# Patent

## Title
Method of prognosing and diagnosing hereditary spastic paraplegia, mutant nucleic acid molecules and polypeptides

## Abstract

A method for diagnosing the presence of hereditary spastic paraplegia (HSP) or predicting the risk of developing HSP in a human subject, comprising detecting the presence or absence of a defect in a gene encoding a polypeptide comprising the sequence of FIG. 9 (SEQ ID NO: 19), in a nucleic acid sample of the subject, whereby the detection of the defect is indicative that the subject has or is at risk of developing HSP.

## Background
RELATED APPLICATIONS
This application is a divisional of U.S. application Ser. No. 11/983,957, filed Nov. 13, 2007 now U.S. Pat. No. 7,989,167, which claims the benefit of U.S. Provisional Application No. 60/858,354, filed on Nov. 13, 2006. The entire teachings of the above applications are incorporated herein by reference.


FIELD OF THE INVENTION
The present invention relates to method of prognosing and diagnosing hereditary spastic paraplegia, mutant nucleic acid molecules and polypeptides.
BACKGROUND OF THE INVENTION
Hereditary Spastic Paraplegia (HSP) has a worldwide prevalence between 1-18 in 100,0001-3 and is characterized by central motor system deficits leading to lower limb spastic paraperesis.4-6 This is due to a “dying back” phenomenon whereby upper motor neurons degenerate progressively, commencing with the longest axons.7,8 HSP can be classified into pure and complicated forms.6 In pure HSP, lower limb spasticity is the only major presenting symptom. Alternatively, in complicated HSP, this spasticity can be accompanied by other neurological or non-neurological symptoms such as ataxia, dementia, mental retardation, deafness, epilepsy, ichthyosis, retinopathy, ocular neuropathy and extrapyramidal disturbances.6,9 There is clinical heterogeneity within families, where age of onset and severity can differ markedly; between families that map to the same locus; and certainly between families which map to separate loci. This complicates genotype-phenotype correlations for HSP.
HSP is also extremely genetically heterogeneous. Eleven genes have been identified out of over 30 loci mapped (SPG1-33). This disease can be transmitted in a dominant (13 loci), a recessive (15 loci) or an X-linked manner (4 loci).9-11 By far the most common locus for the disease is SPG4, with mutations in the microtubule severing protein spastin accounting for  ̃40 percent of dominant HSP cases (MIM604277).12,13 
SPG8 is a pure form of hereditary spastic paraplegia with relatively little interfamilial variability in phenotype. SPG8 is considered to be one of the more aggressive subtypes of HSP with disease onset occurring for patients as early as their 20s or 30s. It was first identified in a Caucasian family as a 6.2 cM region between the markers D8S1804 and D8S1774.14 The family contained 15 patients affected with spasticity, hyperreflexia, extensor plantar reflexes, lower limb weakness, decreased vibration sensation and limited muscle wasting. The candidate region was further reduced to 3.4 cM due to a lower recombinant in a second family, narrowing the interval between markers D8S1804 and D8S1179.15 This family as well as a third Brazilian family linked to SPG8 also presented with pure adult onset HSP.16 For two of the families, a muscle biopsy was performed;14,16 however, no gross histological or histochemical abnormalities were observed. Ragged red fibers have been observed in muscle biopsies of HSP patients with paraplegin mutations.17 These three families thus present with relatively severe, pure spastic paraplegia.
HSP is one of the most genetically heterogeneous diseases, caused by mutations in at least 31 different genes. This means that >0.1% of genes in the human genome can be mutated resulting in one predominant neurological outcome: the degeneration of upper motor neuron axons. This heterogeneity may in part explain why it was originally difficult to identify the eighth HSP locus, SPG8 leading to an expansion of the candidate interval. The eighth HSP locus, SPG8, is on chromosome 8p24.13. It is possible that two spastic paraplegia genes exist on chromosome 8q23-24, and the overlap of linkage results from both loci yielded a region between the two causative genes. This is similar to the SPG33 gene ZFVE27 which is in close proximity to the SPG9 (MIM 601162) and SPG27 (MIM609041) loci.25 Alternatively, one originally reported family may have had a false positive linkage result to chromosome 8.
The present description refers to a number of documents, the content of which is herein incorporated by reference in their entirety.
SUMMARY OF THE INVENTION
More specifically, in accordance with the present invention, there is provided a method for diagnosing the presence of hereditary spastic paraplegia (HSP) or predicting the risk of developing HSP in a human subject, comprising detecting the presence or absence of a defect in a gene encoding a polypeptide comprising the sequence of FIG. 9 (SEQ ID NO: 19), in a nucleic acid sample of the subject, whereby the detection of the defect is indicative that the subject has or is at risk of developing HSP.
In a specific embodiment of the method, said sample comprises DNA. In another specific embodiment, said sample comprises RNA. In another specific embodiment, the defect is a missense or spice site mutation.
In another specific embodiment, the defect comprises a mutation in the gene resulting in a mutant polypeptide in which at least one amino acid residue of FIG. 9 (SEQ ID NO: 19) is substituted with another amino acid residue, and wherein the at least one amino acid residue is selected from the group consisting of an asparagine residue at position 471, a leucine residue at position 619 and a valine residue at position 626. In another specific embodiment, the defect comprises a mutation in the gene resulting in a mutant polypeptide in which amino acid residue 471 of FIG. 9 (SEQ ID NO: 19) is substituted with an aspartate residue, or in which amino acid residue 619 of FIG. 9 (SEQ ID NO: 19) is substituted with a phenylalanine residue or in which amino acid residue 626 of FIG. 9 (SEQ ID NO: 19) is substituted with a phenylalanine residue.
In another specific embodiment, the defect comprises a mutation in the gene, wherein the gene is as set forth in FIG. 8 (SEQ ID NO: 18), the mutation being selected from the group consisting of a substitution of a guanine at position 2205 with another nucleotide, a substitution of a guanine at position 2186 with another nucleotide, and a substitution of an adenine at position 1740 with another nucleotide. In another specific embodiment, the defect comprises a mutation in the gene, wherein the gene is as set forth in FIG. 8 (SEQ ID NO: 18), the mutation being selected from the group consisting of a substitution of a guanine at position 2205 with a thymine, a substitution of a guanine at position 2186 with a cytosine, and a substitution of an adenine at position 1740 with a guanine.
In accordance with another aspect of the present invention, there is provided a method comprising the steps of: a) analyzing a nucleic acid test sample containing the gene; b) comparing the results of said analysis of said sample of step a) with the results of an analysis of a control nucleic acid sample containing a wildtype strumpellin gene, wherein the wildtype strumpellin gene encodes a polypeptide comprising the sequence of FIG. 9 (SEQ ID NO: 19); and c) determining the presence or absence of at least one defect in the strumpellin gene of the test sample.
In another specific embodiment of the method, the nucleic acid sample is amplified prior to analysis. In another specific embodiment, the defect is a mutation in the coding region of the strumpellin gene. In another specific embodiment, the mutation is a missense or splice site mutation.
In another specific embodiment, the defect comprises a mutation in the gene resulting in a mutant polypeptide in which at least one amino acid residue of FIG. 9 (SEQ ID NO: 19) is substituted with another amino acid residue, and wherein the at least one amino acid residue is selected from the group consisting of an asparagine residue at position 471, a leucine residue at position 619 and a valine residue at position 626. In another specific embodiment, the defect comprises a mutation in the gene resulting in a mutant polypeptide in which amino acid residue 471 of FIG. 9 (SEQ ID NO: 19) is substituted with an aspartate residue, or in which amino acid residue 619 of FIG. 9 (SEQ ID NO: 19) is substituted with a phenylalanine residue or in which amino acid residue 626 of FIG. 9 (SEQ ID NO: 19) is substituted with a phenylalanine residue. In another specific embodiment, the defect comprises a mutation in the gene, the gene being as set forth in FIG. 8 (SEQ ID NO: 18), the mutation being selected from the group consisting of a substitution of a guanine at position 2205 with another nucleotide, a substitution of a guanine at position 2186 with another nucleotide, and a substitution of an adenine at position 1740 with another nucleotide. In another specific embodiment, the defect comprises a mutation in the gene, the gene being as set forth in FIG. 8 (SEQ ID NO: 18), the mutation being selected from the group consisting of a substitution of a guanine at position 2205 with a thymine, a substitution of a guanine at position 2186 with a cytosine, and a substitution of an adenine at position 1740 with a guanine.
In another specific embodiment, the analysis is selected from the group consisting of: sequence analysis; fragment polymorphism assays; hybridization assays and computer based data analysis.
In accordance with another aspect of the present invention, there is provided a method of detecting the presence or absence of a mutation in a strumpellin gene, said method comprising the steps of: a) analyzing a nucleic acid test sample containing the gene; b) comparing the results of said analysis of said sample of step a) with the results of an analysis of a control nucleic acid sample containing a wildtype strumpellin gene, wherein the wildtype strumpellin gene comprises the sequence of FIG. 8 (SEQ ID NO: 18); and c) determining the presence or absence of at least one defect in the strumpellin gene of the test sample.
In a specific embodiment, the nucleic acid sample is amplified prior to analysis.
In another specific embodiment, the mutation comprises a mutation in the gene, the mutation being selected from the group consisting of a substitution of a guanine at position 2205 with another nucleotide, a substitution of a guanine at position 2186 with another nucleotide, and a substitution of an adenine at position 1740 with another nucleotide. In another specific embodiment, the mutation comprises a mutation in the gene, the mutation being selected from the group consisting of a substitution of a guanine at position 2205 with a thymine, a substitution of a guanine at position 2186 with a cytosine, and a substitution of an adenine at position 1740 with a guanine.
In accordance with another aspect of the present invention, there is provided a method of selecting a compound, said method comprising: (a) contacting a test compound with at least one biological system displaying a defect in a gene encoding a polypeptide, the polypeptide comprising the sequence of FIG. 9 (SEQ ID NO: 19), wherein the test compound is selected if the polypeptide function, expression or conformation is modified in the presence of the test compound as compared to that in the absence thereof.
In accordance with another aspect of the present invention, there is provided a purified polypeptide comprising a sequence selected from the group consisting of the sequence in FIG. 11 (SEQ ID NO: 21), in FIG. 13 (SEQ ID NO: 23), and in FIG. 15 (SEQ ID NO: 25).
In accordance with another aspect of the present invention, there is provided a purified antibody that binds specifically to the polypeptide of the present invention.
In accordance with another aspect of the present invention, there is provided a method of determining whether a biological sample contains the polypeptide of the present invention, comprising contacting the sample with a purified ligand that specifically binds to the polypeptide, and determining whether the ligand specifically binds to the sample, the binding being an indication that the sample contains the polypeptide.
In a specific embodiment, the ligand is a purified antibody.
In accordance with another aspect of the present invention, there is provided an isolated nucleic acid molecule of no more than 300 nucleotides comprising (a) a sequence of at least 19 contiguous nucleotides of the sequence of FIG. 10 (SEQ ID NO: 20), comprising the nucleotide at position 1740 of FIG. 10; (b) a sequence of at least 19 contiguous nucleotides of the sequence of FIG. 12 (SEQ ID NO: 22), comprising the nucleotide at position 2186 of FIG. 12; (c) a sequence of at least 19 contiguous nucleotides of the sequence of FIG. 14 (SEQ ID NO: 24), comprising the nucleotide at position 2205 of FIG. 14; (d) the complement of the sequence in (a), (b) or (c); or (e) a sequence of at least 19 contiguous nucleotides hybridizable under high stringency conditions to the sequence in (a), (b), (c) or (d).
In accordance with another aspect of the present invention, there is provided a vector comprising the nucleic acid molecule of the present invention. In accordance with another aspect of the present invention, there is provided a recombinant host cell comprising the vector of the present invention.
In accordance with another aspect of the present invention, there is provided an array of nucleic acid molecules attached to a solid support, the array comprising an oligonucleotide hybridizable to one of the nucleic acid molecules of the present invention.
In accordance with another aspect of the present invention, there is provided an isolated nucleic acid molecule comprising the sequence of (a) FIG. 10 (SEQ ID NO: 20); (b) FIG. 12 (SEQ ID NO: 22); (c) FIG. 14 (SEQ ID NO: 24); or (d) the complement of the sequence in (a), (b) or (c). In accordance with another aspect of the present invention, there is provided a vector comprising the nucleic acid molecule of the present invention. In accordance with another aspect of the present invention, there is provided a recombinant host cell comprising the vector of the present invention.
In accordance with another aspect of the present invention, there is provided an isolated nucleic acid molecule encoding a polypeptide comprising the amino acid sequence of (a) FIG. 11 (SEQ ID NO: 21); (b) FIG. 13 (SEQ ID NO: 23); (c) FIG. 15 (SEQ ID NO: 25); or (d) the complement of the sequence in (a), (b) or (c). In accordance with another aspect of the present invention, there is provided a vector comprising the nucleic acid molecule of the present invention. In accordance with another aspect of the present invention, there is provided a recombinant host cell comprising the vector of the present invention.
In specific embodiments of the methods of the present invention, the subject is pre-diagnosed as being a likely candidate for developing HSP.
In accordance with another aspect of the present invention, there is provided a purified polypeptide consisting of a sequence selected from the group consisting of the sequence in FIG. 11 (SEQ ID NO: 21), in FIG. 13 (SEQ ID NO: 23), and in FIG. 15 (SEQ ID NO: 25).
In accordance with another aspect of the present invention, there is provided a method of stratifying a subject having hereditary spastic paraplegia (HSP) comprising: detecting a defect in a strumpellin protein activity and/or in a nucleic acid encoding the protein in a biological sample; whereby the results of the detecting step enables the stratification of the subject having HSP as belonging to a HSP subclass.
Other objects, advantages and features of the present invention will become more apparent upon reading of the following non-restrictive description of specific embodiments thereof, given by way of example only with reference to the accompanying drawings.



BRIEF DESCRIPTION OF THE DRAWINGS
The application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee.
FIG. 1 are pedigrees for families with KIAA0196 mutations. A) Family FSP24, B) Family FSP29, C) Family FSP34, D) Family FSP91. Blackened boxes represent affected individuals, and a diagonal line through the symbol means the individual is deceased. A vertical black bar indicates an individual with an unconfirmed phenotype. Sex of each individual has been masked to preserve confidentiality. Individuals marked “P” represent proximal recombinants and “D” is the distal recombinant. A star indicates that DNA and clinical information have been collected for the particular individual. The age of onset of affected individuals is listed below each symbol, although this information is not available for each patient. All collected affected patients are heterozygous for a c. 2205C→T mutation (pedigrees A, B and C) or a c.A1740G mutation (pedigree D) in KIAA0196 (NCBI accession #NM—014846.3);
FIG. 2 is a region spanning the SPG8 locus. A) Markers defining the borders of each described SPG8 family and their scaled position on chromosome 8q24.13. B) Candidate region used to search for the SPG8-located gene between markers D8S1804 and D8S1774. Genes in the region are shown in their observed orientation. C) The 28-exon KIAA0196 gene drawn to scale with the location of 3 mutations in exons 11, 14 and 15 highlighted;
FIG. 3 presents a mutation analysis of the KIAA0196 gene. A-C) Sequence trace of an HSP patient above the sequence trace of a control individual. Exon 15 (A), 14 (B) and 11 (C) heterozygous point mutations are indicated. D) Multiple sequence alignment for strumpellin homologues surrounding the two coding changes (boxed) (human (SEQ ID NO: 7); orangutan (SEQ ID NO: 8); rat (SEQ ID NO: 9); mouse (SEQ ID NO: 10); dog (SEQ ID NO: 11); chicken (SEQ ID NO: 12); zebrafish (SEQ ID NO: 13); fruit fly (SEQ ID NO: 14); C. elegans (SEQ ID NO: 15); frog (SEQ ID NO: 16); and amoeba (SEQ ID NO: 17). The ProbconsTM (v.1.09) program38 was used for cluster analysis. E) RT-PCR of multiple brain regions using a KIAA0196-specific probe. F) Northern blot of the KIAA0196 transcript using 30 ug of total RNA and a 1 kb C-terminal probe;
FIG. 4 presents a three-dimensional modelling of strumpellin using d1dn1b as a template using SwissProtTM database viewer. Two helices from the 1159aa protein are shown including amino acids 614-634 in one alpha helix and amino acids 662-672 from a nearby alpha helix in the antiparallel direction. A) Residues L619 and V626 are in the same orientation in an alpha helix opposite a second helix in an antiparallel direction. Only residue side-chains which are closest in physical space are shown. B) The L619F mutation adds a bulky phenylalanine side-group which likely exceeds the space available between the two alpha helices C) The V626F mutation. The epsilon carbon of the F626 aromatic ring also may force apart the two alpha-helices and impinges on Q666;
FIG. 5 shows the results of a zebrafish knockdown and rescue of KIAA0196 function. A) The gross morphological features of wildtype zebrafish are depicted at 3 days post fertilization (dpf). B) Injection of a 5 base-pair mismatch morpholino results in no obvious phenotype. C, D) The KIAAMO injected fish present with a severely curly tail (C) or with a slightly curly tail (D). Their heart cavities are also enlarged, which is commonly seen in injected fish. E, F) When the KIAAMO is injected along with normal human KIAA0196 mRNA, the fish partially develop the curly tail (F) or not at all (E) depending on the injected quantity G), H) The phenotype is not alleviated when the KIAAMO is injected with the mutant forms of the human mRNA. These fishes resemble the KIAAMO fish;
FIG. 6 presents an immunohistochemical analysis in zebrafish of the KIAA0196 knockdown phenotype. A) The motor neurons in the ventral roots of zebrafish are segmented and oriented at 3 dpf. The spinal cord consists of the cell bodies of motor neurons and interneuron bundles. The picture was taken near the gut of the fish. B) The mismatch control has a similar motor neuron distribution compared to the wildtype. C, E, F) Zebrafish injected with KIAAMO and fish co-injected with mutant mRNA have shorter, branching motor neurons which are not oriented. D) Wildtype co-injections partially rescue the motor neuron phenotype; the axons are longer and oriented;
FIG. 7 presents a western blot of the KIAA0196 protein. A) A western blot was prepared using whole cell lysates of HeLa cells transiently expressing the different pCS2-KIAA0196 vectors that incorporate a myc-tag (WT, x14 and x15). The PVDF membrane was immunodetected using an antibody (9E10, Invitrogen) directed against the protein myc-tag portion. The KIAA196 protein migrates to its predicted MW (about 134 kDa). The ctl lane corresponds to the untransfected cells. B) A polyclonal antibody was generated against amino acids 652-669 (VPTRLDKDKLRDYAQLGP (SEQ ID NO: 37)) of the KIAA0196 protein. This antibody was able to recognize the wildtype and L619F KIAA0196 protein sequence;
FIG. 8 is the human wildtype KIAA0196 nucleotide sequence (NM—014846.3) (SEQ ID NO: 18);
FIG. 9 is the human wildtype KIAA0196 amino acid sequence (NP—055661) (SEQ ID NO: 19);
FIG. 10 is the mutated human KIAA0196 N471D (c.1740a>g) nucleotide sequence (SEQ ID NO: 20);
FIG. 11 is the mutated human KIAA0196 N471D amino acid sequence (NP—055661) (SEQ ID NO: 21);
FIG. 12 is the mutated human KIAA0196 L619F (c.2186g>c) nucleotide sequence (SEQ ID NO: 22);
FIG. 13 is the mutated human KIAA0196 L619F amino acid sequence (NP—055661) (SEQ ID NO: 23);
FIG. 14 is the mutated human KIAA0196 V626F (c.2205g>t) nucleotide sequence (SEQ ID NO: 24);
FIG. 15 is the mutated human KIAA0196 V626F amino acid sequence (NP—055661) (SEQ ID NO: 25); and
FIG. 16 is a multi-species alignment of the human KIAA0196 (strumpellin) amino acid sequence with other species equivalents: Homo sapiens (Q12768) (SEQ ID NO: 26), Canis familiaris (XP—532327) (SEQ ID NO: 30), Pan troglodytes (XP—519952) (SEQ ID NO: 27), Drosophila melanogastar (CG12272) (SEQ ID NO: 33), Caenorhabditis elegans (CE13235) (SEQ ID NO: 35), Xenopus tropicalis (MGC89323) (SEQ ID NO: 32), Rattus norvegicus (XP—343250) (SEQ ID NO: 29); Danio rerio (BC045490) (SEQ ID NO: 34), Gallus gallus (XP 418441) (SEQ ID NO: 31), Dictyostelium discoideum (EAL63144) (SEQ ID NO: 36), and Mus musculus (NP—705776.2) (SEQ ID NO: 28). The ruler above the alignment corresponds to the amino acid position of the human KIAA0196 protein (NP—055661).



DETAILED DESCRIPTION OF THE INVENTION
Encompassed by the present invention are methods of diagnosing SPG8-associated hereditary spastic paraplegia, or predicting the risk of HSP by detecting mutations associated with the SPG8 locus. The Applicants identified four families linked to the SPG8 locus. Genes were screened in an expanded candidate SPG8 locus defined by these four families along with the British and Brazilian family described previously.15,16 This led to the identification of three point mutations in the KIAA0196 gene encoding the strumpellin protein product in these six families. One mutation, V626F, segregated in four large North American families with European ancestry. An L619F mutation was found in the Brazilian family. The third mutation, N471D, was identified in a smaller family of European origin, and lies in a spectrin domain. None of these mutations were identified in 500 control individuals. Both the L619 and V626 residues are strictly conserved across species and likely have a notable effect on the structure of the protein product, strumpellin. Rescue studies with human mRNA injected in zebrafish treated with morpholino oligonucleotides to knockdown the endogenous protein showed that mutations at these two residues impaired the normal function of the KIAA0196 gene. Recovery of a normal strumpellin activity nevertheless resulted in recovering normal muscle function. To the Applicant knowledge, there is no other gene than the KIAA0196 gene involved in the SPGR-associated hereditary spastic paraplegia.
DEFINITIONS
As used herein the expressions “risk of developing HSP” or “likely candidate for developing HSP” include subjects suspected of having HSP or subjects of which a least one parent has HSP.
As used herein the terms “defect”, “alteration” or “variation” refers to a mutation or polymorphism in the KIAA0196 gene (also referred to herein as the strumpellin gene) that affects the function, expression (transcription or translation) or conformation of the protein (strumpellin) that it encodes. Mutations encompassed by the present invention can be any mutation the KIAA0196 gene that results in the disruption of the function, expression or conformation of the encoded protein, including the complete absence of expression of the encoded protein and can include, for example, missense and nonsense mutations, insertions and deletions. Without being so limited, mutations encompassed by the present invention may alter splicing the mRNA (splice site mutation) or cause a shift in the reading frame (frameshift). Without being so limited, modifications of the function of strumpellin can be observed with methods such as the zebrafish knockouts experiments presented in Example 6 below.
Also encompassed by the present invention are methods of detecting novel mutations of interest in the strumpellin gene that are associated with HSP. A mutation of interest is any mutation detected in a gene sample obtained from a human subject, having, or suspected of having, HSP. For example, the nucleic acid sequence of a strumpellin gene obtained from a human subject can be compared with the nucleic acid sequence of a wild type (control) strumpellin gene and differences in the nucleotide sequence determined. A difference in the nucleotide sequence of the gene from the human subject is indicative of a mutation associated with HSP. Modifications of a protein encoded by the “different” human gene can be analyzed by various methods, for example, in the zebra fish assay described herein, to evaluate expression or function of the encoded protein. Further, the familial history of HSP, or present symptoms of the human subject can be reviewed, and a determination of the association of the novel mutation with HSP can be made. Thus, additional mutations in the strumpellin gene can be associated with, and diagnostic of, HSP.
The articles “a,” “an” and “the” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article.
The term “including” and “comprising” are used herein to mean, and re used interchangeably with, the phrases “including but not limited to” and “comprising but not limited to”.
The terms “such as” are used herein to mean, and is used interchangeably with, the phrase “such as but not limited to”.
As used herein the term “subject” is meant to refer to any mammal including human, mouse, rat, dog, cat, pig, monkey, horse, etc. In a particular embodiment, it refers to a human.
As used herein the term a suitable “control nucleic acid sample” is meant to refer to a nucleic acid sample (RNA, DNA) that does not come from a subject known to suffer from HSP (control subject). For example, the control can be a wild type strumpellin gene which does not contain a variation in its nucleic acid sequence. Also, as used herein, a suitable control can be a fragment or portion of the wilt type gene that does not include the defect/variation that is the mutation of interest (that is, the mutation to be detected in an assay).
As used herein the terms “subject nucleic acid sample” are meant to refer to any biological sample from the subject from whom nucleic acid sample (RNA, DNA) can be extracted, namely any subject tissue or cell type including saliva and blood.
The present invention also relates to methods for the determination of the level of expression of transcripts or translation product of a single gene such as KIAA0196. The present invention therefore encompasses any known method for such determination including real time PCR and competitive PCR, Northern blots, nuclease protection, plaque hybridization and slot blots. For example, assays commonly used to analyze nucleic acid polymorphisms can include sequencing all, or a portion of, the nucleic acid to detect a variation in the nucleotide sequence. Such assays can include fragment polymorphism analysis, nucleic acid hybridization assays and computerized nucleotide or amino acid sequence comparisons
The present invention also concerns isolated nucleic acid molecules including probes. In specific embodiments, the isolated nucleic acid molecules have no more than 300, or no more than 200, or no more than 100, or no more than 90, or no more than 80, or no more than 70, or no more than 60, or no more than 50, or no more than 40 or no more than 30 nucleotides. In specific embodiments, the isolated nucleic acid molecules have at least 20, or at least 30, or at least 40 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 20 and no more than 300 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 20 and no more than 200 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 20 and no more than 100 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 20 and no more than 90 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 20 and no more than 80 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 20 and no more than 70 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 20 and no more than 60 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 20 and no more than 50 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 20 and no more than 40 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 20 and no more than 30 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 30 and no more than 300 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 30 and no more than 200 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 30 and no more than 100 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 30 and no more than 90 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 30 and no more than 80 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 30 and no more than 70 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 30 and no more than 60 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 30 and no more than 50 nucleotides. In other specific embodiments, the isolated nucleic acid molecules have at least 30 and no more than 40 nucleotides.
Probes of the invention can be utilized with naturally occurring sugar-phosphate backbones as well as modified backbones including phosphorothioates, dithionates, alkyl phosphonates and α-nucleotides and the like. Modified sugar-phosphate backbones are generally known. Probes of the invention can be constructed of either ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), and preferably of DNA.
The types of detection methods in which probes can be used include Southern blots (DNA detection), dot or slot blots (DNA, RNA), and Northern blots (RNA detection). Although less preferred, labeled proteins could also be used to detect a particular nucleic acid sequence to which it binds. Other detection methods include kits containing probes on a dipstick setup and the like.
As used herein the terms “detectably labeled” refer to a marking of a probe in accordance with the presence invention that will allow the detection of the mutation of the present invention. Although the present invention is not specifically dependent on the use of a label for the detection of a particular nucleic acid sequence, such a label might be beneficial, by increasing the sensitivity of the detection. Furthermore, it enables automation. Probes can be labeled according to numerous well known methods. Non-limiting examples of labels include 3H, 14C, 32P, and 35S, Non-limiting examples of detectable markers include ligands, fluorophores, chemiluminescent agents, enzymes, and antibodies. Other detectable markers for use with probes, which can enable an increase in sensitivity of the method of the invention, include biotin and radionucleotides. It will become evident to the person of ordinary skill that the choice of a particular label dictates the manner in which it is bound to the probe.
As commonly known, radioactive nucleotides can be incorporated into probes of the invention by several methods. Non-limiting examples thereof include kinasing the 5′ ends of the probes using gamma 32P ATP and polynucleotide kinase, using the Klenow fragment of Pol I of E. coli in the presence of radioactive dNTP (e.g. uniformly labeled DNA probe using random oligonucleotide primers in low-melt gels), using the SP6/T7 system to transcribe a DNA segment in the presence of one or more radioactive NTP, and the like.
The present invention also relates to methods of selecting compounds. As used herein the term “compound” is meant to encompass natural, synthetic or semi-synthetic compounds, including without being so limited chemicals, macromolecules, cell or tissue extracts (from plants or animals), nucleic acid molecules, peptides, antibodies and proteins.
The present invention also relates to arrays. As used herein, an “array” is an intentionally created collection of molecules which can be prepared either synthetically or biosynthetically. The molecules in the array can be identical or different from each other. The array can assume a variety of formats, e.g., libraries of soluble molecules; libraries of compounds tethered to resin beads, silica chips, or other solid supports.
As used herein “array of nucleic acid molecules” is an intentionally created collection of nucleic acids which can be prepared either synthetically or biosynthetically in a variety of different formats (e.g., libraries of soluble molecules; and libraries of oligonucleotides tethered to resin beads, silica chips, or other solid supports). Additionally, the term “array” is meant to include those libraries of nucleic acids which can be prepared by spotting nucleic acids of essentially any length (e.g., from 1 to about 1000 nucleotide monomers in length) onto a substrate. The term “nucleic acid” as used herein refers to a polymeric form of nucleotides of any length, either ribonucleotides, deoxyribonucleotides or peptide nucleic acids (PNAs), that comprise purine and pyrimidine bases, or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. The backbone of the polynucleotide can comprise sugars and phosphate groups, as may typically be found in RNA or DNA, or modified or substituted sugar or phosphate groups. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. The sequence of nucleotides may be interrupted by non-nucleotide components. Thus the terms nucleoside, nucleotide, deoxynucleoside and deoxynucleotide generally include analogs such as those described herein. These analogs are those molecules having some structural features in common with a naturally occurring nucleoside or nucleotide such that when incorporated into a nucleic acid or oligonucleotide sequence, they allow hybridization with a naturally occurring nucleic acid sequence in solution. Typically, these analogs are derived from naturally occurring nucleosides and nucleotides by replacing and/or modifying the base, the ribose or the phosphodiester moiety. The changes can be tailor made to stabilize or destabilize hybrid formation or enhance the specificity of hybridization with a complementary nucleic acid sequence as desired.
As used herein “solid support”, “support”, and “substrate” are used interchangeably and refer to a material or group of materials having a rigid or semi-rigid surface or surfaces. In many embodiments, at least one surface of the solid support will be substantially flat, although in some embodiments it may be desirable to physically separate synthesis regions for different compounds with, for example, wells, raised regions, pins, etched trenches, or the like. According to other embodiments, the solid support(s) will take the form of beads, resins, gels, microspheres, or other geometric configurations.
Any known nucleic acid arrays can be used in accordance with the present invention. For instance, such arrays include those based on short or longer oligonucleotide probes as well as cDNAs or polymerase chain reaction (PCR) products. Other methods include serial analysis of gene expression (SAGE), differential display, as well as subtractive hybridization methods, differential screening (DS), RNA arbitrarily primer (RAP)-PCR, restriction endonucleolytic analysis of differentially expressed sequences (READS), amplified restriction fragment-length polymorphisms (AFLP).
“Stringent hybridization conditions” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as Southern and Northern hybridization are sequence dependent, and are different under different environmental parameters. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl, 1984; Tm 81.5° C.+16.6 (log M)+0.41 (% GC)−0.61 (% form)−500/L; where M is the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. Tm is reduced by about 1° C. for each 1% of mismatching; thus, Tm, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with >90% identity are sought, the Tm can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point I for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point I; moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point I; low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point I. Using the equation, hybridization and wash compositions, and desired T, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a T of less than 45° C. (aqueous solution) or 32° C. (formamide solution), it is preferred to increase the SSC concentration so that a higher temperature can be used. Generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point Tm for the specific sequence at a defined ionic strength and pH.
An example of highly stringent wash conditions is 0.15 M NaCl at 72° C. for about 15 minutes. An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see 64 for a description of SSC buffer). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example medium stringency wash for a duplex of, e.g., more than 100 nucleotides, is 1×SSC at 45° C. for 15 minutes. An example low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4-6×SSC at 40° C. for 15 minutes. For short probes (e.g., about 10 to 50 nucleotides), stringent conditions typically involve salt concentrations of less than about 1.5 M, more preferably about 0.01 to 1.0 M, Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is typically at least about 30° C. and at least about 60° C. for long robes (e.g., >50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. In general, a signal to noise ratio of 2× (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.
Very stringent conditions are selected to be equal to the Tm for a particular probe. An example of stringent conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or Northern blot is 50% formamide, e.g., hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C.
Washing with a solution containing tetramethylammonium chloride (TeMAC) could allow the detection of a single mismatch using oligonucleotide hybridyzation since such mismatch could generate a 10° C. difference in the annealing temperature. The formulation to determine the washing temperature is Tm (° C.)=]−682 (L−1)+97 where L represents the length of the oligonucleotide that will be used for the hybridization. In principle, a single mismatch will generate a 10° C. drop in the annealing so that a temperature of 57° C. should only detect mutants harbouring the T mutation.
The present invention relates to a kit for diagnosing HSP and/or predicting whether a subject is at risk of developing HSP comprising an isolated nucleic acid, a protein or a ligand such as an antibody in accordance with the present invention. For example, a compartmentalized kit in accordance with the present invention includes any kit in which reagents are contained in separate containers. Such containers include small glass containers, plastic containers or strips of plastic or paper. Such containers allow the efficient transfer of reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another. Such containers will include a container which will accept the subject sample (DNA genomic nucleic acid, cell sample or blood samples), a container which contains in some kits of the present invention, the probes used in the methods of the present invention, containers which contain enzymes, containers which contain wash reagents, and containers which contain the reagents used to detect the extension products. Kits of the present invention may also contain instructions to use these probes and or antibodies to diagnose HSP or predict whether a subject is at risk of developing HSP.
As used herein the terminology “biological sample” refers to any solid or liquid sample isolated from a subject. In a particular embodiment, it refers to any solid or liquid sample isolated from a human subject. Without being so limited it includes a biopsy material, blood, saliva, synovial fluid, urine, amniotic fluid and cerebrospinal fluid.
As used herein the terminology “biological system” is a cell, a tissue, an organ or an organism. Without being so limited, organisms include a zebrafish.
As used herein the terminology “blood sample” is meant to refer to blood, plasma or serum.
As used herein the term “purified” in the expression “purified polypeptide” means altered “by the hand of man” from its natural state (i.e. if it occurs in nature, it has been changed or removed from its original environment) or it has been synthesized in a non-natural environment (e.g., artificially synthesized). These terms do not require absolute purity (such as a homogeneous preparation) but instead represents an indication that it is relatively more pure than in the natural environment. For example, a protein/peptide naturally present in a living organism is not “purified”, but the same protein separated (about 90-95% pure at least) from the coexisting materials of its natural state is “purified” as this term is employed herein.
Similarly, as used herein, the term “purified” in the expression “purified antibody” is simply meant to distinguish man-made antibody from an antibody that may naturally be produced by an animal against its own antigens. Hence, raw serum and hybridoma culture medium containing anti-strumpellin antibody are “purified antibodies” within the meaning of the present invention.
As used herein, the term “ligand” broadly refers to natural, synthetic or semi-synthetic molecules. The term “molecule” therefore denotes for example chemicals, macromolecules, cell or tissue extracts (from plants or animals) and the like. Non limiting examples of molecules include nucleic acid molecules, peptides, antibodies, carbohydrates and pharmaceutical agents. The ligand appropriate for the present invention can be selected and screened by a variety of means including random screening, rational selection and by rational design using for example protein or ligand modeling methods such as computer modeling. The terms “rationally selected” or “rationally designed” are meant to define compounds which have been chosen based on the configuration of interacting domains of the present invention. As will be understood by the person of ordinary skill, macromolecules having non-naturally occurring modifications are also within the scope of the term “ligand”. For example, peptidomimetics, well known in the pharmaceutical industry and generally referred to as peptide analogs can be generated by modeling as mentioned above.
Antibodies
As used herein, the term “anti-strumpellin antibody” or “immunologically specific anti-strumpellin antibody” refers to an antibody that specifically binds to (interacts with) a strumpellin protein and displays no substantial binding to other naturally occurring proteins other than the ones sharing the same antigenic determinants as the strumpellin protein. The term antibody or immunoglobulin is used in the broadest sense, and covers monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies, and antibody fragments so long as they exhibit the desired biological activity. Antibody fragments comprise a portion of a full length antibody, generally an antigen binding or variable region thereof. Examples of antibody fragments include Fab, Fab′, F(ab′)2, and Fv fragments, diabodies, linear antibodies, single-chain antibody molecules, single domain antibodies (e.g., from camelids), shark NAR single domain antibodies, and multispecific antibodies formed from antibody fragments. Antibody fragments can also refer to binding moieties comprising CDRs or antigen binding domains including, but not limited to, VH regions (VH, VH-VH), anticalins, PepBodiesTM, antibody-T-cell epitope fusions (Troybodies) or Peptibodies. Additionally, any secondary antibodies, either monoclonal or polyclonal, directed to the first antibodies would also be included within the scope of this invention.
In general, techniques for preparing antibodies (including monoclonal antibodies and hybridomas) and for detecting antigens using antibodies are well known in the art (Campbell, 1984, In “Monoclonal Antibody Technology: Laboratory Techniques in Biochemistry and Molecular Biology”, Elsevier Science Publisher, Amsterdam, The Netherlands) and in Harlow et al., 1988 (in: Antibody A Laboratory Manual, CSH Laboratories). The term antibody encompasses herein polyclonal, monoclonal antibodies and antibody variants such as single-chain antibodies, humanized antibodies, chimeric antibodies and immunologically active fragments of antibodies (e.g. Fab and Fab′ fragments) which inhibit or neutralize their respective interaction domains in Hyphen and/or are specific thereto.
Polyclonal antibodies are preferably raised in animals by multiple subcutaneous (sc), intravenous (iv) or intraperitoneal (ip) injections of the relevant antigen with or without an adjuvant. It may be useful to conjugate the relevant antigen to a protein that is immunogenic in the species to be immunized, e.g., keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, or soybean trypsin inhibitor using a bifunctional or derivatizing agent, for example, maleimidobenzoyl sulfosuccinimide ester (conjugation through cysteine residues), N-hydroxysuccinimide (through lysine residues), glutaraldehyde, succinic anhydride, SOCl2, or R1N═C═NR, where R and R1 are different alkyl groups.
Animals may be immunized against the antigen, immunogenic conjugates, or derivatives by combining the antigen or conjugate (e.g., 100 μg for rabbits or 5 μg for mice) with 3 volumes of Freund's complete adjuvant and injecting the solution intradermally at multiple sites. One month later the animals are boosted with the antigen or conjugate (e.g., with 1⁄5 to 1/10 of the original amount used to immunize) in Freund's complete adjuvant by subcutaneous injection at multiple sites. Seven to 14 days later the animals are bled and the serum is assayed for antibody titer. Animals are boosted until the titer plateaus. Preferably, for conjugate immunizations, the animal is boosted with the conjugate of the same antigen, but conjugated to a different protein and/or through a different cross-linking reagent. Conjugates also can be made in recombinant cell culture as protein fusions. Also, aggregating agents such as alum are suitably used to enhance the immune response.
Monoclonal antibodies may be made using the hybridoma method first described by Kohler et al., Nature, 256: 495 (1975), or may be made by recombinant DNA methods (e.g., U.S. Pat. No. 6,204,023). Monoclonal antibodies may also be made using the techniques described in U.S. Pat. Nos. 6,025,155 and 6,077,677 as well as U.S. Patent Application Publication Nos. 2002/0160970 and 2003/0083293 (see also, e.g., Lindenbaum et al., 2004).
In the hybridoma method, a mouse or other appropriate host animal, such as a rat, hamster or monkey, is immunized (e.g., as hereinabove described) to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the antigen used for immunization. Alternatively, lymphocytes may be immunized in vitro. Lymphocytes then are fused with myeloma cells using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (see, e.g., Goding 1986)).
The hybridoma cells thus prepared are seeded and grown in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells. For example, if the parental myeloma cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (HAT medium), which substances prevent the growth of HGPRT-deficient cells.
This invention will be described herein below, referring to specific embodiments and figures, the purpose of which is to illustrate the invention rather than to limit its scope.
EXAMPLE 1
Material and Methods
Subjects
Protocols were approved by the ethics committee of the Centre hospitalier de l'Université de Montreal (CHUM). Patients gave informed consent after which patient information and blood was collected. DNA was extracted from peripheral blood using standard protocols.
Genotyping and Locus Exclusion
PCR amplified fragments incorporating α-35S-dATP were resolved on 6% denaturing polyacrylamide gels. Alleles were run alongside an M13 mp18 sequence ladder and scored based on allele sizes and frequencies from the Fondation Jean Dausset CEPH database (http://www.cephb.fr/). LOD score calculations and multipoint analysis were performed using the MLINK program of the LINKMAP software package.18 
Mutation Screening
The 28 exons of KIAA0196 were screened by automated sequencing, including at least 50 bp of each intronic region. Primers were designed using the PrimerSelectTM program (Lasergene) and were synthesized by Invitrogen Canada Inc. Primer sequences and amplification conditions for each exon are listed in Table 1 below.







TABLE 1





Primers and conditions for KIAA0196
















KIAA0196x1F
GCCAAGAGTGTTAATCTAGCAAAGTC



(SEQ ID NO: 38)


 


KIAA0196x1R
TTCATGGTTCCCAGAGAAAACACG



(SEQ ID NO: 39)


 


KIAA0196x2F
TCTGCTTTAAGTTTGGGATGTCTA



(SEQ ID NO: 40)


 


KIAA0196x2R
TTAAGATGACCAGTGCCACAGGTA



(SEQ ID NO: 41)


 


KIAA0196x3F
AATATCAAACTGTGGCCCTAAATC



(SEQ ID NO: 42)


 


KIAA0196x3R
TACACCGAGGAGGCTCATAACTTC



(SEQ ID NO: 43)


 


KIAA0196x4F
CATCCCAGCCATCTGTCCTGATAC



(SEQ ID NO: 44)


 


KIAA0196x4R
ACATACACTGCATTTTACCGACAGC



(SEQ ID NO: 45)


 


KIAA0196x5F
AATGGAATTCTACTTTATTGGACT



(SEQ ID NO: 46)


 


KIAA0196x5R
CTCAAAAGGTTTTAAAAGGTTCTACC



(SEQ ID NO: 47)


 


KIAA0196x6F
TGGGCTTTGGAAAAACTGATGTGTCT



(SEQ ID NO: 48)


 


KIAA0196x6R
AAGTTTACCTAAGTGATGTTATGTCC



(SEQ ID NO: 49)


 


KIAA0196x7F
CAAAAAGCAACGTTAATAGGTGTAA



(SEQ ID NO: 50)


 


KIAA0196x7R
ATCATTGCATTAAATTATCTAAGTG



(SEQ ID NO: 51)


 


KIAA0196x8F
TTAATCACAGCCAGAACTAGGATGTAG



(SEQ ID NO: 52)


 


KIAA0196x8R
GACAGGGGAGAGCTTTTCAGGTATGCT



(SEQ ID NO: 53)


 


KIAA0196x9F
TGGCACTCCATGTCAGATTCAACTGT



(SEQ ID NO: 54)


 


KIAA0196x9R
ATGTCTATATTCCCCATTAGG



(SEQ ID NO: 55)


 


KIAA0196x10F
CAGGGTCAATGTTAATTTATAGTGTA



(SEQ ID NO: 56)


 


KIAA0196x10R
AGATGGAGGCCAACTGTGACTCTC



(SEQ ID NO: 57)


 


KIAA0196x11F
TGCTCCAGGCATTTTTGTCG



(SEQ ID NO: 58)


 


KIAA0196x11R
GAACAGACTGCTGGGTGGGTCATA



(SEQ ID NO: 59)


 


KIAA0196x12 and 13F
ATGAGCACCATAGAGTCCATTCAGG



(SEQ ID NO: 60)


 


KIAA0196x12 and 13R
ATTATGCTCTCGTGGAAAAACTGCTA



(SEQ ID NO: 61)


 


KIAA0196x14F
CTTTTTGAAACAAGAAACAGATATACC



(SEQ ID NO: 62)


 


KIAA0196x14R
GGCAAGTAAAAACATCTGTACATCCAC



(SEQ ID NO: 63)


 


KIAA0196x15F
TTTGCAGCATTTTTAGAAGGATTAGC



(SEQ ID NO: 64)


 


KIAA0196x15R
TTCCCCTGAGAATACTGAGGCGAACA



(SEQ ID NO: 65)


 


KIAA0196x16F
GGAGGCCAGGGAAGGGGAGGTTACC



(SEQ ID NO: 66)


 


KIAA0196x16R
GGAATGTCAAACAGCCAGATGATGT



(SEQ ID NO: 67)


 


KIAA0196x17F
ACTTTGCTGAAATAAACAGAGTCC



(SEQ ID NO: 68)


 


KIAA0196x17R
GTAAGGTCTTGTTCGCGATAGGTT



(SEQ ID NO: 69)


 


KIAA0196x18F
AGAACGAATAGTTGACAATCTACTC



(SEQ ID NO: 70)


 


KIAA0196x18R
TGAGGTTTGGGATGTGTACTCTAA



(SEQ ID NO: 71)


 


KIAA0196x19F
AATTATATGGAAAAGGGATAACTAGGT



(SEQ ID NO: 72)


 


KIAA0196x19R
TAAAGGGTCAGAATATGAGTTGACAAG



(SEQ ID NO: 73)


 


KIAA0196x20F
TTGGTGCCGCATGTCCTGTTGAGTC



(SEQ ID NO: 74)


 


KIAA0196x20R
AAGTCTTATCTTCCCAAGTTGAAAC



(SEQ ID NO: 75)


 


KIAA0196x21 and 22F
CCCAGCCTCTGTTCTGCATAGCAT



(SEQ ID NO: 76)


 


KIAA0196x21 and 22R
AAGAACAGATCCAGAAACGGAGAT



(SEQ ID NO: 77)


 


KIAA0196x23F
AAGGCCCAGTGAAGAATTGTCATC



(SEQ ID NO: 78)


 


KIAA0196x23R
CTGAAGAAACTGGGGTGCGTAGAT



(SEQ ID NO: 79)


 


KIAA0196x24F
CTGAGGCTTGAAAAGATTACATCAC



(SEQ ID NO: 80)


 


KIAA0196x24R
CTTCCCCTTTGTCATGAGCTTTCAC



(SEQ ID NO: 81)


 


KIAA0196x25F
TCCCACACTCCCCCTATATTCACCTC



(SEQ ID NO: 82)


 


KIAA0196x25R
AGAAAAGATCTCATATCCGACATAGG



(SEQ ID NO: 83)


 


KIAA0196x26F
GACCCCTGGAATGCCCTACCAATC



(SEQ ID NO: 84)


 


KIAA0196x26R
CTGGCAGGGTGACTAAGGATGGAC



(SEQ ID NO: 85)


 


KIAA0196x27F
GATAGATAGCAGGGATCGTGTTGT



(SEQ ID NO: 86)


 


KIAA0196x27R
AGGCATCTACTGTGAACGACCTAT



(SEQ ID NO: 87)


 


KIAA0196x28F
AAAGGGGCTGTTTCAAGGAGTCG



(SEQ ID NO: 88)


 


KIAA0196x28R
AGTTTTTGAATCATAAGCGAGACG



(SEQ ID NO: 89)









PCR was performed using 50 ng DNA, 20 pmol of each primer, 10× buffer, 0.25 nM dNTPs and 0.15 ul of Taq (Qiagen). Initial denaturation for 5 minutes at 94° C. was followed by 30 cycles of 30 seconds denaturation at 94° C., 30 seconds annealing at 55° C. (for all exons except for exons 15 and 26), and 45 seconds elongation at 72° C. A final extension at 72° C. was performed for 7 minutes. For exon 15, a 50° C. annealing temperature was used, and for exon 26, 10 cycles of a touchdown reaction were performed from 68° C.-63° C., followed by 25 cycles at 63° C.
Variants were first tested in 12 controls by sequencing, followed by allele-specific oligomerization (ASO).19,20 Briefly, 4 μl of PCR product was hybridized onto Hybond-N+TM Nylon membranes (Amersham Biosciences) using a dot blot apparatus. P-32-labelled probes specific to the mutation or normal sequence were hybridized then visualized on autoradiographic film after overnight exposure. ASO primers for exon 11 are 5′-ACTAGAAAACCTTCAAGCT-3′ (SEQ ID NO: 90) (normal) and 5′-ACTAGAAGACCTTCAAGCT-3′ (SEQ ID NO: 91) (mutated). For exon 14, ASO primers of 5′-GGAGAGTTGGTATC-3′ (SEQ ID NO: 92) (normal) and 5′-GGAGAGTTCGTATC-3′ (SEQ ID NO: 93) (mutated) were used. Exon 15 ASO primers were 5′-CACTGAAGGTTTTG-3′ (SEQ ID NO: 94) (normal) and 5′-CACTGAAGTTTTTG-3′ (SEQ ID NO: 95) (mutated).
Protein Sequence Alignment
Cluster analysis was performed using the ProbconsTM v. 1.09 program. Proteins from aligned species included Homo sapiens (Q12768) (SEQ ID NO: 26), Canis familiaris (XP 532327) (SEQ ID NO: 30), Pan troglodytes (XP—519952) (SEQ ID NO: 27), Drosophila melanogastar (CG12272) (SEQ ID NO: 33), Caenorhabditis elegans (CE13235) (SEQ ID NO: 35), Xenopus tropicalis (MGC89323) (SEQ ID NO: 32), Rattus norvegicus (XP—343250) (SEQ ID NO: 29); Danio rerio (BC045490) (SEQ ID NO: 34), Gallus gallus (XP—418441) (SEQ ID NO: 31), Dictyostelium discoideum (EAL63144) (SEQ ID NO: 36), and Mus musculus (NP 705776.2) (SEQ ID NO: 28) (See FIG. 16 for alignment).
Homology Modeling
The size of the strumpellin protein (1159aa) made it prohibitive to obtain a template for the entire protein. Instead, 200 amino acids around the two mutations were selected (aa 501-725) and inputted in the PhyreTM program version 2.039. The template with the highest score was selected, namely 1dn1b from the Neuronal-Sec1 Syntaxin 1a complex. The SwissProtTM database viewer version 3.721 was used to visualize the model concentrating on the alpha helix in which the two mutations lie and on a second alpha helix nearby in 3D space (See FIG. 5). Peptides incorporating one or the other identified point mutation were visualized in the same manner.
Expression Studies
Northern Blot and RT-PCR Analysis
The KIAA0196 cDNA pBluescriptTM clone was kindly provided by the Kazusa DNA Research Institute. A 1 kb probe specific to the c-terminal region of strumpellin was generated by digesting the KIAA0196-pBluescriptTM vector with XhoI and NotI. 30 ug of total RNA per sample was loaded. RNA was extracted from various regions of the brain of a control individual. A reverse-transcriptase reaction was performed using MMLV-RT (Invitrogen). Primers in exons 10 (Forward) and 15 (Reverse) of KIAA0196 were used as described in Table 1 above. GAPD cDNA was amplified as a control.
Constructs
Each mutation was introduced into the KIAA0196 pBluescriptTM clone by site-directed mutagenesis using the primers 5′-CTGGAGAGTTCGTATCCTATGTG-3′ (SEQ ID NO: 96) for the exon 14 variant and 5′-CCTATGTGAGAAAATTTTTGCAGATC-3′ (SEQ ID NO: 97) for the exon 15 variant, along with primers of their complementary sequence. Wildtype and mutant KIAA0196 cDNAs were cloned, upstream of a Myc and His tags, into a pCS2 vector and transcribed in vitro using the SP6 mMESSAGE mMachineTM kit (Ambion) for zebrafish studies. The protein expression from each these constructs was validated following their transient expression in cell culture (HeLa) and subsequent western blot analysis with an anti-Myc antibody. A band at the appropriate height ( ̃134 kDa for KIAA0196) was observed (See FIG. 7).
Zebrafish Knockdown Studies
Morpholino Injections
Wildtype zebrafish were raised and mated as previously described.22 
Antisense morpholinos (AMO) were designed and purchased from Genetools LLC (Philomath, Oreg.). The morpholino sequences were designed against the zebrafish strumpellin ortholog, BC045490. The oligonucleotide, CTCTGCCAGAAAATCAC[CAT]GATG (SEQ ID NO: 98) (KIAA MO) binds to the ATG of the KIAA0196 gene preventing its translation and CTCTcCCAcAAAATgAg[CAT]cATG (SEQ ID NO: 99) (CTL MO) is a five base pair mismatch control. AMO injections were performed as previously described at a concentration of 0.8 mM.23 The rescue injections were performed as mentioned above with a morpholino and mRNA concentration of 0.8 mM and 50 ng/ul respectively.
Immunohistochemistry
Standard protocols were used for immunohistochemistry.22 Briefly, three day old embryos were fixed in 4% paraformaldehyde, washed, and blocked at room temperature. Primary antibodies [anti acetylated tubulin, 1:50 (Sigma)] were added overnight. After extensive washing, the embryos were incubated with the fluorescently labelled secondary antibody Alexa 568 (Molecular Probes). Imaging was performed on an UltraViewTM LCI confocal microscope (Perkin Elmer) using MethamorphTM Imaging software (Universal Imaging Corporation). The statistical significance between the different conditions was calculated using a chi square test.
Clinical Information and Family Details
The SPG8 family FSP24 is from the province of British Columbia, Canada. It is composed of 13 members affected with a spastic gait and lower limb stiffness, 10 of which have been collected (See FIG. 1a). Symptoms were first observed in individuals between the ages of 35 and 53. Intrafamilial phenotypic heterogeneity exists as noted by the symptoms presented and the range in disease severity in patients. Deep tendon reflexes were brisk or increased, and decreased vibration sensation was also noted in three patients. Occasional bladder control problems were also observed. Walking aids were required for some individuals while one is confined to a wheelchair. Together, these features are consistent with a pure, uncomplicated HSP similar to that described for other families linked to the SPG8 locus. Family FSP29 is of European descent residing in the United States. There are 31 affected individuals in the family, and 10 have been collected (See FIG. 1b). Age of onset was quite variable with symptom onset ranging in patients from their twenties to their sixties. The family was negative for mutations in the spastin gene.
EXAMPLE 2
Linkage Analysis
In FSP24, seven markers spanning the candidate region from markers D8S586 to D8S1128 were genotyped in the 10 affected individuals collected (FIG. 1a). The genotyping and locus exclusion were performed as described in Example 1. A disease haplotype segregated with the disease in all 10 affected individuals (See Table 2 below). A recombination event occurred in one individual (FIG. 1a) between markers D8S586 and D8S1804 defining the proximal border of the locus in this family. No lower recombinant was identified nor searched for since the haplotype extended beyond the limits of the SPG8 locus. The maximum LOD score for this family was 3.43 at θ=0 using CEPH allele frequencies for the marker D8S1804, along with a maximum multipoint of 4.20 at marker D8S1799.







TABLE 2







Haplotype comparison between SPG8 linked families











Marker
Position (Mb)
FSP24
FSP29
FSP34





D8S586
121.2
1
11 
11 


D8S1804
124.8
5
3
3


D8S1832
125.4
2
2
NT


D8S1179
125.9
3
9
9


KIAA0196
126.1
L619F
L619F
L619F


rs2293890
126.4
G
C
C


D8S1774
127.5
3
5
4


D8S1128
128.5
7
5
1





Flanking markers in this candidate region are D8S1832 and D8S1774 for family FSP29.


NT = not typed






The same seven markers tested in FSP24 were genotyped for FSP29. A disease haplotype was established for all 10 collected affected individuals that included many informative recombination events. The proximal recombinant occurred between markers D8S1799 and D8S1832 in three affected individuals (FIG. 1b), and the distal recombinant was between markers D8S1774 and D8S1128 for another affected individual (FIG. 1b). This yielded a candidate interval of 3.15 Mb. The maximum LOD score for this family was 5.62 (θ=0) for the marker D8S1179 when using CEPH allele frequencies. Multipoint analysis was also conducted for this family in this region yielding a maximum LOD score of 6.73, 0.5 cM centromeric to the D8S1128 marker.
EXAMPLE 3
Gene Screening and Mutation Analysis
The previously published SPG8 locus spanned 3.4 cM (1.04 Mb) between markers D8S1804 and D8S1179 on chromosome 8q23-8q24. Nine known genes were screened surrounding this candidate region as annotated in the UCSC human genome browser (UCSC golden path, http://www.genome.ucsc.edu/40) May 2004 update along with many clustered ESTs and mRNAs that aligned to the locus without detecting a mutation. It was Therefore opted to redefine the candidate region based on the critical interval determined by an upper recombinant in the FSP29 family at the marker D8S1832 and a lower recombinant at D8S1774 was based on published data (FIG. 2a).14 This increased the size of the region to 5.43 cM (3.15 Mb), which contains 3 additional known genes. In total, 12 genes were sequenced between markers D8S1804 and D8S1174 (FIG. 2b). These additional genes were screened and three mutations were identified in the KIAA0196 gene using the mutation screening method described in Example 1 above (FIG. 2C).
A valine-to-phenylalanine mutation was identified in amino acid 626 for families FSP24 and FSP29 (p.V626F) (FIG. 3a). All affected individuals collected from each family were screened and were positive for this mutation. This G to T nucleotide change is at position 2205 of the mRNA (see FIG. 14). A total of 500 ethnically matched control individuals (400 from North America, and 100 from CEPH) were negative for this mutation after screening by a combination of allele-specific oligomerization (ASO) and sequencing. No unaffected members and spouse controls in any family were positive for the mutation in exon 15. The family previously described by Reid et al.15 was also screened for KIAA0196 and the V626F mutation was identified.
A second mutation was identified in the Brazilian family16 in exon 14, a G to C transition at position 2186 of the mRNA (FIG. 3b). This leucine-to-phenylalanine change (p.L619F) is only 7 amino acids away from the V626F mutation. It was also not found in 500 controls using ASO.
The KIAA0196 gene was screened in probands from 24 additional dominant HSP families that are negative for mutations in both spastin and atlastin, resulting in the identification of two more families with missense mutations in the KIAA0196 gene.
Thus, the frequency of mutations in SPG3A and SPG4-negative autosomal dominant cohort is  ̃8% (2 in 24). FSP34 has the same p.V626F change in its 3 affected collected members. This family is originally from Great Britain, residing in Canada (FIG. 1c). Haplotype analysis of this family with markers D8S1804, D8S1179, D8S1774 and D8S1128 indicated that there is allele sharing between this family and family FSP29 suggesting an ancestral haplotype (Table 2 above). An additional mutation was found in exon 11 in three affected siblings of another North American family of European origin, FSP91 (FIG. 1d). This c.A1740G transition results in an asparagine to aspartate amino acid change (p.N471D), and is not present in the 500 controls tested (FIG. 3c). The Hedera et al. family14 was not screened but it is expected that affected members possess a mutation in the KIAA0196 genes.
Protein sequence alignment was performed as described in Example 1 above. Mutated amino acids at positions 619 and 626 are strictly conserved across all eleven species examined all the way to the social amoeba, Dictyostelium discoideum (FIG. 3D). Indeed, the entire region surrounding these two mutations appears to be functionally relevant for the protein as 73 consecutive amino acids (aa 576-649) are 100% identical between the human, dog, chicken, mouse, rat and orangutan. Despite this high level of conservation, this region is not a known domain, based on NCBI's conserved domain database search, NCBI's BLASTTM search, and the Sanger Institute's Pfam database.41 Position 471 is conserved across all species save for Drosophila melanogastar with a glutamine residue and Xenopus tropicalis with a histidine.
The exon 15 mutation is in the very first nucleotide of the exon, which leads to the speculation that the splicing of this exon might be compromised in these families. Splice site prediction programs including NetGene2TM suggested that the strength of the splice site acceptor may be reduced by 33% in the mutant form.42 However, both normal and mutant alleles were observed in cDNA analysis of patient lymphoblasts using several pairs of primers. The KIAA0196 gene was expressed ubiquitously, including all regions of the brain which were examined by RT-PCR (FIG. 3e). There were no alternative splice isoforms detected in control brain samples and the patient whole blood samples by RT-PCR and northern analysis (FIGS. 3e and 3f). For the full KIAA0196 gene, all spliced ESTs and mRNAs from the UCSC browser, May 2004 draft, were analyzed for potential alternative splice products. One alternative first exon often appears; however, out of the 356 entries, only two (AK223628 and DA202680) contain exons which are skipped. Thus overall, the gene is not frequently spliced, and the two spliced entries may represent spurious transcripts.
EXAMPLE 4
KIAA0196 Profile
The KIAA0196 gene spans 59.7 kilobase pairs of genomic DNA, is 28 exons long and codes for a protein of 1159 amino acids that is named strumpellin herein. The EBI institute's InterPROScanTM program43 predicted a spectrin-repeat containing domain from amino acids 434 to 518. Thus, the mutation at position 471 may abrogate the binding of the spectrin domain with other spectrin-repeat containing proteins. In examining the secondary structure using PSIPRED24, 74% of the protein is considered to be alpha-helical. The program further predicted an α-helix in the protein from amino acids 606 to 644, encompassing the two other mutations which have been identified. The helix consists of a heptameric repeat with hydrophobic residues aligning in inaccessible regions at the center of the helix. The hydrophobic lysine and valine amino acids are seven amino acids apart in the protein sequence; thus it is expected they would be buried in the helix, close in 3D space (FIG. 5a).
Human KIAA0196 gene is known to have previously been implicated in prostate cancer.32 An increase in gene copy number was assayed by real-time quantitative PCR and fluorescence in-situ hybridization, determining over ten-fold overexpression of the gene in PC-3 prostate cancer lines, and in  ̃1⁄3 of advanced prostate cancers examined.32 
Analysis of other species has provided some insight into a potential function for KIAA0196. A 118 kDa homologue of the strumpellin protein was identified as part of a TATA-binding protein-related factor 2 (TRF2) complex in a Drosophila nuclear extract.33 Eighteen proteins were pulled down along with TRF2 in this complex including NURF and SWI, with functions for chromatin remodeling and transcription activation. TRF2 is selective for promoters lacking TATA or CAAT boxes. One protein of the complex is DREF which binds to DRE elements common in controlling genes involved in cell cycle regulation and cell proliferation.34,35 
EXAMPLE 5
Homology Modeling
Homology modeling was performed as described in Example 1 above. Given the high proportion of KIAA0196 considered to be alpha-helical, it is not surprising that the optimal homology modeling candidates are similar in secondary structure composition.
This is true for 1dn1b, a stat-like t-SNARE protein neuronal-Sec1 Syntaxin 1a complex. This is the most appropriate model for strumpellin according to the PhyreTM program. The two mutated residues lie within an alpha-helix from amino acids 619-628 which is in close 3D proximity to another alpha-helix from residues 665-670 (FIG. 4a). A mutation in either Val-626 or Leu-619 to a phenylalanine residue would appear to have significant structural implications given the change in bulkiness between each of the residues. In addition, Tyr-622 points in the same direction from the alpha-helix residue. To have two amino acids with aromatic rings in such a physical proximity could force apart the alignment of the two alpha-helices or induce alterations in the alpha-helix backbone
The one known domain in strumpellin is a spectrin repeat which consists of three α-helices of a characteristic length wrapped in a left-handed coiled coil.26 These spectrin repeats appear in the spectrin/dystrophin/α-actinin family. The spectrin proteins have multiple copies (15-20) of this repeat which can then form multimers in the cell. Spectrin also associates with the cell membrane via spectrin repeats in the ankyrin protein. Likewise, four spectrin repeats are found in α-actinin beside two N-terminal calponin homology domains which anchor the complex to actin.27 This effectively connects the cell membrane with the actin cytoskeletal network. The stability and structure of this network also provides appropriate routes for intracellular vesicular transport, a mechanism already linked to other mutated HSP genes. Proteins with three spectrin repeats or fewer can be considered to have transient association with the spectrin network. The single repeat in strumpellin is more likely to be involved in docking with one of the cytoskeletal spectrin repeats, which could help in protein localization or signal transduction.
Proteins with a spectrin repeat have been identified in other neurological disorders, most notably dystrophin, mutated in myotonic dystrophy (MIM300377).28 The repeat also has been found in a form of cerebellar ataxia (MIM117210).29 β-III spectrin itself is found to be mutated in SCA5.30 While none of the genes mutated in HSP have a spectrin domain, L1CAM (SPG1) has an indirect association.9,31 L1CAM is a single-pass transmembrane protein with a glycosylated extracellular component which facilitates the outgrowth and migration of neurons in the corticospinal tract. The intracellular c-terminus however binds to the spectrin-repeat containing protein, ankyrin, linking the cell membrane to intracellular spectrin. Thus, strumpellin with its spectrin domain may also be involved in this process.
EXAMPLE 6
Zebrafish Rescue Experiments
In order to validate the functional phenotype of SPG8 mutations in vivo, a zebrafish model was developed. Morpholino oligonucleotide knockdown of the KIAA0196 protein ortholog in zebrafish (KIAAMO) was performed as described in Example 1 above. It resulted in an enlarged heart cavity along with a curly tail phenotype which severely impaired the ability of the fish to swim properly. The overall phenotype ranged in severity and was classified in 3 major groups: normal, slightly curly, and severely curly. This phenotype was clearly visible after dechorionating by 1 day post fertilization (dpf). At 3 dpf, wildtype zebrafish are  ̃5 mm long with a straight tail (FIG. 5A). Fish injected with a mismatch-control morpholino (CTLMO) were initially used to titer a KIAAMO specific non-toxic injection dose (FIG. 5b). Injection of the KIAAMO resulted in 66 of 178 (37%) severely curly fish and 50 of 178 (28%) slightly curly fish (See Table 3 below and FIGS. 5c and d).







TABLE 3







Phenotype profile from zebrafish morpholino oligonucleotide


knockdown expressed in percent (total number)














Slight
Severe




Condition
Normal
curve
curve
Dead
Total





KIAA0196
19.1 (34)
28.1 (50)
37.1 (66)
15.7 (28)
178


morpholino


Control
56.1 (83)
24.3 (36)
 7.4 (11)
12.2 (18)
148


morpholino


Wildtype
 63.2 (127)
19.4 (39)
 8.0 (16)
9.5 (9)
201


rescue


Mutant x14
16.0 (32)
37.0 (74)
36.0 (72)
11.0 (22)
200


rescue


Mutant x15
13.2 (29)
37.4 (82)
30.1 (66)
19.2 (42)
219


rescue









The KIAAMO fish had a significantly different distribution of phenotypic groups compared to CTLMO injections (p<0.001). When wildtype human KIAA0196 mRNA was co-injected with KIAAMO, the curly tail phenotype was rescued to levels comparable to CTLMO injections (p=0.51) (FIGS. 5e and f). This suggests that in zebrafish, human KIAA0196 mRNA can compensate for the loss of endogenous zebrafish mRNA. Conversely, co-injection of human KIAA0196 mRNA incorporating either the exon 14 or exon 15 mutation failed to significantly rescue the phenotype (FIG. 5G, H). Injection of mutant exon 14 or exon 15 mRNA alone (without morpholinos) did not lead to curly tail phenotype or influence lethality in zebrafish, suggesting that the two mutations do not exert a dominant negative effect. Approximately 200 embryos were injected per experimental condition (Table 3 above). The difference in distribution between KIAAMO injection alone and KIAAMO co-injection with wildtype mRNA was significant (p<0.001). Similarly, co-injection of wildtype mRNA versus either exon 14 or exon 15 mutant mRNA was significantly different with a p-value<0.001. There was no statistical difference between the co-injection of the exon 14 mutant and the exon 15 mutant (p=0.10).
Upon histochemical analysis of the embryos using an anti-acetylated tubulin stain for growing axons using the method described in Example 1 above, it was found that the motor neurons in the spinal cord did not develop normally (FIG. 6). Motor neuron axons in fish injected with KIAAMO alone or with the mutant mRNAs were shorter and showed abnormal branching. The structure of interneurons in the spinal cord was also different. The absence of the KIAA0196 gene or mutations in this gene during early development thus seemed to hamper axonal outgrowth.
EXAMPLE 7
Production of Antibodies
Three different peptides corresponding to amino acids 62-76 (KGPELWESKLDAKPE (SEQ ID NO: 100), 652-669 (VPTRLDKDKLRDYAQLGP (SEQ ID NO: 37)) and 1132-1147 (YVRYTKLPRRVAEAHV (SEQ ID NO: 101)) were synthesized. The sequence of the first peptide (62-76) corresponds to protein residues present near the amino terminal portion of strumpellin. The sequence of the second peptide (652-669) corresponds to residues found in the middle of the protein. Finally, the sequence of the third peptide (1132-1147) corresponds to residues near the carboxy terminal portion of the protein.
Every month a dose of each peptide was injected to two separate rabbits. These intraperitoneal injections were carried over for a period of five months. A month following each injections, blood samples were collected from each animals and the cellular fraction removed the sera were stored at −80° C. Following the recovery of the last samples where a complete final bleed was achieved, all the animals were euthanized. The sera from the second peptide (652-669) were observed to be the most specific for strumpellin (FIG. 7b).
EXAMPLE 8
Detecting KIAA0196 Mutations in a Subject Sample
The method for detecting a mutation in the KIAA0196 gene involves the amplification of a patient's DNA by the Polymerase Chain Reaction (PCR) using primers designed to specifically recognize flanking genomic sequences of the KIAA0196 gene, such as those listed in Table 1 above. A series of PCR amplifications are necessary to cover the entire coding regions of KIAA0196 and its flanking splice site regions. The product of these amplifications are subsequently sequenced and examined for the presence of mutations using appropriate software (e.g. the SeqManTM program from the DNASTARTM sequence analysis package). Sequences of the patient's DNA amplifications are compared to a reference sequence where no mutation can be found and or to the reference sequences from databases like UCSC.
The optimal PCR reactions for the amplification of KIAA0196 are the following: 50 ng DNA, 20 pmol of each oligonucleotide primer, 10× buffer, 0.25 nM dNTPs and 0.15 ul of Taq (Qiagen). An initial denaturation step of 5 minutes at 94° C. is done and it is followed by 30 cycles of 30 seconds denaturation at 94° C., 30 seconds annealing at 55° C. (for all exons except for exons 15 and 26), and 45 seconds elongation at 72° C. A final extension at 72° C. of 7 minutes is finally performed. In the case of exon 15, a 50° C. annealing temperature was used, and in the case of exon 26, 10 cycles of a touchdown reaction were performed from 68° C.-63° C., followed by 25 cycles at 63° C.
To identify the three specific mutations of the present invention, three separate PCRs were performed using oligonucleotide primers that corresponded to the sequences surrounding exons 11, 14, and 15 with the patients DNA. Following the sequencing of these products, the sequence traces generated by the software were analyzed visually.
EXAMPLE 9
Detecting Mutant KIAA0196 RNA in a Subject Sample
To detect the presence of mutant RNA, PCR reactions may be performed using oligonucleotide primers specific to the cDNA sequence (coding sequences of DNA exclusively, not sequences flanking the different coding regions) of KIAA0196, such as those in Table 4 below. RNA needs to be extracted from patients using standard methods, and a reverse-transcription PCR (RT-PCR) is performed. The cDNA products generated by this reaction are then used as a template for the PCR amplifications. The sequence trace results are then analyzed using appropriate software for the detection of mutations. The type of protein modifications the occurrence of any mutation within the RNA (here represented by the cDNA) can be predicted using a table listing the amino acids produced by the different codons possible.







TABLE 4





Primers for cDNA analysis of the KIAA0196 gene
















KIAA0196rna1F
CCGGGACTGCGGATAGAAGA



(SEQ ID NO: 102)


 


KIAA0196rna1R
AATCCTGTAGCTCTGGCTTAGCATC



(SEQ ID NO: 103)


 


KIAA0196rna2F
TCTGAGTTTATTCCTGCTGTGTTCA



(SEQ ID NO: 104)


 


KIAA0196rna2R
CTCTCGGGATAGTTGGATGGTCTTT



(SEQ ID NO: 105)


 


KIAA0196rna3F
GCTGCTCGATCTTCTGCTGATTCAA



(SEQ ID NO: 106)


 


KIAA0196rna3R
ATCGGATGGCAACATTGCAGTCTCT



(SEQ ID NO: 107)


 


KIAA0196rna4F
TAAGGGAGGAGATGGTTCTGGACA



(SEQ ID NO: 108)


 


KIAA0196rna4R
TCGAGTATCGGCAAGAAACTGACA



(SEQ ID NO: 109)


 


KIAA0196rna5bF
TGAAACCCCTAACCAGAGTGGAGAAA



(SEQ ID NO: 110)


 


KIAA0196rna5R
ATCGTGGGCCTAGCTGAGCATAGT



(SEQ ID NO: 111)


 


KIAA0196rna6F
AGCTTCAGACCCACGACATTATTG



(SEQ ID NO: 112)


 


KIAA0196rna6R
CCACAGGGGTAAACTTGGGTATTG



(SEQ ID NO: 113)


 


KIAA0196rna7F
TTGGCAAAGCATGTACCAGTCCAC



(SEQ ID NO: 114)


 


KIAA0196rna7R
TCTGCATCTGCCCAACCTTCATTA



(SEQ ID NO: 115)


 


KIAA0196rna8F
TCCGCCATTGCCAAAACACAGA



(SEQ ID NO: 116)


 


KIAA0196rna8R
GGCCAATCAGCGCCAGGAACT



(SEQ ID NO: 117)


 


KIAA0196rna9F
GCTTGTCCTGGGACTGCTCACTC



(SEQ ID NO: 118)


 


KIAA0196rna9R
AGAGGCAGTACAAAAATGTGTTCT



(SEQ ID NO: 119)









EXAMPLE 10
Assay to Detect Mutation in Subject Sample
A Western blot is performed using an antibody specific to the KIAA0196 product and protein lysates prepared from patient tissue or lymphoblastoid cell lines to detect mutant protein in a patient's biological sample.
EXAMPLE 11
Identifying Strumpellin-Interacting Proteins
Protein-protein protocols such as the yeast two hybrid (Y2H), GST pulldown and co-immunoprecipitation approaches are used to identify strumpellin-interacting proteins. These three approaches are performed using both normal and mutant strumpellin to establish which interactions may be specific to the mutated forms of the protein, but also to see in some interactions with the normal form of the protein decrease or increase with the mutated proteins. Such interactions with the mutated proteins are to be investigated only in the event that these are stably expressed. Interactions occurring through the spectrin domain of strumpellin in particular is examined.
Although the present invention has been described hereinabove by way of specific embodiments thereof, it can be modified, without departing from the spirit and nature of the subject invention as defined in the appended claims.
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## Claims

1. A purified antibody that binds specifically to one or more peptide epitopes selected from the group consisting of SEQ ID NO: 100; SEQ ID NO: 37 and SEQ ID NO: 101.

2. A method of determining whether a biological sample contains a mutant strumpellin polypeptide comprising:
(a) contacting a biological sample comprising a strumpellin polypeptide with an anti-strumpellin antibody that specifically binds to a mutant strumpellin;
(b) maintaining the sample in contact with the antibody under conditions suitable for specific binding of the antibody to the mutant strumpellin to occur; and
(c) determining whether the antibody specifically bound to the strumpellin polypeptide,
wherein specific binding of the antibody to the strumpellin polypeptide indicates the presence of the mutant strumpellin polypeptide in the sample, wherein the mutant strumpellin polypeptide comprises at least one amino acid residue substitution from the wild-type strumpellin polypeptide that disrupts the spectrum-binding domain of strumpellin, and wherein the wild-type strumpellin polypeptide comprises SEQ ID NO: 19.

3. The method of claim 2, wherein the amino acid residue substitution occurs at one of the following positions in the strumpellin polypeptide: the asparagine residue at position 471; the leucine residue at position 619; or the valine residue at position 626.

4. The method of claim 3, wherein the asparagine at position 471 is substituted with aspartate.

5. The method of claim 4, wherein the polypeptide comprises SEQ ID NO: 21.

6. The method of claim 5, wherein the leucine residue at position 619 is substituted with phenylalanine.

7. The method of claim 6, wherein the polypeptide comprises SEQ ID NO: 23.

8. The method of claim 3, wherein the valine residue at position 626 is substituted with phenylalanine.

9. The method of claim 8, wherein the polypeptide comprises SEQ ID NO: 25.

10. The method of claim 2, wherein the specific binding of the anti-strumpellin antibody to the strumpellin polypeptide is determined by western blot.

11. The method of claim 10, wherein the anti-strumpellin antibody is selected from the group consisting of a polyclonal antibody; a monoclonal antibody; and an antibody fragment.

12. The method of claim 11, wherein the anti-strumpellin antibody specifically binds to one or more peptide epitopes selected from the group consisting of SEQ ID NO: 100; SEQ ID NO: 37; and SEQ ID NO: 101.

13. A method for diagnosing the presence of SPG8-associated hereditary spastic paraplegia (HSP) or predicting the risk of developing HSP in a human subject by determining the presence of a mutated strumpellin polypeptide, the method comprising:
a) contacting a biological sample comprising a strumpellin polypeptide obtained from the human with an anti-strumpellin antibody that specifically binds to a mutated strumpellin polypeptide;
b) maintaining the sample in contact with the antibody under conditions suitable for specific binding of the antibody to the mutated strumpellin to occur; and
c) determining whether the antibody specifically bound to the strumpellin polypeptide, wherein determining specific binding of the antibody to the strumpellin polypeptide indicates the presence of the mutant strumpellin polypeptide in the sample; and
d) identifying that the human subject has, or is at risk of developing, SPG8-associated HSP.

14. The method of claim 13, wherein the amino acid residue substitution occurs at one of the following positions in the strumpellin polypeptide: the asparagine residue at position 471; the leucine residue at position 619; or the valine residue at position 626.

15. The method of claim 14, wherein the asparagine position 471 is substituted with aspartate.

16. The method of claim 15, wherein the polypeptide comprises SEQ ID NO: 21.

17. The method of claim 14, wherein the leucine residue at position 619 is substituted with phenylalanine.

18. The method of claim 17, wherein the polypeptide comprises SEQ ID NO: 23.

19. The method of claim 18, wherein the polypeptide comprises SEQ ID NO: 25.

20. The method of claim 14, wherein the valine residue at position 626 is substituted with phenylalanine.

21. The method of claim 13, wherein the specific binding of the anti-strumpellin antibody to the strumpellin polypeptide is determined by western blot.

22. The method of claim 21, wherein the anti-strumpellin antibody is selected from the group consisting of a polyclonal antibody; a monoclonal antibody; and an antibody fragment.

23. The method of claim 13, wherein the anti-strumpellin antibody specifically binds to one or more peptide epitopes selected from the group consisting of SEQ ID NO: 100; SEQ ID NO: 37 and SEQ ID NO: 101.

24. The method of claim 13, wherein the mutated strumpellin polypeptide comprises at least one amino acid residue substitution from the wild-type strumpellin polypeptide that disrupts the spectrum-binding domain of strumpellin, and wherein the wild-type strumpellin polypeptide comprises SEQ ID NO: 19.