Patent Application
20120071337
The present invention relates to methods and compositions relating to Alzheimer's disease. In particular, the present invention provides methods of diagnostic and prognostic measurement of Alzheimer's disease using differentially expressed proteins.
Alzheimer's disease (AD), the most common cause of dementia in older individuals, is a debilitating neurodegenerative disease for which there is currently no cure. It destroys neurons in parts of the brain, chiefly the hippocampus, which is a region involved in coding memories. Alzheimer's disease gives rise to an irreversible progressive loss of cognitive functions and of functional autonomy. The earliest signs of AD may be mistaken for simple forgetfulness, but in those who are eventually diagnosed with the disease, these initial signs inexorably progress to more severe symptoms of mental deterioration. While the time it takes for AD to develop will vary from person to person, advanced signs include severe memory impairment, confusion, language disturbances, personality and behaviour changes, and impaired judgement. Persons with AD may become non-communicative and hostile. As the disease ends its course in profound dementia, patients are unable to care for themselves and often require institutionalisation or professional care in the home setting. While some patients may live for years after being diagnosed with AD, the average life expectancy after diagnosis is eight years.
In the past, AD could only be definitively diagnosed by brain biopsy or upon autopsy after a patient died. These methods, which demonstrate the presence of the characteristic plaque and tangle lesions in the brain, are still considered the gold standard for the pathological diagnoses of AD. However, in the clinical setting brain biopsy is rarely performed and diagnosis depends on a battery of neurological, psychometric and biochemical tests, including the measurement of biochemical markers such as the ApoE and tau proteins or the beta-amyloid peptide in cerebrospinal fluid and blood.
Better biomarkers are needed for diagnosing AD and other dementias. A biological marker that fulfils the requirements for the diagnostic test for AD would have several advantages. An ideal biological marker would be one that identifies AD cases at a very early stage of the disease, before there is degeneration observed in the brain imaging and neuropathological tests. Detection of a biomarker or panel of biomarkers could be the first indicator for starting treatment as early as possible, and also very valuable in screening the effectiveness of new therapies, particularly those that are focussed on preventing the development of neuropathological changes. A biological marker would also be useful in the follow-up of the development of the disease.
Markers related to pathological characteristics of AD, such as plaques and tangles (Aβ and tau), have been the most extensively studied. The most promising has been from studies of CSF concentration of Aβ(1-40), Aβ(1-42) and tau or the combination of both proteins in AD. Many studies have reported a decrease in Aβ(1-42) in CSF, while the total Aβ protein or Aβ(1-40) concentration remain unchanged (Ida, Hartmann et al. 1996; Kanai, Matsubara et al. 1998; Andreasen, Hesse et al. 1999).
Whilst cerebrospinal fluid (CSF) levels of Aβ and tau are promising biomarkers for diagnosis of AD they are not showing such diagnostic utility in more accessible body fluids. Cerebrospinal fluid is difficult to obtain from human patients. Its collection typically involves a serious invasive technique such as lumbar puncture, which is performed under sedation. This is a highly skilled and complex procedure, requiring qualified and specially trained medical staff. Furthermore, it is time consuming and may require anaesthetic, as well as extended co-operation from the patient. Moreover, collection of cerebrospinal fluid is an uncomfortable and often painful procedure, with prolonged headache being a common symptom, as well as carrying inherent risks of infection and possible paralysis to the patient.
In the light of the limitations of cerebrospinal fluid as a routine clinical sample, considerable interest resides in plasma as a source of biomarkers for neurodegenerative conditions such as Alzheimer's disease. WO 06/035237 describes proteomics studies that identified a number of differentially expressed proteins and described certain methods for the diagnosis of Alzheimer's disease.
However, it remains the case that biomarkers known in the art to be associated with Alzheimer's disease have had limited or insignificant prognostic value. Whilst current clinical diagnosis of Alzheimer's disease based on general neurological symptoms and imprecise cognitive function tests is reasonably robust, it remains a problem to describe, and in particular to predict, the likely progress of disease in living patients. Thus, prognosis, as well as diagnosis, remains a problem in the art in connection with living patients.
The present invention seeks to overcome problem(s) associated with the prior art.
Broadly the present invention is directed to methods, reagents and kits for the diagnostic and prognostic monitoring of patients at risk of or suffering from Alzheimer's disease. More specifically the present invention describes three protein markers whose levels in plasma vary wherein the level of each protein provides information on a certain aspect of a patient's risk of developing the disease, and/or on the rate of progression of any such disease.
In one aspect the present invention provides a method of determining the nature or degree of progression of cognitive decline in Alzheimer's disease in a human or animal subject, the method comprising detecting the level of one or more differentially expressed protein(s) identified by the methods described herein in a tissue sample or body fluid sample from said subject.
In another aspect the present invention provides a method of determining the approximate age of onset Alzheimer's disease in a human or animal subject at risk of developing the disease, the method comprising detecting the level of one or more differentially expressed protein marker(s) identified by the methods described herein in a tissue sample or body fluid sample from said subject.
In another aspect the present invention provides a method of determining an individual's risk of developing Alzheimer's disease, the method comprising detecting the level of one or more differentially expressed protein marker(s) identified by the methods described herein in a tissue sample or body fluid sample from said subject.
In another aspect the present invention provides a method of predicting and/or monitoring the response of a subject with AD to treatment the method comprising detecting the level of one or more differentially expressed protein marker(s) identified by the methods described herein in a tissue sample or body fluid sample from said subject. In this context it is understood that the subject may be a human subject or may be a non-human subject. Non-human subjects include non-vertebrate and vertebrate models of AD including gene amplification, gene knockdown and transgenic models.
In certain embodiments it is preferable to measure levels of the biomarkers of the present invention in serial diagnostic samples taken from the same patient. Changes in the levels of biomarkers with time may provide additional, clinically useful information as to the occurrence, continued rate of progression and/or the response of the patient to treatment for AD.
In each aspect of the invention, reagents and kits useful in performing the methods are provided.
In particular, it is a specific advantage of the invention that the diagnostic and prognostic methods involve assay of particular protein markers (biomarkers) from blood. Blood is easily and quickly collected with minimal invasiveness. Furthermore, collection of blood requires substantially less medical training and qualification than collection of cerebrospinal fluid, making it cheaper and less demanding to obtain. Moreover, risks to the patient can be advantageously minimised or eliminated by basing the methods of the invention on detection in blood.
Furthermore, the inventors identify a defined group of biomarkers which share certain properties, in particular the ability to be detected in blood and to give reliable diagnostic and/or prognostic indications in connection with Alzheimer's disease. Thus, the invention advantageously provides methods for aiding the diagnosis of Alzheimer's disease, and methods for aiding prediction of the prognosis for patients which have Alzheimer's disease. The methods may also be applied in monitoring the effectiveness of treatment of patients suffering from Alzheimer's disease whereby successful treatment is evidenced by a move in the biomarker plasma levels back towards, or back to, that of a non-Alzheimer's state.
Specifically, the present invention identifies and describes proteins that are differentially expressed in the plasma of individuals with Alzheimer's disease relative to their expression in the normal state and, in particular, identifies and describes proteins associated with defining the age of onset and likely rate of cognitive decline in Alzheimer's disease. Further, the present invention provides methods of diagnostic and prognostic measurement of Alzheimer's disease using the differentially expressed proteins. Still further, the present invention provides reagents and kits for the diagnosis and prognostic monitoring of Alzheimer's disease.
Thus the invention provides a method for aiding the diagnosis of Alzheimer's disease in a subject, said method comprising; providing a sample of blood obtained from said subject; assaying the amount of gelsolin present in said sample; comparing the amount of gelsolin present in said sample to a reference amount of gelsolin present in a reference sample from a healthy subject, wherein detection of a gelsolin level in the sample from said subject which is lower than the gelsolin level in the reference sample indicates an increased likelihood of Alzheimer's disease in said subject. It should be understood that the reference sample may be taken from an unrelated healthy subject or may be an earlier sample taken from the same subject prior to the onset of Alzheimer's disease symptoms.
In another aspect, the invention relates to a method for aiding the diagnosis or prognostic monitoring of Alzheimer's disease in a subject, said method comprising; providing a sample of a relevant tissue from said subject; measuring the amount of one or more proteins selected from Gelsolin, C1 protease inhibitor and ceruloplasmin; comparing the amount of said one or more proteins present in said sample to a reference amount of the same proteins in a sample from a healthy subject, wherein detection of a level different to that found in a reference sample indicates an increased likelihood of Alzheimer's disease being present or developing or advancing in said subject.
In another aspect, the invention relates to a method for aiding the diagnosis or prognostic monitoring of Alzheimer's disease in a subject, said method comprising;
(i) providing a sample of a relevant tissue from said subject;
(ii) measuring the amount of gelsolin; and
(iii) measuring the amount of one or more proteins selected from
C1 protease inhibitor;
ceruloplasmin;
clusterin;
complement c3;
serum amyloid P component;
alpha-2-macroglobulin;
gamma-fibrinogen;
complement factor H; or
apolipoprotein E; and
(iv) comparing the amounts of said gelsolin and said one or more proteins present in said sample to a reference amount of the same proteins in a sample from a healthy subject, wherein detection of a level different to that found in a reference sample indicates an increased likelihood of Alzheimer's disease being present or developing or advancing in said subject.
Suitably step (iii) comprises measuring the amount of one or more proteins selected from:
clusterin;
complement c3;
serum amyloid P component;
alpha-2-macroglobulin;
gamma-fibrinogen;
complement factor H; or
apolipoprotein E;
Suitably step (iii) comprises measuring the amount of one or more proteins selected from:
C1 protease inhibitor; or
ceruloplasmin.
In another aspect, the invention relates to a method as described above comprising assaying the levels of each of gelsolin, C1 protease inhibitor and ceruloplasmin in a sample of blood from said subject.
Suitably the sample comprises blood.
More suitably the sample comprises blood plasma.
Suitably said blood plasma may be depleted for one or more of albumin; transferrin; IgG; IgA; antitrypsin or haptoglobin. Suitably such depletion is prior to the analysis step(s) of the methods of the invention.
Suitably said blood plasma has been depleted for each of albumin; transferrin; IgG; IgA; antitrypsin or haptoglobin.
Suitably the protein is detected by western blotting.
Suitably the protein is detected by bead suspension array.
Suitably the protein is detected by planar array.
Suitably the protein is detected by isobaric protein tagging. This embodiment involves all having the same mass. This embodiment may be assayed using a TMTcalibrator type approach.
Suitably the protein is detected by isotopic protein tagging. This embodiment involves having different masses within the same identical chemical structure. This embodiment may be assayed using a TMT-SRM type approach. Suitably an isotopic dilution assay such as AQUA may be used.
Suitably the protein is detected by mass spectrometer-based assay.
Suitably the protein is gelsolin and is detected by reference to one or more of the following peptides of Table B: SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32.
In another aspect, the invention relates to use for diagnostic, prognostic and therapeutic applications, relating to Alzheimer's disease, of a material which recognises, binds to or has affinity for a polypeptide, or a variant or mutant thereof, wherein the polypeptide is selected from gelsolin (SEQ ID NO:1), C1 protease inhibitor (SEQ ID NO:2), or Ceruloplasmin (SEQ ID NO:3).
In another aspect, the invention relates to use as described above of a combination of materials, each of which respectively recognises, binds to or has affinity for one or more of said polypeptide(s), or a variant or mutant thereof.
Suitably the or each material is an antibody or antibody chip.
Suitably the material is an antibody with specificity for one or more of said polypeptide(s), or a fragment, variant or mutant thereof.
In another aspect, the invention relates to an assay device for use in the diagnosis of Alzheimer's disease, which comprises a solid substrate having a location containing a material, which recognizes, binds to or has affinity for a polypeptide, or a fragment, variant or mutant thereof, wherein the polypeptide is selected from gelsolin (SEQ ID NO:1), C1 protease inhibitor (SEQ ID NO:2), or Ceruloplasmin (SEQ ID NO:3).
Suitably the solid substrate has a plurality of locations each respectively containing a material which recognizes, binds to or has affinity for a polypeptide, or a fragment, variant or mutant thereof, wherein the polypeptide is selected from gelsolin (SEQ ID NO:1), C1 protease inhibitor (SEQ ID NO:2), or Ceruloplasmin (SEQ ID NO:3).
Suitably the material is an antibody or antibody chip.
Suitably the assay device as described above has a unique addressable location for each antibody, thereby to permit an assay readout for each individual polypeptide or for any combination of polypeptides.
Suitably the assay device as described above, includes an antibody to a polypeptide wherein the polypeptide is selected from gelsolin (SEQ ID NO:1), C1 protease inhibitor (SEQ ID NO:2), or Ceruloplasmin (SEQ ID NO:3).
Suitably the assay device as described above further has a location containing a material which recognizes, binds to or has affinity for glutathione S transferase P.
Suitably the material is an antibody or antibody chip.
In another aspect, the invention relates to a kit for use in the diagnosis of Alzheimer's disease, comprising an assay device as described above, and means for detecting the amount of one or more of the polypeptides in a sample of body fluid taken from a subject.
In another aspect, the invention relates to a kit for use in the detection of gelsolin polypeptide, said kit comprising one or more of the following peptides of Table B: SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32.
In another aspect, the invention relates to a kit for use in the diagnosis of Alzheimer's disease, comprising one or more of the following peptides of Table B: SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32. Suitably said kit comprises at least one further peptide of Table B.
In one embodiment suitably one or more of said peptides comprises a heavy isotope. Suitably one or more of said peptides comprises several heavy isotopes. Such isotopes may comprise carbon-13 or nitrogen-15. The advantage of this embodiment is that the heavy isotopes provide a different mass to an otherwise unaltered peptide, thereby facilitating its detection/identification.
In one embodiment suitably one or more of said peptides comprises a TMT tag. Suitably said kit comprises a further isotopic TMT tag for labelling of a sample polypeptide. Suitably such a tag may comprise TMT-6.
In another aspect, the invention relates to a method of determining the APOE ε4 genotype of a subject, said method comprising assaying the C1 protease inhibitor level in a sample of blood from said subject.
In another aspect, the invention relates to a method of predicting the age of onset of Alzheimer's disease for a subject, said method comprising assaying the ceruloplasmin levels in a sample of blood from said subject.
Suitably the biomarker is one or more of gelsolin (e.g. SEQ ID NO:1), C1 protease inhibitor (also referred to herein as ‘C1 inhibitor’ or ‘C1 inh’)(e.g. SEQ ID NO:2) or ceruloplasmin (e.g. SEQ ID NO:3). These markers each have the advantage of being detectable in blood.
Thus, the biomarker proteins demonstrated in this study that are important in discriminating AD and NDC are Gelsolin, C1 inhibitor and Ceruloplasmin.
Gelsolin was found in lower levels in AD and correlated with cognitive decline per year. Thus gelsolin is a preferred biomarker according to the present invention.
The two other proteins found in the multivariate analysis to be important for discriminating AD and NDC were C1 inhibitor and Ceruloplasmin. C1 inhibitor protein and Ceruloplasmin were associated with other clinical parameters, i.e. APOE ε4 genotype and age of onset. Whilst these latter proteins did not show a statistically significant difference in plasma protein levels between AD and NDC, they were associated with APOE ε4 genotype and age of onset respectively, and thereby provide means of identifying an individual's risk of developing AD and/or of assessing duration of a diagnosed disease. Thus, all three biomarkers are important in the common area of Alzheimer's disease diagnosis, prognosis, and therapeutic monitoring.
Gelsolin, also called actin-depolymerizing factor (ADF) or Brevin, occurs intracellularly in cytosol and mitochondria, as well as extracellularly in blood plasma. The main function of this 82 kDa sized protein is known to be as a key regulator of actin filament assembly and is regulated by Ca2+ (Sun et al., 1999). Interestingly, a single nucleotide mutation in the Gelsolin gene, which leads to the exchange of an amino acid, is the cause of familial amyloidosis Finnish type (Levy et al., 1990, Maury et al., 1990). Gelsolin has also been related to a familial type of cerebral amyloid angiopathy (Kiuru et al., 1999) and was shown to bind Aβ in a concentration-dependant manner (Chauhan et al., 1999, Ji et al., 2008). Gelsolin inhibits the fibrillization of Aβ peptides and can also defibrillize preformed Aβ fibrils (Ray et al., 2000). It was also shown that Gelsolin plays an important role in inhibiting Aβ-induced cytotoxicity by inhibiting apoptotic mitochondrial changes (Qiao et al., 2005). Amyloid plaques are one of the two main pathological findings in AD and different strategies have been undertaken to decrease the brain plaque load. The increased clearance of Aβ from the central nervous system (CNS) was shown to improve memory function in human (Gilman et al., 2005) and decrease behavioural deficits in transgenic mice (Janus et al., 2000). One strategy to achieve this, also called the peripheral sink hypothesis, is by shifting the Aβ equilibrium between blood plasma and CNS to the periphery (Matsuoka et al., 2003), be it with active or passive immunization or through other Aβ binding proteins including Gelsolin (Matsuoka et al., 2003). In line with this, the induction of peripheral expression of plasma Gelsolin was also shown to reduce brain Aβ and was suggested as a suitable gene-therapeutic approach for the prevention or treatment of AD (Hirko et al., 2007). Given that Gelsolin binds Aβ, reduces the toxicity of Aβ fibrils and lowers the Aβ burden in the CNS, it is plausible that decreased plasma Gelsolin levels in AD, as we demonstrate herein, contribute to a faster disease progression.
Suitably the marker is gelsolin. When the marker is gelsolin, suitably the blood level of gelsolin is compared with a normal or reference blood level of gelsolin. If the level of gelsolin detected in the patient is seen to be lower than the level of gelsolin in the normal or reference sample, this indicates an increased likelihood of the patient having Alzheimer's disease.
Gelsolin levels may also be advantageously used as a predictor of rate of cognitive decline. Specifically, lower gelsolin levels correlate with a greater level of cognitive decline per year. In other words, the degree to which gelsolin levels detected in the blood of a patient are lower than those detected in a normal or reference sample correlates with the degree of cognitive decline expected or predicted year by year for that patient.
Moreover, gelsolin levels are also surprisingly shown to correlate with the disease progression rate. In other words, the lower the level of gelsolin levels found in blood from a patient compared with a normal or reference sample, the faster the disease progression rate predicted for that patient.
It is an advantage of the invention that blood based markers of disease progression are taught herein. Furthermore, it is an advantage of the invention that the levels of blood based biomarkers may be used to predict disease progression rate of that patient.
Plasma protease C1 inhibitor (C1 inh) is an inhibitor of the complement pathway and a member of the so called serpins, serine protease inhibitors. C1 inh is an acute phase protein and its main function is the inhibition of the complement system to prevent spontaneous activation. A deficiency in C1 inh plays a causative role in the development of acquired and hereditary angiodema (Carugati et al., 2001). In AD, an activation of the complement pathway is known to occur already in very early stages (McGeer and McGeer, 2002) and several of its components, including C1 inh, have been shown to be associated with amyloid plaques (Veerhuis et al., 1998, Strohmeyer et al., 2002). C1 inh has recently also been suggested as a biomarker in AD plasma in patients treated with rosiglitazone (Akuffo et al., 2008). However, the role of C1 inh in the disease process remains unclear, since it was shown that C1 inh and CD59 do not effectively inhibit complement activation in AD (Yasojima et al., 1999).
C1 protease inhibitor levels may be advantageously used according to the invention as an indicator of APOE ε4 (APOE epsilon 4) genotype. Suitably levels of C1 protease inhibitor are not used alone in the diagnosis of Alzheimer's disease, but are rather advantageously combined with other markers, or used alone in order to aid the diagnosis of an APOE ε4 genotype.
Ceruloplasmin, also known as ferroxidase, is the major copper-carrying protein in the blood and plays also a role in iron metabolism. Copper deficiency has been attributed as one of the causes for AD and has been extensively studied and reviewed (Gaggelli et al., 2006). Ceruloplasmin levels have been studied in blood (Giometto et al., 1988, Hye et al., 2006, Kessler et al., 2006), CSF (Loeffler et al., 1994) and brain tissue (Connor et al., 1993, Loeffler et al., 1996, Loeffler et al., 2001) with different results. In our study, a significant (positive) correlation of Ceruloplasmin levels with age of onset was established. Due to its main function in copper transport and the observed correlation with age of onset, copper imbalance seems to have a main impact on the onset and course of AD.
The invention advantageously provides the use of ceruloplasmin levels in aiding the diagnosis or prediction of age of onset of Alzheimer's disease. In particular, a positive correlation of ceruloplasmin levels with age of onset of Alzheimer's disease is disclosed herein. Suitably, ceruloplasmin levels are not used alone for the diagnosis of Alzheimer's disease. Suitably, ceruloplasmin levels may be used in combination with other markers in aiding the diagnosis of Alzheimer's disease, or preferably ceruloplasmin levels are used alone in order to aid the prediction of age of onset of Alzheimer's disease for a particular patient.
The invention may be applied as part of a panel of biomarkers in order to provide a more robust diagnosis or prognosis. Moreover, the invention may be applied as part of a panel of biomarkers in order to provide a more complete picture of the disease state or possible outcomes for a given patient.
Suitably, at least one of gelsolin, C1 protease inhibitor, and ceruloplasmin are assayed according to the present invention, suitably in a broader panel of markers according to the present invention.
More suitably, at least two of gelsolin, C1 protease inhibitor and ceruloplasmin are assayed according to the present invention, suitably in a broader panel of markers according to the present invention.
Suitably when two markers are assayed, those markers are gelsolin and C1 protease inhibitor. This permits aiding a diagnosis of disease, together with an indication of the APOE ε4 (“APOE epsilon 4”) genotype, such as in a single assay format, advantageously avoiding performing a separate genotyping test for Apoε4.
Suitably, when two markers are assayed according to the invention, those markers are gelsolin and ceruloplasmin. This offers the advantage of aiding the prediction of age of onset for a particular patient, aiding the diagnosis of whether or not that patient has already developed the disease. Thus, if gelsolin levels are found to be normal, but ceruloplasmin levels indicate a particular age of onset, then re-testing or monitoring of that patient may be advantageously indicated based on the outcome of the gelsolin/ceruloplasmin combined assay.
When two markers are assayed according to the invention, those markers may be C1 protease inhibitor and ceruloplasmin. This combination is not expected to provide a direct indication of diagnosis of a diseased state. This combination offers the advantage of providing descriptive/predictive information about a patient, which may be useful in assessing risk for that particular patient. Moreover, when this combination of markers is used, then issues of counseling regarding a positive diagnosis of Alzheimer's disease are advantageously avoided. Moreover, this combination of markers might be usefully employed as a pre-screen, for example to provide an indication of susceptibility or probability of developing a disease, and patients may be scheduled for a full diagnostic test at an appropriate future point depending on the indications from the ceruloplasmin/C1 protease inhibitor combined results.
Suitably when more than two biomarkers are assayed according to the invention, those biomarkers comprise gelsolin, C1 protease inhibitor and ceruloplasmin. This combination advantageously maximises the amount of information provided to a patient for a given analysis.
Of course, the skilled reader will appreciate that the specific biomarkers of the present invention may be advantageously combined with other markers known in the art. Such extended panels which comprise the specific biomarkers discussed herein are of course intended to be embraced by the invention. Selection of further known markers for testing in such a panel embodiment may be accomplished by the skilled reader according to the appropriate sources. In this context additional biomarkers may relate to AD, to other neurological conditions from which a differential diagnosis of AD is required, or to other diseases commonly associated with patients with AD or whose symptoms mimic those of AD. One such set of additional markers related to AD are provided in WO 06/035237.
Thus a preferred group of markers comprises
Gelsolin (Swiss prot accession number P06396; SEQ ID NO: 1); and one or more proteins selected from
C1 protease inhibitor (SEQ ID NO: 2)
ceruloplasmin (SEQ ID NO: 3)
clusterin (SwissProt accession number P10909; SEQ ID NO:4)
complement c3 (P01024; SEQ ID NO:5)
serum amyloid P component (P02743; SAP; SEQ ID NO:6)
alpha-2-macroglobulin (P01023; A2M; SEQ ID NO:7)
gamma-fibrinogen (P02679; SEQ ID NO:8)
complement factor H (P08603; CFH; SEQ ID NO:9)
apolipoprotein E (P02649; ApoE; SEQ ID NO:10).
In one embodiment the invention provides a method of aiding the diagnosis of Alzheimer's disease in a subject, said method comprising assaying at least two of gelsolin, C1 protease inhibitor and ceruloplasmin in a sample of blood from said subject. Suitably the levels of each of gelsolin, C1 protease inhibitor and ceruloplasmin are assayed in a sample of blood from said subject.
Suitably said subject is a human.
Suitably said subject is a non-human mammal.
Suitably said subject is a rodent.
The sample may be any tissue that can be obtained from a subject suspected of having AD or of being at risk of developing AD. In the context of humans it is preferred that the sample is a body fluid. More preferably the sample is blood. Even more preferred the sample is blood plasma.
In particular, when the biomarker being assayed comprises one or more of gelsolin, C1 protease inhibitor or ceruloplasmin, then suitably cerebrospinal fluid is specifically excluded as the sample. Of course, in further embodiments of the invention involving assay of other biomarkers, cerebrospinal fluid may be analysed as part of a wider analysis.
The sample may comprise a substance derived from blood, such as plasma. Preparation of plasma from whole blood is easily accomplished by the person skilled in the art, such as by centrifugal removal of the cells present in whole blood.
Plasma can be obtained relatively easily and may reflect the sub-proteomes of other organs, including the brain. Both candidate protein panels and gel based proteomics have previously been used in plasma and serum to identify possible biomarkers with some success (Hye et al., 2006, Ray et al., 2007, Baranowska-Bik et al., 2008) but to the best of our knowledge non-gel based proteomics have not previously been used in the search for plasma markers in AD.
One of the problems with the proteomic analysis of blood plasma with mass spectrometry, is the huge dynamic range of plasma proteins. Protein levels span an extraordinary 10 orders of magnitude, which makes the investigation of low(er) abundant proteins nearly impossible (Anderson and Anderson, 2002, Jacobs et al., 2005). The instrumental settings in the LC/MS/MS, where the most prominent peaks in a short period of time are chosen for fragmentation, do not allow for the identification and quantitation of low abundant proteins in unfractionated plasma due to the high abundance of serum albumin and other proteins. This is reflected in a low number of proteins identified. One approach to reduce the dynamic range is to deplete samples of the highest abundant proteins and in this case we exemplify this approach using an immunoaffinity column to remove albumin, transferrin, IgG, IgA, antitrypsin, and haptoglobin. The number of identifiable and quantifiable proteins could be increased considerably and relative protein levels were compared between different samples.
Thus, more suitably, the sample according to the invention may be a processed plasma. For example, plasma may be processed to remove highly abundant proteins, and thereby to increase the number of detectable proteins, or to increase the detectability of proteins present in low absolute concentrations. Techniques for depletion of highly abundant proteins from plasma are well-known in the art. In particular, a multiple affinity removal system may conveniently be used to process plasma for analysis. Exemplary systems are described in the example section of this application.
Furthermore, the sample may suitably comprise plasma proteins. In this embodiment, plasma may be processed as described herein, and may then be subjected to size exclusion chromatography, buffer exchange, or other such treatments in order to arrive at a sample comprising the proteins from said plasma, which may offer advantages such as superior performance in analytical instruments.
The key principle for the properties of the sample, whichever particular form it takes, are that it is, or is derived from, blood.
The reference sample is suitably a sample from a subject that is not suffering from or suspected of suffering from AD. More suitably the reference sample is from a healthy subject. Ideally this is processed and analysed in the same manner as the sample being analysed. However, this may not be practical or desirable in which case the reference sample may be regarded as a reference value previously determined for a healthy subject, such as an abundance or concentration of (e.g.) gelsolin for a normal healthy individual. Ideally the reference sample or value is gender-matched and suitably age-matched, more suitably matched for genetic or ethnic background or other such criteria as are routinely applied in matching of clinical samples to controls, and insofar as the levels of the relevant biomarker in plasma are dependent on such factors. Suitably the reference sample may be an earlier sample taken from the same subject before the onset of Alzheimer's disease.
A marker protein may have its expression modulated, i.e. quantitatively increased or decreased, in patients with Alzheimer's Disease. The degree to which expression differs in normal versus diseased states (or advanced versus early states) need only be large enough to be visualised via standard characterisation techniques, such as silver staining of 2D-electrophoretic gels, measurement of representative peptide ions using isobaric mass tagging and mass spectrometry or immunological detection methods including Western blotting, enzyme-linked immunosorbent assay (ELISA) or radioimmunoassay. Other such standard characterisation techniques by which expression differences may be visualised are well known to those skilled in the art. These include successive chromatographic separations of fractions and comparisons of the peaks, capillary electrophoresis, separations using micro-channel networks, including on a micro-chip, and mass spectrometry methods including multiple reaction monitoring (MRM) and TMTcalibrator (Dayton et al 2009).
Chromatographic separations can be carried out by high performance liquid chromatography as described in Pharmacia literature, the chromatogram being obtained in the form of a plot of absorbance of light at 280 nm against time of separation. The material giving incompletely resolved peaks is then re-chromatographed and so on.
Capillary electrophoresis is a technique described in many publications, for example in the literature “Total CE Solutions” supplied by Beckman with their P/ACE 5000 system. The technique depends on applying an electric potential across the sample contained in a small capillary tube. The tube has a charged surface, such as negatively charged silicate glass. Oppositely charged ions (in this instance, positive ions) are attracted to the surface and then migrate to the appropriate electrode of the same polarity as the surface (in this instance, the cathode). In this electroosmotic flow (EOF) of the sample, the positive ions move fastest, followed by uncharged material and negatively charged ions. Thus, proteins are separated essentially according to charge on them.
Micro-channel networks function somewhat like capillaries and can be formed by photoablation of a polymeric material. In this technique, a UV laser is used to generate high energy light pulses that are fired in bursts onto polymers having suitable UV absorption characteristics, for example polyethylene terephthalate or polycarbonate. The incident photons break chemical bonds with a confined space, leading to a rise in internal pressure, mini-explosions and ejection of the ablated material, leaving behind voids which form micro-channels. The micro-channel material achieves a separation based on EOF, as for capillary electrophoresis. It is adaptable to micro-chip form, each chip having its own sample injector, separation column and electrochemical detector: see J. S. Rossier et al., 1999, Electrophoresis 20: pages 727-731.
Other methods include performing a binding assay for the marker protein. Any reasonably specific binding agent can be used. Preferably the binding agent is labelled. Preferably the assay is an immunoassay, especially between the biomarker and an antibody that recognises the protein, especially a labelled antibody. It can be an antibody raised against part or all of the marker protein, for example a monoclonal antibody or a polyclonal anti-human antiserum of high specificity for the marker protein.
Where the binding assay is an immunoassay, it may be carried out by measuring the extent of the protein/antibody interaction. Any known method of immunoassay may be used. A sandwich assay is preferred. In an exemplary sandwich assay, a first antibody to the marker protein is bound to the solid phase such as a well of a plastics microtitre plate, and incubated with the sample and with a labelled second antibody specific to the protein to be assayed. Alternatively, an antibody capture assay can be used. Here, the test sample is allowed to bind to a solid phase, and the anti-marker protein antibody is then added and allowed to bind. After washing away unbound material, the amount of antibody bound to the solid phase is determined using a labelled second antibody, anti- to the first.
In another embodiment, a competition assay is performed between the sample and a labelled marker protein or a peptide derived therefrom, these two antigens being in competition for a limited amount of anti-marker protein antibody bound to a solid support. The labelled marker protein or peptide thereof can be pre-incubated with the antibody on the solid phase, whereby the marker protein in the sample displaces part of the marker protein or peptide thereof bound to the antibody.
In yet another embodiment, the two antigens are allowed to compete in a single co-incubation with the antibody. After removal of unbound antigen from the support by washing, the amount of label attached to the support is determined and the amount of protein in the sample is measured by reference to standard titration curves established previously.
The binding agent in the binding assay may be a labelled specific binding agent, which may be an antibody or other specific binding agent. The binding agent will usually be labelled itself, but alternatively it may be detected by a secondary reaction in which a signal is generated, e.g. from another labelled substance.
The label may be an enzyme. The substrate for the enzyme may be, for example, colour-forming, fluorescent or chemiluminescent.
An amplified form of assay may be used, whereby an enhanced “signal” is produced from a relatively low level of protein to be detected. One particular form of amplified immunoassay is enhanced chemiluminescent assay. Conveniently, the antibody is labelled with horseradish peroxidase, which participates in a chemiluminescent reaction with luminol, a peroxide substrate and a compound which enhances the intensity and duration of the emitted light, typically 4-iodophenol or 4-hydroxycinnamic acid.
Another form of amplified immunoassay is immuno-PCR. In this technique, the antibody is covalently linked to a molecule of arbitrary DNA comprising PCR primers, whereby the DNA with the antibody attached to it is amplified by the polymerase chain reaction. See E. R. Hendrickson et al., Nucleic Acids Research 23: 522-529 (1995). The signal is read out as before.
The time required for the assay may be reduced by use of a rapid microparticle-enhanced turbidimetric immunoassay such as the type embodied by M. Robers et al., “Development of a rapid microparticle-enhanced turbidimetric immunoassay for plasma fatty acid-binding protein, an early marker of acute myocardial infarction”, Clin. Chem. 1998; 44:1564-1567.
The full automation of any immunoassay contemplated in a widely used clinical chemistry analyser such as the COBAS™ MIRA Plus system from Hoffmann-La Roche, described by M. Robers et al. supra, or the AxSYM™ system from Abbott Laboratories, should be possible and applied for routine clinical diagnosis of Alzheimer's disease.
It is also contemplated within the invention to use (i) an antibody array or ‘chip’, or a bead suspension array capable of detecting one or more proteins that interact with that antibody.
An antibody chip, antibody array or antibody microarray is an array of unique addressable elements on a continuous solid surface whereby at each unique addressable element an antibody with defined specificity for an antigen is immobilised in a manner allowing its subsequent capture of the target antigen and subsequent detection of the extent of such binding. Each unique addressable element is spaced from all other unique addressable elements on the solid surface so that the binding and detection of specific antigens does not interfere with any adjacent such unique addressable element.
A “bead suspension array” is an aqueous suspension of one or more identifiably distinct particles whereby each particle contains coding features relating to its size and colour or fluorescent signature and to which all of the beads of a particular combination of such coding features is coated with an antibody with a defined specificity for an antigen in a manner allowing its subsequent capture of the target antigen and subsequent detection of the extent of such binding. Examples of such arrays can be found at www.luminexcorp.com where application of the xMAP® bead suspension array on the Luminex® 100™ System is described.
Alternatively, the diagnostic sample can be subjected to isobaric mass tagging and LC-MS/MS as described herein. An example of preferred ways of carrying out isobaric protein tagging are set out in the examples section of this application.
Isobaric protein tagging using tandem mass tags has been shown before to be able to determine relative proteins levels in a highly accurate manner (Thompson et al., 2003, Dayon et al., 2008). In addition, numerous reports have been published in the last few years using iTRAQ for protein tagging in various tissues and fluids (Aggarwal et al., 2006). Especially for the discovery of biomarkers in various conditions, iTRAQ has been proved to be a highly suitable tool and has been used in cancer (Maurya et al., 2007, Garbis et al., 2008, Matta et al., 2008, Ralhan et al., 2008) and diabetes research (Lu et al., 2008) as well as in the quest for biomarkers in neurodegenerative disorders (Abdi et al., 2006) albeit in CSF.
Multiple Selected Reaction Monitoring (mSRM or MRM)
MRM is the scan type with the highest duty cycle and is used for monitoring one or more specific ion transition(s) at high sensitivity. Here, Q1 is set on the specific parent m/z (Q1 is not scanning), the collision energy is set to produce the optimal diagnostic charged fragment of that parent ion, and Q3 is set to the specific m/z of that fragment. Only ions with this exact transition will be detected. Historically used to quantify small molecules such as drug metabolites, the same principle can be applied to peptides, either endogenous moieties or those produced from enzymatic digestion of proteins. Again historically experiments were performed using triple quadrupole mass spectrometers but the recent introduction of hybrid instrument designs, which combine quadrupoles with ion traps, enables similar and improved experiments to be undertaken. The 4000QTRAP instrument therefore allows peptide and biomolecule quantitation to be performed at very high specificity and sensitivity using Multiple Reaction Monitoring (MRM). This is largely due to the use of the LINAC® Collision Cell, which subsequently enables many MRM scans to be looped together into one experiment to detect the presence of many specific ions (up to 100 different ions) in a complex mixture. Consequently it is now feasible to measure and quantify multiple peptides from many proteins in a single chromatographic separation. The area under the MRM LC peak is used to quantitate the amount of the analyte present. In a typical quantitation experiment, a standard concentration curve is generated for the analyte of interest. When the unknown sample is then run under identical conditions, the concentration for the analyte in the unknown sample can be determined using the peak area and the standard concentration curve.
The diagnostic sample can be subjected to analysis by MRM on an ion-trap mass spectrometer. Based on the mass spectrometry profiles of the marker proteins described below single tryptic peptides with specific known mass and amino acid sequences are identified that possess good ionising characteristics. The mass spectrometer is then programmed to specifically survey for peptides of the specific mass and sequence and report their relative signal intensity. Using MRM it is possible to survey for up to 5, 10, 15, 20, 25, 30, 40, 50 or 100 different marker proteins in a single LC-MS run. The intensities of the MRM peptides of the specific biomarkers of the present invention in the diagnostic sample are compared with those found in samples from subjects without AD allowing the diagnosis or prognosis of AD to be made.
The MRM assay can be made more truly quantitative by the use of internal reference standards consisting of synthetic absolute quantification (AQUA) peptides corresponding to the MRM peptide of the marker protein wherein one or more atoms have been substituted with a stable isotope such as carbon-13 or nitrogen-15 and wherein such substitutions cause the AQUA peptide to have a defined mass difference to the native, lighter form of the MRM peptide derived from the diagnostic sample. By comparing the relative ion intensity of the native MRM and AQUA peptides the true concentration of the parent protein in the diagnostic sample can thus be determined. General methods of absolute quantitation by such isotope dilution methods are provided in Gerber, Scott A, et al. “Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS” PNAS, Jun. 10, 2003. Vol 100. No 12. p 6940-6945.
In some cases, whilst it is desirable to use isotope-doped standards to provide absolute quantitation in an SRM experiment it is not possible to use the AQUA approach described above. In such cases it is possible to use a pair of isotopic mass tags i.e. two tags with identical chemical structure but different levels of isotopic substitutions giving each a unique mass. Using two forms of the Tandem Mass Tags® (TMT®) that differ in mass by 5 Da it is possible to label standard synthetic reference SRM peptides with a light tag prior to mixing to form a universal reference for all targeted peptides in an assay. Each patient sample is then subjected to trypsin digestion and the resulting peptides labelled with the heavy TMT tag. An aliquot of the TMT-labelled reference peptides is then added to the sample to give a final concentration of reference peptides that is relevant to the target range to be measured in the patient sample. The spiked sample is then subjected to a standard isotope dilution SRM assay and the concentrations of the SRM peptides from the patient sample are calculated by comparing ion intensities of the heavy form against those of the known concentrations of the lighter form.
An alternative form of MS-based assay for the relative or absolute quantitation of regulated peptides identified as biomarker candidates is the TMTcalibrator method developed by Proteome Sciences plc, Known amounts of synthetic peptides representing tryptic fragments of the candidate biomarker(s) with good MS/MS behaviour are labelled with four of the six reagents of the TMT6 set of isobaric mass tags (TMT6-128 to TMT6-131) and mixed in certain ratios. This allows a multi-point calibration curve reflecting physiological and/or disease-modified concentrations to be designed and implemented quickly. Subsequently, a diagnostic sample taken from a patient suffering from or suspected of suffering from AD is labelled with TMT6-126 and the calibration mix is added to the study sample. During MS/MS of individual peptides, the TMT6-reporter ions of the calibrant peptides are produced and used to establish a calibration curve. The absolute amount of the peptide in the study sample is then readily derived by reading the TMT6126 ion intensity against the calibration curve. Further information on TMTcalibrator assays can be obtained from the Proteome Sciences website (www.proteomics.com).
A preferred method of diagnosis comprises performing a binding assay for the marker protein. Any reasonably specific binding partner can be used. Preferably the binding partner is labelled. Preferably the assay is an immunoassay, especially between the marker and an antibody that recognises the protein, especially a labelled antibody. It can be an antibody raised against part or all of it, most preferably a monoclonal antibody or a polyclonal anti-human antiserum of high specificity for the marker protein.
Thus, the marker proteins described above are useful for the purpose of raising antibodies thereto which can be used to detect the increased or decreased concentration of the marker proteins present in a diagnostic sample. Such antibodies can be raised by any of the methods well known in the immunodiagnostics field.
The antibodies may be anti- to any biologically relevant state of the protein. Thus, for example, they can be raised against the unglycosylated form of a protein which exists in the body in a glycosylated form, against a more mature form of a precursor protein, e.g. minus its signal sequence, or against a peptide carrying a relevant epitope of the marker protein.
The sample can be taken from any valid body tissue, especially body fluid, of a mammalian or non-mammalian subject, but preferably blood, plasma, serum or urine. Other usable body fluids include cerebrospinal fluid (CSF), semen and tears. Preferably the subject is a mammalian species such as a mouse, rat, guinea pig, dog or primate. Most preferably the subject is human.
The preferred immunoassay is carried out by measuring the extent of the protein/antibody interaction. Any known method of immunoassay may be used. A sandwich assay is preferred. In this method, a first antibody to the marker protein is bound to the solid phase such as a well of a plastic microtitre plate, and incubated with the sample and with a labelled second antibody specific to the protein to be assayed. Alternatively, an antibody capture assay can be used. Here, the test sample is allowed to bind to a solid phase, and the anti-marker protein antibody is then added and allowed to bind. After washing away unbound material, the amount of antibody bound to the solid phase is determined using a labelled second antibody, anti- to the first.
In another embodiment, a competition assay is performed between the sample and a labelled marker protein or a peptide derived therefrom, these two antigens being in competition for a limited amount of anti-marker protein antibody bound to a solid support. The labelled marker protein or peptide thereof can be pre-incubated with the antibody on the solid phase, whereby the marker protein in the sample displaces part of the marker protein or peptide thereof bound to the antibody.
In yet another embodiment, the two antigens are allowed to compete in a single co-incubation with the antibody. After removal of unbound antigen from the support by washing, the amount of label attached to the support is determined and the amount of protein in the sample is measured by reference to standard titration curves established previously.
The label is preferably an enzyme. The substrate for the enzyme may be, for example, colour-forming, fluorescent or chemiluminescent.
The binding partner in the binding assay is preferably a labelled specific binding partner, but not necessarily an antibody. The binding partner will usually be labelled itself, but alternatively it may be detected by a secondary reaction in which a signal is generated, e.g. from another labelled substance.
It is highly preferable to use an amplified form of assay, whereby an enhanced “signal” is produced from a relatively low level of protein to be detected. One particular form of amplified immunoassay is enhanced chemiluminescent assay. Conveniently, the antibody is labelled with horseradish peroxidase, which participates in a chemiluminescent reaction with luminol, a peroxide substrate and a compound which enhances the intensity and duration of the emitted light, typically 4-iodophenol or 4-hydroxycinnamic acid.
Another preferred form of amplified immunoassay is immuno-PCR. In this technique, the antibody is covalently linked to a molecule of arbitrary DNA comprising PCR primers, whereby the DNA with the antibody attached to it is amplified by the polymerase chain reaction. See E. R. Hendrickson et al., Nucleic Acids Research 23: 522-529 (1995). The signal is read out as before.
The use of a rapid microparticle-enhanced turbidimetric immunoassay such as the type embodied by M. Robers et al., “Development of a rapid microparticle-enhanced turbidimetric immunoassay for plasma fatty acid-binding protein, an early marker of acute myocardial infarction”, Clin. Chem. 1998; 44:1564-1567, significantly decreases the time of the assay. Thus, the full automation of any immunoassay contemplated in a widely used clinical chemistry analyser such as the COBAS™ MIRA Plus system from Hoffmann-La Roche, described by M. Robers et al. supra, or the AxSYM™ system from Abbott Laboratories, should be possible and applied for routine clinical diagnosis of Alzheimer's disease.
Alternatively, the diagnostic sample can be subjected to two dimensional gel electrophoresis to yield a stained gel in which the position of the marker proteins is known and the relative intensity of staining at the appropriate spots on the gel can be determined by densitometry and compared with a corresponding control or comparative gel.
In a yet further embodiment the diagnostic sample can be subjected to analysis by a mass-spectrometer-based assay such as multiple reaction monitoring (MRM) on a triple quadrupole mass spectrometer or on certain types of ion-trap mass spectrometer. For each differentially expressed protein it is possible to identify a set of tryptic peptides with specific known mass (parent mass) and amino acid sequence and which upon fragmentation release fragments of specific mass (fragment mass) that are unique to each protein. The detection of a fragment mass from a defined parent mass ion is known as a transition.
Identification of such proteotypic peptides can be made based on the mass spectrometry profiles of the differentially expressed proteins seen during biomarker discovery, or may be designed in silico using predictive algorithms known to the skilled practitioner. The mass spectrometer is then programmed to specifically survey only for the specific parent mass and fragment mass transitions selected for each protein and reports their relative signal intensity. Using MRM it is possible to survey for up to 5, 10, 15, 20, 25, 30, 40, 50 or 100 different marker proteins in a single LC-MS run. The relative abundances of the proteotypic peptides for each marker protein in the diagnostic sample are compared with those found in samples from subjects without dementia allowing the diagnosis of Alzheimer's disease to be made. Alternatively comparison may be made with levels of the proteins from earlier samples from the same patient thus allowing prognostic assessment of the stage and/or rate of progression of Alzheimer's disease in said patient.
In a further embodiment of the invention the MRM assay can be made more truly quantitative by the use of internal reference standards consisting of synthetic absolute quantification (AQUA) peptides corresponding to the proteotypic peptide of the marker protein wherein one or more atoms have been substituted with a stable isotope such as carbon-13 or nitrogen-15 and wherein such substitutions cause the AQUA peptide to have a defined mass difference to the native proteotypic peptide derived from the diagnostic sample. Once AQUA peptides equivalent to each proteotypic peptide from the differentially expressed biomarkers of Alzheimer's disease have been produced, they can be mixed to form a reference standard that is then spiked into the tryptic digest of the patient sample. The combined sample is then subjected to a programmed mass spectrometer-based assay where the intensity of the required transitions from the native and AQUA peptides is detected. By comparing the relative ion intensity of the native peptides from the sample and the spiked AQUA reference peptides the true concentration of the parent protein in the diagnostic sample can thus be determined. General methods of absolute quantitation are provided in Gerber, Scott A, et al. “Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS” PNAS, Jun. 10, 2003. Vol 100. No 12. p 6940-6945 which is incorporated herein by reference.
In a yet further embodiment of the invention an absolute quantitation can be made by using a TMT-SRM assay. Standard synthetic reference SRM peptides corresponding to the prototypic peptide of the marker protein are labelled with a light TMT tag having no isotope substitutions (light tag) prior to mixing to form a universal reference for all marker proteins in an assay. Each patient sample is then subjected to trypsin digestion and the resulting peptides labelled with the TMT tag having five isotopic substitution (heavy tag). An aliquot of the light TMT-labelled reference peptides is then added to the heavy TMT-labelled sample to give a final concentration of reference peptides that is relevant to the target range to be measured in the patient sample. The spiked sample is then subjected to a standard isotope dilution SRM assay and the concentrations of the SRM peptides from the patient sample are calculated by comparing ion intensities of the heavy form against those of the known concentrations of the lighter form.
Irrespective of the method chosen for measurement of the marker protein, the diagnosis and prognosis of Alzheimer's disease does not necessarily require a step of comparison of the concentration of the marker protein(s) with a control or reference sample but can be carried out with reference to a pre-determined reference value known to represent the presence and/or stage of disease.
The invention can be used to determine the stage and/or rate of progression of dementia in Alzheimer's disease, if desired, with reference to results obtained earlier from the same patient or by reference to standard values that are considered typical of the stage or rate of progression of the disease. In this way, the invention can be used to determine whether, for example after treatment of the patient with a drug or candidate drug, the disease has progressed or not, or that the rate of disease progression has been modified. The result can lead to a prognosis of the outcome of the disease.
The invention further includes the use for a diagnostic (and thus possibly prognostic) or therapeutic purpose of a partner material which recognises, binds to or has affinity for a marker protein specified above. Thus, for example, antibodies to the marker proteins, appropriately humanised where necessary, may be used in treatment. The partner material will usually be an antibody and used in any assay-compatible format, conveniently an immobilised format, e.g. as beads or a chip. Either the partner material will be labelled or it will be capable of interacting with a label.
The invention further includes a kit for use in a method of diagnosis and prognostic monitoring of Alzheimer's disease, which comprises a partner material, as described above, in an assay-compatible format, as described above, for interaction with a marker protein present in the diagnostic sample.
It is further contemplated within the invention to use (i) an antibody chip or array of chips, or a bead suspension array capable of detecting one or more proteins differentially expressed in Alzheimer's disease.
The method may further comprise determining an effective therapy for treating Alzheimer's disease.
In a further aspect, the present invention provides a method of treatment by the use of an agent that will restore the expression of one or more differentially expressed proteins in the Alzheimer's disease state towards that found in the normal state in order to prevent the development or progression of Alzheimer's disease. Preferably, the expression of the protein is restored to that of the normal state.
In a further aspect, the present invention provides a method whereby the pattern of differentially expressed proteins in a tissue sample or body fluid sample of an individual with Alzheimer's disease is used to predict the most appropriate and effective therapy to alleviate the Alzheimer's disease.
Also provided is a method of screening an agent to determine its usefulness in treating Alzheimer's disease, the method comprising:
(a) obtaining a sample of relevant tissue taken from, or representative of, a subject having Alzheimer's disease symptoms, who or which has been treated with the agent being screened;
(b) determining the presence, absence or degree of expression of the differentially expressed protein or proteins in the tissue from, or representative of, the treated subject; and,
(c) selecting or rejecting the agent according to the extent to which it changes the expression, activity or amount of the differentially expressed protein or proteins in the treated subject having Alzheimer's disease symptoms.
Preferably, the agent is selected if it converts the expression of the differentially expressed protein towards that of a normal subject. More preferably, the agent is selected if it converts the expression of the protein or proteins to that of the normal subject.
Also provided is a method of screening an agent to determine its usefulness in treating Alzheimer's disease, the method comprising:
(a) obtaining over time samples of relevant tissue or body fluid taken from, or representative of, a subject having Alzheimer's disease symptoms, who or which has been treated with the agent being screened;
(b) determining the presence, absence or degree of expression of a differentially expressed protein or proteins in said samples; and,
(c) determining whether the agent affects the change over time in the expression of the differentially expression protein in the treated subject having Alzheimer's disease symptoms.
Samples taken over time may be taken at intervals of weeks, months or years. For example, samples may be taken at monthly, two-monthly, three-monthly, four-monthly, six-monthly, eight-monthly or twelve-monthly intervals.
A change in expression over time may be an increase or decrease in expression, compared to the initial level of expression in samples from the subject and/or compared to the level of expression in samples from normal subjects. The agent is selected if it slows or stops the change of expression over time.
In the screening methods described above, subjects having differential levels of protein expression comprise:
(a) normal subjects and subjects having Alzheimer's disease; and,
(b) subjects having Alzheimer's disease symptoms which have not been treated with the agent and subjects having Alzheimer's disease which have been treated with the agent.
The term “diagnosis”, as used herein, includes the provision of any information concerning the existence, non-existence or probability of AD in a patient. It further includes the provision of information concerning the type or classification of the disorder or of symptoms which are or may be experienced in connection with it. It encompasses prognosis of the medical course of the condition. It further encompasses information concerning the age of onset.
The methods described herein are useful for both the diagnosis and/or prognosis of AD. AD may be indicated if one or more markers is present at increased or decreased concentration.
It will be understood that where treatment is concerned, treatment includes any measure taken by the physician to alleviate the effect of AD on a patient. Thus, although reversal of the damage or elimination of the damage or effects of AD is a desirable goal, effective treatment will also include any measures capable of achieving reduction in the degree of damage or severity of the effects or progression.
In one aspect, the invention provides a method of treatment by the use of an agent that will restore the expression of one or more differentially expressed proteins in the AD state towards that found in the normal state in order to prevent the development or progression of AD. Preferably, the expression of the protein is restored to that of the normal state.
In a further aspect, the present invention provides a method whereby the pattern of differentially expressed proteins in a sample from an individual with AD is used to predict the most appropriate and effective therapy to alleviate the neurological damage and/or dementia.
Also provided is a method of screening an agent to determine its usefulness in treating AD, the method comprising:
(a) obtaining a sample from, or representative of, a subject having AD, who or which has been treated with the agent being screened;
(b) determining the presence, absence or degree of expression of a marker protein or proteins as disclosed herein in the sample from, or representative of, the treated subject; and,
(c) selecting or rejecting the agent according to the extent to which it changes the expression, activity or amount of the marker protein or proteins in the treated subject having symptoms of AD.
Preferably, the agent is selected if it converts the expression of the differentially expressed protein towards that of a normal subject. More preferably, the agent is selected if it converts the expression of the protein or proteins to that of the normal subject.
Also provided is a method of screening an agent to determine its usefulness in treating AD, the method comprising:
(a) obtaining over time samples from, or representative of, a subject having AD symptoms, who or which has been treated with the agent being screened;
(b) determining the presence, absence or degree of expression of a marker protein or proteins as disclosed herein in said samples; and,
(c) determining whether the agent affects the change over time in the expression of the marker protein in the treated subject having AD symptoms.
Samples taken over time may be taken at intervals of weeks, months or years. For example, samples may be taken at monthly, two-monthly, three-monthly, four-monthly, six-monthly, eight-monthly or twelve-monthly intervals.
A change in expression over time may be an increase or decrease in expression, compared to the initial level of expression in samples from the subject and/or compared to the level of expression in samples from normal subjects. The agent is selected if it slows or stops the change of expression over time.
In the screening methods described above, subjects having differential levels of protein expression comprise:
(a) normal subjects and subjects having AD symptoms; and,
(b) subjects having AD symptoms which have not been treated with the agent and subjects having AD symptoms which have been treated with the agent.
Antibodies against the marker proteins disclosed herein can be produced using known methods. These methods of producing antibodies include immunising a mammal (e.g. mouse, rat, rabbit, horse, goat, sheep or monkey) with the protein. Antibodies may be obtained from immunised animals using any of a variety of techniques known in the art, and screened, preferably using binding of antibody to antigen of interest. Isolation of antibodies and/or antibody-producing cells from an animal may be accompanied by a step of sacrificing the animal.
As an alternative or supplement to immunising a mammal with a protein, an antibody specific for the protein may be obtained from a recombinantly produced library of expressed immunoglobulin variable domains, e.g. using lambda bacteriophage or filamentous bacteriophage which display functional immunoglobulin binding domains on their surfaces; for instance see WO92/01047. The library may be naive, that is constructed from sequences obtained from an organism which has not been immunised with the protein, or may be one constructed using sequences obtained from an organism which has been exposed to the antigen of interest.
The antibodies may bind or be raised against any biologically relevant state of the protein. Thus, for example, they can be raised against the unglycosylated form of a protein which exists in the body in a glycosylated form, against a more mature form of a precursor protein, e.g. minus its signal sequence, or against a peptide carrying a relevant epitope of the marker protein.
Antibodies may be polyclonal or monoclonal, and may be multispecific (including bispecific), chimeric or humanised antibodies. Antibodies according to the present invention may be modified in a number of ways. Indeed the term “antibody” should be construed as covering any binding substance having a binding domain with the required specificity. Thus, the invention covers antibody fragments, derivatives, functional equivalents and homologues of antibodies, including synthetic molecules and molecules whose shape mimics that of an antibody enabling it to bind an antigen or epitope.
Examples of antibody fragments, capable of binding an antigen or other binding partner, are the Fab fragment consisting of the VL, VH, CI and CH1 domains; the Fd fragment consisting of the VH and CH1 domains; the Fv fragment consisting of the VL and VH domains of a single arm of an antibody; the dAb fragment which consists of a VH domain; isolated CDR regions and F(ab′)2 fragments, a bivalent fragment including two Fab fragments linked by a disulphide bridge at the hinge region. Single chain Fv fragments are also included.
Antibody fragments, which recognise specific epitopes, may be generated by known techniques. For example, such fragments include, but are not limited to, the F(ab′)2 fragments which can be produced by pepsin digestion of the antibody molecule and the Fab fragments which can be generated by reducing the disulfide bridges of the F(ab′)2 fragments. Alternative, Fab expression libraries may be constructed (Huse, et al., 1989, Science 246: 1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity.
The term “monoclonal antibody” as used herein refers to an antibody obtained from a substantially homogenous population of antibodies, i.e. the individual antibodies comprising the population are identical apart from possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies can be produced by the method first described by Kohler and Milstein, Nature, 256:495, 1975 or may be made by recombinant methods, see Cabilly et al, U.S. Pat. No. 4,816,567, or Mage and Lamoyi in Monoclonal Antibody Production Techniques and Applications, pages 79-97, Marcel Dekker Inc, New York, 1987.
In the hybridoma method, a mouse or other appropriate host animal is immunised with the antigen by subcutaneous, intraperitoneal, or intramuscular routes to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the nanoparticles used for immunisation. Alternatively, lymphocytes may be immunised in vitro. Lymphocytes then are fused with myeloma cells using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell, see Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103 (Academic Press, 1986).
The hybridoma cells thus prepared can be seeded and grown in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells. For example, if the parental myeloma cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (HAT medium), which substances prevent the growth of HGPRT-deficient cells.
Preferred myeloma cells are those that fuse efficiently, support stable high level expression of antibody by the selected antibody producing cells, and are sensitive to a medium such as HAT medium.
Culture medium in which hybridoma cells are growing is assayed for production of monoclonal antibodies directed against the protein. Preferably, the binding specificity is determined by enzyme-linked immunoabsorbance assay (ELISA). The monoclonal antibodies of the invention are those that specifically bind to the protein.
In a preferred embodiment of the invention, the monoclonal antibody will have an affinity which is greater than micromolar or greater affinity (i.e. an affinity greater than 10-6 mol) as determined, for example, by Scatchard analysis, see Munson & Pollard, Anal. Biochem., 107:220, 1980.
After hybridoma cells are identified that produce neutralising antibodies of the desired specificity and affinity, the clones can be subcloned by limiting dilution procedures and grown by standard methods. Suitable culture media for this purpose include Dulbecco's Modified Eagle's Medium or RPM1-1640 medium. In addition, the hybridoma cells may be grown in vivo as ascites tumours in an animal.
The monoclonal antibodies secreted by the subclones are suitably separated from the culture medium, ascites fluid, or serum by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
Nucleic acid encoding the monoclonal antibodies of the invention is readily isolated and sequenced using procedures well known in the art, e.g. by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies. The hybridoma cells of the invention are a preferred source of nucleic acid encoding the antibodies or fragments thereof. Once isolated, the nucleic acid is ligated into expression or cloning vectors, which are then transfected into host cells, which can be cultured so that the monoclonal antibodies are produced in the recombinant host cell culture.
A hybridoma producing a monoclonal antibody according to the present invention may be subject to genetic mutation or other changes. It will further be understood by those skilled in the art that a monoclonal antibody can be subjected to the techniques of recombinant DNA technology to produce other antibodies, humanised antibodies or chimeric molecules which retain the specificity of the original antibody. Such techniques may involve introducing DNA encoding the immunoglobulin variable region, or the complementarity determining regions (CDRs), of an antibody to the constant regions, or constant regions plus framework regions, of a different immunoglobulin. See, for instance, EP 0 184 187 A, GB 2 188 638 A or EP 0 239 400 A. Cloning and expression of chimeric antibodies are described in EP 0 120 694 A and EP 0 125 023 A.
An antibody against a marker protein described herein will bind to said protein. Preferably, said antibody specifically binds said protein. By “specific” is meant that the antibody binds to said protein with an affinity significantly higher than it displays for other molecules.
Alzheimer's disease (AD) is a progressive neurodegenerative disorder, where definite diagnosis can only be made post-mortem and where the most promising biomarkers so far are found in cerebrospinal fluid (CSF). A biomarker in blood, more accessible than CSF, has industrial application and utility in aiding diagnosis, as well as in population screening applications.
Differences in plasma proteins may exist between AD patients and non-demented controls (NDC). In the examples, we used isobaric mass tagging to compare the plasma protein levels in slow and fast declining AD patients, as well as in NDC subjects in a carefully designed shotgun proteomic approach. Plasma samples were matched for age, gender and cognitive decline (change in MMSE score per year) and then pooled for analysis. Subsequent relative quantification and statistical analysis generated a list of candidate proteins able to distinguish AD from NDC groups. Selected proteins were validated by Western blot analysis in a larger sample set of 90 probable AD and 50 NDC subjects in total. In this cohort, AD patients displayed significantly lower plasma Gelsolin levels compared to NDC subjects. In addition, Gelsolin levels correlated with disease progression rate and were significantly different in slow and fast declining AD patients. Further, C1 protease inhibitor levels were found to be associated with APOE ε4 genotype and lower Ceruloplasmin levels correlated with an earlier age of onset. Gelsolin is, due to its association with progression rate in AD, as well as due to its reported interaction with amyloid β (Aβ) a robust marker of AD. Moreover, gelsolin may advantageously be further included in a panel of biomarkers, for example for use in the monitoring of treatment response or clinical drug trials.
Thus, we disclose detection of gelsolin as a surrogate marker for progression in Alzheimer's disease. In the examples, this is demonstrated using isobaric protein tagging. This is an exemplary method of detection, but in principle any suitable method of detection may be employed. The particular advantages of this specific technique are demonstrated more fully below and in the examples section.
In addition, it is a key teaching that lower plasma Gelsolin levels are found in Alzheimer's disease and show association with disease progression rate.
We demonstrate in some embodiments how a combination of isobaric mass tagging together with more conventional methods for validation can provide useful information in the development of a biomarker in AD.
Several proteins were found that either occur in different levels in plasma of AD compared to NDC and correlate with disease progression rate or that are associated with additional clinical parameters like ApoE genotype or age of onset.
The term “antibody” includes polyclonal antiserum, monoclonal antibodies, fragments of antibodies such as single chain and Fab fragments, and genetically engineered antibodies. The antibodies may be chimeric or of a single species.
The term “marker protein” or “biomarker” includes all biologically relevant forms of the protein identified, including post-translational modification. For example, the marker protein can be present in the body tissue in a glycosylated, phosphorylated, multimeric or precursor form.
The term “control” refers to a normal human subject, i.e. one not suffering from Alzheimer's disease.
The terminology “increased/decreased concentration . . . compared with a control sample” does not imply that a step of comparing is actually undertaken, since in many cases it will be obvious to the skilled practitioner that the concentration is abnormally high or low. Further, when the stages of AD are being monitored progressively, or when a course of treatment is being monitored, the comparison made can be with the concentration previously seen in the same subject at an earlier stage of progression of the disease, or at an earlier stage of treatment or before treatment has commenced.
The term “diagnosis”, as used herein, includes determining whether a patient has Alzheimer's disease and may also include determining the stage to which it has progressed (or regressed in the course of treatment). The diagnosis can serve as the basis of a prognosis as to the future outcome for the patient.
The term “valid body tissue” or “relevant tissue” means any tissue in which it may reasonably be expected that a marker protein would accumulate in relation to Alzheimer's disease. It may be a cerebrospinal fluid sample or a sample of blood or a blood derivative such as plasma or serum.
The term “antibody array” or “antibody microarray” means an array of unique addressable elements on a continuous solid surface whereby at each unique addressable element an antibody with defined specificity for an antigen is immobilised in a manner allowing its subsequent capture of the target antigen and subsequent detection of the extent of such binding. Each unique addressable element is spaced from all other unique addressable elements on the solid surface so that the binding and detection of specific antigens does not interfere with any adjacent such unique addressable element.
The term “bead suspension array” means an aqueous suspension of one or more identifiably distinct particles whereby each particle contains coding features relating to its size and colour or fluorescent signature and to which all of the beads of a particular combination of such coding features is coated with an antibody with a defined specificity for an antigen in a manner allowing its subsequent capture of the target antigen and subsequent detection of the extent of such binding. Examples of such arrays can be found at www.luminexcorp.com where application of the xMAP® bead suspension array on the Luminex® 100™ System is described.
The term “mass spectrometer-based assay” means a quantitative measurement of a target analyte using the method of multiple reaction monitoring on a triple quadrupole or ion trap mass spectrometer.
The term ‘mutant’ of a biomarker such as a polypeptide biomarker of the invention should have its normal meaning in the art. Mutants are sometimes referred to as ‘variants’ or ‘alleles’. The key is to detect biomarkers as have been set out herein. The biomarkers may possess individual variations in the form of mutations or allelic variants between individuals being studied. Therefore there may be some degree of deviation from the exemplary SEQ ID NOs provided herein. The SEQ ID NOs provided herein are to assist the skilled reader in identifying and working with the polypeptides/biomarkers of the invention and are not intended as a restricted and inflexible definition of the individual polypeptides being assayed. Thus minor sequence differences between the SEQ ID NOs provided and the actual sequences of the polypeptide biomarkers being detected will be expected within the boundaries of normal variation between subjects. This should not affect the working of the invention.
The term ‘comprises’ (comprise, comprising) should be understood to have its normal meaning in the art, i.e. that the stated feature or group of features is included, but that the term does not exclude any other stated feature or group of features from also being present.
It will be appreciated by the skilled worker that the details of the biomarkers discussed herein and in particular the sequences presented for them are given to facilitate their detection. The important information being gathered is the presence or absence (or particular level) of the biomarker in the sample being studied. There is no particular requirement that the full length polypeptide be scored. Indeed, via many of the suitable mass spectrometry based modes of detection set out herein, detection takes place by assaying particular fragments of the polypeptide of interest being present which are thus taken to indicate the presence of the overall biomarker polypeptide in the sample. Therefore the invention embraces the detection of fragments of the polypeptide biomarkers. Moreover, the kits and peptides of the invention may comprise fragments of the polypeptides and need not comprise the full length sequences exemplified herein. Suitably the fragment is sufficiently long to enable its unique identification by mass spectrometry.
Thus a fragment is suitably at least 6 amino acids in length, suitably at least 7 amino acids in length, suitably at least 8 amino acids in length, suitably at least 9 amino acids in length, suitably at least 10 amino acids in length, suitably at least 15 amino acids, suitably at least 25 amino acids, suitably at least 50 amino acids, suitably at least 100 amino acids, or suitably the majority of the biomarker polypeptide of interest. Suitably a fragment comprises a small fragment of the biomarker polypeptide of interest, whilst being long enough to retain an identifiable mass.
Although sequence homology can also be considered in terms of functional similarity (i.e., amino acid residues having similar chemical properties/functions), in the context of the present document it is preferred to express homology in terms of sequence identity. Sequence comparisons can be conducted by eye or, more usually, with the aid of readily available sequence comparison programs. These publicly and commercially available computer programs can calculate percent homology (such as percent identity) between two or more sequences.
Percent identity may be calculated over contiguous sequences, i.e., one sequence is aligned with the other sequence and each amino acid in one sequence is directly compared with the corresponding amino acid in the other sequence, one residue at a time. This is called an “ungapped” alignment. Typically, such ungapped alignments are performed only over a relatively short number of residues (for example less than 50 contiguous amino acids). For comparison over longer sequences, gap scoring is used to produce an optimal alignment to accurately reflect identity levels in related sequences having insertion(s) or deletion(s) relative to one another. A suitable computer program for carrying out such an alignment is the GCG Wisconsin Bestfit package (University of Wisconsin, U.S.A; Devereux et al., 1984, Nucleic Acids Research 12:387). Examples of other software than can perform sequence comparisons include, but are not limited to, the BLAST package, FASTA (Altschul et al., 1990, J. Mol. Biol. 215:403-410) and the GENEWORKS suite of comparison tools.
In the context of the present document, a homologous amino acid sequence is taken to include an amino acid sequence which is at least 40, 50, 60, 70, 80 or 90% identical. Most suitably a polypeptide having at least 90% sequence identity to the biomarker of interest will be taken as indicative of the presence of that biomarker; more suitably a polypeptide which is 95% or more suitably 98% identical at the amino acid level will be taken to indicate presence of that biomarker. Suitably said comparison is made over at least the length of the polypeptide or fragment which is being assayed to determine the presence or absence of the biomarker of interest. Most suitably the comparison is made across the full length of the polypeptide of interest. The same considerations apply to nucleic acid nucleotide sequences.
Alzheimer's disease (AD) is the most common neurodegenerative disorder and affects more than one in eight people over the age of 65 (Blennow et al., 2006). The disease has major financial and other burdens for national health systems and a biomarker to aid early diagnosis or the monitoring of disease progression would be of great value for the development of new treatments and in clinical practice. Considerable progress in the search for a biomarkers has been made with markers derived from the well known pathological lesions—amyloid beta (Aβ) plaques (Glenner et al., 1984) and neurofibrillary tangles (Lee and Trojanowski, 1992)—using a variety of techniques to investigate biochemical changes in the cerebrospinal fluid (CSF), blood and other tissues and fluids. The most promising sources for biomarkers in AD are the CSF or blood plasma, because compared to brain tissue, these fluids are more easily accessible and, in the case of CSF, in close contact with the central nervous system (CNS), where key biochemical changes take place. However, obtaining CSF through lumbar puncture is a relatively invasive procedure and having a biomarker from blood at hand would represent a significant advance. The inventors thus focussed on this aim.
The identification of biomarkers for AD may be addressed using the profiling of blood and CSF samples with highly sensitive methods in order to identify marker(s), i.e. proteins, peptides or metabolites, able to distinguish AD subjects and controls or to provide information about disease progression or response to treatment. Mass spectrometric methods are highly sensitive and therefore suitable for the identification of markers in all kinds of conditions and several reports have been published which used so called shotgun proteomics with isobaric tags to analyse the proteome of CSF samples (Abdi et al., 2006, Choe et al., 2007, Dayon et al., 2008) and blood samples (Hergenroeder et al., 2008) to find altered protein levels in particular diseases or disease stages.
The inventors carried out the comparison of blood from slow declining (SND) and fast declining (FD) AD patients with non-demented control (NDC) subjects. We aimed to identify 1) protein changes between SND and FD patients for disease progression markers and 2) changes between AD patients and NDC to determine proteins, characteristic for the disease pattern. The examples section presents data from samples which were investigated using isobaric protein tagging and mass spectrometry. Changes were further examined and validated by immunoblotting in a larger dataset.
It will be understood by the skilled reader that specific techniques exemplified herein may be varied if desired using readily available alternatives to achieve the same effect. For example, assay of the gelsolin levels in a blood sample may be carried out by western blot or by isobaric protein tagging or by ELISA or by any other suitable means known in the art.
Thus, in some embodiments the invention relates to a method comprising:
a) providing a sample of blood, or a sample comprising protein derived from blood, from a subject
b) optionally extracting the plasma from said blood
c) optionally processing said blood or plasma to produce a sample comprising protein derived from said blood or plasma
d) optionally depleting abundant protein(s) from said blood or plasma
e) optionally size-selecting the proteins from said blood or plasma
f) optionally stabilising the proteins from said blood or plasma
g) optionally concentrating the proteins from said blood or plasma
h) optionally adjusting the buffering of the proteins from said blood or plasma
i) assaying one or more biomarkers such as gelsolin, ceruloplasmin or C1 protease inhibitor in said sample, most suitably gelsolin
j) said assay is suitably determining the concentration or abundance of said biomarker, such as by isobaric protein tagging,
k) comparing the concentration or abundance of said biomarker in the sample from the subject to the concentration or abundance of said biomarker in a sample from a healthy subject, or to a reference sample/value.
Wherein any difference(s) identified in (k) indicate the outcomes set out herein, for example detecting reduced gelsolin levels compared to a sample from a healthy subject or a reference sample indicates increased likelihood of the subject having Alzheimer's disease.
Suitably the sample is provided in vitro. Suitably the methods of the invention are carried out in vitro. Suitably the collection of the sample is not a step of the method of the invention. In this way, suitably the invention is not practised directly on the human or animal body.
Alternatively, the method of the invention may begin with the collection of the sample such as a blood sample.
Various assay devices, kits or materials which recognise, bind to or have affinity for a polypeptide are described. The polypeptide(s) may comprise Gelsolin (Swiss prot accession number P06396; SEQ ID NO: 1). The polypeptide(s) may comprise one or more proteins selected from
C1 protease inhibitor (SEQ ID NO: 2)
ceruloplasmin (SEQ ID NO: 3)
clusterin (SwissProt accession number P10909; SEQ ID NO:4)
complement c3 (P01024; SEQ ID NO:5)
serum amyloid P component (P02743; SAP; SEQ ID NO:6)
alpha-2-macroglobulin (P01023; A2M; SEQ ID NO:7)
gamma-fibrinogen (P02679; SEQ ID NO:8)
complement factor H (P08603; CFH; SEQ ID NO:9)
apolipoprotein E (SEQ ID NO:10).
For any given polypeptide or set of polypeptides being detected by mass spectrometry based assay, the assay may be conducted via MRM techniques mentioned herein. In this embodiment, certain unique peptides and in particular certain transitions are especially advantageous to detect the peptides of interest. These are typically selected to give the highest representation (or combinations may be used such as any or all peptides giving a particular level of representation if multiple fragments/transitions give similar levels). Especially preferred transitions used for monitoring are those mentioned in the accompanying examples and/or figures.
In particular, certain peptides find utility as standards and/or controls in performing assays according to the invention. For example the following peptides are particularly useful in aiding detection of polypeptides mentioned herein:
Especially suitable are:
The peptides in this table each have the advantage of excellent performance in the mass spectrometry assays set out herein. Most preferred are SEQ ID NOs: 30, 31 and 32, which are for detection of gelsolin.
The application is now described by way of example, which examples are intended to be illustrative in nature and not to be understood as limiting the appended claims. In the examples, reference is made to the following figures:
Recent studies indicate that differences in plasma proteins levels may exist between AD patients and non-demented controls (NDC). In the current study, we used isobaric mass tagging to compare the plasma protein levels in 30 probable AD and 15 NDC subjects in a shotgun proteomic discovery experiment. Plasma samples were matched for age, gender and cognitive measures (MMSE scores) and pooled for analysis. Subsequent relative quantification and principal component analysis generated a list of candidate proteins able to distinguish the two groups AD and NDC. The most important proteins, i.e. Gelsolin, C1 protease inhibitor and Ceruloplasmin, were validated by Western blot analysis in a bigger sample set of 90 probable AD and 50 NDC subjects in total.
In this cohort, AD patients displayed significantly lower plasma Gelsolin levels compared to NDC subjects. In addition, Gelsolin levels correlated with disease progression rate and were significantly different in slow and fast declining AD patients. Further, C1 protease inhibitor levels were found to be associated with APOE £4 genotype and lower Ceruloplasmin levels correlated with an earlier age of onset. Gelsolin is, due to its changed levels and its association with progression rate in AD, as well as due to its reported interaction with Amyloid beta (Aβ), an excellent marker. Moreover, this marker should advantageously be included in biomarker panel(s) for AD
The following abbreviations have the given meanings: AD Alzheimer's disease; Aβ Amyloid β; FD Fast decliner; SND Slow/no declining Alzheimer's patients; NDC Non-demented control Alzheimer's patients; APOE Apolipoprotein E; TMT Tandem Mass Tags; (MRM Multiple Reaction Monitoring); C1 inh Plasma protease C1 inhibitor protein; CNS Central nervous system; CSF Cerebrospinal fluid; PBS-T Phosphate buffered saline including 0.01% Tween 20; TCEP Tris(2-carboxyethyl)phosphine; RT Room temperature; TFA Trifluoracetic Acid; RP Reverse Phase; SCX Strong Cation Exchange; LC/MS/MS Liquid Chromatography coupled to tandem mass spectrometry; PCA Principal component analysis; PLS-DA Partial least square discriminant analysis; ROC Response Operator Curve.
The population of the main study was derived from a largely community based population of subjects with Alzheimer's disease and elderly people [Alzheimer's Research Trust (ART) cohort] and were assessed by several cognitive measures including mini mental state examination (MMSE) scale and Alzheimer's disease assessment scale-cognitive subscale (ADAS-cog). The samples were matched for age, gender and baseline MMSE scores between groups and for age, gender and MMSE decline within groups. Samples were collected into EDTA coated glass tubes and stored at −80° C. until further analysis.
For the discovery experiment, plasma samples were analysed from FD and SND groups at baseline (year 1) and after two years (year 3); a single plasma sample was collected from each subject in the NDC group. A total of 15 samples were available per group (75 samples in total) and these were pooled into three sets each of five samples. This results in a total of 15 pools for subsequent analysis. The classification of AD samples to one of the two groups—fast decliners and slow decliners—was performed according to their decline in MMSE scores per year over two years. Samples from patients with a decline of 0-3 points per year on the MMSE scale were classified as slow declining AD patients, whereas samples from patients with an annual decline of 6 or more points on the MMSE scale were assigned to the fast declining group. The samples pooled were matched for age and gender (Table 1a). The fast decliner pools all had a mean age of 78, an average baseline MMSE score of 18-20 and a mean decline of 11 points per year on the MMSE scale. The slow decliner pools on the other hand had an average age of 80-82, a mean baseline MMSE score of 18-21 and an average decline of 2 points per year on the MMSE scale. In comparison, the pools of the NDC had an average age of 78 and were also matched in gender.
For validation purposes, a larger sample set, including the original samples, was used. In total, 90 AD patients were compared to 50 controls (Table 1b). The study was approved by the relevant research ethics committees.
In example 3, protein detection by isobaric protein labelling is demonstrated. This example explains how the sample may advantageously be prepared for such an analysis. Of course if a different analysis is used, then a different sample preparation might be chosen.
In general, sample preparation and labelling with tandem mass tags (TMT) was performed as previously described (Dayon et al., 2008) with minor modifications. To increase the number of detectable proteins, plasma was depleted of the six highest abundant proteins (albumin, transferrin, IgG, IgA, antitrypsin, and haptoglobin) with a multiple affinity removal system (MARS, 5188-5332, Agilent, Palo Alto, Calif.). 300 of pooled plasma were diluted 1:4 by the addition of 900 MARS buffer A, vortexed and spinned down for 1 min at 15,500×g. 100 μl of the supernatant was injected on a 4.6 mm×50 mm MARS column and processed according to the manufacturers instructions. The flow through fractions (1 ml) were collected and transferred to 5 kDa MWCO centrifugal filter devices (Vivaspin 4, VS0414, Sartorius, Goettingen, Germany) for buffer exchange and protein concentration. After the addition of 3 ml 100 mM triethylammonium bicarbonate (TEAB) pH 8.2, the tubes were centrifuged at 2,000×g at 4° C. for 30 min. Subsequently, 3 ml of TEAB were added and centrifuged for 30 min, another 3 ml of TEAB were added and centrifuged for 60 min until the remaining volume was between 50-100 μl. The volume was adjusted to 150 μl and the protein content of each plasma pool was determined with a conventional Bradford assay (Protein Assay, Bio-Rad, Hercules, Calif.).
In principle, protein detection may be by any suitable means known to the skilled reader. The Isobaric Protein Tagging technique is now described by way of example.
To ensure equal protein amounts, 100 μg of protein per sample were transferred to a new tube, 5 μl 2% SDS in H2O (w:w) were added and filled up to 100 μl with 100 mM TEAB. 5.3 μl 20 mM Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) in H2O were added and incubated for 30 min at room temperature (RT). Afterwards, 5.5 μl 150 mM iodoacetamide in acetonitrile (ACN) were added and incubated in the dark for 60 min at RT. Subsequently, 104 of freshly prepared trypsin (Seq. grad modified trypsin, Promega, V5111, Madison, Wis., USA) at 0.4 μg/μl in 100 mM TEAB were added and incubated overnight at 37° C.
The 15 plasma pools were split for analysis into three individual experiments (biological replicates), whereas one of these experiments was repeated three times for technical replication. In each of the three individual experiments, the plasma pools were labelled with 60 mM TMT reporter ions (Proteome Sciences Plc, London, UK) in 40.3 μl ACN for 1 hour at RT as follows: m/z 126.1: FD year 1, 127.1: FD year 3, 128.1: SD year 1, 129.1: SD year 3, 130.1: NDC, 131.1: Dade Behring reference plasma. The Dade Behring plasma was analyzed in all experiments to enable inter-experimental comparison. After incubation, 8 μL of 5% hydroxylamine in H2O (w/v) was added to each tube and mixed for 15 min. The six samples were pooled into a new tube and diluted 1:6 with 5% ACN 0.1% trifluoroacetic acid (TFA) in H2O for reduction of ACN content.
In this example the tagged proteins are detected using mass spectrometry (MS). To avoid negative effects of excessive reagents and high salt content in the MS analysis, the samples were manually purified and desalted on a vacuum manifold (Thames Restek UK Limited, 26077, Saunderton, UK) with reverse phase (RP) columns (Waters Corporation, Oasis HLB cartridge, WAT094225, Milford, Mass., USA) followed by strong cation exchange (SCX) columns prepared from empty cartridges (Macherey-Nagel GmbH & Co KG, 732501, Dueren, Germany) and sepharose suspension (Sigma-Aldrich, SP Sepharose Fast Flow, S1799-100ML, St. Louis, Mo., USA). The eluted sample was lyophilised in a speed vac, dissolved in 2 ml H2O, evacuated to dryness again and stored at −80° C. until further analysis.
For LC/MS/MS analysis, the samples were reconstituted in 100 μl of 50 mM ammonium bicarbonate buffer for 10 min at 37° C. Following, the samples were further diluted (1:60) in ammonium bicarbonate to an approximate concentration of 0.1 μg/μl.
Reversed-phase chromatography was performed using an Ultimate LC system (Dionex, Camberley, UK). Peptides were resolved on a C18 PepMap column (75 μm I.D.) using a three-step linear gradient of 0-48% ACN/0.05% formic acid over 120 min at a flow rate of 200 nL/min. Peptides were ionised by electrospray ionisation using a Z-spray source fitted to a QTof-micro (Waters Ltd, Elstree, UK) operating under Masslynx v4.0 software. The instrument was run in automated switching mode, selecting precursor ions based on their intensity and charge state for sequencing by collision-induced fragmentation. MS/MS was performed using collision energy profiles based on mass/charge (m/z) ratios and optimised for the fragmentation of TMT-labelled peptides. Raw data were recalibrated against internal complement C3 peptides and processed into peak lists using ProteinLynx Global Server v2.2.5 with the following MS/MS processing parameters: smoothing by Savitzky-Golay method, 2 iterations, 4 channels; peak centroiding top 80%, no deisotoping or background subtraction.
Proteins were identified in each TMT experiment by searching the MS peak list data against the IPI human database (release v3.32) as a single search using Mascot (v2.2; http://www.matrixscience.com/). The following parameter specifications were employed: precursor ion mass tolerance 150 ppm, fragment ion mass tolerance 0.6 Da, tryptic peptides with up to three missed cleavages, variable modifications: carbamidomethylation of cysteine, methionine oxidation and TMT labelling of epsilon-amino functions of lysine residues and the peptide N-terminus. The resulting Mascot file contains information about the proteins identified and can be used for manual inspection of the spectra. The peak list files were also processed using TiTRE (v1.6), an in-house developed software, to extract the reporter ion data. This was subsequently associated with the Mascot search results.
Search results were processed to report only assignments with an MS/MS ion score>20 and a rank one sequence assignment. For Mascot MS/MS ion searches, a rank one assignment is the highest scoring sequence match for an MS/MS query. These peptide assignments were evaluated for ‘uniqueness’, i.e. if the assigned sequence only occurred within that protein the assignment was ‘unique’, or if the assigned sequence also was present in other proteins the assignment was ‘non-unique’. Protein hits that were assigned with less than two unique peptides scoring above the Mascot identity score (typically ˜40), which corresponds to a 5% chance of false positive peptide assignment, were validated by manual inspection of the mass spectra for the assigned peptides.
The reporter ion intensities were each expressed as a ratio to the reference plasma standard and converted to log 10 values. Data were normalised by subtracting the median value of the log 10 reporter ion ratios (a global normalisation factor) from each individual value such that median of the normalised log 10 reporter ion ratios was zero.
From previous experience, the minimum threshold at which reporter ion intensities could be reliably determined using the Qtof micro instrument was 40 counts. Below this threshold, the observed protein ratios are not representative of the actual ratios due to poor ion statistics. For this reason, peptides with reporter ion intensities in the reference plasma of below 40 counts were excluded from quantitation. Additionally, peptides that were incompletely labelled with TMT and those containing methionine were removed from the data set. Assignments corresponding to incomplete TMT labelling and/or containing methionine residues were observed to quantitate differently from the main population of assignments and were often not representative of the actual differences in protein amounts. In the latter case, the reporter ion ratios appeared to track differential methionine oxidation between the samples.
The normalised data sets were joined such that proteins identified in different biological replicate experiments were aligned.
The aligned data sets from example 5 were imported into SIMCA-P software (version 11.5). All variables (mean log 10 reporter ion ratios for each protein) were scaled to unit variance and variables with more than 50% of values missing were excluded from the analyses. Initially, the data were summarised using principal components analysis (PCA) to check the presence of strong outliers or other issues in the data set that would need to be addressed. Subsequently, partial least squares—discriminant analysis (PLS-DA) was used to identify proteins that differed between the groups.
To investigate the plasma proteome of slow and fast declining AD patients and of non-demented controls, 15 samples per group, pooled into 3 sets each, were labelled with isobaric protein tags and analyzed by mass spectrometry. A total of 2365 queries were matched to peptide sequences across all five experiments. These peptides related to a total of 152 unique protein sequences. After removal of proteins with more that 50% of the measurements missing, a total of 52 identified proteins had quantitative data available for analysis (Table 2). Multivariate analysis (PLS-DA) was then used to attempt to discriminate the different groups using the mean relative protein concentration data. Following model fitting, cross validation indicated that significant components could not be fitted to data sets containing SD year 1 or year 3 and NDC observations.
A three component model was fitted to the FD year 1 and NDC data set explaining 99.5% of variance in the class data (R2Y).
The proteins most important for discrimination of FD and NDC are highlighted in Table 1. The relative importance of these proteins was judged based on the PLS regression coefficients in the previously described models.
As noted throughout the application, isobaric protein tagging is only one way in which detection of the markers of the invention may be executed. For validation of the data obtained by isobaric protein tagging, selected proteins were analysed by Western blotting in a larger sample set. Plasma samples were diluted as follows: 4 μl raw plasma, 96 μl of PBS containing protease inhibitor cocktail (Complete®, 1836145, Roche Applied Science, Penzberg, Germany) and 100 μl of 2× sample buffer (Laemmli, S3401, Sigma), heated to 100° C. for 5 min, spun down at 15,500×g and separated on SDS polyacrylamide gels (NuPAGE® Novex 4-12% Bis-Tris Midi Gel, 26W, Invitrogen, Carlsbad, Calif., USA). After transfer to 0.2 μm nitrocellulose membranes (Schleicher & Schuell, BA-S 83, Keene, N.H., USA) blots were blocked with 5% non-fat milk in 0.1% PBS-Tween (PBS-T) and probed with antibodies to Ceruloplasmin (ab8813, 1:50000, Abcam, Cambridge, UK) C1 protease inhibitor (ab36992, 1:2000, Abcam) and Gelsolin (ab55070, 1:500, Abcam). Primary antibodies were detected with appropriate secondary antibodies (dilution: 1:10000) conjugated to fluorophors, emitting at wavelengths of either 700 or 800 nm, using a near infrared Odyssey imager (Licor, Lincoln, Nebr., USA). Densitometric analysis was performed using the Odyssey software v2.1.
All samples were run in duplicates and, for adjustment of intensities, a reference plasma sample was run on each gel. Equal volumes of plasma were subjected to immunoblot and subsequent quantitative densitrometry. The ratio of every sample with the reference plasma was build to allow inter-gel quantitative comparisons and the duplicate runs were averaged. When assessing the reproducibility of the duplicate gels, a large positive correlation of 0.84 was found by performing a Pearson correlation. The results were tested for significance by student's t-test using the statistical software program SPSS v15.0. In addition, a response operator curve (ROC) analysis was performed to assess sensitivity and specificity.
In order to confirm the proteomic data, from example 6, selected proteins were analysed by Western blotting to investigate the difference between AD and NDC samples found in the multivariate analysis. A high absolute value of a PLS coefficient indicates a high relative importance of a certain protein in separating respective groups. Therefore we selected 3 proteins—Gelsolin, C1 protease inhibitor (C1 inh) and Ceruloplasmin—with the highest PLS coefficient values (Table 2) for further validation in a larger data set. The data set consisted of the samples used for the initial study and of additional samples to give a total of 90 AD and 50 NDC samples to be compared.
The results were tested for significance using student's t-tests and a highly significant reduction of Gelsolin (p=0.001) levels in plasma from AD patients could be confirmed (
In addition, a ROC analysis for Gelsolin was performed. The area under the curve was highly significant (p=0.001), but the protein did not show favourable test characteristics: Setting specificity at 80% gave a sensitivity value of 44%, whereas setting the sensitivity value to 80% resulted in a specificity value of 39%.
The inventors disclose the first analysis of unfractionated plasma with isobaric protein tags in Alzheimer's disease.
Moreover, using tandem mass tags in a shotgun proteomics discovery experiment, we were able to identify several proteins able to differentiate fast declining Alzheimer's patients and non-demented controls. Selected candidate proteins were validated in a larger dataset with quantitative Western blotting. It was shown that plasma levels of Gelsolin were decreased in AD compared to controls and that the levels also differ between fast and slow declining AD patients. Most important, Gelsolin levels correlated with disease progression.
In addition, C1 protease inhibitor levels were found to be associated with APOE ε4 genotype and lower Ceruloplasmin levels correlated with an earlier age of onset.
Biomarkers for Alzheimer's disease (AD) are urgently needed. Recent studies indicate that differences in plasma proteins levels exist between AD patients and non-demented controls (NDC) suggesting the possibility of a peripheral biomarker for AD. In the current study, we used isobaric mass tagging to compare the plasma protein levels in 30 probable AD and 15 NDC subjects in a shotgun proteomic approach. Plasma samples were matched for age, gender and cognitive measures (MMSE scores) and pooled for analysis. Subsequent relative quantification and principal component analysis generated a list of candidate proteins able to distinguish the two groups AD and NDC. The most important proteins, i.e. Gelsolin, C1 protease inhibitor and Ceruloplasmin, were validated by Western blot analysis in a bigger sample set of 90 probable AD and 50 NDC subjects in total. To further validate some of the findings, multiple reaction monitoring (MRM), a method, which is not only highly specific but also has a very high sensitivity, was used to analyze a subset of samples. In summary, AD patients displayed significantly lower plasma Gelsolin levels compared to NDC subjects. In addition, C1 protease inhibitor levels were found to be associated with ApoE epsilon4 genotype and lower Ceruloplasmin levels correlated with an earlier age of onset. Gelsolin is, due to its changed levels in AD, as well as due to its reported interaction with amyloid beta (Abeta) a highly interesting protein with regards to AD and needs further evaluation.
A general method is shown in
A total of 2365 queries were matched to peptide sequences across all experiments. These peptides related to a total of 152 unique protein sequences. Including only proteins detected in more than 50% of the experiments, a total of 52 identified proteins had quantitative data available for analysis. Multivariate analysis (PLS-DA) generated a list of candidate proteins (Table 1—
Table 1 (
In order to confirm the proteomic data, selected proteins were analysed by Western blotting to investigate the change between AD and NDC extracted by multivariate analysis. Therefore we selected 3 proteins—Gelsolin, C1 protease inhibitor and Ceruloplasmin—with the highest PLS coefficient values (Table 1; bold) at baseline and two years follow-up respectively for further validation in a larger data set. The data set consisted of the samples used for the initial study and of additional samples to give a total of 90 AD and 50 NDC samples to be compared. The results were tested for significance using independent samples t-Test. For the first time, a highly significant reduction (p=0.001) of Gelsolin levels in plasma from AD patients could be established (
In addition, a Response Operator Characteristic (ROC) analysis for Gelsolin was performed (
Use of Gelsolin as a biomarker is merited given its apparent changes in plasma between AD and control subjects, and its previously reported interaction with Ab (Chauhan et al., 1999, Ray et al., 2008).
A number of plasma proteins including gelsolin have emerged as candidate AD biomarkers from discovery exercises. Assays are required for the validation of these candidates; SRM-based approaches are an attractive alternative to ELISAs due to the sensitivity and selectivity of the technique, the capacity to multiplex and the limited availability of antibodies. Here, signature peptides unique to the protein of interest are measured to provide quantitative information of that protein in the sample. Accuracy in the quantitation of the analytes of interest by SRM can be improved by combining with TMT as this allows the incorporation of an internal reference into the analysis. Initial results have demonstrated TMT SRM as an accurate and reproducible method of peptide quantitation. We now move to provide a full TMT SRM assay allowing the evaluation of eight candidate biomarkers in AD and control plasma samples.
Using existing MS/MS data, at least three peptides per protein were selected for quantitation and the representative peptides for Gelsolin are shown in
All peptides were observed in the plasma sample by TMT SRM at varying intensities. To achieve accurate quantitation of each candidate peptide, it was necessary to establish whether there was significant contribution of non-specific signal from the plasma, when no reference peptides were added. TMTzero-labeled plasma was analysed over all TMTzero and TMTsixplex transitions. Signals observed from any TMTzero SRM transitions represented non-specific background. Those transitions which had significant background were subsequently removed from the method.
The establishment of specific and sensitive biomarkers for Alzheimer's disease (AD) is required to assist in the diagnosis and monitoring of disease progression. From discovery exercises, clusterin (SwissProt accession number P10909), complement c3 (P01024), serum amyloid P component (P02743; SAP), alpha-2-macroglobulin (P01023; A2M), gelsolin (P06396), gamma-fibrinogen (P02679) and complement factor H (P08603; CFH) were found to be differentially expressed in an AD versus control samples Additionally, possession of the apolipoprotein e4 allele is the only unequivocal genetic risk factor known to date for late-onset AD and expression of the apolipoprotein E (P02649; ApoE) protein may be altered in AD. These proteins present as potential candidates for which progression of the disease may be monitored. This example details the application of a Tandem Mass Tag Selected Reaction Monitoring (TMT-SRM) assay to a clinical sample cohort (n=20; 10 Alzheimer's disease (AD), 10 controls). The aims of the study were firstly, the validation of western blot (WB) findings for one of the proteins, gelsolin (found to be decreased in AD patients versus control) using an orthogonal technology (TMT SRM) and secondly, to assess the performance of the remaining proteins in an AD cohort by TMT SRM.
Samples were selected based on WB measurements for gelsolin. To give the best chance of detecting a difference between disease and control by TMT-SRM, those samples which showed the highest and lowest concentrations of gelsolin (n=10 per group) were carried forward for analysis.
Existing MS/MS spectra of TMT-labeled plasma datasets, including those from discovery exercises, were mined to determine the most suitable peptides for candidate biomarker validation by SRM. At least three peptides per protein candidate were selected for quantitation (32 in total), 16 of which were observed in discovery exercises. The criteria for the selection of these peptides for SRM were; good high mass fragment ions, no missed cleavages with trypsin, no variable modifications (in-vivo or experimental). Due to the poor endogenous detection and the poor accuracy, precision and reproducibility when plotting previous calibration curves, several of the peptides were removed from the method. This left 22 peptides to be quantitated in this part of the study.
Synthetic versions of each peptide were prepared in-house to act as a reference for quantitation. Previous results demonstrated a variation in the amounts recovered from peptides of the same protein. In order to minimise such variation, peptides of the same protein were combined in an equimolar mixture (62 nmoles/peptide; 8 mixtures in total) prior to TMT-labeling. Each mixture was processed using a typical TMT-SRM workflow consisting of reduction, alkylation, trypsin digestion and chemical labeling of individual samples with TMT. Mixtures were labeled with light TMT (to act as an internal standard for the generation of reverse calibration curves in plasma) and heavy TMT (used for the generation of a reverse calibration curve in plasma and for use as an internal standard for quantitation of the experimental sample set). Both mixtures underwent subsequent purification by solid-phase extraction and strong cation exchange using volatile buffers.
An equal volume of each plasma sample (25 ul) was removed from the stock and diluted 10-fold. From this, 12.5 ul was added to each digestion to give approximately 100 ug of protein per digest. Additionally, a pool of all samples (100 ug per sample; 2 mg of protein in total) was prepared for preparation of calibration curves and for quality control purposes. Following solubilisation with SDS and dilution each sample was reduced, alkylated and digested with trypsin. Samples were labeled with light TMT prior to purification by solid-phase extraction and strong cation exchange using volatile buffers. Samples were lyophilised prior to MS analysis. All samples were processed in triplicate (technical repeats).
SRM analysis was performed on a 4000 QTRAP mass spectrometer (Applied Biosystems) coupled to an Ultimate3000 LC system (Dionex). The mass spectrometer was fitted with a micro-ion spray source for micro litre flow rates, operated in positive ion mode and Q1 and Q3 resolution was set to unit (0.7 FWHM). Peptides were resolved by reversed phase chromatography using a Hypersil gold column (1 mm i.d.×50 mm; 1.9 μm, Thermo Fisher Scientific), over a 14 min gradient of 5-30% ACN/0.2% formic acid at a flow rate of 100 μL/min. Washing and equilibration of the column increased the total run time to 20 min.
Labeled peptides were directly infused into the QTRAP MS and in the first instance selected for MS/MS fragmentation. Optimal MS/MS fragment ions (three) were chosen for each peptide to facilitate maximum detection and specificity of each transition in Q3. All peptides were then measured by SRM by direct infusion using the selected Q3 transitions. The sensitivity of detection of each SRM was further optimised by tuning the collision energy, declustering potential and collision cell exit potential. Peptides were analysed by LC-SRM to define accurate retention times. The final SRM method applied to the analysis of the samples had a SRM scheduling window of 45 sec, 1 sec cycle time, >20 ms dwell time/transition with 5-10 data points at FWHM.
Samples were resuspended in 333.33 μL of 3% ACN/0.2% formic acid. For each individual analysis, 100 ul was aliquoted into a microtitre plate well and lyophilised. All samples were processed in triplicate (analytical repeats). Immediately prior to analysis, samples were resuspended in 25 ul of heavy TMT-labeled peptides (5 fmoles/ul; 100 fm on column). This concentration of sample ensured good detection of the target analyte with no carry-over taken into subsequent runs. Sample (23 μl) was injected on column using a full loop injection (
The experimental samples were analysed in three consecutive sets of 60 samples to provide three analytical repeats. In each set of 60 the run order was shuffled to exclude run-time and run order bias and to ensure that a particular sample was not preceded and followed by the same sample twice. A calibration curve was run immediately prior to running a set of 60 samples with two extra curves ran after the full sample set was completed (five in total). Prior to the analysis of the sample set system checks were undertaken to ensure the MS and LC were performing with optimal sensitivity, mass accuracy, calibration and ion stability. During the analysis of the sample set a reference sample was acquired multiple times to ensure LC-SRM performance was maintained.
SRMs were visualised through Analyst's quantitation wizard (Applied Biosystems). All peak matching was visually verified and peak areas were exported into Microsoft Excel. Transitions were excluded if there was poor peak definition from the background signal. The peak area for each light-labeled transition (experimental plasma sample or pooled plasma sample for quality control) was measured relative to the peak area of the corresponding heavy-labeled transition (synthetic peptide; reference sample). These ratios (L/H) for each transition pair were taken forward for quantitative analysis.
The experimental design was hierarchical (nested) with transitions nested within peptides nested within digests and three replicate measurements made for each digest. We chose an approach to analysis that would give a realistic estimate of the 95% confidence interval, taking into account the variance attributable to all factors in the hierarchy. Three-way analysis of variance was used to separate and estimate the different sources of variation and these were then recombined to give an estimate of the variance of the mean. The variance of the mean was used to estimate the standard error and this, together with a value from the t-distribution was used to estimate the 95% confidence interval around the grand mean.
Gelsolin measurements were correlated to WB results by calculating the Spearman coefficient for each gelsolin peptide (L/H ratio) in each sample, as compared to the corresponding WB sample measurement.
Table shows Gelsolin levels as determined by WB for disease (AD) and control (CTL) samples. High and low gelsolin levels were specifically selected to give the best chance of detecting a difference by TMT-SRM. It can be seen from the mean values of each group that there is ˜4-fold reduction in gelsolin levels in AD as compared to controls.
3.1 Removal of Transitions and Peptides which May Result in Inaccuracies in Quantitation
Transitions were removed from the data analysis if they had poor peak detection or possessed high plasma background (
Four gelsolin peptides were originally included in the method (peptides 27, 29, 30 and 31). Peptide 27 had poor peak detection and so was removed from the data analysis. The remaining three peptides performed similarly, showing a reduction in gelsolin levels of −30% in AD as compared to the control samples (see
From a total of four peptides, two clusterin peptides (peptides 3 and 6) were removed from the data analysis due to poor peak detection. The two remaining peptides cover both the clusterin alpha-chain (peptide 1) and beta-chain (peptide 5). Both peptides show no significant change between AD and control samples (see
The two complement c3 peptides (peptides 8 and 9) showed a similar increase in AD as compared to control subjects (see
One of the CFH peptides (peptide 11) had poor peak detection and was removed from the data analysis. The two remaining peptides (peptides 12 and 13) showed a similar increase in AD as compared to control subjects (see
The two A2M peptides (14 and 15) performed similarly, showing no significant change between AD and control subjects. Previous discovery exercises showed an increase in A2M in AD as compared to controls (see
A high variance was observed one peptide (peptide 18) for all measurements across all samples and so was removed from the data analysis. Gamma-fibrinogen peptides 19 and 20 both showed an increase in AD as compared to controls (see
The two SAP peptides (peptides 22 and 23) showed a similar increase in AD as compared to control subjects (see
The two ApoE peptides (24 and 25) performed similarly, showing no significant change between AD and control subjects (see
The results demonstrate the performance of TMT SRM as a tool for the relative quantitation of candidate biomarkers of AD. Removal of those peptides which had poor peak detection resulted in improved statistics. Peptides of the same protein showed similar differences in AD and control samples, with low variance across all samples (95% CI). The comparison of AD and control samples for the majority of peptides was in agreement with discovery exercises. TMT SRM of gelsolin was found to be highly correlated to WB results. Following on from this, calibration curves will be incorporated into the analysis to calculate the endogenous amounts of each peptide in each sample. Additionally, the dataset will be normalised to a reference sample to account for the differences observed in the L/H ratios of peptides of the same protein. The results demonstrate the good performance of TMT SRM for the relative quantization of a small sample set. Larger cohorts may be quantitated to give in the same manner.
All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described aspects and embodiments of the present invention will be apparent to those skilled in the art without departing from the scope of the present invention. Although the present invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are apparent to those skilled in the art are intended to be within the scope of the following claims.
| Number | Date | Country | Kind |
|---|---|---|---|
| 0901232.9 | Jan 2009 | GB | national |
| 0904209.4 | Mar 2009 | GB | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/GB2010/000107 | 1/26/2010 | WO | 00 | 12/8/2011 |
