Patent Application
20110200564
The present invention generally relates to methods, assays and systems for diagnosing late onset Alzheimer's disease (AD). The invention further relates to methods and compositions for treatment of AD.
Alzheimer's disease (AD) is a devastating neurodegenerative disorder which is clinically characterized by deterioration of memory and cognitive function, progressive impairment of daily living activities, and several neuropsychiatric symptoms. Cummings, J. L., 351 N Engl J. Med. 56 (2004). AD is a genetically complex disease and only four genes have been established to either cause early-onset autosomal dominant AD with complete penetrance (APP, PSEN1 and PSEN2) or to increase susceptibility for late-onset AD with partial penetrance (APOE). Bertram, L. et al., 9 Nat Rev Neurosci 768 (2008). All these four confirmed genes increase the absolute Aβ levels or the ratios of Aβ42 to Aβ40, which enhances the oligomerization of Aβ into neurotoxic assemblies. Bertram, L. et al., 9 Nat Rev Neurosci 768 (2008) and Tanzi R. E. et al., 120 Cell 545 (2005).
To date, more than 200 rare and fully penetrant autosomal-dominant mutations in three genes, the amyloid precursor protein (APP) and presenilin genes (PSEN1 and PSEN2), have been shown to be associated with the early-onset (<60 years) familial form of AD, which accounts for <10% of AD cases [Alzheimer Disease & Frontotemporal Dementia Mutation Database: http://www.molgen.ua.ac.be/ADMutations/]. On the other hand, a common variant, β4, in the gene encoding apolipoprotein E (APOE) is the only confirmed genetic risk factor for the late-onset form of AD (>90% of AD cases). Overall, these four genes together account for <50% of the genetic variance in AD. Tanzi R. E. et al., 120 Cell 545 (2005). However, the heritability of late-onset AD is as high as 80%, and approximately 80% of the late-onset AD genetic variance remains elusive. In the attempt to identify the remaining AD susceptibility genes, a large body of evidence has accrued over the past 20 years, represented by well over 1,000 publications genetically implicating or excluding potential risk factors, the vast majority of which were tested as functional and/or positional candidate genes. Gatz, M. et al., 63 Arch Gen Psychiatry 168 (2006). Several genes besides APOE have yielded evidence (based on meta-analyses) for association with late onset AD, but with only modest effects. Bertram L. et al., 39 Nat Genet. 17 (2007). Risk for late-onset AD is likely influenced by an array of common risk alleles distributed across different genes affecting a variety of biochemical pathways affecting both the etiology and pathogenesis of AD. While the identity and total number of these genes remain elusive, recent estimates suggest that together they have a large impact on disease predisposition in the general population. Gatz, M. et al., 63 Arch Gen Psychiatry 168 (2006). Yet the quest to identify the remaining genes has been challenging due to the complex and heterogeneous nature of the disease.
On the cell and molecular levels, the pathophysiology of AD is characterized by two distinctive features: amyloid plaques comprised primarily of a small peptide named Aβ [Hardy J. et al., 297 Science 353 (2002); Bertram, L. et al., 9 Nat Rev Neurosci 768 (2008); Gady S. et al., 115 J Clin Invest 1121 (2005)], and neurofibrillary tangles composed of hyperphosphorylated tau. While Aβ42 and Aβ40 are the two primary Aβ species, Aβ42 is more prevalent than Aβ40 in amyloid plaques. Considerable genetic, biochemical and molecular biological evidences suggest that the excessive accumulation of Aβ is the primary pathological event leading to AD. Hardy J. et al., 297 Science 353 (2002), Gady S. et al., 115 J Clin Invest 1121 (2005) and Tanzi R. E. et al., 120 Cell 545 (2005). Current drugs available for therapeutic treatment of AD, such as cholinesterase inhibitors (for example, ARICEPT®) and the glutamate antagonist NAMENDA®, treat mainly the symptoms, with no known effects on disease progression. Another drug, dimebolin, which is currently in clinical trials, is a retired antihistamine that is purported to be neuroprotective based on stabilizing mitochondria. Therefore, there is an urgent need for therapeutic interventions for AD.
AD is the leading cause of dementia in the elderly. As the incidence and prevalence of AD rise steadily with increasing longevity, AD threatens to become a catastrophic burden on health care, particularly in developed countries [Alzheimer's Disease Education & Referral Center: http://www.nia.nih.gov/Alzheimers/AlzheimersInformation/GeneralInfo]. While more than 90% of the AD cases are the late-onset form, only APOE-ε4 gene is the only confirmed genetic risk factor for diagnosis of late onset AD. Further, there are very few drugs effective for treatment of AD. As such, there is a strong need for identifying additional late onset AD genes and thus developing methods and assays for diagnosis of increased risk for late onset AD as well as treatment of AD.
Embodiments of the present invention are based on the discovery of four novel late onset AD risk-associated single nucleotide polymorphisms (SNPs), which are rs11159647, rs3826656, rs179943 and rs2049161. These four SNPs have been validated in three additional independent AD family samples composed of nearly 2799 individuals from almost 900 families. Among them, SNP rs11159647 shows the strongest association with late onset AD and acts as a modifier of onset age. Further, the inventors discovered that the CD33 gene, in which SNP rs3826656 resides, is associated with late-onset AD. These additional late onset AD risk-associated SNPs and/or genes in addition to APOE gene allow more accurate and reliable assays and methods for identifying subjects with increased susceptibility for late onset AD. Additionally, while SNP rs179943 resides within the ataxin-1 (ATXN1) gene, the inventors discovered that ATXN1 down-regulation increases Aβ generation in vitro. This effect can be rescued by over-expression of ATXN1. Since accumulation of Aβ can lead to AD pathogenesis, inhibition of Aβ formation by over-expressing ATXN1 or providing externally supplied ATXN1 protein provides a novel therapeutic intervention for treatment of AD.
Accordingly, provided herein are assays and methods for determining an increased risk for developing late onset AD in a subject. In one aspect, the assay and method comprise (a) transforming a biological sample from the subject into at least one detectable target loci for a nucleic acid polymorphism, wherein the target locus is selected from: G/A SNP rs11159647, A/G SNP rs3826656, C/T SNP rs179943, and A/C SNP rs2049161; and (b) detecting presence or absence of at least one AD risk associated allele from the at least one detectable target loci. The AD risk associated alleles include allele A of the G/A SNP rs11159647 locus, allele G of the A/G SNP rs3826656 locus, allele T of the C/T SNP rs179943 locus, and allele C of the A/C SNP rs2049161 locus. Hence, detection of the presence of at least one AD risk associated allele is indicative of increased risk for developing late onset AD in the subject.
In some embodiments, the assay and method for determining an increased risk for developing late onset AD in a subject comprises detecting at least allele A of the G/A SNP rs11159647 locus. In other embodiments, the assay and method described herein comprises detecting at least allele G of the A/G SNP rs3826656 locus. In alternative embodiments, the assay and method described herein comprises detecting at least allele T of the C/T SNP rs179943 locus.
In one embodiment, the assay and method further comprises detecting presence or absence of at least one additional AD risk associated allele. An example of such AD risk associated alleles is APOE-ε4 allele.
Another aspect of the assays and methods for determining an increased risk for developing late onset AD in a subject include measuring the amount of at least one gene associated with the AD risk associated SNPs described herein in a biological sample from the subject, and then comparing the measured amount of the gene to a reference amount.
In one embodiment, at least the amount of ATXN1 gene expression products (e.g., nucleic acid or protein) associated with SNP rs179943 is measured in a biological sample of a subject, and if the amount of the ATXN1 gene expression products is lower than that of the reference amount, the subject is at increased risk for developing late onset AD. The amount of the ATXN1 gene expression products is lower by at least about 10% than the reference ATXN1 amount, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95%, about 98%, about 99% or 100%, including all the percentages between 10-100%.
In another embodiment, at least the amount of CD33 gene expression products (e.g., nucleic acid or protein) associated with SNP rs3826656 is measured in a biological sample of a subject, and if the amount of the CD33 gene expression products is statistically different from that of the reference amount, the subject is at increased risk for developing late onset AD. The amount of the CD33 gene expression products is statistically different from the reference CD33 amount by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95%, about 98%, about 99% or 100%, including all the percentages between 10-100%.
In an alternative embodiment, at least the amount of DLGAP1 [discs, large (Drosophila) homolog-associated protein 1] gene expression products (e.g., nucleic acid or protein) associated with SNP rs2049161 is measured in a biological sample of a subject, and if the amount of the DLGAP1 gene expression products is statistically different from that of the reference amount, the subject is at increased risk for developing late onset AD. The amount of the DLGAP1 gene expression products is statistically different from the reference DLGAP1 amount by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95%, about 98%, about 99% or 100%, including all the percentages between 10-100%.
In various embodiments, the reference amount is measured in a normal healthy subject with no genetic susceptibility for AD. For example, a normal healthy subject is not a carrier of any of the late onset AD risk associated alleles described herein or APOE allele, or is not diagnosed with any forms of AD such as early-onset autosomal-dominant AD, or any neurodegenerative disorders. The reference amount can be from a control sample, a pooled sample of control individuals or a numeric value or range of values based on the same.
In some embodiments, the invention provides methods or assays for determining if an individual is in need of AD treatment or prevention, comprising the steps of determining if the subject carries any of the alleles selected from the group consisting of allele A of the G/A SNP rs11159647 locus, allele G of the A/G SNP rs3826656 locus, allele T of the C/T SNP rs179943 locus, and allele C of the A/C SNP rs2049161 locus. If the subject carries any of the alleles, then the subject can further be administered a treatment or prevention intervention to treat AD symptoms or inhibit development of AD symptoms. These treatment of prevention interventions include, but are not limited to life style advise, including e.g., prescribing an aerobic exercise regime, dietary advise, including increase in intake of omega-3 fatty acids or reduction of sugar or cholesterol rich food intake to lower cholesterol, and administering pharmaceutical agents effective in prevention or treatment of AD.
A further aspect of the invention provides a computer implemented system for determining presence or absence of alleles associated with an increased risk of a subject for developing late onset Alzheimer's disease (AD). The system comprises (a) a determination module configured to identify and detect at least one single nucleotide polymorphism (SNP) in a biological sample of a subject, wherein the SNP is selected from: alleles G/A SNP rs11159647, alleles A/G SNP rs3826656, alleles C/T SNP rs179943, alleles A/C SNP rs2049161, or any combination thereof; (b) a storage module configured to store output data from the determination module; (c) a computing module adapted to identify whether at least one AD risk associated alleles is present or absent in the output data stored on the storage module, wherein the AD risk associated alleles is selected from: allele A of the G/A SNP rs11159647, allele G of the A/G SNP rs3826656, allele T of the C/T SNP rs179943, and allele C of the A/C SNP rs2049161; and (d) a display module for displaying if any of the AD risk associated alleles was identified or not.
In one embodiment, the display module can display the detected alleles.
In various embodiments, the determination module can be further configured to identify and detect the presence or absence of at least one additional AD risk associated allele, e.g., APOE-ε4 allele. In one embodiment, the AD risk associated allele can be associated with early-onset autosomal-dominant AD.
Yet another aspect of the invention relates to a pharmaceutical composition and methods for treating AD in a subject. The method comprises administering to the subject a pharmaceutically acceptable composition comprising ATXN1.
In one embodiment, the ATXN1 is administered as a recombinant ATXN1 protein encoding gene. In such embodiment, the recombinant ATXN1 encoding gene is operably linked to a vector. In some embodiments, a viral vector is used to deliver the ATXN1-encoding gene. In other embodiments, a non-viral vector can be used to deliver the ATXN1-encoding gene.
In some embodiments, the method further comprises diagnosing the individual as having AD prior to administering the pharmaceutical agent. The diagnosing can be performed e.g, using the method of determining the level of ATXN1 or by detecting the presence or absence of any one or more of the alleles associated with AD, such as APOE-ε4, or alleles G/A SNP rs11159647, alleles A/G SNP rs3826656, alleles C/T SNP rs179943, alleles A/C SNP rs2049161.
In some embodiments, the pharmaceutically acceptable composition further comprises a neural stem cell. For example, the neural stem cell is genetically engineered to express or secrete ATXN1.
In one embodiment, the ATXN1 is administered as a protein or a fragment of the protein.
A still yet another aspect of the invention relates to a method for determining if a subject is in need of treatment or prevention for AD. The method comprises the steps of: (a) transforming at least one nucleic acid polymorphism in a locus in a biological sample from the subject into at least one detectable target, wherein the locus is selected from: (i) G/A SNP rs11159647; (ii) A/G SNP rs3826656; (iii) C/T SNP rs179943; and (iv) A/C SNP rs2049161; and (b) detecting presence or absence of at least one AD risk associated allele from the at least one detectable target, wherein the at least one AD risk associated allele is selected from: (v) AD risk associated allele A of the G/A SNP rs11159647 locus; (vi) AD risk associated allele G of the A/G SNP rs3826656 locus; (vii) AD risk associated allele T of the C/T SNP rs179943 locus; and (viii) AD risk associated allele C of the A/C SNP rs2049161 locus; wherein detection of the presence of at least one AD risk associated allele is indicative of the subject in need for treatment or prevention for AD.
In one embodiment, the method further comprises administering a treatment or preventive intervention to the subject, if presence of at least one AD risk-associated allele is detected.
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the leading cause of dementia in the elderly. As the incidence and prevalence of AD rise steadily with increasing longevity, AD threatens to become a catastrophic burden on health care. To date, only four genes have been established to either cause early-onset autosomal dominant AD with complete penetrance (APP, PSEN1 and PSEN2) or to increase susceptibility for late-onset AD with partial penetrance (APOE) [3]. While more than 90% of the AD cases are late-onset AD, approximately 80% of the late-onset AD genetic variance remains elusive [8].
In accordance with the invention, four non-APOE-related novel single nucleotide polymorphisms (SNPs) have been discovered with a significant genome-wide association with a multivariate phenotype of late-onset AD combining affection status and onset age. The four SNPs, which are rs11159647, rs3826656, rs179943 and rs2049161, have been assessed in three additional independent AD family samples composed of nearly 2799 individuals from almost 900 families. Among them, SNP rs11159647 shows the strongest association with late onset AD and acts as a modifier of onset age. It was also discovered in a separate consortium comprising 50,000 AD and 30,000 control cases that the CD33 gene, in which SNP rs3826656 resides, is associated with late-onset AD. Additionally, it was discovered that down-regulation of the ATXN1 gene, in which the SNP rs179943 resides, increases formation of Aβ, which can lead to AD pathogenesis. Further, Aβ generation induced by such ATXN1 down-regulation can be abolished or rescued in vitro by re-introducing the ATXN1 gene into the brain cells.
Accordingly, some embodiments of the invention are generally related to assays, methods and systems for identifying a subject with an increased risk for late-onset AD. In one embodiment, the assays, methods and systems are directed to detection of single nucleotide polymorphisms (SNPs) associated with late-onset AD in a biological sample of a subject. In another embodiment, the assays, methods and systems are directed to determination of the expression level of the corresponding SNP gene product in a biological sample of a subject. Another aspect of the invention is directed to methods and pharmaceutical compositions for therapeutic treatment of AD, e.g., by delivery of the ATXN1 gene, to a subject diagnosed with or at risk of AD.
One aspect of the invention provides a method for determining an increased risk for developing late onset Alzheimer's disease (AD) in a subject, by identifying in a biological sample of the subject the late-onset AD risk associated SNPs and alleles described herein. The method comprises (a) transforming a biological sample from the subject into at least one detectable target locus for a nucleic acid polymorphism, wherein the target locus is selected from: G/A SNP rs11159647, A/G SNP rs3826656, C/T SNP rs179943, and A/C SNP rs2049161; and (b) detecting presence or absence of at least one AD risk associated allele from the at least one detectable target locus. The AD risk associated alleles include allele A of the G/A SNP rs11159647 locus, allele G of the A/G SNP rs3826656 locus, allele T of the C/T SNP rs179943 locus, and allele C of the A/C SNP rs2049161 locus. Hence, detection of the presence of at least one AD risk associated allele is indicative of increased risk for developing late onset AD in the subject. A subject diagnosed with an increased AD risk can further be given life-style advice, dietary advice, follow-up scheduling advice or agents that may assist in preventing or slowing down symptoms or development of Aβ plaque.
As used herein, the term “transforming” or “transformation” refers to changing an object or a substance, e.g., biological sample, nucleic acid or protein, into another substance. The transformation can be physical, biological or chemical. Exemplary physical transformation includes, but not limited to, pre-treatment of a biological sample, e.g., from whole blood to blood serum by differential centrifugation. A biological/chemical transformation can involve at least one enzyme and/or a chemical reagent in a reaction. For example, a DNA sample can be digested into fragments by one or more restriction enzyme, or an exogenous molecule can be attached to a fragmented DNA sample with a ligase. In some embodiments, a DNA sample can undergo enzymatic replication, e.g., by polymerase chain reaction (PCR).
In some embodiments, the assay and method for determining an increased risk for developing late onset AD in a subject comprises detecting at least allele A of the G/A SNP rs11159647 locus in a biological sample of a subject. In other embodiments, the assay and method described herein comprises detecting at least allele G of the A/G SNP rs3826656 locus in a biological sample of a subject. In alternative embodiments, the assay and method described herein comprises detecting at least allele T of the C/T SNP rs179943 locus in a biological sample of a subject.
In some embodiments, detection of at least 2 AD risk associated alleles described herein in a biological sample of a subject is indicative of increased risk for developing late onset AD in the subject. In a particular embodiment, the 2 AD risk associated alleles are allele A of the G/A SNP rs11159647 locus and allele G of the A/G SNP rs3826656 locus.
In some embodiments, detection of at least 3 AD risk associated alleles described herein in biological sample of a subject is indicative of increased risk for developing late onset AD in the subject. In a particular embodiment, the 3 AD risk associated alleles are allele A of the G/A SNP rs11159647 locus, allele G of the A/G SNP rs3826656 locus and allele T of the C/T SNP rs179943 locus.
In some embodiments, the assay and method for determining an increased risk for developing late onset AD in a subject comprises detecting a group of AD risk associated alleles consisting essentially of allele A of the G/A SNP rs11159647 locus, allele G of the A/G SNP rs3826656 locus, allele T of the C/T SNP rs179943 locus and allele C of the A/C SNP rs2049161 locus. In such embodiments, control SNPs (e.g., non-AD related SNPs) can be included.
In one embodiment, the assay and method further comprises detecting presence or absence of at least one additional AD risk associated allele in a biological sample of a subject. An example of such AD risk associated alleles is APOE-ε4 allele.
In some embodiments, the subject can be of European ancestry.
The genomes of all organisms undergo spontaneous mutation in the course of their continuing evolution, generating variant forms of progenitor genetic sequences (Gusella, Ann. Rev. Biochem. 55, 831-854 (1986)). The coexistence of multiple forms of a genetic sequence gives rise to genetic polymorphisms, including SNPs.
Approximately 90% of all polymorphisms in the human genome are SNPs. SNPs are single base positions in DNA at which different alleles, or alternative nucleotides, exist in a population. The SNP position (interchangeably referred to herein as SNP, SNP site, SNP allele or SNP locus) is usually preceded by and followed by highly conserved sequences of the allele (e.g., sequences that vary in less than 1/100 or 1/1000 members of the populations). An individual can be homozygous or heterozygous for an allele at each SNP position. A SNP can, in some instances, be referred to as a “cSNP” to denote that the nucleotide sequence containing the SNP is an amino acid coding sequence.
A SNP can arise from a substitution of one nucleotide for another at the polymorphic site. Substitutions can be transitions or transversions. A transition is the replacement of one purine nucleotide by another purine nucleotide, or one pyrimidine by another pyrimidine. A transversion is the replacement of a purine by a pyrimidine, or vice versa. A SNP can also be a single base insertion or deletion variant referred to as an “in/del” (Weber et al., “Human diallelic insertion/deletion polymorphisms”, Am J Hum Genet October 2002; 71(4):854-62).
A synonymous codon change, or silent mutation/SNP (the terms “SNP” and “mutation” are used herein interchangeably), is one that does not result in a change of amino acid due to the degeneracy of the genetic code. A substitution that changes a codon coding for one amino acid to a codon coding for a different amino acid (i.e., a non-synonymous codon change) is referred to as a missense mutation. A nonsense mutation results in a type of non-synonymous codon change in which a stop codon is formed, thereby leading to premature termination of a polypeptide chain and a truncated protein. A read-through mutation is another type of non-synonymous codon change that causes the destruction of a stop codon, thereby resulting in an extended polypeptide product. While SNPs can be bi-, tri-, or tetra-allelic, the vast majority of the SNPs are bi-allelic, and are thus often referred to as “bi-allelic markers”, or “di-allelic markers”.
A major database of human SNPs is maintained at NCBI as dbSNP, and it contains data for unique human SNPs consisting of 1.1×108 submitted SNP (identified by an “ss” number) and 2.4×107 reference SNP (identified by an “rs” number), as of Build History 131: human—9606 based on GRCh37 available from the NCBI website. The rs numbers are unique, do not change and allow analysis of the particularly identified SNP in any genetic sample. Throughout the specification, the SNPs described herein are identified by an “rs” number. One of skill in the art will be able to determine the position of a specific SNP within a respective chromosome.
The most common type of SNP in humans has alleles A and G. Since DNA is a double helix, the opposite strand has alleles T and C. So an A/G SNP can also be described as a T/C SNP, depending upon orientation. The distribution of the types of SNPs in humans was estimated as follows: 63% A/G (and T/C), 17% A/C (and T/G), 8% CG, 4% AT, and 8% insertion/deletions (Miller, R. D., P. Taillon-Miller, and P. Y. Kwok. 2001. Regions of Low Single-Nucleotide Polymorphism Incidence in Human and Orangutan Xq: Deserts and Recent Coalescences. Genomics 71: 78-88.).
While a SNP could conceivably have three or four alleles, nearly all SNPs have only two alleles. Analysis of the SNPs identified in this study all rely on the two alleles that are listed in connection with each SNP. For example, one of the late-onset AD risk associated SNP described herein, rs11159647 is indicated to have two alleles, A or G. The presence of an allele A at the rs11159647 locus indicates an increased risk for late onset AD.
An association study of a SNP and a specific disorder involves determining the presence or frequency of the SNP allele in biological samples from subjects with the disorder of interest, such as Alzheimer's disease, and comparing the information to that of controls (i.e., individuals who do not have the disorder; controls can be also referred to as “healthy” or “normal” individuals) who are preferably of similar age and race. The appropriate selection of patients and controls is important to the success of SNP association studies. Therefore, a pool of individuals with well-characterized phenotypes is desirable. As shown in Example 1, the AD families that were selected for the genome-wide association analysis had all individuals affected with AD at an onset age greater than or equal to 50 years, and they were all reported to be of similar race, such as of European ancestry.
Association studies can be conducted within the general population and are not limited to studies performed on related individuals in affected families (linkage studies). In some embodiments, methods described in Examples 1 and 2 can be used for association studies to determine AD susceptibility loci.
A SNP can be screened in any biological sample obtained from an individual or a subject diagnosed with or at risk of a disease or disorder, e.g., Alzheimer's disease (AD). If an allele herein discovered as an AD risk allele is identified, the subject can be said to be at greater risk of developing AD than a subject who is not carrying that alleles. Homozygotes for the AD risk allele (e.g., A/A allele carrying subjects) are more at risk than heterozygotes (e.g., A/G-allele carrying subjects).
Particular SNP alleles, sometimes referred to as polymorphisms or polymorphic alleles, of the present invention can be associated with an increased risk of developing AD. In some embodiments the AD is late-onset form. Mutations or alleles identifying a subject with an increased risk of developing a disorder, for example, late onset AD, are also referred to as “susceptibility” alleles, or mutations.
Those skilled in the art will readily recognize that nucleic acid molecules can be double-stranded molecules and that reference to a particular site on one strand refers, as well, to the corresponding site on a complementary strand. In defining a SNP position, SNP allele, or nucleotide sequence, reference to an adenine, a thymine (uridine), a cytosine, or a guanine at a particular site on one strand of a nucleic acid molecule also defines the thymine (uridine), adenine, guanine, or cytosine (respectively) at the corresponding site on a complementary strand of the nucleic acid molecule. Thus, reference can be made to either strand in order to refer to a particular SNP position, SNP allele, or nucleotide sequence. Probes and primers can be designed to hybridize to either strand and SNP genotyping methods disclosed herein can generally target either strand.
Accordingly, the claims are intended to cover analysis of the opposite strand as well. For the opposite-strand analysis, the AD risk associated alleles are (i) allele T of the C/T SNP rs11159647 locus; (ii) allele C of the T/C SNP rs3826656 locus; (iii) allele A of the G/A SNP rs179943 locus; and (iv) allele G of the T/G SNP rs2049161 locus.
Identification method of SNPs can be of either a positive-type (inclusion of an allele) or a negative-type (exclusion of an allele). Positive-type methods determine the identity of a nucleotide contained in a polymorphic site, whereas negative-type methods determine the identity of a nucleotide not present in a polymorphic site. Thus, a wild-type site can be identified either as wild-type or not mutant. For example, at a biallelic polymorphic site where the wild-type allele contains a cytosine and the mutant allele contains adenine, a site can be positively determined to be either adenine or cytosine or negatively determined to be not adenine (and thus cytosine) or not cytosine (and thus adenine).
In one aspect, the nucleic acid sequences of the gene's allelic variants, or portions thereof, can be the basis for probes or primers, e.g., in methods for determining the identity of the allelic variant of the polymorphic region. Thus, in one embodiment, nucleic acid probes or primers can be used in the methods of the present invention to determine whether a subject is at risk of developing disease such as Alzheimer's disease. One of skill in the art can readily access the nucleic acid sequences spanning the SNPs described herein through the NCBI dbSNP database with the “rs” number uniquely assigned to each SNPs described herein. Thus, a skilled artisan can readily design and optimize primers or probes based on the flanking sequences of the SNP loci described herein.
Based on the NCBI dbSNP database, partial flanking DNA sequences for each of the SNPs described herein are shown as follows (by way of an example only):
SNP rs11159647—5′-TATACTCATATAGCAAAGCTGCACAT[A/G]TATCTAACATAACATTGAAATTTTA-3′ (SEQ ID NO: 1);
SNP rs3826656—5′-ATGAGGATGCAGCTACCTCTCTATTA[A/G]TAAGGATGAATGAAGAGTTATCTAG-3′ (SEQ ID NO: 2);
SNP rs179943—5′-AGATGTTGACCTTTTGAAAAAAAAGT[C/T]CCATTTTCATGACAGATTGGCATAA-3′ (SEQ ID NO: 3);
SNP rs2049161—5′-GCTACTTTACTAGTGTATTTCCCAGC[A/C]GTTGACTTGATAATGATTTTTCAAA-3′ (SEQ ID NO: 4); and alleles of the SNP is separated by the symbol “/” within the square bracket. One of skill in the art can design primers based upon the available nucleic acid sequence. For an illustrative purpose only, an exemplary primer pair that can be used for determining the identity of the allelic variant of SNP rs11159647 can be 5′-TATACTCATATAGCAAAGCT-3′ and 5′-ATTTTAAAGTTACAATACAA-3′. Other primers or probes against the SNPs described herein can be designed and optimized for the purpose of the invention.
According to one aspect of the present invention, a method for determining whether a human is homozygous for a polymorphism, heterozygous for a polymorphism, or lacking the polymorphism altogether (i.e. homozygous wildtype) is encompassed. As an exemplary embodiment only, a method to detect the G>A variance in the SNP rs11159647 loci, a method for determining the G-allele, heterozygous for the G- and A-alleles, or homozygous for the G-allele at the SNP loci are provided. Substantially any method of detecting any allele of the late onset AD risk associated SNPs described herein, such as hybridization, amplification, restriction enzyme digestion, and sequencing methods, can be used.
In one embodiment, an allelic discrimination method can be used for identifying the genotype of SNPs described herein. In one embodiment, the allelic discrimination method involves use of a first oligonucleotide probe which anneals with a target portion of the individual's genome. As an illustrative example only, the target portion comprises, for example, the SNP loci at rs11159647. Because the nucleotide residue at this position differs, for example at the position in the G-allele and the A-allele, the first probe is completely complementary to only one of the two alleles. Alternatively, a second oligonucleotide probe can also be used which is completely complementary to the target portion of the other of the two alleles. The allelic discrimination method also involves use of at least one, and preferably a pair of amplification primers for amplifying a reference region, for example, at least a portion of the flanking region including the SNP 11159647 locus.
The probe in some embodiments is a DNA oligonucleotide having a length in the range from about 20 to about 40 nucleotide residues, preferably from about 20 to about 30 nucleotide residues, and more preferably having a length of about 25 nucleotide residues. In one embodiment, the probe is rendered incapable of extension by a PCR-catalyzing enzyme such as Taq polymerase, for example by having a fluorescent probe attached at one or both ends thereof. Although non-labeled oligonucleotide probes can be used in the kits and methods of the invention, the probes are preferably detectably labeled. Exemplary labels include radionuclides, light-absorbing chemical moieties (e.g. dyes), fluorescent moieties, and the like. Preferably, the label is a fluorescent moiety, such as 6-carboxyfluorescein (FAM), 6-carboxy-4,7,2′,7′-tetrachlorofluoroscein (TET), rhodamine, JOE (2,7-dimethoxy-4,5-dichloro-6-carboxyfluorescein), HEX (hexachloro-6-carboxyfluorescein), or VIC.
In some embodiments, the probe can comprise both a fluorescent label and a fluorescence-quenching moiety such as 6-carboxy-N,N,N′,N′-tetramethylrhodamine (TAMRA), or 4-(4′-dimethlyaminophenylazo)benzoic acid (DABCYL). When the fluorescent label and the fluorescence-quenching moiety are attached to the same oligonucleotide and separated by no more than about 40 nucleotide residues, and preferably by no more than about 30 nucleotide residues, the fluorescent intensity of the fluorescent label is diminished. When one or both of the fluorescent label and the fluorescence-quenching moiety are separated from the oligonucleotide, the intensity of the fluorescent label is no longer diminished. In some embodiments, the probe of the present invention has a fluorescent label attached at or near (i.e. within about 10 nucleotide residues of) one end of the probe and a fluorescence-quenching moiety attached at or near the other end. Degradation of the probe by a PCR-catalyzing enzyme releases at least one of the fluorescent label and the fluorescence-quenching moiety from the probe, thereby discontinuing fluorescence quenching and increasing the detectable intensity of the fluorescent labels. Thus, cleavage of the probe (which, as discussed above, is correlated with complete complementarity of the probe with the target portion) can be detected as an increase in fluorescence of the assay mixture.
If different detectable labels are used, more than one labeled probe can be used, and therefore polymorphisms can be performed in multiplex. For example, the assay mixture can contain a first probe which is completely complementary to the target portion of the SNP rs11159647 loci and to which a first label is attached, and a second probe which is completely complementary to the target portion of the another AD risk associated SNP rs3826656 loci. When two probes are used, the probes are detectably different from each other, having, for example, detectably different size, absorbance, excitation, or emission spectra, radiative emission properties, or the like. For example, a first probe can be completely complementary to the target portion of the polymorphism and have FAM and TAMRA attached at or near opposite ends thereof. The first probe can be used in the method of the present invention together with a second probe which is completely complementary to the target portion of another AD risk associated SNP rs3826656 loci and has TET and TAMRA attached at or near opposite ends thereof. Fluorescent enhancement of FAM (i.e. effected by cessation of fluorescence quenching upon degradation of the first probe by Taq polymerase) can be detected at one wavelength (e.g. 518 nanometers), and fluorescent enhancement of TET (i.e. effected by cessation of fluorescence quenching upon degradation of the second probe by Taq polymerase) can be detected at a different wavelength (e.g. 582 nanometers). Using multiplexing methods, more than one SNP described herein can be detected, providing a better diagnosis and more reliable prediction of AD susceptibility in a subject.
Another allelic discrimination method suitable for use in detection of SNPs employs “molecular beacons”. Detailed description of this methodology can be found in Kostrikis et al., Science 1998; 279:1228-1229, which is incorporated herein by reference.
The use of microarrays comprising a multiplicity of sequences, e.g., SNPs described herein and/or APOE allele is becoming increasingly common in the art. Accordingly, a microarray having at least one oligonucleotide probe, as described above, appended thereon, can be used for SNP genotyping.
The polymorphisms of the present invention can be detected directly or indirectly using any of a variety of suitable methods including fluorescent polarization, mass spectroscopy, and the like. Suitable methods comprise direct or indirect sequencing methods, restriction site analysis, hybridization methods, nucleic acid amplification methods, gel migration methods, the use of antibodies that are specific for the proteins encoded by the different alleles of the polymorphism, or by other suitable means. Alternatively, many such methods are well known in the art and are described, for example in T. Maniatis et al., Molecular Cloning, a Laboratory Manual, 2nd Edition, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989), J. W. Zyskind et al., Recombinant DNA Laboratory Manual, Academic Press, Inc., New York (1988), and in R. Elles, Molecular Diagnosis of Genetic Diseases, Humana Press, Totowa, N.J. (1996), and Mamotte et al, 2006, Clin Biochem Rev, 27; 63-75) each herein incorporated by reference.
According to the present invention, any approach that detects mutations or polymorphisms in a gene can be used, including but not limited to single-strand conformational polymorphism (SSCP) analysis (Orita et al. (1989) Proc. Natl. Acad. Sci. USA 86:2766-2770), heteroduplex analysis (Prior et al. (1995) Hum. Mutat. 5:263-268), oligonucleotide ligation (Nickerson et al. (1990) Proc. Natl. Acad. Sci. USA 87:8923-8927) and hybridization assays (Conner et al. (1983) Proc. Natl. Acad. Sci. USA 80:278-282). Traditional Taq polymerase PCR-based strategies, such as PCR-RFLP, allele-specific amplification (ASA) (Ruano and Kidd (1989) Nucleic Acids Res. 17:8392), single-molecule dilution (SMD) (Ruano et al. (1990) Proc. Natl. Acad. Sci. USA 87:6296-6300), and coupled amplification and sequencing (CAS) (Ruano and Kidd (1991) Nucleic Acids Res. 19:6877-6882), are easily performed and highly sensitive methods to determine haplotypes of the present invention (Michalatos-Beloin et al. (1996) Nucleic Acids Res. 24:4841-4843; Barnes (1994) Proc. Natl. Acad. Sci. USA 91:5695-5699; Ruano and Kidd (1991) Nucleic Acids Res. 19:6877-6882).
In some embodiments, restriction enzymes can be utilized to identify variances or a polymorphic site using “restriction fragment length polymorphism” (RFLP) analysis (Lentes et al., Nucleic Acids Res. 16:2359 (1988); and C. K. McQuitty et al., Hum. Genet. 93:225 (1994)). In RFLP, at least one target polynucleotide is digested with at least one restriction enzyme and the resulting restriction fragments are separated based on mobility in a gel. Typically, smaller fragments migrate faster than larger fragments. Consequently, a target polynucleotide that contains a particular restriction enzyme recognition site will be digested into two or more smaller fragments, which will migrate faster than a larger fragment lacking the restriction enzyme site. Knowledge of the nucleotide sequence of the target polynucleotide, the nature of the polymorphic site, and knowledge of restriction enzyme recognition sequences guide the design of such assays. In another embodiment of the present invention, restriction site analysis of particular nucleotide sequence to identify a nucleotide at a polymorphic site is determined by the presence or absence of a restriction enzyme site. A large number of restriction enzymes are known in the art and, taken together, they are capable of recognizing at least one allele of many polymorphisms. However, such single nucleotide polymorphisms (SNPs) rarely result in changes in a restriction endonuclease site. Thus, SNPs are rarely detectable by restriction fragment length analysis.
A number of approaches use DNA ligase, an enzyme that can join two adjacent oligonucleotides hybridized to a DNA template. In Oligonucleotide ligaton assay (OLA) the sequence surrounding the mutation site is first amplified and one strand serves as a template for three ligation probes, two of these are ASO (allele-specific oligonucleotides) and a third common probe. Numerous approaches cane be used for the detection of the ligated products, for example the ASOs with differentially labeled with fluorescent of hapten labels and ligated products detected by fluorogenic of colorimetric enzyme-linked immunosorbent assays (Tobe et al, Nuclic Acid Res, 1996; 24; 3728-32). For electrophorosis-based systems, use of a morbidity modifier taqgs or variation in probe length coupled with fluorescence detection enables the multiplex genotyping of several single nucleotide substitutions in a single tube (Baron et al, 1997; Clinical Chem., 43; 1984-6). When used on arrays, ASOs can be spotted at specific locations or addresses on a chip, PCR amplified DNA can then be added and ligation to labeled oligonucleotides at specific addresses on the array measured (Zhong et al, Proc Natl Acad Sci 2003; 100; 11559-64).
Single base-extension or minisequencing involves annealing an oligonucleotide primer to the single strand of a PCR product and the addition of a single dideoxynucleotide by thermal DNA polymerase. The oligonucleotide is designed to be one base short of the mutation site. The dideoxynucleotide incorporated is complementary to the base at the mutation site. Approaches cans uses different fluorescent tags or haptens for each of the four different dideoxynucleotides (Pastinen et al, Clin Chem 1996, 42; 1391-7). The dideoxynucleotide differ in molecular weight and this is the basis for single-base extension methods utilizing mass-spectrometry, and genotyping based on the mass of the extended oligonucleotide primer, can be used, for example matrix-assisted laser adsorption/ionization time-of flight mass spectrometry or MALDI-TOF (Li et al, Electrophorosis, 1999, 20; 1258-65), which is quantitative and can be used to calculate the relative allele abundance making the approach suitable for other applications such as gene dosage studies (for example for estimation of allele frequencies on pooled DNA samples).
Minisequencing or Microsequencing by MALDI-TOF can be performed by means known by persons skilled in the art. In a variation of the MALDI-TOF technique, some embodiments can use the Sequenom's Mass Array Technology (www.sequenom.com) (Sauser et al, Nucleic Acid Res, 2000, 28; E13 and Sauser et al, Nucleic Acid Res 2000, 28: E100). and also the GOOD Assay (Sauer S et al, Nucleic Acid Res, 2000; 28, E13 and Sauer et al, Nucleic Acid Res, 2000; 28:E100).
In some embodiments, variations of MALDI-TOF can be performed for analysis of variances in the genes associated with SNPs described herein. For example, MALDI and electrospray ioinization (ESI) (Sauer S. Clin Chem Acta, 2006; 363; 93-105) is also useful with the methods of the present invention.
Allele-specific Amplification is also known as amplification refectory mutation system (ARMS) uses allele specific oligonucleotides (ASO) PCR primers and is an well established and known PCR based method for genotyping (Newton et al, J Med Genet, 1991; 28; 248-51). Typically, one of the two oligonucleotide primers used for the PCR binds to the mutation site, and amplification only takes place if the nucleotide of the mutation is present, with a mismatch being refractory to amplification. The resulting PCR Products can be analyzed by any means known to persons skilled in the art. In a variation of the approach, termed mutagenically separated PCR (MS-PCR) the two ARMS primer of different lengths, one specific for the normal gene and one for the mutation are used, to yield PCR procures of different lengths for the normal and mutant alleles (Rust et al, Nucl Acids Res, 1993; 21; 3623-9). Subsequent gel electrophoresis, for example will show at least one of the two allelic products, with normal, mutant or both (heterozygote) genes. A further variation of this forms the basis of the Masscode System™ (www.bioserve.com) which uses small molecular weight tags covalently attached through a photo-cleavable linker to the ARMS primers, with each ARMS primers labeled with a tag of differing weight (Kokoris et al, 2000, 5; 329-40). A catalogue of numerous tags allows simultaneous amplification/genotyping (multiplexing) of 24 different targets in a single PCR reaction. For any one mutation, genotyping is based on comparison of the relative abundance of the two relevant mass tags by mass spectrometry.
Normal or mutant alleles can be genotyped by measuring the binding of allele-specific oligonucleotides (ASO) hybridization probes. In such embodiments, two ASO probes, one complementary to the normal allele and the other to the mutant allele are hybridized to PCR-amplified DNA spanning the mutation site. In some embodiments, the amplified products can be immobilized on a solid surface and hybridization to radiolabelled oligonucleotides such as known as a ‘dot-blot’ assay. In alternative embodiments, the binding of the PCR products containing a quantifiable label (eg biotin or fluorescent labels) to a solid phase allele-specific oligonucleotide can be measured. Alternatively, for a reverse hybridixation assay, or “reverse dot-blot” the binding of PCR products containing a quantifiable fable (for example but not limited to biotin or fluorescent labels) to a solid phase allele-specific oligonucleotide can be measured. In some embodiments, the use of microarrays comprising hundreds of ASO immobilized onto a solid support surfaces to form an array of ASO can also be used for large scale genotyping of multiple single polymorphisms simultaneously, for example Affymetrix GENECHIP® Mapping 10K Array, which can easily be performed by persons skilled in the art.
Homogenous assays, also called “closed tube” arrays, genomic DNA and all the reagents required for the amplification and genotyping are added simultaneously. Genotyping can be achieved without any post-amplification processing. In some embodiments, one such homogenous assay is the 5′ fluorogenic nuclease assay, also known as the TAQMAN® Assay (Livak et al, Genet Anal, 1999; 14:143-9) and in alternative embodiments Melting curve analyses of FRET probes are used. Such methods are carried out using “real-time” theromcyclers, and utilize two dual-labeled ASO hybridization probes complementary to normal and mutant alleles, where the two probes have different reported labels but a common quencher dye. In such embodiments, the changes in fluorescence characteristics of the probes upon binding to PCR products of target genes during amplification enables “real-time” monitoring of PCR amplification and differences in affinity of the fluorogenic probes for the PCR products of normal and mutant genes enables differentiation of genotypes. The approach uses two dual-labeled ASO hybridization probes complementary to the mutant and normal alleles. The two probes have different fluorescent reported dyes but a common quencher dye. When intact, the probes do not fluoresces due to the proximity of the reporter and quencher dyes. During annealing phase of PCR, two probes compete for hybridization to their target sequences, downstream of the primer sites and are subsequently cleaved by 5′ nuclease activity of Thermophilis aquaticus (Taq) polymerase as the primer is extended, resulting in the separation of the reporter dyes from the quencher. Genotyping is determined by measurement of the fluorescent intensity of the two reporter dyes after PCR amplification. Thus, when intact the probes do not fluoresce due to the proximity of the quencher dyes, whereas during the annealing phase of the PCR the probes compete for hybridization of the target sequences and the separation of one of the probes from the quencher which can be detected.
Melting-curve analysis of FRET hybridization is another approach useful in the method of the invention. Briefly, the reaction includes two oligonucleotide probes which when in close proximity forms a fluorescent complex, where one probe often termed the “mutant sensor” probe is designed to specifically hybridize across the mutation site and the other probe (often referred to as the “anchor probe”) hybridizes to an adjacent site. Fluorescent light is emitted by the “donor” excites the “acceptor” fluorphore creasing a unique fluorogenic complex, which only forms when the probes bind to adjacent sites on the amplified DNA. The “sensor” probe is complementary to either the normal or the mutant allele. Once PCR is complete, heating of the sample through the melting temperatures of the probe yields a fluorescent temperature curve which differs for the mutant and normal allele.
A variation of the FRET hybridization method is the LCGREEN™ method, which obviates the requirement for fluorescent labeled probes altogether. LCGREEN™ is a sensitive highly fluorogenic double-stranded DNA (dsDNA) binding dye that is used to detect the dissociation of unlabelled probes (Liew et al, Clin Chem, 2004; 50; 1156-64 and Zhou et al, Clin Chem, 2005; 51; 1761-2). The method uses unlabeled allele-specific oligonucleotides probes that are perfectly complementary either to the mutant or normal allele, and the mismatch of the ASO/template double strand DNA complex results in a lower melting temperature and an earlier reduction in fluorescent signal form the dsDNA binding dye with increasing temperature.
The OLA can also be used for FRET Probes (Chen et al, 1998; 8:549-56), for example, the PCR/ligation mixture can contain PCR primers, DNA polymerase without 5′ nuclease activity, thermal stable DNA ligase and oligonucleotides for the ligation reaction. The ligation of the allele-specific oligonucleotides have a different acceptor fluorophore and the third ligation oligonucleotide, which binds adjacently to the ASO has a donor fluorophore, and the three ligation oligonucleotides are designed to have a lower melting temperature for the PCR primers to prevent their interference in the PCR amplification. Following PCR, the temperature is lowered to allow ligation to proceed, which results in FRET between the donor and acceptor dyes, and alleles can be disconcerted by comparing the fluorescence emission of the two dyes.
Alternatives to homogenous PCR- and hybridization-based techniques are also encompassed. For example, molecular beacons (Tyagi et al, Nat Biotech, 1998; 16: 49-53) and SCORPION® probes (Thelwell et al, Nucleic Acid Res, 2000; 28; 3752-610).
The OLA can also be performed by the use of FRET probes (Chen et al, Genome Res, 1998; 8: 549-56). In such an embodiment, the PCR/ligation mix contains PCR primers, a thermostable DNA polymerase without 5′ exonuclease activity (to prevent the cleavage of ligation probes during the ligation phase), a thermostable DNA ligase as well as the oligonucleotides for the ligation reaction. The ligation of the ASO each have a different acceptor fluorophore and the third ligation oligonucleotide which binds adjacently to the ASO has a donor fluorophore. The three ligation oligonucleotides are designed to habe a lower melting temperature than the annealing temperature for the PCR primers prevent their interference in PCR amplification. Following PCR, the temperature is lowered to allow ligation to proceed. Ligation results in FRET between donor and acceptor dyes, and alleles can be discerned by comparing the fluorescence emission of the two dyes.
Further, variations of the homogenous PCR- and hybridization based techniques to detect polymorphisms are also encompassed in the present invention. For example, the use of Molecular Beacons (Tyagi et al, Nat Biotech 1998; 16; 49-53) and SCORPION® Probes (Thelwell et al, Nucleic Acid Res 2000; 28; 3752-61). Molecular Beacons are comprised of oligonucleotides that have fluorescent reporter and dyes at their 5′ and 3′ ends, with the central portion of the oligonucleotide hybridizing across the target sequence, but the 5′ and 3′ flanking regions are complementary to each other. When not hybridized to their target sequence, the 5′ and 3′ flanking regions hybridize to form a stem-loop structure, and there is little fluorescence because of the proximity of the reported and the quencher dyes. However, upon hybridization to their target sequence, the dyes are separated and there is a large increase in the fluorescence. Mismatched probe-target hybrids dissociate at substantially lower temperatures than exactly matched complementary hybrids. There are a number of variations of the “molecular Beacon” approach. In some embodiments, such a variation includes use of SCORPION® Probes which are similar but incorporate a PCR primer sequence as part of the probe (Thelwell et al, Nucleic Acid Res 2000; 28; 3752-61). In another variation, ‘duplex’ format gives a better fluorescent signal (Solinas et al, Nucleic Acid Res, 2001, 29; E96).
In another embodiment, polymorphisms can be detected by genotyping using a homogenous or real-time analysis on whole blood samples, without the need for DNA extraction or real-time PCR. Such a method is compatible with FRET and TAQMAN® (Castley et al, Clin Chem, 2005; 51; 2025-30) enabling extremely rapid screening for the particular polymorphism of interest.
In FP, the degree to which the emitted light remains polarized in a particular plane is proportional to the speed at which the molecules rotate and tumble in solution. Under constant pressure, temperature and viscosity, FP is directly related to the molecular weight of a fluorescent species. Therefore, when a small fluorescent molecule is incorporated into a larger molecule, there is an increase in FP. FP can be used in for genotyping of polymorphisms of interest (Chen et al, Genome Res, 1999; 9: 492-8 and Latif et al, Genome Res, 2001; 11; 436-40). FP can be utilized in 5′ nuclease assay (as described above), where the oligonucleotide probe is digested to a lower molecule weight species, for example is amenable to analysis by FP, but with the added benefit of not requiring a quencher. For example, Perlkin-Elmers AcycloPrime™-FP SNP Detection Kit can be used as a FP minisequencing method. Following PCR amplification, unicoportated primers and nucleotides are degraded enzymatially, the enzymes heat inactivated and a miniseqencing reaction using DNA polymerase and fluorescent-labelled dideoxynucleotides performed. FP is then measured, typically in a 96- to 386-well plate format on a FP-plate reader.
In some embodiments, the primer extension reaction and analysis is performed using PYROSEQUENCING™ (Uppsala, Sweden) which essentially is sequencing by synthesis. A sequencing primer, designed directly next to the nucleic acid differing between the disease-causing mutation and the normal allele or the different SNP alleles is first hybridized to a single stranded, PCR amplified DNA template from the individual, and incubated with the enzymes, DNA polymerase, ATP sulfurylase, luciferase and apyrase, and the substrates, adenosine 5′ phosphosulfate (APS) and luciferin. One of four deoxynucleotide triphosphates (dNTP), for example, corresponding to the nucleotide present in the mutation or polymorphism, is then added to the reaction. DNA polymerase catalyzes the incorporation of the dNTP into the standard DNA strand. Each incorporation event is accompanied by release of pyrophosphate (PPi) in a quantity equimolar to the amount of incorporated nucleotide. Consequently, ATP sulfurylase converts PPi to ATP in the presence of adenosine 5′ phosphosulfate. This ATP drives the luciferase-mediated conversion of luciferin to oxyluciferin that generates visible light in amounts that are proportional to the amount of ATP. The light produced in the luciferase-catalyzed reaction is detected by a charge coupled device (CCD) camera and seen as a peak in a PYROGRAM™. Each light signal is proportional to the number of nucleotides incorporated and allows a clear determination of the presence or absence of, for example, the mutation or polymorphism. Thereafter, apyrase, a nucleotide degrading enzyme, continuously degrades unincorporated dNTPs and excess ATP. When degradation is complete, another dNTP is added which corresponds to the dNTP present in for example the selected SNP. Addition of dNTPs is performed one at a time. Deoxyadenosine alfa-thio triphosphate (dATPS) is used as a substitute for the natural deoxyadenosine triphosphate (dATP) since it is efficiently used by the DNA polymerase, but not recognized by the luciferase. For detailed information about reaction conditions for the PYROSEQUENCING, see, e.g. U.S. Pat. No. 6,210,891, which is incorporated herein by reference in its entirety.
Other techniques known to persons skilled in the art are also incorporated for use with the present invention, for example see Kwok, Hum Mut 2002; 9; 315-323 and Kwok, Annu Rev Genomic Hum Genetics, 2001; 2; 235-58 for reviews, which are incorporated herein in their entirety by reference. Examples of other techniques to detect variances and/or polymorphisms are the INVADER® Assay (Gut et al, Hum Mutat, 2001; 17:475-92, Shi et al, Clin Chem, 2001, 47, 164-92, and Olivier et al, Mutat Res, 2005; 573:103-110), the method utilizing FLAP endonucleases (U.S. Pat. No. 6,706,476) and the SNPIex genoptyping systems (Tobler et al, J. Biomol Tech, 2005; 16; 398-406.
In one embodiment, a long-range PCR (LR-PCR) is used to detect mutations or polymorphisms of the present invention. LR-PCR products are genotyped for mutations or polymorphisms using any genotyping methods known to one skilled in the art, and haplotypes inferred using mathematical approaches (e.g., Clark's algorithm (Clark (1990) Mol. Biol. Evol. 7:111-122).
For example, methods including complementary DNA (cDNA) arrays (Shalon et al., Genome Research 6(7):639-45, 1996; Bernard et al., Nucleic Acids Research 24(8):1435-42, 1996), solid-phase mini-sequencing technique (U.S. Pat. No. 6,013,431, Suomalainen et al. Mol. Biotechnol. June; 15(2):123-31, 2000), ion-pair high-performance liquid chromatography (Doris et al. J. Chromatogr. A can 8; 806(1):47-60, 1998), and 5′ nuclease assay or real-time RT-PCR (Holland et al. Proc Natl Acad Sci USA 88: 7276-7280, 1991), or primer extension methods described in the U.S. Pat. No. 6,355,433, can be used.
Molecular beacons also contain fluorescent and quenching dyes, but FRET only occurs when the quenching dye is directly adjacent to the fluorescent dye. Molecular beacons are designed to adopt a hairpin structure while free in solution, bringing the fluorescent dye and quencher in close proximity. Therefore, for example, two different molecular beacons are designed, one recognizing the mutation or polymorphism and the other the corresponding wildtype allele. When the molecular beacons hybridize to the nucleic acids, the fluorescent dye and quencher are separated, FRET does not occur, and the fluorescent dye emits light upon irradiation. Unlike TaqMan probes, molecular beacons are designed to remain intact during the amplification reaction, and must rebind to target in every cycle for signal measurement. TaqMan probes and molecular beacons allow multiple DNA species to be measured in the same sample (multiplex PCR), since fluorescent dyes with different emission spectra can be attached to the different probes, e.g. different dyes are used in making the probes for different disease-causing and SNP alleles. Multiplex PCR also allows internal controls to be co-amplified and permits allele discrimination in single-tube assays. (Ambion Inc, Austin, Tex., TechNotes 8(1)-February 2001, Real-time PCR goes prime time).
Another method to detect mutations or polymorphisms is by using fluorescence tagged dNTP/ddNTPs. In addition to use of the fluorescent label in the solid phase mini-sequencing method, a standard nucleic acid sequencing gel can be used to detect the fluorescent label incorporated into the PCR amplification product. A sequencing primer is designed to anneal next to the base differentiating the disease-causing and normal allele or the selected SNP alleles. A primer extension reaction is performed using chain terminating dideoxyribonucleoside triphosphates (ddNTPs) labeled with a fluorescent dye, one label attached to the ddNTP to be added to the standard nucleic acid and another to the ddNTP to be added to the target nucleic acid.
Alternatively, an INVADER® assay can be used (Third Wave Technologies, Inc (Madison, Wis.)). This assay is generally based upon a structure-specific nuclease activity of a variety of enzymes, which are used to cleave a target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof in a sample (see, e.g. U.S. Pat. No. 6,458,535). For example, an INVADER® operating system (OS), provides a method for detecting and quantifying DNA and RNA. The INVADER® OS is based on a “perfect match” enzyme-substrate reaction. The INVADER® OS uses proprietary CLEAVASE® enzymes (Third Wave Technologies, Inc (Madison, Wis.)), which recognize and cut only the specific structure formed during the INVADER® process which structure differs between the different alleles selected for detection, i.e. the disease-causing allele and the normal allele as well as between the different selected SNPs. Unlike the PCR-based methods, the INVADER® OS relies on linear amplification of the signal generated by the INVADER® process, rather than on exponential amplification of the target.
In the INVADER® process, two short DNA probes hybridize to the target to form a structure recognized by the CLEAVASE® enzyme. The enzyme then cuts one of the probes to release a short DNA “flap.” Each released flap binds to a fluorescently-labeled probe and forms another cleavage structure. When the CLEAVASE® enzyme cuts the labeled probe, the probe emits a detectable fluorescence signal.
Mutations or polymophisms can also be detected using allele-specific hybridization followed by a MALDI-TOF-MS detection of the different hybridization products. In the preferred embodiment, the detection of the enhanced or amplified nucleic acids representing the different alleles is performed using matrix-assisted laser desorption ionization/time-of-flight (MALDI-TOF) mass spectrometric (MS) analysis described in the Examples below. This method differentiates the alleles based on their different mass and can be applied to analyze the products from the various above-described primer-extension methods or the INVADER® process.
In one embodiment, a haplotyping method can be used for the purpose of the invention. A halotyping method is a physical separation of alleles by cloning, followed by sequencing. Other methods of haplotyping include, but are not limited to monoallelic mutation analysis (MAMA) (Papadopoulos et al. (1995) Nature Genet. 11:99-102) and carbon nanotube probes (Woolley et al. (2000) Nature Biotech. 18:760-763). U.S. Patent Application No. US 2002/0081598 also discloses a useful haplotying method which involves the use of PCR amplification.
Computational algorithms such as expectation-maximization (EM), subtraction and PHASE are useful methods for statistical estimation of haplotypes (see, e.g., Clark, A. G. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 7, 111-22. (1990); Stephens, M., Smith, N. J. & Donnelly, P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet. 68, 978-89. (2001); Templeton, A. R., Sing, C. F., Kessling, A. & Humphries, S. A cladistic analysis of phenotype associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations. Genetics 120, 1145-54. (1988)).
Other methods for genetic screening can be used within the scope of the present invention, for example, to detect mutations in genomic DNA, cDNA and/or RNA samples. Methods commonly used, or newly developed or methods yet unknown are encompassed for used in the present invention. Examples of newly discovered methods include for example, but are not limited to; SNP mapping (Davis et al, Methods Mol Biology, 2006; 351; 75-92); Nanogen Nano Chip, (keen-Kim et al, 2006; Expert Rev Mol Diagnostic, 6; 287-294); Rolling circle amplification (RCA) combined with circularable oligonucleotide probes (c-probes) for the detection of nucleic acids (Zhang et al, 2006: 363; 61-70), luminex XMAP system for detecting multiple SNPs in a single reaction vessel (Dunbar S A, Clin Chim Acta, 2006; 363; 71-82; Dunbar et al, Methods Mol Med, 2005; 114:147-1471) and enzymatic mutation detection methods (Yeung et al, Biotechniques, 2005; 38; 749-758).
Methods used to detect point mutations include denaturing gradient gel electrophoresis (“DGGE”), restriction fragment length polymorphism analysis (“RFLP”), chemical or enzymatic cleavage methods, direct sequencing of target regions amplified by PCR (see above), single strand conformation polymorphism analysis (“SSCP”) and other methods well known in the art.
One method of screening for point mutations is based on RNase cleavage of base pair mismatches in RNA/DNA or RNA/RNA heteroduplexes. As used herein, the term “mismatch” is defined as a region of one or more unpaired or mispaired nucleotides in a double-stranded RNA/RNA, RNA/DNA or DNA/DNA molecule. This definition thus includes mismatches due to insertion/deletion mutations, as well as single or multiple base point mutations.
In such embodiments, protection from cleavage agents (such as a nuclease, hydroxylamine or osmium tetroxide and with piperidine) can be used to detect mismatched bases in RNA/RNA DNA/DNA, or RNA/DNA heteroduplexes (see, e.g., Myers et al. (1985) Science 230:1242). In general, the technique of “mismatch cleavage” starts by providing heteroduplexes formed by hybridizing a control nucleic acid, which is optionally labeled, e.g., RNA or DNA, comprising a nucleotide sequence of the allelic variant of the gene of interest with a sample nucleic acid, e.g., RNA or DNA, obtained from a tissue sample. The double-stranded duplexes are treated with an agent which cleaves single-stranded regions of the duplex such as duplexes formed based on basepair mismatches between the control and sample strands. For instance, RNA/DNA duplexes can be treated with RNase and DNA/DNA hybrids treated with S1 nuclease to enzymatically digest the mismatched regions. In other embodiments, either DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine whether the control and sample nucleic acids have an identical nucleotide sequence or in which nucleotides they are different. See, for example, U.S. Pat. No. 6,455,249, Cotton et al. (1988) Proc. Natl. Acad. Sci. USA 85:4397; Saleeba et al. (1992) Methods Enzy. 217:286-295. In another embodiment, the control or sample nucleic acid is labeled for detection.
U.S. Pat. No. 4,946,773 describes an RNaseA mismatch cleavage assay that involves annealing single-stranded DNA or RNA test samples to an RNA probe, and subsequent treatment of the nucleic acid duplexes with RNaseA. For the detection of mismatches, the single-stranded products of the RNaseA treatment, electrophoretically separated according to size, are compared to similarly treated control duplexes. Samples containing smaller fragments (cleavage products) not seen in the control duplex are scored as positive.
Other investigators have described the use of RNaseI in mismatch assays. The use of RNaseI for mismatch detection is described in literature from Promega Biotech. Promega markets a kit containing RNaseI that is reported to cleave three out of four known mismatches.
In other embodiments, alterations in electrophoretic mobility is used to identify the particular allelic variant. For example, single strand conformation polymorphism (SSCP) can be used to detect differences in electrophoretic mobility between mutant and wild type nucleic acids (Orita et al. (1989) Proc Natl. Acad. Sol USA 86:2766; Cotton (1993) Mutat. Res. 285:125-144 and Hayashi (1992) Genet Anal Tech Appl 9:73-79). Single-stranded DNA fragments of sample and control nucleic acids are denatured and allowed to renature. The secondary structure of single-stranded nucleic acids varies according to sequence, the resulting alteration in ejectrophoretic mobility enables the detection of even a single base change. The DNA fragments can be labeled or detected with labeled probes. The sensitivity of the assay can be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence. In another preferred embodiment, the subject method utilizes heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility (Keen et al. (1991) Trends Genet. 7:5).
Gel Migration Single strand conformational polymorphism (SSCP; M. Orita et al., Genomics 5:8 74-8 79 (1989); Huinphfies et al., In: Molecular Diagnosis of Genetic Diseases, R. Elles, ed. pp 321-340 (1996)) and temperature gradient gel electrophoresis (TGGE; R. M. Wartell et al., Nucl. Acids Res. 18:2699-2706 (1990)) are examples of suitable gel migration-based methods for determining the identity of a polymorphic site. In SSCP, a single strand of DNA will adopt a conformation that is uniquely dependent of its sequence composition. This conformation is usually different, if even a single base is changed. Thus, certain embodiments of the present invention, SSCP can be utilized to identify polymorphic sites, as wherein amplified products (or restriction fragments thereof of the target polynucleotide are denatured, then run on a non-denaturing gel. Alterations in the mobility of the resultant products are thus indicative of a base change. Suitable controls and knowledge of the “normal” migration patterns of the wild-type alleles can be used to identify polymorphic variants.
In yet another embodiment, the identity of the allelic variant is obtained by analyzing the movement of a nucleic acid comprising the polymorphic region in polyacrylamide gels containing a gradient of denaturant, which is assayed using denaturing gradient gel electrophoresis (DGGE) (Myers et al. (1985) Nature 313:495). When DGGE is used as the method of analysis, DNA will be modified to insure that it does not completely denature, for, example by adding a GC clamp of approximately 40 bp of high-melting GC rich DNA by PCR. In a further embodiment, a temperature gradient is used in place of a denaturing agent gradient to identify differences in the mobility of control and sample DNA (Rosenbaum and Reissner (1987) Biophys Chem 265:1275).
Others have described using the MutS protein or other DNA-repair enzymes for detection of single-base mismatches. Alternative methods for detection of deletion, insertion or substitution mutations that can be used in the practice of the present invention are disclosed in U.S. Pat. Nos. 5,849,483, 5,851,770, 5,866,337, 5,925,525 and 5,928,870, each of which is incorporated herein by reference in its entirety. Several methods have been developed to screen polymorphisms and some examples are listed below. The reference of Kwok and Chen (2003) and Kwok (2001) provide overviews of some of these methods, both of these references are specifically incorporated by reference.
Examples of identifying polymorphisms and applying that information in a way that yields useful information regarding patients can be found, for example, in U.S. Pat. No. 6,472,157; U.S. Patent Application Publications 20020016293, 20030099960, 20040203034; WO 0180896, all of which are hereby incorporated by reference.
In another embodiment, multiplex PCR procedures using allele-specific primers can be used to simultaneously amplify multiple regions of a target nucleic acid (PCT Application WO89/10414), enabling amplification only if a particular allele is present in a sample. Other embodiments using alternative primer-guided nucleotide incorporation procedures for assaying polymorphic sites in DNA can be used, and have been described (Komher, J. S. et al., Nucl. Acids. Res. 17:7779-7784 (1989); Sokolov, B. P., Nucl. Acids Res. 18:3671 (1990); Syvanen, A.-C., et al., Genomics 8:684-692 (1990); Kuppuswamy, M. N. et al., Proc. Nad. Acad. Sci. (U.S.A) 88:1143-1147 (1991); Bajaj et al. (U.S. Pat. No. 5,846,710); Prezant, T. R. et al., Hum Mutat. 1: 159-164 (1992); Ugozzoli, L. et al., GATA 9:107-112 47 (1992); Nyr6n, P. et al., Anal. Biochem. 208:171-175 (1993)).
Other known nucleic acid amplification procedures include transcription-based amplification systems (Malek, L. T. et al., U.S. Pat. No. 5,130,238; Davey, C. et al., European Patent Application 329,822; Schuster et al.) U.S. Pat. No. 5,169,766; Miller, H. I. et al., PCT-Application WO89/06700; Kwoh, D. et al., Proc. Natl. Acad. Sci. (U.S.A) 86:1173 Z1989); Gingeras, T. R. et al., PCT Application WO88/10315)), or isothermal amplification methods (Walker, G. T. et al., Proc. Natl. 4cad Sci. (U.S.A) 89:392-396 (1992)) can also be used.
Another method to determine genetic variation is using “gene chips” as described in Examples 1 and 2. Probes can be affixed to surfaces for use as “gene chips.” Such gene chips can be used to detect genetic variations by a number of techniques known to one of skill in the art. In one technique, oligonucleotides are arrayed on a gene chip for determining the DNA sequence of a by the sequencing by hybridization approach, such as that outlined in U.S. Pat. Nos. 6,025,136 and 6,018,041. The probes of the present invention also can be used for fluorescent detection of a genetic sequence. Such techniques have been described, for example, in U.S. Pat. Nos. 5,968,740 and 5,858,659. A probe also can be affixed to an electrode surface for the electrochemical detection of nucleic acid sequences such as described by Kayyem et al. U.S. Pat. No. 5,952,172 and by Kelley, S. O. et al. (1999) Nucleic Acids Res. 27:4830-4837.
Another aspect of the invention provides methods and assays for determining an increased risk for developing late onset Alzheimer's disease (AD) in a subject, by determining in a biological sample of the subject the level of at least one gene associated with the late-onset AD risk SNPs and alleles described herein. The methods and assays described herein include (a) transforming the gene expression product into a detectable gene target; (b) measuring the amount of the detectable gene target; and (c) comparing the amount of the detectable gene target to an amount of a reference, wherein if the amount of the detectable gene target is statistically different from that of the amount of the reference, the subject is at increased risk for developing late onset AD.
In some embodiments, the reference can be a normal healthy subject with no genetic susceptibility for AD. For example, a normal healthy subject is not a carrier of any of the late onset AD risk associated alleles described herein or APOE allele, or is not diagnosed with any forms of AD such as early-onset autosomal-dominant AD, or any neurodegenerative disorders. The reference can be also a control sample, a pooled sample of control individuals or a numeric value or range of values based on the same.
In some embodiments, the gene associated with the late onset AD risk SNP rs179943 is ATXN1. ATXN1 is also known as aliases ATX1, D6S504E, SCA1. In such embodiments, at least the amount of ATXN1 gene expression products (e.g., nucleic acid or protein) can be measured in a biological sample of a subject. If the amount of the ATXN1 gene expression products is lower than that of the reference amount, the subject is at increased risk for developing late onset AD. The amount of the ATXN1 gene expression products is lower by at least about 10% than the reference ATXN1 amount, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95%, about 98%, about 99% or 100%, including all the percentages between 10-100%.
In some embodiments, the gene associated with the late onset AD risk SNP rs3826656 is CD33. CD 33 is also known as aliases FLJ00391, SIGLEC-3, SIGLEC3, and p67, as well as designated as CD33 antigen (gp67), gp67, myeloid cell surface antigen CD33, sialic acid binding Ig-like lectin 3, and sialic acid-binding Ig-like lectin 3. In such embodiments, at least the amount of CD33 gene expression products (e.g., nucleic acid or protein) can be measured in a biological sample of a subject. In other embodiments, the gene associated with the late onset AD risk SNP rs2049161 is discs, large (Drosophila) homolog-associated protein 1 (DLGAP1). DLGAP1 is also known as aliases DAP-1, DAP-1-ALPHA, DAP-1-BETA, GKAP, MGC88156, SAPAP1, and hGKAP, as well as designated as OTTHUMP00000174377, OTTHUMP00000174378, PSD-95/SAP90 binding protein 1, PSD-95/SAP90-binding protein 1, 'SAP90/PSD-95-associated protein 1, disks large-associated protein 1, and guanylate kinase-associated protein. In such embodiments, at least the amount of CD33 and/or DLGAP1 gene expression products (e.g., nucleic acid or protein) can be measured in a biological sample of a subject. If the amount of the CD33 and/or DLGAP1 gene expression products is statistically different from that of the reference amount, the subject is at increased risk for developing late onset AD. The amount of the CD33 or DLGAP1 gene expression products is statistically different from the reference amount by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95%, about 98%, about 99% or 100%, including all the percentages between 10-100%.
In some embodiments, the invention also provides assays to identify a subject with an increased risk for developing late onset AD. In one embodiment, the assay comprises or consists essentially of a system for transforming and identifying at least one nucleic acid polymorphism in a SNP locus described herein in a biological sample of a subject, and a system for computing the likelihood of the subject getting late onset AD on the basis of comparison of the identified nuclei acid at the SNP locus against the late onset AD risk associated alleles described herein. If the computing or comparion system, which can be a computer implemented system, indicates that at least one of the allele at the SNP locus is identical to the corresponding AD risk associated allele, the subject from which the sample is collected can be diagnosed with increased susceptibility for late onset AD.
In another embodiment of the assays described herein, the assay comprises or consists essentially of a system for transforming and measuring the amount of at least one gene expression product associated with the amount in the test sample to a reference amount. In such embodiments, the gene expression product can be ATXN1, CD33 and/or DLGAP1. The reference amount can be obtained either from a control sample, which can be a biological sample from a normal and healthy individual free of any neurodegenerative disorder, e.g., AD. If the comparison system, which can be a computer implemented system, indicates that the amount of the measured gene expression product is statistically different from that of the reference amount, the subject from which the sample is collected can be diagnosed with increased risk for late onset AD.
Methods to measure gene expression products associated with late onset AD risk associated SNPs described herein are well known to a skilled artisan. Such methods to measure gene expression products, e.g., protein level, include ELISA (enzyme linked immunosorbent assay), western blot, immunoprecipitation, immunofluorescence using detection reagents such as an antibody or protein binding agents. Alternatively, a peptide can be detected in a subject by introducing into a subject a labeled anti-peptide antibody and other types of detection agent. For example, the antibody can be labeled with a radioactive marker whose presence and location in the subject is detected by standard imaging techniques, particularly useful are methods that detect the allelic variant of a peptide expressed in a subject and methods which detect fragments of a peptide in a sample.
For example, antibodies and ELISA kits for ATXN1, CD33 and DLGAP1 are commercially available and can be used for the purpose of the invention. Alternatively, since the amino acid sequences for ATXN1, CD33 and DLGAP1 are known and publicly available at NCBI website, one of skill in the art can raise their own antibodies against these proteins of interest for the purpose of the invention.
The amino acid sequences of ATXN1, CD33 and DLGAP1 have been assigned NCBI accession numbers for different species such as human, mouse and rat. In particular, the NCBI accession numbers for the amino acid sequences of human ATXN1, human CD33 and human DLGAP1 are included herein. For the human ATXN1 protein, the NCBI accession number for the amino acid sequence is either NP—000323 or NP—001121636 (due to the presence of two transcript variants). However, both the two transcript variants encode the same ATXN1 protein (SEQ ID NO: 7). For the human CD33 protein, the NCBI accession number for the amino acid sequence is NP—001763 (SEQ ID NO: 9), NP—001076087 (SEQ ID NO: 11) or NP—001171079 (SEQ ID NO: 13), each of which represents a different CD33 isoform. For the human DLGAP1 protein, the NCBI accession number for the amino acid sequence is NP—004737 (SEQ ID NO: 15) or NP—001003809 (SEQ ID NO: 17), each of which represents an alpha or a beta isoform, respectively.
In alternative embodiments, antibodies directed against wild type or mutant peptides encoded by the allelic variants of the gene of interest, for example ATXN1, can also be used in AD diagnostics. Such diagnostic methods can be used to detect abnormalities in the level of expression of the peptide, or abnormalities in the structure and/or tissue, cellular, or subcellular location of the peptide.
In another embodiment, immunohistochemistry (“IHC”) and immunocytochemistry (“ICC”) techniques can be used. IHC is the application of immunochemistry to tissue sections, whereas ICC is the application of immunochemistry to cells or tissue imprints after they have undergone specific cytological preparations such as, for example, liquid-based preparations. Immunochemistry is a family of techniques based on the use of an antibody, wherein the antibodies are used to specifically target molecules inside or on the surface of cells. The antibody typically contains a marker that will undergo a biochemical reaction, and thereby experience a change color, upon encountering the targeted molecules. In some instances, signal amplification can be integrated into the particular protocol, wherein a secondary antibody, that includes the marker stain or marker signal, follows the application of a primary specific antibody. However, this detection method could be considered invasive for the invention as ATXN1, CD33 or DLGAP1 are not secreted proteins. Therefore, a biopsy would be required to determine the protein levels of those gene expression products in the brain and thus is less desirable.
Accordingly, in one embodiment, the gene expression products as described herein can be instead determined by determining the level of messenger RNA (mRNA) expression of genes associated with SNPs described herein (e.g., ATXN1, CD33, and DLGAP1). Such molecules can be isolated, derived, or amplified from a biological sample, such as body fluids. Detection of mRNA expression is known by persons skilled in the art, and comprise, for example but not limited to, PCR procedures, RT-PCR, Northern blot analysis, differential gene expression, RNA protection assay, microarray analysis, hybridization methods etc.
The nucleic acid sequences of ATXN1, CD33 and DLGAP1 have been assigned NCBI accession numbers for different species such as human, mouse and rat. In particular, the NCBI accession numbers for the nuclei acid sequences of human ATXN1, human CD33 and human DLGAP1 are included herein. For the human ATXN1 mRNA, the NCBI accession number for the nucleic acid sequence is NM—000332 (SEQ ID NO: 5) or NM—001128164 (SEQ ID NO: 6), each of which represents a different transcript variant. However, both the two transcript variants encode the same ATXN1 protein (SEQ ID NO: 7). For the human CD33 mRNA, the NCBI accession number for the nucleic acid sequence is NM—001772 (SEQ ID NO: 8), NM—001082618 (SEQ ID NO: 10) or NM—001177608 (SEQ ID NO: 12), each of which represents a different transcript variant for each CD33 isoform. For the human DLGAP1 mRNA, the NCBI accession number for the nucleic acid sequence is NM—004746 (SEQ ID NO: 14) or NM—001003809 (SEQ ID NO: 16), each of which represents a transcript for an alpha or a beta isoform, respectively. Accordingly, a skilled artisan can design an appropriate primer based on the known sequence for determining the mRNA level of the respective gene.
Nucleic acid and ribonucleic acid (RNA) molecules can be isolated from a particular biological sample using any of a number of procedures, which are well-known in the art, the particular isolation procedure chosen being appropriate for the particular biological sample. For example, freeze-thaw and alkaline lysis procedures can be useful for obtaining nucleic acid molecules from solid materials; heat and alkaline lysis procedures can be useful for obtaining nucleic acid molecules from urine; and proteinase K extraction can be used to obtain nucleic acid from blood (Roiff, A et al. PCR: Clinical Diagnostics and Research, Springer (1994)).
In general, the PCR procedure describes a method of gene amplification which is comprised of (i) sequence-specific hybridization of primers to specific genes within a nucleic acid sample or library, (ii) subsequent amplification involving multiple rounds of annealing, elongation, and denaturation using a DNA polymerase, and (iii) screening the PCR products for a band of the correct size. The primers used are oligonucleotides of sufficient length and appropriate sequence to provide initiation of polymerization, i.e. each primer is specifically designed to be complementary to each strand of the genomic locus to be amplified.
In an alternative embodiment, mRNA level of gene expression products described herein can be determined by reverse-transcription (RT) PCR and by quantitative RT-PCR (QRT-PCR) or real-time PCR methods. Methods of RT-PCR and QRT-PCR are well known in the art.
Systems for Identifying a Subject with Increased Risk for Late Onset AD
Embodiments of the invention also provide for systems (and computer readable media for causing computer systems) to perform a method for determining presence or absence of alleles associated with an increased risk of a subject for developing late onset AD. In one embodiment, provided herein is a system comprising: (a) a determination module configured to identify and detect at least one single nucleotide polymorphism (SNP) in a biological sample of a subject, wherein the SNP is selected from: alleles G/A SNP rs11159647, alleles A/G SNP rs3826656, alleles C/T SNP rs179943, alleles A/C SNP rs2049161, or any combination thereof; (b) a storage module configured to store output data from the determination module; (c) a computing module adapted to identify from the output data at least one of AD risk associated alleles is present in the output data stored on the storage module, wherein the AD risk associated alleles is selected from: allele A of the G/A SNP rs11159647, allele G of the A/G SNP rs3826656, allele T of the C/T SNP rs179943, and allele C of the A/C SNP rs2049161; and (d) a display module for displaying if any of the AD risk associated alleles was identified or not, and/or displaying the detected alleles.
Embodiments of the invention can be described through functional modules, which are defined by computer executable instructions recorded on computer readable media and which cause a computer to perform method steps when executed. The modules are segregated by function for the sake of clarity. However, it should be understood that the modules/systems need not correspond to discreet blocks of code and the described functions can be carried out by the execution of various code portions stored on various media and executed at various times. Furthermore, it should be appreciated that the modules can perform other functions, thus the modules are not limited to having any particular functions or set of functions.
The computer readable storage media can be any available tangible media that can be accessed by a computer. Computer readable storage media includes volatile and nonvolatile, removable and non-removable tangible media implemented in any method or technology for storage of information such as computer readable instructions, data structures, program modules or other data. Computer readable storage media includes, but is not limited to, RAM (random access memory), ROM (read only memory), EPROM (erasable programmable read only memory), EEPROM (electrically erasable programmable read only memory), flash memory or other memory technology, CD-ROM (compact disc read only memory), DVDs (digital versatile disks) or other optical storage media, magnetic cassettes, magnetic tape, magnetic disk storage or other magnetic storage media, other types of volatile and non-volatile memory, and any other tangible medium which can be used to store the desired information and which can accessed by a computer including and any suitable combination of the foregoing.
Computer-readable data embodied on one or more computer-readable media may define instructions, for example, as part of one or more programs that, as a result of being executed by a computer, instruct the computer to perform one or more of the functions described herein, and/or various embodiments, variations and combinations thereof. Such instructions may be written in any of a plurality of programming languages, for example, Java, J#, Visual Basic, C, C#, C++, Fortran, Pascal, Eiffel, Basic, COBOL assembly language, and the like, or any of a variety of combinations thereof. The computer-readable media on which such instructions are embodied may reside on one or more of the components of either of a system, or a computer readable storage medium described herein, may be distributed across one or more of such components.
The computer-readable media may be transportable such that the instructions stored thereon can be loaded onto any computer resource to implement the aspects of the present invention discussed herein. In addition, it should be appreciated that the instructions stored on the computer-readable medium, described above, are not limited to instructions embodied as part of an application program running on a host computer. Rather, the instructions may be embodied as any type of computer code (e.g., software or microcode) that can be employed to program a computer to implement aspects of the present invention. The computer executable instructions may be written in a suitable computer language or combination of several languages. Basic computational biology methods are known to those of ordinary skill in the art and are described in, for example, Setubal and Meidanis et al., Introduction to Computational Biology Methods (PWS Publishing Company, Boston, 1997); Salzberg, Searles, Kasif, (Ed.), Computational Methods in Molecular Biology, (Elsevier, Amsterdam, 1998); Rashidi and Buehler, Bioinformatics Basics: Application in Biological Science and Medicine (CRC Press, London, 2000) and Ouelette and Bzevanis Bioinformatics: A Practical Guide for Analysis of Gene and Proteins (Wiley & Sons, Inc., 2nd ed., 2001).
The functional modules of certain embodiments of the invention include at minimum a determination module, a storage module, a computing module, and a display module. The functional modules can be executed on one, or multiple, computers, or by using one, or multiple, computer networks. The determination module has computer executable instructions to provide e.g., allelic variance etc in computer readable form.
The determination module can comprise any system for detecting a signal elicited from the SNPs described herein in a biological sample. In some embodiments, such systems can include an instrument, e.g., for genotyping such as Pyrosequencer described earlier. In another embodiment, the determination module can comprise multiple units for different functions, such as implication and hybridization. In one embodiment, the determination module can be configured to perform the genotyping methods described in the Examples, including restriction enzyme digestion, ligation, PCR, purification, labeling, incubation and hybridization.
In some embodiments, the determination module can be further configured to identify and detect the presence of at least one additional AD risk associated allele, such as APOE-ε4 allele, or other AD alleles such as APP, PSEN1, and PSEN2.
The information determined in the determination system can be read by the storage module. As used herein the “storage module” is intended to include any suitable computing or processing apparatus or other device configured or adapted for storing data or information. Examples of electronic apparatus suitable for use with the present invention include stand-alone computing apparatus, data telecommunications networks, including local area networks (LAN), wide area networks (WAN), Internet, Intranet, and Extranet, and local and distributed computer processing systems. Storage modules also include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage media, magnetic tape, optical storage media such as CD-ROM, DVD, electronic storage media such as RAM, ROM, EPROM, EEPROM and the like, general hard disks and hybrids of these categories such as magnetic/optical storage media. The storage module is adapted or configured for having recorded thereon, for example, sample name, alleleic variants, and frequency of each alleleic variant. Such information may be provided in digital form that can be transmitted and read electronically, e.g., via the Internet, on diskette, via USB (universal serial bus) or via any other suitable mode of communication.
As used herein, “stored” refers to a process for encoding information on the storage module. Those skilled in the art can readily adopt any of the presently known methods for recording information on known media to generate manufactures comprising expression level information.
In one embodiment of any of the systems described herein, the storage module stores the output data from the determination module. In additional embodiments, the storage module stores the reference information such as late onset AD risk associated alleles at the SNPs described herein, and/or the wild-type allele in subjects who do not have symptoms associated with AD.
The “computing module” can use a variety of available software programs and formats for computing the genotype frequency at the SNPs described herein and identifying the presence or absence of at least one of AD risk associated alleles described herein. Genotyping algorithms are well established in the art. A skilled artisan is readily able to determine the appropriate genotyping algorithms based on the size and quality of the sample. Genotyping algorithms, e.g., DM or BRLMM, and statistics tools for data analysis described in Examples can be implemented in the computing module of the invention. In one embodiment, the computing module further comprises a comparison module, which compares the genotype determined at the SNPs described herein with the AD risk associated alleles and/or wide-type alleles. By way of an example, when the allelic variant at SNP rs11159647 is determined to be A allele, a comparison module can compare or match the output data—A-allele—with the AD risk associated allele A and/or with the wild-type allele G at such locus that have been pre-stored in the storage module. During the comparison or matching process, the comparison module can determine whether the identified allele at the rs11159647 locus is identical to the AD associated allele A or the wild-type allele G at the locus. In some circumstances, if the identified allele at rs11159647 is neither allele A nor allele G, the comparison module can generate an output indicating undetermined risk for AD. In various embodiments, the comparison module can be configured using existing commercially-available or freely-available software for comparison purpose, and may be optimized for particular data comparisons that are conducted.
The computing and/or comparison module, or any other module of the invention, can include an operating system (e.g., UNIX) on which runs a relational database management system, a World Wide Web application, and a World Wide Web server. World Wide Web application includes the executable code necessary for generation of database language statements (e.g., Structured Query Language (SQL) statements). Generally, the executables will include embedded SQL statements. In addition, the World Wide Web application may include a configuration file which contains pointers and addresses to the various software entities that comprise the server as well as the various external and internal databases which must be accessed to service user requests. The Configuration file also directs requests for server resources to the appropriate hardware—as may be necessary should the server be distributed over two or more separate computers. In one embodiment, the World Wide Web server supports a TCP/IP protocol. Local networks such as this are sometimes referred to as “Intranets.” An advantage of such Intranets is that they allow easy communication with public domain databases residing on the World Wide Web (e.g., the GenBank or Swiss Pro World Wide Web site). Thus, in a particular preferred embodiment of the present invention, users can directly access data (via Hypertext links for example) residing on Internet databases using a HTML interface provided by Web browsers and Web servers.
The computing and/or comparison module provides a computer readable comparison result that can be processed in computer readable form by predefined criteria, or criteria defined by a user, to provide a content-based in part on the comparison result that may be stored and output as requested by a user using an output module, e.g., a display module.
In some embodiments, the content displayed on the display module can be an allele genotype identified in the biological sample of the subject together with a reference allele. For example, the reference allele can be an AD risk associated allele or a wild-type allele. In some embodiments, the content displayed on the display module can be a numerical value indicating the probability of getting late onset AD. In such embodiments, the probability can be expressed in percentages or a fraction of getting late onset AD. For example, higher percentage or a fraction closer to 1 indicates a higher likelihood of a subject going to be affected with late onset AD. In some embodiments, the content displayed on the display module can be single word or phrases to qualitatively indicate the likelihood of a subject going to be affected with late onset AD. For example, a word “unlikely” can be used to indicate a lower risk for late onset AD, while “likely” can be used to indicate a high risk for late onset AD.
In one embodiment of the invention, the content based on the computing and/or comparison result is displayed on a computer monitor. In one embodiment of the invention, the content based on the computing and/or comparison result is displayed through printable media. The display module can be any suitable device configured to receive from a computer and display computer readable information to a user. Non-limiting examples include, for example, general-purpose computers such as those based on Intel PENTIUM-type processor, Motorola PowerPC, Sun UltraSPARC, Hewlett-Packard PA-RISC processors, any of a variety of processors available from Advanced Micro Devices (AMD) of Sunnyvale, Calif., or any other type of processor, visual display devices such as flat panel displays, cathode ray tubes and the like, as well as computer printers of various types.
In one embodiment, a World Wide Web browser is used for providing a user interface for display of the content based on the computing/comparison result. It should be understood that other modules of the invention can be adapted to have a web browser interface. Through the Web browser, a user can construct requests for retrieving data from the computing/comparison module. Thus, the user will typically point and click to user interface elements such as buttons, pull down menus, scroll bars and the like conventionally employed in graphical user interfaces.
Systems and computer readable media described herein are merely illustrative embodiments of the invention for identifying at least one nucleic acid polymorphism at the SNPs described herein in a subject and determining a risk of the subject for susceptibility to late onset AD, and therefore are not intended to limit the scope of the invention. Variations of the systems and computer readable media described herein are possible and are intended to fall within the scope of the invention.
The modules of the machine, or those used in the computer readable medium, may assume numerous configurations. For example, function may be provided on a single machine or distributed over multiple machines.
Provided herein are methods, assays and systems for determining an increased risk for developing late onset AD in a subject by identifying the SNPs described herein or corresponding gene expression products in a biological sample of the subject. The term “biological sample” as used herein denotes a sample taken or isolated from a biological organism, e.g., tissue cell culture supernatant, cell lysate, a homogenate of a tissue sample from a subject or a fluid sample from a subject. Exemplary biological samples include, but are not limited to, blood, sputum, urine, spinal fluid, pleural fluid, nipple aspirates, lymph fluid, the external sections of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, milk, feces, sperm, cells or cell cultures, serum, leukocyte fractions, smears, tissue samples of all kinds, embryos, etc. The term also includes both a mixture of the above-mentioned samples such as whole human blood containing mycobacteria as well as food samples that contain free or bound nucleic acids or cells containing nucleic acids. The term “biological sample” also includes untreated or pretreated (or pre-processed) biological samples.
A “biological sample” can contain cells from subject, but the term can also refer to non-cellular biological material, such as non-cellular fractions of blood, saliva, or urine, that can be used to measure gene expression levels or determine SNPs. In some embodiments, the sample is from a resection, biopsy, or core needle biopsy. In addition, fine needle aspirate samples can be used. Samples can be either paraffin-embedded or frozen tissue.
The sample can be obtained by removing a sample of cells from a subject, but can also be accomplished by using previously isolated cells (e.g. isolated by another person). In addition, the biological sample can be freshly collected or a previously collected sample. Furthermore, the biological sample can be utilized for the detection of the presence and/or quantitative level of a biomolecule of interest. Representative biomolecules include, but are not limited to, DNA, RNA, mRNA, polypeptides, and derivatives and fragments thereof. In some embodiments, the biological sample can be used for SNP determination for diagnosis of a disease or a disorder, e.g., Alzheimer's disease, using the methods, assays and systems of the invention.
In some embodiments, biological sample is a biological fluid. Examples of biological fluids include, but are not limited to, saliva, bone marrow, blood, serum, plasma, urine, sputum, cerebrospinal fluid, an aspirate, tears, and any combinations thereof.
In some embodiments, the biological sample is an untreated biological sample. As used herein, the phrase “untreated biological sample” refers to a biological sample that has not had any prior sample pre-treatment except for dilution and/or suspension in a solution. Exemplary methods for treating a biological sample include, but are not limited to, centrifugation, filtration, sonication, homogenization, heating, freezing and thawing, and any combinations thereof.
In some embodiments, the biological sample is a frozen biological sample, e.g., a frozen tissue or fluid sample such as urine, blood, serum or plasma. The frozen sample can be thawed before employing methods, assays and systems of the invention. After thawing, a frozen sample can be centrifuged before being subjected to methods, assays and systems of the invention.
In some embodiments, the biological fluid sample can be treated with at least one chemical reagent, such as a protease inhibitor. In some embodiments, the biological fluid sample is a clarified biological fluid sample, for example, by centrifugation and collection of a supernatant comprising the clarified biological fluid sample.
In some embodiments, a biological sample is a pre-processed biological sample, for example, supernatant or filtrate resulting from a treatment selected from the group consisting of centrifugation, filtration, sonication, homogenization, lysis, thawing, amplification, purification, restriction enzyme digestion ligation and any combinations thereof. In some embodiments, a biological sample can be a nucleic acid product amplified after polymerase chain reaction (PCR). The term “nucleic acid” used herein refers to DNA, RNA, or mRNA.
In some embodiments, the biological sample can be treated with a chemical and/or biological reagent. Chemical and/or biological reagents can be employed to protect and/or maintain the stability of the sample, including biomolecules (e.g., nucleic acid and protein) therein, during processing. One exemplary reagent is a protease inhibitor, which is generally used to protect or maintain the stability of protein during processing. In addition, or alternatively, chemical and/or biological reagents can be employed to release nucleic acid or protein from the sample.
The skilled artisan is well aware of methods and processes appropriate for pre-processing of biological samples required for determination of SNPs or expression of gene expression products as described herein.
The present invention further provides methods for treating AD in a subject. Among the four SNPs described herein, rs179943 resides within the ataxin-1 (ATXN1) gene, which has been previously shown to cause a neurodegenerative disorder, spinocerebellar ataxia type 1 (SCA1), through a gain-of-function mechanism utilizing its polyglutamine tract and functional domains [13]. SCA1 is a neurodegenerative disease characterized by ataxia, progressive motor deterioration, and loss of Purkinje cells in the cerebellum [13, 14]. However, the role of ATXN1 in neurodegeneration in AD is unknown.
Ataxin-1 (ATXN1) Gene
ATXN1 (synonyms: ATX1, D6S504E; SCA1) spans 450 kb of genomic DNA and is located on 6p22.3, a chromosomal region that had been previously linked to AD in the recent genetic linkage screen by Dr: Tanzi's group [15]. ATXN1 is organized into 9 exons [14]. The AD risk-conferring SNP rs179943 is located at position 16,506,297 in the intron region between exons 8 and 9 [6]. The coding region consists of 2448 bp nucleotides and lies in exons 8 and 9. ATXN1 contains a CAG trinucleotide repeat regionlocated in exon 8, which encodes the polyglutamine sequence tract. Expansion of the CAG repeat is implicated in causing a polyglutamine-induced gain-of-function in the protein, and is associated with eight other diseases [13]. These related diseases are: SCA2 (expansion by ATXN2), SCA3 (also called Machado-Joseph disease; by ATXN3 expansion), SCA6 (by ATXN6 expansion), SCA7 (by the expansion of TATA binding protein 7), SCA17 (by ATXN17 expansion), Huntington's disease (by Huntingtin expansion), Dentatorubrai-pallidoiuysian atrophy (as also called Haw River syndrome; by expansion of atrophin-1), and Spinobulbar muscular atrophy (also called Kennedy disease; by expansion of androgen receptor). In SCA1, the number of CAG repeats in the normal population ranges from 6-42 with those greater than 21 being interrupted with 1-3 CAT trinucleotides; however, the number in SCA1 patients is 39-82 with no interruption. It is shown that the length of the polyglutamine repeats is a significant contributor to the onset age of SCA1 [13].
The ATXN1 protein is constitutively expressed in the brain and elsewhere [13] with an expression level that is about 2.5 fold higher when compared to average protein expression levels, and it is localized to the nucleus and cytoplasm. Several domains and amino acids have been known to play important roles in ATXN1 functions, such as the Ataxin-1 and HBP1 module (AXH) domain [16], the nuclear localization sequence (NLS), and amino acid Ser776, which can undergo phosphorylation. The AXH domain contains the protein binding and RNA binding motifs that allow ATXN1 to interact with other proteins and RNAs. Its homolog, HBP1 (abbreviated from HMG Box Containing Protein 1) is a transcription factor and affects chromatin regulation and gene expression. ATXN1 has more than 200 interacting partners to date including histone deacetylase 3 (HDAC3) (involved in gene expression regulation), ubiquilin4 (involved in ubiquitin-protease degradation), and capicua (involved in SCA1 neuropathology) [13, 17, 18]. By utilizing its AXH domain and interacting partners, ATXN1 plays an important role in RNA metabolism, gene expression regulation, and protein degradation [19].
It is known that the pathogenesis of ATXN1 in SCA1 is primarily through a gain-of-function mechanism caused by the expanded polyglutamine tract, which acts on ATXN1's interacting partners through several functional domains and causes neurotoxicity and nuclear inclusion body formation primarily in Purkinje cells in the cerebellum [13]. Despite the ability of these findings to explain the mechanism behind SCA1, the cellular and molecular mechanism of ATXN1-mediated neurodegeneration in AD is unknown. Determining ATXN1 mediated pathological events in AD will help to develop a better understanding of AD pathogenesis as a whole and to identify novel AD therapeutic targets.
In accordance with the invention, ATXN1 is a viable target for therapeutic treatment of AD. It is demonstrated in Examples 4 to 10 that downregulation of the ataxin-1 (ATXN1) gene increases Aβαformation in the brain cells in vitro and that over-expression of ATXN1 in those brain cells can inhibit Aβ accumulation. Accordingly, provided herein is a method for treatment of AD in a subject by administering to the subject a pharmaceutically acceptable composition comprising ATXN1.
As used herein, the terms “treatment” and “treating,” with respect to treatment of AD, means preventing the progression for the disease, or altering the course of the disorder (for example, but not limited to, slowing the progression of the disorder), or reversing a symptom of the disorder or reducing one or more symptoms and/or one or more biochemical markers in a subject, preventing one or more symptoms from worsening or progressing, promoting recovery or improving prognosis. For example, in the case of AD treatment, therapeutic treatment refers to reducing the cognitive deterioration in a subject and/or inhibiting or reducing the level of Aβ in the brain of a subject that is already inflicted with AD. Measurable lessening includes any statistically significant decline in a measurable marker or symptom, such as measuring Aβ in the brain by PET scan, or assessing the cognitive improvement with neuropsychological tests such as verbal and perception after treatment.
In one embodiment, the ATXN1 is administered to the subject as a protein. The term “protein” used herein, in reference to the ATXN1 protein, refers to a recombinant protein. The recombinant ATXN1 protein can be an intact ATXN1 protein or a fragment thereof comprising protein-protein or RNA binding motifs. In some embodiments, the ATXN1 protein administered to a subject in need thereof can be a fragment of the ATXN1 protein comprising a conserved domain thereof, such as AXH domain (located from 574aa to 688aa) and ATXN1_C (capicua transcriptional repressor modulator) domain (located from 415aa to 445aa). In some embodiments, the fragment of the ATXN1 protein can comprise the nuclear localization sequence (NLS) or the domain comprising an amino acid Ser776. Direct administration of the protein requires production of therapeutic amounts of the protein and repeated delivery to the central nervous system (CNS) to achieve therapeutically effective levels. Large scale production of recombinant proteins for therapeutic uses is well understood in the art. Administration of a protein typically provides only transient efficacy, requiring frequent dosing, for example multiple administrations per day, often by intravenous injection.
In one embodiment, the ATXN1 is administered to a subject as a recombinant ATXN1 protein encoding gene. In some embodiments, the recombinant ATXN1 protein encoding gene, can encode a fragment of the ATXN1 protein, for example, a conserved domain thereof, such as the AXH domain or the ATXN1_C domain. In some embodiments, the recombinant ATXN1 protein encoding gene can encode the nuclear localization sequence (NLS), or the domain comprising an amino acid Ser776.
Gene therapy has the advantage of potentially long-term therapeutic benefit with only one, or perhaps a limited number, of administrations. These methods allow clinicians to introduce DNA coding for a gene of interest directly into a patient (in vivo gene therapy) or into cells isolated from a patient or a donor (ex vivo gene therapy). Therapeutic proteins produced by transduced cells after gene therapy may be maintained at a relatively constant level in the CNS of a subject, as compared to a protein that is administered directly, which will typically vary greatly in concentration between the time right after administration of a first dose and the time immediately before the succeeding dose. Such sustained production of a therapeutic cytokine is particularly appropriate in the treatment of chronic diseases, such as neurodegenerative diseases, e.g., AD.
Administration of gene therapy vectors can be performed intracranially or extracranially with known techniques. Stem cells have been shown to cross blood-brain barrier and home towards injury in brain. Thus, for example stem cells engineered to produce secreted ATXN1 protein can be administered intravenously and would be expected to reach areas of brain wherein ATXN1 is lacking and causing structural changes.
Further, regulatable genetic constructs using small molecule inducers have been developed that might be included in vectors to be used in gene therapy embodiments of the present invention. Rivera et al. (1996) Nat. Med. 2:1028-32; No et al. (1996) Proc. Natl. Acad. Sci. USA, 93:3346-51; Gossen and Bujard (1992) Proc. Natl. Acad. Sci. USA 89:5547-51; the GeneSwitch® system (Valentis, Inc., Burlingame, Calif.). These systems are based on the use of engineered transcription factors whose activity is controlled by a small molecule drug, and a transgene whose expression is driven by the regulated transcription factor. One such system, based on induction by rapamycin (referred to herein as the “dimerizer system”), involves formation of a functional transcription factor from two synthetic fusion proteins dependent upon addition of rapamycin. Rivera et al. (1996) Nat. Med. 2:1028-32; Pollock et al. (2000) Proc. Natl. Acad. Sci. USA 97:13221-26. The dimerizer system is a component of the ARGENT Transcription Technology platform of ARIAD Pharmaceuticals, Inc. (Cambridge, Mass.). See U.S. Pat. Nos. 6,043,082 and 6,649,595; Rivera et al. (1999) Proc. Natl. Acad. Sci. USA 96:8657-62.
DNA may be introduced into a patient's cells in several ways. There are transfection methods, including chemical methods such as calcium phosphate precipitation and liposome-mediated transfection, and physical methods such as electroporation. In general, transfection methods are not suitable for in vivo gene delivery. Genes can be delivered using “naked” DNA in plasmid form. There are also methods that use recombinant viruses. Current viral-mediated gene delivery methods employ retrovirus, adenovirus, herpes virus, pox virus, and adeno-associated virus (AAV) vectors. Of the more than one hundred gene therapy trials conducted, more than 95% used viral-mediated gene delivery. C. P. Hodgson, Bio/Technology 13, 222-225 (1995).
In one embodiment, the recombinant ATXN1 encoding gene is operably linked to a vector. In general, as used herein, the term “vector” refers to any genetic element, such as a plasmid, phage, transposon, cosmid, chromosome, virus, virion, etc., that is capable of replication when associated with the proper control elements and that can transfer gene sequences to cells. Thus, the term includes cloning and expression vehicles, as well as viral vectors. By “recombinant vector” is meant a vector that includes a heterologous nucleic acid sequence, or “transgene,” that is capable of expression in vivo.
In additional embodiments, it can be desirable to fuse the gene of interest to immunoglobulin molecules, for example the Fc portion of a mouse IgG2a with a noncytolytic mutation, to provide for sustained expression. Such a technique has been shown to provide for sustained expression of cytokines, especially when combined with electroporation. See e.g. Jiang et al. (2003) J. Biochem. 133:423-27; Adachi et al. (2002) Gene Ther. 9:577-83.
It should be understood that the vectors delivered by the methods of the present invention be combined with other suitable compositions and therapies for AD.
Plasmid-Directed Gene Delivery
The recombinant ATXN1 encoding gen can be delivered using non-viral plasmid-based nucleic acid delivery systems, as described in U.S. Pat. Nos. 6,413,942, 6,214,804, 5,580,859, 5,589,466, 5,763,270 and 5,693,622, all incorporated herein by reference in their entireties. Plasmids will include the gene of interest operably linked to control elements that direct the expression of the gene in a target cell, which control elements are well known in the art. Plasmid DNA can be guided by a nuclear localization signal or like modification.
Alternatively, plasmid vectors encoding the gene of interest can be packaged in liposomes prior to delivery to a subject or to cells, as described in U.S. Pat. Nos. 5,580,859, 5,549,127, 5,264,618, 5,703,055, all incorporated herein by reference in their entireties. For a review of the use of liposomes as carriers for delivery of nucleic acids, see, Hug and Sleight (1991) Biochim. Biophys. Acta. 1097:1-17; Straubinger et al. (1983) in Methods of Enzymology Vol. 101, pp. 512-27; de Lima et al. (2003) Current Medicinal Chemistry, Volume 10(14): 1221-31. The DNA can also be delivered in cochleate lipid compositions similar to those described by Papahadjopoulos et al. (1975) Biochem. Biophys. Acta. 394:483-491. See also U.S. Pat. Nos. 4,663,161 and 4,871,488, incorporated herein by reference in their entireties. In one embodiment, the plasmid vector is complexed with Lipofectamine 2000 at a ratio of 3 μl of Lipofectamine per μg of DNA. Wang et al. (2005) Mol. Therapy. 12(2):314-320.
Biolistic delivery systems employing particulate carriers such as gold and tungsten may also be used to deliver genes of interest. The particles are coated with the gene to be delivered and accelerated to high velocity, generally under reduced pressure, using a gun powder discharge from a “gene gun.” See, e.g., U.S. Pat. Nos. 4,945,050, 5,036,006, 5,100,792, 5,179,022, 5,371,015, and 5,478,744, all incorporated herein by reference in their entireties.
A wide variety of other methods can be used to deliver the vectors. Such methods include DEAE dextran-mediated transfection, calcium phosphate precipitation, polylysine- or polyornithine-mediated transfection, or precipitation using other insoluble inorganic salts, such as strontium phosphate, aluminum silicates including bentonite and kaolin, chromic oxide, magnesium silicate, talc, and the like. Other useful methods of transfection include electroporation, sonoporation, protoplast fusion, peptoid delivery, or microinjection. See, e.g., Sambrook et al (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratories, New York, for a discussion of techniques for transforming cells of interest; and Feigner, P. L. (1990) Advanced Drug Delivery Reviews 5:163-87, for a review of delivery systems useful for gene transfer. Exemplary methods of delivering DNA using electroporation are described in U.S. Pat. Nos. 6,132,419; 6,451,002, 6,418,341, 6,233,483, U.S. Patent Publication No. 2002/0146831, and International Publication No. WO/0045823, all of which are incorporated herein by reference in their entireties.
Plasmid vectors can also be introduced directly into the CNS by intrathecal (IT) injection, as described herein in greater detail with regard to protein administration. Plasmid DNA can be complexed with cationic agents such as polyethyleneimine (PEI) or Lipofectamine 2000 to facilitate uptake. See, e.g., Wang et al. (2005) Mol. Therapy. 12(2):314-320. In one embodiment, a plasmid vector encoding ATXN1 is complexed with PEI (25 kDa, Sigma-Aldrich, San Diego, Calif.) in a 5% glucose solution at a N/P ratio of approximately 15, where N represents PEI nitrogen and P represents DNA phosphate. Based on results obtained with pain relieving medications, intrathecal delivery may be expected to significantly reduce the required dose of a plasmid vector, e.g. up to ten-fold when compared with intravenous delivery, although such results may not apply to IT delivery of DNA-based therapeutic agents.
Retroviruses provide a convenient platform for gene delivery. A selected gene can be inserted into a vector and packaged in retroviral particles using techniques known in the art. The recombinant virus can then be isolated and delivered to cells of the subject either in vivo or ex vivo. A number of retroviral systems have been described. See, e.g., U.S. Pat. No. 5,219,740; Miller and Rosman (1989) BioTechniques 7:980-90; Miller, A. D. (1990) Human Gene Therapy 1:5-14; Scarpa et al. (1991) Virology 180:849-52; Burns et al. (1993) Proc. Natl. Acad. Sci. USA 90:8033-37; Boris-Lawrie and Temin (1993) Curr. Opin. Genet. Develop. 3:102-09.
Replication-defective murine retroviral vectors are widely used gene transfer vectors. Murine leukemia retroviruses include a single stranded RNA molecule complexed with a nuclear core protein and polymerase (pol) enzymes, encased by a protein core (gag), and surrounded by a glycoprotein envelope (env) that determines host range. The genomic structure of retroviruses includes gag, pol, and env genes and 5′ and 3′ long terminal repeats (LTRs). Retroviral vector systems exploit the fact that a minimal vector containing the 5′ and 3′ LTRs and the packaging signal are sufficient to allow vector packaging, infection and integration into target cells, provided that the viral structural proteins are supplied in trans in the packaging cell line. Fundamental advantages of retroviral vectors for gene transfer include efficient infection and gene expression in most cell, types, precise single copy vector integration into target cell chromosomal DNA and ease of manipulation of the retroviral genome.
Adenoviral Gene Delivery
In one embodiment of the subject invention, a nucleotide sequence encoding ATXN1 is inserted into an adenovirus-based expression vector. Unlike retroviruses, which integrate into the host genome, adenoviruses persist extrachromosomally thus minimizing the risks associated with insertional mutagenesis (Haj-Ahmad and Graham (1986) J. Virol. 57:267-74; Bett et al. (1993) J. Virol. 67:5911-21; Mittereder et al. (1994) Human Gene Therapy 5:717-29; Seth et al. (1994) J. Virol. 68:933-40; Barr et al. (1994) Gene Therapy 1:51-58; Berkner, K. L. (1988) BioTechniques 6:616-29; and Rich et al. (1993) Human Gene Therapy 4:461-76).
The adenovirus genome is a linear double-stranded DNA molecule of approximately 36,000 base pairs with the 55-kDa terminal protein covalently bound to the 5′ terminus of each strand. Adenoviral (“Ad”) DNA contains identical Inverted Terminal Repeats (“ITRs”) of about 100 base pairs with the exact length depending on the serotype. The viral origins of replication are located within the ITRs exactly at the genome ends.
Adenoviral vectors have several advantages in gene therapy. They infect a wide variety of cells, have a broad host-range, exhibit high efficiencies of infectivity, direct expression of heterologous genes at high levels, and achieve long-term expression of those genes in vivo. The virus is fully infective as a cell-free virion so injection of producer cell lines is not necessary. With regard to safety, adenovirus is not associated with severe human pathology, and the recombinant vectors derived from the virus can be rendered replication defective by deletions in the early-region 1 (“E1”) of the viral genome. Adenovirus can also be produced in large quantities with relative ease. For all these reasons vectors derived from human adenoviruses, in which at least the E1 region has been deleted and replaced by a gene of interest, have been used extensively for gene therapy experiments in the pre-clinical and clinical phase.
Adenoviral vectors for use with the present invention can be derived from any of the various adenoviral serotypes, including, without limitation, any of the over 40 serotype strains of adenovirus, such as serotypes 2, 5, 12, 40, and 41. The adenoviral vectors used herein are replication-deficient and contain the gene of interest under the control of a suitable promoter, such as any of the promoters discussed below with reference to adeno-associated virus. For example, U.S. Pat. No. 6,048,551, incorporated herein by reference in its entirety, describes replication-deficient adenoviral vectors that include the human gene for ATXN1 under the control of the Rous Sarcoma Virus (RSV) promoter.
Other recombinant adenoviruses of various serotypes, and comprising different promoter systems, can be created by those skilled in the art. See, e.g., U.S. Pat. No. 6,306,652, incorporated herein by reference in its entirety.
Moreover, “minimal” adenovirus vectors as described in U.S. Pat. No. 6,306,652 will find use with the present invention. Such vectors retain at least a portion of the viral genome required for encapsidation (the encapsidation signal), as well as at least one copy of at least a functional part or a derivative of the ITR. Packaging of the minimal adenovirus vector can be achieved by co-infection with a helper virus or, alternatively, with a packaging-deficient replicating helper system.
Other useful adenovirus-based vectors for delivery of ATXN1 gene include the “gutless” (helper-dependent) adenovirus in which the vast majority of the viral genome has been removed. Wu et al. (2001) Anesthes. 94:1119-32. Such “gutless” adenoviral vectors produce essentially no viral proteins, thus allowing gene therapy to persist for over a year after a single administration. Parks (2000) Clin. Genet. 58:1-11; Tsai et al. (2000) Curr. Opin. Mol. Ther. 2:515-23. In addition, removal of the viral genome creates space that can be used to insert control sequences that provide for regulation of transgene expression by systemically administered drugs (Burcin et al. (1999) Proc. Natl. Acad. Sci. USA 96:355-60), adding both safety and control of virally driven protein expression. These and other recombinant adenoviruses will find use with the present methods.
Adeno Associated Virus (AAV) Gene Delivery
One viral system that has been used for gene delivery is AAV. AAV is a parvovirus which belongs to the genus Dependovirus. AAV has several attractive features not found in other viruses. First, AAV can infect a wide range of host cells, including non-dividing cells. Second, AAV can infect cells from different species. Third, AAV has not been associated with any human or animal disease and does not appear to alter the biological properties of the host cell upon integration. Indeed, it is estimated that 80-85% of the human population has been exposed to the virus. Finally, AAV is stable at a wide range of physical and chemical conditions, facilitating production, storage and transportation.
The AAV genome is a linear single-stranded DNA molecule containing approximately 4681 nucleotides. The AAV genome generally comprises an internal non-repeating genome flanked on each end by inverted terminal repeats (ITRs). The ITRs are approximately 145 base pairs (bp) in length. The ITRs have multiple functions, including serving as origins of DNA replication and as packaging signals for the viral genome.
The internal non-repeated portion of the genome includes two large open reading frames, known as the AAV replication (rep) and capsid (cap) genes. The rep and cap genes code for viral proteins that allow the virus to replicate and package the viral genome into a virion. In particular, a family of at least four viral proteins is expressed from the AAV rep region, Rep 78, Rep 68, Rep 52, and Rep 40, named according to their apparent molecular weight. The AAV cap region encodes at least three proteins, VP1, VP2, and VP3.
AAV is a helper-dependent virus; that is, it requires co-infection with a helper virus (e.g., adenovirus, herpesvirus or vaccinia) in order to form AAV virions in the wild. In the absence of co-infection with a helper virus, AAV establishes a latent state in which the viral genome inserts into a host cell chromosome, but infectious virions are not produced. Subsequent infection by a helper virus rescues the integrated genome, allowing it to replicate and package its genome into infectious AAV virions. While AAV can infect cells from different species, the helper virus must be of the same species as the host cell. Thus, for example, human AAV will replicate in canine cells co-infected with a canine adenovirus.
Adeno-associated virus (AAV) has been used with success in gene therapy. AAV has been engineered to deliver genes of interest by deleting the internal nonrepeating portion of the AAV genome (i.e., the rep and cap genes) and inserting a heterologous gene (in this case, the gene encoding the anti-inflammatory cytokine) between the ITRs. The heterologous gene is typically functionally linked to a heterologous promoter (constitutive, cell-specific, or inducible) capable of driving gene expression in the patient's target cells under appropriate conditions.
Recombinant AAV virions comprising a ATXN1 gene can be produced using a variety of art-recognized techniques. In one embodiment, a rAAV vector construct is packaged into rAAV virions in cells co-transfected with wild-type AAV and a helper virus, such as adenovirus. See, e.g., U.S. Pat. No. 5,139,941.
Alternatively, plasmids can be used to supply the necessary replicative functions from AAV and/or a helper virus. In one embodiment of the present invention, rAAV virions are produced using a plasmid to supply necessary AAV replicative functions (the “AAV helper functions”). See e.g., U.S. Pat. Nos. 5,622,856 and 5,139,941, both incorporated herein by reference in their entireties. In another embodiment, a triple transfection method is used to produce rAAV virions. The triple transfection method is described in detail in U.S. Pat. Nos. 6,001,650 and 6,004,797, which are incorporated by reference herein in their entireties. The triple transduction method is advantageous because it does not require the use of an infectious helper virus during rAAV production, enabling production of a stock of rAAV virions essentially free of contaminating helper virus. This is accomplished by use of three vectors for rAAV virion production: an AAV helper function vector, an accessory function vector, and a rAAV expression vector. One of skill in the art will appreciate, however, that the nucleic acid sequences encoded by these vectors can be provided on two or more vectors in various combinations. Vectors and Cell lines necessary for preparing helper virus-free rAAV stocks are commercially available as the AAV Helper-Free System (Catalog No. 240071) (Stratagene, La Jolla, Calif.).
The AAV helper function vector encodes AAV helper function sequences (i.e., rep and cap) that function in trans for productive rAAV replication and encapsidation. Preferably, the AAV helper function vector supports efficient rAAV virion production without generating any detectable replication competent AAV virions (i.e., AAV virions containing functional rep and cap genes). An example of such a vector, pHLP19, is described in U.S. Pat. No. 6,001,650. The rep and cap genes of the AAV helper function vector can be derived from any of the known AAV serotypes. For example, the AAV helper function vector may have a rep gene derived from AAV-2 and a cap gene derived from AAV-6. One of skill in the art will recognize that other rep and cap gene combinations are possible, the defining feature being the ability to support rAAV virion production.
The accessory function vector encodes nucleotide sequences for non-AAV-derived viral and/or cellular functions upon which AAV is dependent for replication (the “accessory functions”). The accessory functions include those functions required for AAV replication, including, without limitation, genes involved in activation of AAV gene transcription, stage specific AAV mRNA splicing, AAV DNA replication, synthesis of cap expression products, and AAV capsid assembly. Viral-based accessory functions can be derived from any of the well-known helper viruses such as adenovirus, herpesvirus (other than herpes simplex virus type-1), and vaccinia virus. In one embodiment, the accessory function plasmid pLadeno5 can be used. See U.S. Pat. No. 6,004,797. This plasmid provides a complete set of adenovirus accessory functions for AAV vector production, but lacks the components necessary to form replication-competent adenovirus.
Unlike stocks of rAAV vectors prepared using infectious helper virus, stocks prepared using an accessory function vector (e.g. the triple transfection method) do not contain contaminating helper virus because no helper virus is added during rAAV production. Even after purification, for example by CsCl density gradient centrifugation, rAAV stocks prepared using helper virus still remain contaminated with some level of residual helper virus. When adenovirus is used as the helper virus in preparing a stock of rAAV virions, contaminating adenovirus can be inactivated by heating to temperatures of approximately 60° C. for 20 minutes or more. This treatment effectively inactivates only the helper virus since AAV is extremely heat stable, while the helper adenovirus is heat labile. Although heat inactivating of rAAV stocks may render much of the contaminating adenovirus non-infectious, it does not physically remove the helper virus proteins from the stock. Such contaminating viral protein can elicit undesired immune responses in subjects and are to be avoided if possible. Contaminating adenovirus particles and proteins in rAAV stocks can be avoided by use of the accessory function vectors disclosed herein.
Recombinant AAV Expression Vectors
Recombinant AAV expression vectors can be constructed using standard techniques of molecular biology. rAAV vectors comprise a transgene of interest (e.g. a gene encoding ATXN1 or a fragment thereof) flanked by AAV ITRs at both ends. rAAV vectors are also constructed to contain transcription control elements operably linked to the transgene sequence, including a transcriptional initiation region and a transcriptional termination region. The control elements are selected to be functional in a mammalian target cell.
The nucleotide sequences of AAV ITR regions are known. See, e.g., Kotin (1994) Human Gene Therapy 5:793-801; Berns “Parvoviridae and their Replication” in Fundamental Virology, 2nd Edition, (B. N. Fields and D. M. Knipe, eds.) for the AAV-2 sequence. AAV ITRs used in the vectors of the invention need not have a wild-type nucleotide sequence, and may be altered, e.g., by the insertion, deletion or substitution of nucleotides. Additionally, AAV ITRs may be derived from any of several AAV serotypes, including without limitation, AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7 and AAV-8, etc. Furthermore, 5′ and 3′ ITRs which flank a selected nucleotide sequence in an AAV expression vector need not necessarily be identical or derived from the same AAV serotype or isolate, so long as they function as intended, i.e., to allow for excision and rescue of the sequence of interest from a host cell genome or vector, and to allow integration of the DNA molecule into the recipient cell genome when AAV Rep gene products are present in the cell.
Suitable transgenes for delivery in AAV vectors will be less than about 5 kilobases (kb) in size. In one embodiment, a complete ATXN1 gene can be delivered with AAV vectors. In other embodiments, a DNA sequence encoding a fragment of the ATXN1 protein, such as the AXH domain, the nuclear localization sequence (NLS), or the domain comprising an amino acid Ser776, can be delivered with AAV vectors. The selected polynucleotide sequence is operably linked to control elements that direct the transcription thereof in the subject in vivo. Such control elements can comprise control sequences normally associated with the selected gene. Alternatively, heterologous control sequences can be employed. Useful heterologous control sequences generally include those derived from sequences encoding mammalian or viral genes. Examples include, but are not limited to, neuron-specific enolase promoter, a GFAP promoter, the SV40 early promoter, mouse mammary tumor virus LTR promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (HSV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), a rous sarcoma virus (RSV) promoter, synthetic promoters, hybrid promoters, and the like. In addition, sequences derived from nonviral genes, such as the murine metallothionein gene, will also find use herein. Such promoter sequences are commercially available from, e.g., Stratagene (San Diego, Calif.).
The AAV expression vector harboring a transgene of interest bounded by AAV ITRs can be constructed by directly inserting the selected sequence(s) into an AAV genome that has had the major AAV open reading frames (“ORFs”) excised. Other portions of the AAV genome can also be deleted, so long as enough of the ITRs remain to provide replication and packaging functions. Such constructs can be designed using techniques well known in the art. See, e.g., U.S. Pat. Nos. 5,173,414 and 5,139,941; International Publication Nos. WO 92/01070 and WO 93/03769; Lebkowski et al. (1988) Molec. Cell. Biol. 8:3988-96; Vincent et al. (1990) Vaccines 90 (Cold Spring Harbor Laboratory Press); Carter (1992) Current Opinion in Biotechnology 3:533-39; Muzyczka (1992) Current Topics in Microbiol. and Immunol. 158:97-129; Kotin (1994) Human Gene Therapy 5:793-801; Shelling and Smith (1994) Gene Therapy 1:165-69; and Zhou et al. (1994) J. Exp. Med. 179:1867-75.
AAV ITR-containing DNA fragments can be ligated at both ends of a selected transgene using standard techniques, such as those described in Sambrook et al., supra. For example, ligations can be accomplished in 20 mM Tris-Cl pH 7.5, 10 mM MgCl2, 10 mM DTT, 33 μg/ml BSA, 10 mM-50 mM NaCl, and either 40 μM ATP, 0.01-0.02 (Weiss) units T4 DNA ligase at 0° C. (for “sticky end” ligation) or 1 mM ATP, 0.3-0.6 (Weiss) units T4 DNA ligase at 14° C. (for “blunt end” ligation). Intermolecular “sticky end” ligations are usually performed at 30-100 μg/ml total DNA concentrations (5-100 nM total end concentration).
Suitable host cells for producing rAAV virions of the present invention from rAAV expression vectors include microorganisms, yeast cells, insect cells, and mammalian cells. Such host cells are preferably capable of growth in suspension culture, a bioreactor, or the like. The term “host cell” includes the progeny of the original cell that has been transfected with an rAAV virion. Cells from the stable human cell line, 293 (readily available through the American Type Culture Collection under Accession Number ATCC CRL1573) are preferred in the practice of the present invention. The human cell line 293 is a human embryonic kidney cell line that has been transformed with adenovirus type-5 DNA fragments (Graham et al. (1977) J. Gen. Virol. 36:59), and expresses the adenoviral E1a and E1b genes (Aiello et al. (1979) Virology 94:460). The 293 cell line is readily transfected, and provides a particularly convenient platform in which to produce rAAV virions.
Other Viral Vectors for Gene Delivery
Additional viral vectors useful for delivering the nucleic acid molecules of interest include those derived from the pox family of viruses, including vaccinia virus and avian poxvirus. By way of example, vaccinia virus recombinants expressing a gene of interest can be constructed as follows. DNA carrying the gene is inserted into an appropriate vector adjacent to a vaccinia promoter and flanking vaccinia DNA sequences, such as the sequence encoding thymidine kinase (TK). This vector is then used to transfect cells that are simultaneously infected with vaccinia. Homologous recombination serves to insert the vaccinia promoter and the gene into the viral genome. The resulting TK-recombinant can be selected by culturing the cells in the presence of 5-bromodeoxyuridine and picking viral plaques resistant thereto.
Alternatively, avipoxviruses, such as the fowlpox and canarypox viruses, can be used to deliver the genes. Recombinant avipox viruses expressing immunogens from mammalian pathogens are known to confer protective immunity when administered to non-avian species. The use of avipox vectors in human and other mammalian species is advantageous with regard to safety because members of the avipox genus can only productively replicate in susceptible avian species. Methods for producing recombinant avipoxviruses are known in the art and employ genetic recombination, as described above with respect to the production of vaccinia viruses. See, e.g., WO 91/12882; WO 89/03429; and WO 92/03545.
Molecular conjugate vectors, such as the adenovirus chimeric vectors, can also be used for gene delivery. Michael et al. (1993) J. Biol. Chem. 268:6866-69 and Wagner et al. (1992) Proc. Natl. Acad. Sci. USA 89:6099-6103. Members of the Alphavirus genus, for example the Sindbis and Semliki Forest viruses, may also be used as viral vectors for delivering the ATXN1 gene or a fragment thereof. See, e.g., Dubensky et al. (1996) J. Virol. 70:508-19; WO 95/07995; WO 96/17072.
Neural Stem Cell Therapy
Recent studies have shown that intracranially or intravenously injected neural stem cells (NSCs) or neural precursor cells migrate towards central nervous system (CNS) locus with injury or pathology. This chemotropic property of NSCs has been utilized for cell-based therapies to treat diverse neurological diseases as described in Brustle O. et al., 6 Current Opinion in Neurobiology. 688 (1996), Flax J. D., et al., 16 Nature Biotechnology. 1033. (1998); Kim S. U., 24. Neuropathology. 159 (2004); Lindvall O et al., 10 (suppl) Nature Medicine. S42 (2004); Goldman S., 7. Nature Biotechnology. 862 (2005); Muller F. et al., 7 Nature Reviews Neuroscience. 75 (2006); Lee, J. P., et al. 13 Nature Medicine 439 (2007) and Kim S. U. et al., 87 Journal of Neuroscience Research 2183 (2009).
Accordingly, in some embodiments of the method for treating AD in a subject, a pharmaceutically acceptable composition comprising a neural stem cell and the ATXN1 gene can be administered to the subject.
In one embodiment, the neural stem cell is genetically engineered to express or secrete ATXN1. Because NSCs can be engineered to package and release replication-defective retroviral particles or replication-conditional herpes virus vectors which, in turn, may serve as vectors for the transfer of genes to CNS cells, neural progenitor/stem cells should serve to magnify the efficacy of viral-mediated gene delivery to large regions in the brain. In such embodiments, the neural stem cell can comprise a vector as described above encoding the ATXN1 gene. Additional vectors that can be used for the purpose of the invention inclue herpes simplex virus vectors, SV 40 vectors, polyoma virus vectors, papilloma virus vectors, picarnovirus vectors, vaccinia virus vectors, and a helper-dependent or gutless adenovirus. In one embodiment, the vector can be a herpes simplex type 1 virus (HSV-1). In a further embodiment, the vector can be a replication-dependent HSV-1 vector which has been engineered to lack ribonucleotide reductase activity. Methods for preparing genetically engineered neural stem cells and compositions thereof for therapeutic treatment have been described in U.S. Pat. Nos. 7,393,526 and 7,655,224, the contents of which are incorporated herein by reference in their entirety.
For administration to a subject, neural stem cells comprising ATXN1 can be provided in a pharmaceutically acceptable composition. A pharmaceutically acceptable composition can comprise at least one neural stem cell comprising ATXN1, formulated together with one or more pharmaceutically acceptable carriers (additives) and/or diluents. As described in detail below, the pharmaceutical composition of the present invention can be specially formulated for various administration routes known in the art. A skilled artisan will be able to adapt the formulation for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), gavages, lozenges, dragees, capsules, pills, tablets (e.g., those targeted for buccal, sublingual, and systemic absorption), boluses, powders, granules, pastes; (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous, intravascular or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; (3) ocularly, (4) intracranially, or (5) nasally. Additionally, the pharmaceutical acceptable composition can be implanted into a patient or injected using a drug delivery system. See, for example, Urquhart, et al., Ann. Rev. Pharmacol. Toxicol. 24: 199-236 (1984); Lewis, ed. “Controlled Release of Pesticides and Pharmaceuticals” (Plenum Press, New York, 1981); U.S. Pat. No. 3,773,919; and U.S. Pat. No. 3,270,960, content of all of which is herein incorporated by reference.
As used herein, the term “pharmaceutically acceptable” refers to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
As used herein, the term “pharmaceutically acceptable carrier” means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient. Some examples of materials which can serve as pharmaceutically-acceptable carriers include: (i) sugars, such as lactose, glucose and sucrose; (ii) starches, such as corn starch and potato starch; (iii) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, methylcellulose, ethyl cellulose, microcrystalline cellulose and cellulose acetate; (iv) powdered tragacanth; (v) malt; (vi) gelatin; (vii) lubricating agents, such as magnesium stearate, sodium lauryl sulfate and talc; (viii) excipients, such as cocoa butter and suppository waxes; (ix) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (x) glycols, such as propylene glycol; (xi) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (xii) esters, such as ethyl oleate and ethyl laurate; (xiii) agar; (xiv) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (xv) alginic acid; (xvi) pyrogen-free water; (xvii) isotonic saline; (xviii) Ringer's solution; (xix) ethyl alcohol; (xx) pH buffered solutions; (xxi) polyesters, polycarbonates and/or polyanhydrides; (xxii) bulking agents, such as polypeptides and amino acids (xxiii) serum component, such as serum albumin, HDL and LDL; (xxiv) C2-C12 alcohols, such as ethanol; and (xxv) other non-toxic compatible substances employed in pharmaceutical formulations. Wetting agents, coloring agents, release agents, coating agents, sweetening agents, flavoring agents, perfuming agents, preservative and antioxidants can also be present in the formulation.
The term “administer” or “administration” as used herein refers to the placement of a composition into a subject by a method or route which results in at least partial localization of the composition at a desired site such that desired effect is produced, such as intracranially to brain or specific areas of brain. Stereotactic means can be used to guide intracranial administration if desired. Routes of administration suitable for the methods of the invention include both local and systemic administration. Generally, local administration results in more of the composition being delivered to a specific location as compared to the entire body of the subject, whereas, systemic administration can result in delivery to essentially the entire body of the subject. However, it is envisioned that chemotropic property of NSCs can guide the cells to a specific location with a tissue injury, e.g., brain, even with systemic administration.
A composition described herein can be administered by any appropriate route known in the art including, but not limited to, oral or parenteral routes, including intravenous, intramuscular, subcutaneous, transdermal, and nasal administration.
Exemplary modes of administration include, but are not limited to, injection, infusion, instillation, inhalation, or ingestion. “Injection” includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intraventricular, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, sub-capsular, subarachnoid, intraspinal, intracerebro spinal, and infrasternal injection and infusion.
In some embodiments, the pharmaceutically acceptable composition comprising at least one neural stem cell and the ATXN1 gene can be administered to an individual systemically or intracranially. In a particular embodiment, the neural stem cells and/or the pharmaceutical acceptable composition can be administered intravascularly, including intravenously. In one embodiment, the neural stem cells and/or the pharmaceutical acceptable composition can also be administered using intra-CSF or intraosseous injection.
In various embodiments of the method of treatment, the neural stem cells that can be used according to the present invention include, but are not limited to, neural stem cells, HSN-1 cells, fetal pig cells and neural crest cells, bone marrow derived neural stem cells, and hNT cells. The HSN-1 cells useful according to the invention can be prepared as described in, e.g., Ronnett et al. [Science 248, 603-605, 1990]. The preparation of neural crest cells in described in U.S. Pat. No. 5,654,183. The hNT cells useful according to the present invention can be prepared as described in, e.g, Konubu et al. [Cell Transplant 7, 549-558, 1998].
Subjects amenable to methods of treatment are subjects that have been diagnosed with Alzheimer's disease. Methods for diagnosing Alzheimer's disease are well known in the art. For example, the stage of Alzheimer's disease can be assessed using the Functional Assessment Staging (FAST) scale, which divides the progression of Alzheimer's disease into 16 successive stages under 7 major headings of functional abilities and losses: Stage 1 is defined as a normal adult with no decline in function or memory. Stage 2 is defined as a normal older adult who has some personal awareness of functional decline, typically complaining of memory deficit and forgetting the names of familiar people and places. Stage 3 (early Alzheimer's disease) manifests symptoms in demanding job situation, and is characterized by disorientation when traveling to an unfamiliar location; reports by colleagues of decreased performance; name- and word-finding deficits; reduced ability to recall information from a passage in a book or to remember a name of a person newly introduced to them; misplacing of valuable objects; decreased concentration. In stage 4 (mild Alzheimer's Disease), the patient may require assistance in complicated tasks such as planning a party or handling finances, exhibits problems remembering life events, and has difficulty concentrating and traveling. In stage 5 (moderate Alzheimer's disease), the patient requires assistance to perform everyday tasks such as choosing proper attire. Disorientation in time, and inability to recall important information of their current lives, occur, but patient can still remember major information about themselves, their family and others. In stage 6 (moderately severe Alzheimer's disease), the patient begins to forget significant amounts of information about themselves and their surroundings and require assistance dressing, bathing, and toileting. Urinary incontinence and disturbed patterns of sleep occur. Personality and emotional changes become quite apparent, and cognitive abulia is observed. In stage 7 (severe Alzheimer's disease), speech ability becomes limited to just a few words and intelligible vocabulary may be limited to a single word. A patient can lose the ability to walk, sit up, or smile, and eventually cannot hold up the head.
Other alternative diagnostic methods for AD include, but not limited to, cellular and molecular testing methods disclosed in U.S. Pat. No. 7,771,937, U.S. Pat. No. 7,595,167, U.S. Pat. No. 5,580,748, and PCT Application No.: WO2009/009457, the content of which is incorporated by reference in its entirety. Additionally, protein-based biomarkers for AD, some of which can be detected by non-invasive imaging, e.g., PET, are disclosed in U.S. Pat. No. 7,794,948, the content of which is incorporated by reference in its entirety.
Genes involved in AD risk can be used for diagnosis of AD, including the SNPs described herein. Accordingly, in one embodiment, the methods provided herein for identifying a nucleic acid polymorphism in a biological sample can also be used for screening AD in a subject. Such AD “risk genes” increase the risk of developing AD. In addition, one example of other AD risk genes is apolipoprotein E-ε4 (APOE-ε4). APOE-ε4 is one of three common forms, or alleles, of the APOE gene; the others are APOE-e2 and APOE-e3. APOE provides the blueprint for one of the proteins that carries cholesterol in the bloodstream. Everyone inherits a copy of some form of APOE from each parent. Those who inherit one copy of APOE-ε4 have an increased risk of developing AD. Those who inherit two copies have an even higher risk, but not a certainty of developing AD. In addition to raising risk, APOE-ε4 may tend to make symptoms appear at a younger age than usual. Other AD risk genes in addition to APOE-e4 are well established in the art. Some of them are disclosed in US Pat. App. No.: US 2010/0249107, US 2008/0318220, US 2003/0170678 and PCT Application No.: WO 2010/048497, the content of which is incorporated by reference in its entirety. Genetic tests are well established in the art and are available, for example for APOE-e4. A subject carrying the APOE-e4 allele can, therefore, be identified as a subject at risk of developing AD.
In further embodiments, subjects with Aβ burden are amenable to the methods described herein. Such subjects include, but not limited to, the ones with Down syndrome, Huntington disease, the unaffected carriers of APP or presenilin gene mutations, and the late onset AD risk factor, apolipoprotein E-ε4.
In some embodiments, AD patients that are currently receiving other AD therapeutic treatment can also be subjected to the methods of treatment as described herein.
In some embodiments, a subject who has been diagnosed with an increased risk for developing AD, e.g., using the diagnostic methods and assays described herein or any AD diagnostic methods known in the art, can be subjected to the methods of treatment as described herein.
A still yet another aspect of the invention relates to a method for determining if a subject is in need of treatment or prevention for AD. The method comprises the steps of: (a) transforming at least one nucleic acid polymorphism in a locus in a biological sample from the subject into at least one detectable target, wherein the locus is selected from: (i) G/A SNP rs11159647; (ii) A/G SNP rs3826656; (iii) C/T SNP rs179943; and (iv) A/C SNP rs2049161; and (b) detecting presence or absence of at least one AD risk associated allele from the at least one detectable target, wherein the at least one AD risk associated allele is selected from: (v) AD risk associated allele A of the G/A SNP rs11159647 locus; (vi) AD risk associated allele G of the A/G SNP rs3826656 locus; (vii) AD risk associated allele T of the C/T SNP rs179943 locus; and (viii) AD risk associated allele C of the A/C SNP rs2049161 locus; wherein detection of the presence of at least one AD risk associated allele is indicative of the subject in need for treatment or prevention for AD.
In one embodiment, the method further comprises administering a treatment or preventive intervention to the subject, if presence of at least one AD risk-associated allele is detected.
In some embodiments, the subject with at least one AD risk-associated allele but no AD symptoms, including undetectable level of amyloid-beta protein in the brain and/or no detectable cognitive impairment can be administered with a preventive treatment. These treatment of prevention interventions include, but are not limited to life style advice, including e.g., prescribing an aerobic exercise regime to exercise the body and/or mental exercises to keep brain active, dietary advice, including increase in intake of omega-3 fatty acids, fruits and vegetables, fish or poultry, whole-grain breads and cereals, or reduction of sugar or cholesterol rich food intake to lower cholesterol, and administering pharmaceutical agents effective in prevention or treatment of AD.
In some embodiments, the subject having at least one AD risk-associated allele and exhibiting AD symptoms, i.e. diagnosed with AD, can be treated with the methods of treatment described herein. In some embodiments, the subject diagnosed with AD can-be treated with a drug known in the art such as cholinesterase inhibitors (for example, ARICEPT®), the glutamate antagonist NAMENDA® and dimebolin, which is currently in clinical trials. The subject diagnosed with AD can further be advised on changes in life style and/or diet to slow down the progression of AD. Accordingly, the term “treatment or prevention for AD” will encompass treating a subject diagnosed with AD to slow down or ameliorate at least one symptom associated with AD, or treating a subject with an increased risk for AD, e.g, carrying an AD risk associated allele described herein to avoid or delay the onset of AD. The term “prevention” as used herein refers to a complete avoidance of symptoms, such as cognitive impairment or measurable markers of AD, level of Aβ in the brain, or delay the onset of AD. Inhibition of AD development is also considered a preventive measure even if it does not confer a complete avoidance of AD symptoms. The term “inhibition” as used in reference to the development of a disease (e.g., AD) refer to a reduced severity or degree of any one or more of those symptoms or markers, relative to those symptoms or markers arising in a control or non-treated individual with a similar likelihood or susceptibility of developing AD, or relative to symptoms or markers likely to arise based on historical or statistical measures of populations affected by AD. By “reduced severity” is meant at least about 20% in the severity or degree of a symptom or measurable marker, e.g., level of Aβ in the brain, relative to a control, such as without administration of the treatment described herein, e.g., at least about 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99% or even 100% (i.e., no or non-detectable level of cognitive impairment or measurable markers, e.g., Aβ level).
Kits for determining if a subject is at increased risk of developing Alzheimer's disease will include at least one reagent specific for detecting for the presence or absence of the AD risk associated SNPs described herein or antibodies specific for detecting the gene expression products (e.g., ATXN1, CD33 and/or DLGAP1) associated with AD risk associated SNPs, and instructions for observing that the subject is at increased risk of developing Alzheimer's disease if the presence of at least one of the SNPs described herein is detected. The kit may optionally include a nucleic acid for detection of the gene of interest.
Diagnostic kits for carrying out antibody assays may be produced in a number of ways. In one embodiment, the diagnostic kit comprises (a) an antibody which binds ATXN1, CD33 and/or DLGAP1 conjugated to a solid support and (b) a second antibody which binds ATXN1, CD33 and/or DLGAP1 conjugated to a detectable group. The reagents may also include ancillary agents such as buffering agents and protein stabilizing agents, e.g., polysaccharides and the like. The diagnostic kit may further include, where necessary, other members of the signal-producing system of which system the detectable group is a member (e.g., enzyme substrates), agents for reducing background interference in a test, control reagents, apparatus for conducting a test, and the like. A second embodiment of a test kit comprises (a) an antibody as above, and (b) a specific binding partner for the antibody conjugated to a detectable group. Ancillary agents as described above may likewise be included. The test kit may be packaged in any suitable manner, typically with all elements in a single container along with a sheet of printed instructions for carrying out the test. In other embodiments, the diagnostic kits can comprise primers or probes for detection of mRNA level of ATXN1, CD33 and/or DLGAP1 gene.
Unless otherwise explained, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Definitions of common terms in diseases and disorders, separation and detection techniques can be found in The Merck Manual of Diagnosis and Therapy, 18th Edition, published by Merck Research Laboratories, 2006 (ISBN 0-911910-18-2); Robert S. Porter et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).
It should be understood that this invention is not limited to the particular methodology, protocols, and reagents, etc., described herein and as such may vary. The terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention, which is defined solely by the claims.
Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term “about.” The term “about” when used in connection with percentages may mean±1%.
The singular terms “a,” “an,” and “the” include plural referents unless context clearly indicates otherwise. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of this disclosure, suitable methods and materials are described below. The abbreviation, “e.g.” is derived from the Latin exempli gratia, and is used herein to indicate a non-limiting example. Thus, the abbreviation “e.g.” is synonymous with the term “for example.”
All patents and other publications identified throughout the specification are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the present invention. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the contents of these documents are based on the information available to the applicants and do not constitute any admission as to the correctness of the dates or contents of these documents.
The term “subject” includes, but is not limited to, humans, nonhuman primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs, and the like. The term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be covered. In one embodiment, the subject is a mammal. In one embodiment, the subject is a human subject.
The terms “significantly different from,”, “statistically significant,” and similar phrases refer to comparisons between data or other measurements, wherein the differences between two compared individuals or groups are evidently or reasonably different to the trained observer, or statistically significant (if the phrase includes the term “statistically” or if there is some indication of statistical test, such as a p-value, or if the data, when analyzed, produce a statistical difference by standard statistical tests known in the art).
As used herein, the term “comprising” means that other elements can also be present in addition to the defined elements presented. The use of “comprising” indicates inclusion rather than limitation.
The term “consisting of” refers to the components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment.
As used herein the term “consisting essentially of” refers to those elements required for a given embodiment. The term permits the presence of elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment of the invention
This invention is further illustrated by the following example which should not be construed as limiting.
The contents of all references cited throughout this application, examples, as well as the figures and tables are incorporated herein by reference in their entirety.
The examples presented herein relate to identification of non-APOE-related Alzheimer's disease susceptibility loci and demonstration of biological roles of ataxin 1 (ATXN1) in AD pathogenesis. In accordance with the invention, in some embodiments, the methods, assays and compositions described herein can be used for diagnosis of late onset AD and/or treatment of AD. Throughout this application, various publications are referenced. The disclosures of all of the publications and those references cited within those publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains. The following examples are not intended to limit the scope of the paragraphs to the invention, but are rather intended to be exemplary of certain embodiments. Any variations in the exemplified methods which occur to the skilled artisan are intended to fall within the scope of the present invention.
Participants. All datasets tested in this project were originally collected for the study of genetic factors in AD using family-based methods (see Table 1 for a detailed summary of sample characteristics).
All studies were approved by the institutional review boards of the appropriate institutions and all subjects gave informed consent for their participation. With the exception of the CAG sample (see below), the majority of pedigrees analyzed here were nuclear families ascertained on the basis of multiple affected, generally lacking parental genotypes. In addition to containing at least one affected relative pair, many pedigrees also had DNA available from additional affected or unaffected individuals (Supplementary Table 1). These were mostly siblings, and only a minority of additional subjects stemmed from more extended branches (most of these are part of the NIMH sample). The diagnosis of “definite”, “probable” or “possible” AD was made according to NINCDS/ADRDA (ref. 21) criteria in all samples. Age of onset for all AD cases was determined by a clinician based on an interview with a knowledgeable informant and review of any available records.
NIMH families. This sample was collected as part of the National Institute of Mental Health Genetics Initiative Study (ref. 11), and is comprised of a total of 1528 subjects from 457 families. Only families in which all affected family members showed an onset age ≧50 years, and in which DNA was available from at least two affected family members were included in these analyses, i.e. 1439 individuals from 436 families. Of these, 1376 individuals from 410 families were of Caucasian ancestry and used for the initial 500 K screening. Fifty eight individuals from 24 families were of African descent and were included in the follow-up analyses.
NIA and NCRAD families. Both of these datasets were obtained from the National Repository of Research on Alzheimer's Disease (NCRAD), and ascertainment and collection details can be found at the NCRAD website. For this study, families of Caucasian ancestry were included only when DNA was available from at least two first degree relatives (concordant or discordant) and all individuals in which were affected with AD showed onset ages ≧50 years. For the NIA collection this was comprised of 1,040 samples from 329 pedigrees, and for NCRAD 1,108 samples from 331 pedigrees.
CAG families. Samples in this dataset were recruited under the auspices of the “Consortium on Alzheimer's Genetics” (see ref. 22 for more details). Probands were included only if they had at least one unaffected living sibling willing to participate in the study described herein. As for the other replication samples, only families of Caucasian ancestry and with onset ages >50 years were included in the study, i.e., 483 individuals from 215 sibships.
Genotyping assay. Two chips (Nsp and Sty) were used to genotype 500,668 SNPs of the GENECHIP® Human Mapping 500 K Array Set in 1505 individuals comprising the publicly available NIMH AD genetics population. Each of the two chips assayed approximately 250,000 SNPs per sample. Genotyping was carried out according to manufacturer's protocol except for the following modifications: Restriction enzyme digestion, ligation, Polymerase Chain Reaction (PCR) and purification were completed in 96 well plates containing 92 samples and four blanks. The PCR normalization step was performed using a Biomek F/X robot. After normalization, PCR products were divided into four separate 96-well plates each containing only 23 samples. Both the fragmentation and labeling steps were performed on 23 samples at a time, while maintaining a constant temperature using cold blocks. For the hybridization step, samples were denatured in hybridization cocktail for 10 minutes at 99° C. and 2 minutes at 49° C. using an MJ Tetrad, then were transferred immediately to an external heating block kept at a constant temperature of 49° C. Prior to sample injection, the 500 K arrays were warmed in hybridization ovens at 49° C. for at least 10 minutes. During sample injection the arrays were maintained at 40 to 49° C. and were immediately returned to the hybridization oven for 19 to 27 hours of incubation at 49° C. Post-hybridization wash, staining, and detection followed the manufacturer's protocol. Modifications to the manufacturer's protocol increased the quality and quantity of data obtained from each chip assay. The average genotype call rates (see Genotyping data analysis for detail) increased from 87.5% to 97.3% and from 94.8% to 96.1% for Nsp and Sty arrays, respectively. Out of the entire sample, data from only eight arrays on a total of 5 DNA samples failed to exceed a 93% call rate threshold necessary to be included in the analyses.
In addition to the chip-based genotypes, all four SNPs implied by the GWA analyses as well as APOE SNPs rs429358 and rs7412 were genotyped in all four sample sets using high-efficiency fluorescence polarization (HEFP) detection of a single-base extension assay (ref. 24). The HEFP procedures were essentially identical to those previously described in Bertram et al. (ref. 22). Neither genotyping method showed evidence for Mendelian errors for these four SNPs, although the power used herein to detect such inconsistencies is low owing to the lack of parental genotypes and relatively small family size.
Genotyping-calling algorithm. Genotype calls were based on the Bayesian Robust Linear Model with Mahalanobis Distance algorithm (BRLMM; ref. 23), which was developed for yielding greater call rates without affecting accuracy or reproducibility of the data. Overall, an average SNP genotype call rate of 98.95% was achieved. SNPs with genotype call rates below 90% (5,758 markers [1.1%]) were excluded. In addition, all SNPs located on the X-chromosome (10,388 markers [2.1%]) were excluded, resulting in 484,522 markers used in the whole-genome association analyses. SNPs on the X-chromosome were excluded because there is currently no method available for association testing of these markers in family-based settings.
Only genotype calls passing a stringent quality control threshold were accepted, in which 93% of the SNPs on a 250K array yielded a genotype (using the DM algorithm at a confidence threshold of 0.33). Of the 3,010 500K GENECHIPs® necessary to complete genotyping of the family-based sample set, only eight chips failed to meet or exceed the 93% call rate threshold. The DM algorithm calculates genotypes for one sample at a time, relying on assumptions about the behavior of SNP allele signals. However, an alternative genotype-calling algorithm was recently developed by Rabbee & Speed termed Bayesian Robust Linear Modeling using Mahalanobis Distance (BRLMM; ref. 23). The BRLMM method simultaneously analyzes data from multiple-chips, calling genotypes via multiple-sample cluster analysis. BRLMM accounts for probe effects on variation in allele signal intensity of individual SNPs in making genotype calls. This new algorithm is an improvement over DM in terms of overall call rates, accuracy and detection of heterozygous genotypes. Both Affymetrix and The Broad Institute (MIT/Harvard) have shown improved efficacy of genotyping calling using BRLMM on their datasets.
The DM and BRLMM genotype-calling algorithms were compared with respect to call rates, accuracy and concordance on the 500 K data set. Initial analysis of the data with BRLMM increased the number of heterozygous genotypes (
Overall, genotype calls made by DM and BRLMM were in close agreement with one another, and the concordance increased with data from chips having higher initial DM call rates, indicating that higher call rate data is more reliable (
Because the BRLMM algorithm processes chips in batches and uses a clustering algorithm to make genotype calls, the effects of batch size and/or batch composition on call rate were determined. Experiments were carried out with batch sizes of 50 and 100 chip-data CEL files. Samples with moderate (93%), good (95%) and excellent (98%) chip call rates (ref. 1) were tested and processed in varying batch environments. Single test samples (e.g. 93% initial DM call rate) were grouped with samples that had (1) Like or similar call rates (e.g. 93%), (2) Mixed call rates (samples with call rates ranging between 93% and 99%), or (3) Unlike or dissimilar call rates (e.g. 98%). CEL data files were analyzed in “like”, “mixed”, and “unlike” environments with the BRLMM algorithm. The “mixed” environment was designed to emulate the batch composition one would obtain if processing batches were built randomly. It was determined that batch composition does make a difference in genotype calling efficacy. Specifically, call rates for the test samples were substantially improved when processed with data files of similar call rates (
Chips from the “good” (95%) and “excellent” (98%) call rate (ref. 1) classes showed a similar pattern to the “moderate” chips when analyzed in the three different batch environments with BRLMM, however this trend was not absolute. The majority of the cases tested showed improved call rates when analyzed in “like” environments as compared to “mixed” or “unlike” environments, with a few exceptions (
Based on the analysis above, a novel ‘workflow’ was developed for maximizing SNP call rates while maintaining high accuracy and reproducibility of the data. DM was used as an initial quality measure for individual chips, and then re-analyzed the raw data with the BRLMM algorithm in appropriately defined clusters. Using this method the average chip call rates across the entire sample set improved to 98.95% with BRLMM (
Association analyses. Association analyses were performed using PBAT (v3.6), an extension (ref. 25) of the Family-Based Association Test (FBAT) program (ref. 26). To maximize statistical power, AD affection status and age-of-onset were tested jointly, using the multivariate extension of the FBAT-approach, FBAT-GEE (ref. 16). To minimize the multiple testing problem, the weighted Bonferroni-testing strategy by Ionita-Laza et al (ref. 13) which is an extension of the VanSteen algorithm (ref. 27) was applied. On the basis of the between-family information which is statistically independent from the FBAT-statistic (ref. 27), the testing strategy evaluates the evidence for association at a population-level and then estimates the conditional power of the FBAT-GEE statistic for each marker in the first step. The FBAT-GEE statistic contains affection status and time-to-onset as phenotypes, coded either as logrank-statistic or Wilcoxon statistic. The choice of which statistic to use in the association test is determined on the basis of the highest conditional power estimate for each coding. In the second step of the testing strategy, FBAT-statistics are computed for all markers. Since none of the phenotypic traits used herein were quantitative, the conditional power was estimated based on the non-parametric extension of the conditional mean model approach to dichotomous traits and time-to-onset variables proposed by Jiang et al (ref. 17). Their significance is assessed based on individually adjusted alpha-levels that maintain the overall type-1 error and that are weighted on the basis of the conditional-power estimate for the corresponding marker according to their conditional-power estimates. The computation of the weights is described in detail in Ionita-Laza et al (2007) (ref. 13).
The approach applied herein used the following tuning parameters: the size of the first partition was 5 and the parameter was set to 2. When the weighted Bonferroni-approach was applied to the 809,208 P-values of the FBAT-GEE statistic for AD affection status and time-to-onset, 4 of the SNPs reached genome-wide significance (thresholds for genome-wide significance are P<5×10−3 for markers rs11159647, rs179943, and rs2049161, and P<4.88×10−6 for rs3826656). Affection status was coded with an offset of 0.10 (approximate prevalence of AD among individuals over 65 years). Sensitivity analyses using offsets ranging from 0.05 to 0.2 did not change the results appreciably (data not shown). The age of onset variable was constructed using the Wilcoxon approach (ref. 17). While SNPs on the X-chromosome and those with low call rates or poor reproducibility across duplicated genotypes were excluded from the analyses (16,146 SNPs), SNPs that deviated from Hardy-Weinberg Equilibrium (HWE), which affected a total of ˜85,000 SNPs at P=0.01, and ˜56,000 at P=0.001, were retained. Approximately half of the HWE-deviating SNPs showed low minor allele frequencies 0.10). Inclusion of HWE-deviating SNPs was based on the assumption that most departures from HWE in this context are caused by mis-calling heterozygous genotypes. Under these circumstances dominant and recessive models, which treat the heterozygous genotype and one of the homozygous genotypes as one category will provide test results that are fairly robust against such genotyping errors. This was the case for marker rs326656 which significantly deviated from HWE (P=1×10−23) in the 500 K dataset, but not in the families of the follow-up samples (all P-values >0.05) which were genotyped using the high-efficiency fluorescence polarization (HEFP) technology. Re-genotyping of this SNP by HEFP in the NIMH families resolved the HWE deviation (P=0.6), decreasing the statistical significance to P=0.04 in the FBAT-GEE analyses. FBAT-GEE test statistics were only calculated for SNPs in which the number of informative families was at least 20 (i.e. 404,604 SNPs out of the 484, 522 SNPs with available genotypes). The 404,604 SNPs were tested under additive and dominant transmission models. Accordingly, all nominal P-values were adjusted conservatively for 2×404,604=809,208 comparisons, using the weighted Bonferroni method by Ionita-Laza et al (ref. 13). P-values on the combined samples were calculated using the method described by Fisher (ref. 28) taking into account the direction of the transmissions in each individual sample. Pairwise LD estimations were performed in Haploview (v3.32) on the 500 K SNP chip genotype data in Caucasian NIMH families (using the re-genotyped data for rs4777936) as well as on genotype data available on the International HapMap Consortium website (Public Release #22 based on NCBI build 36 [dbSNP b126]).
In the first stage of the study, 1,376 individuals were screened from 410 Caucasian families from the National Institute of Mental Health (NIMH) Genetics Initiative Study sample, the largest uniformly ascertained and evaluated AD family sample to date (Refs. 11, 12). Methods for both the genotyping assay and genotype-calling algorithm were optimized to increase quality and quantity of the data (see Methods and Materials in Example 1). After removal of all 10,388 X-chromosome markers, as well as 5,758 SNPs that did not pass genotype quality assessment or showed a minor allele frequency (MAF) that resulted in less than 20 informative families, a total of 404,604 (80.8%) SNPs were used for the whole-genome screening. Statistical analyses as described in Example 1 were performed in PBAT using affection status and age of onset as a multivariate phenotype in the FBAT-GEE statistic whose P-values were adjusted based on the weighted Bonferroni-testing strategy by Ionita-Laza et al (ref. 13). The Q-Q plot displaying observed vs. expected P-values shows that the overall alpha-level is maintained, despite a slight departure from the expected values for the smallest P-values (
The association of the non-APOE markers with AD was further assessed in three additional and independently collected family samples of Caucasian ancestry (“NIA”, “NCRAD”, “CAG” described in Methods and Materials), by genotyping the same SNPs for which association was observed in the genome-wide analyses. The vast majority of these families are made up of sibships (either concordant or discordant for AD), with a total of 2,689 individuals (1,816 affecteds and 845 unaffecteds). Upon combining results across all three replication samples (using Fisher's combined probability test), significant association with the multivariate phenotype was observed for two of the four SNPs tested ([1-tailed] p-values 0.00002 [rs11159647] and 0.007 [rs3826656]; Table 3;
Next, it was sought to investigate whether any of the four identified SNPs showed association in the two recently published AD GWA analyses, for which genotype data were made publicly available. Since the two recent AD GWA published data did not include subject-level age-of-onset information, only test statistics using affection status could be calculated (Table 4). rs11159647 on chromosome 14q, the SNP demonstrating the strongest association with AD in the family-based analyses, revealed nominally significant association with the same allele in the TGEN dataset ([1-tailed] p=0.04; ref. 7). Meanwhile, rs2049161 on chromosome 18p showed nominally significant association in the GSK dataset ([1-tailed] p=0.045; ref. 10). It should be noted that this latter SNP rs2049161 was the only marker not showing any consistent evidence of association in the family-based replication samples. rs179943 did not show evidence of association in either of the two previously published GWA screens, no analyses could be performed for rs3826656 as it was missing from both case-control GWA datasets.
In the two previous studies (refs. 14 and 15), it was assessed whether or not any of the currently most promising putative AD susceptibility loci (based on a recent freeze of the AlzGene database), including all five recently pinpointed by the two high-density case-control GWA studies (refs. 7 and 10), showed association in the four family datasets tested herein. After combining results across all four family datasets using the same analytical methodology as applied herein; it was observed in the previous studies that there was nominally significant association with variants in ACE (MIM 106180), CHRNB2 (MIM 118507), GAB2 (MIM 606203), TF (MIM 190000), and an as yet unidentified locus on chromosome 7p15.2. Of these, GAB2 (ref. 7) and the 7p15.2 locus (ref. 9) were originally implicated by GWA association analyses. However, the level of statistical support for each of those loci was several orders of magnitude smaller (i.e. combined P-values ranging between 0.03 and 0.002) than that observed for the chromosome 14 locus identified herein. Variants in other recently reported potential AD genes, such as SORL1 (MIM 602005) and GOLM1 (a.k.a. GOLPH2, MIM 606804; see AlzGene database for detail) did not show any significant evidence in those analyses.
Presented herein is the first GWA analysis using family-based methods in the field of AD. For two of the four non-APOE SNPs, the initial evidence for genetic association was replicated in three independent collections of Caucasian AD families, while a third SNP showed at least a trend towards association in the analyses limited to affection status. Moreover, for the SNP exhibiting the strongest and most consistent family-based association with AD in the analyses, rs11159647, statistically significant association of the same risk-allele with AD was also observed in an independent collection of cases and controls that had been probed with the same 500 K SNP array (ref. 7). Collectively, these data strongly indicates the presence of a genuine AD susceptibility locus in the vicinity of marker rs11159647 on chromosome 14q31.2. In addition, the analyses shown herein highlight two further putative AD loci located on chromosomes 6p22 and 19q13. Further, a quantitative analysis approach combining the two most widely available phenotypes in AD samples, i.e. age of onset and affection status, were used. This has the advantage of increasing power while ensuring consistency of the findings across both phenotypes (refs. 16, 17). Power calculations reveal that minimally ˜700 combined cases and controls are required to detect the additively transmitted rs11159647 risk effect (i.e. an allelic OR of ˜1.4) at α=0.05 in order to achieve 80% power, and minimally ˜2,300 and ˜8600 samples for the more modest risk effects of SNPs rs3826656 and rs179943, respectively. Additionally, the association signal for rs11159647 maps to the distal end of a genetic linkage region identified in a whole-genome linkage screen of the NIMH sample (Blacker, 2003; ref 12), as well as in an independent collection of Caribbean Hispanic families using age of onset as phenotype (Lee, 2007; ref. 29). In previous reports, most of the linkage evidence originated from families with an “early/mixed” onset age, i.e., those families in which at least one affected family member showed onset age prior to 65 years (ref. 12). This is in good agreement with the decrease in onset age observed herein in individuals carrying the A-allele at rs11159647. A similar observation was made with the whole-genome linkage signal encompassing the APOE region on chromosome 19q13, which was also most pronounced in families with an “early/mixed” onset age (ref. 12). Notably, the other two putative signals implied by the GWA and follow-up analyses described herein map to chromosomes 6p22 and 19q13, which were also discussed by genome-wide linkage analyses (refs. 12, 8). However, the prior-art studies do not specifically describe the AD risk-associated loci on chromosomes 6p22 and 19q13.
The statistical and genetic epidemiological evidence strongly indicates the presence of a putative AD gene on chromosome 14q, and additional loci on chromosomes 6p22 and 19q13. Yet the potential functional and pathophysiological consequences of the findings remain elusive. According to the UCSC genome browser (hg18, NCBI Build 36.1), the genomic region in the vicinity of the AD-associated SNP, rs11159647, on chromosome 14q31 does not contain any genes known in the database of NCBI Reference Sequence (RefSeq). This SNP resides at position 83,844,962 bp on chromosome 14 in an intron of the gene predicted by a program Genscan, NT—026437.1360 (
SNP rs179943, on 6p22.3 at position 16,506,297 bp, resides within an intron of the ataxin-1 (ATXN1) gene, in which an elongated polyglutamine tract causes the progressive neurodegenerative disease, spinocerebellar ataxia (SCA1 [MIM 164400]), characterized by progressive degeneration of the cerebellum, brain stem and spinal cord (ref. 19). SNP, rs3826656, on 19q33 at position 6,418,175 bp, resides in a region that contains no known RefSeq genes. However, this SNP resides in a predicted Genscan gene, NT—011109.848, spanning 126,319 bp. The 3′ portion of this locus overlaps with the gene encoding human protein CD33 (MIM 159590). CD33, also known as SIGLEC3, maps to 19q13.3 and encodes a cell surface receptor on cells of monocytic or myeloid lineage. It is also a member of the SIGLEC family of lectins that bind sialic acid and regulate the innate immune system via the activation of caspase-dependent and caspase-independent cell death pathways (ref. 20). Finally, rs2049161, on 18p11.31 at position 4,117,583 bp, resides within an intron of BC040718, a gene of currently unknown function. However, rs2049161 can be associated with the gene DLGAP1, which also maps on chromosome 18, at 18p11.31 according to Entrez Gene and encodes disc, large (Drosophila) homolog-associated protein 1 and BC040718.
Alzheimer's disease (AD) is a genetically complex and heterogeneous disorder. To date four genes have been established to either cause early-onset autosomal dominant AD (APP, PSEN1, PSEN2 [refs. 1-4]), or to increase susceptibility for late-onset AD (APOE [ref. 5]). However, the heritability of late-onset AD is as high as 80% (ref. 6), and much of the phenotypic variance remains unexplained to date. A genome-wide association (GWA) analysis was performed using 484,522 single nucleotide polymorphisms (SNPs) on a large (1,376 samples from 410 families) sample of Caucasian AD families. Presented herein is the first study to employ a family-based whole genome association approach to AD. Five SNPs showing either significant or marginally significant genome-wide association with a multivariate phenotype combining affection status and onset age as a multivariate phenotype was identified. One of these signals (P=5.7×10-14) was elicited by SNP rs4420638 and likely reflects APOE-ε4, which maps 11 kb proximal (r2=0.78). The other four signals were tested in three additional independent AD family samples comprised of nearly 2,700 individuals from almost 900 families. Two of these SNPs showed significant association in the replication samples (combined P-values 0.007 and 0.00002). The SNP (rs11159647, on chromosome 1401) with the strongest association signal also showed evidence of association with the same allele in GWA data generated in an independent sample of ˜1,400 AD cases and controls (P=0.04). The study presented herein provides strong evidence for the existence of at least one previously undescribed AD gene (e.g., rs11159647) that, like APOE-ε4, primarily acts as a modifier of onset age. The replication of these associations in three independent AD family samples—and in the case of rs11159647 also in one independent case-control GWA dataset—strongly indicates the existence of AD susceptibility loci that warrant follow-up in additional independent samples as well as in functional genomic analyses.
AD is a genetically complex disease and only four genes have been established to either cause early-onset autosomal dominant AD with complete penetrance (APP, PSEN1 and PSEN2) or to increase susceptibility for late-onset AD with partial penetrance (APOE)[3]. All these four confirmed genes increase the absolute Aβ levels or the ratios of Aβ42 to Aβ40, which enhances the oligomerization of Aβ into neurotoxic assemblies [3, 5]. To date approximately 80% of the late-onset AD genetic variance remains elusive[8]. Example 2 demonstrates the four novel late-onset AD susceptibility loci identified in a genome-wide association screen (GWAS) that achieved genome-wide statistical significance (beyond APOE). Among the four AD susceptibility loci, rs 179943 resides within an intron of the Ataxin 1(ATXN1) gene, and ATXN1 has been shown to cause spinocerebellar ataxia type 1 (SCA1). As a different neurodegenerative disease from AD, SCA1 is characterized by ataxia, progressive motor deterioration, and loss of Purkinje cells in the cerebellum [10, 11].
It has been shown that ATXN1 leads to SCA1 through a primary gain-of-function mechanism through the expanded polyglutamine tract and functional domains [11]. However, the cellular and molecular mechanism by which ATXN1 contributes to AD pathogenesis is still unknown. Determining ATXN1-mediated pathological events in AD will help develop a better understanding of AD pathogenesis and identify novel AD therapeutic targets. Thus, this Example contains methods and materials that were used to elucidate the biological roles of ATXN1 and address the molecular mechanism by which ATXN1 affects AD pathogenesis in later Examples.
Cell culture and mouse primary cortical neuron culture. The H4 human neuroglioma cell line stably over-expressing human APP751 (H4-APP751) has been previously reported in Xie et al. (2007 and 2005) [12, 13]. The stable H4-APP-C99 cell line stably over-expressing APP-C99 has been previously described in Xie et al. (2005) [13]. APP-C99, the product of β-secretase, contains α- and γ-secretase (but not β-secretase) sites. The stable H4-APP-C99 cell line provides a valid system to assess whether any effects on APP processing are dependent on β-secretase. These cell lines were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 units/ml penicillin, 100 μg/ml streptomycin, and 200 ug/ml G418. Mouse primary cortical neurons were from Brainbits (E18) and were cultured in B27/Neurobasal medium supplemented with 1× GlutaMAX (Invitrogen).
Plasmids, chemicals and antibodies. The ATXN1-cDNA that over-expresses ATXN1 (Origene Inc. #: SC314762: SEQ ID NO: 18) was inserted into a pCMV derived vector (Origene Inc. #: PCMV6XL5). The BACE1-myc fusion plasmid has been previously reported [37]. The APP C-terminal antibody (targeting the last 19 amino acids of APP751, APP750 or APP695; A8717; 1:1000) was purchased from Sigma. The sAPPβ antibody (targeting ISEVKM, the C-terminus of human sAPPβ wild type, 2 ug/ml or 1:50) was from IBL. The 6E10, anti-APP antibody was purchased from Covance and utilized for detection of sAPPα (1:1000). The ATXN1 antibodies (76-3 and 76-8) were from the UC Davis/NIH NeuroMab Facility (1:1000). β-Actin antibody (1:10,000) was purchased from Sigma. The HRP-conjugated secondary antibodies (anti-mouse and anti-rabbit) (1:10,000) were purchased from Pierce.
Small interfering RNAs (siRNAs). siRNA duplexes were obtained from Dharmacon, Inc. Four different individual on-target siRNAs were synthesized to target different regions of ATXN1: (A). GGGAATAGGTTTACACAAA (SEQ ID NO: 19); (B). GGTCTAATGTAGGCAAGTA (SEQ ID NO: 20); (C). CCAGCCAGCTCTTTGATTT (SEQ ID NO: 21); (D). GAAGAACGGCTCTGTTAAA (SEQ ID NO: 22). A smart-pool on-target siRNA was also obtained from Dharmacon, Inc in which the four siRNAs were combined in equal molar concentrations (represented by ATXN1-construct E siRNA). The control siRNA was a scrambled siRNA from Dharmacon, Inc. The smart-pool accell siRNA targeting mouse ATXN1 and control accell siRNA were obtained from Dharmacon, Inc.
Transfection. Transfections of on-target siRNAs were performed using the 96-well nucleofection shuttle system from Lonza (previously Amaxa; SF solution; DS137 program) and have been reported previously [12, 14]. Cells were mixed with siRNA or plasmid DNA, and resuspended in transfection solution according to the manufacturer's protocol. The transfected cells were harvested 48 h after transfection. The mouse primary cortical neurons were transfected with the accell ATXN1 siRNA or control siRNAs as recommended by the manufacturer's protocols and harvested 72 h after transfection.
Aβ measurement. Aβ measurement was performed following the manufacturer's suggested protocols and was described previously [15]. In brief, Aβ40 and Aβ42 levels (pg/ml) were quantified using a sandwich enzyme-linked immunosorbent (ELISA) assay (Wako and Signet). Aβ40 and Aβ42 levels were normalized to the protein concentrations from the cell lysates. Normalized Aβ40 and Aβ42 values from the treatments were represented as relative values by comparing to control treatment, which were set as 100% or 1.
Cell lysis and protein amount quantification. Cells were lysed in the Mammalian Protein Extraction Reagent (Thermoscientific) with 1× Halt protease inhibitor cocktail (Thermoscientific). The lysates were collected and centrifuged at 13,000 rpm for 20 minutes. Pellets were discarded and supernatants were transferred into a new Eppendorf tube [16]. Total proteins were quantified by the BCA protein assay kit (Pierce) [16].
Western blotting analysis. Western blotting analysis was carried out by the method previously described in Hiltunen et al. (2006) and Zhang et al. (2007) [15, 16]. Briefly, after centrifugation and protein concentration measurement, an equal amount of each protein sample was applied to electrophoresis followed by membrane transfer, antibody incubation, and signal development. The VersaDoc imaging system (Bio-Rad) was used to develop the blots and the software Quantity One (Bio-Rad) was used to quantify the proteins of interest by subtracting the background, following the protocols previously described in Hiltunen et al. (2006) and Zhang et al. (2007) [15, 16].
RNA extraction and quantitative polymerase chain reaction. RNA was extracted using the RNeasy mini kit (Qiagen Inc.) and was previously described in Hiltunen et al. [15]. RNA concentration was measured using the Nanoprop ND-1000 Spectrophotometer (Themofisher Inc.). Equal quantities of RNA samples were subjected to cDNA synthesis using the SuperScript III first strand synthesis system (Invitrogen). A multi-plex system was used to measure the relative amount of cDNA. Primers/probes that targeted the gene of interest were labeled with FAM490 (Applied Biosystems, Inc.; ATXN1: Hs00165656_ml or Mm00485928_m1; APP: Hs01552283_m1 or Mm00431827_m1; BACE1: Hs00201573_m1). The house-keeping gene, β-actin, was used as the endogenous control and was labeled with a VIC/MGB probe (Applied Biosystems, Inc.; human #: 4326315E; mouse #: 4352341E). 1:10 diluted cDNAs were mixed with 2×PCR Universal Master Mix (Applied Biosystems, Inc.) and amplified using an iCycler Real-Time PCR System following the manufacturer's directions (Bio-Rad). To determine differences in mRNA levels from the treatments, the ΔΔCt method was utilized [17].
Alamar Blue assay. The Alamar Blue assay was a non-invasive way to assess cell viability and proliferation and has been previously reported in Antczak et al. [38]. The Alamar Blue was purchased from Invitrogen and the assay was performed according to the manufacturer's recommended protocol. Alamar Blue dye (the commercial name for resazurin) was directly added to culture medium at a final concentration of 10% (v/v), medium was collected at certain time intervals, and the fluorescence intensity was read on the Criterion Analyst AD high-throughput fluorescence detection system (Molecular Devices) using a 530-560 nm excitation wavelength and a 590 nm emission wavelength. The fluorescence readout from ATXN1 siRNA treatment was compared to the readout from the control siRNA treatment and represented as changes in percentage.
Data analysis. Aβ40 and Aβ42, as well as sAPPα and sAPPβ levels were normalized to the BCA values from the same cell lysates [14]. β-Actin was used in the Western blotting analysis or quantitative PCR analysis to account for any differences in loading. The levels of proteins, e.g. ATXN1, C83, and full length APP, were normalized to the corresponding values from the same lane. The normalized sAPPα and sAPPβ values were divided by normalized full length APP levels from each sample. The values from the ATXN1 siRNA treatment were normalized to control siRNA treatment. The samples for each treatment were from at least three for each experimental group and were demonstrated as means±SEM. A two-tailed t-test, as appropriate, was used to compare the differences between two groups. The Bonferroni correction analysis was used to correct for multiple comparisons within a single experiment. P value≦0.05 was considered statistically significant.
The effect of down-regulation of endogenous ATXN1 on alteration of Aβ levels was investigated herein. The experimental conditions under which ATXN1 siRNA treatment could significantly decrease ATXN1 protein levels in stable H4-APP751 cells was first established. H4-APP751 cells were transfected with different ATXN1 siRNAs (siATXN1) or control siRNA (siCtr1) using the Amaxa nucleofector[13, 14]. Cells were harvested 48 hours post transfection and cell lysates were prepared for Western blot analysis. The ATXN1 antibody (76-3) has been reported previously and was used to detect ATXN1 protein [18]. β-Actin, a house keeping gene, was used as a negative control. All the ATXN1 siRNA treatments significantly decreased ATXN1 protein levels by quantitative analysis compared to control siRNA treatment (siATXN1-A: 79.5%; siATXN1-B: 85.0%; siATXN1-C, 74.5%; siATXN1-D: 78.3%; siATXN1-E: 81.1%) (p<0.01) (
The Aβ40 and Aβ42 levels in the conditioned medium were next measured 48 h after the transfection. Aβ40 and Aβ42 levels were measured using ELISA and normalized to the cell lysate protein concentration from the same sample. All of the five different ATXN1 siRNA treatments increased Aβ40 levels compared to control siRNA treatment (43.3%, 73.3%, 99.0%, 80.9%, and 102.1% by siATXN1-construct A, B, C, D, and E, respectively) (
It was also sought to assess whether ATXN1 siRNA treatment increased the ratio of Aβ42 to Aβ40. It has been shown that most familial AD mutations in APP, PSEN1, and PSEN2 increase the ratio of Aβ42 to Aβ40, which drives the aggregation of Aβ into neurotoxic oligomeric assemblies [3, 5]. The ratio of Aβ42:Aβ40 in cells treated with ATXN1 siRNAs had no significant difference compared to cells treated with control siRNA (p>0.05) (
Next, the down-regulation effect of ATXN1 on Aβ levels was validated by over-expression of ATXN1. H4-APP751 cells were transfected with control siRNA (siCtr1) and/or ATXN1 siRNA (siATXN1), as well as the empty vector (pCMV) and/or ATXN1-cDNA and applied to Western blotting analysis and ELISA as described in Methods and Materials. The combination of siATXN1/pCMV treatment significantly decreased ATXN1 protein levels compared to the siCtr1/pCMV treatment (
The effects of ATXN1 knock-down on Aβ40 and Aβ42 levels was also investigated in naïve H4 cells other than H4-APP751 cells. Naïve H4 cells were transiently transfected with control siRNA or the ATXN1 siRNA and harvested 48 h post transfection. Cell lysates were applied to Western blotting analysis. ATXN1 antibody (76-3) was utilized to reveal the ATXN1 protein. Quantitative Western blotting analysis showed that ATXN1 siRNA treatment significantly decreased ATXN1 protein levels by 85.7% (p<0.01 versus control) (
The effect of ATXN1 knock-down on Aβ40 and Aβ42 levels was validated in mouse primary cortical neurons. The mouse cortical neurons were transfected with ATXN1 accell siRNA or control siRNA and harvested 72 h post transfection. Cell lysates were applied to quantitative Western blotting analysis and ATXN1 antibody (76-8) was utilized to reveal the ATXN1 protein. ATXN1 siRNA treatment significantly decreased ATXN1 protein levels by 40.0% compared to control siRNA treatment (p<0.05) (
Mutant ATXN1 with polyglutamine repeats could utilize a gain-of-function mechanism and induce cytotoxicity and apoptosis [39], which may increase Aβ levels by activating caspase-3 activity [40-43]. Thus, it was sought to determine whether ATXN1 knock-down potentiates Aβ levels by activating caspase-3 and inducing cytotoxicity or apotosis. The Alamar blue assay was first used to test cell viability [38]. Stable H4-APP751 cells were transiently transfected with the control siRNA or the different ATXN1 siRNAs using the Amaxa nucleofactor. Alamar blue was added to transfected cells 36 hours after transfection and cells were harvested 12 hours after treatment. The fluorescence readouts from the ATXN1 siRNA treatment were compared to those from the control siRNA treatment. There were no differences on the fluorescence levels between the ATXN1 and the control siRNA treatments (p>0.05) (
Then the effect of ATXN1 down-regulation on caspase-3 activation was determined. Full-length caspase-3 protein is 35 kDa, which undergoes cleavage and produces a 17 kDa cleavage fragment during apoptotic in vitro [42,44]. The caspase-3 activation process can be represented and quantified by comparing the ratio of cleaved caspase-3 fragment levels to full length caspase-3 levels [45]. In the experiment, stable H4-APP751 cells were transiently transfected with control siRNA or ATXN1 siRNA. Cell lysates were collected 48 h post transfection and applied to Western blotting analysis. Cells treated with 100 nM staurosporine (STS) for 12 hours were used as a positive control for caspase-3 activation and the caspase-3 fragment. ATXN1 (76-3) antibody was used to detect the ATXN1 protein. Caspase-3 antibody was used to detect full length caspase-3 and the 17 kDa cleaved caspase-3 fragment. β-actin was used to normalize the protein levels in each gel lane for comparison. Quantitative Western blotting analysis revealed that the ATXN1 siRNA treatment did not alter caspase-3 activation in comparison with the control siRNA treatment (p>0.05) (
As shown in Examples 4 and 5, knock-down of ATXN1 increased Aβ levels. It was first determined that the increased Aβ levels driven by down-regulation of ATXN1 was not contributed by the effect of silencing ATXN1 on cell viability or induction of apoptosis in Example 6 (
Next, the effect of knock-down of ATXN1 on APP protein levels and its proteolytic processing was assessed. Stable H4-APP751 cells were transfected with different ATXN1 siRNAs and control siRNA. Conditioned medium and cell lysates were collected 48 h post transfection and subjected to Western blotting analysis. Antibody APP8717 was used to detect full length APP and its C-terminal fragments (CTFs). β-Actin antibody was used as the loading control. The ATXN1 siRNAs (siATXN1-C, D & E) did not change full length APP levels (p>0.05), whereas the ATXN1 siRNA (siATXN1-A & B) modestly increased full length APP levels by approximately 30% (p<0.05) (
It was next sought to examine whether ATXN1 down-regulation affected APP processing by assessing the ratios of its proteolytic cleavage fragments levels to full length (FL) APP levels. ATXN1 siRNA treatments did not significantly alter the absolute C83 levels compared to control (p>0.05) (
Then the effects of ATXN1 down-regulation on APP processing were assessed in naïve H4 cells and mouse primary cortical neurons. Naïve H4 cells were transfected with human ATXN1 siRNA or control siRNA. Mouse primary cortical neurons were transfected with mouse accell ATXN1 siRNA or control siRNA. Cells were harvested and applied to Western blotting analysis. Antibody APP8717 was used to detect full length APP. β-Actin antibody was used to detect β-actin which was used a loading control. The ATXN1 siRNA treatment did not significantly change full length APP levels in naïve H4 cells (p>0.05) (
Aβ is produced by a sequential proteolytic cleavage of a type I transmembrane protein, β-amyloid precursor protein (APP) [6]. The initial cleavage of APP can occur through α- or β-secretase (or BACE1). α-secretase cleavage produces sAPPα and the α-C-terminal fragment (α-CTF or C83); β-secretase cleavage produces sAPPβ and β-C-terminal fragment (β-CTF or C99). Following trophic factor deprivation, sAPPβ can be further cleaved by an unidentified protease, to produce N-APP, which contains the N-terminal 286 amino acids of APP [7]. C83 and C99 can be further cleaved by γ-secretase to produce P3 or Aβ.
To further study APP proteolytic processing, secreted APP products, including sAPPα and sAPPβ, were assessed in the conditioned medium. 6E10 antibody was used to detect sAPPα protein. sAPPα levels were quantified and normalized to the cell lysate protein levels from the same samples. The ratio of sAPPα to full length APP was calculated by dividing normalized sAPPα values by full length APP values (normalized to β-actin) from the same samples. ATXN1 siRNA treatment did not change the absolute sAPPα levels compared to control siRNA treatment (p>0.05) (
The sAPPβ protein levels in the cell medium (detected by the sAPPβ antibody) was quantified and normalized to the cell lysate protein levels. The normalized sAPPβ levels were then compared to full length APP levels (normalized to β-actin). Each of the ATXN1 siRNA treatments increased sAPPβ levels and the ratio of sAPPβ to APP-FL compared to control siRNA treatment (
Next, stable H4-APP-C99 cells were utilized for validation of ATXN1 knock-down increasing Aβ levels and APP processing through β-secretase. The stable H4-APP-C99 cell line has saturated β-secretase activity and provides a valid system to assess whether any effects on APP processing are dependent on β-secretase [12]. First, H4-APP-C99 cells were transiently transfected with ATXN1 siRNA and control siRNA. Cells were harvested 48 h post transfection and applied to Western blotting analysis and ELISA. ATXN1 siRNA treatment markedly decreased ATXN1 protein levels (
Collectively, the data presented herein showed that ATXN1 significantly altered the levels of Aβ and sAPPβ. To determine whether there was a correlation between the levels of Aβ40 or Aβ42, and sAPPβ, the data presented herein was consolidated and a linear regression analysis was performed. Levels of sAPPβ were plotted with levels of Aβ40 or Aβ42 from the same samples, and were represented as a percentage change by comparing the siATXN1-treated samples to the control. The x-axis was represented by the percentage changes in sAPPβ levels, and the y axis was represented by the percentage change in Aβ40 or Aβ42 levels. This analysis revealed a significant correlation between sAPPβ and Aβ40 (p<0.05;
It has been reported that both wild type and extended polyglutamine mutant ATXN1 proteins can function as transcriptional regulators [19, 20]. Thus, it was sought to examine whether ATXN1 knock-down increased Aβ levels by affecting APP transcription. Naïve H4 cells or mouse primary cortical neurons were transfected with control siRNA or ATXN1 siRNA as described in the Methods and Materials. Cell lysates were subjected to RNA extraction and quantitative PCR analysis utilizing the corresponding human or mouse ATXN1 probe to detect ATXN1 mRNA levels. β-Actin was utilized as the internal control. ATXN1 mRNA levels from ATXN1 siRNA treatment were compared to the levels from control siRNA treatment. The data showed that ATXN1 siRNA treatment significantly decreased ATXN1 mRNA levels by 82.0% in naïve H4 cells (p<0.01) (
Because knock-down of ATXN1 had a trend to increase APP protein levels in H4-APP751 cells, the effect of ATXN1 down-regulation on altering APP turn-over rate was determined. H4-APP751 cells were transfected with ATXN1 siRNA or control siRNA for 42 h, and then treated with 40 μg/ml cycloheximide for a different time period (0 h, 3 h, or 6 h). Cells were harvested and cell lysates were subjected to Western blotting analysis as described in Methods and Materials. The data showed that there existed no significant differences in the protein levels of full length APP at the times of 3 h and 6 h of cycloheximide treatment (p>0.05 versus controls at corresponding time point (
To assess the mechanism through which ATXN1 affects BACE1 activity, the endogenous BACE1 mRNA and protein levels were determined under the treatment of ATXN1 knock-down. Stable H4-APP751 cells or naïve H4 cells were transfected with the ATXN1 siRNA and control siRNA using the Amaxa nucleofector and harvested 48 h post transfection, followed by either quantitative PCR or Western blotting analysis. The ATXN1 (76-3) antibody was used to detect the ATXN1 protein.
Mounting evidence has shown that extended polyglutamine mutant ATXN1 is associated with the disease SCA1, however, little is known about its endogenous functions. Matilla and colleagues have performed a study focused on assessing whether loss-of-function of ATXN1 affects the pathophysiology of SCA1[21]. Notably, mice homozygous and heterozygous for ATXN1 (or Sca1 in the ref. 21) null mutation were viable and fertile (consistent with the in vitro experiment in Example 6 that ATXN1 knock-down does not reveal cytotoxicity), and they did not display any signs of ataxia or loss of cerebellar Purkinje cells. Further, Matilla et al. discussed that ATXN1 was important in learning tasks mediated by the hippocampus and the cerebellum. For example, these Sca1 null mice displayed neurobehavioral abnormalities and were severely impaired in the spatial version of the Morris water maze test, suggesting the presence of motor learning deficits. Additionally, paired-pulse facilitation (PPF) was significantly decreased in Sca1 null mice of both homozygous and heterozygous genetic backgrounds, though they revealed normal long-term potentiation (LTP) and post-tetanic potentiation (PTP) analyses in area CA1 of the hippocampus compared to control mice.
Examples 3-10 present an in vitro functional study of ATXN1 in Aβ formation and indicate that ATXN1 loss-of-function potentiates APP processing and increases Aβ levels. Additionally, it has been recently suggested that alteration in Aβ levels may cause learning and neurobehavioral abnormalities [3, 22]. Therefore, the learning and memory loss in SCA1 null mice may be caused by elevated Aβ levels. The mechanism of ATXN1 loss-of-function in AD is different from its primary role in SCA1, which is primarily a gain-of-function caused by its extended polyglutamine tract [25].
We showed that ATXN1 is an important AD candidate gene, the function of which affects AD phenotype. The polymorphism identified in the GWAS is located in an intron region nearby the 5′ untranslated region. ATXN1 has been shown to undergo alternative splicing [10]. Defects of alternative splicing can alter protein functions, and are emerging as major contributors to AD and other neurodegenerative diseases [23, 24]. Accordingly, it is possible that the polymorphism in ATXN1 can affect the alternative splicing of ATXN1, which lead to a loss-of-function effect in ATXN1 protein. Without wishing to be bound by theory, the loss-of-function of ATXN1 can potentiate β-secretase processing of APP and increases Aβ levels, ultimately leading to AD. Accordingly, modulating ATXN1 levels by over-expression can be an effective AD therapeutic approach because ATXN1 cDNA over-expression leads to decreases in both Aβ40 and Aβ42 levels. Due to the complex network that exists between ATXN1 and its interacting partners [11, 18, 26], the ATXN1-mediated pathogenesis in AD and SCA1 is complex and can be affected by multiple other risk components, e.g. genetic and environmental factors.
Modulation of APP processing, e.g. maturation, trafficking, as well as shedding by its secretases plays important roles in AD pathogenesis and could be used in AD therapeutic strategies [15, 31-33]. It has been shown that cholesterol-lowering drug, named statins, can stimulate APP ectodomain shedding. There is as of yet no evidence suggesting that wild-type ATXN1 may directly affect protein trafficking. However, it has been discussed that over-expression of mutant ATXN1 with extended polyglutamine tracts in transgenic mice has been associated with altered membrane protein trafficking [34]. It is demonstrated herein that ATXN1 loss-of-function in vitro increases both Aβ40 and Aβ42 levels, but not the ratio of Aβ42:Aβ40, which is usually observed in mutations of familial AD γ-secretase components, e.g. PSEN1 and PSEN2[14, 35, 36]. This suggests that ATXN1 knock-down increases Aβ levels by a mechanism other than through γ-secretase, which is in agreement with the results presented herein that down-regulation of ATXN1 increases Aβ levels via potentiating β-secretase processing of APP. Although the underlying mechanism by which ATXN1 affects β-secretase cleavage of APP is not clear, the process can possibly be influenced by mediating BACE1 or APP trafficking in discreet subcellular locations, and thereby affecting their interaction and proteolytic activity [31].
Without wishing to be bdoung by a theory, we propose that the possible pathogenesis of ATXN1 loss-of-function can be not only limited to increasing Aβ levels, but also related with possibly potentiating the levels of N-APP, the further cleavage product of sAPPβ. A recent paper by Nikolaev et al. showed that N-APP, the 286 amino acid N-terminal fragment of APP, a proteolytic product of the O-secretase-derived secreted form of APP (sAPPβ), could bind the death receptor, DR6, and lead to neurodegeneration [7]. Accordingly, it is envisioned that ATXN1 loss-of-function increases sAPPβ levels, which can lead to an increase in N-APP level that ultimately bind to the DR6 receptor and cause neuronal death. It was sought to detect the N-APP protein in the ATXN1 and control siRNA treated samples described herein, but the existence of N-APP could be not confirmed, which was most probably due to low antibody specificity.
Collectively, we demonstrate that down-regulation of ATXN1 increases both Aβ40 and Aβ42 levels by potentiating β-secretase processing of APP. Without wishing to be bound by theory, ATXN1 can function as a significant risk modifier of late-onset AD by a mechanism of loss-of-function. Targeting ATXN1 provide, therefore, an important approach in developing AD therapeutics.
It is understood that the foregoing detailed description and examples are illustrative only and are not to be taken as limitations upon the scope of the invention. Various changes and modifications to the disclosed embodiments, which will be apparent to those of skill in the art, may be made without departing from the spirit and scope of the present invention. Further, all patents and other publications identified are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the present invention. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents.
This application claims benefit under 35 U.S.C. §119(e) of provisional application No. 61/256,128, filed on Oct. 29, 2009, the content of which is incorporated herein by reference in its entirety.
This invention was made with government support under Grant No. U24NS050606 awarded by the National Institute of Health (NIH). The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 61256128 | Oct 2009 | US |
