased head circumference (Folstein and Rosen-Sheidley, 2001).
The incidence of autism falls significantly with decreasing degree of relatedness to an affected individual indicating that a single-gene model is unlikely to account for most cases of autism (Jorde et al., 1990). A reported segregation analysis was most consistent with a polygenic mode of inheritance (Jorde et al., 1991). The most parsimonious genetic model is one in which several genes interact with one another to produce the autism phenotype (Folstein and Rosen-Sheidley, 2001).
Considerable indirect evidence indicates a possible role for autoimmunity in autism. One study found more family members with autoimmune diseases in families with an autistic proband compared with control probands (Comi et al., 1999). A few studies reported that haplotypes at the Major Histocompatibility Complex (MHC) locus present in some children with autism, or their mothers, might predipose their autistic children to autoimmunity (Burger and Warren, 1998). In two studies, autoantibodies to certain brain tissues and proteins, including myelin basic protein, neurofilament proteins and vascular epithelium were found more often in autistic children compared to controls (Singh et al., 1993; Connolly et al., 1999; Weizman et al., 1982).
Although most autism cases are consistent with the proposed mechanism of oligogenicity and epistasis, a minority have been seen in association with chromosomal abnormalities and with disorders that have specific etiologies. Smalley (1997) stated that approximately 15 to 37% of cases of autism have a comorbid medical condition, including 5 to 14% with a known genetic disorder or chromosomal anomaly. Chromosome anomalies involving almost all human chromosomes have been reported. These include autosomal aneuploidies, sex-chromosome anomalies, deletions, duplications, translocations, ring chromosomes, inversions and marker chromosomes (Gillberg, 1998). Most common are abnormalities of the Prader Willi/Angelman Syndrome region on chromosome 15. Association of autism and a Mendelian condition or genetic syndrome included untreated phenylketonuria, fragile X syndrome, tuberous sclerosis and neurofibromatosis. Recently, Carney et al. (2003) identified mutations in the MECP2 (methyl CpG-binding protein 2) gene in two females with autism who do not have manifestations of Rett syndrome caused in 80% of the cases by mutations in the MECP2 gene.
Different groups are conducting genome scans related to autism or the broader phenotypes of ASDs. This approach appears very promising, because it is both systematic and model free. In addition, it has already been shown to be successful. Thus, positive linkage results have been obtained even by analysing comparatively small study groups. More important, some findings have already been replicated. The most consistent result was obtained for chromosome 7q, but there is also considerable overlap on chromosomes 2q and 16p (Folstein and Rosen-Sheidley, 2001). Considerable progress in identifying chromosomal regions have also been made on chromosome 15 and X. Mutations in two X-linked genes encoding neuroligins NLGN3 and NLGN4 have been identified in siblings with autism spectrum disorders (Jamain et al., 2003). Several lines of evidence support the fact that mutations in neuroligins are involved in autistic disorder. First, the reported mutations cause severe alterations of the predicted protein structure. Second, deletions at Xp22.3 that include NLGN4 have been reported in several autistic children. Third, a mutation in NLGN4 appeared de novo in one affected individual's mother.
The present invention now discloses the identification of a human autism susceptibility gene, which can be used for the diagnosis, prevention and treatment of autism, autism spectrum disorders, and autism-associated disorders, as well as for the screening of therapeutically active drugs.
The present invention more particularly discloses the identification of a human autism susceptibility gene, which can be used for the diagnosis, prevention and treatment of autism and related disorders, as well as for the screening of therapeutically active drugs. The invention more specifically discloses certain alleles of the pituitary homeobox transcription factor 1 (PITX1) gene related to susceptibility to autism and representing novel targets for therapeutic intervention. The present invention relates to particular mutations in the PITX1 gene and expression products, as well as to diagnostic tools and kits based on these mutations. The invention can be used in the diagnosis of predisposition to, detection, prevention and/or treatment of Asperger syndrome, pervasive developmental disorder, childhood disintegrative disorder, mental retardation, anxiety, depression, attention deficit hyperactivity disorders, speech delay or language impairment, epilepsy, metabolic disorder, immune disorder, bipolar disease and other psychiatric and neurological diseases including schizophrenia.
The invention can be used in the diagnosis of predisposition to or protection from, detection, prevention and/or treatment of autism, an autism spectrum disorder, or an autism-associated disorder, the method comprising detecting in a sample from the subject the presence of an alteration in the PITX1 gene or polypeptide, the presence of said alteration being indicative of the presence or predisposition to autism, an autism spectrum disorder, or an autism-associated disorder. The presence of said alteration can also be indicative for protecting from autism.
A particular object of this invention resides in a method of detecting the presence of or predisposition to autism, an autism spectrum disorder, or an autism-associated disorder in a subject, the method comprising detecting the presence of an alteration in the PITX1 gene locus in a sample from the subject, the presence of said alteration being indicative of the presence of or the predisposition to autism, an autism spectrum disorder, or an autism-associated disorder. An alteration being indicative of the presence of or the predisposition to autism, an autism spectrum disorder, or an autism-associated disorder is an alteration with a preferential transmission to autists. Alternatively, an alteration being indicative of the presence of or the predisposition to autism, an autism spectrum disorder, or an autism-associated disorder is an alteration with a higher frequency in autists compared to non affected individuals.
An additional particular object of this invention resides in a method of detecting the protection from autism, an autism spectrum disorder, or an autism-associated disorder in a subject, the method comprising detecting the presence of an alteration in the PITX1 gene locus in a sample from the subject, the presence of said alteration being indicative of the protection from autism, an autism spectrum disorder, or an autism-associated disorder. An alteration being indicative of the protection from autism, an autism spectrum disorder, or an autism-associated disorder is an alteration with a preferential non-transmission to autists. Alternatively, an alteration being indicative of the protection from autism, an autism spectrum disorder, or an autism-associated disorder is an alteration with a lower frequency in autists compared to non affected individuals.
Another particular object of this invention resides in a method of assessing the response of a subject to a treatment of autism, an autism spectrum disorder, or an autism-associated disorder, the method comprising detecting the presence of an alteration in the PITX1 gene locus in a sample from the subject, the presence of said alteration being indicative of a particular response to said treatment.
A further particular object of this invention resides in a method of assessing the adverse effect in a subject to a treatment of autism, an autism spectrum disorder, or an autism-associated disorder, the method comprising detecting the presence of an alteration in the PITX1 gene locus in a sample from the subject, the presence of said alteration being indicative of an adverse effect to said treatment.
This invention also relates to a method for preventing autism, an autism spectrum disorder, or an autism-associated disorder in a subject, comprising detecting the presence of an alteration in the PITX1 gene locus in a sample from the subject, the presence of said alteration being indicative of the predisposition to autism, an autism spectrum disorder, or an autism-associated disorder; and, administering a prophylactic treatment against autism, an autism spectrum disorder, or an autism-associated disorder.
In a preferred embodiment, said alteration is one or several SNP(s) or a haplotype of SNPs associated with autism. Preferably, said SNP(s) are selected from those disclosed in Tables 1a and 1b, more preferably those disclosed in Tables 3-8. More preferably, said SNP associated with autism can be selected from the group consisting of SNP6 and SNP33. More preferably, said haplotype associated with autism comprises or consists of several SNPs selected from SNPs disclosed in Tables 1a and 1b. Preferably, said SNPs are selected from the group consisting of those disclosed in Tables 3-8. In a preferred embodiment, said haplotype associated with autism comprises or consists of several SNPs selected from the group consisting of SNP6, SNP33, SNP25, SNP27, SNP29, SNP31 and SNP33. In a particular embodiment, said haplotype associated with autism comprises or consists of several SNPs selected from the group consisting of SNP1, SNP3, SNP4, SNP6, SNP7, SNP21 and SNP22. Still more preferably, said haplotype is selected from the haplotypes disclosed in Tables 4, 6, 7 and 8.Optionally, the haplotypes disclosed in the present invention can comprise one or several additonal SNPs. More preferably, said SNP associated with autism can be SNP6 or SNP33. In a most preferred embodiment, said haplotype consists of or comprises SNP24, SNP25 and SNP40, preferably with the alleles 1-2-1, respectively. In another most preferred embodiment, said haplotype consists of or comprises SNP23, SNP25 and SNP33, preferably with the alleles 1-2-1, respectively. In a further most preferred embodiment, said haplotype consists of or comprises SNP25, SNP27, SNP29, SNP31, and SNP33 preferably with the alleles 2-1-1-1-1, respectively.
Preferably, the alteration in the PITX1 gene locus is determined by performing a hydridization assay, a sequencing assay, a microsequencing assay, an oligonucleotide ligation assay, a confirmation based assay, a melting curve analysis, a denaturing high performance liquid chromatography (DHPLC) assay or an allele-specific amplification assay.
A particular aspect of this invention resides in compositions of matter comprising primers, probes, and/or oligonucleotides, which are designed to specifically detect at least one SNP or haplotype associated with autism in the genomic region including the PITX1 gene, or a combination thereof. Preferably, said SNP(s) are selected from those disclosed in Tables 1a and 1b, more preferably those disclosed in Tables 3-8. More preferably, said SNP associated with autism can be selected from the group consisting of SNP6 and SNP33. More preferably, said haplotype associated with autism comprises or consists of several SNPs selected from SNPs disclosed in Tables 1a and 1b. Preferably, said SNPs are selected from the group consisting of those disclosed in Tables 3-8. In a preferred embodiment, said haplotype associated with autism comprises or consists of several SNPs selected from the group consisting of SNP6, SNP33, SNP25, SNP27, SNP29, SNP31 and SNP33. In a particular embodiment, said haplotype associated with autism comprises or consists of several SNPs selected from the group consisting of SNP1, SNP3, SNP4, SNP6, SNP7, SNP21 and SNP22. Still more preferably, said haplotype is selected from the haplotypes disclosed in Tables 4, 6, 7 and 8.Optionally, the haplotypes disclosed in the present invention can comprise one or several additonal SNPs. More preferably, said SNP associated with autism can be SNP6 or SNP33. In a most preferred embodiment, said haplotype consists of or comprises SNP24, SNP25 and SNP40, preferably with the alleles 1-2-1, respectively. In another most preferred embodiment, said haplotype consists of or comprises SNP23, SNP25 and SNP33, preferably with the alleles 1-2-1, respectively. In a further most preferred embodiment, said haplotype consists of or comprises SNP25, SNP27, SNP29, SNP31 and SNP33, preferably with the alleles 2-1-1-1-1, respectively.
The invention also resides in methods of treating autism and/or associated disorders in a subject through a modulation of PITX1 expression or activity. Such treatments use, for instance, PITX1 polypeptides, PITX1 DNA sequences (including antisense sequences and RNAi directed at the PITX1 gene locus), anti-PITX1 antibodies or drugs that modulate PITX1 expression or activity.
The invention also relates to methods of treating individuals who carry deleterious alleles of the PITX1 gene, including pre-symptomatic treatment or combined therapy, such as through gene therapy, protein replacement therapy or through the administration of PITX1 protein mimetics and/or inhibitors.
A further aspect of this invention resides in the screening of drugs for therapy of autism or associated disorder, based on the modulation of or binding to an allele of PITX1 gene associated with autism or associated disorder or gene product thereof.
A further aspect of this invention includes antibodies specific of PITX1 polypeptide fragments and derivatives of such antibodies, hybridomas secreting such antibodies, and diagnostic kits comprising those antibodies. More preferably, said antibodies are specific to a PITX1 polypeptide or a fragment thereof comprising an alteration, said alteration modifying the activity of PITX1.
The invention also concerns a PITX1 gene or a fragment thereof comprising an alteration. The invention further concerns a PITX1 polypeptide or a fragment thereof comprising an alteration. Preferably, said alteration modifies the activity of PITX1. In a particular embodiment, said alteration is selected from the mutation disclosed in Table 11.
A total of 2263 BAC clones with an average spacing of 1.2 Mega base pairs between clones representing the whole human genome were tested for linkage using GenomeHIP. Each point corresponds to a clone. Significant evidence for linkage was calculated for clone BACA4ZA08 (p-value 6.4×10−7). The whole linkage region encompasses a region from 134095595 base pairs to 135593528 base pairs on human chromosome 5. The p-value 2×10−5 corresponding to the significance level for significant linkage was used as a significance level for whole genome screens as proposed by Lander and Kruglyak (1995).
The present invention discloses the identification of PITX1 as a human autism susceptibility gene. Various nucleic acid samples from 114 families with autism were submitted to a particular GenomeHIP process. This process led to the identification of particular identical-by-descent fragments in said populations that are altered in autistic subjects. By screening of the IBD fragments, we identified the pituitary homeobox transcription factor 1 gene on chromosome 5q31.1 (PITX1) as a candidate for autism and related phenotypes. This gene is indeed present in the critical interval and expresses a functional phenotype consistent with a genetic regulation of autism. SNPs of the PITX1 gene were also identified, as being correlated to autism in human subjects. SNP6 and SNP33, located in the PITX1 gene locus was found to be associated with autism. Haplotypes disclosed in Tables 4, and 6-8 comprising several SNPs selected from the group consisting of SNP1, SNP3, SNP4, SNP6, SNP7, SNP21, SNP22, SNP23, SNP24, SNP25, SNP27, SNP29, SNP31, SNP33, SNP36, SNP39 and SNP40 have also been identified as associated with autism.
The present invention thus proposes to use PITX1 gene and corresponding expression products for the diagnosis, prevention and treatment of autism, autism spectrum disorders, and autism-associated disorders, as well as for the screening of therapeutically active drugs.
DEFINITIONS
Autism and autism spectrum disorders (ASDs): Autism is typically characterized as part of a spectrum of disorders (ASDs) including Asperger syndrome (AS) and other pervasive developmental disorders (PPD). Autism shall be construed as any condition of impaired social interaction and communication with restricted repetitive and stereotyped patterns of behavior, interests and activities present before the age of 3, to the extent that health may be impaired. AS is distinguished from autistic disorder by the lack of a clinically significant delay in language development in the presence of the impaired social interaction and restricted repetitive behaviors, interests, and activities that characterize the autism-spectrum disorders (ASDs). PPD-NOS (PPD, not otherwise specified) is used to categorize children who do not meet the strict criteria for autism but who come close, either by manifesting atypical autism or by nearly meeting the diagnostic criteria in two or three of the key areas.
Autism-associated disorders, diseases or pathologies include, more specifically, any metabolic and immune disorders, epilepsy, anxiety, depression, attention deficit hyperactivity disorder, speech delay or language impairment, motor incoordination, mental retardation, schizophrenia and bipolar disorder.
The invention may be used in various subjects, particularly human, including adults, children and at the prenatal stage.
Within the context of this invention, the PITX1 gene locus designates all PITX1 sequences or products in a cell or organism, including PITX1 coding sequences, PITX1 non-coding sequences (e.g., introns), PITX1 regulatory sequences controlling transcription, translation and/or stability (e.g., promoter, enhancer, terminator, etc.), as well as all corresponding expression products, such as PITX1 RNAs (e.g., mRNAs) and PITX1 polypeptides (e.g., a pre-protein and a mature protein). The PITX1 gene locus also comprise surrounding sequences of the PITX1 gene which include SNPs that are in linkage disequilibrium with SNPs located in the PITX1 gene. For example, the PITX1 locus comprises surrounding sequences comprising SNPs disclosed in Tables 1a and/or 1b.
As used in the present application, the term “PITX1 gene” designates the pituitary homeobox transcription factor 1 gene on human chromosome 5q31.1, as well as variants, analogs and fragments thereof, including alleles thereof (e.g., germline mutations) which are related to susceptibility to autism and autism-associated disorders. The PITX1 gene may also be referred to as paired-like homeodomain transcription factor pituitary homeobox 1, PTX1, backfoot, mouse, homolog of, BFT, pituitary OTX-related factor, POTX.
The term “gene” shall be construed to include any type of coding nucleic acid, including genomic DNA (gDNA), complementary DNA (cDNA), synthetic or semi-synthetic DNA, as well as any form of corresponding RNA. The term gene particularly includes recombinant nucleic acids encoding PITX1, i.e., any non naturally occurring nucleic acid molecule created artificially, e.g., by assembling, cutting, ligating or amplifying sequences. A PITX1 gene is typically double-stranded, although other forms may be contemplated, such as single-stranded. PITX1 genes may be obtained from various sources and according to various techniques known in the art, such as by screening DNA libraries or by amplification from various natural sources. Recombinant nucleic acids may be prepared by conventional techniques, including chemical synthesis, genetic engineering, enzymatic techniques, or a combination thereof. Suitable PITX1 gene sequences may be found on gene banks, such as Unigene Cluster for PITX1 (Hs.84136) and Unigene Representative Sequence NM—002653. A particular example of a PITX1 gene comprises SEQ ID No: 1 or 37.
The term “PITX1 gene” includes any variant, fragment or analog of SEQ ID No 1 or 37 or of any coding sequence as identified above. Such variants include, for instance, naturally-occurring variants due to allelic variations between individuals (e.g., polymorphisms), mutated alleles related to autism, alternative splicing forms, etc. The term variant also includes PITX1 gene sequences from other sources or organisms. Variants are preferably substantially homologous to SEQ ID No 1 or 37, i.e., exhibit a nucleotide sequence identity of at least about 65%, typically at least about 75%, preferably at least about 85%, more preferably at least about 95% with SEQ ID No 1 or 37. Variants and analogs of a PITX1 gene also include nucleic acid sequences, which hybridize to a sequence as defined above (or a complementary strand thereof) under stringent hybridization conditions.
Typical stringent hybridisation conditions include temperatures above 30° C., preferably above 35° C., more preferably in excess of 42° C., and/or salinity of less than about 500 mM, preferably less than 200 mM. Hybridization conditions may be adjusted by the skilled person by modifying the temperature, salinity and/or the concentration of other reagents such as SDS, SSC, etc.
A fragment of a PITX1 gene designates any portion of at least about 8 consecutive nucleotides of a sequence as disclosed above, preferably at least about 15, more preferably at least about 20 nucleotides, further preferably of at least 30 nucleotides. Fragments include all possible nucleotide lengths between 8 and 100 nucleotides, preferably between 15 and 100, more preferably between 20 and 100.
A PITX1 polypeptide designates any protein or polypeptide encoded by a PITX1 gene as disclosed above. The term “polypeptide” refers to any molecule comprising a stretch of amino acids. This term includes molecules of various lengths, such as peptides and proteins. The polypeptide may be modified, such as by glycosylations and/or acetylations and/or chemical reaction or coupling, and may contain one or several non-natural or synthetic amino acids. A specific example of a PITX1 polypeptide comprises all or part of SEQ ID No: 2 (NP—002644).
The terms “response to a treatment” refer to treatment efficacy, including but not limited to ability to metabolise a therapeutic compound, to the ability to convert a pro-drug to an active drug, and to the pharmacokinetics (absorption, distribution, elimination) and the pharmacodynamics (receptor-related) of a drug in an individual.
The terms “adverse effects to a treatment” refer to adverse effects of therapy resulting from extensions of the principal pharmacological action of the drug or to idiosyncratic adverse reactions resulting from an interaction of the drug with unique host factors. “Side effects to a treatment” include, but are not limited to, adverse reactions such as dermatologic, hematologic or hepatologic toxicities and further includes gastric and intestinal ulceration, disturbance in platelet function, renal injury, generalized urticaria, bronchoconstriction, hypotension, and shock.
DIAGNOSIS
The invention now provides diagnosis methods based on a monitoring of the PITX1 gene locus in a subject. Within the context of the present invention, the term “diagnosis” includes the detection, monitoring, dosing, comparison, etc., at various stages, including early, pre-symptomatic stages, and late stages, in adults, children and pre-birth. Diagnosis typically includes the prognosis, the assessment of a predisposition or risk of development, the characterization of a subject to define most appropriate treatment (pharmacogenetics), etc.
The present invention provides diagnostic methods to determine whether an individual is at risk of developing autism, an autism spectrum disorder, or an autism-associated disorder or suffers from autism, an autism spectrum disorder, or an autism-associated disorder resulting from a mutation or a polymorphism in the PITX1 gene locus. The present invention also provides methods to determine whether an individual is likely to respond positively to a therapeutic agent or whether an individual is at risk of developing an adverse side effect to a therapeutic agent.
A particular object of this invention resides in a method of detecting the presence of or predisposition to autism, an autism spectrum disorder, or an autism-associated disorder in a subject, the method comprising detecting in a sample from the subject the presence of an alteration in the PITX1 gene locus in said sample. The presence of said alteration is indicative of the presence or predisposition to autism, an autism spectrum disorder, or an autism-associated disorder. Optionally, said method comprises a previous step of providing a sample from a subject. Preferably, the presence of an alteration in the PITX1 gene locus in said sample is detected through the genotyping of a sample.
Another particular object of this invention resides in a method of detecting the protection from autism, an autism spectrum disorder, or an autism-associated disorder in a subject, the method comprising detecting the presence of an alteration in the PITX1 gene locus in a sample from the subject, the presence of said alteration being indicative of the protection from autism, an autism spectrum disorder, or an autism-associated disorder.
In a preferred embodiment, said alteration is one or several SNP(s) or a haplotype of SNPs associated with autism. Preferably, said SNP(s) are selected from those disclosed in Tables 1a and 1b, more preferably those disclosed in Tables 3-8. More preferably, said SNP associated with autism can be selected from the group consisting of SNP6 and SNP33. More preferably, said haplotype associated with autism comprises or consists of several SNPs selected from SNPs disclosed in Tables 1a and 1b. Preferably, said SNPs are selected from the group consisting of those disclosed in Tables 3-8. In a preferred embodiment, said haplotype associated with autism comprises or consists of several SNPs selected from the group consisting of SNP6, SNP33, SNP25, SNP27, SNP29, SNP31 and SNP33. In a particular embodiment, said haplotype associated with autism comprises or consists of several SNPs selected from the group consisting of SNP1, SNP3, SNP4, SNP6, SNP7, SNP21 and SNP22. Still more preferably, said haplotype is selected from the haplotypes disclosed in Tables 4, 6, 7 and 8.Optionally, the haplotypes disclosed in the present invention can comprise one or several additonal SNPs. More preferably, said SNP associated with autism can be SNP6 or SNP33. In a most preferred embodiment, said haplotype consists of or comprises SNP24, SNP25 and SNP40, preferably with the alleles 1-2-1, respectively. In another most preferred embodiment, said haplotype consists of or comprises SNP23, SNP25 and SNP33, preferably with the alleles 1-2-1, respectively. In a further most preferred embodiment, said haplotype consists of or comprises SNP25, SNP27, SNP29, SNP31, and SNP33 preferably with the alleles 2-1-1-1-1, respectively.
Another particular object of this invention resides in a method of assessing the response of a subject to a treatment of autism, an autism spectrum disorder, or an autism-associated disorder, the method comprising (i) providing a sample from the subject and (ii) detecting the presence of an alteration in the PITX1 gene locus in said sample.
Another particular object of this invention resides in a method of assessing the response of a subject to a treatment of autism, an autism spectrum disorder, or an autism-associated disorder, the method comprising detecting in a sample from the subject the presence of an alteration in the PITX1 gene locus in said sample. The presence of said alteration is indicative of a particular response to said treatment. Preferably, the presence of an alteration in the PITX1 gene locus in said sample is detected through the genotyping of a sample.
A further particular object of this invention resides in a method of assessing the adverse effects of a subject to a treatment of autism, an autism spectrum disorder, or an autism-associated disorder, the method comprising detecting in a sample from the subject the presence of an alteration in the PITX1 gene locus in said sample. The presence of said alteration is indicative of adverse effects to said treatment. Preferably, the presence of an alteration in the PITX1 gene locus in said sample is detected through the genotyping of a sample.
In a preferred embodiment, said alteration is one or several SNP(s) or a haplotype of SNPs associated with autism. Preferably, said SNP(s) are selected from those disclosed in Tables 1a and 1b, more preferably those disclosed in Tables 3-8. More preferably, said SNP associated with autism can be selected from the group consisting of SNP6 and SNP33. More preferably, said haplotype associated with autism comprises or consists of several SNPs selected from SNPs disclosed in Tables 1a and 1b. Preferably, said SNPs are selected from the group consisting of those disclosed in Tables 3-8. In a preferred embodiment, said haplotype associated with autism comprises or consists of several SNPs selected from the group consisting of SNP6, SNP33, SNP25, SNP27, SNP29, SNP31 and SNP33. In a particular embodiment, said haplotype associated with autism comprises or consists of several SNPs selected from the group consisting of SNP1, SNP3, SNP4, SNP6, SNP7, SNP21 and SNP22. Still more preferably, said haplotype is selected from the haplotypes disclosed in Tables 4, 6, 7 and 8.Optionally, the haplotypes disclosed in the present invention can comprise one or several additonal SNPs. More preferably, said SNP associated with autism can be SNP6 or SNP33. In a most preferred embodiment, said haplotype consists of or comprises SNP24, SNP25 and SNP40, preferably with the alleles 1-2-1, respectively. In another most preferred embodiment, said haplotype consists of or comprises SNP23, SNP25 and SNP33, preferably with the alleles 1-2-1, respectively. In a further most preferred embodiment, said haplotype consists of or comprises SNP25, SNP27, SNP29, SNP31 and SNP33, preferably with the alleles 2-1-1-1-1, respectively.
In an additional embodiment, the invention concerns a method for preventing autism, an autism spectrum disorder, or an autism-associated disorder in a subject, comprising detecting the presence of an alteration in the PITX1 gene locus in a sample from the subject, the presence of said alteration being indicative of the predisposition to autism, an autism spectrum disorder, or an autism-associated disorder; and, administering a prophylactic treatment against autism, an autism spectrum disorder, or an autism-associated disorder. Said prophylactic treatment can be a drug administration. Said prophylactic treatment can also be a behavioral therapy.
Diagnostics, which analyse and predict response to a treatment or drug, or side effects to a treatment or drug, may be used to determine whether an individual should be treated with a particular treatment drug. For example, if the diagnostic indicates a likelihood that an individual will respond positively to treatment with a particular drug or behavioral therapy, the drug may be administered to the individual. Conversely, if the diagnostic indicates that an individual is likely to respond negatively to treatment with a particular drug, an alternative course of treatment may be prescribed. A negative response may be defined as either the absence of an efficacious response or the presence of toxic side effects.
Clinical drug trials represent another application for the PITX1 SNPs. One or more PITX1 SNPs indicative of response to a drug or to side effects to a drug may be identified using the methods described above. Thereafter, potential participants in clinical trials of such an agent may be screened to identify those individuals most likely to respond favorably to the drug and exclude those likely to experience side effects. In that way, the effectiveness of drug treatment may be measured in individuals who respond positively to the drug, without lowering the measurement as a result of the inclusion of individuals who are unlikely to respond positively in the study and without risking undesirable safety problems.
Clinical trials to assess the utility of a behavioural therapy are also an application for the PITX1 SNPs. One or more PITX1 SNPs indicative of response to a behavioural therapy or to side effects to a behavioral therapy may be identified using the methods described above. Thereafter, potential participants in clinical trials of such a therapy may be screened to identify those individuals most likely to respond favorably to the therapy and exclude those likely to experience side effects. In that way, the effectiveness of behavioral treatment may be measured in individuals who respond positively to the therapy, without lowering the measurement as a result of the inclusion of individuals who are unlikely to respond positively in the study and without risking undesirable safety problems.
The alteration may be determined at the level of the PITX1 gDNA, RNA or polypeptide. Optionally, the detection is determined by performing a hydridization assay, a sequencing assay, a microsequencing assay, an oligonucleotide ligation assay, a confirmation based assay, a melting curve analysis, a denaturing high performance liquid chromatography (DHPLC) assay (Jones et al, 2000) or an allele-specific amplification assay. In a particular embodiment, the detection is performed by sequencing all or part of the PITX1 gene or by selective hybridisation or amplification of all or part of the PITX1 gene. More preferably a PITX1 gene specific amplification is carried out before the alteration identification step.
An alteration in the PITX1 gene locus may be any form of mutation(s), deletion(s), rearrangement(s) and/or insertions in the coding and/or non-coding region of the locus, alone or in various combination(s). Mutations more specifically include point mutations. Deletions may encompass any region of one, two or more residues in a coding or non-coding portion of the gene locus, such as from two residues up to the entire gene or locus. Typical deletions affect smaller regions, such as domains (introns) or repeated sequences or fragments of less than about 50 consecutive base pairs, although larger deletions may occur as well. Insertions may encompass the addition of one or several residues in a coding or non-coding portion of the gene locus. Insertions may typically comprise an addition of between 1 and 50 base pairs in the gene locus. Rearrangement includes inversion of sequences. The PITX1 gene locus alteration may result in the creation of stop codons, frameshift mutations, amino acid substitutions, particular RNA splicing or processing, product instability, truncated polypeptide production, etc. The alteration may result in the production of a PITX1 polypeptide with altered function, stability, targeting or structure. The alteration may also cause a reduction in protein expression or, alternatively, an increase in said production.
In a particular embodiment of the method according to the present invention, the alteration in the PITX1 gene locus is selected from a point mutation, a deletion and an insertion in the PITX1 gene or corresponding expression product, more preferably a point mutation and a deletion. The alteration may be determined at the level of the PITX1 gDNA, RNA or polypeptide.
In this regard, the present invention now discloses a SNP in the PITX1 gene and certain haplotypes, which include SNPs selected from the group consisting of SNP1, SNP3, SNP4, SNP6, SNP7, SNP21 and SNP22, that are associated with autism. The SNPs are reported in the following Table 1a.
In any method according to the present invention, one or several SNP in the PITX1 gene and certain haplotypes comprising SNP in the PITX1 gene and surrounding regions, more particularly those disclosed in the present invention, can be used in combination with other SNP or haplotype associated with autism, an autism spectrum disorder, or an autism-associated disorder and located in other gene(s).
In another variant, the method comprises detecting the presence of an altered PITX1 RNA expression. Altered RNA expression includes the presence of an altered RNA sequence, the presence of an altered RNA splicing or processing, the presence of an altered quantity of RNA, etc. These may be detected by various techniques known in the art, including by sequencing all or part of the PITX1 RNA or by selective hybridisation or selective amplification of all or part of said RNA, for instance.
In a further variant, the method comprises detecting the presence of an altered PITX1 polypeptide expression. Altered PITX1 polypeptide expression includes the presence of an altered polypeptide sequence, the presence of an altered quantity of PITX1 polypeptide, the presence of an altered tissue distribution, etc. These may be detected by various techniques known in the art, including by sequencing and/or binding to specific ligands (such as antibodies), for instance.
As indicated above, various techniques known in the art may be used to detect or quantify altered PITX1 gene or RNA expression or sequence, including sequencing, hybridisation, amplification and/or binding to specific ligands (such as antibodies). Other suitable methods include allele-specific oligonucleotide (ASO), oligonucleotide ligation, allele-specific amplification, Southern blot (for DNAs), Northern blot (for RNAs), single-stranded conformation analysis (SSCA), PFGE, fluorescent in situ hybridization (FISH), gel migration, clamped denaturing gel electrophoresis, denaturing HLPC, melting curve analysis, heteroduplex analysis, RNase protection, chemical or enzymatic mismatch cleavage, ELISA, radio-immunoassays (RIA) and immuno-enzymatic assays (IEMA).
Some of these approaches (e.g., SSCA and CGGE) are based on a change in electrophoretic mobility of the nucleic acids, as a result of the presence of an altered sequence. According to these techniques, the altered sequence is visualized by a shift in mobility on gels. The fragments may then be sequenced to confirm the alteration.
Some others are based on specific hybridisation between nucleic acids from the subject and a probe specific for wild type or altered PITX1 gene or RNA. The probe may be in suspension or immobilized on a substrate. The probe is typically labeled to facilitate detection of hybrids.
Some of these approaches are particularly suited for assessing a polypeptide sequence or expression level, such as Northern blot, ELISA and RIA. These latter require the use of a ligand specific for the polypeptide, more preferably of a specific antibody.
In a particular, preferred, embodiment, the method comprises detecting the presence of an altered PITX1 gene expression profile in a sample from the subject. As indicated above, this can be accomplished more preferably by sequencing, selective hybridisation and/or selective amplification of nucleic acids present in said sample.
Sequencing
Sequencing can be carried out using techniques well known in the art, using automatic sequencers. The sequencing may be performed on the complete PITX1 gene or, more preferably, on specific domains thereof, typically those known or suspected to carry deleterious mutations or other alterations.
Amplification
Amplification is based on the formation of specific hybrids between complementary nucleic acid sequences that serve to initiate nucleic acid reproduction.
Amplification may be performed according to various techniques known in the art, such as by polymerase chain reaction (PCR), ligase chain reaction (LCR), strand displacement amplification (SDA) and nucleic acid sequence based amplification (NASBA). These techniques can be performed using commercially available reagents and protocols. Preferred techniques use allele-specific PCR or PCR-SSCP. Amplification usually requires the use of specific nucleic acid primers, to initiate the reaction.
Nucleic acid primers useful for amplifying sequences from the PITX1 gene or locus are able to specifically hybridize with a portion of the PITX1 gene locus that flank a target region of said locus, said target region being altered in certain subjects having autism, an autism spectrum disorder, or an autism-associated disorder. Examples of such target regions are provided in Tables 1a and 1b.
Primers that can be used to amplify PITX1 target region comprising SNPs as identified in Table 1 may be designed based on the sequence of Seq Id No 1 or on the genomic sequence of PITX1. In a particular embodiment, primers may be designed based on the sequence of SEQ ID Nos 3-26.
Another particular object of this invention resides in a nucleic acid primer useful for amplifying sequences from the PITX1 gene or locus including surrounding regions. Such primers are preferably complementary to, and hybridize specifically to nucleic acid sequences in the PITX1 gene locus. Particular primers are able to specifically hybridise with a portion of the PITX1 gene locus that flank a target region of said locus, said target region being altered in certain subjects having autism, an autism spectrum disorder, or an autism-associated disorder.
The invention also relates to a nucleic acid primer, said primer being complementary to and hybridizing specifically to a portion of a PITX1 coding sequence (e.g., gene or RNA) altered in certain subjects having autism, an autism spectrum disorder, or an autism-associated disorder. In this regard, particular primers of this invention are specific for altered sequences in a PITX1 gene or RNA. By using such primers, the detection of an amplification product indicates the presence of an alteration in the PITX1 gene locus. In contrast, the absence of amplification product indicates that the specific alteration is not present in the sample.
Typical primers of this invention are single-stranded nucleic acid molecules of about 5 to 60 nucleotides in length, more preferably of about 8 to about 25 nucleotides in length. The sequence can be derived directly from the sequence of the PITX1 gene locus. Perfect complementarity is preferred, to ensure high specificity. However, certain mismatch may be tolerated.
The invention also concerns the use of a nucleic acid primer or a pair of nucleic acid primers as described above in a method of detecting the presence of or predisposition to autism, an autism spectrum disorder, or an autism-associated disorder in a subject or in a method of assessing the response of a subject to a treatment of autism, an autism spectrum disorder, or an autism-associated disorder.
Selective Hybridization
Hybridization detection methods are based on the formation of specific hybrids between complementary nucleic acid sequences that serve to detect nucleic acid sequence alteration(s).
A particular detection technique involves the use of a nucleic acid probe specific for wild type or altered PITX1 gene or RNA, followed by the detection of the presence of a hybrid. The probe may be in suspension or immobilized on a substrate or support (as in nucleic acid array or chips technologies). The probe is typically labeled to facilitate detection of hybrids.
In this regard, a particular embodiment of this invention comprises contacting the sample from the subject with a nucleic acid probe specific for an altered PITX1 gene locus, and assessing the formation of an hybrid. In a particular, preferred embodiment, the method comprises contacting simultaneously the sample with a set of probes that are specific, respectively, for wild type PITX1 gene locus and for various altered forms thereof. In this embodiment, it is possible to detect directly the presence of various forms of alterations in the PITX1 gene locus in the sample. Also, various samples from various subjects may be treated in parallel.
Within the context of this invention, a probe refers to a polynucleotide sequence which is complementary to and capable of specific hybridisation with a (target portion of a) PITX1 gene or RNA, and which is suitable for detecting polynucleotide polymorphisms associated with PITX1 alleles which predispose to or are associated with autism, an autism spectrum disorder, or an autism-associated disorder. Probes are preferably perfectly complementary to the PITX1 gene, RNA, or target portion thereof. Probes typically comprise single-stranded nucleic acids of between 8 to 1000 nucleotides in length, for instance of between 10 and 800, more preferably of between 15 and 700, typically of between 20 and 500. It should be understood that longer probes may be used as well. A preferred probe of this invention is a single stranded nucleic acid molecule of between 8 to 500 nucleotides in length, which can specifically hybridise to a region of a PITX1 gene or RNA that carries an alteration.
A specific embodiment of this invention is a nucleic acid probe specific for an altered (e.g., a mutated) PITX1 gene or RNA, i.e., a nucleic acid probe that specifically hybridises to said altered PITX1 gene or RNA and essentially does not hybridise to a PITX1 gene or RNA lacking said alteration. Specificity indicates that hybridisation to the target sequence generates a specific signal which can be distinguished from the signal generated through non-specific hybridisation. Perfectly complementary sequences are preferred to design probes according to this invention. It should be understood, however, that certain a certain degree of mismatch may be tolerated, as long as the specific signal may be distinguished from non-specific hybridisation.
Particular examples of such probes are nucleic acid sequences complementary to a target portion of the genomic region including the PITX1 gene or RNA carrying a point mutation as listed in Table 1 above. More particularly, the probes can comprise a sequence selected from the group consisting of SEQ ID Nos 3-26 or a fragment thereof comprising the SNP or a complementary sequence thereof.
The sequence of the probes can be derived from the sequences of the PITX1 gene and RNA as provided in the present application. Nucleotide substitutions may be performed, as well as chemical modifications of the probe. Such chemical modifications may be accomplished to increase the stability of hybrids (e.g., intercalating groups) or to label the probe. Typical examples of labels include, without limitation, radioactivity, fluorescence, luminescence, enzymatic labeling, etc.
The invention also concerns the use of a nucleic acid probe as described above in a method of detecting the presence of or predisposition to autism, an autism spectrum disorder, or an autism-associated disorder in a subject or in a method of assessing the response of a subject to a treatment of autism, an autism spectrum disorder, or an autism-associated disorder.
Oligonuleotide Ligation
The oligonucleotide ligation assay is a method consists of designing 3 specific primers per SNP with two primers carrying the SNP-base specific 3′ end and one common primer that starts 5′ with the next base in the target sequence. The two allele specific primers carry a tag of unique sequences that determine each allele. Primers are annealed to the target sequence and a ligation reaction will join the allele specific primer with the common primer if the allele specific 3′-base is present. A short fluorescent dye labelled probe homologous to the tag of unique sequence, is then hybridised to the immobilized product enabling the detection of the corresponding allele. An oligo-ligation kit is commercially available (SNPlex, Applied Biosystems, Foster City).
Specific Ligand Binding
As indicated above, alteration in the PITX1 gene locus may also be detected by screening for alteration(s) in PITX1 polypeptide sequence or expression levels. In this regard, a specific embodiment of this invention comprises contacting the sample with a ligand specific for a PITX1 polypeptide and determining the formation of a complex.
Different types of ligands may be used, such as specific antibodies. In a specific embodiment, the sample is contacted with an antibody specific for a PITX1 polypeptide and the formation of an immune complex is determined. Various methods for detecting an immune complex can be used, such as ELISA, radioimmunoassays (RIA) and immuno-enzymatic assays (IEMA).
Within the context of this invention, an antibody designates a polyclonal antibody, a monoclonal antibody, as well as fragments or derivatives thereof having substantially the same antigen specificity. Fragments include Fab, Fab′2, CDR regions, etc. Derivatives include single-chain antibodies, humanized antibodies, poly-functional antibodies, etc.
An antibody specific for a PITX1 polypeptide designates an antibody that selectively binds a PITX1 polypeptide, namely, an antibody raised against a PITX1 polypeptide or an epitope-containing fragment thereof. Although non-specific binding towards other antigens may occur, binding to the target PITX1 polypeptide occurs with a higher affinity and can be reliably discriminated from non-specific binding.
In a specific embodiment, the method comprises contacting a sample from the subject with (a support coated with) an antibody specific for an altered form of a PITX1 polypeptide, and determining the presence of an immune complex. In a particular embodiment, the sample may be contacted simultaneously, or in parallel, or sequentially, with various (supports coated with) antibodies specific for different forms of a PITX1 polypeptide, such as a wild type and various altered forms thereof.
The invention also concerns the use of a ligand, preferably an antibody, a fragment or a derivative thereof as described above, in a method of detecting the presence of or predisposition to autism, an autism spectrum disorder, or an autism-associated disorder in a subject or in a method of assessing the response of a subject to a treatment of autism, an autism spectrum disorder, or an autism-associated disorder.
The invention also relates to a diagnostic kit comprising products and reagents for detecting in a sample from a subject the presence of an alteration in the PITX1 gene or polypeptide, in the PITX1 gene or polypeptide expression, and/or in PITX1 activity. Said diagnostic kit according to the present invention comprises any primer, any pair of primers, any nucleic acid probe and/or any ligand, preferably antibody, described in the present invention. Said diagnostic kit according to the present invention can further comprise reagents and/or protocols for performing a hybridization, amplification or antigen-antibody immune reaction.
The diagnosis methods can be performed in vitro, ex vivo or in vivo, preferably in vitro or ex vivo. They use a sample from the subject, to assess the status of the PITX1 gene locus. The sample may be any biological sample derived from a subject, which contains nucleic acids or polypeptides. Examples of such samples include fluids, tissues, cell samples, organs, biopsies, etc. Most preferred samples are blood, plasma, saliva, urine, seminal fluid, etc. Pre-natal diagnosis may also be performed by testing fetal cells or placental cells, for instance. The sample may be collected according to conventional techniques and used directly for diagnosis or stored. The sample may be treated prior to performing the method, in order to render or improve availability of nucleic acids or polypeptides for testing. Treatments include, for instant, lysis (e.g., mechanical, physical, chemical, etc.), centrifugation, etc. Also, the nucleic acids and/or polypeptides may be pre-purified or enriched by conventional techniques, and/or reduced in complexity. Nucleic acids and polypeptides may also be treated with enzymes or other chemical or physical treatments to produce fragments thereof. Considering the high sensitivity of the claimed methods, very few amounts of sample are sufficient to perform the assay.
As indicated, the sample is preferably contacted with reagents such as probes, primers or ligands in order to assess the presence of an altered PITX1 gene locus. Contacting may be performed in any suitable device, such as a plate, tube, well, glass, etc. In specific embodiments, the contacting is performed on a substrate coated with the reagent, such as a nucleic acid array or a specific ligand array. The substrate may be a solid or semi-solid substrate such as any support comprising glass, plastic, nylon, paper, metal, polymers and the like. The substrate may be of various forms and sizes, such as a slide, a membrane, a bead, a colunm, a gel, etc. The contacting may be made under any condition suitable for a complex to be formed between the reagent and the nucleic acids or polypeptides of the sample.
The finding of an altered PITX1 polypeptide, RNA or DNA in the sample is indicative of the presence of an altered PITX1 gene locus in the subject, which can be correlated to the presence, predisposition or stage of progression of autism, an autism spectrum disorder, or an autism-associated disorder. For example, an individual having a germ line PITX1 mutation has an increased risk of developing autism, an autism spectrum disorder, or an autism-associated disorder. The determination of the presence of an altered PITX1 gene locus in a subject also allows the design of appropriate therapeutic intervention, which is more effective and customized. Also, this determination at the pre-symptomatic level allows a preventive regimen to be applied.
Linkage Disequilibirum
Once a first SNP has been identified in a genomic region of interest, more particularly in PITX1 gene locus, the practitioner of ordinary skill in the art can easily identify additional SNPs in linkage disequilibrium with this first SNP. Indeed, any SNP in linkage disequilibrium with a first SNP associated with autism or an associated disorder will be associated with this trait. Therefore, once the association has been demonstrated between a given SNP and autism or an associated disorder, the discovery of additional SNPs associated with this trait can be of great interest in order to increase the density of SNPs in this particular region.
Identification of additional SNPs in linkage disequilibrium with a given SNP involves: (a) amplifying a fragment from the genomic region comprising or surrounding a first SNP from a plurality of individuals; (b) identifying of second SNPs in the genomic region harboring or surrounding said first SNP; (c) conducting a linkage disequilibrium analysis between said first SNP and second SNPs; and (d) selecting said second SNPs as being in linkage disequilibrium with said first marker. Subcombinations comprising steps (b) and (c) are also contemplated.
Methods to identify SNPs and to conduct linkage disequilibrium analysis can be carried out by the skilled person without undue experimentation by using well-known methods.
These SNPs in linkage disequilibrium can also be used in the methods according to the present invention, and more particularly in the diagnosic methods according to the present invention.
For example, a linkage locus of Crohn's disease has been mapped to a large region spanning 18 cM on chromosome 5q31 (Rioux et al., 2000 and 2001). Using dense maps of microsatellite markers and SNPs across the entire region, strong evidence of linkage disequilibrium (LD) was found. Having found evidence of LD, the authors developed an ultra-high-density SNP map and studied a denser collection of markers selected from this map. Multilocus analyses defined a single common risk haplotype characterised by multiple SNPs that were each independently associated using TDT. These SNPs were unique to the risk haplotype and essentially identical in their information content by virtue of being in nearly complete LD with one another. The equivalent properties of these SNPs make it impossible to identify the causal mutation within this region on the basis of genetic evidence alone.
Causal Mutation
Mutations in the PITX1 gene which are responsible for autism or an associated disorder may be identified by comparing the sequences of the PITX1 gene from patients presenting autism or an associated disorder and control individuals. Based on the identified association of SNPs of PITX1 and autism or an associated disorder, the identified locus can be scanned for mutations. In a preferred embodiment, functional regions such as exons and splice sites, promoters and other regulatory regions of the PITX1 gene are scanned for mutations. Preferably, patients presenting autism or an associated disorder carry the mutation shown to be associated with autism or an associated disorder and controls individuals do not carry the mutation or allele associated with autism or an associated disorder. It might also be possible that patients presenting autism or an associated disorder carry the mutation shown to be associated with autism or an associated disorder with a higher frequency than controls individuals.
The method used to detect such mutations generally comprises the following steps: amplification of a region of the PITX1 gene comprising a SNP or a group of SNPs associated with autism or an associated disorder from DNA samples of the PITX1 gene from patients presenting autism or an associated disorder and control individuals; sequencing of the amplified region; comparison of DNA sequences of the PITX1 gene from patients presenting autism or an associated disorder and control individuals; determination of mutations specific to patients presenting autism or an associated disorder.
Therefore, identification of a causal mutation in the PITX1 gene can be carried out by the skilled person without undue experimentation by using well-known methods.
For example, the causal mutations have been identified in the following examples by using routine methods.
Hugot et al. (2001) applied a positional cloning strategy to identify gene variants with susceptibly to Crohn's disease in a region of chromosome 16 previously found to be linked to susceptibility to Crohn's disease. To refine the location of the potential sucecptibility locus 26 microsatellite markers were genotyped and tested for association to Crobn's disease using the transmission disequilibrium test. A borderline significant association was found between one allele of the microsatellite marker D16S136. Eleven additional SNPs were selected from surrounding regions and several SNPs showed significant association. SNP5-8 from this region were found to be present in a single exon of the NOD2/CARD15 gene and shown to be non-synonymous variants. This prompted the authors to sequence the complete coding sequence of this gene in 50 CD patients. Two additional non-synonymous mutations (SNP12 and SNP13) were found. SNP13 was most significant associated (p=6×10-6) using the pedigree transmission disequilibrium test. In another independent study, the same variant was found also by sequencing the coding region of this gene from 12 affected individuals compared to 4 controls (Ogura et al., 2001). The rare allele of SNP13 corresponded to a 1-bp insertion predicted to truncate the NOD2/CARD15 protein. This allele was also present in normal healthy individuals, albeit with significantly lower frequency as compared to the controls.
Similarly, Lesage et al. (2002) performed a mutational analyses of CARD15 in 453 patients with CD, including 166 sporadic and 287 familial cases, 159 patients with ulcerative colitis (UC), and 103 healthy control subjects by systematic sequencing of the coding region. Of 67 sequence variations identified, 9 had an allele frequency >5% in patients with CD. Six of them were considered to be polymorphisms, and three (SNP12-R702W, SNP8-G908R, and SNP13-1007fs) were confirmed to be independently associated with susceptibility to CD. Also considered as potential disease-causing mutations (DCMs) were 27 rare additional mutations. The three main variants (R702W, G908R, and 1007fs) represented 32%, 18%, and 31%, respectively, of the total CD mutations, whereas the total of the 27 rare mutations represented 19% of DCMs. Altogether, 93% of the mutations were located in the distal third of the gene. No mutations were found to be associated with UC. In contrast, 50% of patients with CD carried at least one DCM, including 17% who had a double mutation.
The present invention also provides novel targets and methods for the screening of drug candidates or leads. The methods include binding assays and/or functional assays, and may be performed in vitro, in cell systems, in animals, etc.
A particular object of this invention resides in a method of selecting compounds active on autism, an autism spectrum disorder, or an autism-associated disorder, said method comprising contacting in vitro a test compound with a PITX1 gene or polypeptide according to the present invention and determining the ability of said test compound to bind said PITX1 gene or polypeptide. Binding to said gene or polypeptide provides an indication as to the ability of the compound to modulate the activity of said target, and thus to affect a pathway leading to autism, an autism spectrum disorder, or an autism-associated disorder in a subject. In a preferred embodiment, the method comprises contacting in vitro a test compound with a PITX1 polypeptide or a fragment thereof according to the present invention and determining the ability of said test compound to bind said PITX1 polypeptide or fragment. The fragment preferably comprises a binding site of the PITX1 polypeptide. Preferably, said PITX1 gene or polypeptide or a fragment thereof is an altered or mutated PITX1 gene or polypeptide or a fragment thereof comprising the alteration or mutation.
A particular object of this invention resides in a method of selecting compounds active on autism, autism spectrum disorders, and autism-associated disorders, said method comprising contacting in vitro a test compound with a PITX1 polypeptide according to the present invention or binding site-containing fragment thereof and determining the ability of said test compound to bind said PITX1 polypeptide or fragment thereof. Preferably, said PITX1 polypeptide or a fragment thereof is an altered or mutated PITX1 polypeptide or a fragment thereof comprising the alteration or mutation.
In a further particular embodiment, the method comprises contacting a recombinant host cell expressing a PITX1 polypeptide according to the present invention with a test compound, and determining the ability of said test compound to bind said PITX1 and to modulate the activity of PITX1 polypeptide. Preferably, said PITX1 polypeptide or a fragment thereof is an altered or mutated PITX1 polypeptide or a fragment thereof comprising the alteration or mutation.
The determination of binding may be performed by various techniques, such as by labeling of the test compound, by competition with a labeled reference ligand, etc.
A further object of this invention resides in a method of selecting compounds active on autism, an autism spectrum disorder, or an autism-associated disorder, said method comprising contacting in vitro a test compound with a PITX1 polypeptide according to the present invention and determining the ability of said test compound to modulate the activity of said PITX1 polypeptide. Preferably, said PITX1 polypeptide or a fragment thereof is an altered or mutated PITX1 polypeptide or a fragment thereof comprising the alteration or mutation.
A further object of this invention resides in a method of selecting compounds active on autism, an autism spectrum disorder, or an autism-associated disorder, said method comprising contacting in vitro a test compound with a PITX1 gene according to the present invention and determining the ability of said test compound to modulate the expression of said PITX1 gene. Preferably, said PITX1 gene or a fragment thereof is an altered or mutated PITX1 gene or a fragment thereof comprising the alteration or mutation.
In an other embodiment, this invention relates to a method of screening, selecting or identifying active compounds, particularly compounds active on autism, an autism spectrum disorder, or an autism-associated disorder, the method comprising contacting a test compound with a recombinant host cell comprising a reporter construct, said reporter construct comprising a reporter gene under the control of a PITX1 gene promoter, and selecting the test compounds that modulate (e.g. stimulate or reduce) expression of the reporter gene. Preferably, said PITX1 gene promoter or a fragment thereof is an altered or mutated PITX1 gene promoter or a fragment thereof comprising the alteration or mutation.
In a particular embodiment of the methods of screening, the modulation is an inhibition. In another particular embodiment of the methods of screening, the modulation is an activation.
The above screening assays may be performed in any suitable device, such as plates, tubes, dishes, flasks, etc. Typically, the assay is performed in multi-wells plates. Several test compounds can be assayed in parallel. Furthermore, the test compound may be of various origin, nature and composition. It may be any organic or inorganic substance, such as a lipid, peptide, polypeptide, nucleic acid, small molecule, etc., in isolated or in mixture with other substances. The compounds may be all or part of a combinatorial library of products, for instance.
A further object of this invention is a pharmaceutical composition comprising (i) a PITX1 polypeptide or a fragment thereof, a nucleic acid encoding a PITX1 polypeptide or a fragment thereof, a vector or a recombinant host cell as described above and (ii) a pharmaceutically acceptable carrier or vehicle.
The invention also relates to a method of treating or preventing autism, an autism spectrum disorder, or an autism-associated disorder in a subject, the method comprising administering to said subject a functional (e.g., wild-type) PITX1 polypeptide or a nucleic acid encoding the same.
An other embodiment of this invention resides in a method of treating or preventing autism, an autism spectrum disorder, or an autism-associated disorder in a subject, the method comprising administering to said subject a compound that modulates, preferably that activates or mimics, expression or activity of a PITX1 gene or protein according to the present invention. Said compound can be an agonist or an antagonist of PITX1, an antisense or a RNAi of PITX1, an antibody or a fragment or a derivative thereof specific to a PITX1 polypeptide according to the present invention. In a particular embodiment of the method, the modulation is an inhibition. In another particular embodiment of the method, the modulation is an activation.
The invention also relates, generally, to the use of a functional PITX1 polypeptide, a nucleic acid encoding the same, or a compound that modulates expression or activity of a PITX1 gene or protein according to the present invention, in the manufacture of a pharmaceutical composition for treating or preventing autism, an autism spectrum disorder, or an autism-associated disorder in a subject. Said compound can be an agonist or an antagonist of PITX1, an antisense or a RNAi of PITX1, an antibody or a fragment or a derivative thereof specific to a PITX1 polypeptide according to the present invention. In a particular embodiment of the method, the modulation is an inhibition. In another particular embodiment of the method, the modulation is an activation.
The present invention demonstrates the correlation between autism, autism spectrum disorders, and autism-associated disorders and the PITX1 gene locus. The invention thus provides a novel target of therapeutic intervention. Various approaches can be contemplated to restore or modulate the PITX1 activity or function in a subject, particularly those carrying an altered PITX1 gene locus. Supplying wild-type function to such subjects is expected to suppress phenotypic expression of autism, autism spectrum disorders, and autism-associated disorders in a pathological cell or organism. The supply of such function can be accomplished through gene or protein therapy, or by administering compounds that modulate or mimic PITX1 polypeptide activity (e.g., agonists as identified in the above screening assays).
The wild-type PITX1 gene or a functional part thereof may be introduced into the cells of the subject in need thereof using a vector as described above. The vector may be a viral vector or a plasmid. The gene may also be introduced as naked DNA. The gene may be provided so as to integrate into the genome of the recipient host' cells, or to remain extra-chromosomal. Integration may occur randomly or at precisely defined sites, such as through homologous recombination. In particular, a functional copy of the PITX1 gene may be inserted in replacement of an altered version in a cell, through homologous recombination. Further techniques include gene gun, liposome-mediated transfection, cationic lipid-mediated transfection, etc. Gene therapy may be accomplished by direct gene injection, or by administering ex vivo prepared genetically modified cells expressing a functional PITX1 polypeptide.
Other molecules with PITX1 activity (e.g., peptides, drugs, PITX1 agonists, or organic compounds) may also be used to restore functional PITX1 activity in a subject or to suppress the deleterious phenotype in a cell.
Restoration of functional PITX1 gene function in a cell may be used to prevent the development of autism, an autism spectrum disorder, or an autism-associated disorder or to reduce progression of said diseases. Such a treatment may suppress the autism-associated phenotype of a cell, particularly those cells carrying a deleterious allele.
Further aspects and advantages of the present invention will be disclosed in the following experimental section, which should be regarded as illustrative and not limiting the scope of the present application.
A further aspect of this invention resides in novel products for use in diagnosis, therapy or screening. These products comprise nucleic acid molecules encoding a PITX1 polypeptide or a fragment thereof, vectors comprising the same, recombinant host cells and expressed polypeptides.
More particularly, the invention concerns an altered or mutated PITX1 gene or a fragment thereof comprising said alteration or mutation. The invention also concerns nucleic acid molecules encoding an altered or mutated PITX1 polypeptide or a fragment thereof comprising said alteration or mutation. Said alteration or mutation modifies the PITX1 activity. The modified activity can be increased or decreased. The invention further concerns a vector comprising an altered or mutated PITX1 gene or a fragment thereof comprising said alteration or mutation or a nucleic acid molecule encoding an altered or mutated PITX1 polypeptide or a fragment thereof comprising said alteration or mutation, recombinant host cells and expressed polypeptides.
A further object of this invention is a vector comprising a nucleic acid encoding a PITX1 polypeptide according to the present invention. The vector may be a cloning vector or, more preferably, an expression vector, i.e., a vector comprising regulatory sequences causing expression of a PITX1 polypeptide from said vector in a competent host cell.
These vectors can be used to express a PITX1 polypeptide in vitro, ex vivo or in vivo, to create transgenic or “Knock Out” non-human animals, to amplify the nucleic acids, to express antisense RNAs, etc.
The vectors of this invention typically comprise a PITX1 coding sequence according to the present invention operably linked to regulatory sequences, e.g., a promoter, a polyA, etc. The term “operably linked” indicates that the coding and regulatory sequences are functionally associated so that the regulatory sequences cause expression (e.g., transcription) of the coding sequences. The vectors may further comprise one or several origins of replication and/or selectable markers. The promoter region may be homologous or heterologous with respect to the coding sequence, and may provide for ubiquitous, constitutive, regulated and/or tissue specific expression, in any appropriate host cell, including for in vivo use. Examples of promoters include bacterial promoters (T7, pTAC, Trp promoter, etc.), viral promoters (LTR, TK, CMV-IE, etc.), mammalian gene promoters (albumin, PGK, etc), and the like.
The vector may be a plasmid, a virus, a cosmid, a phage, a BAC, a YAC, etc. Plasmid vectors may be prepared from commercially available vectors such as pBluescript, pUC, pBR, etc. Viral vectors may be produced from baculoviruses, retroviruses, adenoviruses, AAVs, etc., according to recombinant DNA techniques known in the art.
In this regard, a particular object of this invention resides in a recombinant virus encoding a PITX1 polypeptide as defined above. The recombinant virus is preferably replication-defective, even more preferably selected from E1- and/or E4-defective adenoviruses, Gag-, pol- and/or env-defective retroviruses and Rep- and/or Cap-defective AAVs. Such recombinant viruses may be produced by techniques known in the art, such as by transfecting packaging cells or by transient transfection with helper plasmids or viruses. Typical examples of virus packaging cells include PA317 cells, PsiCRIP cells, GPenv+ cells, 293 cells, etc. Detailed protocols for producing such replication-defective recombinant viruses may be found for instance in WO95/14785, WO96/22378, U.S. Pat. No. 5,882,877, U.S. Pat. No. 6,013,516, U.S. Pat. No. 4,861,719, U.S. Pat. No. 5,278,056 and WO94/19478.
A further object of the present invention resides in a recombinant host cell comprising a recombinant PITX1 gene or a vector as defined above. Suitable host cells include, without limitation, prokaryotic cells (such as bacteria) and eukaryotic cells (such as yeast cells, mammalian cells, insect cells, plant cells, etc.). Specific examples include E. coli, Kluyveromyces or Saccharomyces yeasts, mammalian cell lines (e.g., Vero cells, CHO cells, 3T3 cells, COS cells, etc.) as well as primary or established mammalian cell cultures (e.g., produced from fibroblasts, embryonic cells, epithelial cells, nervous cells, adipocytes, etc.).
The present invention also relates to a method for producing a recombinant host cell expressing a PITX1 polypeptide according to the present invention, said method comprising (i) introducing in vitro or ex vivo into a competent host cell a recombinant nucleic acid or a vector as described above, (ii) culturing in vitro or ex vivo the recombinant host cells obtained and (iii), optionally, selecting the cells which express the PITX1 polypeptide.
Such recombinant host cells can be used for the production of PITX1 polypeptides, as well as for screening of active molecules, as described below. Such cells may also be used as a model system to study autism. These cells can be maintained in suitable culture media, such as DMEM, RPMI, HAM, etc., in any appropriate culture device (plate, flask, dish, tube, pouch, etc.).
1. GenomeHIP platform to identify the chromosome 5 susceptibility gene
The GenomeHIP platform was applied to allow rapid identification of an autism susceptibility gene.
Briefly, the technology consists of forming pairs from the DNA of related individuals. Each DNA is marked with a specific label allowing its identification. Hybrids are then formed between the two DNAs. A particular process (WO00/53802) is then applied that selects all fragments identical-by-descent (IBD) from the two DNAs in a multi step procedure. The remaining IBD enriched DNA is then scored against a BAC clone derived DNA microarray that allows the positioning of the IBD fraction on a chromosome.
The application of this process over many different families results in a matrix of IBD fractions for each pair from each family. Statistical analyses then calculate the minimal IBD regions that are shared between all families tested. Significant results (p-values) are evidence for linkage of the positive region with the trait of interest (here autism). The linked interval can be delimited by the two most distant clones showing significant p-values.
In the present study, 114 families from the United States (114 independent sib-pairs) concordant for strict autism (as defined by ADI-R) were submitted to the GenomeHIP process. The resulting IBD enriched DNA fractions were then labeled with Cy5 fluorescent dyes and hybridised against a DNA array consisting of 2263 BAC clones covering the whole human genome with an average spacing of 1.2 Mega base pairs. Non-selected DNA labeled with Cy3 was used to normalize the signal values and compute ratios for each clone. Clustering of the ratio results was then performed to determine the IBD status for each clone and pair.
By applying this procedure, several BAC clones were identified (BACA19ZB03, BACA16ZG06, BACA4ZA08 and BACA11ZF12) spanning approximately 1.5 megabases in the region on chromosome 5 (bases 134 095 595 to 135 593 528), which showed significant evidence for linkage to autism (p<6.40E-07).
Table 2: Linkage results for chromosome 5 in the PITX1 locus: Indicated is the region corresponding to 4 BAC clones with evidence for linkage. The start and stop positions of the clones correspond to their genomic locations based on NCBI Build34 with respect to the start of the chromosome (p-ter).
2. Identification of an Autism Susceptibility Gene on Chromosome 5
By screening the aforementioned 1.5 Megabases in the linked chromosomal region, we identified the pituitary homeobox transcription factor 1 (PITX1) gene as a candidate for autism and related phenotypes. This gene is indeed present in the critical interval, with evidence for linkage delimited by the clones outlined above.
The PITX1 gene encodes a member of the RIEG/PITX homeobox family, an expanding family of bicoid-related vertebrate homeobox genes. Members of this family are involved in organ development, in particular, the brain and facies, and left-right asymmetry. Lamonerie et al. (1996) cloned and characterized a mouse transcription factor gene (called Ptx1 by them) on the basis of its ability to activate pituitary transcription of the proopiomelanocortin gene (POMC). Six hormones are derived from the POMC gene: ACTH, lipotropin, alpha-MSH, beta-MSH, endorphin, and one other. ACTH and beta-lipotropin (beta-LPH) are derived from a large precursor peptide. Each of these hormones is known to include smaller peptides having distinct biologic activities: alpha-melanotropin (alpha-MSH) and corticotropin-like intermediate lobe peptide (CLIP) are formed from ACTH; gamma-LPH and beta-endorphin are peptide components of beta-LPH. Beta-MSH is contained within gamma-LPH.
The PTX1, PTX2, and PTX3 genes define a novel family of transcription factors, the PTX subfamily, within the paired-like class of homeodomain factors. In mice, Ptx1 and Ptx2 gene expression has been detected in the area of the pituitary primordium and is maintained throughout development in the Rathke pouch and adult pituitary. Pellegrini-Bouiller et al. (1999) demonstrated the expression of the PTX1, PTX2, and PTX3 genes in the normal human pituitary and in the different types of human pituitary adenomas.
Tremblay et al. (1998) reported that most pituitary hormone-coding gene promoters are activated by Ptx1 and so Ptx1 appears to be a general regulator of pituitary-specific transcription. In addition, Ptx1 action is synergized by cell-restricted transcription factors to confer promoter-specific expression. Antisense RNA experiments performed in alphaT3-1 cells that express the alphaGSU gene showed that expression of endogenous alphaGSU is highly dependent on Ptx1 whereas many other genes are not affected. The only other gene found to be highly dependent on Ptx1 for expression was the gene for the Lim3/Lhx3 transcription factor. Thus, Ptx1 is upstream of Lim3/Lhx3 in a cascade of regulators that appear to work in a combinatorial code to direct pituitary-, lineage-, and promoter-specific transcription.
Shapiro et al. (2004) described naturally occurring variants in regulatory regions of PITX1 in stickleback fish that result in differing patterns of PITX1 gene expression and functional differences in pelvic anatomy. They emphasize that regulatory regions of homeobox genes such as PITX1 may be found at numerous distantly spaced sites and as far as several 100's of kilobases from the gene.
Szeto et al. (1999) found that Pitx1-deleted mice exhibited striking abnormalities in morphogenesis and growth of the hindlimb. Mice homozygous for the Pitx1 targeted mutation die immediately or shortly after birth. A small number of Pitx1-null mice show embryonic lethality after E11.5. The hindlimb of Pitx1-null mice is significantly shorter. The size of the pelvis is also markedly reduced. Examination of thyroid-stimulating hormone beta, luteinizing hormone beta, and the common glycoprotein alpha subunit expression suggests that both the number of gonadotropes and thyrotropes, as well as the level of luteinizing hormone beta and thyroid-stimulating hormone beta transcripts and protein within the individual cells, are diminished. Interestingly, the level of TSH beta transcripts is most severely reduced in the rostral tip thyrotrope population, which does not require Pit-1 for TSH beta gene activation. Growth hormone expression in somatotropes appears unchanged, whereas the number and expression levels of POMC gene in the intermediate lobe melanotropes appear normal between E15.5 and P0. There is a consistent increase in the levels of both number of, and ACTH transcripts and peptide levels in the anterior pituitary corticotropes.
Chamberlain and Herman (1990) proposed a novel biochemical model in which a subgroup of autistic individuals may have a hypersecretion of pineal melatonin that produces a cascade of biochemical effects including a corresponding hyposecretion of pituitary proopiomelanocortin (POMC) peptides and a hypersecretion of hypothalamic opioid peptides and serotonin (5-HT). Autism may reflect a dysfunction in the pineal-hypothalamic-pituitary-adrenal axis that modulates POMC and 5-HT systems of the brain. This model is consistent with numerous clinical investigations implicating hypersecretion of brain 5-HT and opioid peptides in autism.
Curin et al. (2003) found that individuals with autism have significantly lower serum concentrations of cortisol (p<10(−6)), and significantly higher concentrations of ACTH (p=0.002) than control age- and sex-matched subjects. Also, prolactin concentrations in autistic patients with epilepsy were significantly higher when compared with normal subjects. The observed hormonal changes are consistent with a dysfunction of the hypothalamic-pituitary-adrenal axis in individuals with autism.
3. Association Study
The same families that have been used for the linkage study were also used to test for association between a specific phenotype (here autism) in question and the genetic marker allele or haplotypes containing a specific marker allele using the transmission disequilibrium test (TDT). The TDT is a powerful association test as it is insensitive to population stratification problems in the tested sample. Briefly, the segregation of alleles from heterozygous parents to their affected offspring is tested. The portion of alleles transmitted to the affected offspring compared to the non-transmitted alleles is compared to the ratio expected under random distribution. A significant excess of allele transmission over the expected value is evidence for an association of the respective allele or haplotype with the studied autism phenotype.
An alternative test is the pedigree disequilibrium test (PDT) that remains more powerful even when there is misclassification of unaffected individuals (Martin et al. 2000). Simulations suggest that there may be advantages to using the PDT even if the data consist of independent families without extended family information.
The results of this analysis show that certain alleles of the PITX1 gene are positively associated with autism and therefore increase the susceptibility to disease. In the tested population, the allele G of SNP6 is correlated with autism as determined by TDT (p-value=0.028) and PDT (p-value=0.0044). In contrast, the allele T of SNP6 is significantly under-transmitted to autistic individuals showing that this allele helps protect from the disease.
Examples of the transmission of the alleles to autists are given in Table 3.
Table 3, Note 1:
The frequency in this column for the PDT test is the population frequency.
In addition, haplotypes were constructed for SNP1, SNP3, SNP4, SNP6, SNP7, SNP21 and SNP22 to identify the phase for all SNPs.
The results of this analysis in the tested population showed that certain haplotypes, all characterized by the presence of allele G at SNP6 are strongly associated with autism, while certain haplotypes devoid of allele G are preferentially not transmitted to autists. An example is the haplotype A-G-A for SNP3-SNP6-SNP22, p=3.68×10−5. Haplotypes that carry allele T instead of allele G at SNP6 show significant evidence to be under-represented in autistic subjects. An example is the haplotype A-T-A for SNP3-SNP6-SNP22, p=0.000218.
Preferential transmission of certain haplotypes was also demonstrated by calculation of an odds ratio. An odds ratio greater than 1 means that the tested genetic allele is associated with the disease and therefore that the allele increases the susceptibility to disease. There is a negative association if the odds ratio is smaller than 1 showing that the tested genetic allele helps to protect from the disease. For example, the odds ratio for transmission of the haplotype A-G-G for SNP3-SNP6-SNP22 is 4.32, with p=3.62×10−5.
Examples of haplotypes with preferential transmission and non-transmission of SNP6 to autists are given in Table 4.
To increase the information content and narrow down the interval of association, the SNP density in the PITX1 gene was increased to approximately one SNP every 2.5 kb. Several additional markers showed positive single point results in the PITX1 gene. The strongest association was observerd for marker SNP33 with allele 1 being transmitted more frequently to autists than expected by chance, while allele 2 was preferentially non-transmitted to autists (p=0.001674). Interestingly, this marker is identical to SNP6 which was already found to be associated in the previous analysis. Examples of alleles transmitted and non-transmitted to autists are shown in Table 5.
Haplotypes were also constructed to determine the phase and analysed for association in the complete sample set used for linkage analysis as described above. The results of this analysis in the tested population showed that certain haplotypes are strongly associated with autism, of which all are characterized by the presence of allele 2 at marker SNP25, allele 1 at marker SNP27, allele 1 at marker SNP29, allele 1 at marker SNP31 or allele 1 at marker SNP33, respectively. The most significant result was obtained for haplotype 1-2-1 for markers SNP24, SNP25 and SNP40 with a p-value of 2.24×1003. While certain haplotypes characterised by allele 1 at marker SNP25, allele 2 at marker SNP27 or allele 2 at marker SNP40, respectively, are preferentially not transmitted to autists.
Examples of haplotypes with preferential transmission and non-transmission to autists from the complete data set are given in Table 6.
N: number,
T: haplotypes transmitted,
NT: haplotypes non-transmitted
This family set includes samples from different ethnic groups represented within the population of the USA. In order to adjust for any population stratification effects, the haplotype analysis was repeated for each ethnic group. Significant association was found for several haplotypes in the Caucasian population. An example for a haplotype being transmitted more often to autistis is haplotype 1-2-1 for markers SNP23, SNP25 and SNP33 (p=4.44×10−3), while haplotype 1-2-2 for markers SNP25, SNP29 and SNP31 was preferentially not transmitted to autists (p=0.006).
Examples of haplotypes with preferential transmission and non-transmission to autists from the Caucasian data set are given in Table 7.
N: number,
T: haplotypes transmitted to autists,
NT: haplotypes non-transmitted to autists
A second independent set of 167 trio families (set 2) was studied for replication of the 5 association that has been observed in the families providing evidence for linkage (set 1) as described above.
As this second family set (set 2) also includes samples from different ethnic groups represented within the population of the USA, like set 1, the haplotype analysis was performed for each ethnic group separately in order to adjust for potential population stratification effects. Significant association was found for several haplotypes in the Caucasian population characterised by the presence of alleles 2, 1, 1, 1, or 1 for markers SNP25, SNP27, SNP29, SNP31 and SNP33. An example for a haplotype being transmitted more often to autistis is haplotype 2-1-2 for markers SNP25, SNP27 and SNP32 (p=5.93×10−3) while the haplotype 2-2-1 for markers SNP25, SNP26 and SNP27 was more frequently not transmitted to autists (p=0.04).
Examples of haplotypes with preferential transmission and non-transmission to autists from the Caucasian data set in family set 2 are given in Table 8.
N: number,
T: haplotypes transmitted,
NT: haplotypes non-transmitted
In summary, haplotype analysis in Caucasians showed positive replication of haplotype 2-1-1-1-1 for markers SNP25, SNP27, SNP29, SNP31 and SNP33 in set 2 (p=3.2×10−3 in set 1 and p=6.85×10−3 in set 2) as shown in Table 9 below.
4. Identification of Nucleotide Changes
96 unrelated affected individuals were included in the mutation screen. Primers were designed to amplify the coding region of the PITX1 gene. The sequences of the primers are provided below in Table 10:
The resulting amplification products were directly sequenced in one direction using dye-terminator sequencing chemistry to identify rare nucleotide changes (mutations) and polymorphisms (allele frequency>1%) in the gene.
A total of 10 nucleotide changes were detected in the coding region of the gene plus the flanking intron regions in close proximity of the splice sites (for positions see table 11). Two of these resulted in changes of the amino-acids in the respective codons, as illustrated in table 11.
Two deletions, MUT1 and MUT9, were identified in the untranslated region. MUT1 was detected in the 5′UTR. Two point mutations, MUT2 and MUT3, were also detected in the 5′UTR. These mutations could have an effect on the transcriptional level of the PITX1 RNA. MUT9 was discovered in the 3′UTR and could affect the stability of the RNA.
Two non-synonymous mutations, MUT6 and MUT7, were also found which could have an effect on the function of the protein.
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| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/IB05/02319 | 6/30/2005 | WO | 12/13/2006 |
| Number | Date | Country | |
|---|---|---|---|
| 60584130 | Jul 2004 | US |
