Patent Application
20190324017
The invention relates to methods for screening a compound for Parkinson's disease treatment and to compounds for Parkinson's disease treatment.
Parkinson's disease (PD) is the second most common neurodegenerative brain disease. The characteristic motor symptoms including rigidity, imbalance and uncontrollable shaking are all familiar to the general public. To date, there is no cure for PD and motor symptoms can only be alleviated to increase the quality of life of patients. Overall, 2% of the world's population over 65 suffers from this debilitating disease and the incidence of PD is set to double in the next 20 years due to the demo-graphic development of the.
The protein DJ-1, which is encoded by PARK7 (or “DJ-1 gene”) is involved in a variety of biological processes including transcriptional regulation, chaperone-like functions, oxidative stress response and mitochondrial protection. DJ-1 has a small 20 kDa domain, which in solutions forms a dimer to become active. DJ-1 has multiple functions and is cytoprotective. The DJ-1 gene was first described as an oncogene in 1997 and shortly thereafter DJ-1 was found to regulate male fertility. In 2003, Bonifati and colleagues described four PD patients in a Dutch and three PD patients in an Italian family with mutations in DJ-1.
The gene encoding DJ-1 is composed of seven exons with exon 1 not coding. DJ-1 consists of 189 amino acids and belongs to the Thj1/Pfp1 superfamily. It is highly conserved among different species, homologues are found in all aerobic species from prokaryotes to eukaryotes and the amino acid residues are highly conserved, including the presumably most important residues for PD, namely C106, located in a nucleophile elbow, shown as ball and stick. The cysteine in position 106 of the peptide sequence is highly oxidisable and responds to oxidative stress/ROS by forming a sulfinic acid. DJ-1 with oxidised C106 is thought to be less stable and therefore becomes inactive. Interestingly, when C106 was replaced with other amino acids, DJ-1 lost its neuro protective activity. Only oxidised DJ-1 gets transported to the mitochondria where it acts mitoprotective.
The precise biochemical functions of DJ-1 in PD, however, are unclear. One reason might be that no post mortem brain samples from PD patients with DJ-1 mutations reached autopsy to study the pathology in these cases.
Another reason is the broad spectrum of publications describing different and partially quite vague functions of this small protein. DJ-1 is ubiquitously expressed. In the human brain, it is found in neurons and astrocytes. In sporadic PD patients, a strong expression is seen in reactive astrocytes, but it is not accumulating in the pathognomonic Lewy bodies (Bandopadhyay et al., 2004, Neumann et al., 2004, Rizzu et al., 2004).
Mutations in DJ-1 cause approximately 1% of all PD cases world-wide. However, there is a variation seen in the frequency of DJ-1 mutations between different ethnic groups. Caucasians: 0.83% in familial cases and 0.99% in sporadic cases and 0.54% copy number variations, Asians: 3.03% in familial cases, Arabs: 0.74% in sporadic cases and Ashkenazi Jews: 1.96% in sporadic cases. The mutations result in an early-onset with slow progression (except for the compound heterozygous c.317_322del:p.106_108del mutation) of the disease. For many of the mutations, the effect is still unknown including the previously described c.G192C mutation (corresponding to the p.E64D mutation) (Hering et al., 2004, Human Mutation 24:321-329).
The p.E64D mutation was first found in a male Turkish patient. He developed PD symptoms at the age of 34 (Hering et al., 2004). Hering et al have also studied the p.E64D mutation of DJ-1. For this purpose, HEK293 cells were transfected with cDNA encoding a DJ1 mutant comprising the p.E64D mutation. They observed that the recombinantly expressed DJ-1 E64D mutant displayed only a mild reduction in the protein level compared to the wild-type DJ-1. Hering et al further reported that the overall structure of the monomer and dimer of the p.E64D mutant are essentially the same as those of the wild-type DJ-1. Thus, they suggested that the p.E64D may affect binding of DJ-1 to another protein, thus causing deleterious effects by disrupting this interaction.
The results of Hering et al. 2004 were also confirmed by Malgieri and Eliezer, 2007, Protein Science, 17:855-868, who expressed p.E64D mutant of DJ-1 in E. coli using cDNA. In their study, Malgieri and Eliezer further reported that no significant change in thermodynamic stability occurs due to the p.E64D mutation. They also suggest that this mutation most likely alters interactions of DJ-1 with other cellular partners that are crucial for proper execution of its function.
The inventors of the present invention, however, have surprisingly found out that the c.G192C in the genome leads to a loss of DJ-1 proteins in the affected cells. This is because the inventors have recognized the importance of studying patient-derived primary cells instead of recombinantly expressed DJ-1 proteins. The inventors of the present invention have further conducted experiments using qPCR and an in vitro splicing assay, which showed that a splicing defect caused complete skipping of the mutation-carrying exon 3 in the pre-mRNA. This result could only be obtained because the inventors of the present invention have recognized the importance of studying the mutated gene in its native environment, instead of studying the gene expression using cDNA as for example conducted by Hering et al., 2004 or Malgieri and Eliezer, 2007.
After deciphering the pathogenic mechanism of the c.G192C, the inventors of the present invention were able to establish a method for screening a compound for Parkinson's disease treatment.
The invention thus envisions a method for screening a compound for Parkinson's disease treatment, comprising contacting a cell having a DJ-1 gene containing a c.192G>C mutation with a compound of interest; and testing whether said compound of interest prevents skipping of exon 3 of said DJ-1 gene, thereby identifying said compound as candidate for Parkinson's disease treatment. It is understood that the method is preferably an in vitro method.
The term “DJ-1 gene” also known as “PARK7” gene, as used herein refers to a nucleic acid sequence encoding the DJ-1 protein. It is understood that this nucleic acid sequence is preferably a genomic nucleic acid sequence, i.e. comprising introns and exons. It is also understood that the term “DJ-1” gene preferably relates to a human DJ-1 gene. It is envisioned by the invention that the term “DJ-1” gene preferably relates to a “native DJ-1” gene, i.e. a naturally occurring genomic sequence of the DJ-1 gene, which preferably has no known association with a pathologic phenotype of the carrier of said native DJ-1 gene, especially no association with an increased probability of developing Parkinson's disease. In humans, the DJ-1 gene is located at chromosome band 1p36.23. It is further envisioned that the term “DJ-1 gene” preferably relates to the human gene having the cytogenetic location: 1p36.23 having the genomic coordinates (GRCh38): 1:7,961,653-7,985,281 (UCSC Genome Browser on Human December 2013 (GRCh38/hg38) Assembly) as described in OHIM entry 602533 in the version of 15 Jun. 2015.
The term “exon 3” of the “DJ-1” gene, when relating to a human “DJ-1” gene, preferably relates to the sequence set forth in SEQ ID NO: 3. It may also relate to a homolog of SEQ ID NO: 3.
The term “homolog” of a given gene (sequence) or protein (sequence) generally relates to a gene (sequence) or protein (sequence) having at least about 70%, preferably at least about 75%, preferably at least about 80%, preferably at least about 85%, preferably at least about 90%, preferably at least about 91%, preferably at least about 92%, preferably at least about 93%, preferably at least about 94%, preferably at least about 95%, preferably at least about 96%, preferably at least about 97%, preferably at least about 98%, preferably at least about %, preferably at least about 99% sequence identity to said given gene (sequence) or protein (sequence).
“Percent (%) sequence identity” with respect to a nucleic acid or an amino acid sequence disclosed herein is defined as the percentage of nucleic acid or amino acid residues in a candidate sequence that are pair-wise identical with the nucleic acid or amino acid residues in a reference sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publically available computer software such as BLAST, ALIGN, or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximum alignment over the full length of the sequences being compared.
The terms “mutated”, “mutant” and “mutation” in reference to a nucleic acid or a polypeptide refers to the exchange, deletion, or insertion of one or more nucleotides or amino acids, respectively, compared to a naturally occurring nucleic acid or polypeptide, i.e. to a reference sequence that can be taken to define a wild-type.
It is understood in this regard that the term “position”, when used in accordance with the present invention, means the position of a nucleic acid or an amino acid within a nucleic acid or amino acid sequence depicted herein. This position may be indicated relative to a resembling native sequence, e.g. a sequence of a naturally occurring IgG domain or chain. The term “corresponding” as used herein also includes that a position is not necessarily, or not only, determined by the number of the preceding nucleotides/amino acids. Thus, the position of a given amino acid in accordance with the present invention which may be substituted may vary due to deletion or addition of amino acids elsewhere in the antibody chain.
Thus, under a “corresponding position” in accordance with the present invention it is to be understood that nucleic acids or amino acids may differ in the indicated number but may still have similar neighbouring nucleic acids or amino acids. Said nucleic acids or amino acids which may be exchanged, deleted or added are also encompassed by the term “corresponding position”. In order to determine whether a nucleic acid or an amino acid residue in a given nucleic acid or amino acid sequence corresponds to a certain position in the nucleic acid or amino acid sequence of a naturally occurring gene or protein, the skilled person can use means and methods well-known in the art, e.g., alignments, either manually or by using computer programs such as BLAST2.0, which stands for Basic Local Alignment Search Tool or ClustalW or any other suitable program which is suitable to generate sequence alignments.
An “exon” refers to a defined section of nucleic acid that encodes for a protein, or a nucleic acid sequence that is represented in the mature form of an RNA molecule after either portions of a pre-processed (or precursor) RNA have been removed by splicing. The mature RNA molecule can be a messenger RNA (mRNA) or a functional form of a non-coding RNA, such as rRNA or tRNA. The human DJ-1 gene has 8 exons.
An “intron” refers to a nucleic acid region (within a gene) that is not translated into a protein. An intron is a non-coding section that is transcribed into a precursor mRNA (pre-mRNA), and subsequently removed by splicing during formation of the mature RNA.
“Exon skipping” refers generally to the process by which an entire exon, or a portion thereof, is removed from a given pre-processed RNA, and is thereby excluded from being present in the mature RNA, such as the mature mRNA that is translated into a protein. Hence, the portion of the protein that is otherwise encoded by the skipped exon is not present in the expressed form of the protein.
As used herein, the terms “treat”, “treatment” or “therapy” refer to alleviation, attenuation (e.g. of progression), or prevention of a pathological state, such as a disease.
Further envisaged herein is a compound for treating Parkinson's disease. Preferably, the compound is for the treatment of early onset Parkinson's disease. The compound may be for treatment of idiopathic Parkinson Disease. The Parkinson Disease may be caused by or is associated with aberrant splicing. The aberrant splicing may be caused by or is associated with a mutation in e.g. PARK7, PINK1, GBA, or PARK2. The Parkinson disease may be caused by or is associated with a U1-dependent splicing defect. The compound is also preferably for treating PARK7-associated Parkinson's disease, in particular for treating Parkinson's disease associated with a c.G192C mutation in the PARK7 gene.
It is envisioned that the cell used in the methods of the present invention comprises at least one allele of the DJ-1 gene, preferably two. It is further envisioned that the cell has a c.192G>C mutation in at least one allele of the DJ-1 gene. In this context it is noted that “c.192G>C” and “c.G192C” are used synonymously and interchangeably throughout the application and both terms relate to a G->C substitution at position 192 of a reference nucleic acid sequence. In is further envisioned that the cell preferably has two alleles of the DJ-1 gene and that both alleles of the DJ-1 gene have a c.192G>C mutation.
As used herein, the term “allele(s)” means any of one or more alternative forms of a gene at a particular locus. In a diploid cell of an organism, alleles of a given gene are located at a specific location or locus (loci plural) on a chromosome. One allele is present on each chromosome of the pair of homologous chromosomes.
It is further envisioned that the c.192G>C mutation in a DJ-1 gene may lead to a p.E64D amino acid exchange in the DJ-1 protein.
A cell according to the invention may preferably be an isolated cell. The cell may be any cell, but is preferably a mammalian cell, such as a human cell, a mouse cell, a rat cell, a dog cell, a rabbit cell, a swine cell, a cattle cell, a monkey cell, an ape cell. Most preferably, the cell is a human cell.
It is envisioned that the cell used in the methods of the invention is a human cell or a human cell line. This human cell line preferably contains a DJ-1 gene having a c.192G>C mutation, preferably a c.192G>C mutation in both alleles of the DJ-1 gene. Said human cell line may be a primary fibroblast cell, an immortalized fibroblast cell, an induced pluripotent stem cell (iPSC), a small-molecule-derived neuronal precursor cell (smNPC), or a midbrain-specific dopaminergic neuro (mDA), each of which may preferably be obtained from a patient having at least one c.192G>C mutation in a DJ-1 gene. It is understood that the step of obtaining the cell line from the subject may preferably be excluded from the methods of the invention.
It is further envisioned that the DJ-1 gene containing a c.192G>C mutation that is comprised in the cell used in the methods of the invention may be fused to a reporter gene. As used herein, the term “reporter gene” refers to any gene whose expression can be measured.
A reporter gene may preferably not have any untranslated regions (UTRs). A reporter gene may preferably be a contiguous open reading frame. A reporter gene can have a previously determined reference range of detectable expression.
A reporter gene can express a screenable marker. Exemplary screenable markers include: green fluorescent protein (GFP) or any other fluorescent protein, a β-glucuronidase or uidA gene (GUS) which encodes an enzyme for which various chromogenic substrates are known; a gene which encodes an enzyme for which various chromogenic substrates are known (e.g., PADAC, a chromogenic cephalosporin); a luciferase gene; a tyrosinase gene, which encodes an enzyme capable of oxidizing tyrosine to DOPA and dopaquinone which in turn condenses to melanin; and α-galactosidase, which can be used in colormetric assays. A preferred screenable marker is GFP.
Included within the terms “screenable marker genes” are also genes that encode a secretable marker whose secretion can be detected as a method of identifying or selecting for transformed cells. Examples include markers that encode a secretable antigen that can be identified by antibody interaction, or even secretable enzymes, which can be detected utilizing their inherent biochemical properties. Secretable proteins fall into a number of classes, including small, diffusible proteins which are detectable, (e.g., by ELISA), or small active enzymes which are detectable in extracellular solution (e.g., α-amylase, β-lactamase, phosphinothricin transferase). Other possible selectable or screenable marker genes, or both, are apparent to those of skill in the art.
It is further envisioned by the present invention that the step of testing whether said compound of interest prevents skipping of exon 3 of said DJ-1 gene can be conducted using any method that is known to the skilled person and that is suitable for detection of such a exon skipping. Suitable methods include, but are not limited to, western blot, qPCR, mass spectrometry, detection of reporter gene activity, a microscopy-based assay, or a FACS-based assay.
The invention further envisions a compound which prevents skipping of exon 3 of the DJ-1 gene for use in a method of treatment of Parkinson's disease. Such compound is preferably obtainable by a method for screening a compound for Parkinson's disease treatment described herein.
According to the present invention, such a compound may be a mutated U1 snRNA allowing the U1 complex to bind to the mutant pre-mRNA. Such a mutated U1 snRNA thus may allow correct splicing of the c.192G>C mutant pre-mRNA. Such a mutated U1 snRNA may preferably have the nucleotide sequence shown in SEQ ID NO: 7.
As used herein, “snRNA” (or “small nuclear ribonucleic acid”), is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcribed by either RNA polymerase II or RNA polymerase III, and studies have shown that their primary function is in the processing of pre-messenger RNA (hnRNA) in the nucleus. A snRNA may further be associated with a set of specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins (snRNP) that may form the splicesosome.
Another compound that may be for use in a method of treatment of Parkinson's disease according to the invention is an optionally substituted C1-C10 alkyl carboxylic acid. Such a compound may be butyric acid. Such a compound may also comprise at least one aryl and/or at least one heteroaryl substituent.
As used herein, “alkyl” refers to a straight-chain, or branched alkyl group having 1 to 10 carbon atoms. Exemplary alkyl groups include methyl, ethyl, propyl, isopropyl, butyl, isobutyl, sec-butyl, tert-butyl, pentyl, isoamyl, neopentyl, 1-ethylpropyl, 3-methylpentyl, 2,2-dimethylbutyl, 2,3-dimethylbutyl, hexyl, octyl, etc. The alkyl moiety of alkyl-containing groups, such as alkoxy, alkoxycarbonyl, and alkylaminocarbonyl groups, has the same meaning as alkyl defined above. Alkyl groups may be optionally substituted.
As used herein, “aryl” refers to an aromatic group preferably having in the range of 6 up to 14 carbon atoms, preferably 6 carbon atoms. A “substituted aryl” refers to aryl groups further bearing one or more substituents.
As herein, “heteroaryl” refers to arylic groups containing one or more heteroatoms (e.g., N, O, S, or the like) as part of the ring structure, and preferably having in the range of 3 up to 14 carbon atoms.
A preferred compound that may be for use in a method of treatment of Parkinson's disease according to the invention is a compound having the structural formula (I):
wherein R1 is optionally substituted aryl or optionally substituted heteroaryl; and n is an integer of from 0 to 8. R1 may preferably be an unsubstituted aryl, preferably a unsubstituted phenyl. Moreover, n may be 0, 1, 2, 3, 4, 5, 6, 7, or 8, preferably 2. A preferred compound may be 4-phenylbutyric acid.
A further compound that may be for use in a method of treatment of Parkinson's disease according to the invention is a compound having the structural formula (II):
wherein R2 is hydrogen or optionally substituted alkyl; and X is hydrogen or halogen. R2 is preferably hydrogen or an unsubstituted alkyl, preferably hydrogen or methyl. X is preferably hydrogen or chlorine. Preferred compounds are those in which R2 is hydrogen and X is hydrogen; in which R2 is hydrogen and X is a halogen, preferably chlorine; in which R2 is an unsubstituted alkyl, preferably methyl, and X is a halogen, preferably chlorine, such as a compound where R2 is methyl and X is chlorine. A preferred compound is N6-furfuryladenine (also referred to as “kinetin”). Another preferred compound is 2-chloro-N-[(furan-2-yl)methyl]-7H-purin-6-amine (also referred to as “rectas”). Another preferred compound is 2-chloro-N-[(furan-2-yl)methyl]-N-methyl-7H-purin-6-amine (also referred to as “MolPort-032-631-702” or “032.631.702”).
The present invention further envisions a method of treating Parkinson's disease comprising administering to a subject a compound useful for the treatment of Parkinson's disease as described herein. It is understood that the compound may preferably administered in a therapeutically effective amount. It is further understood that the subject is preferably in need of the administration, e.g. that the subject suffers from Parkinson's disease or has a c.192G>C mutation in the DJ-1 gene in at least one allele, preferably both alleles. The subject is preferably human.
A compound used for treatment of Parkinson's disease as described herein may typically be administered in the form of a pharmaceutical composition. The present invention thus further provides a pharmaceutical composition comprising, as an active agent, a compound used for treatment of Parkinson's disease as disclosed herein, and, optionally, one or more pharmaceutically excipient(s). Accordingly, the use of a compound used for treatment of Parkinson's disease as disclosed herein for the manufacture of a pharmaceutical composition or medicament, preferably for the treatment of Parkinson's disease is also envisaged herein.
A pharmaceutical composition for use in a method of treatment of Parkinson's disease may comprise one or more compounds which prevents skipping of exon 3 of the DJ-1 gene. Such one or more compounds may be compounds which prevents skipping of exon 3 of the DJ-1 gene may be compounds that are described herein. The pharmaceutical composition may comprise at least two compounds which prevents skipping of exon 3 of the DJ-1 gene that are described herein. The pharmaceutical composition may comprise an optionally substituted C1-C10 alkyl carboxylic acid and a compound having the structural formula (II). The optionally substituted C1-C10 alkyl carboxylic acid may be butyric acid or a salt thereof, or a substituted C1-C10 alkyl carboxylic acid or a salt thereof that comprises at least one aryl and/or at least one heteroaryl substituent, or a compound having the structural formula (I) or a salt thereof. The optionally substituted C1-C10 alkyl carboxylic acid is preferably 4-phenyl butyric acid or a salt thereof. The compound of having the structural formula (II) may be N6-furfuryladenine, 2-chloro-N-[(furan-2-yl)methyl]-7H-purin-6-amine, or 2-chloro-N-[(furan-2-yl)methyl]-N-methyl-7H-purin-6-amine. The compound of having the structural formula (II) is preferably 2-chloro-N-[(furan-2-yl)methyl]-7H-purin-6-amine. The pharmaceutical composition preferably comprises 4-phenyl butyric acid or a salt thereof, such as the sodium salt thereof, and 2-chloro-N-[(furan-2-yl)methyl]-7H-purin-6-amine.
The term “pharmaceutical composition” particularly refers to a composition suitable for administering to a human. However, compositions suitable for administration to non-human animals are generally also encompassed by the term.
The pharmaceutical composition and its components (i.e. active agents and optional excipients) are preferably pharmaceutically acceptable, i.e. capable of eliciting the desired therapeutic effect without causing any undesirable local or systemic effects in the recipient. Pharmaceutically acceptable compositions of the invention may for instance be sterile or non-sterile. Specifically, the term “pharmaceutically acceptable” may mean approved by a regulatory agency or other generally recognized pharmacopoeia for use in animals, and more particularly in humans.
A compound used for treatment of Parkinson's disease as described herein is preferably present in the pharmaceutical composition in a therapeutically effective amount. By “therapeutically effective amount” is meant an amount of the active agent that elicits the desired therapeutic effect. Therapeutic efficacy and toxicity can be determined by standard procedures, e.g. in cell culture or in test animals, e.g., ED50 (the dose therapeutically effective in 50% of the population) and LD50 (the dose lethal to 50% of the population). The dose ratio between therapeutic and toxic effects is the therapeutic index, and it can be expressed as the ratio, ED50/LD50. Pharmaceutical compositions that exhibit large therapeutic indices are preferred.
The term “excipient” includes fillers, binders, disintegrants, coatings, sorbents, antiadherents, glidants, preservatives, antioxidants, flavoring, coloring, sweeting agents, solvents, co-solvents, buffering agents, chelating agents, viscosity imparting agents, surface active agents, diluents, humectants, carriers, diluents, preservatives, emulsifiers, stabilizers and tonicity modifiers. It is within the knowledge of the skilled person to select suitable excipients for preparing the desired pharmaceutical composition of the invention. Exemplary carriers for use in the pharmaceutical composition of the invention include saline, buffered saline, dextrose, and water. Typically, choice of suitable excipients will inter alia depend on the specific active agent used, the disease to be treated, and the desired formulation of the pharmaceutical composition.
The present invention further provides pharmaceutical compositions comprising one or more of the active agents specified above and one or more additional active agents that are suitable for treatment of the disease to be treated. Examples of active ingredients suitable for combinations include levodopa (or L-DPOA), a dopamine agonists such as bromocriptine, pergolide, pramipexole, ropinirole, piribedil, cabergoline, apomorphine, and lisuride, a MAO-B inhibitor (monoamine oxidase inhibitor) such as selegiline or rasagilines, amantadine, anticholinergics, clozapine, cholinesterase inhibitors, modafinil, donepezil, quetiapine, ziprasidone, aripiprazole, or paliperidone.
The exact dosage of the compound used for treatment of Parkinson's disease as described herein (or the pharmaceutical composition comprising the same) will be ascertainable by one skilled in the art using known techniques. Suitable dosages provide sufficient amounts of the compound used for treatment of Parkinson's disease as described herein and are preferably therapeutically effective.
As is known in the art, adjustments for purpose of the treatment (e.g. remission maintenance vs. acute flare of disease), route, time and frequency of administration, time and frequency of administration formulation, age, body weight, general health, sex, diet, severity of the disease state, drug combination(s), reaction sensitivities, and tolerance/response to therapy may be required. Suitable dosage ranges for compound used for treatment of Parkinson's disease as described herein or its derivatives can be determined using data obtained from cell culture assays and animal studies and may include the ED50. It is recognized that treatment may require a single administration of a therapeutically effective dose or multiple administrations of a therapeutically effective dose of the compound used for treatment of Parkinson's disease as described herein. E.g., the compound used for treatment of Parkinson's disease as described herein (or a pharmaceutical composition comprising the same) might be administered daily, every 3 to 4 days, every week, or once every two weeks, or once within a month depending on formulation, half-life and clearance rate of the particular compound or composition.
A variety of routes are applicable for administration of the pharmaceutical composition described herein. Typically, administration may be accomplished enterally or parenterally. Methods of enteral delivery include oral application, for example as a tablet or capsule or int the form of powder or granulate. Methods of parenteral delivery include topical, intra-arterial, intramuscular, subcutaneous, intramedullary, intrathecal, intraventricular, intravenous, intraperitoneal, intrauterine, intravaginal, sublingual or intranasal administration.
The pharmaceutical compositions of the invention can be formulated in various forms, e.g. in solid, liquid, gaseous or lyophilized form and may be, for instance, in the form of a tablet, a pill, a capsule, a powder, a granule, a solution, an ointment, a cream, transdermal patches, a gel, an aerosol, suspensions, emulsions, syrups, liquids, elixirs, extracts, tincture or fluid extracts or in a form which is particularly suitable for the desired method of administration. Processes known per se for producing medicaments are indicated in 22nd edition of Remington's Pharmaceutical Sciences (Ed. Maack Publishing Co, Easton, Pa., 2012) and may include, for instance conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes. After pharmaceutical compositions of the invention have been prepared, they can be placed in an appropriate container and labeled for treatment of an indicated condition. Such labeling would for instance include amount, frequency and method of administration.
It must be noted that as used herein, the singular forms “a”, “an”, and “the”, include plural references unless the context clearly indicates otherwise. Thus, for example, reference to “a reagent” includes one or more of such different reagents and reference to “the method” includes reference to equivalent steps and methods known to those of ordinary skill in the art that could be modified or substituted for the methods described herein.
Unless otherwise indicated, the term “at least” preceding a series of elements is to be understood to refer to every element in the series. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the present invention.
The term “and/or” wherever used herein includes the meaning of “and”, “or” and “all or any other combination of the elements connected by said term”.
The term “about” or “approximately” as used herein means within 20%, preferably within 10%, and more preferably within 5% of a given value or range. It includes, however, also the concrete number, e.g., about 20 includes 20.
Throughout this specification and the claims which follow, unless the context requires otherwise, the word “comprise”, and variations such as “comprises” and “comprising”, will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integer or step. When used herein the term “comprising” can be substituted with the term “containing” or “including” or sometimes when used herein with the term “having”.
When used herein “consisting of” excludes any element, step, or ingredient not specified in the claim element. When used herein, “consisting essentially of” does not exclude materials or steps that do not materially affect the basic and novel characteristics of the claim.
In each instance herein any of the terms “comprising”, “consisting essentially of” and “consisting of” may be replaced with either of the other two terms.
It should be understood that this invention is not limited to the particular methodology, protocols, material, reagents, and substances, etc., described herein and as such can vary. The terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention, which is defined solely by the claims.
All publications and patents cited throughout the text of this specification (including all patents, patent applications, scientific publications, manufacturer's specifications, instructions, etc.), whether supra or infra, are hereby incorporated by reference in their entirety. Also references to database entries of amino acid or nucleic acid sequences include the sequences themselves and all database entries of amino acid or nucleic acid sequences that are referred to are hereby incorporated by reference in their entirety. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention. To the extent the material incorporated by reference contradicts or is inconsistent with this specification, the specification will supersede any such material.
SEQ ID NO 1: cDNA sequence of human wild type (wt) PARK7 (DJ-1)
SEQ ID NO 2: cDNA sequence of human c.192G>C PARK7 (DJ-1) mutant
SEQ ID NO 3: exon 3 of human wild type (wt) PARK7 (DJ-1)
SEQ ID NO 4: exon 3 of human c.192G>C PARK7 (DJ-1) mutant
SEQ ID NO 5: amino acid sequence of human DJ-1 wild type (wt) protein
SEQ ID NO 6: amino acid sequence human DJ-1 E64D mutant
SEQ ID NO 7: mutated U1 snRNA
SEQ ID NO 8: fragment of U1 snRNA
SEQ ID NO 9: fragment of DJ-1 RNA (wt)
SEQ ID NO 10: fragment of DJ-1 RNA (c.192G>C)
SEQ ID NO 11: fragment of mutated U1 snRNA
SEQ ID NO 12: wt DJ-1 mRNA
SEQ ID NO: 13: Δex3 DJ-1 mRNA
The following examples illustrate the invention. These examples should not be construed as to limit the scope of this invention. The examples are included for purposes of illustration and the present invention is limited only by the claims.
Reprogramming of both homozygous c.192G>C DJ-1 mutation carriers and the heterozygous c.192G>C DJ-1 mutation carrier was performed using retroviral vectors expressing the classical four ‘Yamanaka factors’. A minimum of 20 clones per individual was picked, passaged and stocks were frozen down for subsequent characterization of the clones. Characterization included tests about pluripotency and stem cell characteristics of the clones. Therefore, qPCR was performed to ensure silencing of the four exogenous viral factors and endogenous expression of pluripotency markers, ICC was used to show the expression of stem cell markers. Furthermore, the picked clones were tested for major chromosomal aberrations and mutations via G-banding and a genotyping microarray analysis. Additionally, the mutation carrying exon 3 of DJ-1 was sequenced in all clones to verify the correct genotype. Likewise, the ability of the clones to differentiate in cell types of all three germ layers was tested by ICC after differentiating the clones. At least two different clones per one individual were correctly characterized and a sufficient number of stocks was frozen down.
Loss of DJ-1 function is a rare cause of familial PD. To calculate the steady state DJ-1 protein levels in different healthy individuals in comparison to the c.192G>C DJ-1 mutation carriers, samples from the respective individuals were analyzed on a low percentage SDS-PAGE gel (4% acrylamide). We took cell lysates from three different female human control individuals and from two different male human control individuals. Lysates from fibroblasts of family members of the c.192G>C DJ-1 family were taken as well. Lysates were taken from individual IV.9 who is a female heterozygous c.192G>C DJ-1 mutation carrier, from individual III.7, who is a male heterozygous c.192G>C DJ-1 mutation carrier and from individual III.11 and III.13 who are both homozygous c.192G>C DJ-1 mutation carriers; III.11 being female and premotor diseased and III.13 being the male index patient with motor symptoms.
DJ-1 proteins were examined by immunoblotting using a DJ-1 specific antibody (
Primary fibroblasts from patients are a useful tool but at the same time they only grow very slow and particularly from older people they become senescent after a certain times of passaging. To not lose the ability to work with fibroblasts from the c.192G>C DJ-1 family we immortalized fibroblasts using a lentiviral vector expressing SV40. This opened the opportunity to work with cells from patients that grow faster and can be used at higher passages.
To test if the immortalization had an effect on DJ-1 protein level and to see if the c.192G>C DJ-1 mutation still results in undetectable DJ-1 protein in immortal cells we repeated the Western blot for DJ-1 in this cell type which has a higher metabolic rate. Indeed DJ-1 protein could not be detected in both homozygous c.192G>C DJ-1 mutation carriers. The DJ-1 protein level of the heterozygous c.192G>C DJ-1 mutation carrier was reduced to about 20% of the amount seen in the healthy control (
The findings on DJ-1 protein level in c.192G>C DJ-1 mutation carriers raised interest in the underlying effect of the mutation. In a first experiment, RNA from patient derived fibroblasts was isolated, transcribed into cDNA and amplified DJ-1 by PCR. Agarose gel revealed a reduced length of c.192G>C DJ-1 carrying cDNA and a normal size band as well as the short band in the heterozygous c.192G>C carrying cDNA. cDNA from a healthy control served as positive control for correct length (
Subsequently, these results led us to sequence the amplified cDNA to find out which sequence segment was missing in the cDNA of c.192G>C DJ-1 mutation carriers. Sequencing result shows that the end of DJ-1 exon 2 is directly followed by the beginning of exon 4. Complete sequence of DJ-1 exon 3 was missing or skipped.
After obtaining these results, we wanted to validate the finding of skipping of DJ-1 exon 3 in c.192G>C DJ-1 mutation carrying cells. Therefore, minigene assay to assess the effect of DJ-1 exon 3 on splicing was performed.
Minigene assay is used to analyze splicing of an exon of interest by cloning it into a vector (pSPL3) between two given exons (Exon A and Exon B) and subsequent analysis of the cDNA by rtPCR and sequencing (
In the minigene assay we tested wt exon 3 of the control and mutant exon 3 (carrying the c.192G>C DJ-1 mutation) from the index patient. At the same time minigene constructs were tested where the wt exon 3 was mutated to carry the c.192G>C mutation and the corrected exon from the index patient now carrying the wt allele. Agarose gel electrophoresis (
The c.192G>C DJ-1 mutation in exon 3 which does not lead to a premature stop codon and which does not cause a frameshift in the RNA caused the skipping of exon 3 in the minigene assay. In addition to the correction of the mutation in the patient exon 3 and the mutating of exon 3 to carry the c.192G>C DJ-1 mutation from a healthy control in the minigene, sequencing of the entire DJ-1 locus of the patient's DNA was performed. This was done in order to have a second confirmation that the c.192G>C DJ-1 mutation suffices to cause skipping of exon 3 in c.192G>C DJ-1 mutation carriers and other sequence variants can be excluded.
The minigene assay showed, in an artificial system, that the c.192G>C DJ-1 mutation which lies at the end of exon 3 leads to skipping of the respective exon. Skipping of this exon does not lead to a frameshift or a premature stop codon.
Next, we wanted to verify our minigene assay results in the different cell types available from the c.192G>C DJ-1 mutation carriers. Therefore, cells were grown under standard conditions, harvested, RNA was extracted and transcribed into cDNA. Quantitative qPCR was performed using cDNA and two different pairs of primers for amplification. One primer pair to detect correctly spliced DJ-1 as well as cDNA lacking exon 3 and another primer pair where one primer is complementary with exon 2 and exon 3, leading to only correctly spliced (with exon 3) DJ-1 cDNA detected by qPCR. qPCR was performed with cDNA from immortalized fibroblasts (
qPCR results generated with primers that detect normal and misspliced DJ-1 cDNA show a reduction which is not significant of DJ-1 RNA expression in all c.192G>C DJ-1 mutation carriers (
When looking at the qPCR results in iPSCs derived from these fibroblasts one sees a reduction in RNA expression of DJ-1 with and without skipping of exon 3 of the c.192G>C DJ-1 mutation carriers. With two clones (homozygous premotor diseased c4 and homozygous affected c4) being particularly low (
Further experiments aimed at analyzing why the c.192G>C base exchange leads to missplicing of DJ-1 pre-mRNA and skipping of exon 3 during the splicing process. Hypothesized mechanism of splicing of pre-mRNA carrying the c.192G>C DJ-1 mutation is shown (
As the c.192G>C DJ-1 mutation lies in the splice donor site normally it would get recognized by the U1 snRNP which is initiating the formation of the spliceosome. U1 snRNP recognizes the 5′ splice site through base pairing at the 5′ end. Of note, a hundred percent match is not necessary. In case of DJ-1 exon 3 in the wt situation there are already four mismatches between U1 snRNA and the splice donor site (
To test this hypothesis, one base of the U1 snRNA was modified in the sense that it matches the c.192G>C mutation in DJ-1 exon 3, namely C>G were exchanged as indicated in cyan (
In a splicing reaction where C>G mutant U1 snRNP is present and recognizes the splice donor sequence of c.192G>C mutant DJ-1 exon 3 skipping of this exon does not take place.
In order to test the hypothesis, the previously performed minigene experiment was repeated and a plasmid expressing c.192G>C U1 snRNA was co-transfected.
The minigene construct expressing wt exon 3 resulted in the inclusion of the exon 3 when the minigene assay was performed with the minigene construct alone, when wt U1 snRNP was co-transfected and when c.192G>C U1 snRNA was co-transfected, this is shown by the long prominent bands on the agarose gel picture in (
As c.192G>C U1 snRNA was able to rescue skipping of c.192G>C DJ-1 mutation carrying exon 3 in the minigene assay in HEK cells, the next step was to test the effect of c.192G>C U1 snRNA in patient-derived cells.
Immortalised fibroblasts of the index patient carrying the c.192G>C DJ-1 mutation were electroporated with empty vector, wt U1 snRNA or c.192G>C U1 snRNA, respectively. Electroporation with wt U1 snRNA caused a significant increase in DJ-1 RNA expression of normal RNA and RNA lacking DJ-1 exon 3 in comparison to electroporation with empty vector or c.192G>C U1 snRNA. c.192G>C U1 snRNA also caused higher RNA levels in comparison to empty vector (
The c.192G>C mutation causes mis-splicing of the DJ-1 pre mRNA upon which Exon 3 is spliced out. Although the resulting shorter ΔEx3-mRNA is present in the patient derived small molecule-derived neuronal precursor cells (smNPC), the protein levels of DJ-1 are reduced to an almost undetectable level. The ΔEx3-mRNA is, although stably expressed in the cells, not translated into protein. Even overexpression of a recombinant ΔEx3-mRNA that doesn't undergo splicing does not translate into expression of a truncated ΔEx3-DJ-1 protein. However, overexpression of recombinant full length DJ-1 restores DJ-1 full length mRNA and protein levels in patient derived.
Both constructs (ΔEx3 and full length DJ-1) were delivered to cells by stable transduction using lentiviral vectors. The vectors co-express GFP and population of successfully transduced cells were enriched by FACS sorting for GFP+ cells to an purity of over 80%. (
As the DJ-1 ΔEx3-mRNA does not get translated into protein we aimed to rescue the pathological skipping of exon 3 genetically in the patient-derived cell model. By stably transducing the cells with a specifically designed mutated U1 snRNA (U1mut) that will allow the U1 complex to bind again to the mutant pre-mRNA, the amount of correctly spliced DJ-1 RNA was predicted to increase in the cell model. A lentiviral vector encoding wild type U1 snRNA (U1wt) was used as control to account for effects on protein levels that occur due to general increase of U1 levels in the cells. These lentiviral vectors were co-expressing GFP for later enrichment of transduced cells.
The enriched population of U1 transduced cells indeed showed a rescue of DJ-1 protein only when transduced with the mutant U1 snRNA (
Both rescue strategies, expression of DJ-1 full length and U1mut, increase level of full length RNA and protein levels not only in smNPC but also in DIV14 neurons differentiated from smNPC (
The genetic rescue shows that the DJ-1 protein can be successfully restored in patient cells after identification of the underlying mechanism by correcting the splicing defect.
This opens the opportunity for a second strategy to rescue DJ-1 protein level, the use of small chemical compounds. The patient-derived smNPC were used to screen for active compounds. Here, our experiments identified 4-Phenylbutric acid as active in rescuing DJ-1 protein expression in concentrations of 150 μM and 300 μM as shown by Western blot (
Since exon 3 skipping is in frame, a shorter DJ-1 peptide would be expected, that is identical to the wt protein except for the deleted 34 amino acids encoded by exon 3. Strikingly, no truncated protein can be detected (
Next, we investigated the predicted centroid secondary structure of mRNA, where 47.1% of the bases were predicted to be unpaired for wt DJ-1, while only 40.3% were unpaired for the Δex3 variant. This difference in the number of unpaired bases in the native mRNA structure is also reflected by a slightly higher predicted minimum free energy (˜271.1 kcal/mol) as compared to the Δex3 variant (˜273.1 kcal/mol). These energy predictions can only provide indicative estimates, but structure visualizations (
We hypothesized a synergistic effect of RECTAS when combined with PB to rescue DJ-1 in c.192G>C carriers. Therefore, DIV 30 neurons differentiated from the two patient-derived smNPC clones were treated for 4 days with 1 mM PB and indicated concentrations of RECTAS. mRNA levels of full-length DJ-1 were measured by qPCR. Compared to the untreated and the solvent control treated neurons correctly spliced full-length DJ-1 mRNA was significantly increased after treatment with 1 mM PB and 50 μM RECTAS. Four days treatment with 1 mM PB and RECTAS concentrations of 10 μM and 25 μM increased the amount of correctly spliced mRNA in a dose-dependent manner (
We also tested the effect of RECTAS and PB as a single treatment for rescuing DJ-1 in c.192G>C carriers. The experiments were carried out with patient-derived neurons as described above. As shown in
Here we describe a novel mechanistic concept for the pathogenic role of the PD-associated c.192G>C mutation in PARK7. In contrast to a missense mutation that was predicted to cause instability of E64D mutant DJ-1 protein, we identified a drastic reduction of DJ-1 protein levels in patient-based cellular models due to U1-dependent mis-splicing of pre-mRNA. The demonstration of the disease-causing Δex3 DJ-1 mRNA splice variant as cause of the drastically reduced expression of DJ-1 protein reported here underscores the relevance of access to patient material for functional studies in order to validate predictions and define the underlying molecular pathology as basis for precision medicine approaches.
The observed discrepancy between the overall amount of mutant pre-mRNA and the drastically reduced levels of DJ-1 protein in homozygous c.192G>C carriers indicated the involvement of pathological mRNA processing and/or translation and argued against nonsense-mediated decay (NMD) as underlying mechanism. In our case, the c.192G>C mutation in the DJ-1 gene leads to an in-frame deletion of exon 3 without a PTC and therefore mutant mRNA was predicted to encode a smaller protein lacking the 34 amino acids encoded by exon 3. However, neither mass spectroscopy nor Western blot with different antibodies directed against different epitopes of DJ-1 revealed a truncated protein encoded by Δex3 DJ-1 pre-mRNA (
In order to prove a U1-mediated pathogenic splicing mechanism underlying loss of DJ-1 function in PD, we performed genetic rescue experiments. This may open avenues for future gene transfer strategies to the central nervous system, as options for viral vectors delivered to the brain are becoming safer and more effective.
Here, we successfully applied an advanced literature mining approach for prioritization of candidate drugs to revert molecular and cellular phenotypes associated with mis-splicing of DJ-1 in homozygous carriers of the c.192G>C mutation. The novel combination of a RECTAS with PB significantly increased mRNA and protein levels of DJ-1 in patient-based cells across different tissues (
Our findings on the combination of RECTAS and PB as causative treatment for DJ-1 deficiency have an immediate impact for homozygous carriers of the c.192G>C mutation, and may qualify for treatment at the prodromal stage of PD for addressing neuroprotective strategies in PD. As a first drug candidate for correction of aberrant splicing, recently kinetin underwent clinical assessments for pharmacokinetics, safety and effectiveness in vivo (Axelrod, F. B. et al. Kinetin improves IKBKAP mRNA splicing in patients with familial dysautonomia. Pediatr. Res. 70, 480-3 (2011); Shetty, R. S. et al. Specific correction of a splice defect in brain by nutritional supplementation. Hum. Mol. Genet. 20, 4093-101 (2011)). Within a clinical trial kinetin was well-tolerated, safe, and resulted in increased levels of correctly spliced mRNA in vivo. This indicates that drugs targeting U1-mediated splicing defects have a high potential to become a therapeutic tool and supports future clinical trials.
The therapeutic potential of combined RECTAS and PB treatment for targeting defective splicing is further substantiated by additional mutations in monogenic PD. Homozygous mutations in PARK7 affecting the 5′ consensus splice site for U1 were described as a c.91-2AG mutation in an Iranian family and a c.317-322del mutation in a Turkish family. Moreover, a novel c.1488+1 G>A mutation in the PINK1 gene was shown to affect a U1 binding site and cause an in-frame deletion of exon 7 (Samaranch, L. et al. PINK1-linked parkinsonism is associated with Lewy body pathology. Brain 133, 1128-42 (2010)). Interestingly, as for the c.192G>C mutation in PARK7, no NMD of the mutant PINK1 mRNA was observed in affected carriers.
These findings already indicate that the pathogenic relevance of exonic splicing mutations may be underestimated in PD, as it is known to represent a common cause for human diseases with approximately 15% of all mutations caused by aberrant spliceosome function, that translates into defective pre-mRNA processing (Nissim-Rafinia, M. & Kerem, B. Splicing regulation as a potential genetic modifier. Trends Genet. 18, 123-7 (2002)). To further assess the potential role of splicing-related mutations in PD, we performed an exploratory analysis of exonic mutations affecting U1-mediated splicing using publicly available databases including whole exome sequencing results from the PPMI study (Parkinson Progression Marker Initiative. The Parkinson Progression Marker Initiative (PPMI). Prog. Neurobiol. 95, 629-35 (2011).). We found a significantly higher burden of rare exonic variants affecting U1 snRNA binding sites in 380 PD patients compared to 162 control samples (n=109, P-value=0.015, OR=1.55, CI=1.05-2.29), with the majority of the burden defined by brain expressed genes (P-value=0.047, OR=1.50, CI=0.95-2.38). These results are in line with a recent study showing that approximately 10% of pathogenic missense variants predicted to alter protein code are essentially disrupting splicing (Soemedi, R. et al. Pathogenic variants that alter protein code often disrupt splicing. Nat. Genet. (2017). doi:10.1038/ng.3837). This supports our findings of an enrichment of missense and synonymous disease-associated variants in the exon boundary and underscores the therapeutic potential of compounds acting on pathological splicing.
Our study illustrates the promise for treatment concepts in precision medicine in PD that focus on genetic and molecular stratification. In order to account for the increasingly recognized heterogeneity in PD and other neurodegenerative disorders, new strategies have to be developed for the stratification of patients along shared pathogenic mechanisms.
Variant Annotation and Filtering:
In the current study we only focused on the intronic 5′ splice single nucleotide variants (SNVs). Multi-allellic variants were decomposed by using variant-tests (Tan, A., Abecasis, G. R. & Kang, H. M. Unified representation of genetic variants. Bioinformatics 31, 2202-2204 (2015)) and left normalized by bcftools (Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009)). Variants were annotated by using ANNOVAR (Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164-e164 (2010)) version 2016December05 using RefSeq gene annotations and the dbNSFP v3.0 (Liu, X., Wu, C., Li, C. & Boerwinkle, E. dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs. Hum. Mutat. 37, 235-241 (2016)) prediction scores. Only rare variants, as defined by variants with a MAF<0.05 in the current dataset and also European population of public databases such as 1000 genomes (The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68-74 (2015)), ExAC (release 0.3), and the Exome variant server (http://evs.gs.washington.edu/EVS/) were selected. In order to prioritize the 5′ splice variants based on their deleteriousness, we used three different scores. The first score is generated by using the MaxEntScan method (Yeo, G. & Burge, C. B. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol. J. Comput. Mol. Cell Biol. 11, 377-394 (2004).) which is based on the maximum entropy principle. The other two scores were ensemble scores (dbscSNV_ADA and dbscSNV_RF) generated from multiple splice site prediction tools (Jian, X., Boerwinkle, E. & Liu, X. In silico prediction of splice-altering single nucleotide variants in the human genome. Nucleic Acids Res. 42, 13534-13544 (2014)) which are available as part of dbNSFP database (Liu, X., Wu, C., Li, C. & Boerwinkle, E. dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs. Hum. Mutat. 37, 235-241 (2016)).
Generation of MaxEntScan score:
In the current study we only focused on the variants present in the consensus splice site positions i.e., +3 to −6 from the exon/intron boundary. To prioritize such variants using MaxEntScan method, for each SNV that lies in the consensus splice site region (SNVsplice) a wild type 9 mer (WT) was extracted from the reference genome (hg19). Then the variant was introduced within the WT by using the python module pyfaidx (Shirley, M. D., Ma, Z., Pedersen, B. S. & Wheelan, S. J. Efficient ‘pythonic’ access to FASTA files using pyfaidx. (PeerJ PrePrints, 2015).), hence creating a mutated consensus splice site (MUT) sequence for each variant. In the next steps the scores were calculated for both WT and MUT sequences by using the scripts provided in the MaxEntScan website (http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html). The relative percentage change (maxentscan_change) was calculated by using the formula below and all the variant sites were annotated with the WTscore and maxentscan_change.
Deleterious splice site variants (SNVsplicedef) were defined as SNVs with the following criteria: WTscore>5 and maxentscan_change>70 and dbscSNV_ADA score>0.9 and dbscSNV_RF score>0.9. If the ensemble scores are not available for any particular variant only MaxEntScan methods (WTscore>5 and maxentscan_change>70) was used.
Burden Tests:
To test the genome-wide differential burden of SNVsplicedef variants in cases compared to the controls CMCFisherExact test available part of rvtests (Zhan, X., Hu, Y., Li, B., Abecasis, G. R. & Liu, D. J. RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data. Bioinformatics 32, 1423-1426 (2016)) with default parameters was used and one sided P-values were reported. CMCFisherExact test collapses the variants in the given regions (gene or gene-set) and performs the fisher exact test. We used a list of brain expressed genes to see if there is an increased burden in the brain expressed genes (n=14,177) compared to the non-brain expressed genes (n=6,428).
Results:
Burden Analysis:
After the filtering based on ethnicity, cryptic relatedness and quality parameters the final dataset comprised of 380 PD and 162 control samples. A total of 128 SNVsplicedef variants were included in the final analysis. We observed a genome-wide significant burden in cases compared to the controls (P-value=0.021, OR=1.49, CI=1.02-2.18). The signal is coming mainly from the exonic SNVsplicedef variants (n=109, P-value=0.015, OR=1.55, CI=1.05-2.29) rather than the intronic ones (n=19, P-value=0.24, OR=1.34, CI=0.68-2.65). In the exonic SNVsplicedef variants majority of the burden is caused by the brain expressed genes (P-value 0.047, OR=1.50, CI=0.95-2.38), compared to the genes that are not expressed in brain (P-value 0.12, OR=1.37, CI=0.84-2.23). The SNVsplicedef variants are provided in the supplemental table 1, along with their respective case-control counts.
Research co-funded by the Fonds National de la Recherche Luxembourg (FNR) under grant number FNR/P13/6682797/Krüger
The invention illustratively described herein may suitably be practiced in the absence of any element or elements, limitation or limitations, not specifically disclosed herein. Additionally, the terms and expressions employed herein have been used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by exemplary embodiments and optional features, modification and variation of the inventions embodied therein herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention.
The invention has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein.
Other embodiments are within the following claims. In addition, where features or aspects of the invention are described in terms of Markush groups, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group.
| Number | Date | Country | Kind |
|---|---|---|---|
| LU93116 | Jun 2016 | LU | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP17/63554 | 6/2/2017 | WO | 00 |
