EP3924973A1 - Blood-based screen for detecting neurological diseases in primary care settings - Google Patents
Blood-based screen for detecting neurological diseases in primary care settingsInfo
- Publication number
- EP3924973A1 EP3924973A1 EP20754956.9A EP20754956A EP3924973A1 EP 3924973 A1 EP3924973 A1 EP 3924973A1 EP 20754956 A EP20754956 A EP 20754956A EP 3924973 A1 EP3924973 A1 EP 3924973A1
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- European Patent Office
- Prior art keywords
- disease
- biomarkers
- alzheimer
- dementia
- neurological
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- 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.)
- Pending
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- G16B40/20—Supervised data analysis
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/158—Expression markers
Definitions
- the present invention relates in general to the field of screening, detecting and discriminating between neurological diseases within primary care settings, and more particularly, to biomarkers for the detection, screening, and discriminating patients with neurological diseases.
- Another such invention is taught in United States Patent No. 8,008,025, issued to Zhang and directed to biomarkers for neurodegenerative disorders. Briefly, this inventor teaches methods for diagnosing neurodegenerative disease, such as Alzheimer's Disease, Parkinson's Disease, and dementia with Lewy body disease by detecting a pattern of gene product expression in a cerebrospinal fluid sample and comparing the pattern of gene product expression from the sample to a library of gene product expression pattern known to be indicative of the presence or absence of a neurodegenerative disease. The methods are also said to provide for monitoring neurodegenerative disease progression and assessing the effects of therapeutic treatment. Also provided are kits, systems and devices for practicing the subject methods.
- United States Patent Application Publication No. 2013/0012403, filed by Hu is directed to Compositions and Methods for Identifying Autism Spectrum Disorders.
- This application is directed to microRNA chips having a plurality of different oligonucleotides with specificity for genes associated with autism spectrum disorders.
- the invention is said to provide methods of identifying microRNA profiles for neurological and psychiatric conditions including autism spectrum disorders, methods of treating such conditions, and methods of identifying therapeutics for the treatment of such neurological and psychiatric conditions.
- the method is said to include quantitating the amount of alpha-sy nuclein and total protein in a cerebrospinal fluid (CSF) sample obtained from the subject and calculating a ratio of alpha-synuclein to total protein content; comparing the ratio of alpha-synuclein to total protein content in the CSF sample with the alpha-synuclein to total protein content ratio in CSF samples obtained from healthy neurodegenerative disease-free subjects; and determining from the comparison whether the subject has a likelihood to develop neurodegenerative disease or making a diagnosis of neurodegenerative disease in a subject. It is said that a difference in the ratio of alpha- synuclein to total protein content indicates that the subject has a likelihood of developing a neurodegenerative disease or has developed a neurodegenerative disease.
- CSF cerebrospinal fluid
- the present invention includes a method for detecting biomarkers within a primary care setting comprising: measuring a level of four or more biomarkers selected from IL1, IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, adiponectin, MIP1, eotaxin3, sVCAMl, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and a-synuclein in a sample separated from a human subject in the primary care setting with neurological disease with a nucleic acid, an immunoassay or an enzymatic activity assay.
- the first four biomarkers are used in the analysis, namely, IL1, IL7, TNFa, and IL5.
- the neurological disease is selected from the group consisting of Alzheimer’s Disease, Parkinson’s Disease, Down’s syndrome, Frontotemporal dementia, Dementia with Lewy Bodies.
- the neurological disease is selected from the group consisting of Alzheimer’s Disease or Parkinson’s Disease.
- the neurological disease is selected from the group consisting of Alzheimer’s Disease or Dementia with Lewy Bodies.
- the neurological disease is selected from the group consisting of Parkinson’s Disease or Dementia with Lewy Bodies.
- the neurological disease is selected from the group consisting of Alzheimer’s Disease, Parkinson’s Disease, or Dementia with Lewy Bodies.
- the method detects 5, 6, 7, 8, 9, 10, 11, 12, or 13 biomarkers of neurological diseases.
- the sample is serum or plasma.
- the method further comprises the step of obtaining the following parameters: patient age, and a neurocognitive screening tests, wherein the combination of four or more biomarkers (e.g., serum- or plasma-based, age and the neurocognitive screening tests) are at least 90% accurate in a primary care setting for the determination of Alzheimer’s disease when compared to a control subject that does not have a neurological disease or disorder.
- a profile comprises age, and one or more biomarkers selected from sVCAMl, IL5, B2M, IL6, IL1, adiponexin, Eotaxin, MIP1 and IL10.
- the first four biomarkers are used in the analysis, namely, sVCAMl, IL5, B2M, and IL6.
- a profile comprises NFL, PPY, FABP3, IL18, IL7, TARC, TPO, a-syn, Eotaxin3 and IL5, and further comprises Ab40, Ab42, tau, alpha- syn, and NfL.
- a profile for identifying Dementia with Lewy Bodies from other neurode generative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin, MIP1 and IL10.
- a profile for identifying Parkinson’s disease from other neurode generative diseases comprises ICAM1, VCAM1, Ab42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6.
- the method further comprises the step of determining one or more of the following parameters: sleep disturbance (yes/no), visual hallucinations (yes/no), psychiatric/personality changes (yes/no), age, neurocognitive screening, and four or more biomarkers for the accurate detection and discrimination between neurode generative diseases.
- the level of expression identified by nucleic acid, an immunoassay or an enzymatic activity assay is selected from fluorescence detection, chemiluminescence detection, electrochemiluminescence detection and patterned arrays, reverse transcriptase -polymerase chain reaction, antibody binding, fluorescence activated sorting, detectable bead sorting, antibody arrays, microarrays, enzymatic arrays, receptor binding arrays, allele specific primer extension, target specific primer extension, solid-phase binding arrays, liquid phase binding arrays, fluorescent resonance transfer, or radioactive labeling.
- the method is used to screen in the primary setting uses a higher specificity than sensitivity, wherein the specificity is in the range of 0.97 to 1.0, and the sensitivity is in the range of 0.80 to 1.0.
- a profile for identifying Dementia with Lewy Bodies from other neurodegenerative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin3, MIP1 and IL10 or the biomarkers in Figure 7.
- a profile for identifying Parkinson’s disease from other neurodegenerative diseases comprises ICAM1, VCAM1, Ab42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6.
- a profile for identifying Parkinson’s disease from negative controls comprises NFL, PPY, FABP3, and IL18, and may further comprise one or more biomarkers selected from IL7, TARC, TPO, a-syn, Eotaxin3 and IL5.
- the neurological disease is determined from the biomarkers found in Figures 7 - 11, which will often be used in order.
- the present invention includes a method for detecting biomarkers in a human patient with neurological disease, the method comprising: detecting a level of four or more proteins selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and a-synuclein by separating the proteins in a sample separated from a human subject in the primary care setting with neurological disease contained in the sample and a molecular marker by electrophoresis; contacting the separated proteins with four or more antibodies that each specifically bind to four or more proteins selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO,
- a profile for identifying Parkinson’s disease from negative controls comprises NFL, PPY, FABP3, and IL18, and may further comprise one or more biomarkers selected from IL7, TARC, TPO, a-syn, Eotaxin3 and IL5.
- the first four biomarkers are used in the analysis for detecting Alzheimer’s disease, namely, IL7, TNFa, IL5, and IL6.
- the secondary antibody comprises a fluorescence label, chemiluminescence label, an electrochemiluminescence label, the separation is on a patterned array, an antibody arrays, a fluorescent resonance transfer label, or a radioactive label.
- the neurological disease is selected from the group consisting of Alzheimer’s Disease, Parkinson’s Disease, Down’s syndrome, Frontotemporal dementia, Dementia with Lewy Bodies. In another aspect, the neurological disease is selected from the group consisting of Alzheimer’s Disease or Parkinson’s Disease. In another aspect, the neurological disease is selected from the group consisting of Alzheimer’s Disease or Dementia with Lewy Bodies. In another aspect, the neurological disease is selected from the group consisting of Parkinson’s Disease or Dementia with Lewy Bodies. In another aspect, the neurological disease is selected from the group consisting of Alzheimer’s Disease, Parkinson’s Disease, or Dementia with Lewy Bodies.
- the method detects 5, 6, 7, 8, 9, 10, 11, 12, or 13 biomarkers of neurological diseases.
- the sample is serum or plasma.
- the method further comprises the step of obtaining the following parameters: patient age, and a neurocognitive screening tests, wherein the combination of four or more biomarkers, age and the neurocognitive screening tests) are at least 90% accurate in a primary care setting for the determination of Alzheimer’s disease when compared to a control subject that does not have a neurological disease or disorder.
- a profile comprises age, sVCAMl, IL5, B2M, IL6, IL1, adiponexin, Eotaxin, MIP1 and IL10.
- the first four biomarkers are used in the analysis, namely, sVCAMl, IL5, B2M, and IL6.
- a profile comprises NFL, PPY, FABP3, IL18, IL7, TARC, TPO, a-syn, Eotaxin3 and IL5, and further comprises Ab40, Ab42, tau, alpha-syn, and NfL.
- a profile for identifying Dementia with Lewy Bodies from other neurode generative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin, MIP1 and IL10.
- a profile for identifying Parkinson’s disease from other neurode generative diseases comprises fCAMf, VCAMi, Ab42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6.
- the method further comprises the step of determining one or more of the following parameters: sleep disturbance (yes/no), visual hallucinations (yes/no), psychiatric/personality changes (yes/no), age, neurocognitive screening, and four or more biomarkers for the accurate detection and discrimination between neurodegenerative diseases.
- the level of expression identified by nucleic acid, an immunoassay or an enzymatic activity assay is selected from fluorescence detection, chemiluminescence detection, electrochemiluminescence detection and patterned arrays, reverse transcriptase-polymerase chain reaction, antibody binding, fluorescence activated sorting, detectable bead sorting, antibody arrays, microarrays, enzymatic arrays, receptor binding arrays, allele specific primer extension, target specific primer extension, solid-phase binding arrays, liquid phase binding arrays, fluorescent resonance transfer, or radioactive labeling.
- the method is used to screen in the primary setting uses a higher specificity than sensitivity, wherein the specificity is in the range of 0.97 to 1.0, and the sensitivity is in the range of 0.80 to 1.0.
- a profile for identifying Dementia with Lewy Bodies from other neurodegenerative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin, MIP1 and IL10.
- a profile for identifying Parkinson’s disease from other neurodegenerative diseases comprises fCAMf, VCAMi, Ab42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6.
- a profile for identifying Parkinson’s disease from negative controls comprises NFL, PPY, FABP3, and IL18, and may further comprise one or more biomarkers selected from IL7, TARC, TPO, a-syn, Eotaxin3 and IL5.
- the neurological disease is determined from the biomarkers found in Figures 7 - 11, which will often be used in order.
- the present invention includes a method of selecting subjects for a clinical trial to evaluate a candidate drug believed to be useful in treating neurological diseases, the method comprising: measuring a level of four or more biomarkers selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAMI, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and a-synuclein in a sample separated from a human subject in the primary care setting with neurological disease with a nucleic acid, an immunoassay or an enzymatic activity assay; and determining if the subject should participate in the clinical trial based on the results of the identification of the neurodegenerative disease profile of the subject obtained from the step (a), wherein the subject is only selected if the neurodegenerative disease profile if the candidate drug is likely to be useful in beating the neurological disease.
- the first four biomarkers are used in the analysis, namely, IL7, TNFa, IL5, and IL6.
- a profile for identifying Dementia with Lewy Bodies from other neurodegenerative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin, MIP1 and IL10.
- a profile for identifying Parkinson’s disease from other neurodegenerative diseases comprises ICAM1, VCAM1, Ab42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6.
- a profde for identifying Parkinson’s disease from negative controls comprises NFL, PPY, FABP3, and IL18, and may further comprise one or more biomarkers selected from IL7, TARC, TPO, a-syn, Eotaxin3 and IL5.
- the neurological disease is determined from the biomarkers found in Figures 7 - 11, which will often be used in order.
- the present invention includes a method of evaluating the effect of a treatment for a neurological disease, the method comprising: treating a patient for a neurological disease; measuring a level of four or more biomarkers selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and a-synuclein in a sample separated from a human subject in the primary care setting with neurological disease with a nucleic acid, an immunoassay or an enzymatic activity assay; and determining if the treatment reduces the expression of the one or more biomarkers that is statistically significant as compared to any reduction occurring in the second subset of patients that have not been treated or from a prior sample obtained from the patient, wherein a statistically significant reduction indicates that the treatment is useful
- the first four biomarkers are used in the analysis, namely, IL7, TNFa, IL5, and IL6.
- a profile for identifying Dementia with Lewy Bodies from other neurodegenerative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin, MIP1 and IL10.
- a profile for identifying Parkinson’s disease from other neurodegenerative diseases comprises ICAM1, VCAM1, Ab42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6
- a profile for identifying Parkinson’s disease from negative controls comprises NFL, PPY, FABP3, and IL18, and may further comprise one or more biomarkers selected from IL7, TARC, TPO, a-syn, Eotaxin3 and IL5.
- the neurological disease is determined from the biomarkers found in Figures 7 - 11, which will often be used in order.
- the present invention includes a method and/or apparatus for screening for neurological disease within a primary care setting comprising: obtaining a blood test sample from a subject in the primary care setting; measuring two or more biomarkers in the blood sample selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and/or a-synuclein; comparing the level of the one or a combination of biomarkers with the level of a corresponding one or combination of biomarkers in a normal blood sample; measuring an increase in the level of the two or more biomarkers in the blood test sample in relation to that of the normal blood sample, which indicates that the subject is likely to have a neurological disease; identifying the neurological disease based on the two biomarkers measured; and selecting a course of
- At least one of the biomarker measurements is obtained by a method selected from the group consisting of immunoassay and enzymatic activity assay.
- the first four biomarkers are used in the analysis, namely, IL7, TNFa, IL5, and IL6.
- the method further comprises advising the individual or a primary health care practitioner of the change in calculated risk.
- the method further comprises advising the individual or a primary health care practitioner of the change in calculated risk.
- the method uses 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 biomarkers to distinguish between neurological diseases.
- the isolated biological sample is serum or plasma.
- the sample is a serum sample and upon the initial determination of a neurological disease within the primary care clinic, providing that primary care provider with information regarding the specific type of specialist referral appropriate for that particular blood screen finding and directing the individual to a specialist for that neurological disease and treatment in accordance therewith.
- the neurological diseases are selected from Alzheimer’s Disease, Parkinson’s Disease, Down’s syndrome, Frontotemporal dementia, Dementia with Lewy Bodies, and neurodegenerative disease.
- the method further comprises the step of refining the analysis by including the following parameters: patient age, and a neurocognitive screening tests, wherein the combination of two or more serum-based markers, age and the neurocognitive screening tests are at least 90% accurate in a primary care setting for the determination of Alzheimer’s disease when compared to a control subject that does not have a neurological disease or disorder.
- the method further comprises the step of determining one or more of the following parameters: sleep disturbance (yes/no), visual hallucinations (yes/no), psychiatric/personality changes (yes/no), age, neurocognitive screening, and two or more serum-based markers for the accurate detection and discrimination between neurodegenerative diseases.
- the level of expression of the various proteins is measured by at least one of fluorescence detection, chemiluminescence detection, electrochemiluminescence detection and patterned arrays, reverse transcriptase-polymerase chain reaction, antibody binding, fluorescence activated sorting, detectable bead sorting, antibody arrays, microarrays, enzymatic arrays, receptor binding arrays, allele specific primer extension, target specific primer extension, solid-phase binding arrays, liquid phase binding arrays, fluorescent resonance transfer, or radioactive labeling.
- the method is used to screen in the primary setting used a higher specificity than sensitivity, wherein the specificity is in the range of 0.97 to 1.0, and the sensitivity is in the range of 0.80 to 1.0.
- a profile for identifying Dementia with Lewy Bodies from other neurodegenerative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin, MIP1 and IL10.
- a profile for identifying Parkinson’s disease from other neurodegenerative diseases comprises ICAM1, VCAM1, Ab42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6.
- a profile for identifying Parkinson’s disease from negative controls comprises NFL, PPY, FABP3, and IL18, and may further comprise one or more biomarkers selected from IL7, TARC, TPO, a-syn, Eotaxin3 and IL5.
- the neurological disease is determined from the biomarkers found in Figures 7 - 11, which will often be used in order.
- Another embodiment of the present invention includes a method and apparatus for distinguishing between one or more neurological disease states; the method comprising: obtaining from at least one biological sample isolated from an individual suspected of having a neurological disease measurements of biomarkers comprising the biomarkers IL-7 and TNFa; adding the age of the subject and the results from one or more neurocognitive screening tests from the subject (clock drawing, verbal fluency, list learning, sleep disturbances, visual hallucinations, behavioral disturbances, motor disturbances); calculating the individual's risk for developing the neurological disease from the output of a model, wherein the inputs to the model comprise the measurements of the two biomarkers, the subject’s age and the results from one or more cognitive tests, and further wherein the model was developed by fitting data from a longitudinal study of a selected population of individuals and the fitted data comprises levels of the biomarkers, the subject’s age and the results from one or more cognitive tests and neurological disease in the selected population of individuals; and comparing the calculated risk for the individual to a previously calculated risk obtained from at least one earlier
- At least one of the biomarker measurements is obtained by a method selected from at least one of fluorescence detection, chemiluminescence detection, electrochemiluminescence detection and patterned arrays, reverse transcriptase-polymerase chain reaction, antibody binding, fluorescence activated sorting, detectable bead sorting, antibody arrays, microarrays, enzymatic arrays, receptor binding arrays, allele specific primer extension, target specific primer extension, solid-phase binding arrays, liquid phase binding arrays, fluorescent resonance transfer, or radioactive labeling.
- two or more of the methods for biomarker measurement are used to cross-validate the neurological disease.
- the method further comprises advising the individual or a health care practitioner of the change in calculated risk.
- the method further comprises advising the individual or a health care practitioner of the change in calculated risk.
- the biomarkers further comprise one or more biomarkers selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and/or a-sy nuclein.
- the first four biomarkers are used in the analysis, namely, IL7, TNFa, IL5, and IL6.
- the method uses 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 biomarkers to distinguish the neurological disease.
- the isolated biological sample is serum or plasma.
- the sample is a serum sample and upon the initial determination of a neurological disease, directing the individual to a specialist for that neurological disease.
- the neurological diseases are selected from Alzheimer’s Disease, Down’s syndrome, Frontotemporal dementia, Dementia with Lewy Bodies, Parkinson’s Disease, and dementia.
- the method is used to exclude one or more neurological diseases selected from Alzheimer’s Disease, Down’s syndrome, Frontotemporal dementia, Dementia with Lewy Bodies, Parkinson’s Disease, and dementia.
- the method is used to screen in the primary setting used a higher specificity than sensitivity, wherein the specificity is in the range of 0.97 to 1.0, and the sensitivity is in the range of 0.80 to 1.0.
- the present invention also includes a method of performing a clinical trial to evaluate a candidate drug believed to be useful in treating neurological diseases, the method comprising: (a) measuring an two or more biomarkers selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and/or a-synuclein from one or more blood samples obtained from patients suspected of having a neurological disease, the patient’s age, and results from one or more neurocognitive screening tests of the patient; (b) administering a candidate drug to a first subset of the patients, and a placebo to a second subset of the patients; (c) repeating step (a) after the administration of the candidate drug or the placebo; and (d) determining if the candidate drug reduces the expression of the one
- the method further comprises the steps of obtaining one or more additional blood samples from the patient after a predetermined amount of time and comparing the levels of the biomarkers from the one or more additional samples to determine disease progression.
- the method further comprises the steps of treating the patient for a pre-determined period of time, obtaining one or more additional blood samples from the patient after the predetermined amount of time and comparing the levels of the biomarkers from the one or more additional samples to determine disease progression.
- the first four biomarkers are used in the analysis, namely, IL7, TNFa, IL5, and IL6.
- a profile for identifying Dementia with Lewy Bodies from other neurode generative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin, MIP1 and IL10.
- a profile for identifying Parkinson’s disease from other neurode generative diseases comprises ICAM1, VCAM1, Ab42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6.
- a profile for identifying Parkinson’s disease from negative controls comprises NFL, PPY, FABP3, and IL18, and may further comprise one or more biomarkers selected from IL7, TARC, TPO, a-syn, Eotaxin3 and IL5.
- the neurological disease is determined from the biomarkers found in Figures 7 - 11, which will often be used in order.
- the present invention also includes a method of selecting subjects for a clinical trial to evaluate a candidate drug believed to be useful in treating neurological diseases, the method comprising: (a) measuring an two or more biomarker selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and/or a-synuclein in a blood samples obtained from the subject, the patient’s age and the results from one or more neurocognitive screening tests to determine a neurode generative disease profile; and (b) determining if the subject should participate in the clinical trial based on the results of the identification of the neurodegenerative disease profile of the subject obtained from the step (a), wherein the subject is only selected if the neurodegenerative disease profile if the candidate drug is likely to be useful in treating the
- the present invention also includes a method of evaluating the effect of a treatment for a neurological disease, the method comprising: treating a patient for a neurological disease; measuring two or more biomarkers from a blood samples obtained from patients suspected of having a neurological disease, the patient’s age, and results from one or more cognitive tests of the patient; and determining if the treatment reduces the expression of the one or more biomarkers that is statistically significant as compared to any reduction occurring in the second subset of patients that have not been treated or from a prior sample obtained from the patient, wherein a statistically significant reduction indicates that the treatment is useful in treating the neurological disease.
- the present invention also includes a method of aiding diagnosis of neurological diseases, comprising: obtaining a blood sample from a human individual; comparing normalized measured levels of IL-7 and TNFa biomarkers from the individual's blood sample to a reference level of each neurological disease diagnosis biomarker; wherein the group of neurological disease diagnosis biomarkers comprises IL-7 and TNFa; and obtaining the patient’s age and results from one or more cognitive tests of the patient; wherein the reference level of each neurological disease diagnosis biomarker comprises a normalized measured level of the neurological disease diagnosis biomarker from one or more blood samples of human individuals without neurological disease ; and wherein levels of neurological disease diagnosis biomarkers greater than the reference level of each neurological disease diagnosis biomarker, the patient’s age and the patient’s results from one or more cognitive tests indicate a greater likelihood that the individual suffers from neurological disease.
- the present invention also includes a method of level of expression of IL-7 and TNF alpha in the blood are elevated when compared to the reference level indicates a greater likelihood that the individual suffers from the neurological disease.
- the method further comprises the step of determining the blood levels of one or more biomarkers selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and/or a-synuclein.
- the method uses 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 biomarkers to distinguish the neurological disease.
- the levels of CRP and IL10 are lower when compared to the reference level indicates a greater likelihood that the individual suffers from the neurological disease.
- the method further comprises the steps of obtaining one or more additional blood samples from the patient after a predetermined amount of time and comparing the levels of the biomarkers from the one or more additional samples to determine disease progression.
- the isolated blood sample is serum sample.
- the blood sample is a serum sample and upon the initial determination of a neurological disease, directing the individual to a specialist for that neurological disease.
- the neurological diseases are selected from Alzheimer’s Disease, Parkinson’s Disease, and dementia.
- the method is used to screen in the primary setting used a higher specificity than sensitivity, wherein the specificity is in the range of 0.97 to 1.0, and the sensitivity is in the range of 0.80 to 1.0.
- the present invention also includes a rapid-screening kit for aiding diagnosis of a neurological disease in a primary care setting, comprising: one or more reagents for detecting the level of expression of IL-7 and TNFa in a blood sample obtained from a human individual, and one or more neurological screening test sheets; and instructions for comparing normalized measured levels of the IL-7 and TNFa biomarkers from the individual’s blood sample to a reference level, the patient’s age and the patient’s results from the neurological screening tests; wherein the reference level of each neurological disease diagnosis biomarker comprises a normalized measured level of the neurological disease diagnosis biomarker from one or more blood samples of human individuals without neurological disease; and wherein levels of neurological disease diagnosis biomarkers less than the reference level of each neurological disease diagnosis biomarker indicate a greater likelihood that the individual suffers from neurological disease, wherein the test is at least 90% accurate.
- the level of expression of IL-7 and TNF alpha in the blood are elevated when compared to the reference level indicates a greater likelihood that the individual suffers from the neurological disease.
- the kit further comprises one or more reagents for detecting the level of expression markers selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and/or a-synuclein.
- the levels of CRP and IL10 are lower when compared to the reference level indicates a greater likelihood that the individual suffers from the neurological disease.
- the sample is a serum sample and upon the initial determination of a neurological disease, directing the individual to a specialist for that neurological disease.
- the neurological diseases are selected from Alzheimer’s Disease, Down’s syndrome, Frontotemporal dementia, Dementia with Lewy Bodies, Parkinson’s Disease, and dementia.
- the level of expression of the various proteins is measured at least one of the nucleic acid, the protein level, or functionally at the protein level.
- the level of expression of the various proteins is measured by at least one of fluorescence detection, chemiluminescence detection, electrochemiluminescence detection and patterned arrays, reverse transcriptase-polymerase chain reaction, antibody binding, fluorescence activated sorting, detectable bead sorting, antibody arrays, microarrays, enzymatic arrays, receptor binding arrays, allele specific primer extension, target specific primer extension, solid-phase binding arrays, liquid phase binding arrays, fluorescent resonance transfer, or radioactive labeling.
- a profile for identifying Dementia with Lewy Bodies from other neurodegenerative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin, MIP1 and IL10.
- a profile for identifying Parkinson’s disease from other neurodegenerative diseases comprises ICAM1, VCAM1, Ab42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6.
- a profile for identifying Parkinson’s disease from negative controls comprises NFL, PPY, FABP3, and IL18, and may further comprise one or more biomarkers selected from IL7, TARC, TPO, a-syn, Eotaxin3 and IL5.
- the neurological disease is determined from the biomarkers found in Figures 7 - 11, which will often be used in order.
- the present invention also includes a method of determining one or more neurological disease profiles that best matches a patient profde, comprising: (a) comparing, on a suitably programmed computer, the level of expression of IL-7 and TNFa in a blood sample from a patient suspected of having one or more neurological diseases with reference profdes in a reference database to determine a measure of similarity between the patient profde and each the reference profdes; (b) identifying, on a suitably programmed computer, a reference profde in a reference database that best matches the patient profde based on a maximum similarity among the measures of similarity determined in step (a); and (c) outputting to a user interface device, a computer readable storage medium, or a local or remote computer system; or displaying, the maximum similarity or the disease of the disease cell sample of the reference profde in the reference database that best matches the patient profde.
- the method further comprises the step of determining the level of expression of one or more markers from a blood sample further selected from, in order, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and/or a- synuclein.
- the method uses 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 biomarkers to distinguish the neurological disease.
- the method is used to screen in the primary setting used a higher specificity than sensitivity, wherein the specificity is in the range of 0.97 to 1.0, and the sensitivity is in the range of 0.80 to 1.0.
- the first four biomarkers are used in the analysis, namely, IL7, TNFa, IL5, and IL6.
- a profde for identifying Dementia with Lewy Bodies from other neurodegenerative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin, MIP1 and IL10.
- a profde for identifying Parkinson’s disease from other neurodegenerative diseases comprises ICAM1, VCAM1, Ab42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6.
- the method further comprising the step of determining the level of expression of one or more markers from a blood sample selected from IL7, TNFa, IL5, IL6, CRP, IL10, TNC, ICAM1, FVII, 1309, TNFR1, A2M, TARC, eotaxin3, VCAM1, TPO, FABP, IL18, B2M, SAA, PPY, DJI, and/or a-synuclein.
- the method further comprises measuring 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 biomarkers to distinguish the neurological disease.
- the method further comprises screening a patient in a primary setting used a higher specificity than sensitivity, wherein the specificity is in the range of 0.97 to 1.0, and the sensitivity is in the range of 0.80 to 1.0.
- the method further comprises using four biomarkers for identifying Dementia with Lewy Bodies from other neurodegenerative diseases comprises sVCAMl, IL5, B2M, and IL6, and may further comprise one or more biomarkers selected from IL1, adiponexin, Eotaxin, MIP1 and IL10.
- the method further comprises using four biomarkers for identifying Parkinson's disease from other neurodegenerative diseases comprises ICAM1, VCAM1, AB42, and B2M, and may further comprise one or more biomarkers selected from Tenacin C, AB40, TNF-a, PPY, TARC, and IL6.
- the method further comprises using four biomarkers for identifying Alzheimer's disease selected from IL7, TNFa, IL5, and IL6.
- a profile for identifying Parkinson’s disease from negative controls comprises NFL, PPY, FABP3, and IL18, and may further comprise one or more biomarkers selected from IL7, TARC, TPO, a-syn, Eotaxin3 and IL5.
- the neurological disease is determined from the biomarkers found in Figures 7 - 11, which will often be used in order.
- Figure 1 shows data from the Neurodegenerative Panel 1 that assays THPO, FABP3, PPY, IL18, and 1309 on an MSD platform from two control participants in duplicate. As can be seen, the assays are highly reliable;
- Figure 2 is a box Plot of Random Forest Risk Scores for AD vs. normal controls (NC);
- Figure 3 is a receiver operation characteristic (ROC) plot of serum biomarker profile
- Figure 4 is a Gini Plot from Random Forest Biomarker Model
- Figure 5 is a receiver operation characteristic (ROC) plot of serum biomarker profile
- Figure 6 highlights the importance of the relative profiles in distinguishing between neurodegenerative diseases. The relative profiles across disease states varied.
- Figure 7 shows a ROC curve and variable importance plot for Step 1 - discriminating Lewy body disease from normal controls.
- Figure 8 shows a ROC curve and variable importance plot.
- Figure 9 shows a ROC Curve and Variable Importance Plot for Proteomic Profile for Detecting Neurodegenerative Disease.
- Figure 10 shows a ROC Curve and Variable Importance Plot for Proteomic Profile for Distinguishing PD from Other Neurodegenerative Diseases.
- Figure 11 shows a support vector machines (SVM) importance score for Proteomic Profile for Distinguishing PD from Other Neurodegenerative Diseases.
- SVM support vector machines
- the phrase“primary care clinic”,“primary care setting”,“primary care provider” are used interchangeably to refer to the principal point of contact/consultation for patients within a health care system and coordinates with specialists that the patient may need.
- the phrase“specialist” refers to a medical practice or practitioner that specializes in a particular disease, such as neurology, psychiatry or even more specifically movement disorders or memory disorders.
- IL7 - interleukin-7 TNFa -tumor necrosis factor alpha
- IL5 - interleukin-5 IL6- interleukin-6
- CRP- C-reactive protein IL10 - interleukin- 10
- TNC- Tenascin C ICAM1 -intracellular adhesion molecule 1, FVII - factor VII, 1309 - chemokine (C-C motif) ligand 1, TNFR1 - tumor necrosis factor receptor 1, A2M - alpha-2-microglobulin, TARC - Chemokine (C-C Motif) Ligand i7, eotaxin3, VCAMi - Vascular Cell Adhesion Molecule 1, TPO - Thrombopoietin, FABP3 - fatty acid binding protein 3, IL
- neurodegenerative disorders such as AD, Parkinson's disease, mild cognitive impairment (MCI) and dementia and neurological diseases include multiple sclerosis, neuropathies.
- MCI mild cognitive impairment
- the present invention will find particular use in detecting AD and for distinguishing the same, as an initial or complete screen, from other neurodegenerative disorders such as Parkinson’s Disease, Frontotemporal dementia, Dementia with Lewy Bodies, and Down’s syndrome.
- AD patient As used herein, the terms“Alzheimer's patient”,“AD patient”, and“individual diagnosed with AD” all refer to an individual who has been diagnosed with AD or has been given a probable diagnosis of Alzheimer's Disease (AD).
- AD Alzheimer's Disease
- DLB Delivery with Lewy bodies
- DLB Diseased with Lewy bodies
- DS Down’s syndrome
- DS “individual diagnosed with Down’s syndrome”
- DS “individual diagnosed with Down’s syndrome” all refer to an individual who has been diagnosed with DS or has been given a diagnosis of DS.
- neurological disease biomarker refers to a biomarker that is a neurological disease diagnosis biomarker.
- neurological disease biomarker protein refers to any of: a protein biomarkers or substances that are functionally at the level of a protein biomarker.
- methods for“aiding diagnosis” refer to methods that assist in making a clinical determination regarding the presence, or nature, of the neurological disease (e.g., AD, PD, DLB, FTD, DS or MCI), and may or may not be conclusive with respect to the definitive diagnosis.
- a method of aiding diagnosis of neurological disease can comprise measuring the amount of one or more neurological disease biomarkers in a blood sample from an individual.
- the term“stratifying” refers to sorting individuals into different classes or strata based on the features of a neurological disease. For example, stratifying a population of individuals with Alzheimer's disease involves assigning the individuals on the basis of the severity of the disease (e.g., mild, moderate, advanced, etc.).
- the term“predicting” refers to making a finding that an individual has a significantly enhanced probability of developing a certain neurological disease.
- biological fluid sample refers to a wide variety of fluid sample types obtained from an individual and can be used in a diagnostic or monitoring assay.
- Biological fluid sample include, e.g., blood, cerebral spinal fluid (CSF), urine and other liquid samples of biological origin. Commonly, the samples are treatment with stabilizing reagents, solubilization, or enrichment for certain components, such as proteins or polynucleotides, so long as they do not interfere with the analysis of the markers in the sample.
- a“blood sample” refers to a biological sample derived from blood, preferably peripheral (or circulating) blood.
- a blood sample may be, e.g., whole blood, serum or plasma.
- serum is preferred as the source for the biomarkers as the samples are readily available and often obtained for other sampling, is stable, and requires less processing, thus making it ideal for locations with little to refrigeration or electricity, is easily transportable, and is commonly handled by medical support staff.
- a “normal” individual or a sample from a“normal” individual refers to quantitative data, qualitative data, or both from an individual who has or would be assessed by a physician as not having a disease, e.g., a neurological disease. Often, a“normal” individual is also age- matched within a range of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 years with the sample of the individual to be assessed.
- treatment refers to the alleviation, amelioration, and/or stabilization of symptoms, as well as delay in progression of symptoms of a particular disorder.
- “treatment” of AD includes any one or more of: (1) elimination of one or more symptoms of AD, (2) reduction of one or more symptoms of AD, (3) stabilization of the symptoms of AD (e.g., failure to progress to more advanced stages of AD), and (4) delay in onset of one or more symptoms of AD delay in progression (i.e., worsening) of one or more symptoms of AD; and (5) delay in progression (i.e., worsening) of one or more symptoms of AD.
- fold difference refers to a numerical representation of the magnitude difference between a measured value and a reference value, e.g., an AD biomarker, a Parkinson’s biomarker, a dementia biomarker, or values that allow for the differentiation of one or more of the neurological diseases.
- a“reference value” can be an absolute value, a relative value, a value that has an upper and/or lower limit, a range of values; an average value, a median value, a mean value, or a value as compared to a particular control or baseline value.
- a reference value is based on an individual sample value, such as for example, a value obtained from a sample from the individual with e.g., a neurological disease such as AD, Parkinson’s Disease, or dementia, preferably at an earlier point in time, or a value obtained from a sample from an neurological disease patient other than the individual being tested, or a“normal” individual, that is an individual not diagnosed with AD, Parkinson’s Disease, or dementia.
- the reference value can be based on a large number of samples, such as from AD patients, Parkinson’s Disease patients, dementia patients, or normal individuals or based on a pool of samples including or excluding the sample to be tested.
- the phrase“a predetermined amount of time” is used to describe the length of time between measurements that would yield a statistically significant result, which in the case of disease progression for neurological disease can be 7 days, 2 weeks, one month, 3 months, 6 months, 9 months, 1 year, 1 year 3 months, 1 year 6 months, 1 year 9 months, 2 years, 2 years 3 months, 2 years 6 months, 2 years 9 months, 3, 4, 5, 6, 7, 8, 9 or even 10 years and combinations thereof.
- the phrases“neurocognitive screening tests”, or“cognitive test” are used to describe one or more tests known to the skilled artisan for measuring cognitive status or impairment and can include but is not limited to: a 4-point clock drawing test, an verbal fluency test, trail making test, list learning test, and the like. The skilled artisan will recognize and know how these tests can be modified, how new tests that measure similar cognitive function can be developed and implemented for use with the present invention.
- PET Ab imaging were made available at even $1,000 per exam (less than a third to one tenth of the actual cost) and only 1 million elders were screened annually within primary care settings (there are 40 million Americans age 65+), the cost would be $1 billion (U.S. dollars) annually for neurodegenerative screening. If a blood-based screener were made available at $100/person, the cost would be $100 million annually. If 15% tested positive and went on to PET Ab imaging ($150 million), the cost savings of this screen - follow-up procedure would be $750 million dollars annually screening less than one fortieth of those who actually need annual screening.
- a blood-based tool can easily fit the role as the first step in the multi-stage diagnostic process for neurodegenerative diseases with screen positives being referred to specialist for confirmatory diagnosis and treatment initiation. In fact, this is the process already utilized for the medical fields of cancer, cardiology, infectious disease and many others.
- Example 1 Screening patients for neurode generative diseases.
- Another substantial advancement comes from the current procedure. Specifically, the procedure can also be utilized for screening patients prior to entry into a clinical trial.
- a major impediment to therapeutic trials aimed at preventing, slowing progression, and/or treating AD is the lack of biomarkers available for detecting the disease 14, 15.
- the validation of a blood-based screening tool for AD could significantly reduce the costs of such trials by refining the study entry process. If imaging diagnostics (e.g., Ab neuroimaging) are required for study entry, only positive screens on the blood test would be referred for the second phase of screening (i.e., PET scan), which would drastically reduce the cost for identification and screening of patients.
- imaging diagnostics e.g., Ab neuroimaging
- the new methods for screening of the present invention facilitate recruitment, screening, and/or selection of patients from a broader range of populations and/or clinic settings, thereby offering underserved patient populations the opportunity to engage in clinical trials, which has been a major limitation to the majority of previously conducted trials 16.
- the present inventors provide for the first time, data that demonstrates the following: a novel procedure can detect and discriminate between neurodegenerative diseases with high accuracy.
- the current novel procedure which can be utilized for implementation as the first line screen within primary care settings that leads to specific referrals to specialist providers for disease confirmation and initiation of treatment.
- Non-AD Patients Down’s Samples. Serum samples were obtained from 11 male patients diagnosed with Down’s syndrome (DS) from the Alzheimer’s Disease Cooperative Studies core at the University of California San Diego (UCSD). Parkinson’s disease Samples. Serum samples from 49 patients (28 males and 21 females) diagnosed with Parkinson’s disease (PD) came from the University of Texas Soiled Medical Center (UTSW) Movement Disorders Clinic. Dementia with Lewy Bodies (DLB) and Frontotemporal dementia (FTD) Samples. Serum samples from 11 DLB and 19 FTD samples were obtained from the UTSW Alzheimer’s Disease Coordinating Center (ADCC).
- ADCC UTSW Alzheimer’s Disease Coordinating Center
- Serum sample collection TARCC and UTSW ADC serum samples were collected as follows: (1) non-fasting serum samples was collected in 10 ml tiger-top tubes, (2) allowed to clot for 30 minutes at room temperature in a vertical position, (3) centrifuged for 10 minutes at 1300 x g within one hour of collection, (4) 1.0 ml aliquots of serum were transferred into cryovial tubes, (5) FreezerworksTM barcode labels were firmly affixed to each aliquot, and (6) samples placed into -80° C freezer for storage until use in an assay. Down’s syndrome serum samples were centrifuged at 3000rpm for 10 minutes prior to aliquoting and storage in a -80° C freezer.
- Plasma (1) non-fasting blood was collected into 10 ml lavender-top tubes and gently invert 10- 12 times, (2) centrifuge tubes at 1300 x g for 10 minutes within one hour of collection, (3) transfer 1 ml aliquots to cryovial tubes, (4) affix FreezerworksTM barcode labels, and (5) placed in -80° C freezer for storage.
- ECL electrochemiluminescence
- MSD Meso Scale Discovery
- the markers assayed were from a previously generated and cross-validated AD algorithm (17,19,29) and included: fatty acid binding protein (FABP3), beta 2 microglobulin, pancreatic polypeptide (PPY), sTNFRl, CRP, VCAM1, thrombopoeitin (THPO), a2 macroglobulin (A2M), exotaxin 3, tumor necrosis factor a, tenascin C, IL-5, IL6, IL7, IL10, IL18, 1309, Factor VII, TARC, SAA, and ICAM1, a-synuclein.
- Figure 1 illustrates the reliability of the MSD assay of the present invention.
- the ROC (receiver operation characteristic) curves were analyzed using R package AUC (area under the curve) was calculated using R package DiagnosisMed (V 0.2.2.2).
- the sample was randomly divided into training and test samples separately for serum and plasma markers.
- the RF model was generated in the training set and then applied to the test sample.
- Logistic regression was used to combine demographic data (i.e. age, gender, education, and APOE4 presence [yes/no]) with the RF risk score as was done in the present inventors’ prior work (17,19,29,32).
- Clinical variables were added to create a more robust diagnostic algorithm given the prior work documenting a link between such variables and cognitive dysfunction in AD (33-36).
- the biomarker risk score was limited to the smallest set of markers that retained optimal diagnostic accuracy as a follow-up analysis.
- support vector machines (SVM) analysis was utilized for multi-classification of all diagnostic groups.
- NC normal controls
- SVM is based on the concept of decision planes that define decision boundaries and is primarily a method that performs classification tasks by constructing hyperplanes in a multidimensional space that separates cases of different class labels.
- An SVM-based method was used with five-fold cross-validation to develop the classifier for the combined samples, and then applied the classifier to predict the combined samples.
- Table 2 Statistical results for AD biomarker sensitivity and specificity and area under the receiver operating characteristic curve (AUC).
- Figure 3 shows a ROC plot for a serum biomarker profile using 21 serum biomarkers.
- the plasma-based algorithm yielded much lower accuracy estimates of SN, SP, and AUC of 0.65, 0.79, and 0.76, respectively. Therefore, the remaining analyses focused solely on serum. Inclusion of age, gender, education and APOE4 into the algorithm with the RF biomarker profile increased SN, SP, and AUC to 0.95, 0.90, and 0.98, respectively (Table 2). Next the RF was re-run to determine the optimized algorithm with the smallest number of serum biomarkers.
- Figure 4 shows a Gini Plot from Random Forest Biomarker Model demonstrating variable importance and differential expression.
- Figure 5 shows a ROC plot using only the top 8 biomarkers for the AD algorithm.
- Figure 6 highlights the importance of the relative profiles in distinguishing between neurodegenerative diseases.
- the relative profiles across disease states varied. For example, A2M and FVII are disproportionately elevated in DLB and FTD whereas TNFa is disproportionately elevated in AD and lowest in PD and DLB whereas PPY is lowest in PD and highest in DLB.
- PPV/NPV are dependent on base rates of disease presence 44 .
- AD it is estimated that the base rate of disease presence in the community is 11% of those age 65 and above 13 as compared to 50% or more in specialty clinic settings.
- PPV and NPV are based on Bayesian statistics and calculated as outlined here:
- PPV positive predictive value
- SN sensitivity
- BR base rate
- RC remaining cases
- NPV negative predictive value
- SP specificity.
- the screen and/or algorithm of the present invention is very accurate and can be used within a community-based setting, that is, at the primary point-of-care. This is in comparison to the minimal requirements to be acceptable based on the 1998 Consensus Report where PPV was less than 35% (see Table 4).
- the current approach (1) is highly accurate at detecting Alzheimer’s disease; (2) is highly accurate at detecting and discriminating between neurodegenerative diseases; (3) can be implemented within primary care settings as the first step in a multi-stage diagnostic process; and (4) the combination of specific serum biomarkers and select neurocognitive screening assessments can refine the screening process with excellent accuracy.
- Table 6 shows the selection of the specialist for referral, and hence the course of treatment, based on the results of the screen of the two or more biomarkers measured at the primary care center or point of care.
- the inventors sought to determine if a proteomic profde approach developed to detect Alzheimer’s disease would distinguish patients with Lewy body disease from normal controls, and if it would distinguish dementia with Lewy bodies (DLB) from Parkinson’s disease (PD).
- DLB dementia with Lewy bodies
- PD Parkinson’s disease
- the proteomic profde described herein distinguished the DLB-PD group from controls with a diagnostic accuracy of 0.97, sensitivity of 0.91 and specificity of 0.86.
- the proteomic profile distinguished the DLB from PD groups with a diagnostic accuracy of 0.92, sensitivity of 0.94 and specificity of 0.88.
- Lewy Body disease is the second most common neurodegenerative disease and clinically may present with dementia as Dementia with Lewy bodies (DLB), or without dementia as Parkinson’s disease (PD).
- DLB was first characterized as a dementia by Kosaka [1] and operationalized diagnostic criteria were initially put forth by McKeith [2] in 1992. Patients who meet consensus criteria for DLB commonly have Lewy -related pathology [3] at autopsy, and in a large dementia autopsy series [4], 25% were found to have Lewy -related pathology.
- the core clinical features of DLB include parkinsonism, fluctuating cognition, fully formed visual hallucinations and a history of probable REM behavior disorder.
- the inventors’ work on blood-based biomarkers of Alzheimer’s disease (AD) and PD has consistently shown that a multi-marker approach identifying biomarker profiles of disease presence can yield excellent results [26-28]
- the inventors’ blood-based biomarker profile provides a cost- and time-effective method for establishing a rapidly scalable multi-tiered neurodiagnostic process [29, 30] for detecting neurodegenerative disease, including DLB.
- the inventors generated and cross-validated the AD proteomic profile across platforms[26, 32], cohorts[26, 28, 29, 33, 34], species (human, mouse)[32], tissue (brain, serum, plasma)[32] and ethnicities (non-Hispanic white, Mexican American)[26, 35], which is currently being prospectively tested in primary care settings.
- This same approach was highly accurate in discriminating PD from AD.
- the proteomic profile approach to detecting AD [29, 32] is successful in (1) detecting neurodegenerative disease due to synucleinopathy (DLB and PD vs controls) and (2) discriminating amongst neurodegenerative disease due to synucleinopathy (i.e.
- DLB vs PD DLB vs PD
- the DLB patients also underwent, neuropsychological testing, had pathologic confirmation of diffuse or transitional Lewy body disease., and were specifically selected for this study if they had a documented response to cholinesterase inhibitors based the work described above showing that DLB cases who respond to these medications are less likely to have imaging-based AD comorbid pathology [18] Normal controls were recruited through the ADRC and were all cognitively normal based on neuropsychological testing. All PD-dementia (PDD) cases were not included in this study.
- Plasma samples were assayed via a multi-plex biomarker assay platform using electrochemiluminescence (ECL) lab using the QuickPlex from Meso Scale Discovery per the inventors’ previously published methods using commercially available kits [29, 32]
- ECL electrochemiluminescence
- the MSD platform has been used extensively to assay biomarkers associated with a range of human diseases including AD [38-41]
- ECL technology uses labels that emit light when electronically stimulated, which improves the sensitivity of detection of many analytes at very low concentrations.
- ECL measures have well established properties of being more sensitive and requiring less volume than conventional ELISAs [40], the gold standard for most assays.
- the inventors recently reported the analytic performance of each of these markers for >1,300 samples across multiple cohorts and diagnoses (normal cognition, MCI, AD) [29]
- the assays are reliable and, in the inventors’ experience with these assays, again show excellent spiked recovery, dilution linearity, coefficients of variation, as well as detection limits. Inter- and intra-assay variability has been excellent.
- Internal QC protocols are implemented in addition to manufacturing protocols including assaying consistent controls across batches and assay of pooled standards across lots. To further improve assay performance, assay preparation was automated using a customized Hamilton Robotics StarPlus system.
- Statistical Analysis were conducted using the R (V 3.3.3) statistical software [42], SPSS 24 (IBM) and SAS.
- Support vector machine (SVM) analyses were conducted to create proteomic profiles specifically for control versus Lewy Body Disease and then DLB vs PD.
- SVM is based on the concept of decision planes that define decision boundaries and is primarily a classifier method that performs classification tasks by constructing hyperplanes in a multidimensional space that separates cases of different class labels. Diagnostic accuracy was calculated via receiver operating characteristic (ROC) curves.
- ROC receiver operating characteristic
- Step 2 SVM analysis was restricted only to those with Lewy Body Disease to discriminate DLB from PD (Step 2) with resulting diagnostic accuracy statistics generated.
- This two-step process was utilized to allow for the overall algorithm to be more robust and avoid multi-level analyses simultaneously, which reduces risk for error and sample over-identification. Additionally, as described hereinabove, the inventors have demonstrated that the overall profile differs amongst neurode generative diseases and, therefore, the multi-step process capitalizes on these overall proteomic profile fluctuations.
- AD cases were analyzed to provide preliminary analyses on a three-step approach to (1) detect neurode generative disease (Alzheimer’s disease [AD]/DLB/PD) from controls, (2) discriminate dementia (AD/DLB) from PD and (3) discriminate AD from DLB. These AD cases were also evaluated and clinically diagnosed by the Mayo ADRC. Demographic characteristics of the AD cases are provided in Table 7.
- Step 1 the SVM-based proteomic profile was highly accurate in detecting Lewy Body disease (DLB and PD) as compared to normal controls.
- the overall AUC of the proteomic profile was 0.94 with a sensitivity (SN) of 0.99 and specificity (SP) of 0.64.
- SN sensitivity
- SP specificity
- inclusion of demographic variables increased the overall accuracy somewhat with an overall AUC was 0.97 with an decreased SN to 0.91 but increased SP to 0.86.
- Table 8 shows all of the correct and incorrect predictions while the variable importance plot and ROC curve are presented in Figure 7.
- Table 8 Diagnostic accuracy of blood test in Step 1 - discriminating control from Lewy body disease
- Step 2 the overall SVM-proteomic profile also showed good accuracy at distinguishing DLB from PD.
- Table 9 shows the all classifications (correct and incorrect) while the variable importance plot and ROC curve are presented in Figure 8.
- the inventors conducted preliminary analyses on a three-step algorithmic approach. Here the full algorithm was applied (proteins + demographic variables).
- Table 9 shows the diagnostic accuracy of blood test in Step 2 - Discriminating between Dementia with Lewy bodies and Parkinson’s disease.
- AUC 0.9204 [0102]
- DLB synucleinopathy
- AUC 0.92
- Recent work demonstrates that a CSF-based a- synuclein seeding technology can also achieve strong diagnostic accuracy in detecting neurodegenerative disease due to synucleinopathy (93% sensitivity and 100% specificity). While that work requires cross- validation in larger studies, the advancement of the current work in tandem is promising for a sensitive and specific time- and cost-effective multi-step approach for broad-based screening of DLB for prospective studies, clinical trials and routine clinical practice.
- the top 10 markers for discriminating DLB/PD from controls were as follows: age, sVCAMl, IL5, B2M, IL6, IL1, Adipo, Eotaxin, MIP1 and IL10.
- the top 4 biomarkers are sVCAMl, IL5, B2M, IL6, followed by, in order, IL1, Adipo, Eotaxin, MIP1 and IL10.
- the top variable was age in both models.
- the top 2 proteins in this profile were the bottom 2 in the profile for discriminating DLB from PD.
- B2M, IL6, adiponectin, and eotaxin overlapped in the top 10 markers in the algorithm (5 out of top 10).
- the profile was a mix of inflammatory, metabolic and vascular dysfunction, but at different levels between the categories.
- the inventors have found that the AD profile is heavily inflammatory in nature as compared to PD and controls. In fact, the AD in adults with Down syndrome is also heavily inflammatory in nature. Therefore, while there are certainly disease-overlapping pathological processes depicted in this work, the profiles are different amongst categories.
- Prior work has demonstrated that there is a range of biological dysfunction across numerous neurodegenerative diseases. When tau and Ab are present in DLB, they tend to occur at far less densities than what is typically seen in AD.
- the inventors have created and validated a proteomic signature for detecting AD across cohorts, species (humans, mice) and tissue (serum, plasma, brain) [26, 28, 29, 32]
- the inventors have proposed a multi-tiered neurodiagnostic process for detecting neurodegenerative disease beginning in primary care clinics using blood-based biomarkers [29, 30] which is now being prospectively studied in primary care settings (i.e. Alzheimer’s Disease in Primary Care [ADPC] study).
- the inventors have also demonstrated that the inventors’ multi-protein algorithmic approach can discriminate AD from PD [32] as well as controls from“neurodegenerative disease” (i.e.
- AD AD, PD, DLB, Down Syndrome
- the synucleinopathy profile and DLB vs PD profile is different from the AD profile.
- Additional preliminary analyses were provided here to support the notion that the multi-marker, multi-step profile can also discriminate DLB and PD from AD. Given the sample size, these results are preliminary, but strongly supportive of further work. Therefore, the current work takes a significant step forward in the area of blood-biomarkers for detecting neurodegenerative diseases as it sets the stage for a large-scale, multi-level proteomic-bioinformatic model that takes into account disease-specific profiles across numerous neurodegenerative diseases. The current team is currently assaying large numbers of samples across disease states in order to test this model.
- the inventors sought to further validate the proteomic profile approach for detecting Alzheimer’s disease would detect Parkinson’s disease (PD) and distinguish PD from other neurodegenerative diseases describe hereinabove.
- PD Parkinson’s disease
- the first step proteomic profile distinguished neurodegenerative diseases from controls with a diagnostic accuracy of 0.94.
- the second step profile distinguished PD cases from other neurode generative diseases with a diagnostic accuracy of 0.98.
- the proteomic profde differed in step 1 versus step 2 suggesting that a multi-step proteomic profde algorithm to detecting and distinguishing between neurode generative diseases may be optimal.
- This example demonstrates the utility of a multi-tiered blood-based proteomic screening method for detecting individuals with neurode generative disease and then distinguishing P D from other neurodegenerative diseases.
- Parkinson’s disease is the second most common neurodegenerative disease affecting over 1% of people age 65 and over in the United States[l].
- the cost of PD to society was reported to be $23 billion annually in the U.S. in 2005 [2] Considering the estimated 15% growth in the elderly U.S. population during the last decade, these costs can be expected to increase dramatically as the population ages.
- Neuropathologically, PD is a progressive disorder of unknown cause affecting multiple neurotransmitter systems. Common non-motor features of the disease include autonomic failure, urinary incontinence, hallucinations, and dementia[3].
- DMTs disease modifying therapies
- a major impediment to treatment developments and clinical trials for neurodegenerative diseases is the lack of a sensitive, easily -obtained biomarker of disease presence [4-8]
- The“cornerstone” to the development of novel DMTs in PD is the identification and validation of biomarkers of disease presence and progression[9] .
- CSF neuroimaging and cerebrospinal
- AD Alzheimer’s disease
- DaT-SPECT dopamine transporter single photon emission CT
- Blood-based biomarkers have potential to serve as the initial step in the neurodiagnostic process used in large-scale screening, in primary care settings[19], as well as screening into novel clinical trials, the latter of which will result in substantial cost savings to the overall trial itself.
- the goal of the first-step is to screen out those patients who should not undergo more expensive and invasive confirmatory diagnostic procedures [19] This is the same model utilized by cancer biomarkers that have received both regulatory and reimbursement approval[24].
- the present inventors work on blood-based biomarkers of Alzheimer’s disease (AD) has consistently shown that a multi-marker approach identifying biomarker profiles of disease presence can yield excellent results [28-30]
- This blood-based biomarker profile approach provides a cost- and time-effective method for establishing a rapidly scalable multi-tiered neurodiagnostic process [19, 31] for detecting neurode generative disease, including PD.
- appropriate referrals can be made for subsequent specialty exanimations and confirmatory diagnostic biomarkers (imaging, CSF), following the multi stage models used for diagnosing cancer [24] .
- HBS Harvard Biomarker Study
- HBS is a longitudinal, case-control study that tracks clinical phenotypes and linked biospecimens of individuals with neurodegenerative diseases and controls without neurologic disease. High-quality biosamples and high-resolution clinical phenotypes are longitudinally tracked over time.
- HBS was designed for the primary goal of developing biomarkers that track disease progression and allow go/no go decisions in phase II clinical trials.
- the HBS specifically fosters research across neurodegenerative diseases, such as the proof-of-concept study described here.
- HBS has been published extensively[15, 33-40]
- Plasma samples were assayed using two technological platforms.
- the proteomic assays were conducted using two automated systems.
- the electrochemiluminescence (ECL) assays from the work hereinabove is a previously validated AD blood screen that captured via the multi-plex platform, QuickPlex from Meso Scale Discovery with assay preparation performed via automation using the Hamilton Robotics StarPlus system. The inventors reviewed this analytic performance for each of these markers for >1,300 samples across multiple cohorts and diagnoses (normal cognition, MCI, AD).
- the inventors also examined the impact of demographic factors (age, gender, education) on the proteomic profile to ensure that the inventors’ proteomic profde performs better than demographics alone and to determine if simple demographic characteristics that are easily obtained can somehow add to the algorithm.
- the inventors’ utilized the same approach described above, beginning with the discovery phase. Specifically, the inventors sought to expand on the work described above to determine if the same protein analytes used in the inventors’ AD Blood Test algorithm can achieve the same sensitivity and specificity for detecting PD.
- Statistical Analysis were conducted using R (V 3.3.3) statistical software [44] and SPSS 24 (IBM). Diagnostic accuracy was calculated via receiver operating characteristic (ROC) curves.
- SVM analyses were utilized to discriminate controls from neurodegenerative disease (i.e. PD/Other) with resulting diagnostic accuracy statistics generated (Step 1).
- SVM analysis was restricted only to PD versus Other neurodegenerative disease (Step 2).
- SVM analyses were conducted with internal 5-fold cross-validation.
- the two-step approach was used to capitalize on these differences to increase accuracy and also to allow for the overall algorithm to be more robust and avoid multi-level analyses simultaneously. The latter reduces risk for error and sample over identification.
- Step 1 the SVM-based proteomic profile was highly accurate in detecting neurodegenerative disease (PD and Other) as compared to normal controls.
- the overall AUC was 0.94 with an observed sensitivity (SN) of 0.92 and specificity (SP) of 0.65.
- Table 11 shows all of the correct and incorrect predictions while the variable importance plot and ROC curve are presented in Figure 1. Inclusion of demographic factors did not significantly change the AUC.
- the overall SVM-proteomic profile also showed excellent accuracy at distinguishing PD from other neurodegenerative diseases.
- Table 3 shows all classifications (correct and incorrect) while the variable importance plot and ROC curve are presented in Figure 10. Inclusion of demographic factors did not significantly change the AUC.
- Table 12 Classification Accuracy for Proteomic Profile for Distinguishing PD from Other
- the overall profiles for discriminating PD/Other neurodegenerative diseases from controls was different than the profde for discriminating PD from Other neurodegenerative diseases as was the case described above.
- the top 10 markers for discriminating neurodegenerative diseases from controls were as follows: NFL, PPY, FABP3, IL18, IL7, TARC, TPO, a-syn, Eotaxin3 and IL5.
- the top 10 variables for discriminating PD from Other neurodegenerative diseases were ICAM1, VCAM1, Ab42, B2M, Tenacin C, Ab40, TNF-a, PPY, TARC, and IL6.
- Figure 11 shows a support vector machines (SVM) importance score for proteomic profde for distinguishing pd from other neurodegenerative diseases. While age and gender are included in the graph, these are not part of the biomarkers for use with the present invention. The most important markers in these results are: SAA, IL6, IL10, and sICAMl . These are primary four biomarkers in this analysis. One or more additional biomarkers can also be used in the evaluation, in order: 1309, IL5, sVCAMl, TARC, TNFa, PPY, Eotaxin 3, IL7, A2M, CRP, B2M, IL18, TPO, FABP3, Factor VII, and Tenacin C. The same analysis applies for each of the figures.
- SVM support vector machines
- the first four biomarkers can be used to obtain an initial determination. Further refinement of that determination can be provided by adding each of the one or more additional biomarkers from the graphs, with the order provided in the graph from top to bottom having a preference and/or greater impact on the determination.
- the combined algorithm with the inventors’ ECL and Simoa assays resulted in an increases SP to 0.94.
- the current study further demonstrates that the proteomic profile approach of the present invention can be applied to detecting PD and distinguishing PD from other neurodegenerative diseases.
- the current AUC was 0.94 with an observed SN of 0.92 and SP of 0.65.
- the present invention provides clinicians and companies with a rapidly scalable tool (or tools) that can streamline and increase access (while cost containing) to novel clinical trials to improve patient outcomes.
- the present invention allows for the rapid identification of neurodegenerative disease profiles from as few as 4 biomarkers, with increasing sensitivity by the addition of one or more of the following biomarkers. While the skilled artisan will understand from the figures that each additional biomarkers will add more specificity and/or sensitivity to the analysis. In some cases the next biomarker does not necessarily have to be used in order, but rather, can includes any of the additional biomarkers (after the first four) selected from the list in any combination and amount.
- biomarker may go up or down, which is relative to the expression in a normal cell, or may be relative to the expression in another neurodegenerative disease, as the case may be.
- a relative biomarker expression analysis based on the teachings in the present specification, will be known to the skilled artisan without undue experimentation.
- a special technical effect of the present invention is the identification and use of novel biomarkers obtained from, for example, a retrospective analysis of patients for which biological samples were obtained prior to having a neurological disease, followed by a correlation following the initiation of disease, from which novel biomarkers have been identified having a higher specificity and/or sensitivity that previously obtained.
- This analysis can be done in a primary care setting, which is the first contact with a medical professional that may or may not be an expert in the neurological arts, but from which the patient can be directed to an expert based on the initial neurological diseases is identified.
- Another special technical effect of the present invention is, thus, being able to initiate the correct treatment (or avoid a treatment that is contraindicated for that specific neurological disease), at the earliest possible time.
- Yet another special technical effects is being able to have a robust initial identification of a possible disease without the need for expensive (CAT, MRI or other no-invasive scans), invasive procedures such as obtaining a neurological biopsy, or both, and to do so in a primary care setting.
- the words“comprising” (and any form of comprising, such as“comprise” and“comprises”),“having” (and any form of having, such as“have” and“has”), “including” (and any form of including, such as“includes” and“include”) or“containing” (and any form of containing, such as “contains” and“contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps.
- words of approximation such as, without limitation,“about”,“substantial” or “substantially” refer to a condition that when so modified is understood to not necessarily be absolute or perfect but would be considered close enough to those of ordinary skill in the art to warrant designating the condition as being present.
- the extent to which the description may vary will depend on how great a change can be instituted and still have one of ordinary skilled in the art recognize the modified feature as still having the required characteristics and capabilities of the unmodified feature.
- a numerical value herein that is modified by a word of approximation such as “about” may vary from the stated value by at least ⁇ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or 15%.
- compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.
- Alzheimer's Association 2013 Alzheimer's Disease Facts and Figures. Alzheimer's & Dementia. 2013;9(2): l-72.
- Kantarci K., et al., Multimodality imaging characteristics of dementia with Lewy bodies. Neurobiology of aging, 2012. 33(9): p. 2091-105.
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