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EP2867678A2 - Séquences marqueurs pour la maladie de parkinson et leur utilisation - Google Patents

Séquences marqueurs pour la maladie de parkinson et leur utilisation

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Publication number
EP2867678A2
EP2867678A2 EP13744447.7A EP13744447A EP2867678A2 EP 2867678 A2 EP2867678 A2 EP 2867678A2 EP 13744447 A EP13744447 A EP 13744447A EP 2867678 A2 EP2867678 A2 EP 2867678A2
Authority
EP
European Patent Office
Prior art keywords
seq
sequences
homologous
nucleic acid
disease
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP13744447.7A
Other languages
German (de)
English (en)
Inventor
Helmut E. Meyer
Caroline MAY
Dirk WOITALLA
Christian Stephan
Martin Eisenacher
Michael TUREWICZ
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Leibniz Institut fuer Analytische Wissenschaften ISAS eV
Original Assignee
Leibniz Institut fuer Analytische Wissenschaften ISAS eV
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Leibniz Institut fuer Analytische Wissenschaften ISAS eV filed Critical Leibniz Institut fuer Analytische Wissenschaften ISAS eV
Priority to EP13744447.7A priority Critical patent/EP2867678A2/fr
Publication of EP2867678A2 publication Critical patent/EP2867678A2/fr
Withdrawn legal-status Critical Current

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Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6893—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to diseases not provided for elsewhere
    • G01N33/6896—Neurological disorders, e.g. Alzheimer's disease
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/28—Neurological disorders
    • G01N2800/2835—Movement disorders, e.g. Parkinson, Huntington, Tourette

Definitions

  • the present invention relates to new marker sequences for Parkinson's disease and the diagnostic use thereof together with a method for screening potential active substances for Parkinson's disease by means of these marker sequences. Furthermore, the invention relates to a diagnostic device containing marker sequences of this type for Parkinson's disease, in particular a protein biochip and the use thereof .
  • Protein biochips have become established as screening instruments.
  • the cDNA of a particular tissue is hereby cloned into a bacterial or an eukaryotic expression vector, such as, e.g., yeast.
  • the vectors used for the expression are generally characterized in that they carry inducible promoters that may be used to control the time of protein expression.
  • expression vectors have sequences for so-called affinity epitopes or affinity proteins, which on the one hand permit the specific detection of the recombinant fusion proteins by means of an antibody directed against the affinity epitope, and on the other hand the specific purification via affinity chromatography (IMAC) is rendered possible.
  • affinity epitopes or affinity proteins which on the one hand permit the specific detection of the recombinant fusion proteins by means of an antibody directed against the affinity epitope, and on the other hand the specific purification via affinity chromatography (IMAC) is rendered possible.
  • the gene products of a cDNA expression library from human fetal brain tissue in the bacterial expression system Escherichia coli were arranged in high-density format on a membrane and could be successfully screened with different antibodies. It was possible to show that the proportion of full-length proteins is at least 66%.
  • the recombinant proteins from the library could be expressed and purified in a high-throughput manner (Braun P., Hu, Y., Shen, B., Halleck, A., Koundinya, M., Harlow, E. and LaBaer, J. (2002) Proteome-scale
  • antibody-presenting arrangements are likewise described (Lai et al (2002) Antibody arrays: An embryonic but rapidly growing technology, DDT, 7, 143-149; Kusnezow et al. (2003), Antibody microarrays: An evaluation of production parameters, Proteomics, 3, 254-264).
  • Parkinson's disease also called primary or idiopathic parkinsonism is the second most common neurodegenerative disorder in the elderly. With no available biomarker the diagnosis of PD is still based on clinical criteria (Gibb and Lees, 1988) . Not all cases of PD are diagnosed
  • Parkinson's disease is a common neurodegenerative disorder for which no biomarker is available to aid diagnosis or to monitor disease progression. Extracellular fluid markers of proteins involved in the pathology of Parkinson's disease are thought to be promising candidates, but no specific biomarker could be identified yet. Marker sequences and the diagnostic use thereof for Parkinson's disease, in
  • the present invention provides biomarkers for Parkinson's disease, in particular marker sequences and the use thereof for protein biochips and diagnosis.
  • the provision of specific marker sequences permits the reliable diagnosis and stratification of patients with Parkinson's disease, in particular by means of a protein biochip and test kits.
  • the identified Parkinson's disease specific marker sequences are suitable for early
  • amplifying neuroinflammation such as generation of
  • antibodies may play a critical role in the
  • Antibodies are candidates for biomarkers in neurodegenerative disorders.
  • Antibodies are highly stable proteins, which are easily accessible e.g. in blood or also saliva and can be easily measured with protein microarrays, ELISA, or other methods. For these reasons they could be seen as a good starting point to find candidates for an early diagnosis, with a high sensitivity and specificity and perhaps the ability to monitor disease progression.
  • a protein array-based screening strategy for the discovery of PD disorder-specific autoantibodies was developed. Sera samples, clinical and other data of PD patients, diseased and healthy controls are collected in an ongoing clinical study called ParkChip.
  • Protein arrays displaying more than 9,500 different human proteins were incubated with serum and used for the detection of PD-specific autoantibody signatures in human blood.
  • the performance of this protein array allowed the identification of marker sequences SEQ ID No. 1 - 37 that discriminate PD patients from reference groups .
  • the invention therefore relates to a marker sequence for Parkinson's disease, wherein the marker sequence is selected from the group of protein sequences SEQ ID No. 1 -
  • nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37.
  • the invention further relates to a method for identifying marker sequences for Parkinson's disease by means of differential screening of samples from healthy test subjects (healthy persons), samples from patients with other neurodegenerative diseases (DC) and samples from patients with Parkinson's disease.
  • DC neurodegenerative diseases
  • the invention relates to a marker sequence for Parkinson's disease identified by means of differential screening of samples from healthy persons and samples from patients with Parkinson's disease and wherein the marker sequence is selected from the group of protein sequences SEQ ID No. 1 -
  • nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37.
  • the invention further relates to the use of marker
  • sequences for the diagnosis of Parkinson's disease wherein at least one marker sequence is selected from the group of protein sequences SEQ ID No. 1 - 37, homologous of SEQ ID No. 1 - 37, partial sequences of SEQ ID No. 1 - 37, nucleic acid sequences encoding for SEQ ID No. 1 - 37, nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37, nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37 and is determined on or from a patient to be examined.
  • marker sequence (s) according to the invention or “marker sequence (s) for Parkinson's disease” or “marker sequence (s) " relates to one or more sequences selected from the group of protein sequences SEQ ID No. 1 - 37,
  • nucleic acid sequences encoding for SEQ ID No. 1 - 37 nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37
  • nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37.
  • Parkinson's disease (PD) is defined e.g., according to Pschyrembel, de Gruyter, 263st edition (2012), Berlin) . According to the invention Parkinsonism is also enclosed in rougeParkinson's disease".
  • the term “Parkinsonism” is used for a motor syndrome whose main symptoms are tremor at rest, stiffness, slowing of movement and postural instability. Parkinson's disease (Parkinsonian syndromes) can be divided into four subtypes according to their origin: primary or idiopathic, secondary or acquired, hereditary parkinsonism, and Parkinson plus syndromes or multiple system degeneration.
  • Parkinson's disease is the most common form of parkinsonism and is usually defined as “primary” parkinsonism, meaning parkinsonism with no external identifiable cause. According to the invention Parkinson's disease encloses also "familial Parkinson's disease” and “sporadic Parkinson's disease” and cognitivemovement disorder”. It can be recognized for example by several non- motor types of symptoms such as sensory deficits, cognitive difficulties or sleep problems. Parkinson plus diseases are primary Parkinsonism's which present additional features. They include multiple system atrophy, progressive
  • PD posterior to anterior aortic hyperplasia
  • corticobasal degeneration dementia with Lewy bodies.
  • PD is considered a synucleinopathy due to an abnormal
  • Parkinson's disease relates to Morbus Parkinson.
  • the invention relates to the diagnosis of Parkinson's disease, wherein at least one marker sequence is selected from the group of protein sequences SEQ ID No. 1 - 37, homologous of SEQ ID No. 1 - 37, partial sequences of SEQ ID No. 1 - 37, nucleic acid sequences encoding for SEQ ID No. 1 - 37, nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37, nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37 and is determined on or from a patient to be examined.
  • the invention relates to the use of the marker sequences according to the invention as biomarker for PD.
  • At least 2 to 5 or 10 preferably 30 to 50 marker sequences or 50 to 100 or more marker sequences are determined on or from a patient to be examined, in particular such respectively from the group SEQ ID No. 1 - 37.
  • the marker sequences according to the invention can likewise be combined, supplemented, fused or expanded likewise with known biomarkers for this indication.
  • the determination of the marker sequences is carried out outside the human body and the determination is carried out in an ex vivo / in vitro diagnosis .
  • the invention relates to the use of marker sequences as diagnostic agents, wherein at least one marker sequence is selected from the group of protein sequences SEQ ID No. 1 - 37, homologous of SEQ ID No. 1 - 37, partial sequences of SEQ ID No. 1 - 37, nucleic acid sequences encoding for SEQ ID No. 1 - 37, nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37, nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37.
  • the invention relates to a method for the diagnosis of Parkinson's disease, wherein a. ) at least one marker sequence is selected from the group of protein sequences SEQ ID No. 1 - 37, homologous of SEQ ID No. 1 - 37, partial sequences of SEQ ID No. 1 - 37, nucleic acid sequences encoding for SEQ ID No. 1 - 37, nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37, nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37 and is applied to a solid support and b. ) is brought into contact with body fluid or tissue extract of a patient and c. ) the detection of an interaction of the body fluid or tissue extract with the marker sequences from a.) is carried out.
  • the invention therefore likewise relates to diagnostic agents for the diagnosis of Parkinson's disease comprising at least one marker sequence selected from the group of protein sequences SEQ ID No. 1 - 37, homologous of SEQ ID No. 1 - 37, partial sequences of SEQ ID No. 1 - 37, nucleic acid sequences encoding for SEQ ID No. 1 - 37, nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37, nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37.
  • the detection of an interaction of this type can be carried out, for example, by a probe, in particular by an antibody.
  • the invention therefore likewise relates to the object of providing a diagnostic device or an assay, in particular a protein biochip, which permits a diagnosis or examination for Parkinson's disease.
  • the invention relates to a method for the stratification, in particular risk stratification and/or therapy control of a patient with Parkinson's disease, wherein at least one marker sequence selected from the group of protein sequences SEQ ID No. 1 - 37, homologous of SEQ ID No. 1 - 37, partial sequences of SEQ ID No. 1 - 37, nucleic acid sequences encoding for SEQ ID No. 1 - 37, nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37, nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37 is determined on a patient to be examined.
  • Parkinson's disease in new or established subgroups of Parkinson's disease is also covered, as well as the
  • diagnosis for the purposes of this invention means the positive determination of Parkinson's disease by means of the marker sequences according to the invention as well as the assignment of the patients to Parkinson's disease.
  • diagnosis covers medical diagnostics and examinations in this regard, in particular in-vitro diagnostics and laboratory diagnostics, likewise proteomics and nucleic acid blotting. Further tests can be necessary to be sure and to exclude other diseases.
  • diagnosis therefore likewise covers the differential diagnosis of Parkinson's disease by means of the marker sequences according to the invention and the prognosis of Parkinson's disease.
  • Stratification or therapy control for the purposes of this invention means that the method according to the invention renders possible decisions for the treatment and therapy of the patient, whether it is the hospitalization of the patient, the use, effect and/or dosage of one or more drugs, a therapeutic measure or the monitoring of a course of the disease and the course of therapy or etiology or classification of a disease, e.g., into a new or existing subtype or the differentiation of diseases and the patients thereof.
  • patient means any test subject - human or mammal - with the proviso that the test subject is tested for Parkinson's disease.
  • marker sequences for the purposes of this invention means that the protein (polypeptide, peptide) and / or the nucleic acid, e.g. RNA / cDNA / DNA encoding for the polypeptide or protein is significant for Parkinson's disease.
  • the cDNA or the polypeptide or protein that can be obtained thereof can exhibit an interaction with substances from the body fluid or tissue extract of a patient with Parkinson's disease (e.g., antigen (epitope) / antibody (paratope) interaction) .
  • At least one marker sequence is selected from the group of protein sequences SEQ ID No. 1 - 37, homologous of SEQ ID No. 1 - 37, partial sequences of SEQ ID No. 1 - 37, nucleic acid sequences encoding for SEQ ID No. 1 - 37, nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37, nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37 and is determined on a patient to be examined.
  • An interaction of this type is, e.g., a bond, in particular a binding substance on at least one marker sequence according to the invention or in the case of a cDNA the hybridization with a suitable substance under selected conditions, in particular stringent
  • stringent hybridization conditions hybridization in 4 x SSC at 65°C (alternatively in 50% formamide and 4 x SSC at 42°C), followed by several washing steps in 0.1 x SSC at 65°C for a total of approximately one hour.
  • An example of less stringent hybridization conditions is hybridization in 4 x SSC at 37°C, followed by several washing steps in 1 x SSC at room temperature .
  • substances of this type are constituents of a body fluid, in particular blood, whole blood, blood plasma, blood serum, patient serum, urine, cerebrospinal fluid, synovial fluid or of a tissue extract of the patient.
  • the marker sequences according to the invention can be present in a significantly higher or lower expression rate or concentration that indicates Parkinson's disease.
  • At least one marker sequence is selected from the group of protein sequences SEQ ID No. 1 - 37, homologous of SEQ ID No. 1 - 37, partial sequences of SEQ ID No. 1 - 37, nucleic acid sequences encoding for SEQ ID No. 1 - 37, nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37, nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37 and is determined on a patient to be examined in comparison to a control, e.g. a person without Parkinson's disease like for example a healthy person.
  • the relative sick/healthy expression rates of the marker sequences for Parkinson's disease according to the invention are hereby determined for example by means of proteomics or nucleic acid
  • the marker sequences have a recognition signal that is addressed to the substance to be bound (e.g., antibody, nucleic acid) .
  • the recognition signal is an epitope and/or a paratope and/or a hapten and for a cDNA is a hybridization or binding region.
  • the marker sequence recognizes (e.g. hybridizes, binds, ..) to an autoantibody which is significant for Parkinson's disease .
  • Autoantibodies that are significant for Parkinson's disease are either expressed only in case of Parkinson's disease or the levels of these autoantibodies vary significantly in case of Parkinson's disease, e.g. they are more or less expressed in case of Parkinson's disease in comparison to the levels of the respective autoantibody levels in a control like for example healthy persons.
  • the marker sequences can especially be used to determine autoantibody profiles that are specific for early detection of Parkinson's disease and/or diagnosis of
  • Autoantibody profiles in this respect relate to the amount of one or more autoantibodies that are specifically expressed, e.g. up- or down regulated in Parkinson's disease.
  • the autoantibody profiles relate therefore in one aspect to the composition (one or more autoantibodies) of the profile and in another aspect to the amount or
  • the marker sequence binds to / recognizes one or more autoantibodies that are more or less expressed during development, establishment, therapy and/or progression of Parkinson's disease.
  • one or more marker sequence can be used.
  • the invention comprises the use of at least one marker sequence.
  • two, three, four, five, six seven, eight, nine or ten or more, e.g. 15 or 20 or more marker sequences are used together or sequentially .
  • the marker sequences according to the invention are the subject matter of sequence listing and can be clearly identified by the sequences SEQ ID No. 1 - 37.
  • the marker sequences also cover those modifications of the cDNA sequence and the
  • amino acid sequence as chemical modification, such as citrullination, acetylation, phosphorylation, glycosylation or poly (A) strand and other modifications known to one skilled in the art.
  • Homologous sequences according to the invention are homologous protein / peptide or nucleic acid sequences, in particular of SEQ ID No. 1 - 37 that display an identity of at least 70 % or 80 %, preferred 90 % or 95 %, most preferred 96 % or 98 % or more, e.g. 98 % or 99 % homology with the respective protein, peptide or nucleic acid sequences or the respective partial sequences.
  • Partial sequences according to the invention are parts of the respective protein / peptide sequences, in particular of SEQ ID No. 1 - 37, and the nucleic acids encoding theses partial proteins or peptides. These parts are missing one or more amino acids or nucleotides respectively in
  • partial sequences or fragments of the marker sequences according to the invention are likewise covered.
  • Another object of the invention relates to an arrangement of marker sequences containing at least one marker sequence selected from the group of protein sequences SEQ ID No. 1 - 37, homologous of SEQ ID No. 1 - 37, partial sequences of SEQ ID No. 1 - 37, nucleic acid sequences encoding for SEQ ID No. 1 - 37, nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37, nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37.
  • the arrangement contains at least 2 to 5 or 10, for example 2, 3, 4 or 5, preferably 30 to 50 different marker sequences or 50 to 100 or more different marker sequences.
  • array is synonymous with “array, " and if this "array” is used to identify substances on marker sequences, this is to be understood to be an “assay” or diagnostic device.
  • the arrangement is designed such that the marker sequences represented on the arrangement are present in the form of a grid on a solid support.
  • the term "assay” or diagnostic device likewise comprises those embodiments of a device, such as ELISA, bead-based assay, line assay, Western Blot, immunochromatographic methods (e.g., lateral flow immunoassays) or similar immunological single or multiplex detection measures.
  • a protein biochip in accordance with the invention is a systematic
  • the marker sequences of the arrangement are fixed on a solid support, but preferably spotted or immobilized even printed on, i.e. applied in a reproducible manner.
  • One or more marker sequences can be present multiple times in the totality of all marker sequences and present in different quantities based on one spot.
  • the marker sequences can be standardized on the solid support (i.e., by means of serial dilution series of, e.g., human
  • the respective marker sequence can be represented in different quantities in one more regions on a solid support. This permits a variation of the sensitivity.
  • the regions can have a totality of marker sequences, i.e., a sufficient number of different marker sequences, in particular 2 to 5 or 10 or more and
  • nucleic acids and/or proteins optionally more nucleic acids and/or proteins, in
  • biomarkers At least 96 to 25,000 (numerical) or more from different or identical marker sequences and further nucleic acids and/or proteins, in particular biomarkers are preferred. Furthermore preferred are more than 2,500, in particular preferred 10,000 or more different or identical marker sequences and optionally further nucleic acids and/or proteins, in particular biomarkers .
  • the invention therefore relates to an assay or a protein biochip comprising an arrangement containing marker sequences according to the invention.
  • the marker sequences are present as clones.
  • Clones of this type can be obtained, for example, by means of a cDNA expression library according to the invention (Biissow et al. 1998 (supra)) .
  • such expression libraries containing clones are obtained using expression vectors from a cDNA expression library comprising the cDNA marker sequences.
  • These expression vectors preferably contain inducible promoters. The induction of the expression can be carried out, e.g., by means of an inductor, such as IPTG. Suitable expression vectors are described in Terpe et al. (Terpe T Appl)
  • Expression libraries can be produced according to standard works, such as Sambrook et al, "Molecular Cloning, A laboratory handbook, 2nd edition (1989), CSH press, Cold Spring Harbor, New York.
  • Expression libraries are also preferred which are tissue-specific (e.g., human tissue, in particular human organs) .
  • tissue-specific e.g., human tissue, in particular human organs
  • expression libraries can be obtained by exon-trapping .
  • a synonym for expression library is expression bank.
  • Uniclone® library protein biochips or corresponding expression libraries that do not exhibit any redundancy
  • Uniclone® library protein biochips or corresponding expression libraries that may be produced, for example, according to the teachings of WO 99/57311 and WO 99/57312.
  • Uniclone® library protein biochips or corresponding expression libraries that may be produced, for example, according to the teachings of WO 99/57311 and WO 99/57312.
  • These preferred Uniclone libraries have a high portion of non-defective fully expressed proteins of a cDNA expression library.
  • the clones can also be, but not limited to, transformed bacteria, recombinant phages or transformed cells from mammals, insects, fungi, yeasts or plants.
  • the clones are fixed, spotted or immobilized on a solid support .
  • the invention therefore relates to an arrangement wherein the marker sequences are present as clones.
  • the marker sequences can be present in the respective form of a fusion protein, which contains, for example, at least one affinity epitope or tag.
  • the tag may be one such as contains c-myc, his tag, arg tag, FLAG, alkaline phosphatase, VS tag, T7 tag or strep tag, HAT tag, NusA, S tag, SBP tag, thioredoxin, DsbA, a fusion protein, preferably a cellulose-binding domain, green fluorescent protein, maltose-binding protein, calmodulin-binding protein, glutathione S-transferase or lacZ .
  • solid support covers embodiments such as a filter, a membrane, a bead, for example a magnetic or fluorophore-labeled bead, a silica wafer, glass, metal, ceramics, plastics, a chip, a target for mass spectrometry or a matrix.
  • a filter for example PVDF, nitrocellulose or nylon (e.g., Immobilon P Millipore, Protran Whatman, Hybond N+ Amersham) can be used.
  • the arrangement corresponds to a grid with the dimensions of a microtiter plate (8 - 12 wells strips, 96 wells, 384 wells or more), a silica wafer, a chip, a target for mass spectrometry, or a matrix.
  • the invention relates to the use of at least one marker sequence for example an arrangement, a protein biochip or an assay according to the invention for
  • the invention therefore likewise relates to the use of an arrangement according to the invention or an assay for screening active substances for Parkinson's disease .
  • the invention relates to a method for identifying and characterizing a substance for Parkinson's disease, characterized in that at least one marker sequence for example an arrangement, a protein biochip or an assay according to the invention is a.) brought into contact with at least one substance to be tested and b.) a binding success is detected.
  • at least one marker sequence for example an arrangement, a protein biochip or an assay according to the invention is a.) brought into contact with at least one substance to be tested and b.) a binding success is detected.
  • the substance to be tested can be any native or non-native biomolecule, a synthetic chemical molecule, a mixture or a substance library.
  • the binding success is evaluated, which, for example, is carried out using commercially available image analyzing software (GenePix Pro (Axon Laboratories), Aida (Ray test), ScanArray (Packard Bioscience).
  • the visualization of protein-protein interactions according to the invention can be performed, for example, using fluorescence labelling, biotinylation, radioisotope labelling or colloid gold or latex particle labelling in the usual way.
  • a detection of bound antibodies is carried out with the aid of secondary antibodies, which are labelled with commercially available reporter molecules (e.g., Cy, Alexa, Dyomics, FITC or similar fluorescent dyes, colloidal gold or latex particles), or with reporter enzymes, such as alkaline phosphatase, horseradish
  • Readout is conducted, e.g., using a microarray laser scanner, a CCD camera or visually.
  • the invention relates to a drug/active substance or prodrug developed for Parkinson's disease and obtainable through the use of the assay or protein biochip according to the invention.
  • the invention therefore likewise relates to a target for the treatment and therapy of
  • Parkinson's disease wherein the target is selected from the group of protein sequences SEQ ID No. 1 - 37, homologous of SEQ ID No. 1 - 37, partial sequences of SEQ ID No. 1 - 37, nucleic acid sequences encoding for SEQ ID No. 1 - 37, nucleic acid sequences encoding for homologous of SEQ ID No. 1 - 37, nucleic acid sequences encoding for partial sequences of SEQ ID No. 1 - 37 and nucleic acids encoding for partial sequences of homologous of SEQ ID No. 1 - 37.
  • the invention likewise relates to the use of the marker sequences according to the invention, preferably in the form of an arrangement, as an affinity material for carrying out an apheresis or in the broadest sense a blood lavage, wherein substances from body fluids of a patient with Parkinson's disease, such as blood or plasma, bind to the marker sequences according to the invention and consequently can be selectively withdrawn from the body fluid.
  • the diagnosis of PD is still a challenge. Especially at early stages the clinical signs and symptoms of PD can overlap with other neurodegenerative diseases (Tolosa et al. , 2006) . Up to now no suitable biomarker for PD could be identified. Most studies have focused on the detection of a single protein known to be involved in the
  • the screening platform allows a simultaneous analysis in a high-throughput manner.
  • a three step approach
  • autoantibodies can be divided into three subgroups: 1) autoantibodies to proteins involved in the pathological cascade of the disease, 2) autoantibodies possibly related to therapeutic interventions and 3) autoantibodies to proteins with unknown biological significance.
  • SEPT4 Septin 4
  • BAG5 BCL2-associated athanogene 5
  • SEPT4 has been localized also in Lewy bodies in the SN of PD patients (Ihara et al . , 2007) . SEPT4 could be further detected together with ⁇ -synuclein in the presynaptic terminals of dopaminergic neurons, suggesting a physiological association (Ihara et al. , 2003) . Additionally, in a-synuclein A53T transgenic mice the loss of septin4 enhanced neuropathology (Ihara et al. , 2007) . Recoverin is known to be a neuronal calcium sensor (Nagao and Hayashi, 2009) . The intracellular Ca 2+ -concentration is essential for neurotransmitter release and other neuronal processes. Another member of that protein family,
  • BAG5 is another candidate marker known to regulate the E3 ubiquitin ligase CHIP.
  • ubiquitin ligases is to target substrate proteins for degradation where a-synuclein is a prominent substrate (Kalia et al. , 2011) . BAG5 is also shown to inhibit also Parkin E3 ligase activity (Kalia et al. , 2004).
  • mutations in the parkin gene were identified as a cause of autosomal recessive PD (Kitada et al. , 1998) . Since then, more than one hundred different mutations of that candidate gene have been described (West and Maidment, 2004) . Genetic and biochemical studies revealed that mutations induce a loss of parkin function, leading to the hypothesis that the accumulation of parkin substrates causes neurotoxicity and results in the death of dopaminergic neurons .
  • the aim and complexity of the biomarker candidate selection procedure was to find a suitable panel of proteins that discriminates the main groups HC, DC and PD .
  • the M score provided by Prospector has been used to rate the discriminating power of particular proteins for biomarker candidate pre-selection .
  • the M score has revealed proteins with sub-group differences.
  • Other pre-selection methods e.g., t-test or Mann-Whitney U test
  • had been not able to detect these sub-groups Love, 2007, Sboner et al. , 2009.
  • the list assembling approach has solved two tasks. On the one hand, the multiclass problem of finding biomarker candidates to distinguish PD patients from HC and DC has been solved. On the other hand, the aim to exclude biomarker candidates discriminating
  • Expression Omnibus under GSE29654 and GSE296766 is composed of microarrays from different lots neither clinical class distribution nor protein exclusion or other batch
  • the unistep pre-selection method that has been used in this study has been combined with two other approaches (manual and wrapper approach) to enhance biomarker candidate detection.
  • the wrapper approach that has been used in this study is a widely used multivariate feature selection method (Saeys et al . , 2007, Kohavi R. and John, 1997) for optimal variable set detection when the number samples is very much smaller than the number of variables (so called "n ⁇ p" problems; this is
  • Figure 1 The biomarker candidate selection procedure that has been performed in this study.
  • four two group comparisons arrays incubated with HC sera vs. arrays incubated with PD sera, arrays incubated with DC sera vs. arrays incubated with PD sera, arrays incubated with HC sera vs. arrays incubated with DC sera and all arrays from one of the ProtoArray lots vs. all arrays from the other lot (“lot 1 vs. lot 2”)
  • For the corresponding results that have been sorted by means of M score thresholds have been set to identify the respective most discriminative proteins for the four comparisons and to discard all proteins that not match these thresholds.
  • the four reduced lists have been assembled by restoring the proteins in the HC vs. PD list that are contained in the DC vs. PD list and that have been discarded previously ("+") . Then, all proteins that are contained in the HC vs. DC and in the lot 1 vs. lot 2 lists are discarded from the HC vs. PD list ("-") .
  • the resulting list has contained 284 preliminary biomarker candidates. This list has been used for manual and wrapper biomarker selection ("manual" and "wrapper”) as described in the text. Finally, the resulting lists containing 22 and 14 proteins, respectively, have been assembled to the final biomarker candidate list containing 37 proteins.
  • Figure 2 Exemplary Single Feature Scatter Plot.
  • All 144 data points are intensity values of a particular protein measured on 72 protein arrays incubated with HC sera (left) and 72 protein arrays incubated with PD sera (right) .
  • ParkCHIP data (in log scale) are shown where 117 arrays from one lot ("batch 1") are displayed in the lower part and the 99 arrays from the other lot ("batch 2") are displayed in the upper part of each diagram.
  • a) raw data in b) data after cyclic loess normalization in c) data after vsn normalization and in d) data after quantile normalization is shown.
  • Figure 4 Exemplary two-microarray plots ("same-same plots") of ProtoArray pairs are shown; left: raw intensities, right: log intensities; details: In a) raw data (intensity values) of two technical replicates (different microarrays incubated with the same serum) from the same lot is drawn (average coefficient of variation (CV) : 7.9%) . b) shows the corresponding plot with log-scale data of the same
  • microarrays like in e) (CV: 2.9%) .
  • raw data of two microarrays incubated with different sera from different lots is drawn (CV: 47.2%) .
  • h) shows the corresponding plot with log-scale data of the same microarrays like in g) (CV: 8.1%) .
  • Example 1 Material and methods Subjects and samples
  • ParkCHIP is an on-going cross-sectional study of cases with PD, diseased controls with other neurodegenerative diseases (DC), and healthy controls (HC) . All together over 2,500 participants were screened for inclusion criteria. This analysis was conducted with a subset of 72 triplets where a PD patient was matched 1:1:1 by gender and age to two controls (DC and HC) . Non-eligible were subjects with severe cognitive impairment, drug addiction, and being HIV positive. Socio-demographic characteristics of the triplets and of the diseases of DC are shown in Tables 1 and 2. The diseases of DC comprised neurodegenerative other than PD and autoimmune disorders. Subjects with neurodegenerative disorders other than PD were diagnosed according to the guidelines for the specific disease. Eligible were PD cases with validated diagnosis according to the diagnostic criteria of the Parkinson ' s UK Brain Bank (Hughes et al. , 1992) . Furthermore, patients had to fulfil at least four supportive criteria, with an excellent response to
  • HC dopaminergic medication as obligate inclusion criteria. Patients not on therapy underwent functional imaging via Single Photon Emission Computed Tomography (SPECT) . HC were unrelated to cases and comprised subjects without
  • Venous blood samples were taken from an antecubital vein through an indwelling catheter for the protein microarray analysis and for the determination of routine laboratory parameters.
  • Blood samples for routine laboratory parameters were collected in EDTA tubes containing 100 L of 0.5% sodium disulfite solution and in 5 mL tubes for serum preparation (Kabevette® V serum Gel S831 V, Kabe
  • Example 3 Statistical analysis of protein microarray data and biomarker candidate selection ("feature selection")
  • Step 1 For the first step the software Prospector provided by the ProtoArray vendor has been used (current version 5.2 can be downloaded from Life Technologies' web site (http://www.lifetechnologies.com)). Due to its sensitivity for unknown biological subgroups Prospector's minimal M Statistic ("M score", proposed in Love B., 2007) is an appropriate measure to score the proteins concerning two group discrimination. After importing the normalized data into Prospector four comparisons with two groups each have been computed. These comparisons are: HC vs. PD, DC vs. PD, HC vs. DC and lot 1 vs. lot 2. Thus, Prospector has computed altogether four comparison result lists each containing about 9,500 proteins and a corresponding M score.
  • M score proposed in Love B., 2007
  • Step 2 In the second step the four lists from step 1 have been assembled by the following procedure: First, all proteins that had been discarded from the original HC vs. PD list but not from the DC vs. PD list during step 1 have been restored in the HC vs. PD list (including their corresponding HC vs. PD M score values) . Thus, proteins that discriminate HC and PD as well as DC and PD have been finally included. Then, all proteins contained in the HC vs. DC list and the lot 1 vs. lot 2 list have been deleted from the HC vs. PD list. Thus, proteins that discriminate HC and DC as well as the two different ProtoArray
  • Step 3 In step 3 the remaining 284 biomarker candidates have been further narrowed down by a manual and an
  • classification accuracy The whole procedure including split has been repeated ten times to avoid a selection bias caused by the splitting step. Finally, the average accuracy of the ten sub-run accuracy values has been computed to assess the overall performance of the biomarker candidates.
  • classification results for the group comparisons HC vs. PD, DC vs. PD and HC vs. DC have been compared to analogous classification results based on all ParkCHIP samples with randomly mixed group assignments (hereafter referred to as groups "A", "B” and "C”) .
  • Alzheimer's disease 4 5. .56
  • Corticobasal degeneration 2 2. .78
  • Tourette's syndrome 1 1. .39
  • Gallagher DA Goetz CG
  • Stebbins G Stebbins G
  • Lees AJ Schrag A.
  • Goldberg DE Genetic algorithms in search, optimization, and machine learning. Repr . with corr . ed. Reading, Mass. [u.a.]: Addison-Wesley; 1989.
  • Parkinson disease a population-based case-control study. Eur J Neurol. 2011 Nov; 18 ( 11 ): 1336-42.
  • TNF-alpha Tumor necrosis factor-alpha
  • Kalia LV Kalia SK, Chau H, Lozano AM, Hyman BT, McLean PJ.
  • Ubiquitinylation of alpha-synuclein by carboxyl terminus Hsp70-interacting protein (CHIP) is regulated by Bcl-2- associated athanogene 5 (BAG5).
  • Bcl-2- associated athanogene 5 BAG5

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Abstract

La présente invention concerne de nouvelles séquences marqueurs pour la maladie de Parkinson et l'utilisation diagnostique de celles-ci conjointement à un procédé de criblage de substances potentiellement actives pour la maladie de Parkinson au moyen de ces séquences marqueurs. En outre, l'invention concerne un dispositif diagnostique contenant ces séquences marqueurs pour la maladie de Parkinson, en particulier une biopuce de protéine et son utilisation.
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DE69921982T2 (de) 1998-04-30 2005-12-29 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Neuartiges verfahren zur identifizierung von klonen mit einer gewünschten biologischen eigenschaft, ausgehend von einer expressionsgenbank
WO1999057312A1 (fr) 1998-04-30 1999-11-11 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Nouveau procede permettant la selection de clones dans une banque d'expression et comprenant un rearrangement
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CLEMENS R. SCHERZER ET AL: "Molecular markers of early Parkinson's disease based on gene expression in blood", PNAS, vol. 104, no. 3, 16 January 2007 (2007-01-16), pages 955 - 960, XP055019562, DOI: 10.1073/pnas.0610204104 *
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