Patent Application
20160097780
Alzheimer's disease (AD) is a chronic neurodegenerative disease currently identified by progressive cognitive impairment and loss of memory leading to severe dementia. AD is typically a disease of the elderly, most prevalent in persons over the age of 65. It is the leading cause of dementia in the elderly and with an increasingly higher life expectancy, the prevalence in the population is only set to increase. AD is not typically life threatening, however as the disease progresses to severe dementia, patients are unable to care for themselves and usually require full time professional care.
There is currently no known cure for AD, but there are treatments that can slow the progression of the disease. Therefore a method that can identify patients with AD and potentially monitor their response to treatment would be an invaluable assay (tool for clinicians).
Current methods of diagnosis of AD involve mental assessment (such as MMSE), CT/MRI, measurement of cerebrospinal fluid for specific Tau or Beta-amyloid isoforms known in the art to be associated with AD or genotyping for genetic risk factors such as Apolipoprotein E4 (ApoE4 variant); there are currently no clinically validated blood biomarkers of AD. Deficiencies of these methods can include a lack of specificity, they can be open to errors in interpretation, and may be highly invasive; generally a true diagnosis can only be made post mortem. There are currently no routinely used biomarker methods to assist the positive diagnosis for AD.
The pathogenesis of AD is not fully understood, but pathological investigations of patients revealed the presence of neurofibrillary tangles (caused by accumulation of Tau protein) and Beta-amyloid plaques. There is also widespread neuronal and synaptic loss, which is thought to underlie the reduced cognitive and mnemonic function. The formation of plaques has been shown to cause neurodegeneration, however the causes of plaque formation are unknown. Diagnostic tests that identify specific isoforms of these proteins have been the main focus in diagnostic assay development. However, the presence of these proteins may indicate that the disease has progressed past a therapeutically viable stage and therefore earlier risk markers may be more beneficial.
There have been several inventions describing methods for diagnosing AD using blood biomarkers, these include; EP 2293075 A2 and WO 2011/143597 Al. EP2293075 identified several markers expressed in blood platelets using 2-D gel electrophoresis, which were differentially expressed between AD and control patients. These included variants of proteins which may correspond to a genetic susceptibility to AD. A further invention was described by these inventors (EP2507638) in which protein biomarkers were combined in an algorithm along with genotyping to improve the diagnostic model. In this algorithm patients whom were ApoE4 positive were more likely to have AD, as were patients whom were ApoE4 negative, but expressed two copies of the wild-type glutathione S-transferase 1 Omega (wtGSTO) gene. In the context of this previous invention, wtGSTO was defined as any GSTO gene which did not contain the rs4825 mutation (which encodes an Aspartic acid instead of an Alanine at residue 140 [A140D]). This invention highlights the effectiveness of combining blood-based biomarkers and genotyping to assist in the diagnosis of disease. WO 2011/143597 A1 identified multiple biomarkers that are differentially expressed between serum of AD and control patients using multiplexed assays. In this invention, greater accuracy of diagnosis is observed when using multiple combinations of biomarkers combined with clinical measurements and demographic variables using Random forests to develop a classification algorithm. However, these methods have not found clinical utility and there is an urgent need for a method that can be used routinely to aid the diagnosis of AD.
The present invention relates to methods and compositions for the diagnosis of Alzheimer's disease.
The present invention identifies and describes proteins that are differentially expressed in the Alzheimer's disease state relative to their expression in the normal state.
According to the first aspect of the invention, there is provided a method of diagnosing
Alzheimer's disease in a subject, comprising detecting two or more differentially expressed proteins chosen from Table 1 in a sample taken from the subject, whereby one of these is Afamin. More specifically, a method comprising detecting levels of Afamin and any of Alpha-1 antichymotrypsin, Alpha-2-macroglobulin, Apolipoprotein B100, complement C3, Serine threonine kinase TBK-1, vitamin D binding protein, alpha-1-B glycoprotein, hemopexin, serum albumin, ceruloplasmin, alpha-2-antiplasmin, apolipoprotein A1, complement factor H, IgG, IgG fc binding protein, hornerin, fibrinogen or complement C5 in a sample taken from a subject. Preferably the sample is serum or plasma.
According to a further aspect of the invention, the relative levels of the differentially expressed proteins are used in conjunction with the ApoE or GSTO1 genotype or phenotype of a subject to increase the ability to differentiate between patients at risk of developing or having AD and those who are not at risk or do not have AD.
According to a further aspect of the invention, a method of detecting differentially expressed proteins chosen from Table 1 in a sample taken from a subject is provided wherein a specific probe for the protein is attached to the surface of a device. The respective levels of these proteins in a sample are calculated based on their ability to compete with biotinylated tracer substance. The tracer substance is modified plasma, where proteins contained have been conjugated to biotin.
According to a further aspect of the invention, a method for predicting the likelihood that a subject can be defined as suffering from or at risk of developing Alzheimer's disease, through developing a categorical prediction model using statistical modelling or machine learning methods. Such methods may include, but are not limited to; perceptron neural networks, support vector machines, logistic regression, decision trees and random forests.
The present invention describes a biomarker-based method to aid in the diagnosis of Alzheimer's disease (AD). Specifically the measurement of relative levels or concentration of biomarkers within a fluid sample taken from a patient suspected of having or at risk of developing Alzheimer's disease are measured. In the context of the current invention, the utility for diagnosing AD has been used as way of an example. However, it is envisaged that the invention may also be used for monitoring the progression of AD and diagnosing and monitoring other forms of dementia and cognitive disorders, these include but are not limited to; Parkinson's dementia, Lewy body dementia, Vascular dementia, mild cognitive impairment, frontotemporal dementia. The term ‘biomarker’, in the context of the current invention, refers to a molecule present in a biological sample of a patient, the levels of which in said biological fluid may be indicative of Alzheimer's disease. Such molecules may include peptides/proteins or nucleic acids and derivatives thereof; the term ‘relative levels’, in the context of the current invention refers to the light intensity or absorbance reading (However the invention is not restricted to measurement using these techniques, the skilled person will be aware of other methods for measuring biological molecules that do not utilise measuring the properties of visible light to determine a measurement) from a biological assay that results from comparing the levels of the biomarker in a given biological sample to a reference material with a known concentration (this concentration may be zero) of the biomarker or level by which the biomarker within a biological sample directly competes with a reference material known to contain said biomarker to bind to a specific probe for said biomarker, the latter method generates a level inversely related to the concentration of the biomarker; the term ‘probe’ in the context of the current invention, refers to a synthetic or biological molecule that specifically binds to a region of a biomarker; the term ‘at risk of developing Alzheimer's disease’, in the context of the current invention, refers to a patient that displays early clinical signs; such as mild cognitive impairment (MCI) or vascular dementia determined by methods known in the art (such as MMSE), has family history of Alzheimer's disease, has genetic prevalence for Alzheimer's disease or is classified ‘at risk’ due to lifestyle (e.g. age, diet, general health, occupation, geographical location); the term ‘genetic prevalence’ in the context of the current invention, can imply that the patients genome contains specific genotypes for certain proteins which are known in the art to be altered in patients who develop AD, such proteins include, but are not limited to, Apolipoprotein E (ApoE) and Glutathione S-Transferase Omega 1 (GSTO), this may be determined through genotyping or identifying the disease relevant form of the expressed protein in a biological fluid from the patient. More specifically, the number of alleles encoding ApoE4 and wild-type GSTO (wtGSTO) variants shall be determined. The term wtGSTO, in the context of the current invention, refers to any variant of GSTO that does not contain the rs4825 mutation in the genomic sequence, or an alanine to aspartic acid substitution at residue 140 of the protein sequence. The invention describes various biomarkers for use in diagnosing AD either alone or in combination with other diagnostic methods or as complementary biomarkers. A complementary biomarker in the current context implies a biomarker that can be used in conjunction with other biomarkers for AD.
A first aspect of the invention describes a method for diagnosing AD in a patient suspected of having, at risk of developing or of having AD which comprises taking an in vitro sample from the patient, determining the relative level or concentration of Afamin and one or more biomarkers chosen from Table 1 and establishing the significance of the relative level(s) or concentration(s) of Afamin and one or more biomarkers. The significance of the relative level or concentration is gauged by comparing said relative level or concentration to a control value for the specific biomarker. The control value is derived from determining the relative level or concentration of said biomarker in a biological sample taken from an individual(s) who does not have AD, as determined by clinical assessment. For Afamin, the relative level or concentration in a patient with AD is reduced compared with a control value. A preferred embodiment of the invention utilises a method employing a combination of Afamin and at least one other biomarker chosen from Alpha-1 antichymotrypsin, Alpha-2-macroglobulin, Apolipoprotein B100, complement C3, Serine threonine kinase TANK Binding Kinase-1 (TBK1), vitamin D binding protein, alpha-1-B glycoprotein, hemopexin, serum albumin, ceruloplasmin, alpha-2-antiplasmin, apolipoprotein A1, complement factor H, IgG, IgG fc binding protein, hornerin, fibrinogen or complement C5. A further preferred embodiment the invention uses a method whereby the relative level or concentration of Afamin is divided by the relative level or concentration of Alpha-1 antichymotrypsin to produce a ratio of Afamin/Alpha-1 antichymotrypsin. The term ‘ratio’ in the context of the current embodiment of the invention, relates to dividing the value of one biomarker by the other, this value should be the same for both biomarkers and can be represented as a weight or moles of biomarker in a given volume (concentration) or by a light intensity or absorbance level generated by means of an assay (relative level). A further embodiment of the invention utilises the value of the ratio of Afamin/Alpha-1 antichymotrypsin in combination with relative levels or concentration of one or more biomarkers chosen from Alpha-1 antichymotrypsin, Alpha-2-macroglobulin, Apolipoprotein B100, complement C3, Serine threonine kinase TBK-1, vitamin D binding protein, alpha-1-B glycoprotein, hemopexin, serum albumin, ceruloplasmin, alpha-2-antiplasmin, apolipoprotein A1, complement factor H, IgG, IgG fc binding protein, hornerin, fibrinogen or complement C5. For example, a preferred combination of the current invention is the ratio of Afamin/Alpha-1 antichymotrypsin in combination with the relative level or concentration of Complement C3. Another preferred combination of the invention is the ratio of Afamin/Alpha-1 antichymotrypsin in combination with the relative level or concentration of serine threonine kinase TBK-1.
A further aspect of the invention is directed to the use of one or more of Afamin, Alpha-1 antichymotrypsin, Alpha-2-macroglobulin, Apolipoprotein B100, complement C3, Serine threonine kinase TBK-1, vitamin D binding protein, alpha-1-B glycoprotein, hemopexin, serum albumin, ceruloplasmin, alpha-2-antiplasmin, apolipoprotein A1, complement factor H, IgG, IgG fc binding protein, hornerin, fibrinogen or complement C5 as complementary biomarkers of AD. As complementary biomarkers they may be used for AD diagnosis in conjunction with other clinical evidence such as mental state assessment (MMSE), neurological imaging, Beta-amyloid peptides, phosphorylated Tau, ApoE genotype, and wild-type GSTO 1 genotype (wtGSTO). In the context of the current invention, this clinical evidence may be added to the predictive model, based on the output measurement. For example, ApoE status of a patient may be determined through genotyping, by identifying the disease relevant form of protein that is expressed at the genetic level (DNA and/or RNA), or by detecting the presence of the specific expressed form of the protein from a fluid sample taken from the patient. In the context of the current invention, this output is expressed as either a dichotomised value, whereby the patient is either positive for the ApoE4 gene or protein or not; or as an ordinal output for the number of ApoE4 alleles present in the patients genomic DNA (0-2), which can be calculated using relative levels of the gene or protein within a sample taken from the patient.
Biomarker relative levels or concentrations can be determined by contacting the sample with probes, preferably immobilised on a substrate, specific for each of the biomarkers included in the combination of biomarkers. Interactions between biomarker and its respective probe can be monitored and quantified using various techniques that are well-known in the art. An example of a suitable technique is an enzyme-linked immunosorbent assay (ELISA). Performing an ELISA involves at least one antibody with specificity for a particular antigen. The sample with an unknown amount of antigen is immobilized on a solid support (usually a polystyrene microtiter plate) either non-specifically (via adsorption to the surface) or specifically (via capture by another antibody specific to the same antigen, in a “sandwich” ELISA). After the antigen is immobilized, the detection antibody is added, forming a complex with the antigen. The detection antibody can be covalently linked to an enzyme, or can itself be detected by a secondary antibody that is linked to an enzyme through bioconjugation. Between each step, the plate is typically washed to remove any proteins or antibodies that are not specifically bound. After the final wash step, the plate is developed by adding an enzymatic substrate to produce a visible signal, which indicates the quantity of antigen in the sample.
In a preferred embodiment of the current invention the ‘sample’ as referred to herein is serum or plasma, however it may be any sample from a patient from which biomarker levels or concentrations can be determined. These include but are not limited to whole blood, urine, saliva, cerebrospinal fluid and platelets.
The substrate comprises at least two, preferably three or four probes, each probe specific to an individual biomarker. As used herein, the term ‘specific’ means that the probe binds only to one of the biomarkers of the invention, with negligible binding to other biomarkers of the invention or to other analytes in the biological sample being analysed. This ensures that the integrity of the diagnostic assay and its result using the biomarkers of the invention is not compromised by additional binding events.
The substrate can be any surface able to support one or more probes, but is preferably a biochip. A “Biochip” is a general term for a reaction platform for hosting chemical, biochemical, proteomic or molecular tests, as may be required for medical diagnosis, drug detection, etc. Typically, a Biochip comprises an inert substrate, such as silicon, glass or ceramic (often of the order of about 1 cm2 or less in surface area), on which one or a plurality of reaction sites is provided. The sites generally carry one or more ligands, for example, one or more antibodies, selected for the test (or “assay”) to be performed, adsorbed to the surface of the chip for activation upon combination with a sample applied to the chip (e.g. a blood sample) and/or a reagent. The reactions can be detected using a number of alternative techniques, including detection of chemiluminescence generated by the reaction. Some biochips carry a very large number (hundreds or thousands) of such tests sites, typically arranged in a grid or array, making it possible to carry out numerous assays simultaneously, and using the same single specimen. When identifying the various biomarkers/proteins of the invention it will be apparent to the skilled person that as well as identifying the full length protein, the identification of a fragment or several fragments of a protein is possible, provided this allows accurate identification of the protein. Similarly, although a preferred probe of the invention is a polyclonal or monoclonal antibody, other probes such as aptamers, molecular imprinted polymers, phages, short chain antibody fragments and other antibody-based probes may be used. The invention also allows for nucleic acid sequence probes.
Preferably, a solid state device is used in the methods of the present invention, preferably the Biochip Array Technology system (BAT) (available from Randox Laboratories Limited). More preferably, the Evidence Evolution and Evidence Investigator apparatus (available from Randox Laboratories) may be used to determine the levels of biomarkers in the sample.
The accuracy of statistical methods used in accordance with the present invention can be best described by their receiver operating characteristics (ROC). The ROC curve addresses both the sensitivity, the number of true positives, and the specificity, the number of true negatives, of the test. Therefore, sensitivity and specificity values for a given combination of biomarkers are an indication of the accuracy of the assay. For example, if a biomarker combination has sensitivity and specificity value of 80%, out of 100 patients, 80 will be correctly identified from the determination of the presence of the particular combination of biomarkers as positive for disease, while out of 100 patients who do not have disease 80 will accurately test negative for the disease.
If two or more biomarkers are to be used in the diagnostic method a suitable mathematical or machine learning classification model, such as logistic regression equation, can be derived. The logistic regression equation might include other variables such as age and gender of the patient. The ROC curve can be used to assess the accuracy of the logistic regression model. The logistic regression equation can be used independently or in an algorithm to aid clinical decision making. Although a logistic regression equation is a common mathematical/statistical procedure used in such cases and is preferred in the context of the present invention, other mathematical/statistical, decision trees or machine learning procedures can also be used.
By way of example, a logistic regression equation applicable to the present invention (at a classification cut-off value of 0.5) for the biomarker combination for indication of AD versus non-AD (control) in a patient suspected of having or being at risk of developing AD is calculated as follows;
As further example, a decision tree may be grown where a decision branch is grown from each node (sub-population) to divide the population into classification groups.
Plasma normalisation was conducted as per US 2009/0136966. Briefly human plasma was normalised by removing high abundance proteins utilising the propriety method. Firstly, high abundance proteins were removed using Multiple Affinity Removal System (MARS) technology. The resultant plasma was then loaded on to a Multi-ImmunoAffinity Normalisation (MIAN) column, where normalisation stringency was adjusted by altering the flow rate. The flow-throw and wash samples were combined to give a differentially normalised sample. Some of this normalised plasma was then ubiquitously biotinylated to provide a tracer substance, known as Quantiplasma™.
Monoclonal antibodies were produced as per US 2009/0136966. Normalised plasma was used as an immunogen to generate polyclonal antibodies. B-cells were then isolated and monoclonal hybridomas were generated. Initial selection of hybridomas was done using an ELISA. Plates were coated with mouse Ig gamma-Fc specific GAM, and then incubated with the mAb hybridoma supernatant, following a wash step this complex was then incubated with the Quantiplasma™ and finally an enzyme-substrate reaction was induced to detect the binding of the biotinylated plasma (Quantiplasma™) to the mAb. This selection identified more than 1000 mAb. To identify the protein targets of monoclonal antibodies used in this study, western blotting, immunoprecipitation and mass spectrometry techniques were employed. There are, however, some antigens that could not be identified at this time, but as they are known to be present in the human plasma proteome they have been included.
Serum samples were obtained from 19 clinically confirmed Alzheimer's disease (AD) patients and 19 age/gender-matched control participants with normal cognitive function. These samples were frozen shortly after collection and stored at (−80° C.) until analysis was performed. Additional clinical information was gathered for these subjects, this included basic personal and family medical history. Further to this, ApoE and GSTO genotype were determined through methods known in the art. For each patient, genomic DNA was isolated and the presence of DNA that encodes each of the 3 isoforms of ApoE (E2, E3, E4) or GSTO (wild-type, mutant A140 [rs4825]) were determined utilising polymerase chain reaction (PCR) techniques. Further analysis allowed the allelic frequency of each of the isoforms to be determined through methods known in the art.
A panel of 69 mAb antibodies (Table 1) were selected out of a catalogue of >1000 generated as per Section 2. Antibodies were then evaluated by competitive immunoassay. They were first immobilised on a biochip platform (9mm×9mm), which was the substrate for the immunoreactions. The semi-automated bench top analyser Evidence Investigator was used (EV3602, Randox Laboratories Ltd., Crumlin, UK, patents-EP98307706, EP98307732, EP0902394, EP1227311, EP1434995 and EP1354623). The assay principle is based on competition for binding sites of the monoclonal antibody between free antigen (the patient sample) and labelled tracer plasma (Quantiplasma™).
Sample and reagents are added to the biochip and incubated under controlled conditions. Following addition of substrate, a light signal is generated which is then detected using digital imaging technology. The system incorporates dedicated software to automatically process, report and archive the data generated. The level of a specific protein in the patient sample is determined by comparing the difference between the light signal (RLU) at the position of the respective antibody on a biochip containing sample and the tracer (test) and a biochip containing just the tracer (blank). A ratio between test and control samples is determined as;
with a high ratio indicating a relatively high level of the protein specific for its respective mAb present in the sample, and a low ratio indicating relatively little or none of the protein present in the sample. Ratios for AD patients and control patients for all mAbs were determined (Example
As an example of how multiple markers identified by this study may be combined to provide a model to classify a patient whose disease state is unknown, we have used logistic regression as a method of model determination. Initial investigation showed that using the relative levels of Afamin (BSI0268) combined with that of Alpha-1-antichymotrypsin (BSI0221) generated a model with an AUC of 0.906 (
| Number | Date | Country | Kind |
|---|---|---|---|
| 1303936.7 | Mar 2013 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2014/054185 | 3/4/2014 | WO | 00 |
