Patent Application
20240319203
The present invention relates to a method to determine hyperphosphorylated Tau, and in particular Tau phosphorylated on the Serine residue in position 396 (S396) of Tau, in human cerebrospinal Fluid (CSF) using a trypsin digestion and a Liquid Chromatography/Mass Spectrometry workflow (LC-MS).
A method to follow progression of Tau pathology in Tau pathologies such as Alzheimer's disease (AD) or Down's syndrome can be of great relevance in order to diagnose patients or monitor their disease stage. Currently there is great clinical need for diagnostic and predictive biomarkers, as well as biomarkers for classification purposes, to identify patients in the early stages of Tau pathology, such as seen for patients with mild cognitive impairment (MCI) who may later progress to AD.
Promising cerebrospinal fluid (CSF) biomarker candidates are total Tau protein and phosphorylated Tau protein (pTau) which may prove to have sufficient diagnostic accuracy and predictive power. The present inventors have developed an assay that is able to detect hyperphosphorylated Tau using Tau protein phosphorylated at serine 396 (pS396) and has shown that this analysis/biomarker can show effect of e.g. antibody treatment in transgenic mouse expressing high levels of human Tau and Taupatology.
The inventors of the present invention have found a reliable method of measuring pS396-Tau using a method that takes advantage of the fact that trypsin does not cleave after amino acid Lysine 395 when Tau is phosphorylated at Serine 396 (pS396), which is a hall mark in hyperphosphorylated Tau phathology. Hence only a Tau protein which is not phosphorylated at this site will be cleaved by Trypsin and will yield the peptide SPVVSGDTSPR (SEQ ID NO: 1), where S is the unphosphorylated S396 serine.
The Tau protein is a highly complex structure consisting of (at least) 6 proteoforms (ranging from 352 to 441 amino acids and containing more than 80 possible sites for post-translational modifications (PTMs). The heterogenous structure is a challenge for mass spectrometric analysis of the protein, since the mass of the signature peptide of interest may vary depending on possible PTMs.
In this invention, the signature peptide of interest contains Serine 396. The cleavage points of Trypsin are the carbonyl (C) side of the amino acids Lys (K) and Arg (R), except if the following amino acid is phosphorylated. Hence, for analysis of pS396-Tau, tryptic cleavage yields the signature peptide TDHGAEIVYK[p]SPVVSGDTSPR (SEQ ID NO: 2). However, this peptide may (or may not) be phosphorylated on the amino acids T386, Y394, S400, T403 and S404. The various possible combinations of these phosphorylations result in hundreds of different peptides, which will each have a specific chromatographic retention time and/or molecular mass for LC-MS analysis. If direct quantitative analysis of the signature peptide containing pS396 were to be performed using LC-MS, it would require quantification of each individual variation of phosphorylated peptide. This approach would require extensive analytical work, and more important, the analytical signal for pS396 would be “diluted” into these various peptides. Since the expected concentrations of pS396 in human CSF are in the low pM range, the requirements for sensitivity of the mass spectrometer will likely be a limitation if applying such a direct analysis.
Therefore, an aspect of the invention lies in the tryptic digestion of the sample obtained from CSF. In this invention an indirect analytical approach is applied that allows the analysis to be focused on a single human Tau derived peptide SPVVSGDTSPR [aa 396-406] (SEQ ID NO: 1).
The method takes advantage of the fact that phosphorylation on S396 prevents trypsin from cleaving the protein chain at this position, and tryptic digestion of S396-phosphorylated Tau protein will therefore yield the peptide TDHGAEIVYK[p]SPVVSGDTSPR (SEQ ID NO: 2). Hence only Tau protein not phosphorylated at S396 will be cleaved by Trypsin in the first workflow and yield the peptide SPVVSGDTSPR (SEQ ID NO: 1) (after removing all possible phosphorylations with phosphatase treatment). Hence the workflow 1 analysis of SPVVSGDTSPR corresponds to the amount of unphosphorylated S396.
In workflow 2 a second tryptic digest is applied. The peptide SPVVSGDTSPR (SEQ ID NO: 1) will be unaffected of this treatment, whereas TDHGAEIVYKSPVVSGDTSPR will now be cleaved between amino acids Lysine 395 and Serine 396 since the peptide is no longer phosphorylated at Serine 396 (removed by the phosphatase treatment). Hence the second tryptic digest yields additional amounts of SPVVSGDTSPR and the workflow 2 analysis corresponds to the sum of unphosphorylated S396 and phosphorylated S396 (equivalent to total amount of Tau).
The difference of the amount of SPVVSGDTSPR [396-406] (SEQ ID NO: 1) measured in workflow 1 and workflow 2 hence equals the amount of Tau protein originally phosphorylated at S396 (pS396-Tau).
The present invention relates to a method of measuring pS396 Tau in a CSF sample comprising the steps of
The method can be used in diagnosing a patient with a Tau pathology or monitoring the disease of a patient with a Tau pathology. Alternatively, it's believed that the method can be used to monitor the treatment effect of patients with a Tau pathology.
Top panes (A+B) show the analytical peaks after first tryptic digest and dephosphorylation: A: The analytical peak for TDHGAEIVYKSPVVSGDTSPR correspond to Tau phosphorylated on S396 (miscleavage) whereas B: SPVVSGDTSPR correspond to Tau not phosphorylated on S396.
The bottom panes (C+D) show analytical peaks obtained after second tryptic digest: C: TDHGAEIVYKSPVVSGDTSPR is not detectable as this is now cleaved at the Lysine 395 site (S396 is no longer phosphorylated). D: The analytical peak for SPVVSGDTSPR increases with an area corresponding the peak in pane A. This additional area corresponds to the amount of Tau phosphorylated at S396 (pS396).
In the control antibody treated mice, it can be observed that the measured concentrations of tau(396-406) and pS396 is higher in the old compared to young mice. Furthermore, in the old mice (with Tau pathology) a dose dependent reduction of tau(396-406) and pS396 is observed after treatment with anti-Tau hIgG.
The present invention relates to an assay measuring the amount of Tau phosphorylated at the Serine residue S396 (pS396) in a human cerebrospinal fluid (CSF) sample. The aim is to get a measure of hyperphosphorylated Tau in the CSF of subjects by measuring pS396, particular in subjects where a diagnosis is desired or where the effect of a treatment is to be determined or monitored. These subjects are suffering or suspected to be suffering from a Tau pathology such as Alzheimer's disease (AD) and Down's Syndrome.
The inventors of the present invention have used analysis of pS396 Tau as an indirect measure of hyperphosphorylated Tau in CSF. By using a tryptic cleavage step, the inventors of the present invention have taken the advantage of trypsins inability to cleave Tau just before the Serine residue 396 (S396) in Tau when phosphorylated.
An aspect of the invention therefore lies in the tryptic digestion of the sample obtained from CSF. If Tau is unphosphorylated at the position S396 trypsin can cleave just before residue S396 and generate a peptide SPVVSGDTSPR [amino acids 396-406]. This fragment is dominant in e.g. healthy subjects without Tau pathology. During the disease stages of a Tau pathology (e.g. AD), Tau will become hyperphosphorylated and the residue S396 will also be phosphorylated. Phosphorylation at S396, generating pS396, will block trypsin's ability to cleave, and tryptic digestion will therefore not give the signature peptide SPVVSGDTSPR. Instead, it will yield a larger peptide TDHGAEIVYKSPVVSGDTSPR.
In one aspect, the invention relates to a method comprising the steps of
The measured SPVVSGDTSPR in step ii) above will measure the portion of SPVVSGDTSPR corresponding to unphosphorylated S396 in the CSF sample, because trypsin is only able to cleave between amino acids Lysine 395 and Serine 396 if Serine 396 is unphosphorylated.
In step iii), a second tryptic digest is applied after the dephosphorylation step in step ii). The portion of phoshorylated and uncleaved Tau peptide TDHGAEIVYKSPVVSGDTSPR from step i) will now be cleaved between amino acids Lysine 395 and Serine 396 since Tau is no longer phosphorylated at Serine 396. Hence the second tryptic digest yields additional amounts of SPVVSGDTSPR corresponding to the sum of unphosphorylated S396 and phosphorylated S396 (total amount of Tau).
Further, the difference of the amount of SPVVSGDTSPR measured directly after step i) (unphosphorylated S396) and the amount of SPVVSGDTSPR measured after the second digestion in step iii) (total Tau) is the amount of Tau protein phosphorylated at S396. IGSTENLK [260-267] serves as a reference peptide since this peptide does not contain any phosphorylation sites, and the same concentrations should be measured before and after the second tryptic digest step. This serves as a confirmatory peptide for measurement of the total concentration of Tau protein.
The trypsin digested peptides in step i) are subjected to a solid phase extraction (SPE) prior to dephoshorylation treatment in order to remove residues of trypsin prior to the dephosphorylation step (to avoid cleavage at S396 when phosphorylation is removed). Prior to dephosphorylation, pH is adjusted to 5.5. At this pH the enzymatic activity of trypsin is minimized whereas the activity of Lambda Protein Phosphatase (λPP) is maintained. In step v) a suitable method for analysis of Tau protein in the above-described assay can be an LC-MS analysis of peptides, Tau(396-406) and Tau(260-267).
The method according to the invention can be used to assess or monitor the Tau pathology of a subject such as a mammal (mouse or monkey) and in particular a human.
The Tau pathology can be seen in many diseases such as Alezheimer's Disease, Down's Syndrome, Argyrophilic Grain Disease (AGD), Psychosis, particularly Psychosis due to AD or Psychosis in patients with AD, apathy due to AD or apathy in patients with AD, psychiatric symptoms of patients with Lewy body dementia, Progressive Supranuclear Palsy (PSP), Frontotemporal dementia (FTD or variants thereof), TBI (traumatic brain injury, acute or chronic), Corticobasal Degeneration (CBD), Picks Disease, Primary age-related Tauopathy (PART), Neurofibrillary tangle-predominant senile dementia, Dementia pugilistica, Chronic traumatic encephalopathy, stroke, stroke recovery, neurodegeneration in relation to Parkinson's disease, Parkinsonism linked to chromosome, Lytico-Bodig disease (Parkinson-dementia complex of Guam), Ganglioglioma and gangliocytoma, Meningioangiomatosis, Postencephalitic parkinsonism, Subacute sclerosing panencephalitis, Huntington's disease, lead encephalopathy, tuberous sclerosis, Hallervorden-Spatz disease and lipofuscinosis. It is envisaged that the method disclosed above, can be used for diagnosing a patient with a Tau pathology, such as Alzheimer's or Down's syndrome. Further, it is believed that the method will also be useful for monitoring the disease of a subject with a Tau pathology.
It is further envisaged that the method disclosed above, can be used for monitoring the treatment effect in a subject with a Tau pathology, such as Alzheimer's or Down's syndrome. In particular, it is believed that the method is useful to monitor any treatments that may be targeting the Tau pathology such as anti-Tau antibody treatment.
Lambda Protein Phosphatase (λPP, 50 μL of 400 000 units/mL) and 10 mM Manganese(II)chloride (1 mL of 10 mM MnCl2) was obtained from Bioke.
Sep-Pak® tC18 100 mg 96-well SPE plate was obtained from Waters, US. Phosphatase inhibitor cocktail Ill was obtained from Sigma Aldrich.
Trypsin (from porcine pancreas, T0303) was obtained from Sigma Aldrich Trypsin inhibitor was obtained from Sigma Aldrich
Human CSF obtained from BioIVT or PrecisionMed
Mouse CSF obtained from own laboratory. CSF sampled from rtg4510 mice expressing human ON4R tau harbouring a disease associated mutation P301L.
Following Reagents are Prepared Freshly During Sample Preparation. Details of Preparation are Described Under Sample Preparation:
Stock solution 15N-Tau protein (1.00 mg/mL) (=21.6 μM, MW=46353.2 g/mol)Dissolve an equivalent of 100 μg in 100 μL 0.1% Tween20 in PBS
Stock Solution pS396 Tau Protein (˜1.20 mg/mL) (=26.1 μM, MW=45902.2 g/Mol)
This solution is used to demonstrate method suitability and determine the lowest percentage of S396-phosphorylation that reliable can be measured
Frozen CSF samples were thawed at room temperature and homogenized by slowly inverting (at least 5 times) and vortexing for 30 seconds. Samples are centrifuged for 1 minute at approximately 500× g and 20° C. and 200 μL sample is pipetted into a 1 mL plate. Add 10.0 μL 0.1% Tween 20 in PBS to the (double) blanks and add 10.0 μL internal standard working solution (2.7 nM 15N-Tau protein) to all other wells.
Prepare the digestion mix 1 freshly as described under materials and reagents (100 μg/mL trypsin). Mix 100 μL 5 mg/mL trypsin in 1 mM HCl solution with 4900 UL digestion solvent (250 mM ABC in water) in a tube. Add 40.0 μL of the freshly prepared digestion to each well and vortex the plate for 60 minutes at 1200 rpm (thermomixer) and 37° C.
Prepare the digestion stop solution freshly (1.00 mg/mL). Weigh an amount of approximately 1.5 mg trypsin inhibitor and dissolve in the required volume of Milli-Q to achieve a concentration of 1.00 mg/mL.
Add 12.0 μL of the freshly prepared digestion stop solution to each well and vortex the plate for 2 minutes at 1200 rpm (thermomixer or mixmate) and 37° C.
Add 60.0 μL of digestion solvent (250 mM ABC in water) and 300 μL of 0.1% Tween 20 in PBS to each well and vortex-mix.
A solid-phase extraction step is applied to remove residues of trypsin prior the dephosphorylation step (to avoid cleavage at S396 when phosphorylation is removed) and the concentrate the sample.
Condition the SPE-columns (Sep-Pak® tC18 100 mg) with 500 μL methanol followed by condition with 1000 μL Milli-Q water. Load the complete sample onto the SPE-columns. Wash the SPE-columns twice with 1000 μL SPE wash (100 mM ammonium acetate pH=5.5).
Place the SPE plate on a (clean) 500 μL plate and centrifuge the SPE plate on the 500 μL plate for 1 minute at 400*g to collect all the remaining SPE wash (waste). Elute the samples with 450 UL methanol into a new clean 500 μL LoBind plate deep well plate.
Evaporate the solvent to dryness at 65° C. under a gentle stream of nitrogen for approximately 45 minutes and reconstitute the samples with 20.0 L dephosphorylation solvent (100 mM Ammonium acetate pH=5.5). At this pH the enzymatic activity of trypsin is minimized whereas the activity of Lambda Protein Phosphatase (λPP) is maintained.
Prepare the MnCl2 3.125 mM solution by mixing 1000 μL of 10 mM MnCl2 with 2200 UL Milli-Q in a tube. Add 20.0 μL of the (freshly) prepared 3.125 mM MnCl2 solution to the samples. Prepare the λPP solution fresh, by mixing 50.0 μL λPP solution (containing 20 000 units) with 500 μL Milli-Q in the original cup. Add 10.0 μL of the (freshly) prepared λPP solution to the samples and vortex the plate for 120 minutes at 1200 rpm (thermomixer) and 37° C.
Add 50.0 μL dephosphorylation solvent (100 mM Ammonium acetate pH=5.5) to the plate and vortex the plate for 1 minute at 1200 rpm (thermomixer) and 37° C.
Transfer 50.0 μL of the sample to a new 500 μL protein plate. This sample will be used in workflow 2 and undergo a second tryptic digest (workflow 2 plate).
To the original plate, add 50.0 μL 1% formic acid in water and vortex the plate for 1 minute at 1200 rpm and RT. This plate is ready for LC-MS/MS analysis.
Prepare the digestion mix 2 freshly (300 μg/mL trypsin) by mixing 300 μL 5 mg/mL trypsin in 1 mM HCl solution with 4700 μL 250 mM ABC solution in a tube. Add 30.0 μL of the freshly prepared digestion mix 2 to each well of the workflow 2 plate and vortex for 60 minutes at 1200 rpm (thermomixer) and 37° C.
Stop the digestion by adding 20.0 μL 1% formic acid in water to the workflow 2 plate and vortex the plate for 1 minute at 1200 rpm and 37° C. This plate is now ready for LC-MS/MS analysis.
Separation from interfering endogenous compounds is achieved by LC-MS/MS using an Acquity HSS T3 (100×2.1 mm, 1.8 μm) analytical column, set at 30° C., and 0.1% formic acid and 0.5% DMSO in water as mobile phase A and methanol as mobile phase B. An 11-minute gradient at a flow rate of 0.500 mL/min is applied running at 5% mobile phase B for the first 1 minute, linearly increasing to 14% B after 9 min, followed by a step to 90% B which is maintained for 1 min before decreasing back to 5% B. Injection volume is 40 μL.
The expected retention time for SPVVSGDTSPR [396-406] is 7.2 min and for IGSTENLK [260-267] it is 6.5 min.
A SCIEX triple quad 6500 mass spectrometer equipped with a turbo ion spray source is used for detection in positive ion mode. The turbo ionspray source is operated in the positive ion mode at an ion spray voltage of 5500V and at a temperature of 500° C. Curtain gas is set at 30.
Quantification is based on multiple reaction monitoring (MRM) using the transitions specified in Table below. A linear (Analyst) calibration curve with a 1/x2 weighting factor is used ranging from 2 to 100 pM Total Tau protein in CSF.
15N-IGSTENLK
15N-SPVVSGDTSPR
| Number | Date | Country | Kind |
|---|---|---|---|
| 21190078.2 | Aug 2021 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2022/071958 | 8/4/2022 | WO |
