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US20170037476A1 - Differential diagnosis of eczema and psoriasis - Google Patents

Differential diagnosis of eczema and psoriasis Download PDF

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US20170037476A1
US20170037476A1 US15/304,364 US201515304364A US2017037476A1 US 20170037476 A1 US20170037476 A1 US 20170037476A1 US 201515304364 A US201515304364 A US 201515304364A US 2017037476 A1 US2017037476 A1 US 2017037476A1
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psoriasis
eczema
ccl27
markers
seq
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Kilian EYERICH
Carsten Schmidt-Weber
Bettina KNAPP
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Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt GmbH
Klinikum Rechts der Isar der Technischen Universitaet Muenchen
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Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt GmbH
Klinikum Rechts der Isar der Technischen Universitaet Muenchen
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Assigned to Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), KLINIKUM RECHTS DER ISAR DER TECHNISCHEN UNIVERSITÄT MÜNCHEN reassignment Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: EYERICH, Kilian, SCHMIDT-WEBER, CARSTEN, KNAPP, Bettina
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    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/24—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/40—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against enzymes
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6881—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids from skin
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/22—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against growth factors ; against growth regulators
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/24—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
    • C07K16/244—Interleukins [IL]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2866—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against receptors for cytokines, lymphokines, interferons
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • C—CHEMISTRY; METALLURGY
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/20—Dermatological disorders
    • G01N2800/205—Scaling palpular diseases, e.g. psoriasis, pytiriasis

Definitions

  • the present invention relates to a method of diagnosing eczema and/or psoriasis, wherein said method differentiates between eczema and psoriasis, and comprises determining the expression of at least two markers in a sample taken from an individual, wherein said at least two markers are selected from CCL27, NOS2, IL36G, KLK13, SOST, NPTX1, PLA2G4D, GDA, IL36A, TGM1, CLEC4G, IL13, TCN1, TMPRSS11D and RHCG, provided that said at least two markers consist of or comprise (a) CCL27 and NOS2; (b) CCL27 and KLK13; (c) IL36G and KLK13; (d) CCL27 and IL36G; (e) NOS2 and IL36G; (f) NOS2 and KLK13; (g) SOST; or (h) NPTX1; and assessing on the basis of the expression of said at least two markers
  • IL-4 itself is a useful therapy of psoriasis (Ghoreshi K et al. Nat Med 9, 40-6 (2003)). Therefore, also in such a setting it is to be expected that the treatment which ameliorates eczema will have a negative impact on psoriasis. This problem is further aggravated by the fact that for a significant fraction of patients a clear distinction between psoriasis and eczema is not possible, even for experienced clinicians, the reason being that either disease may manifest itself in different forms, wherein the established clinical parameters may fail to correctly distinguish between certain forms of eczema and certain forms of psoriasis.
  • Guttman-Yassky E et al. J Allergy Clin Immunol 124, 1235-1244 (2009)
  • Kamsteeg M et al. (Br J Dermatol 162, 568-578 (2010)) describe classifiers to be used in distinguishing between atopic dermatitis and psoriasis based on gene expression levels.
  • the classifier of Guttman-Yassky et al. (loc. cit.) requires thirteen genes and that of Kamsteeg et al. (loc. cit.) seven genes. Independent validation of the respective classifier with patient data not used for training is not provided.
  • the present invention relates to a method of diagnosing eczema and/or psoriasis, wherein said method differentiates between eczema and psoriasis, and comprises determining the expression of at least two markers in a sample taken from an individual, wherein said at least two markers are selected from CCL27, NOS2, IL36G, KLK13, SOST, NPTX1, PLA2G4D, GDA, IL36A, TGM1, CLEC4G, IL13, TCN1, TMPRSS11D and RHCG, provided that said at least two markers consist of or comprise (a) CCL27 and NOS2; (b) CCL27 and KLK13; (c) IL36G and KLK13; (d) CCL27 and IL36G; (e) NOS2 and IL36G; (f) NOS2 and KLK13; (g) SOST; or (h) NPTX1; and assessing on the basis of the expression of said
  • the present invention relates to a method of diagnosing eczema and/or psoriasis, wherein said method differentiates between eczema and psoriasis, and comprises determining the expression of at least two markers in a sample taken from an individual, wherein said at least two markers are selected from CCL27, NOS2, IL36G, KLK13, SOST, NPTX1, PLA2G4D, GDA, IL36A, TGM1, CLEC4G, IL13, TCN1, TMPRSS11D and RHCG, provided that said at least two markers consist of or comprise (a) CCL27 and NOS2; (b) CCL27 and KLK13; (c) IL36G and KLK13; (d) CCL27 and IL36G; (e) NOS2 and IL36G; (f) NOS2 and KLK13; (g) SOST; or (h) NPTX1.
  • Psoriasis and eczema are inflammatory skin diseases known to the clinician; see introductory section above and references cited there.
  • the term “expression” has its art-established meaning and defines, in a quantitative sense, the degree of transcription and/or translation of a given gene. Accordingly, it is understood that the method of diagnosing according to the first aspect of the present invention may, in preferred embodiments, employ mRNA expression data and/or protein expression data. Means and methods for determining expression data are detailed further below.
  • the method of diagnosing employs at least two markers to be selected from the list of fifteen markers presented above, wherein furthermore one of the requirements (a) to (h) has to be met. Accordingly, it is understood that the language “said at least two markers comprise” relates to any one of items (a) to (h), and the language “said at least two markers consist of” relates to any one of items (a) to (f).
  • markers are used. While also three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen or the whole set of fifteen markers may be used, it is a surprising achievement of the present inventors to provide very small sets of markers, namely two markers, which—despite the small size of the set—yield excellent classifiers to be used in the assessment whether the individual is afflicted with eczema and/or psoriasis. Their good performance has been cross-validated, i.e. by testing them on data sets which were not used for training. This is an important distinction from the prior art which not only uses larger sets of markers, but also fails to independently cross-validate the respective classifier.
  • the group of two markers consisting of CCL27 and NOS2 may be expanded by adding one or more markers from the thirteen remaining markers of the list of fifteen provided above, it is particularly preferred to exclusively use the expression of CCL27 and NOS2 for the purpose of diagnosing eczema and/or psoriasis and furthermore differentiating between these two diseases.
  • the gene names used in the definition of the first aspect of the present invention are standard art-established gene names. Table 1 below provides the full names and functional annotations of these genes.
  • FIG. 1A presents the expression data (mRNA levels) of the fifteen genes for the two diseases and furthermore gene specific cut-offs separating expression levels characteristic of psoriasis from those characteristic of eczema. Cut-off values are also given in Table 2 below.
  • the most preferred classifier i.e. the method of diagnosing according to the first aspect, wherein said at least two markers are exactly two markers which are CCL27 and NOS2, yields correct results where the established diagnostic gold standard, namely visual inspection of the patient by the experienced clinician and histological analysis fail.
  • the predictor classified a patient as suffering from eczema which patient, based on clinical parameters, was initially diagnosed as having psoriasis. Only the initially surprising result delivered by the method according to the present invention prompted the clinicians to go back and review once more clinical and histological features of this patient.
  • the therapy initially chosen and targeted at psoriasis did not improve the patient's condition, thereby confirming that clinical diagnosis was wrong and the method of the present invention correct.
  • a second case of particular interest was a patient which, from clinical and histological aberration, could not be assigned unambiguously.
  • established methods failed to distinguish between psoriasis and eczema.
  • the classifier according to the present invention instead clearly established eczema.
  • said at least two markers are at least three markers and consist of or comprise: (i) CCL27, NOS2 and IL36G; or (j) CCL27, KLK13 and IL36G.
  • a key aspect of the present invention is the identification and validation of particularly small and particularly powerful sets of markers. This is defined by the embodiments disclosed above. Once the sets of markers to be used being established, various methods are at the skilled person's disposal to make use of the markers for diagnostic purposes, namely the assessment whether the individual is afflicted with eczema and/or psoriasis.
  • said diagnosing is effected by a classifier.
  • classifier has its art-established meaning and refers to a computer-implemented algorithm. Said algorithm, when fed with patient data (in the present case expression levels) yields an output which assigns the respective patient either to the group of psoriasis patients or the group of eczema patients. Thus, assessment whether the individual is afflicted with eczema and/or psoriasis is preferably effected by a classifier.
  • the results provided by the method of the first aspect may be compared, complemented or validated by established clinical methods, in particular visual inspection of the patient and/or histological analysis of a sample taken from the patient. Histological hallmarks of psoriasis on the one hand and eczema on the other hand, in particular in clear-cut cases (which, as noted above, does not apply to all patients) are well-known in the art; see, for example, Bieber (loc. cit.) and Nestle (loc. cit.).
  • said classifier is obtainable by analyzing said expression of said at least two markers in samples taken from individuals suffering from eczema and in samples taken from individuals suffering from psoriasis; or (b) said method further comprises calculating said classifier by analyzing said expression of said at least two markers in samples taken from individuals suffering from eczema and in samples taken from individuals suffering from psoriasis.
  • the method of the present invention may optionally further comprise the step of building said classifier, or, in the alternative, may make use of a previously established classifier.
  • training of the classifier in accordance with item (b) does not pose particular challenges with regard to the choice of patients the samples of which are to be used for classifier training. Preference is given to patients with clear-cut clinical symptoms of the respective disease. Preferred are furthermore large cohorts of patients.
  • analyzing is by means of support vector machines (SVMs), generalized linear models (GLMs), linear discriminant analysis, decision trees, decision rules, neural networks, Bayes regression methods, and/or nearest neighbor methods; see, e.g. Bishop (Pattern Recognition and Machine Learning (Information Science and Statistics), Springer, ISBN:0387310738 (2007)).
  • SVMs support vector machines
  • LLMs generalized linear models
  • linear discriminant analysis decision trees
  • decision rules decision rules
  • neural networks e.g. Bishop (Pattern Recognition and Machine Learning (Information Science and Statistics), Springer, ISBN:0387310738 (2007)).
  • expression data is normalized prior to analysis. Normalization can be effected by dividing expression data for a given marker from a diseased sample by the expression level of the same marker from a healthy sample. In either case, averages are preferred. Furthermore, it is preferred to use the logarithms of the expression levels (see, for example, FIG. 1 ).
  • a linear SVM is used, wherein, to the extent mRNA expression data are used, it is most preferred that the negative intercept (rho) is given by 0.22 with a 99% confidence interval (CI) of [ ⁇ 1.24, 0.89].
  • CI confidence interval
  • NOS2 CCL27 center 0.84 [0.25, 1.46] ⁇ 0.47 [ ⁇ 0.87, ⁇ 0.13] scale 1.15 [0.86, 1.37] 0.7 [0.48, 0.84] w 1.7 [ ⁇ 2.14, 2.13] ⁇ 0.32 [ ⁇ 0.63, 0.63]
  • FIG. 1B As enclosed herewith or FIG. 1B as such for classification purposes.
  • said patient upon determining the normalized mRNA expression levels of NOS2 and CCL27 of a patient to be classified, said patient is classified by determining whether its expression data fall into the area labelled “psoriasis” or into the area labelled “eczema”.
  • said eczema is selected from atopic eczema (also known as atopic dermatitis), contact dermatitis, nummular dermatitis and dyshidrotic eczema.
  • atopic eczema also known as atopic dermatitis
  • contact dermatitis also known as atopic dermatitis
  • nummular dermatitis and dyshidrotic eczema.
  • said psoriasis is selected from psoriasis vulgaris, psoriasis inversa and psoriasis pustulosa.
  • said expression is expression (a) at the mRNA level and/or (b) at the protein level.
  • said determining is effected by PCR, preferably real-time PCR.
  • PCR is used for determining the mRNA level.
  • Preferred primers to be used are disclosed further below in conjunction with kits of the present invention.
  • PCR is well known in the art and is employed to make large numbers of copies of a target sequence.
  • PCR comprises three major steps, which typically are repeated for 30 or 40 cycles. This is done on an automated cycler device, which can heat and cool containers with the reaction mixture in a very short time.
  • the first step is denaturation, e.g. at 94° C. During the denaturation, the double strand melts to form single stranded DNA. Concomitantly, all enzymatic reactions are stopped. These enzymatic reactions include, for example, the extension reaction of a previous PCR cycle.
  • the second step is annealing, e.g. at 54° C.
  • Bonds are constantly formed and broken between the single stranded primer and the single stranded template. The more stable bonds last a bit longer (primers that match exactly) and on the formed double stranded DNA comprising template and primer, the polymerase can attach and starts copying the template. Once a few bases are built in, the bonds are sufficiently strong between the template and the primer such that it does not break anymore.
  • the third step is an extension step which is performed at a temperature of, for example, 72° C. This is the ideal temperature for polymerase activity.
  • the primers where there are a few bases built in, already exhibit a stronger binding to the template as compared to primers that are on positions with no exact match, which in turn get loose again (because of the higher temperature as compared to the annealing step) and do not give rise to an extension of the fragment.
  • Real-time PCR is a specific type of PCR, where the process of amplification can be monitored directly and in real time, which permits a significantly more precise determination of expression levels than conventional end-point PCR. It may either employ a specific probe, in the art also referred to as TaqMan probe, which has a reporter dye covalently attached at the 5′ end and a quencher at the 3′ end. After the TaqMan probe has been hybridized in the annealing step of the PCR reaction to the complementary site of the polynucleotide being amplified, the 5′ fluorophore is cleaved by the 5′ nuclease activity of Taq polymerase in the extension phase of the PCR reaction.
  • specific primers may be combined with a fluorescent dye (SYBR green) that binds to double stranded DNA.
  • SYBR green fluorescent dye
  • said determining is effected by antibodies, in particular by antibodies which are specific for the given marker protein.
  • Antibodies are preferably used for determining the above mentioned protein level.
  • Antibodies may be labeled, or bound antibodies may in turn be detected by using labeled (secondary) antibodies.
  • Preferred labels are fluorescent, luminescent and radioactive labels. Particularly preferred are fluorescent labels.
  • the latter type of detection scheme is also known in the art as immunofluorescence.
  • a further art-established alternative are enzyme-linked immunosorbent assays (ELISA).
  • antibody includes monoclonal antibodies, polyclonal antibodies, single chain antibodies, or fragments thereof that specifically bind said peptide or polypeptide, also including bispecific antibodies, synthetic antibodies, antibody fragments, such as Fab, a F(ab 2 )′, Fv or scFv fragments etc., or a chemically modified derivative of any of these.
  • Monoclonal antibodies can be prepared, for example, by the techniques as originally described in Köhler G and Milstein C, Nature 256 495-7 (1975), and Galfré G and Milstein C, Meth. Enzymol. 73 3-46 (1981), which comprise the fusion of mouse myeloma cells to spleen cells derived from immunized mammals with modifications developed by the art.
  • antibodies or fragments thereof to the aforementioned peptides can be obtained by using methods which are described, e.g., in Harlow and Lane “Antibodies, A Laboratory Manual”, CSH Press, Cold Spring Harbor, 1988.
  • surface plasmon resonance as employed in the BIAcore system can be used to increase the efficiency of phage antibodies which bind to an epitope of the peptide or polypeptide of the invention (Schier, Human Antibodies Hybridomas 7 97-105 (1996); Malmborg, J. Immunol. Methods 183 7-13 (1995)).
  • the production of chimeric antibodies is described, for example, in WO89/09622.
  • a further source of antibodies to be utilized in accordance with the present invention are so-called xenogenic antibodies.
  • the general principle for the production of xenogenic antibodies such as human antibodies in mice is described in, e.g., WO 91/10741, WO 94/02602, WO 96/34096 and WO 96/33735.
  • Antibodies to be employed in accordance with the invention or their corresponding immunoglobulin chain(s) can be further modified using conventional techniques known in the art, for example, by using amino acid deletion(s), insertion(s), substitution(s), addition(s), and/or recombination(s) and/or any other modification(s) known in the art either alone or in combination.
  • polyclonal antibody also relates to derivatives of said antibodies which retain or essentially retain their binding specificity. Whereas particularly preferred embodiments of said derivatives are specified further herein below, other preferred derivatives of such antibodies are chimeric antibodies comprising, for example, a mouse or rat variable region and a human constant region.
  • scFv fragment single-chain Fv fragment
  • scFv fragment single-chain Fv fragment
  • the antibody, fragment or derivative thereof specifically binds the target protein.
  • the term “specifically binds” in connection with the antibody used in accordance with the present invention means that the antibody etc. does not or essentially does not cross-react with (poly)peptides of similar structures. Cross-reactivity of a panel of antibodies etc. under investigation may be tested, for example, by assessing binding of said panel of antibodies etc. under conventional conditions (see, e.g., Harlow and Lane, (1988), loc. cit.) to the (poly)peptide of interest as well as to a number of more or less (structurally and/or functionally) closely related (poly)peptides.
  • said antibody or antibody binding portion is or is derived from a human antibody or a humanized antibody.
  • humanized antibody means, in accordance with the present invention, an antibody of non-human origin, where at least one complementarity determining region (CDR) in the variable regions such as the CDR3 and preferably all 6 CDRs have been replaced by CDRs of an antibody of human origin having a desired specificity.
  • CDR complementarity determining region
  • the non-human constant region(s) of the antibody has/have been replaced by (a) constant region(s) of a human antibody.
  • the antibody is preferably labeled or is to be detected by labeled compounds such as labeled secondary antibodies.
  • labeled compounds such as labeled secondary antibodies.
  • said sample is a skin sample affected by the disease such as a slice of skin or a skin biopsy affected by the disease. Slices may be obtained by using a microtome.
  • said sample is preprocessed in order to obtain a homogenous phase. Determining expression of at least two markers is then effected in said homogenous phase.
  • classifying, or, more generally, diagnosing can also be effected directly on a stained skin sample such as a skin biopsy or a slice of skin.
  • Staining is preferably obtained by the above disclosed method employing antibodies.
  • a stained skin sample is subjected to image analysis. For exemplary implementations using either Fourier transformation and/or convolution, reference is made to Example 6.
  • said sample is a skin sample and said expression is a expression at the protein level
  • said determining the expression is effected by staining of said skin sample
  • said diagnosing is effected by image analysis of the stained skin sample.
  • morphological distribution in particular morphological distribution at a level of cellular morphology of markers in accordance with the present invention may be used for the purpose of diagnosing.
  • Staining is preferably effected by immunofluorescence, preferably of slices of skin.
  • Image analysis preferably involves Fourier transformation and/or convolution.
  • both eczema and psoriasis are inflammatory skin diseases which generally effect part, but not all of the skin of a given patient.
  • choosing disease affected skin samples is the method of choice.
  • said individual is Caucasian.
  • the present invention provides a kit comprising or consisting of means for quantifying the expression of at least two markers selected from CCL27, NOS2, IL36G, KLK13, SOST, NPTX1, PLA2G4D, GDA, IL36A, TGM1, CLEC4G, IL13, TCN1, TMPRSS11D and RHCG, provided that said at least two markers consist of or comprise (a) CCL27 and NOS2; (b) CCL27 and KLK13; (c) IL36G and KLK13; (d) CCL27 and IL36G; (e) NOS2 and IL36G; (f) NOS2 and KLK13; (g) SOST; or (h) NPTX1.
  • said means are primers, wherein the primers for the respective genes are as follows: CCL27: SEQ ID NOs: 1 and 2; NOS2: SEQ ID NOs: 3 and 4; IL36G: SEQ ID NOs: 5 and 6; KLK13: SEQ ID NOs: 7 and 8; SOST: SEQ ID NOs: 9 and 10; NPTX1: SEQ ID NOs: 11 and 12; PLA2G4D: SEQ ID NOs: 13 and 14; GDA: SEQ ID NOs: 15 and 16; IL36A: SEQ ID NOs: 17 and 18; TGM1: SEQ ID NOs: 19 and 20; CLEC4G: SEQ ID NOs: 21 and 22; IL13: SEQ ID NOs: 23 and 24; TCN1: SEQ ID NOs: 25 and 26; TMPRSS11D: SEQ ID NOs: 27 and 28; RHCG: SEQ ID NOs: 29 and 30.
  • said means are antibodies which are specific for the given marker protein.
  • said kit further comprises one or more of the following: (a) means for obtaining a skin sample; (b) means for isolating or enriching RNA from a skin sample; (c) means for performing PCR; and (d) means for preparing tissue sections.
  • the kit according to the second aspect of the present invention further comprises a manual comprising instructions for performing the method of the first aspect of the present invention.
  • the present invention provides use of at least two markers selected from CCL27, NOS2, IL36G, KLK13, SOST, NPTX1, PLA2G4D, GDA, IL36A, TGM1, CLEC4G, IL13, TCN1, TMPRSS11D and RHCG, provided that said at least two markers consist of or comprise (a) CCL27 and NOS2; (b) CCL27 and KLK13; (c) IL36G and KLK13; (d) CCL27 and IL36G; (e) NOS2 and IL36G; (f) NOS2 and KLK13; (g) SOST; or (h) NPTX1 for diagnosing eczema and/or psoriasis in a sample taken from an individual.
  • each embodiment mentioned in a dependent claim is combined with each embodiment of each claim (independent or dependent) said dependent claim depends from.
  • a dependent claim 2 reciting 3 alternatives D, E and F and a claim 3 depending from claims 1 and 2 and reciting 3 alternatives G, H and I
  • the specification unambiguously discloses embodiments corresponding to combinations A, D, G; A, D, H; A, D, I; A, E, G; A, E, H; A, E, I; A, F, G; A, F, H; A, F, I; B, D, G; B, D, H; B, D, I; B, E, G; B, E, H; B, E, I; B, F, G; B, F, H; B, F, I; C, D, G; C, D, H; C, D, I; C,
  • FIG. 1 A first figure.
  • B A disease classifier consisting of NOS2 (y-axis) and CCL27 (x-axis) accurately separates psoriasis and eczema patients in a training set consisting of 19 patients (9 psoriasis, 10 eczema). Shown are data samples of the training set after log transformation and scaling.
  • the crosses indicate the support vectors, the circles indicate the remaining data samples of the training set.
  • the square shows one initially mis-classified patient, the squares with discontinued contour a clinically and histologically unclear patient illustrated in D.
  • Scale bars indicate 100 ⁇ m in overview and 50 ⁇ m in islets, respectively.
  • CCL27 staining pattern distinguishes psoriasis from eczema.
  • marker genes were selected according to the following criteria: genes with most predominant difference between psoriasis and eczema; and functional annotation as epidermal, immune related, and metabolic genes.
  • SVMs support vector machines
  • the measurements of the selected 15 genes were transformed using the logarithm to the base 10.
  • a two-sample, two-sided Welch's t-test followed by a Bonferroni p-value correction was used to test for differential expression.
  • To train the classifier a 10-fold cross-validation was used.
  • Primers amplifying genes of interest were designed using the publicly accessible Primer3 software (http://frodo.wi.mit.edu/primer3/). The used primers are given in the sequence listing.
  • Cytokines that were exclusively induced in eczematous lesions were IL-6 and the Th2 cytokine IL-13, with a trend for a higher induction of other Th2 cytokines IL-4, IL-5, and IL-10 in eczematous as compared to psoriatic skin.
  • chemokines CCL17 and CCL18 were up-regulated in eczematous lesions to a higher degree than in psoriatic skin.
  • CCL27 was down-regulated significantly in psoriatic skin.
  • CXCL1 and CXCL8 (IL-8) showed a stronger up-regulation in psoriatic plaques, with CXCL8 being exclusively regulated in psoriatic skin.
  • AMPs antimicrobial peptides
  • DEFB4 and DEFB103B as well as the S100 proteins S100A7A, S100A7, S100A8, S100A9, and S100A12 were significantly up-regulated in both diseases.
  • induction of all detected AMPs was much higher in psoriatic than in eczematous skin.
  • the IL-20 induced Kallikrein-related peptidases KLK6, KLK9, and KLK13 demonstrated to induce AMPs, were exclusively up-regulated in psoriatic, but not in eczematous skin.
  • SPRR1A, SPRR1B, SPRR2A, SPRR2B, SPRR2C, SPRR2D, LCE3C, and cornifelin were exclusively up-regulated in psoriatic plaques.
  • LCE3A, LCE3D, and LCE3E were up-regulated in both psoriasis and eczema skin, but to a higher degree in psoriasis.
  • LCE1B, and LCE5A were down-regulated both in psoriatic and eczematous skin, but to a higher degree in eczema.
  • KRT6A, KRT6B, KRT6C, KRT16 and KRT75 highly up-regulated in psoriatic skin and KRT2, KRT19 as well as KRT77 down-regulated more in psoriatic than in eczematous skin.
  • the late differentiation genes of the filaggrin family FLG and FLG2 were also down-regulated in both psoriatic and eczematous skin.
  • hornerin was up-regulated more in psoriatic than in eczematous as compared to non-involved skin.
  • aldo-keto reductase family members AKR1B15, AKR1B10 and the peptidase inhibitor PI3 were up-regulated in both psoriatic and eczematous skin, but more in psoriasis.
  • the 15 genes of the invention (Table1, FIG. 1A ) were included in a validation cohort with 19 patients (9 for psoriasis, 10 for eczema) to train a classifier. Expression of the selected 15 genes was detected using real-time PCR in all 19 patients and a two-sample, two-sided Welch's t-test on the log-transformed measurements followed by a Bonferroni p-value correction was used to assign each of the 15 genes with a p-value.
  • the primer sequences used for real-time PCR are given in table S4.
  • CCL27 and NOS2 were the genes with lowest adjusted p-values (for significantly up and down regulation, respectively, of psoriasis versus eczema).
  • SVMs support vector machines
  • An average accuracy of 100% was achieved ( FIG. 1B ).
  • FIG. 1D Besides patients with a given diagnosis from clinical and histological evaluation, one patient was tested where the gold standard methods could not distinguish between psoriasis and eczema ( FIG. 1D ).
  • the histological evaluation was conflicting, with a plump acanthosis, partially missing stratum granulosum and parakeratosis accounting for psoriasis.
  • T cell epidermotropism and very few neutrophils with missing microabscesses were more typical for eczema.
  • the two biopsies were classified as eczema with a probability above 99%, indicating the classifier might be useful even in cases where established gold standard diagnostic tools fail.
  • the proposed disease classifier of psoriasis and eczema based on the markers NOS2 and CCL27 is valid at the level of immunofluorescence. This has been confirmed using data from 118 patients. Paraffin-embedded skin biopsies from psoriasis, eczema, and clinically as well as histologically unclear skin lesions were stained for DAPI (nuclear staining), NOS2, and CCL27. In line with the results obtained from PCR analysis at RNA level, psoriasis sections stained strongly positive for NOS2, but hardly for CCL27. In contrast, eczema sections were positive for CCL27, but NOS2 staining was very weak to absent ( FIG. 2 ). In conclusion, the proposed classifier to distinguish psoriasis from eczema is valid at protein expression level, as demonstrated using immunofluorescence double stainings.
  • the proposed markers NOS2 and CCL27 allow to distinguish psoriasis from eczema based on their protein expression pattern.
  • CCL27 distributes homogenously over the cytoplasm in psoriasis sections, while eczema samples are characterized by a clear nuclear staining pattern ( FIG. 3 ).
  • the first method is based on Fourier transformation which decomposes an image into its frequencies in a two-dimensional space (sine and cosine components).
  • Sharp edges which can be seen in the DAPI channel as well as in the CCL27 channel of eczema—where clear borders between positive nuclei and rather negative cytoplasm are found—are represented by high frequencies, whereas ubiquitous cytoplasmatic occurrence pf CCL27 as seen in psoriasis is represented by low edges and as such by low frequencies.
  • Similar frequency power densities between the two channels are resulting in quotients close to 1, distinct frequency power densities in quotients close to 0.
  • the second method is based on convolution.
  • both color channels of each part of the image are sequentially compared with each other in windows of 32 ⁇ 32 pixel.
  • For each image both values are represented by one dot in a 2 dimensional coordinate system. A line is plotted at maximal separation of both groups.

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