# Patent

## Title
KASPP (LRRK2) gene, its production and use for the detection and treatment of neurodegenerative disorders

## Abstract

The present invention refers to a newly discovered gene named KASPP for Kinase Associated with Parkinsonism with Pleiomorphic Pathology or alternatively named LRRK2 for Leucine-Rich Repeat Kinase 2, its production, biochemical characterization and use for the detection and treatment of neurodegenerative disorders, such as Parkinson disease (PD) including, without limitation, sporadic PD, Alzheimer disease (AD), amyotrophic lateral sclerosis (ALS), and other synucleinopathies and/or tauopathy as well as several polymorphisms and mutations in the KASPP/LRRK2 gene segregated with PD.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a divisional of U.S. patent application Ser. No. 11/665,875, filed Apr. 19, 2007, which is the U.S. National Stage of International Application No. PCT/EP2005/010428, filed Sep. 27, 2005, which claims benefit of U.S. Provisional Patent Application Nos. 60/620,893, filed Oct. 21, 2004, and 60/621,169, filed Oct. 22, 2004, each of which is hereby incorporated by reference.


STATEMENT AS TO FEDERALLY FUNDED RESEARCH
This invention was made with government support under NS040256 awarded by National Institute of Neurological Disorders and Stroke. The government has certain rights in the invention.


The present invention refers to a newly discovered gene named KASPP for Kinase Associated with Parkinsonism with Pleiomorphic Pathology or alternatively named LRRK2 for Leucine-Rich Repeat Kinase 2, its production, biochemical characterization and use for the detection and treatment of neurodegenerative disorders, such as Parkinson disease (PD) including, without limitation, sporadic PD, Alzheimer disease (AD), amyotrophic lateral sclerosis (ALS), and other synucleinopathies and/or tauopathy as well as several polymorphisms and mutations in the KASPP/LRRK2 gene segregated with PD.
Parkinson's disease (PD) is the second most neurodegenerative disorder affecting 1-2% of the population aged 65 and older characterized by a progressive loss of dopaminergic neurons of the substantia nigra, associated with the formation of fibrillar aggregates composed of α-synuclein and other proteins (Lewy bodies and Lewy neurites). In most cases, PD occurs as a sporadic disease of unknown etiology, but in rare instances, point mutations or multiplications of the α-synuclein gene can cause autosomal-dominant parkinsonism which resembles the sporadic disease in many aspects. Recessive forms of parkinsonism have been recognized, which are caused by mutations in the genes for parkin (Kitada T. et al., Nature, 392, 605-608, 1998), DJ-1 (Bonifati V. et al., Science, 299, 256-259, 2002) and PINK1 (Valente E. M. et al., Science, 304 (5674), 1158-1160, 2004). Additional loci have been mapped on chromosomes 2p (Gasser T. et al., Nat. Genet., 18, 262-265, 1998), 12cen (Funayama M. et al., Ann. Neurol., 51(3), 296-301, 2002), 1q (Hicks A. A. et al., Ann. Neurol., 52(5), 549-555, 2002), and 2q (Pankratz N. et al., Am. J. Hum. Genet., 72(4), 1053-1057, 2003). In more than 10% of patients with PD one or more relatives are also affected by this disorder (Elbaz et al., Neurology, 52:1876-82, 1999). However, genetic causes are only very rarely found.
As α-synuclein aggregation is a pathologic feature both in the common sporadic and a dominantly inherited form of PD, and also in other neurodegenerative diseases, such as dementia with Lewy bodies (DLB) and multiple systems atrophy (MSA), those diseases have collectively been called “synucleinopathies”. Other forms of parkinsonism are associated with the accumulation of filaments composed of the microtubule associated protein tau (MAPT). Mutations in this gene explain at least a subgroup of families with frontotemporal dementia with parkinsonism (FTDP-17; Ghetti B. et al., “Frontotemporal dementia and parkinsonism linked to chromosome 17 associated with tau gene mutations (FTDP-17)”. In: Dickson D. W., “Neurodegeneration: the molecular pathology of dementia and movement disorders” ISN Neuropath Press, Basal, 86-102, 2003), while sporadic cases with tau pathology most commonly present as progressive supranuclear palsy (PSP) or corticobasal degeneration (CBD). Based on the putative central role of the tau protein in these diseases, they have been called “tauopathies”.
Recently it has been shown that two large families with autosomal-dominant late-onset parkinsonism (families A and D) are linked to the PARKS-locus on chromosome 12p11.2-q13.1 (OMIM# 607060), originally mapped in a Japanese family by Funayama et al. (Funayama et al., Ann. Neurol., 51(3), 296-301, 2002; Zimprich A. et al., Am. J. Hum. Genet., 74(1), 11-19, 2004).
Now, a haplotype analysis refined the candidate region to a 13 Mb interval between flanking markers D12S1692 and D12S85. A total of 29 genes have been sequenced in that region in two patients from each family (see Table 1).
A whole gene, part of that had previously been deposited under DKFZp434H211 (Accession: XM—058513), has been amplified from human brain cDNA using overlapping primers corresponding to published sequences of various ESTs and mRNAs. Nevertheless, it became clear from cross-species sequence alignments that the DKFZp434H211 clone was incomplete towards the 5′-end.
Surprisingly, several mutations, including missense mutations and a splice site mutation, have been found in newly discovered large gene coding for a multifunctional protein, which is referred to as Kinase ASsociated with Parkinsonism with Pleiomorphic Pathology, KASPP. KASPP spans a genomic region of 144 Kb and comprises 51 exons and encodes 2527 amino acids (see SEQ ID NOS: 1 and 2 and FIG. 4). The gene can also be named Leucine-Rich Repeat Kinase 2, LRRK2, because it is the only gene in the human genome encoding a kinase containing leucine rich repeats which was very surprising. KASPP/LRRK2 is a 285 kD protein.
Therefore, the present invention is directed to an isolated nucleic acid molecule comprising a polynucleotide sequence selected from:

    (a) nucleotides 1 to 9104 of SEQ ID NO: 1 or 2;
    (b) nucleotides 1 to 7584 of SEQ ID NO: 1 or 2;
    (c) nucleotides 1 to 7581 of SEQ ID NO: 1 or 2;
    (d) a nucleotide sequence coding for the protein sequence of SEQ ID NO: 1 or 2 or for the protein sequence of SEQ ID NO: 1 or 2 containing at least one of the mutations depicted in SEQ ID NO: 1 or 2, respectively;
    (e) a nucleotide sequence complementary to either of the nucleotide sequences in (a), (b), (c) or (d); and/or
    (f) a nucleotide sequence which hybridizes under high stringency conditions to any of the nucleotide sequences in (a), (b), (c), (d) or (e).


SEQ ID NO: 2 is particularly preferred because it reflects the amino acid sequence of human KASPP/LRRK2 and the human nucleotide sequence coding for the human KASPP/LRRK2.
Examples of polynucleotides selected from paragraph (f), above are the specific mutations, variants and polymorphisms described herein.
A polymorphism generally is the occurrence of different forms of nucleic acids or proteins in individual organisms or in organisms of the same species, independent of sexual variations. According to the present invention two different polymorphisms have been found for the human KASPP/LRRK2. One shows a variation from cytosine to thymidine at position 635 (c635t) causing a change in the amino acid sequence from serine to leucine (S212L) (see SEQ ID NOS: 4 and 5). The other shows a variation from thymidine to cytosine at position 7190 causing a change in the amino acid sequence from methionine to threonine (M2397T) (see SEQ ID NOS: 6 and 7).
Examples of high stringency hybridization conditions can be found e.g. in Ausubel, F. M. et al., Current protocols in Molecular Biology, John Wily & Sons, Inc., New York, N.Y. (1989). In a particular example, a filter, e.g. a nitrocellulose filter, is incubated overnight at 68° C. with a probe in a hybridization solution e.g. containing 50% formamide, high salt (either 5×SSC [20×: 3M NaCl/0.3M trisodium citrate] or 5×SSPE [20×: 3.6M NaCl/0.2M NaH2PO4/0.02M EDTA, pH 7.7]), 5× Denhardt's solution, 1% SDS, and 100 μg/ml denatured salmon sperm DNA. This is followed by several washes with buffer, e.g. in 0.2×SSC/0.1% SDS at a temperature selected based on the desired stringency and the melting temperature (Tm) of the DNA hybrid. For example, 68° C. are appropriate for high stringency hybridization.
The present invention is also directed to a fragment of the inventive nucleic acid molecule specified above containing at least one of the 51 exons and/or coding for at least one of the five domains as specified in FIGS. 4A-4K, FIGS. 5A-5C, and/or FIGS. 11A or 11B of the present specification. The boundaries of the exons as specified in FIGS. 4A-4K are applicable for the nucleotide sequences of SEQ ID NO:1 and SEQ ID NO:2.
In addition, the nucleic acid molecule as specified under (f) above may consist of 10 to 50 nucleotides, preferably from 10 to 35 nucleotides, in particular from 20 to 35 nucleotides. Such nucleic acid molecule can be used as a probe or primer for the detection of the polynucleotide of the present invention, in particular for the detection of a mutation thereof as explained in more details below.
Another example of a fragment is a nucleic acid coding for the immunogenic peptide of SEQ ID NO: 3 and the peptide itself.
Such fragments may be produced synthetically e.g. by nucleic acid synthesis or by a PCR or TR-PCR reaction.
Therefore, another embodiment of the present invention is directed to a nucleic acid molecule containing at least one of the mutations depicted in FIGS. 17A-17K or FIGS. 18A-18K, preferably only one of the mutations depicted in FIGS. 17A-17K or FIGS. 18A-18K, e.g., the mutation/s at position 2378, 2789, 3287, 3342, 3364, 3683, 4321, 5096 and/or 6059. In addition, the polymorphisms c635t and t7190c are also a specific embodiment of the present invention.
Surprisingly, is has been discovered that in family A (Y1699C; 5096A>G) and in family D (R1441C; 4321C>T) both mutations segregated with disease in the families (for pedigree structures see FIG. 1) and were not found in more than 1000 control individuals, nor in 300 sporadic PD-patients.
In Family A, 16 individuals were typed (8 unaffecteds, 8 affecteds). All affecteds were heterozygous for the mutation and all unaffecteds aged over 60 were wild-type. Individuals IV:1 and IV:2 (family A) were not included in our initial linkage analysis (Zimprich A. et al., 2004, supra), both individuals have now been genotyped. Recalculation of the two-point LOD scores using the mutation as a marker gives maximum LOD scores of 3.78 at θ=0.
In Family D, 34 individuals were typed (10 affecteds and 24 unaffecteds), all affecteds were heterozygous for the 4321C>T (2.1441C) mutation; out of the 24 clinically unaffected, genotyped individuals, only two were aged over 60 years and were mutation carriers. These individuals are at risk and likely to be presymptomatic given that the average age of onset in this family is 65 years according to Wszolek Z. K. et al., Neurology, 62(9), 1619-1622, 2004.
To estimate the prevalence of KASPP/LRRK2-mutations among PD-families, one index patient from 44 additional families with PD, 32 consistent with autosomal dominant parkinsonism and 12 affected sib-pairs, were subsequently sequenced.
Surprisingly, two further miss-sense and one putative splice site mutation have been identified, all in families with typical late onset PD, compatible with a dominant transmission: (I1122V; 3364A>G) in family 21; (I2020T; 6059T>C) in family 32, and (L1114L; 3342A>G) in family 38, which is 6 by away from the exon/intron border. Affected individuals in a further family (469) were found to carry the same mutation as family D (R1441C; 4321C>T). Those two families are not known to be related, nor did they share haplotypes for the closest flanking microsatellite repeat markers D12S2194, D12S1048 or three newly developed intragenic repeat markers, indicating that the mutations are extremely ancient or arose independently (for pedigree structures see FIG. 2).
Again, the mutations segregated with the disease in all families and none of them were found in controls. Three of the amino acid substitutions (R1441C, Y1699C and I1122T) are additionally highly conserved across species (see FIG. 3).
Screening the entire coding region of the KASPP/LRRK2 gene in a cohort of 53 apparently unrelated families with apparently autosomal mode of inheritance, seven more families with amino acid substitutions or one splice site mutation have been identified. Mutations in the KASPP/LRRK2 gene, therefore, account for 13% of familiar PD in our total cohort.
In the second study four novel mutations (R793M, Q930R, S1096C and S1228T) have been identified. Therefore, together with the published mutation, until now, 10 missense mutations and one splice site mutation have been described.
The KASPP/LRRK2 gene consists of 51 exons comprising five conserved domains (see FIGS. 5 and 7) indicating that it belongs to a recently defined ROCO protein family (Bosgraaf L. et al. Biochim. Biophys. Acta., 1643 (1-3), 5-10, 2003).
The five conserved domains are in detail:
(1) N-terminal leucine-rich repeat (LRR) consisting of 12 strands of a 22-28 amino acid motif, present in a tandem array; (2) ROC (Ras of complex) domain indicating the affiliation of the protein to the Ras/GTPase superfamily; (3) COR (C-terminal of Roc) domain; (4) tyrosine kinase catalytic domain (MAPKKK) and (5) C-terminal WD-40 domain.
Proteins containing LRRs are associated with diverse functions, such as hormone receptor interactions, enzyme inhibition, cell adhesion, cellular trafficking, splicing and substrate binding for ubquitination, a common property involves protein-protein interaction (Kobe B. et al., Curr. Opin. Struct. Biol., 11(6), 725-723, 2001). In particular, the N-terminal LRR and the C-terminal WD-40 propeller structure are assembly points for larger protein complexes. Ras/GTPase domains are involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras, in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase (Ridley A. J. Trends Cell. Biol, 2001). In particular, the fusion of a Ras-like domain with a MAPKKK domain indicates the function of KASPP/LRRK2 in intramolecular signal transduction. Furthermore, KASPP/LRRK2 should also function as a scaffolding protein like Ksr (Kinase suppressor of Ras). The KASPP/LRRK2 kinase domain shows also similarity to the RIR and Mixed lineage kinases which are part of the TKL-(thyrosine kinase like) branch of the human kinome indicating an involvement in stress-induced cell signalling and mediation of apoptosis. The COR domain is characteristic for this protein family and shows no significant sequence homology to any domain or protein today. Enzymes with a tyrosine kinase catalytic domain belong to an extensive family of proteins which share a conserved catalytic core common to both serine/threonine and tyrosine protein kinases. They exert their function by catalyzing the transfer of the gamma-phosphate of ATP to tyrosine residues on protein substrates (Hubbard S. R. et al. Annu. Rev. Biochem., 69, 373-398, 2000). The WD40 domain is implicated in signal transduction, pre-mRNA processing and cytoskeleton assembly (Smith T. F. et al., Trends Biochem. Sci., 24(5), 181-185, 1999).
In view of the present invention three Roco proteins of the Roco-protein family exist now in mammals: LRRK1, DAP-kinase (death associated protein kinase) and KASPP/LRRK2 of the present invention. The mammalian DAP-kinase, for example, should be involved in cytosceletal rearrangements and/or induction of apoptosis dependent on its activity.
The biochemical analysis of KASPP/LRRK2 and its Parkinson disease-associated variant, I2020T, bearing a mutation located next to the DFG motif (DYG in KASPP/LRRK2) at the beginning of the activation loop of the kinase domain which is highly conserved in almost all MAPKKK, indicates according to the present invention that KASPP/LRRK2 acts as a true protein kinase at cytoskeletal and membraneous structure within the cell. In addition, the found increase (approximately 30-50%) in the kinase activity of the I2020T mutant is consistent with mutations in homologous positions of other kinases like B-Raf associated with cancer (Dibb, N. J. et al. (2004), Nat. Rev. Cancer, 4, 718-727). It is also worth to be noted that this mutation is a dominant feature. In addition to an overall gain in kinase activity, the mutation could also alter substrate specificity. As with oncogenic kinase variants, kinase inhibitors could then be considered as a treatment option. The effectiveness of such therapeutic strategy has been proven with respect to specifically inhibiting the bcr-abl protein kinase within chronic myeloic leukemia (CML) through the kinase inhibitor 2-phenylaminopyrimidine STI571 (Gleevec), a small-molecule tyrosine kinase inhibitor for the treatment of CML (Chalandon, Y. & Schwaller, J., Haematologica, 90, 949-968, 2005).
In summary, the biochemical analysis of KASPP/LRRK2 and its I2020T mutant according to the present inventions shows that KASPP/LRRK2 shares common features with other MAPKKK, such as autophosphorylation, dimerisation or interaction with kinase specific chaperones. The autokinase activity of the mutant I2020T, localised within the activation loop of the KASPP/LRRK2 kinase domain is increased when compared to wild-type KASPP/LRRK2 according to the present invention. In view of its multimodular structure, KASPP/LRRK2 should be involved in functions as diverse as maintenance of microtubular ultrastructure and dynamics, vesicular trafficking (ER, Golgi compartment) and/or cytoskeletal rearrangements.
Interestingly, all ten mutations are within these conserved domains (FIG. 7). The R793M mutation, however, is located in exon 19 which is part of the ancyrin repeat region (amino acid 678-806), that seems to take part in protein-protein interactions.
In contrast to previous reports the so far most common mutation (G2019S; 6055G>A, Hernandez D G et al., Ann Neurol, 57: 453-6, 2005) was not detected in any of the families investigated but only in one patient with sporadic PD. Moreover, this mutation was found in only one out of 340 patients with sporadic PD. Therefore, the predominance of this mutation (Gilks et al., Lancet, 365: 415-6, 2005; Toft et al., Lancet, 365: 1229-30, 2005) can not be established for all populations. The screening in familial and sporadic PD patients showed frequencies of the G2019S mutation up to 7% in familial and almost 1% in sporadic PD cases, however, no association could be demonstrated of this mutant with the non-mendelian sporadic form of PD in a recent study of the inventors. In the present cohort comprising 340 patients with sporadic PD the novel R793M was additionally found in one sporadic patient. Therefore, KASPP/LRRK2 mutations account for only 0.6% of sporadic PD cases in the present population.
In three families the specific variation did not cosegregate with one family member each: In family DE022, the Q930R only three of the four family members affected by the disease were mutation carriers (FIG. 6b), in family E in fact only one of the two family members with PD phenotype was carrier of the S1096C mutation (FIG. 6f), and the splice site mutation cosegregating with PD in one previously investigated family (DE038) was only found in one of the clinically affected sisters (T112888) (FIG. 6c). As none of these variations was found in any of the 1200 controls investigated and the splice site variation affected two distinct PD families it is likely that they are causative for the disease, although incomplete penetrance at least in family DE022 could indicate that additional factors may contribute to manifestation of the disease in affected subjects. This may be due to phenocopies in these three families, as the high prevalence of PD in the population makes it well possible that other causes of PD occur in a family affected by KASPP/LRRK2 mutations. Disease phenocopy is not uncommon in PD. It has been described in the original α-synuclein A53T kindred (Polymeropoulos et al., Science, 276: 2045-7, 1997), in a family with the KASPP/LRRK2 G2019S mutation (Hernandez et al., 2005, supra), but also in family D with the KASPP/LRRK2 R1441C mutation.
Three of the present mutations affect at least two families. For two of these (R793M and I2020T) haplotype analysis revealed a common haplotype indicating a common founder. None of the families was aware of a possible relation to the respective family although the two families harbouring the I2020T mutation lived in the same geographic region. The same mutation has also been described in the Japanese family, who served as the basis for the original defining of the PARK8 locus (Funayama et al., Ann Neurol., 57: 918-21, 2005).
The R793M mutation, detected in two distinct families with the same haplotype, was also found in one patient with sporadic PD and one control person. Because of technical problems in assessing this CG rich exon call rate of the population screened was low (about 50% in three different tries). Therefore, it may well be, that this mutation is more frequent in apparently sporadic PD patients. Also, the possibility of a polymorphism needs to be taken into account, if this variation was detected in more controls. However, finding of a possible common founder in the two families with the mutation is an indication for a disease related amino-acid substitution. Common founders are also suggested for other families affected by mutations in the KASPP/LRRK2 gene (Mata et al., Neurosci Lett, 382: 309-311, 2005).
Mode of inheritance of KASPP/LRRK2 mutations is autosomal dominant. It has been suggested that penetrance of KASPP/LRRK2 mutations is age dependent (DiFonzo et al., Lancet, 365: 412-5, 2005; Toft et al., 2005, supra) accounting for the reduced penetrance in some families. In the present families reduced penetrance was only observed in mutations of exons 19 and 21 located before the highly conserved LRR domain. This indicates that mutations in this region are less severe and have to be associated with other so far unknown factors for disease manifestation. From the splice site mutation of exon 24 onwards, penetrance was complete, although one splice mutation carrier (DE038, III-1) had only slight resting tremor for several years, while his sister (III-3), mother and uncle were affected by severe PD.
In all families with definite documentation of age of onset an earlier recognitions of first Parkinsonian signs was observed in the younger generations. So far, there are no known pathomechanism that allow the hypothesis of anticipation. Rather, a greater awareness of a possible affliction and a more thorough investigation in families in whom PD has already been diagnosed could account for the earlier diagnoses.
The clinical presentation of KASPP/LRRK2 mutation carriers varies within families and between families affected by the same mutation. In general the typical phenotype of PD with resting tremor, bradykinesia, rigidity and olfactory dysfunction can be observed. Interestingly, tremor, the main and naming feature of some of the initially described to families (Paisan-Ruiz et al., Neuron, 44: 595-600, 2004) was neither the main initial nor the leading symptom in many of our PD patients. Two patients did not report any resting tremor in their medical history. Rather, the typical pattern of different subtypes known from idiopathic PD could be observed. All patients reported a substantial relief of symptoms after application of dopaminergic treatment, which was hampered by halluzinations in only the one patient with DLBD-phenotype (Diffuse Lewy Body Disease-phenotype).
In patients with KASPP/LRRK2 mutations a frequent, the patient strongly afflicting symptom seems to be sleeping abnormality. Eight out of 10 patients (80%) reported to suffer from difficulties of either falling a sleep, staying a sleep or both. According to several studies, sleeping disturbancies occur in about 40-75% of PD patients (Lees et al., Clin Neuropharmacol., 11:512-519, 1988; Kumar et al., Mov Disord, 17: 775-781, 2002), but only the minority (about 20%) reports sleeping abnormalities as a problem (Lees et al., 1988, supra). In the present study 80% stated that sleeping disturbances were indeed a problem. More detailed assessment on sleeping behaviour and pattern are to be decided, whether this symptom is more pronounced in KASPP/LRRK2 mutations carriers, possibly indicating an earlier involvement of the respective systems. Postural instability occurs late in the course of the disease. As also described by others (Paisan-Ruiz et al., Ann Neurol., 57:365-72, 2005) dementia is not a common finding in KASPP/LRRK2 associated PD and seems to occur rather late in the disease process. The same holds true for hallucinations in our patient cohort, occurring either late in the disease process or in combination with dementia. In the present cohort, one patient presented with the typical clinical picture of DLBD. Autopsy of one subject with dementia in our first cohort revealed diffuse Lewy Body pathology in one family affected by the Y1699C mutation. Description of the same phenotype in an other patient in this study affected by a different mutation favours the hypothesis that the clinical presentation of DLBD may be caused by the same pathophysiological alterations as the clinical picture of PD. Obviously specific pathophysiological changes (in this case caused by mutations in the KASPP/LRRK2 gene) may lead to the clinical and histopathological entity of both: PD and DLBD.
In our first study one patient showed mild signs of motor neuron disease. In the second study, however, motor neuron symptoms were neither clinically nor electrophysiologically disclosed in any patient investigated.
Structural neuroimaging revealed slight to marked atrophy in all 4 patients investigated, although disease duration was only 3-12 years in these and only one was classified as demented (Table 4). This contrasts findings of idiopathic PD, where structural MRI is usually normal and atrophy only occurs with disease progression, usually associated with dementia. The patient with the clinical presentation of DLBD had marked signs of microangiopathy, which may also be causative for an atypical Parkinsonian syndrome. The clinical presentation with fluctuation of vigilance, good response to L-dopa hampered by hypersensitivity and dementia developing over a short period of time, however, makes the diagnosis of DLBD more likely.
TCS revealed SN hyperechogenicity—the typical sign for idiopathic PD, found in more than 90% of PD patients (Berg et al., 2001, supra; Walter et al., J Neural Transm, 109:191-196, 2002)—on at least one side of KASPP/LRRK2 mutation carriers. Interestingly, SN hyperechogenicity was only moderate in all patients investigated, as opposed to idiopathic PD, where it is marked in 73-79% of the patients. This highly characteristic finding is supposed to be associated with an increase in tissue iron content and possible alterations in iron binding, antedating the manifestation of disease onset (Berg et al., 1999, supra: Berg et al., Neural Transm, 109:191-196, 2002). An only moderate hyperechogenicity of the SN in KASPP/LRRK2 associated PD may argue for a different course of underlying pathomechanisms, which may finally lead to less iron accumulation in KASPP/LRRK2 associated than in idiopathic PD. Similarly, the slower disease progress, documented by less although typically located reduction of F-Dopa uptake in PET examinations (Hernandez et al., 2005, supra) favours the hypothesis of a different course of the disease.
In conclusion, in two consecutive studies it has been shown that KASPP/LRRK2 mutations account for about 13% of apparently autosomal dominantly inherited PD and sib pairs in the population investigated. Although the phenotype varies within and between families affected by the same mutations it is very similar to the clinical presentation of idiopathic PD. The causal relation between disease manifestation and variation is not equally clear for all variations described. In three families the specific variations did not co-segregate with one family member each affected by the disease. As none of these mutations was found in 1200 control persons, and one variation was found in two distinct PD families phenocopies is indicative.
Moreover, two patients with the clinical presentation of DLBD should lead to the consideration of KASPP/LRRK2 mutations in families with the simultaneous occurrence of DLBD and PD.
As already pointed out above mutations have been found in different functional domains but it is unclear which of them are related to neurodegeneration. However, KASPP/LRRK2 may be central to a range of neurodegenerative processes because our findings show that (i) KASPP/LRRK2-mutations appear to be a numerically important cause of autosomal-dominant parkinsonism (6 independent mutations in 34 families with dominant inheritance) and (ii) affected individuals with KASPP/LRRK2 mutations exhibit strikingly variable pathologic changes, representing aspects of several of the major neurodegenerative diseases.
Using cell fractionation and carbonate extraction the present invention discloses that KASPP/LRRK2 is associated partially with mitochondria, the cytoskeleton and microsomal membranes, which is an indication that KASPP/LRRK2 is involved in cytoskeletal rearrangements. No KASPP/LRRK2 was found in the cytoplasm. Further, the autokinase activity of KASPP/LRRK2 is not significantly changed in the disease-associated I2020T mutant compared with wild-type, indicating that the autosomal dominant effect is caused by a toxic gain of function rather than loss of function. The I2020T mutation is located next to the conserved motif DFG (DYG in LRRK2) at the beginning of the activation segment of the kinase domain (Ross O. A. & Farrer M. J. Biochem. Soc. Trans., 33, 586-590, 2005) and in the mutation a hydrophobic leucine residue is exchanged by a polar threonine residue. This is also an indication that associated Parkinson's disease is caused by altered substrate specificity or higher KASPP/LRRK2 activity. Homodimerization and association with the HSP90/p50cdc37 chaperone-system further indicate that the KASPP/LRRK2 function and activation mechanisms are similar to other MAPKKK. These effects serve as a basis for the development of a suitable screening assay and/or the development of a pharmaceutical or a diagnostic agent as described below in detail.
Autopsies performed on affected individuals uniformly demonstrated neuronal loss and gliosis in the substantia nigra as the pathological substrate of parkinsonism. However, α-synuclein pathology (Lewy-bodies, LBs) typical for PD was seen only in one case from family D. In another case from this family widespread LB's was more consistent with diffuse Lewy Body disease (DLB). Even more intriguingly, senile plaques and neurofibrillary tangles (NFTs) as well as prominent tau deposits were demonstrated in 3 other brains from both large kindreds. Spinal cord pathology consistent with a diagnosis of amyotrophic lateral sclerosis (ALS) was found in affected members of family A.
Hence, KASPP/LRRK2 is likely to be central to the aetiology of all neurodegenerative diseases such as PD, Alzheimer disease (AD) and amyotrophic lateral sclerosis (ALS) and pathologies, including synucleinopathy and tauopathy, associated with a clinical phenotype of parkinsonism.
It has previously been shown that tau and α-synuclein pathologies may be closely linked. Tau-aggregations have been found in the brains of patients carrying pathogenic A53T α-synuclein mutations (Kotzbauer P. T. et al., Exp. Neurol., 187(2), 279-288, 2004; Duda J. E. et al., Acta Neuropathol. Berl., 104, 7-11, 2002) Similarly, the major pathogenic protein aggregating in AD has been shown to promote fibrillization of tau and formation of neurofibrillary tangles in an animal model (Gotz J., Science, 293, 1491-1495, 2001). Interestingly, a genomic region overlapping the PARK8 locus has been identified in a linkage study of familial Alzheimer disease (Scott W. K. et al. Am. J. Hum. Genet., 66(3), 922-932, 2000). Evidence for linkage was derived in a large part from families with at least one member with autopsy proven diffuse Lewy body disease. Whether this linkage result reflects variants in the KASPP/LRRK2 gene remains to be determined.
The expression pattern of KASPP/LRRK2 was subsequently examined in brain and other tissues. Human brain and multiple tissue Northern blots were hybridized with a 1078 by 3′ cDNA probe and found expression in most brain regions, albeit at a very low levels. Two transcripts of about 9 kb and 8 kb, respectively, and multiple bands at lower sizes were found. The two transcript sizes might be explained by alternative splicing and/or the alternative use of polyadenylation sites.
As low overall expression levels in brain precluded a detailed analysis of its regional distribution by Northern blotting, real-time RT-PCR was done using RNA isolated from adult and fetal whole brain as well as from different brain regions in order to assess quantitative gene expression and alternative splicing. Primers have been designed to generate specific PCR products for exon1-8, exon13-19 and exon 31-39, respectively. Within the same tissue or brain region transcript levels of all three assays showed no significant differences. Consistent expression in most brain regions have been found, slightly higher in putamen, substantia nigra and heart. The highest expression levels were observed in lung. The cDNA analysis, within in multiple tissues, confirms in silico prediction that at least 11 exons may be alternatively spliced. In adult human brain tissue, exon 6 was constitutively expressed within the full length mRNA.
In view of the above, the present invention is also directed to a vector, preferable an expression vector, containing the nucleic acid molecule of the present invention, to a cell containing the nucleic acid or the vector of the present invention and to a transgenic animal containing the nucleic acid or the vector of the present invention.
A vector can be a plasmid or phage DNA or any other DNA sequence into which DNA can be inserted to be cloned. The vector can replicate autonomously in a host cell, and can be further characterized by one or a small number of endonuclease recognition sites at which such DNA sequences can be cut in a determinable fashion and into which DNA can be inserted. The vector can further contain a marker suitable for use in the identification of cells transformed with the vector. Markers, for example, are tetracycline resistance genes or ampicillin resistance genes.
In a further embodiment the vector can be in the form of an expression vector containing an expression cassette which comprises the nucleic acid molecule of the present invention, but preferably also further comprising expression control sequences which are operatively linked to the nucleic acid molecule. The expression control sequences are chosen so that they allow expression of the encoded polypeptide in a host. For example a nucleic acid sequence encoding a polypeptide of the present invention can be isolated and cloned into an expression vector and the vector can then be transformed into a suitable host cell for expression of the polypeptide of the invention. Such a vector can be a plasmid, a phagemid or a cosmid. For example, a nucleic acid molecule of the invention can be cloned in a suitable fashion into prokaryotic or eukaryotic expression vectors, preferably into eukaryotic expression vectors and more preferably into expression vectors allowing expression in a mammalian and in particular in a human cell which is known to a person skilled in the art. Such expression vectors typically comprise at least one promoter and can also comprise a signal for translation initiation of the reading frame encoding the polypeptide and—in the case of prokaryotic expression vectors—a signal for translation termination, while in the case of eukaryotic expression vectors the expression cassette preferably comprises expression signals for transcriptional termination and polyadenylation. Examples of suitable eukaryotic expression vectors are well known for the person skilled in the art, e.g. for the expression in insect cells via baculovirus vectors, and for expression in mammalian cells, e.g. the SV40 or CMV vectors, the sindbisvirus expression system, or an adenovirus expression system, a Semliki Forest Virus-based expression system, or a lentivirus-based expression system. The molecular biological methods for the production of these expression vectors are also well known to the skilled person, as well as the methods for transfecting host cells and culturing such transfected host cells. In a preferred embodiment the above-mentioned expression control sequences specify induced expression of the polypeptide of the invention, that is induced transcription of the messenger RNA encoding the polypeptide of the invention upon addition or withdrawal of an external signal, such as a small chemical like tetracycline or a hormone like Ecdysone, but the extracellular signal can also be an increase or decrease in temperature or ionizing radiation. Also, inducible expression can be brought about by inducible translation initiation of the messenger RNA or a system in which mRNA stability is controlled in an inducible fashion. Examples of expression control sequences allowing induction of polypeptide production are reviewed in the following publications: the TET-off/TET-on system, suitable for both cell cultures and transgenic animals, but also the expression control system based on Cre-recombinase based methods, predominantly for use in transgenic animals. A further inducible expression system, for use in both cell culture and transgenic animals is based on the insect hormone Ecdysone. Another inducible expression system is the GAL4 system, which has been successfully applied with mice, zebrafish and Drosophila, and allows conditional expression at 26-29 degrees, or also a Rapamycin based conditionals expression system. A temperature-sensitive expression system is based on a Sindbis virus expression cassette and predominantly suitable for controlled expression in cell culture systems.
Another aspect of this invention relates to a cell comprising a nucleic acid or a vector of the present invention. Such a cell can be a mammalian, non-human cell inside or outside of the animal body or a human cell outside of the human body. But it can also be an insect cell, like a drosophila cell, in culture or in the context of a transgenic insect, like a transgenic Drosophila. It can also be a nematode cell, like, for example, present in transgenic C. elegans. Preferred host cells are mammalian, and particularly human, neuronal cells, microglia cells, astrocytes, oligodendrocytes, fibroblasts, monocytes, and macrophages and other non-neuronal primary cells, which can be kept in primary tissue culture and can be made capable of expressing the polypeptide of the invention by introducing the nucleic acid/or the expression cassette of the invention, for example by transfection with such a nucleic acid or expression cassette. Other means of introducing the nucleic acid and/or the expression cassette of the invention to the above-mentioned primary cells are “gene gun” approaches, mRNA transfer, viral infection, microinjection or liposomal nucleic acid transfer, to name but a few. Other suitable host cells are mammalian cells like HEK cells, HELA cells, PC12 cells, CHO cells, JURKAT cells, mouse 3T3 fibroblasts, mouse hepatoma cells, human neuroblastoma cells, but also established cancer cell lines, particularly neuronal cell lines, of mammalian and particularly of human origin.
The nucleic acid and/or the expression cassette of the invention can also be introduced into those cells by the above-mentioned nucleic acid transfer methods. Particularly preferred are stably transformed cell lines wherein the expression of the polypeptide of the invention is inducible. Since expression of the polypeptide of the invention may show increased neuropathology, it may be preferred that in such host cells the expression of the polypeptide of the invention is usually very low or off, for example during the generation of a stably transformed cell line, and only for experimental purposes and after establishment of such a stably transformed cell line the expression of the polypeptide of the invention is turned on by addition of a suitable stimulus, like e.g. a hormone like Ecdysone or a small chemical like the antibiotic tetracycline. Again, the above described examples of expression control sequences allowing induction of polypeptide production are suitable for this purpose, like the TET-off/TET-on system, the Cre-recombinase based methods, the Ecdysone system, the GAL4 system, Rapamycin-based systems, or the above described temperature-sensitive expression system based on a Sindbis virus expression cassette.
Another aspect of the invention relates to transgenic animals which comprise a host cell of the invention. Particularly preferred are transgenic flies, like transgenic Drosophila, transgenic nematodes, like transgenic C elegans, transgenic fish, like transgenic zebra fish, and transgenic non-human mammals, like transgenic rodents (mice, rats).
Meanwhile, the generation of transgenic animals are within the general skill of a person skilled in the art. In addition, it is pointed out that under the control of tissue-specific promoters expression could be targeted to the CNS in mice and others. Most tissue-specific to promoters could be used, for example, also in the context of viral vectors. In the following, tissue-specific promoters of rodents are listed. Expression in astrocytes: GFAP-promoter, macrophage colony-stimulating factor (c-fms). Expression in neurons: synapsin promoter, thy-1 promoter, neuron-specific rat enolase promotor (NSE), L7 promoter (Purkinje cells), dopamine beta-hydroxylase (DBH) promoter (predominantly in the peripheral nervous is system), brain dystrophin promoter, calmodulin gene II and III promoter (CaMII, CaMIII), human and murine neurofilament light gene promoter (NF-L), human hypoxanthine phosphoribosyltransferase (hHPRT) promoter, corticotropin-releasing hormone (CRH), T alpha 1 alpha-tubulin promoter, murine low-affinity NGF receptor promoter, hippocalcin gene promoter, olfactory marker protein (OMP) promoter (olfactory neurons), GABA(A) receptor alpha 6 subunit promoter, GABA(A) receptor delta subunit promoter, tyrosine hydroxylase (TH) promoter, mouse vesicular acetylcholine transporter (VAChT), mouse glutamate decarboxylase 65 and mouse glutamate decarboxylase 67 genes promoters, brain-specific promoter of the human FGF1, gonadotropin-releasing hormone (GnRH) promoter, N-methyl-D-aspartate receptor 2A subunit gene promoter; mouse metabotropic glutamate receptor subtype 6 (mGluR6) upstream sequence, Rod photoreceptor cGMP phosphodiesterase (PDE6), human blue opsin promoter and rhodopsin promoter (retina). Neuron-restrictive silencer elements: Neuron-restrictive silencer elements (NRSEs). Expression in oligodendrocytes: MBP (myelin basic protein), proteolipid protein (PLP) promoter.
Furthermore, the present invention is directed to a protein encoded by a nucleotide sequence of the present invention, in particular a protein containing the amino acid sequence of SEQ ID NO: 1 or 2 or at least one of the mutations depicted in SEQ ID NO: 1 or 2, such as the mutation R793M, Q930R, S1096C, L1114L, I1122V, S1228T, R1441C, Y1699C and/or I2020T.
It is particularly pointed out that the present invention encompasses also proteins which contain one or more amino acid substitutions in the KASPP/LRRK2 protein but still retains essentially its function. Such amino acid substitutions may be semi-conservative or conservative and more preferably a conservative amino acid residue exchange. In the following table such amino acid substitutions are exemplified.
















Conservative
Semi-conservative



Amino acid
substitution
substitution









A
G; S; T
N; V; C



C
A; V; L
M; I; F; G



D
E; N; Q
A; S; T; K; R; H



E
D; Q; N
A; S; T; K; R; H



F
W; Y; L; M; H
I; V; A



G
A
S; N; T; D; E; N; Q



H
Y; F; K; R
L; M; A



I
V; L; M; A
F; Y; W; G



K
R; H
D; E; N; Q; S; T; A



L
M; I; V; A
F; Y; W; H; C



M
L; I; V; A
F; Y; W; C;



N
Q
D; E; S; T; A; G; K; R



P
V; I
L; A; M; W; Y; S; T; C; F



Q
N
D; E; A; S; T; L; M; K; R



R
K; H
N; Q; S; T; D; E; A



S
A; T; G; N
D; E; R; K



T
A; S; G; N; V
D; E; R; K; I



V
A; L; I
M; T; C; N



W
F; Y; H
L; M; I; V; C



Y
F; W; H
L; M; I; V; C










For example, changing from A, F, H, I, L, M, P, V, W or Y to C is semi-conservative if the new cysteine remains as a free thiol. Furthermore, the skilled person knows that glycines at sterically demanding positions should not be substituted and that P should not be introduced into parts of the protein which have an alpha-helical or a beta-sheet structure.
The present invention is also directed to the manufacturing of the proteins by methods already explained above. In short such method comprises

    (a) culturing a cell of the present invention under suitable conditions; and
    (b) isolating the protein produced by the cultured cell.


Another preferred embodiment of the present invention is directed to a method of detecting a mutation at position 2378, 2789, 3287, 3342, 3364, 3683, 4321, 5096 and/or 6059 in the nucleic acid molecule of SEQ ID NO: 1 or 2 in a sample, the method comprising:

    (a) contacting said sample with the nucleic acid molecule according to the present invention, and
    (b) detecting the presence of the mutation.


Preferably, the sample is selected from

    (a) a sample, in particular a biopsy, from human tissue or cells, in particular from the brain, in particular putamen or substantia nigra; heart, lung and/or blood lymphocytes; Or
    (b) RNA and/or DNA from a sample, in particular a biopsy, from human tissue or cells, in particular from the brain, in particular putamen or substantia nigra; heart, lung and/or blood lymphocytes;


In general, the detection can be carried out by Southern blot hybridization, Northern blot hybridization, PCR or RT-PCR including real-time RT-PCR, techniques which are well known to a person skilled in the art. The mutation can also be detected by radiography, fluorescence, chemiluminescence, or any combination thereof. Preferably automated sequencing can be carried out, an electrophoresis method run basically in a capillary (column) combined with fluorescence.
Other methods for detection and/or quantification of the amount of polynucleotides, i.e. for the methods according to the invention allowing e.g. the determination of the level of expression of a polynucleotide containing a mutation, are real time methods known in the art as the TaqMan® method disclosed in WO92/02638. This method exploits the exonuclease activity of a polymerase to generate a signal. In detail, the (at least one) target nucleic acid component is detected by a process comprising contacting the sample with an oligonucleotide containing a sequence complementary to a region of the target nucleic acid component and a labeled oligonucleotide containing a sequence complementary to a second region of the same target nucleic acid component sequence strand, but not including the nucleic acid sequence defined by the first oligonucleotide, to create a mixture of duplexes during hybridization conditions, wherein the duplexes comprise the target nucleic acid annealed to the first oligonucleotide and to the labeled oligonucleotide such that the 3′-end of the first oligonucleotide is adjacent to the 5′-end of the labeled oligonucleotide. Then this mixture is treated with a template-dependent nucleic acid polymerase having a 5′ to 3′ nuclease activity under conditions sufficient to permit the 5′ to 3′ nuclease activity of the polymerase to cleave the annealed, labeled oligonucleotide and release labeled fragments. The signal generated by the hydrolysis of the labeled oligonucleotide is detected and/or measured. TaqMan® technology eliminates the need for a solid phase bound reaction complex to be formed and made detectable. Other methods include e.g. fluorescence resonance energy transfer (FRET) between two adjacently hybridized probes as used in the LightCycler® format described in U.S. Pat. No. 6,174,670.
A preferred protocol if the polynucleotide is in form of a transcribed nucleotide is a method where total RNA is isolated, cDNA and, subsequently, cRNA is synthesized and biotin is incorporated during the transcription reaction. The purified cRNA is applied to commercially available arrays which can be obtained e.g. from Affymetrix. The hybridized cRNA is then detected. The arrays are produced by photolithography or other methods known to experts skilled in the art.
Consequently, the method can be carried out on an array, e.g. in a robotics system or using microfluidics.
The present invention is also directed to a diagnostic kit containing at least one nucleic acid molecule of the present invention for diagnosing a neuronal disease, in particular a neurodegenerative disorder, especially Parkinson Disease (PD) including, without limitation, sporadic PD, Alzheimer Disease (AD), amyotrophic lateral sclerosis (ALS), synucleinopathy and/or tauopathy, in combination with suitable auxiliaries. Suitable auxiliaries, as used herein, include buffers, enzymes, labelling compounds, and the like. In a preferred embodiment, the nucleic acid molecule contained in the kit is a nucleic acid molecule which is capable of hybridizing to the mRNA corresponding to at least one nucleic acid molecule of the present invention. Preferably, the nucleic acid molecule is attached to a solid support, e.g. a polystyrene microtiter dish, nitrocellulose membrane, glass surface or to non-immobilized particles in solution. Alternatively, the diagnostic kit contains one or more means necessary for automated sequencing.
The present invention refers also to a pharmaceutical containing at least one nucleic acid molecule or a protein of the present invention which can be used for the prevention or treatment of a neurodegenerative disorder, especially Parkinson disease including, without limitation, sporadic PD, AD, amyotrophic lateral sclerosis (ALS), synucleinopathy and/or tauopathy. Therefore, the nucleic acid molecule or protein of the present invention can also be used for the preparation of a medicament for treating a neurodegenerative disorder as e.g. exemplified above.
Another embodiment of the present invention is directed to a method for screening a pharmaceutical or diagnostic agent, the method comprising:

    (a) providing at least one nucleic acid molecule or a protein of the present invention,
    (b) providing a test compound, and
    (c) measuring or detecting the influence of the test compound on the expression activity of the nucleic acid molecule or the protein.


For example, the test compound is provided in the form of a chemical compound library. According to the present invention the term “chemical compound library” refers to a plurality of chemical compounds that have been assembled from any of multiple sources, including chemically synthesized molecules and natural products, or that have been generated by combinatorial chemistry techniques.
The influence of the test compound can be measured or detected in a heterogeneous or homogeneous assay. As used herein, a heterogeneous assay is an assay which includes one or more washing steps, whereas in a homogeneous assay such washing steps are not necessary. The reagents and compounds are only mixed and measured. Heterogeneous assays are, for example, ELISA, DELFIA, SPA and flashplate assays. Alternative homogeneous assays are, for example, TR-FRET, FP, ALPHA and gene assays.
The method can also be carried out on an array or using whole cells, e. g. in a robotics system or using microfluidics.
Methods for preparing such arrays using solid phase chemistry and photolabile protecting groups are disclosed, for example, in U.S. Pat. No. 5,744,305. These arrays can also be brought into contact with test compound or compound libraries and tested for interaction, for example binding or changing conformation.
Whole cells usually grow at the bottom of multiwell plates and are fixed and permeabilized, blocked and incubated with e.g. a primary (P)-specific antibody against the substrate of interest. Then, e.g. Europium labelled or HRP conjugated secondary antibodies in conjunction with specific chemiluminescent or colorimetric substances, e.g. as described above, are utilized to generate the signal. In combination with the use of a microscope not only the amount of (P)-specific antibodies can be quantified on the single cell level, but also phosphorylation-induced translocations of a substrate or morphological changes of the cells.
The method can also be carried out in form of a high-through put screening system. In such a system advantageously the screening method is automated and miniaturized, in particular it uses miniaturized wells and microfluidics controlled by a roboter.
An example for a pharmaceutical or diagnostic agent which can be found by the screening assay of the present invention is an antibody or antibody derivative specifically binding a protein of the present invention.
Therefore, the present invention is also directed to an antibody or antibody derivative which specifically binds a protein of the present invention.
The antibody is either polyclonal or monoclonal, preferably it is a monoclonal antibody. The term antibody derivative is understood as also meaning antigen-binding parts of the inventive antibody, prepared by genetic engineering and optionally modified antibodies, such as, for example, chimeric antibodies, humanized antibodies, multifunctional antibodies, bi- or oligospecific antibodies, single-stranded antibodies, F(ab) or F(ab)2 fragments, which are all well known for a person skilled in the art.
The antibodies of the present invention can also be produced by immunization of a mammal with an immunogenic peptide and/or recombinantly using standard protocols. A particularly preferred immunogenic peptide is the peptide with the amino acid sequence “CRMGIKTSEG TPGFRAPEVA RGNVIYNQQA D” (SEQ ID NO:3) because it represents the kinase domain of KASPP/LRRK2 (amino acids Nos. 2025-2055) and shows homology between mouse and human of 100%.
The antibodies and antibody derivatives of the present invention can be used e.g. for the diagnosis and/or prevention and/or treatment of a neuronal disease, in particular a neurodegenerative disorder, especially Parkinson disease (PD) including, without limitation, sporadic PD, Alzheimer disease (AD), amyotrophic lateral sclerosis (ALS), synucleinopathy and/or tauopathy, but also for the identification of other pharmacologically active substances. Particular uses of the antibodies and/or antibody derivatives of the present invention are e.g. in Western blots, immuno precipitation, immuno fluorescence or ELISA.
The invention will now be further illustrated below with the aid of the Figures, Tables, Sequence Listings and Examples, without being restricted hereto.
DESCRIPTION OF THE TABLES, THE SEQUENCES AND THE FIGURES


    Table 1 shows the 29 genes and its sources which have been sequenced in the candidate region D12S1692-D12S85. “KASPP/LRRK2” is the abbreviation of the new gene of the present invention.
    Table 2 shows primer sequences for haplotype analysis of the second study consisting of two flanking and three intragenic markers.
    Table 3 shows the frequency of the mutations of the second study. Mutational screening was performed in 53 PD families additional to the 34 families of the first study, 337 patients with sporadic PD and 1200 matched controls.
    Table 4 shows the clinical and neuroimaging features of affected members of the families of the second study. Not all subjects could be investigated with the same methods, which is indicated with nd (not done). No change in comparison with normal is indicated with na (no alteration). y year,  ̃ongoing at the time of examination, B bradykinesia, R rigidity, RT resting tremor. For brief evaluation of olfaction a sniffing test consisting of 8 different odours (/8) was used.
    Table 5 shows the neuropsychological assessment of the second study. Tests applied for intelligence (LPS-K), executive function (Tower of London), interference (CWIT), dementia CERAD 1-8; concentration (D2) as well as mood (BDI) and quality of life (PDQ-39. ↓ performance below,  ̃average and I above average of matched healthy controls.
    SEQ ID NO: 1 shows the nucleotide sequence and the amino acid sequence of a KASPP/LRRK2 including the sites of the particular mutations found in the specified families (bold face).
    SEQ ID NO: 2 shows the nucleotide sequence and the amino acid sequence of human KASSP/LRRK2 including the sites of the particular mutations found in the specified families (bold face).
    SEQ ID NO: 3 shows the amino acid sequence of the peptide used for the production of monoclonal antibodies against KASSP/LRRK2.
    SEQ ID NO: 4 shows the relevant section of the amino acid sequence of the S212L polymorphism of human KASSP/LRRK2. The variation is shown in bold face.
    SEQ ID NO: 5 shows the relevant section of the nucleic acid sequence of the c634t polymorphism of human KASSP/LRRK2. The variation is shown in bold face.
    SEQ ID NO: 6 shows the relevant section of the amino acid sequence of the M2397T polymorphism of human KASSP/LRRK2. The variation is shown in bold face.
    SEQ ID NO: 7 shows the relevant section of the amino acid sequence of the t7190c polymorphism of human KASSP/LRRK2. The variation is shown in bold face.





BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the pedigree structure of the two largest families: A (German-Canadian), D (Western Nebraska) and with mutations. Blackened symbols denote affected family members; asterisks (*): individuals typed for the mutation, m: mutation carrier and wt: wildtype. To protect the confidentiality of these results, the genotypes of some unaffected individuals of families A and D are not shown.
FIG. 2 shows pedigree structure of smaller families with mutations. Blackened symbols denote affected family members; asterisks (*): individuals typed for the mutation, m: mutation carrier and wt: wildtype. To protect the confidentiality of these results, the genotypes of some unaffected individuals of family 469 are not shown.
FIG. 3 shows the three across species highly conserved amino acid substitutions R1441C, Y1699C and I1122T (SEQ ID NOs:21-39).
FIGS. 4A-4K show the nucleotide (SEQ ID NO:20) and amino acid sequence (SEQ ID NO:8) of KASPP/LRRK2 as well as the location of the exons 1-51. The vertical lines mark the last and the first nucleotides of the exon, respectively.
FIGS. 5A-5C show A: exon positions; B: schematic drawing of KASPP/LRRK2 with domains, primer positions for cDNA amplification and positions of mutations; and C: Protein alignment of three mutations conserved among hs: Homo sapiens (SEQ ID NOs:40, 45, and 50), mm: Mus musculus (SEQ ID NOs:41, 46, and 51), rn: Rattus norvegicus (SEQ ID NOs:42, 47, and 52), ce: C. elegans (SEQ ID NOs:43, 48, and 53) and dm: Drosophila melanogaster (SEQ ID NOs:44, 49, and 54).
FIGS. 6A-6F show pedigree structures of families with KASPP/LRRK2 mutation. Except for family DE038 which is shown to demonstrate cosegregation in the first family investigated and DE032 (FIG. 6E), which is displayed to demonstrate the same haplotypes in the two families affected by the I2020T mutation, all pedigrees display novel families.
Blackend symbols denote family members with the clinical presentation of PD; “+” denotes a genotyped individual, with “M” for mutation carriers and “wt” for wild-type KASPP/LRRK2. The dotted symbols in FIG. 6F denote family members with the clinical presentation of tremor. To protect confidentiality the genotype of some unaffected family members are not shown. Moreover, the gender of individuals in the youngest generation of family E is disguised.
FIGS. 7A and 7B show A; exon positions; and B: schematic drawing of KASPP/LRRK2 with domains and positions of mutations.
FIG. 8 shows the autophosphorylation of wild type and mutated KASPP/LRRK2. In the upper panel an autoradiogram of an SDS-PAGE blotted onto PVDF membranes is shown. γ-32P-ATP incorporation (1 h) into KASPP/LRRK2 wildtype and I2020T mutant is visualized using a phosphoimaging system. A loading control by immunoblotting with anti FLAG M2 is shown in the lower panel. All samples shown are form the same experiment and were separated on the same gel.
FIGS. 9 (A) shows a scheme of the KASPP/LRRK2-domain structure and the used Tag-fusion constructs of LRRK2.

    
    
        (B) shows SDS gel separation of associated proteins co-isolated by tandem affinity purification of KASPP/LRRK2-kinase domain (lane 1) and a vector control (lane 2). The proteins were visualized by colloidal coomassie staining.
        (C) shows coimmuno-precipitation. Two FLAG tagged LRRK2-baits (full-length and kinase domain) were tested for interaction with HA tagged full length KASPP/LRRK2. The co-precipitated HA-tagged KASPP/LRRK2 was visualized by immuno-blotting (3F10 anti HA, upper panel). A loading control for the bait-constructs is shown in the lower panel (immuno-blot: anti Flag M2). FIG. 15 (B) is the same figure as FIG. 9 (C) in a better shape.
    
    


FIG. 10 shows the immunofluorescence of different cell structures.
FIG. 11 (A) shows cell fractionation of HEK293 cells over expressing KASPP/LRRK2-Flag. The different pellet fractions 700×g pellet (cell pellet), the 10.000×g pellet (10K pellet), 160.000×g pellet (160K pellet) and the cytosolic fraction (160K supernatant) are shown. The localization of LRRK2-Flag is shown in the first lane. The localization of specific markers for the cytoskeleton (beta-tubulin), mitochondrial membranes (Tom20) and the endoplasmic reticulum membrane (Sec61-alpha) are shown below.

    
    
        (B) shows carbonate extraction of the 160K pellet fraction. The starting material is shown in column 1, the pellet fraction in column 2 and the supernatant fraction in column 3. LRRK2-flag is shown in the first lane. For quality control of the extraction, immuno-blots for several ER-marker proteins have been provided: a luminal ER marker (BiP/GRP78, a 78 kD glucose regulated protein), a peripheral cytosolic ER-associated marker (p97, VCP) and an integral ER membrane marker (Sec61-alpha).
    
    


FIG. 12 (A) shows a further overview of KASPP/LRRK2-domain structure and constructs. The kinase domain of human KASPP/LRRK2 (1), the full-length LRRK2 (2) and a disease associated LRRK2 mutant 12020T (3) were cloned in frame into a modified pcDNA3.0, containing a C-terminal affinity tag. The I2020T mutation is localised, as marked, in the kinase domain of KASPP/LRRK2. Additionally, wild-type KASPP/LRRK2 was C-terminally tagged with a Hemagglutinin (HA) epitope (4) and a GFP (green fluorescent protein)-tag (5).

    
    
        (B) shows LRRK2-tag and LRRK2 I2020T-tag constructs expressing an approximately 280 kD protein in HEK293 cells, visualised by Western-blotting after SDS-PAGE.
    
    


FIG. 13 shows KASPP/LRRK2 appearing in the particulate fractions upon subcellular fractionation and is associated with membranes.

    
    
        (A) shows KASPP/LRRK2 co-sediments with membranes. HEK293 cells were fractionated into a cell pellet (700×g) an organelle pellet (10K pellet), a soluble cytosolic fraction (cytosol) and a microsomal fraction (160 k pellet). The fractions were analysed by SDS-PAGE and Western blotting with antibodies against the Flag-tag, TOM20 (mitochondria), PMP70, (peroxisomes), BiP/GRP78, (ER lumen), Sec61α (ER membrane), p50cdc37 (cytosol) and β-tubulin (microtubules).
        (B) shows an alkaline extraction of KASPP/LRRK2. The 160K pellet was treated with 100 mM sodium carbonate. Membrane and soluble fraction (pellet and supernatant, respectively) were separated by centrifugation and analysed as in (A) using antibodies against the integral ER membrane protein Sec61α, the cytosolic ER-associated protein p97/VCP and the luminal ER protein BiP/GRP78.
    
    


FIG. 14 shows that KASPP/LRRK2-GFP localises to mitochondria, endoplasmic KASPP/LRRK2-GFP (GFP fluorescence shown in the middle panel) were immunostained for a) mitochondria (TOM20), b) endoplasmic reticulum (PDI), c) Golgi (58K Golgi) d) peroxisomes (PMP70), e) intermediate filaments (vimentin), f) microtubular cytoskeleton (β-tubulin) and g) Phalloidin-Tritc (actin cytoskeleton). The right panel depicts digitally merged images taken from the same micrograph section and merges green fluorescence (GFP), red alexa 568 staining (specific markers) and nuclear staining with DAPI.
FIG. 15 shows that KASPP/LRRK2 dimerises and interacts with HSP90 and p50cdc37.

    
    
        (A) shows co-purification of differently tagged KASPP/LRRK2-constructs: HA-tagged full-length KASPP/LRRK2 was tested for its ability to interact with two different tagged KASPP/LRRK2 baits (a full-length and a kinase domain only construct). The constructs were co-expressed transiently in HEK293 cells prior to cell-lysis and purification. The result of the co-purification of HA-tagged KASPP/LRRK2 with the Step/Flag-tagged baits is shown in the upper left panel (pellet). The co-precipitated HA-tagged KASPP/LRRK2 was visualised by Western blotting (3F10 anti-HA).
        (B) is the same figure as as FIG. 9 (C) in a better shape.
        Controls: In order to demonstrate equal expression of KASPP/LRRK2-HA a Western blot (anti-HA) of the supernatants is shown (upper right panel). An equal loading of purified bait-proteins was ensured by Western blotting (anti-tag, lower left panel). Purification efficiency of Strep/Flag-tagged baits was determined by Western blotting of the depleted supernatants: after their affinity binding to the beads, no detectable bait protein remains in the supernatants (lower right panel).
    
    


FIG. 16 shows western blots of HEK293 cells with different hybridoma supernatants. The first western blot shows the result of a lysate of HEK293 cells which overexpress KASPP/LRRK2 (named “LRRK2”). The other western blot shows the result of a lysate of HEK293 cells transfected with an empty vector (named “vector”).
FIGS. 17A-17K show the nucleotide sequence (SEQ ID NO:1) and the amino acid sequence (SEQ ID NO:8) of a KASPP/LRRK2 including the sites of the particular mutations found in the specified families (bold face).
FIGS. 18A-18K show the nucleotide sequence (SEQ ID NO:2) and the amino acid sequence (SEQ ID NO:9) of a KASPP/LRRK2 including the sites of the particular mutations found in the specified families (bold face).
FIG. 19 shows the amino acid sequence of the peptide used for the production of monoclonal antibodies against KASSP/LRRK2 (SEQ ID NO:3), the relevant section of the amino acid sequence of the S212L polymorphism of human KASSP/LRRK2 (variation shown in bold; SEQ ID NO:4), the relevant section of the nucleic acid sequence of the c634t polymorphism of human KASSP/LRRK2 (variation shown in bold; SEQ ID NO:5), the relevant section of the amino acid sequence of the M2397T polymorphism of human KASSP/LRRK2 (variation shown in bold;
SEQ ID NO:6), and the relevant section of the amino acid sequence of the t7190c polymorphism of human KASSP/LRRK2 (variation shown in bold; SEQ ID NO:7).



Clones:



















 1) 4E1
 2) 4A11
 3) 3G3
 4) 7F1
 5) 2H8



 6) 2D7
 7) 4A8
 8) 2B5
 9) 4G11
10) 3G6



11) 4G11
12) 3D9
13) 4H11
14) 4F12
15) 4B7.










EXAMPLES OF THE FIRST STUDY
Example 1
Genetic Analysis
DNA Extraction
Genomic DNA from peripheral blood lymphocytes was extracted using standard protocols and after obtaining informant's consent from all participating family members.
Sequence Analysis
Genomic sequences and annotations were obtained from the National center for Biotechnology Information (NCBI) and University of California Santa Cruz (UCSC). Primers for mutation screening were designed using Primer3 software integrated into script to allow for automated primer design. Exon sequences and exon-intron boundaries were amplified with intronic primers and sequenced them directly by BigDye Terminator Cycle sequencing kit (Applied Biosystems). Between Markers D12S1692 and D12S85 a total of 29 genes or RNAs were sequenced (see Table 1).
Haplotype analysis
Haplotypes were constructed by hand using the repeat markers previously used for linkage analysis (Zimprich, A. et al., 2004, supra). Intragenic markers for haplotype analysis for fam 469 and fam D were established by searching the whole gene for repeat polymorphisms by use of a “tandem repeat finding program” (http://c3.biomath.mssm.edu/trf.html). Polymorphic repeats were found in intron 5 (caa), intron 20 (atct) and intron 29 (ac).
Linkage analysis
Twopoint LOD scores were calculated using the MLINK program (V 5.10) in its FASTLINK implementation (V4.1P). Phenocopy rate was set at 0.01, penetrance for the heterozygous state and homozygous mutation carriers at 0.90. The allele frequency of the disease causing allele was set at 0.001, as was the frequency of the mutation used as the marker.
Screening of Mutations and Polymorphisms
For mutations 2000, for polymorphisms at least 1200 control chromosomes from a mixed European descent were screened as controls. In addition 300 patients were screened with sporadic parkinson's disease. Genotyping was performed on a MALDI-TOF mass-spectrometer (Sequenom MassArray system) using the homogeneous mass-extension (hME) process for producing primer extension products (Tang K. et al., Proc. Natl. Acad. Sci USA, 96, 10016-10020, 1999).
Amplifikation of KASPP/LRRK2
The complete coding sequence of KASPP/LRRK2 was amplified from human brain cDNA by using Marathon-Ready cDNA (BD Biosciences Clontech). Primers were set to amplify three overlapping fragments from exon1-21 (P1f, P1r), from exon 20-35 (p2f, p2r) and exon 34-51 (p3f, p3r) (see FIG. 5). Sequence information were derived from published the mRNA of DKFZp434H211. PCR products were run on agarose gel to check its length and integrity.
Example 2
Northern blot Analysis
Northern blot analysis was performed according to the manufacturers protocols (BD Biosciences). For hybridization a KASPP/LRRK2 cDNA fragment was used (bp 6577-7655; corresponding to exon 45-3′UTR.
Example 3
LightCycler Experiments
mRNAs from different human tissues were purchased from BD Biosciences, (Clontech BD Sciences, Palo Alto, USA) and were reverse transcribed with the Transciptor First Strand cDNA Synthesis Kit (Roche Applied Sciences, Mannheim, Germany) according to the manufacturers protocol. For real-time amplification of KASPP/LRRK2 three specific PCR products spanning exon1 to 8, exon13 to 19 and exon 31 to 39 were quantified using the
LightCycler Instrument (Roche Applied Sciences, Mannheim, Germany). Fluorescence-labeled hybridization probes providing maximum specificity were used for product detection. Calculation of sample concentrations were performed using the fit-point algorithm. The Phorphobilinogen deaminase (h-PBGD) gene, a low-copy housekeeping to gene, was used as an external standard and absolutely quantified using the (h-PBGD Housekeeping Gene Set, Roche-Applied Science). Relative transcript levels were calculated as ratios of Park8/PBGD normalized to adult whole brain adult expression as 100%
EXAMPLES OF THE SECOND STUDY
Subjects and Methods
Subjects
DNA of 51 index patients from PD families compatible with an autosomal dominant mode of inheritance of PD or with a mode of inheritance that could not be assigned to a typical Mendelian trait, as well as two affected sib pairs were analyzed for mutations in the KASPP/LRRK2 gene. Clinical diagnosis was based on published criteria (Hughes et al., J Neurol Neurosurg Psychiatry; 55:181-4, 1992) and severity of the disease was rated according to the Unified Parkinson's Disease Rating Scale (UPDRS) (Fahn et al., Recent Developments in Parkinson's Disease. New York: Macmillan,153-163, 1987) and Hoehn and Yahr staging. In one family (family E) typical Parkinsonian features were only found in one member (III-11), while all other affected family members presented primarily with postural tremor. Moreover, all novel and known mutations were investigated in a cohort of 337 patients with apparently sporadic PD (204 male, 133 female, mean age 53±13 years) and a cohort of 1200 subjects without any extrapyramidal disorders matched for age±5 years and sex. Allele frequency of the polymorphism N551K; 1653C>G was investigated in 888 of these control subjects.
DNA of patients with familial and sporadic PD was obtained from our gene bank, while DNA of control subjects comprised the Kora cohort obtained form the National Research Center of Environment and Health/Munich, Germany. All patients and controls had given informed consent to mutational screenings, which was approved by the local ethical committee.
Mutational Screening
Genomic DNA was isolated from peripheral blood using standard protocols. Mutational screening in patients of families with autosomal dominant PD was performed for all exons and exon-intron boundaries of the KASPP/LRRK2 gene by direct sequencing of both strands using the BigDye Terminator Cycle sequencing kit (Applied Biosystems) with the same primers and under the same condition as described above.
Mutational screening in patients with sporadic PD and control subjects was performed using an ABI 7900 Allelic Detection system. As described above genotyping was performed on a MALDI-TOF mass-spectrometer (Sequenom Mass Array system) using the homogeneous mass-extension (hME) process for producing primer extension products.
In families with identical mutations haplotype analysis of the KASPP/LRRK2 region was performed. Haplotypes were constructed using 5 fluorescent-labeled microsatellite markers, two flanking and three intragenic (Table 2). DNA fragments containing the polymorphic marker sequences were amplified by PCR. Fluorescently labelled PCR products were analyzed on an ABI 3100 automated sequencer with a fluorescence detection system.
DNA extraction from Brain Tissue
In the large family with only one patient with the clinical picture of PD and many others affected by symptoms resembling essential tremor (family E), blood for DNA extraction was only available of the PD patient. To disclose a possible association of a KASPP/LRRK2 mutation and clinical features of essential tremor DNA was extracted from a microscope slide with paraffin-embedded brain tissue (cerebellum) of one family member with this phenotype (III-7).
Deparaffinisation was performed using xylene and ethanol followed by a proteinase K digestion. The probe was then purified using phenol/chloroform extraction and finally precipitated with LiCl and Ethanol.
Clinical Investigations
The index patients of families with mutations in the KASPP/LRRK2 gene were invited for a genetic consultation and clinical and neuroimaging investigations under an approved protocol. After informed consent was given a thorough neurological examination was performed and olfactory function was tested using sniffing sticks (Daum et al., Nervenarzt, 71:643-50, 2000). A neuropsychological test battery sensitive for dementia, concentration, planning, as well as intelligence was chosen (Table 5). To evaluate mood and sensitivity patients were asked to complete the Becks Depressions Inventar (BDI) and the PDQ-39 Parkinson's Disease Quality of Life Questionaire.
Electrophysiological investigations comprised neurography of the right tibial and sural nerve, and elektromyography of the quadriceps to discern subclinical changes in motor unit potentials and possible abnormal spontaneous activity. Moreover, magnet evoked potentials were performed in all patients without contraindications.
Neuroimaging
Structural neuroimaging comprised transcranial ultrasound (TCS) and magnet resonance imaging (MRI).
For TCS a phased-array ultrasound system equipped with a 2.5-MHz transducer with an axial resolution of approximately 0.7 mm and a lateral resolution of about 3 mm (Elegra, Siemens, Erlangen, Germany) was used. The examination was performed through a preauricular acoustic bone window with a penetration depth of 16 cm and a dynamic range of 45 dB as described previously (Berg et al., Ultrasound Med Biol, 25: 901-904, 1999). The SN was identified within the butterfly-shaped structure of the mesencephalic brainstem as clearly as possible, scanning from both temporal bone windows, then the area of hyperechogenic signals in the SN-region was encircled and measured (Berg et al., 1999, supra, Berg et al., J Neurol, 248:684-689, 2001). An area of SN hyperechogenicity ≦0.19 cm2 was classified as normal, an area >0.19 and ≦0.24 cm2 as moderately and an are of >0.24 cm2 as markedly hyperechogenic (Berg et al., 1999, supra).
MRI was performed on a Magnetom Avanto 1.5 Tesla, Siemens AG, Germany.
Results
Mutational Screening
Screening the entire coding region of the KASPP/LRRK2 gene of one index patient each from 55 families identified 7 novel families with amino acid substitutions (FIG. 6a-f). Four of these are novel missense mutations: R793M; 2378G>T in family DE041 and to family T11239, Q930R; 2789A>G in family DE022; S1096C; 3287C>G in family E and S1228T; 3683G>C in family DE031. The missense mutation R793M was also found in one patient with sporadic PD and one control person.
The so far most common amino acid substitution G2019S; 6055G>A was only found in one sporadic PD patient, who showed typical levodopa responsive Parkinson's disease with an age of onset of XX and no additional clinical features. Moreover one additional patient was detected with the already above described splice site mutation 3342A>G (family T11288) and one more family with the above described 12020T mutation (family T10738).
Except for the R793M mutation, which was found in one control person none of the mutations were found in the control group (Table 3). There was no significant difference in the minor allele frequency of the known N551K; 1653C>G polymorphism between patients with sporadic PD (6.5%) and control subjects (7.3%).
Haplotype Analysis
Haplotype analysis revealed common haplotypes for the two novel families affected by the R793M mutation as well as for family T10758 and family DE032 affected by the I2020T mutation, indicating common founders for these mutations (FIGS. 6a and 6e). Although members of family DE032 and T10758 were not aware of common ancestors, they originate from the same geographical area (Baden Wurttemberg, Southern Germany).
Family T11239 and DE041 were recruited from more distinct geographical areas (Baden Württemberg family T11239 and Hesse family DE041). Members of these families were also not aware of common ancestors. For the A3342G splice site mutation no common haploptype was found in the affected families (DE038 and T11288).
Clinical Findings
Extensive clinical a neuroimaging examination revealed the features listed in Table 4.
All patients investigated had typical signs of Parkinson's disease. However, features differed between members within the same family affected by the same mutation as well as between different families with the same mutation. Moreover, penetrance was found to vary for different mutations.
Common Findings in Patients with KASPP/LRRK2 Mutations
All mutation carriers with clinically apparent PD had the typical Parkinsonian features including bradykinesia, tremor and rigidity. Moreover, all patients experienced substantial relief of symptoms after application of L-dopa, although therapy was complicated in one patient (T11288 II-5) by hallucinations. Estimation of olfactory function by application of 8 sniffing sticks revealed a moderate to severe loss of identification capacity in three of 5 subjects. Postural instability was only found late in the disease course. Hallucinations were reported seldom and only occurred after long disease duration or associated with dementia, whereas sleep disturbances were reported by 80% (Table 4).
Intrafamily Differences in Clinical Presentation
R793M: Two sisters are affected with a difference of age of onset of 15 years. While at disease onset II-1 had only slight postural tremor on the right side, the initial symptom of II-2 was resting tremor on the left side. An equivalent type of PD developed in II-2 while II-1 showed no resting tremor at all but an akinetic-rigid type of PD (FIG. 6a).
Q930R: Span of age of onset was 21 years among the three members of the same generation affected. Only brother III-7 developed severe dementia and hallucinations after more than 20 years of disease duration (FIG. 6b).
3342A>G: While sister II-7 of family T11288 presented with typical Parkinsonian features, the clinical picture of early severe dementia, hypersensitivity to dopaminergic halluzinations and daytime sleepiness with fluctuation of vigilance resembled DLBD in II-5. However, mutational analysis revealed the wt allele in II-7. A phenocopy for the more typical PD presentation must therefore be postulated, while the atypical DLBD-type was indeed associated with the 3342A>G splice site mutation. However, the fact that this variation co-segregated with the mutation in the above described family DE038 is an indication for a mutation rather than a benign polymorphism.
Interfamily Differences in Clinical Presentation for the Same Mutation
R793M: While in III-3 of family T11239 speaking was impossible because of severe tongue dyskinesia, the affected sisters of family 41 did not show any atypical signs except of postural tremor in II-1 (FIG. 6a).
3342A>G: In family T11288 both sisters and in the reported family DE038 father and III-1 were severely affected by the disease. III-3, however, did not show any Parkinsonian symptoms except of minimal resting tremor of the right thumb for more than 15 years (FIG. 6c).
Age of Onset
Mean age of onset in the novel families was 58±14 years. However, age of onset differed between members of the same family. In offsprings of mutation carriers of the three novel families, in whom clear data of ancestors was available (Table 4) the diagnosis if PD was established earlier and also investigation of an additional family member in family DE032 revealed and earlier diagnosis (41 years), while mean age of onset was 54 (48-59 years) in generation I-III (FIG. 6e).
Penetrance
Combining findings of the second study and the first study a clear autosomal dominant mode of inheritance was found in at least one affected family for the splice site mutation of exon 24, and for the missense mutations of exon 25, exon 27, exon 31, and exon 41. No strong genetic pattern was found in families affected by missense mutations in exon 19, 21 and 24.
Exon 19; R793M: In family T11239 only the uncle of the index patient was affected, while the father who died at the age of 68 did no show any extrapyramidal sign during life time. In family DE041 two sisters showed typical signs of PD during life time, while none of the parents who died both at the age of 74 showed any Parkinsonian signs (FIG. 6a).
Exon 21, Q930R: Of nine sisters and brothers in family DE022 three were affected by the mutation and had clinical signs of PD, while one other sister and brother, also mutation carrier are not affected by PD at an age of more than 70 years. Neither the mother (II-3), who died at the age of 90 years nor her brother (II-2), who died at 75 years of age showed any Parkinsonian features during life time. The cousin of the affected members of the to family (III-4) displayed signs for typical PD but was not carrier for the Q930R mutation, indicating sporadic PD in this family member. However, her sister (III-3), was found to have the mutation. Having already reached the age of 77, she has no clinical signs allowing the diagnosis of PD. Both II-3 and II-2 must have been mutation carriers. The fact that none of them and also III-3 have not shown any Parkinsonian features during life time argues for incomplete penetrance of this mutation.
Exon 24, S1096C: In this large family with an additional tremor phenotype (1f) only III-12 was mutation carrier, affected by PD. One child of his brother, who showed only features of essential tremor but no Parkinsonian symptoms until death at the age of 66 years, is also mutation carrier, indicating incomplete penetrance for this mutation as well.
Phenocopies and Simultaneous Occurrence of Tremor
One family member with typical PD of DE022, associated with the Q930R mutation and one of the sisters of family T11288, (A3342G splice site mutation of the other sister), again with typical Parkinsonian features had wt alleles, arguing for idiopathic PD in these cases.
In family E an autosomal dominant inheritance of tremor is evident (FIG. 6f). Two family members (III-7 and III-11) showed typical Parkinsonian features during life time, in III-11 the S1096C mutation was detected. As there was no blood available of III-7, DNA extracted from brain tissue was investigated. However, in this patient the C3287G mutation could not be detected, indicating a different cause for Parkinson's disease. Of one of the siblings with a tremor phenotype (III-19, presenting with postural and vocal tremor) also only wild type alleles could be identified. The only family member with a tremor phenotype carrying the S1096C mutation must have been the brother of III-12, as one of his children is also mutation carrier. However, as the mutation could not be detected in III-19 incomplete penetrance of Parkinsonian symptomes in a subject also affected by tremor is more likely than an association of tremor with the mutation in this family.
Neuropsychological Findings
Of the 5 patients examined in a thorough neuropsychological investigation, three were able to complete the whole test battery. In all three intelligence was above average of a matched control group (LPS-K), suggesting that subtle neuropsychological deficits may well be compensated. Still, all three showed deficits in executive functions (Tower of London) and had high interference scores (CWIT) indicating incapacity to blind overstimulation (Table 5). This pattern is in accordance with neuropsychological deficits in idiopathic PD. The two others investigated were graded as demented. In patient III-3 of family T11239 MMSE was 22. Additionally, severe tongue dystonia prevented accomplishing the CERAD. In patient II-5 of family T11288 with 3342A>G splice site mutation exhaustability and dementia thwarted completing of neuropsychological testing.
TCS and MRI Findings
TCS: Moderate hyperechogenicity, at least on one side, was found in all but one patient with LRRK2 mutations. Interestingly, none of the patients displayed marked SN hyperechogenicity. MRI showed mild to marked atrophy in the 4 patients investigated (Table 4). The patient with the DLBD phenotype had additionally some evidence for microangiopathy.
BIOCHEMICAL CHARACTERIZATION OF KASPP/LRRK2
Material and Methods
Plasmid and Cloning
Human KASPP/LRRK2 was cloned via PCR from cDNA which has been generated from lymphoblast mRNA. KASPP/LRRK2 was cloned domain-wise in six fragments. Each fragment was cloned into pcDNA3.0 (Invitrogen) and verified by sequencing. The full length sequence was generated by subsequent fusion of the sub-constructs. The HA and FLAG tag were introduced at the 3′ end (c-terminus) of the constructs. The I2020T mutation was introduced into KASPP/LRRK2 by site-directed mutagenesis using the QuikChange® II mutagenesis kit (Stratagene). For fluorescence microscopy, humanised GFP cDNA, derived from pFRED143 (Ludwig, E. et al., J. Virol., 73, 8279-8289, 1999)), was cloned in frame at the 3′ end (c-terminus) of KASPP/LRRK2.
Cell Culture
HEK293 cells were cultured in DMEM supplemented with 10% FBS at 37° C. and 5% CO2. For immuno precipitation (IP), tandem affinity purification or cell fractionation experiments cells were transfected with Effectene® (Qiagen) and kept under full medium for additional 48 h.
Electrophoresis and Immunoblotting
For immunoblotting analyses protein samples were separated by SDS-PAGE and transferred onto Hybond-P PVDF membranes (GE Healthcare). After blocking non-specific binding sites with 5% dry milk in TBST (1 h, RT) (25 mM Tris pH 7.4, 150 mM NaCl, 0.1% Tween-20) membranes were incubated overnight at 4° C. with primary antibodies in blocking buffer (mouse anti-Bip/GRP78 (BD), 1:1000; mouse anti-p50cdc37 (BD), 1:1000; rat anti-HA 5F10, 1.3 μg/ml; mouse anti-p97/VCP (Progen), 1:1000; rabbit anti-PMP70 (Prof. Dr. A. Völkl, University of Heidelberg, Germany), 1:1000; rabbit anti-Sec61α (Acris), 1:1000; mouse anti-TOM20 (BD), 1:1000; mouse anti β-tubulin (Sigma), 1:2000), washed with TBST and incubated for 1 h with horseradish peroxidase (HRP)-coupled secondary antibodies. Membranes were washed and antibody-antigen complexes were visualized using the ECL+chemiluminescence detection system (GE Healthcare) on Hyperfilms (GE Healthcare). For the HA epitope the monoclonal anti HA 5F10 (Roche) was used in a concentration of 1.3 μg/ml (5% dry milk). For the FLAG epitope, the HRP-coupled monoclonal anti-FLAG M2 antibody (Sigma) was used in a dilution of 1:1000 (5% dry milk) Further antibodies are used with the following dilutions: mouse anti β-Tubulin (Sigma) 1:2000; rabbit anti Sec61-α (Acris) 1:1000; mouse anti TOM20 (BD) 1:1000; mouse anti Bip/GRP78 (BD) 1:1000; mouse anti p97/VCP (ProGen) 1:1000).
Cell Fractionation
Cells were harvested via trypsinisation, washed once with cold PBS, resuspended in cold homogenisation buffer (20 mM HEPES pH 7.4, 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM EGTA, 1 mM DTT, 250 mM sucrose, protease inhibitor cocktail (Roche)) and homogenized. Homogenates were centrifuged at 700×g for 10 min to pellet nuclei, debris, and non-disrupted cells (cell pellet). The supernatant was centrifuged at 10,000×g for 20 min to obtain the 10K pellet. Cytosol and 160K pellet were prepared by ultracentrifugation of the 10K supernatant (160,000×g for 1 h).
Carbonate Extraction
160K fractions were diluted with 100 mM (final concentration) sodium carbonate pH 11.5 and for 30 min on ice. The suspensions were centrifuged for 1 h at 160,000×g at 4° C. The supernatants were recovered and proteins precipitated with 10% trichloracetic acid. Membrane pellets and precipitated proteins were subjected to SDS-PAGE and Western blotting analyses.
Immuno Precipitation (IP)
For interaction assays FLAG-tagged KASPP/LRRK2 was lysed for 1 h in lysis buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5% Nonidet-P40, protease inhibitors (Roche), 1 mM orthovanadate) for 1 h at 4° C. After sedimentation of nuclei (10 min, 10.000 g, 4° C.), the supernatant was incubated with anti FLAG M2 agarose beads (Sigma) for 2 h at 4° C. After incubation, beads were washed 4× in lysis buffer and eluted with SDS-gel sample buffer.
Tandem Affinity Purification
The tandem affinity purification was done with a c-terminal tandem affinity purification tag consisting of a tandem StrepII tag and a Flag epitope (Strep/Flag-tag). HEK293 cells transiently expressing the Strep/Flag-tagged constructs were lysed in 50 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5% Nonidet-P40, protease inhibitors and 1 mM orthovanadate for 1 h at 4° C. Following sedimentation of nuclei, the cleared supernatant was incubated for 2 h at 4° C. with streptactin superflow (IBA). Prior to washing, the lysates with suspended resin were transferred to microspin columns (GE Healthcare). Washing (1× with lysis buffer and 2× with TBS) was done in the microspin columns. Washing solution was removed from the columns by centrifugation (10 s, 2,000×g) after each washing step. Protein baits were eluted with desthiobiotin (2 mM in TBS). The eluates were used for LRRK2 co-precipitation experiments of LRRK2-Strep/Flag constructs vs. LRRK2-HA.
For MS analysis, a second purification step was added. For this step, the eluates were transferred to anti-Flag M2 agarose (Sigma) and incubated for 2 h at 4° C. The beads were washed 3× with TBS in microspin columns. Proteins were eluted with Flag peptide (Sigma) in PBS at 200 μg/ml peptide. After purification samples were separated by SDS-PAGE and stained with colloidal coomassie according to standard protocols prior to MS identification (Neuhoff, V. et al., Electrophoresis, 9, 255-262, 1988).
Mass Spectrometry
The proteins were identified by MALDI-MS and MSMS on an AB3700 (Applied Biosystems) instrument. Tryptic in gel proteolysis was done after standard protocols (Shevchenko, A. et al., Anal. Chem. 68, 850-858, 1996). Peptides were spotted on steal targets with the dried droplet method using alpha-cyano-4-hydroxycinnamic acid (Sigma) as matrix (Shevchenko, A. et al., supra). Obtained MS and MS/MS spectra were analysed by GPS explorer software suite (Applied Biosystems).
Kinase Activity Assays (Autophosphorylation Assay)
For kinase assays (autophoshorylation assays), Strep/Flag-tagged full-length wild-type LRRK2 or LRRK2-I2020T variant were transiently expressed in HEK293 cells (4x14 cm culture dishes per construct, 2×14 cm dishes for the vector control). After cell lysis and removal of the nuclei, the purification of LRRK2 variants was done by immunoprecipitation with anti-Flag M2 agarose. The resin was washed 3× in lysis buffer. The tagged proteins were not eluted, since the kinase assays were directly performed on the resin. Each sample was divided in 4 aliquots and stored in TBS+10% glycerol at −80° C. until use.
For the kinase assay, one aliquot of each condition (wild-type LRRK2 and LRRK2-I2020T) was divided into three sub-aliquots (1/2, 1/3, 1/6). Each sub-aliquot, as well as one aliquot of the vector control was incubated with 50 μM ATP, 0.3 μCi [γ-32P] ATP in 30 μl assay buffer (25 mM Tris-HCl pH 7.5, 5 mM β-glycerophosphate, 2 mM DTT, 0.1 mM orthovanadate; 10 mM MgCl2; Cell Signaling) for 1 h at 30° C. Reaction was stopped with Laemmli buffer. Protein samples were resolved by SDS-PAGE and transferred onto Hybond-P PVDF membranes (GE Healthcare). Imaging was done on a phosphoimager system (BioRad). Equal loading was ensured by Western blotting analyses (anti-Flag M2).
Immunofluorescence
HEK293 cells were grown on glass coverslips prior to transfection with GFP-tagged wild-type LRRK2. To avoid cell detachment, coverslips were pre-treated with poly-D-lysine (Sigma) and laminin (Sigma). 48 h post-transfection cells were fixed for 15 min with 4% paraformaldehyde at RT. Fixed cells were permeabilised with PBS containing 0.1% Triton-X 100 for 5 min, blocked with PBS containing 0.1% Tween-20 and 1% BSA and incubated 3 h at RT with primary antibodies in blocking solution [mouse anti-58K Golgi, 1:100 (Abeam); mouse anti-PDI (protein disulfide isomerase), 1:100 (Abcam); rabbit anti-PMP70 (70 kD peroxisomal membrane protein), 1:200; mouse anti-TOM20 (translocase outer mitochondrial membrane protein), 1:500 (BD); mouse anti-β-Tubulin, 1:500 (Sigma); mouse anti-Vimentin, 1:200 (Sigma)]. Coverslips were rinsed six times with PBS and labelled for 1 h with alexa 568-conjugated goat anti-mouse, goat anti-rabbit IgG (Invitrogen) or Phalloidin-TRITC (1:10,000, Sigma). For nuclear staining the solution also contained 1 μg/ml 4,6-diamnodiphenyl-2-phenylindole (DAPI, Sigma). Coverslips were washed six times with PBS, mounted with FluorSave (Calbiochem) and evaluated by fluorescence microscopy using a Zeiss Apotome equipped with Cy3, FITC and Dapi optical filter sets. The obtained images provide an axial resolution comparable to confocal microscopy (Garini, Y. et al., Curr. Opin. Biotechnol., 16, 3-12, 2005).
Results
KASPP/LRRK2 is a Membrane-Associated 280 kD Protein
For functional and biochemical studies, KASPP/LRRK2 was cloned from human cDNA and generated a series of constructs for the expression of Hemagglutinin (HA), Strep/Flag and green fluorescent protein (GFP)-tagged LRRK2 fusion proteins (FIG. 12A). HEK293 cells that were transiently transfected with c-terminal Strep/Flag-tagged wild-type human KASPP/LRRK2, express a  ̃280 kD protein recognised by anti-Flag antibody (FIG. 12B). The observed molecular weight corresponds to that expected for KASPP/LRRK2. An additional weaker signal could be also detected in some cases at  ̃180 kD that is most likely an N-terminal degradation product of KASPP/LRRK2.
In order to determine the subcellular localisation of KASPP/LRRK2, two approaches were used: subcellular fractionation and fluorescence microscopy. For detection of the subcellular distribution of KASPP/LRRK2 in vitro, transfected cells were fractionated by differential centrifugation. The distribution of subcellular organelles in the obtained fractions was then analysed by antibodies specific for mitochondria (TOM20), cytoskeleton (β-tubulin), peroxisomes (PMP70), microsomes (BiP/GRP78, Sec61α) and soluble cytosolic proteins (p50cdc37). LRRK2 was found only in membranous fractions (both 10K and 160K pellets), i.e., fractions enriched in mitochondria (10K pellet) and microsomal membranes (160K pellet) but was absent from the cytosol (FIG. 13A).
In order to investigate whether KASPP/LRRK2 is a membrane-associated or an integral membrane protein, the 160K pellet was treated with sodium carbonate, pH 11.5 (Fujiki, Y. et al., J. Cell Biol., 93, 97-102, 1982). KASPP/LRRK2, together with other known membrane-associated proteins, the luminal ER marker BiP/GRP78 (78 kD glucose regulated protein) and peripheral cytosolic ER-associated marker VCP (valosin-containing protein), was extracted from microsomal membranes, whereas the integral membrane protein Sec61α was recovered in the membrane pellet (FIG. 13B). This provides evidence for KASPP/LRRK2 being a membrane-associated protein rather than integrated into membranes.
Additionally, HEK293 cells that expressed recombinantly Strep/Flag-tagged KASPP/LRRK2 kinase-domain were subjected to subcellular fractionation. In contrast to full-length KASPP/LRRK2, the kinase-domain construct was found in the cytosol, whereas little or no fusion-protein was detected in the particulate fractions (both, 10K and 160K pellet, FIG. 13A). Thus, the kinase-domain is not implicated in the association of KASPP/LRRK2 to membranous structures.
LRRK2 Co-Localises with Discrete Cytoplasmic Structures
Immunofluorescence microscopy was used to determine the subcellular localisation of GFP-tagged KASPP/LRRK2 transiently expressed in HEK293 cells. After fixation, cells were permeabilised and co-immunolabelled with antibodies specific for distinct subcellular structures. In HEK293 cells, GFP-tagged KASPP/LRRK2 demonstrated a cytoplasmic distribution (FIG. 314 column 2). Partial co-localization was observed with inner cellular structures, i.e., mitochondria (TOM20), ER (PDI) and Golgi (58K Golgi). In contrast, no overlap was observed with peroxisomes (PMP70). No co-localization was found with the actin cytoskeleton (Phalloidin-Tritc) and intermediate filaments (Vimentin). However, the strongest co-localisation was an overlap with β-tubulin, suggesting an interaction between KASPP/LRRK2 and the microtubular cytoskeleton. Thus, KASPP/LRRK2 is a cytoplasmic protein associated with a subset of inner cellular membranes, i.e., mitochondria, ER and Golgi, and with the microtubular cytoskeleton.
Autophosphorylation Levels Between I2020T Mutant and Wildtype KASPP/LRRK2
Kinase-domain signatures can be easily detected by bioinformatical tools. Nevertheless, it is necessary to verify the kinase activity of KASPP/LRRK2 by biochemical assays. Furthermore, a comparison of wildtype and mutated KASPP/LRRK2 will contribute to the understanding of the mutation's nature, whether it is a gain- or loss of function mutation.
The wildtype full length protein vs. the I2020T mutant variant was tested for its ability for auto-phosphorylation. No significant differences in the autophosphorylation levels have been observed between the I2020T variant and the wild-type (FIG. 8). This confirms that both, KASPP/LRRK2 and the disease-associated mutation I2020T in the kinase domain of KASPP/LRRK2, possess kinase activity. Quantification of autophosphorylation rates revealed an increase in activity of the I2020T mutant compared to wild-type KASPP/LRRK2 of about 30-50%. This finding may be the basis for the development of an appropriate screening assay for modulating compounds, in particular inhibitors, of the increased kinase activity of the I2020T mutant, as e.g. further described herein.
KASPP/LRRK2 Homodimerization
The kinase domain of LRRK2 is predicted to belong to the class of MAPKKK. A characteristic of such kinases is the formation of dimers. Moreover, for Raf-1 and MLK-3 (mixed lineage kinase 3), one of the closest relatives of LRRK2 in vertebrates, homo-dimerisation is required for activity.
In a first approach, KASPP/LRRK2 was tested for its ability to interact with itself by co-precipitation experiments. Therefore, tandem Flag-tagged KASPP/LRRK2 baits were co-expressed with HA-tagged full length KASPP/LRRK2. As shown in FIG. 9a, the full length KASPP/LRRK2 bait could pull out HA-KASPP/LRRK2 whereas a bait-protein containing only the kinase domain showed no interaction with full length KASPP/LRRK2. Thus, KASPP/LRRK2 interacts with itself indicating formation of homodimers or oligomers of higher order.
In a second approach, differently-tagged KASPP/LRRK2 proteins and co-transfected HEK293 cells were utilized with two constructs for expression of HA and the Strep/Flag-tagged KASPP/LRRK2 fusion proteins, with the intention that a certain fraction of cells expressing two different KASPP/LRRK2 fusion proteins would to address the question of dimerisation by co-precipitation experiments. In addition to the full-length LRRK2 protein, a Strep/Flag-tagged version of the kinase domain only was used (FIG. 12). A comparison of purifications with all three tags showed the best results for streptactin, which almost completely precipitates the tagged proteins. Therefore, streptactin was used for precipitation of KASPP/LRRK2 fusion proteins from solubilised cells co-expressing HA and Strep/Flag-tagged KASPP/LRRK2. As shown in FIG. 15A (lower part) by an anti-Flag antibody, both, the full-length and the KASPP/LRRK2 kinase domain baits were precipitated with the same efficiency. Analysis of the precipitated proteins with the anti-HA antibody showed that only the full-length KASPP/LRRK2 bait could pull out HA-tagged KASPP/LRRK2, whereas the kinase domain did not display any interaction with full-length KASPP/LRRK2 (FIG. 15A, upper left panel). Thus, only full-length KASPP/LRRK2 interacts with itself forming homodimers or oligomers of higher order.
KASPP/LRRK2 Interaction with HSP90 and its Co-chaperone p50cdc37 
To identify proteins which interact with the KASPP/LRRK2 kinase domain tandem affinity purification experiments were performed with a tag system. The purified protein complexes were subjected to SDS page (FIG. 9b). The interacting proteins were identified using mass spectrometry. As shown in FIG. 10b the isolated kinase domain of KASPP/LRRK2 is associated with HSP90 and its co-chaperone p50cdc37. The full-length KASPP/LRRK2, however, binds to HSP90 and p50cdc37 to a very low extend. The interaction with the HSP90/p50cdc37 chaperone-system is shown for several kinases, including the MAPKKK Raf-1 and MLK-3. In both instances, they do not serve as substrates but associate as chaperones participating in maintenance of proper folding of the kinase. This experiment is a further evidence that KASPP/LRRK2 possesses kinase activity and is active in transfected cells.
KASPP/LRRK2 Association with Microsomal Membranes
Information of the localization of KASPP/LRRK2 will help to understand its in vivo function. Using fluorescence microscopy experiments with a c-terminal GFP tagged construct it was shown that KASPP/LRRK2 is cytoplasmic distributed in HEK293 and COST cells (FIG. 10). By immuno co-staining there was no clear co localisation observed with any cellular structure like cytoskeleton or organelles. However, by co-staining with TOM20 and TIM23 partial overlap with mitochondria was obtained.
To further analyze the subcellular localization of this protein, a cell fractionation was performed (FIG. 11a). Surprisingly, no KASPP/LRRK2 was found in the cytosol. However, high amounts of KASPP/LRRK2 were found in the analyzed membranous fractions (both 10K and 160K pellets), i.e. fractions enriched with mitochondria (10K-pellet) and microsomal membranes (160 k pellet).
In order to test if KASPP/LRRK2 is an integral membrane or a membrane-associated protein, carbonate extraction of the microsomal membrane fraction (160K pellet) was applied. Since KASPP/LRRK2 could be extracted with carbonate (FIG. 11b) it is a membrane-associated protein rather than being integrated into the membrane. Thus, KASPP/LRRK2 is a protein with cytoplasmic but not cytosolic distribution and demonstrates strong association to membranes.
GENERATION OF MONOCLONAL ANTIBODIES AGAINST KASPP/LRRK2
General
The immunization, generation of hybridoma clones and ELISA for positive clones against peptide #2025 used for the immunization were carried out according to standard protocols. The antibody producing clones were tested for sensitivity and specificity against KASPP/LRRK2. Peptide #2025 with the amino acid sequence “CRMGIKTSEG TPGFRAPEVA RGNVIYNQQA D” (SEQ ID NO:3) represents the kinase domain of KASPP/LRRK2 (amino acids Nos. 2025-2055). This particular peptide was chosen because the homology of the sequences between mouse and human is 100%.
Test Conditions for Sensitivity and Specificity of the Generated Antibodies
A lysate of HEK293 cells overexpressing recombinant KASPP/LRRK2 and a control lysate of HEK 293 cells transfected with an empty vector were separated in a PAGE gels (8%). The probe was applied in a broad slot over the whole gel. After electrophoretic separation the separated lysates were transferred on PVDF membranes (western blot procedure). After the transfer the membranes were first blocked with blocking buffer (5% low-fat milk powder, BioRad, in TBS-Tween 20) for 1 h with the effect that unspecific adsorption of the antibodies to the membrane was avoided. Thereafter the blots were incubated with the positively tested hybridoma supernatants for 3 h (ELISA for testing the affinity to the peptide). The incubation was carried out in a multiscreen chamber (BioRad). The chamber allows the incubation of a blot with different primary antibodies. The membranes were taken form the chambers for washing (4×5 min in TBST buffer). Then. the incubation was carried out with a HRP (horse reddish peroxidase) coupled secondary antibody (anti rat IgG) for 1 h. After the incubation the blots were washed with TBST (4 ×10 min). The detection of the antibody reaction was done with the help of chemolumineszenz (ECL+, GE Healthcare) and exposition of a film (hyperfilm, GE Healthcare).
Result
The results of the above described Western blots are shown in FIG. 16. Clone 3G6 (No. 10) and 4B7 (No. 15) (peptide #2025) produced a specific signal. A signal was specific if (a) it appeared at the position of the correct molecular weight (280 kD) and (b) it appeared stronger or only for the lysate of the KASSP/LRRK2 overexpressing cells.










TABLE 1







Gene Symbol
Accession Nr.









PKP2
NM_001005242



ALG10
NM_032834



CPNE8
NM_153634



KIF21A
NM_017641



ABCD2
NM_005164



FLJ40126
NM_173599



SLC2A13
NM_052885



KASPP/LRRK2




MUC19
AY236870



CNTN1
NM_001843



PDZRN4
NM_013377



LOC283464
BC039145



YAF2
NM_005748



MADP-1
NM_033114



PPHLN1
NM_201438



PRICKLE1
NM_153026



ADAMTS20
NM_025003



DKFZp434G1415
NM_031292



IRAK4
NM _016123



PTK9
NM_002822



DKFZp434K2435
NM_032256



NELL2
NM_006159



PLEKHA9
NM_015899



DKFZp451M105
AL832340



FLJ14711
AK027617



FLJ22820
AK026473



SLC38A1
NM_030674



SLC38A2
NM_018976



SLC38A4
NM_018018



















TABLE 2





Location
Forward
Reverse







D12s2194
F_GAGGACTATGATTGCCATGG
R_AGGGCATACAAAATGTCCCT


D12s1048
F_GGTCTGCTTAGGTCCCTTTT
R_AAGGAACCAAGGAGTGGAAG


Intragenic_1
F_TTCAGATGTTTGGGGCAAGT
R_CATGAAGACTGTGAATGGTTTG


Intragenic_2
F_CCAGACAGAAGTCTGAAGGACA
R_TCCAAAACAGACAAGAGGTTGA


Intragenic_3
F_ATGAAGCCTTGGCTCTTCAA
R_TCCCAATTCAAAATTTTAGTGC





















TABLE 3







PD Families
Idiopathic
Controls



Variant
Exon
(n = 55)
PD (n = 337)
(n = 1200)
Family




















R793M; 
19
2
1
1
DE041


2378G>T




T11239


Q930R; 
21
1
0
0
DE022


2789A>G







S1096C; 
24
1
0
0
famE


3287C>G







L1114L; 
24
1
0
0
DE038


3342A>G




T11288


S1228T; 
27
1
0
0
DE031


3683G>C







G2019S; 
41
0
1
0
Hernandez DG


6055G>A




et al. (2005)


I2020T; 
41
1
0
0
DE032


6059T>C




T10738

















TABLE 4








Family/Patient

















DE022/








DE041/
III-5//







T11239
II-1//II-2
III-6//III-7
Fam. E
T11288/II-5
DE031/III-1//III-2
T10738/II-2





Mutation
R793M
R793M
Q930R
S1096C
3342A > G
S1228T
12020T


Age at onset (y)
42
55//70
68//58//47

77
49//49
57



uncle: 79




father: 62
father: 59








granny: 68



Disease duration
25~
14~//10~
8~//19//30

4~
8~//12~
3~


Initial symtom
B/RT
PT//RT
B, RT//B//

B
RT//B, RT
B, RT





B, RT






Response to L-
+
+//+
+//+//+
+
+
+//+
+


dopa









Bradykinesia
+
+//+
+//+//+

+
+//+
+


Rigidity
+
+//+
+//+//+

+
+//+
+


Resting Tremor
+
−//+
+//+//+

−
+//+
+


Postural
+
+//+
−//+//+

+
−//−
−


instability









Sleeping
+
+//−
+//+//+

+
−//+
+


disturbances









Long-term
+
+//+
+//+//+

−
+//+
−


complications









Hallucinations
+
−//−
−//−//+

+
−//−
−


Additional
Tongue
−


Dementia




findings
dystonia



L-dopa 









hypersensitivity




Sniffing test
2/8
nd
nd
nd
7/8
5/8//5/8
7/8


Electro-
na
nd
nd
nd
na
na//na
Na


neurography









Electro-
na
nd
nd
nd
na
na//na
Na


myography









Magnet evoked
na
nd
nd
nd
na
na//na
Na


potentials









TCS (r; l)
0.21; 0.24
nd
nd
nd
0.24; 0.19
0.23; 0.24//
0.16; 0.17








0.22; 0.24



MRI
nd,
nd
nd
nd
global atrophy,
slightly increased atrophy in
Slight 



because of



microangiopathy
both, slight microangiopathie
frontotemporally



electrodes




in III-2
enhanced atrophy

















TABLE 5








Family/Patient













T11239
T11288/II-5
DE031/III-1//
DE031/III-2
T10738/II-2





Mutation
R793M
3342A > G

S1228T
12020T


LPS-K/SPM (IQ)
/90↓
75↓↓/
111↑/
117↑/
120↑/


Tower of London (PR)
xx
—
6↓↓
27↓
xx


CWIT (T-Value INT)
—
(63)
37
41
41


CERAD 1 (Verbal Fluency)
—
 6
20~
31↑
36↑


CERAD 2 (Boston Naming Test)
—
12
14~
15~
14-


CERAD 3 (MMSE)
22
24
30~
30~
29~


CERAD 4 (Word List Memory)
—
10
19~
22~
29↑


CERAD 5 (Constructional Praxis)
—
 7
10~
10~
11~


CERAD 6.1 (Word List Recall)
—
 1
 7~
 7~
10↑


CERAD 7.1 (Word List Recognition)
—
10
 9
10
10


CERAD 8 (Recall of Constructional Praxis)
—
 2
10~
13↑
12↑


D2-Test (Concentration)
—
—
38
46
46


BDI
23↑
11
 3
 9
 7.5


PDQ-39 (PDSI)
40.4
25.6
 8.8
18.6
23.6

## Claims

1. A method of detecting a mutation at position 4321 in the nucleic acid molecule of SEQ ID NO: 1 or 2 in a sample, the method comprising:
(a) contacting a sample with a probe consisting of 10 to 50 nucleotides for the detection of said mutation, wherein said probe hybridizes under high stringency conditions to any of the polynucleotide sequences (i), (ii), (iii), (iv), or (v):
(i) a polynucleotide sequence selected from nucleotides 1 to 9104 of SEQ ID NO: 1 or 2;
(ii) a polynucleotide sequence selected from nucleotides 1 to 7584 of SEQ ID NO: 1 or 2;
(iii) a polynucleotide sequence selected from nucleotides 1 to 7581 of SEQ ID NO: 1 or 2;
(iv) a polynucleotide sequence selected from a nucleotide sequence coding for the protein sequence of SEQ ID NO:8 or 9 or for the protein sequence of SEQ ID NO:8 or 9 containing at least one of the mutations depicted in SEQ ID NO: 1 or 2; or
(v) a polynucleotide sequence selected from a nucleotide sequence complementary to any of the nucleotide sequences of (i), (ii), (iii), or (iv):
wherein the polynucleotide sequence codes for the protein sequence of SEQ ID NO. 8 or 9 containing a mutation at position 1441, and wherein said high stringency conditions comprise hybridization at 68° C. in a solution comprising 50% formamide, 5×SSC (Sodium and sodium Citrate buffer) or 5× SSPE (Sodium, Sodium Phosphate, and EDTA buffer at pH 7.7), 5× Denhardt's solution, 1% Sodium Dodecyl Sulfate (SDS), and 100 μg/ml denatured salmon sperm DNA, followed by washing at 68° C. in a buffer comprising 0.2 SSC and 0.1% SDS, and


(b) detecting the presence of the mutation in the nucleic acid of the sample.

2. The method of claim 1, wherein the sample is selected from
(a) a biopsy from human tissue or cells; or
(b) RNA or DNA from a biopsy from human tissue or cells.

3. The method of claim 1, wherein the detecting of the mutation comprises Southern blot hybridization, Northern blot hybridization, PCR, RT-PCR, real-time RT-PCR or automated sequencing.

4. The method of claim 1, wherein the detecting of the mutation comprises radiography, fluorescence, chemiluminescence, or any combination thereof.

5. The method of claim 1, wherein the method is carried out on an array.

6. The method of claim 1, wherein the method is carried out in a robotics system.

7. The method of claim 1, wherein the method is carried out using microfluidics.

8. The method of claim 1, wherein said probe consists of 10 to 35 nucleotides.

9. The method of claim 1, wherein said probe consists of 20 to 35 nucleotides.

10. The method of claim 2, wherein said sample is from the brain.

11. The method of claim 10, wherein said sample is from putamen or substantia nigra.

12. The method of claim 2, wherein said sample is from heart, lung, or blood lymphocytes.

13. The method of claim 2, wherein said RNA or DNA is from the brain.

14. The method of claim 13, wherein said RNA or DNA is from putamen or substantia nigra.

15. The method of claim 2, wherein said RNA or DNA is from heart, lung, or blood lymphocytes.

16. The method of claim 1, wherein said method is diagnostic of a neurodegenerative disorder selected from the group consistent of Parkinson disease (PD), sporadic PD, Alzheimer disease (AD), amyotrophic lateral sclerosis (ALS), synucleinopathy, and tauopathy.