Method for the direct diagnostic detection of genetically caused pathogenic point mutations

[0002] The present invention relates to a method according to the generic part of claim 1.

[0003] Mutations on the gene level often cause inappropriate amino acids to be incorporated in proteins which are encoded in the corresponding gene segment which has mutated. This may result in pathologic phenomena, e.g., sickle-cell anaemia. Examinations of the presence of mutations which are responsible for pathologic conditions are usually performed on the DNA level. Such examinations are cumbersome, and their evaluation takes very long as a rule.

[0004] Thus, an object of the invention has been to provide a method by which the presence of mutations can be established quickly and reliably.

[0005] According to the invention, this object is achieved by a method with the features as defined in claim 1.

[0006] The method according to the invention serves to recognize mutations in organisms by comparing a deviation, Caused by a mutation, of the amino acid composition of a protein expressed in the region of the mutation (protein to be examined) with a corresponding protein which is expressed by a wild type lacking the mutation. The method according to the invention is characterized in that

[0007] a sample is taken from the organism at a site where the protein to be examined is expressed, can be detected and/or plays a physiological role;

[0008] either the protein is concentrated or purified by methods of protein analysis, followed by a determination of its molecular weight, or

[0009] a determination of the molecular weight of the protein to be examined is performed without a pretreatment of the sample.

[0010] The invention advantageously relates to a quick method for a qualitative and quantitative medical-diagnostic analysis on the protein level of the substitution of single amino acids with pathogenic or non-pathogenic effects on the organism. The medical-diagnostic analysis is preferably performed by a combination of enzymatic or chemical cleavage of the isolated peptide, chromatographical separation of the fragments and analysis by mass spectrometry, both direct LC/MS and indirect MALDI-MS, and analysis, e.g., by capillary electrophoresis. By comparing protein samples from healthy subjects with those of ill subjects, the method described is suitable for establishing new, as yet unknown mutations and quantifying the expression and incorporation of wild type to mutant.

[0011] The obtaining of samples from an organism, especially by biopsy, can be considered a basis of the method according to the invention. As the sites where the samples are taken, sites are selected in which the protein to be examined is expressed, detectable or plays a physiological role, e.g., in muscle fiber bundles or tissue pieces from organs, especially hearts. The samples are advantageously processed in such a way that the substitution of a single amino acid can be unambiguously detected by mass-spectrometric, chromatographical and/or electrophoretical methods, and the expression and incorporation ratio of wild type to mutant can be quantitatively determined. Thus, it becomes possible by a direct protein analysis as well to diagnose the causes of a genetically caused disease at an early stage and to identify as yet unknown mutations by a comparative analysis of samples from healthy subjects and samples from ill subjects.

[0012] By using the highly sensitive “matrix-assisted laser-induced desorption and ionization time-of-flight mass spectrometry” (MALDI-MS) in combination with liquid chromatography, especially using columns with an inner diameter of ≦1 mm (microbore and capillary columns), the detection can be effected even with minute sample quantities.

[0013] As compared to the as yet performed analyses of the DNA coding for the proteins, the method is characterized in that the detection of the mutation and the determination of the expression and incorporation ratio is effected in a significantly shorter period of time. An analysis can be performed within one week, in contrast to the usual times required for DNA analysis, ranging from several weeks to half a year.

[0014] It is an advantage that a specific cleavage of the protein recovered from biopsy samples for diagnostic purposes is performed with selective enzymes, endoproteinases, or by chemical reagents, and the fragments obtained by such cleavage are separated by chromatographical methods and characterized in terms of their molecular weights either directly (LC/MS) or indirectly (MALDI-MS). The distribution in the separation and the molecular weight, determined by mass spectrometry, is unambiguous evidence for each fragment of the protein.

[0015] With smaller proteins, i.e., those having a molecular weight of up to 100,000 Dalton, the amino acid substitutions can be directly determined with the method described, without a preliminary cleavage into fragments. The accuracy of the measurement enables the precise determination of deviations in molecular weight of <5 Dalton and thus the detection of both wild type and mutant in the presence of each other. The precise localization of the amino acid substitution can be effected by the above described cleavage.

[0016] Thus, it is possible to characterize all proteins involved in a physiologically functional structure, e.g., muscle, in terms of genetically caused pathogenic and non-pathogenic amino acid substitutions.

[0017] Since the amino acid sequences of a lot of proteins are already known due to the sequencing of the human genome and all human proteins will be elucidated in a few years, a protein can be analyzed for mutations by means of the method herein described by selecting the appropriate cleavage which can be achieved by one skilled in the art by per se known methods.

[0018] It can be of great importance that this method may also be adapted for clinical-diagnostic use in the recognition of the causes of diseases and, through an optimization of the separation and detection conditions, also for the systematic screening of patient samples for particular, defined mutations.

[0019] Using appropriate equipment, the method described may also be automated to a large extent. For the procedure as described, the duration of an analysis is in the range of a few days whereas DNA analysis takes several weeks to months. At the same time, all proteins involved in a physiologically functional structure can be analyzed by this method.

[0020] Unlike the conventional methods for the detection of point mutations by analyzing the genomic DNA or cDNA, this method allows the quantification of the expression and incorporation of the mutant in the physiologically functional structure, especially if, due to the presence of a diploid set of chromosomes in the nucleus, both forms of the respective protein are expressed and it is not known in what ratio the two forms are present in the functional form.

[0021] The invention further allows evidence of the identity of the wild type and of the mutant to be furnished by chemical sequence analysis or by amino acid analysis.

[0022] A preferred embodiment of the method according to the invention comprises the cleavage of the protein to be examined with suitable enzymes or chemical reagents, and a combination of chromatographical methods, especially high-pressure liquid chromatography with capillary columns (MB-HPLC), and mass spectrometry.

[0023] The invention will be further illustrated by using the heavy chain of the β-isoform of myosin as an example. Point mutations in the heavy chain of the ⊖-isoform of myosin, e.g., substitution of the amino acid methionine for the amino acid valine in position 606, may result in hypertrophic cardiomyopathy, a genetically caused thickening of certain heart walls which may lead to sudden death. According to the invention, the detection of the mutation is possible by a combination of enzymatic cleavage and LC/MS.

[0024] FIGS. 1aand 1bshow the analysis of the peptide fragments of human cardiac β-myosin heavy chain (β-MHC) by means of a coupling of high performance liquid chromatography (HPLC) with mass spectrometry (MS). In this example, the presence of the heterozygotic mutant Val606Met, i.e., substitution of valin in position 606 of β-MHC, was looked for. FIG. 1ashows two marked ranges in which the fragment with a substituted amino acid and a molecular weight of 1507.5 could be detected in addition to the original fragment, the wild type fragment having a molecular weight of 1475.5, in a person for whom the substitution had been proven on the gene level. For comparison, FIG. 1bshows the analysis of a β-MHC sample of a person with no point mutation in this gene. In this case, only the wild type fragment can be detected; in the range in which the mutated fragment was eluted in FIG. 1a, this peptide is completely lacking. Thus, it becomes possible to detect mutated β-MHC in a person's muscle fibers.

[0025] In order to support this finding which is only substantiated by the observed shift in molecular weight of +32 by the amino acid substitution of Val by Met, fragments of an enzymatic cleavage were separated by HPLC, and the fractions were examined for the presence of peptides with molecular weights of 1475.5 and 1507.5 using mass spectrometry.

[0026] These peptides could be found in such fractions as corresponded to the above showed LC/MS analysis. FIGS. 2aand 2bshow the mass spectra of these peptide fractions; in addition to the peptides to be detected, a large number of other peptides from β-MHC are also present.

[0027] The sequences of the peptides detected in the fractions were confirmed by collision-induced fragmentation by means of the coupling of two mass spectrometers (CID-MS/MS). The distances between the fragment ions designated as b and y correspond to the amino acids of the peptides with high specificity. From these distances, the sequence of the peptide can be established fully or in part. Problems are only encountered with the amino acids Leu and Ile which have no difference in molecular weight at all, and Lys and Gln which are different by only 0.04 unit masses. Since the enzymatic cleavage was performed with an enzyme which specifically cleaves behind Lys, the sequence determination can be based on the assumption that amino acids at the end of the peptide are Lys.

[0028] The CID-MS/MS spectra are shown in FIGS. 3aand 3b. The distance between b5 and b6 clearly shows the shift caused by the amino acid substitution while all other distances between the fragment ions remain unchanged. The evaluation yielded DPLNETVVGLYQK (SEQ ID No. 1) as the sequence for the wild type, and DPLNETVMGLYQK (SEQ ID No. 2) as the sequence for the mutant. Comparisons performed in data bases yielded no homology of the CID-MS/MS spectra with other proteins, except for very homologous β-MHCs from other species. Thus, the presence of the mutation in the muscle fibers could be clearly proven on a molecular level.

[0029] The stated techniques are not suitable for quantifying the degree of the incorporation of wild type to mutant. Because of the different ionization probabilities and the interference by other peptides present in the mixtures, the amount of peptide cannot be concluded from the results of mass spectrometry. For a quantification, another separation method is recommendable as a quantitative detection method, namely capillary zone electrophoresis. In this method which is based on other specific parameters than those of HPLC, peptides are separated in. unmodified glass capillaries, filled with buffers, with an inner diameter of 0.05 to 0.075 mm and a length of 50 cm in a strong electric field. The buffer employed has a pH value of 2.5 (100 mM phosphate buffer) in order to exclude electroendoosmotic fluxes of the buffer itself and to confer a positive charge to all peptides. In this system, the peptides of the identified fractions were separated. A commercially available peptide (low-pH mobility marker of Applied Biosystems) was added in the same amounts as an internal standard, in order to be able to compare, on one hand, the peak areas of the peptides to be compared, and to consider variations in the elution time in the different runs. The peptides to be detected themselves were identified in further separations by coinjection with a synthetic peptide of the same sequence. From the peak height and also from the peak area, a relative incorporation of the mutant of 10 to 15% of the total β-MHC was calculated. This experiment was performed with 5 different preparations, but from one patient. The thus measured values for the mutant β-MHV Val606Met were always between 10 and 15%. The capillary zone electrophoreses are shown in FIGS. 4aand 4b, the marked peptide (*) is the added internal standard, peptide (1) is the fragment of the wild type of the β-MHC, and peptide (2) is the fragment of the mutant of the β-MHC.

[0030] It is interesting that the sample examined does not show any symptoms of the familial hypertrophic cardiomyopathy. Therefore, it can be considered that a low degree of incorporation does not result in externally visible changes in muscle function.

[0031] The method according to the invention can-generally be applied to all mutants of the β-MHC. As yet, several fragments which are potential carriers of mutations were successfully identified; these fragments are underlined in FIG. 5, and the amino acids written below the continuous sequence are the as yet known substitutions. The method according to the invention can further be applied to all mutations having a pathogenic effect. For diagnostic purposes, this method may be used for the early recognition of the development of hereditary diseases;. in addition to gene analysis, a direct forecast of the risk of a severe disease or of the course of the disease can be made for every patient by analyzing the functioning proteins from the organism.

[0032] LC/MS analysis of fragments of the heavy chain of the β-isoform of myosin (β-MHC) obtained with endoproteinase Lys-C

[0033] The basis of the selective cleavage is the isolation of the β-MHC from muscle fibers of the soleus muscle which are obtained from biopsies by dissolution in a high salt buffer and precipitation of the β-MHC by decreasing the salt concentration. The collected β-MHC may be washed with water to remove disturbing soluble components.

[0034] For preparing the fragments to be analyzed, the precipitated β-MHC is slurried in 200 μl of 100 mM ammonium .hydrogencarbonate buffer, pH 8.2, and incubated with endoproteinase Lys-C (Boehringer Mannheim) at 37° C. for more than 24 hours. The solution is then subjected to freeze-drying, and the residue is dissolved in 100 μl of 0.1 M trifluoroacetic acid in water.

[0035] To remove undissolved components, the sample is filtered through an 0.2 μm cellulose acetate filter at a maximum of 10,000×g, and 20 to 50 μl aliquots are applied on the MB-HPLC column. The separation is performed through a reverse phase C18 column with an inner diameter of 1 mm and a length of 100 mm at a flow rate of 20 μl/min. The elution of the peptides is effected by a linear increase of 0.5%/min of the acetonitrile concentration in the buffer, from 10% acetonitrile in 0.06% TFA in water to 80% acetonitrile in 0.05% TFA in water. The eluting peptides are directed through a fused silica capillary and a UV detector directly into the electrospray ionization device of the quadrupole mass spectrometer (SCIEX API III, Perkin-Elmer, Langen). In the mass spectrometer, the m/z (mass to charge) values are determined over a range of from 400 to 2400 amu (atomic mass units) every 4.2 seconds. From the recorded total ion chromatogram and the respective mass spectra, the fragment of the wild type and of the mutant can be detected by computer aided evaluation.

[0036] After the separation described, a sample of the non-mutated β-MHC was analyzed together with the synthetic peptides having the sequences of the non-mutated and mutated fragments under the same conditions. The molecules which had been found are in the ranges in which the synthetic peptides are eluted.

[0037] FIG. 1: Top part: Total ion chromatogram of the separation of the fragments of the mutated β-MHC obtained with endoproteinase Lys-C.

[0038] Middle part: Detection of the non-mutated fragment in the cross-hatched range (1) of the top figure. The non-mutated fragment has a molecular weight of 1475.5 amu.

[0039] Bottom part: Detection of the mutated fragment in the crosshatched range (2) of the top figure. The mutated fragment has a molecular weight of 1507.5 amu.

[0040] Detection of the fragments of the wild type and the mutant of the β-MHC by means of the MALDI-MS technique

[0041] As described in Example 1, the cleavage of the β-MHC was effected by incubation with endoproteinase Lys-C and a subsequent separation on a reverse phase C18 column under the conditions stated above. In this Example, instead of direct coupling with the mass spectrometer, an automated fraction collector collects fractions for 2 minutes each, and 0.5 μl each of these fractions is mixed with 1 μl of a suitable matrix substance, usually α-hydroxycinnamic acid or sinapic acid, dissolved in 60% acetonitrile and 0.2% TFA, on a support for MALDI-MS. The determination of the molecular weights is then performed in a MALDI-MS (Vestec, Houston) using an external standard, i.e., two known synthetic peptides, for calibrating the measurement.

[0042] In the corresponding fractions from Example 1, these measurements yielded the expected masses of 1477.5 and 1507.5 amu.

[0043] Thus, the mutated fragments can be unambiguously detected by means of MALDI-MS as well.

[0044] Analysis of the fractions from Example 2 by means of capillary electrophoresis

[0045] The fractions from Example 2 were separated by capillary electrophoresis (Beckmann P/ACE 2000, Beckmann, Munich) using fused silica capillaries with an inner diameter of 75 μm in a 100 mM sodium phosphate buffer, pH 8.0, at a voltage of 15 to 17 kV. The detection of the peptides was effected by means of a UV detector at 200 nm.

[0046] By coinjecting the synthetic peptides in a second separation run, the identity of the natural non-mutated and mutated fragments could be shown.