# Patent

## Title
Methods and means related to diseases

## Abstract

The present invention relates to the fields of genetics and oncology and provides methods for detecting cutaneous T-cell lymphomas (CTCL) or susceptibility to CTCL. Specifically, the present invention relates to a novel method for the diagnosis and follow-up of CTCL or CTCL subtype, the method comprising determination of expression of one or more genes, gene fragments or gene products. The present invention further relates to a novel method of detecting the response to CTCL therapy, the method comprising determining expression of one or more genes or gene fragments or gene products in a biological sample. The present invention further relates to a novel method of developing or improving CTCL therapy or developing anti-CTCL medicament, the method comprising screening agents affecting one or several of the genes or gene products. The present invention further relates to a novel method of treating CTCL patients, the method comprising affecting one or several of the genes or gene products. The present invention further relates to a novel test kit, the kit comprising the necessary means for detecting one or more genes, gene fragments or gene products. The present invention also relates to a use of one or more genes, gene fragments or gene products for determination, diagnosis or follow-up of CTCL or CTCL subtype and for detection of the response to CTCL therapy. The present invention also relates to a use of one or more target molecules for CTCL therapy or for the preparation of a medicament for treating CTCL.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a 371 National Phase Entry Application of co-pending International Application PCT/F12006/050577, filed 21 Dec. 2006, which designated the U.S. and which claims the benefit under 35 U.S.C. §119(e) of U.S. Provisional Application 60/753,268, filed 22 Dec. 2005.


FIELD OF THE INVENTION
The present invention relates to the fields of genetics and oncology and provides methods for detecting cutaneous T-cell lymphomas (CTCL) or susceptibility to CTCL. Specifically, the present invention relates to a novel method for the diagnosis and follow-up of CTCL or CTCL subtype, the method comprising determination of expression of one or more genes, gene fragments or gene products. The present invention further relates to a novel method of detecting the response to CTCL therapy, the method comprising determining expression of one or more genes or gene fragments or gene products in a biological sample. The present invention further relates to a novel method of developing or improving CTCL therapy or developing anti-CTCL medicament, the method comprising screening agents affecting one or several of the genes or gene products. The present invention further relates to a novel method of treating CTCL patients, the method comprising affecting one or several of the genes or gene products. The present invention further relates to a novel test kit, the kit comprising the necessary means for detecting one or more genes, gene fragments or gene products. The present invention also relates to a use of one or more genes, gene fragments or gene products for determination, diagnosis or follow-up of CTCL or CTCL subtype and for detection of the response to CTCL therapy. The present invention also relates to a use of one or more target molecules for CTCL therapy or for the preparation of a medicament for treating CTCL.
BACKGROUND OF THE INVENTION
Primary cutaneous T-cell lymphomas (CTCL) represent a group of malignancies of mature T lymphocytes, which show a homing preference for skin. CTCL most often occurs in people aged between 40 and 60 and the two major clinical variants of CTCL are mycosis fungoides (MF) or Sezary syndrome (SzS).
Mycosis fungoides (MF), the most common type of CTCL, presents with skin lesions showing epidermotrophic clonal T lymphocytes (Willemze R et al. Blood 90:354-371, 1997). CTCL may also present in a leukaemic form with erythrodermic skin involvement and lymphadenopathy (Sezary syndrome, SzS), and 10-20% of MF cases transform to large T-cell lymphoma with time (Willemze R et al. Blood 90:354-371, 1997, Willemze R et al. Blood 105:3768-3785, 2005). Ten-year relative survival of MF, the most benign form of the cutaneous T-cell lymphomas ranges from 100% to 41%, depending on the degree of skin involvement. Patients with SzS have a prognosis with an estimated 5-year survival of 15% (Willemze R et al. Blood 90: 354-71, 1997). Therefore, many patients with advanced disease do not respond to therapy and furthermore, many patients having some response to therapy will later suffer a relapse. Thus, there is an urgent need for life-saving therapeutics.
The molecular mechanisms leading to CTCL are still largely unknown. Previously performed microarray studies have found no uniform gene expression signatures (Kari L et al. J Exp Med 197:1477-1488, 2003, van Doorn R et al. Cancer Res 64:5578-5586, 2004, Tracey L et al. Blood 102:1042-1050, 2003), most likely due to a wide range of different experimental designs and microarray platforms used. On one hand, an expression profile suggesting upregulation of genes involved in TNF signaling pathway was found among MF skin samples (Tracey L et al. Blood 102:1042-1050, 2003). On the other hand, among SzS samples, many Th2-specific transcription factors (like Gata-3 and JunB) were found overexpressed, while underexpressed genes included CD26, Stat4, and IL-1 receptors in one study (Kari L et al. J Exp Med 197:1477-1488, 2003) and decreased expression of some tumor suppressor genes such as TGF-β receptor 11 with overexpression of EphA4 and Twist in an other study (van Doorn R et al. Cancer Res 64:5578-5586, 2004). Due to the different probe and sample sets, and to the lack of publicly available raw data of array hybridizations, comparison of the published data is difficult. Recently, the very low concordance in array profiles obtained with the same samples on different devices has been clearly demonstrated (Tan P K et al. Nucleic Acids Res 31:5676-5684, 2003, Marshall E. Science 306:630-631, 2004). To get a better comprehension of CTCL pathogenesis, we analyzed fresh cells from various tissues of both SzS and MF, and compared their expression profiles with DNA copy number data, since DNA copy number changes contribute to variation in gene expression (Pollack J R et al. Proc Natl Acad Sci USA 99:12963-12968, 2002).
Helper T (Th) cells are essential for developing an immune response by activating antigen-specific effector cells and recruiting cells of the innate immune system such as macrophages and mast cells. Th1 commitment relies on the local production of IL-12, and Th2 development is promoted by IL-4 in the absence of IL-12. Th1 cells participate in cell-mediated immunity and control intracellular pathogens. The cytokines produced by Th1 cells stimulate phagocytosis and destruction of microbial pathogens. Th2 cells are essential for antibody-mediated immunity by stimulating the production of antibodies. Thus, Th2 cells participate in controlling extracellular pathogens. Excessive Th1 responses are involved in many autoimmune diseases, whereas excessive Th2 responses are known to lead for example to chronic diseases, including allergies, asthma, and chronic bronchitis. Increased Th2 cytokine levels have also been revealed in various malignancies including CTCL (Kari L et al. J Exp Med 197:1477-1488, 2003).
Profound understanding of CTCL improves the possibilities of diagnosing or curing the disease. None of the previous documents describes CTCL specific genes or gene products presented in this patent application (Kari L et al. J Exp Med 197:1477-1488, 2003, van Doorn R et al. Cancer Res 64:5578-5586, 2004, Tracey L et al. Blood 102:1042-1050, 2003, and US2005074761). Therefore, this invention provides novel tools for CTCL diagnostics and therapeutics.
BRIEF DESCRIPTION OF THE INVENTION
An object of the present invention is to provide novel solutions for the above problems.
Thus, a group of novel genes has been shown to associate with CTCL or susceptibility to CTCL.
The object of the invention is to provide novel methods and means for detecting CTCL or susceptibility to CTCL, such methods and means allowing an early diagnosis of the disease.
Another object of the invention is to provide novel methods and means for the prediction, diagnosis and follow-up of CTCL or CTCL subtype, such methods and means being specific and reliable and allowing identification as early as possible.
Yet another object of the invention is to provide novel methods and means for detecting the response to CTCL therapy, such methods and means allowing selection of specific and effective treatment for a patient.
Still another object of the invention is to provide novel biomarkers useful in detection of CTCL or potential for developing CTCL.
Still another object of the invention is to provide novel biomarkers useful in diagnosing CTCL or CTCL subtype as well as following up CTCL or CTCL subtype.
Still another object of the invention is to provide novel biomarkers useful in detecting the response to therapy of CTCL.
Still another object of the invention is to introduce new possibilities for combating the disease and for the recovery of the patient by providing novel biomarkers useful as target molecules for therapies or prevention of CTCL.
Still another object of the invention is to provide a diagnostic kit for detecting novel CTCL associated genes, gene fragments or gene products.
Yet another object of the invention is to provide novel methods and means for developing or improving CTCL therapy.
Still another object of the invention is to provide novel methods and means for developing anti-CTCL medicament.
Yet another object of the invention is to provide novel methods and means for treating CTCL.
The present invention relates to a novel method for detection of CTCL or susceptibility to CTCL, characterized by determining expression of one or more genes, gene fragments or gene products selected from the group comprising or consisting of S4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9 in a biological sample, whereby under- or overexpression of one or more of said genes, gene fragments or gene products indicates CTCL or susceptibility to CTCL.
The present invention relates to a novel method for detection of CTCL or susceptibility to CTCL, characterized by determining expression of MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9 genes, gene fragments or gene products in a biological sample, whereby under- or overexpression of one or more of said genes or gene products indicates CTCL or susceptibility to CTCL.
The present invention further relates to a novel method for the diagnosis and follow-up of CTCL or CTCL subtype, characterized by determining expression of one or more genes, gene fragments or gene products selected from the group comprising MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9 in a biological sample, whereby under- or overexpression of one or more of said genes, gene fragments or gene products indicates CTCL or susceptibility to CTCL or CTCL subtype.
The present invention further relates to a novel method of detecting the response to CTCL therapy, characterized by determining expression of one or more genes, gene fragments or gene products selected from the group comprising MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9, in a biological sample, whereby normalization of under- or overexpression of one or more of said genes, gene fragments or gene products indicates response of CTCL therapy.
The present invention further relates to a novel diagnostic kit, characterized by comprising the necessary means for detecting one or more genes, gene fragments or gene products selected from the group comprising MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9.
The present invention further relates to uses of one or more genes, gene fragments or gene products selected from the group comprising MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9 for determining CTCL, for the diagnosis and follow-up of CTCL or CTCL subtype, and for detecting the response to therapy of CTCL.
The present invention further relates to a use of one or more genes, gene fragments or gene products selected from the group comprising MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5 and LIR9 as target molecules for CTCL therapy.
The present invention also relates to a method for developing or improving CTCL therapy, the method comprising screening of agents affecting one or several of the genes or gene products selected from the group comprising MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9, whereby an agent having said effect allows developments and improvements of CTCL therapy.
The present invention also relates to a method for developing anti-CTCL medicament, the method comprising screening of agents affecting one or several of the genes or gene products thereof selected from the group comprising MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9, whereby an agent having said effect is tested as a medicament.
The present invention also relates to a method for treating CTCL patients, characterized by affecting one or several of the genes or gene products selected from the group comprising MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9.



BRIEF DESCRIPTION OF THE DRAWINGS
In the following the invention will be described in greater detail by means of preferred embodiments with reference to the attached drawings, in which
FIG. 1 shows substantial differences that were observed in gene expression profiles in SzS PBMC, MF CD4+ and skin biopsy samples, compared to corresponding control samples. The most differentially (p<0.05 and fold change>3) expressed genes between patient and control samples are shown: SzS PBMC (A), MF skin biopsies (B), MF CD4+ cells (C) and MF PBMC (D). The expression of the genes selected for further analysis from each category is displayed: SzS PBMC (E), MF skin biopsies (F), MF CD4+ cells (G) and MF PBMC (H). In Figures: P=patients, C=controls, red=upregulated (brightest red=fold change value 3), green=downregulated (brightest green=fold change value−3).
FIG. 2A shows genes distinguishing between Sezary syndrome (P1-4) and mycosis fungoides (P5-9). The analysis was performed by comparing the Sezary syndrome and mycosis fungoides PBMC samples together and selecting the genes distinguishing these two subtypes. The genes that were also differentially regulated between control samples and either Sezary syndrome or mycosis fungoides samples were included in the final data.
FIG. 2B shows a subset of genes found to change in a similar manner both in SzS (P1-4) and MF (P5-9) PBMC samples when compared to controls (C1-5).
FIG. 3A shows quantitative PCR, performed on 10 genes.
FIG. 3B shows the downregulation of TBX21 gene in PBMC samples of both SzS (P1-4 and SzS1-2) and MF patients (P5-9 and MF1).
FIG. 4A shows gene expression profiles by chromosome arms in four SzS PBMC (patients P1-4) and three MF skin samples (patients P5, P7, P8).
FIG. 4B shows gene expression ratios of Szs PBMC and MF PBMC mapped to chromosome 12q.
FIG. 4C shows combined CGH profiles of three Sezary syndrome (blood samples) and three mycosis fungoides (skin samples) patients.
FIG. 5 shows that the gene expression profile reflected the size of tumor burden in an SzS patient. The gene expression profile of patient P2 (Table 1) was analyzed before (pre thr) and after (post thr) cancer therapy. Among the probe sets differentially regulated in SzS and control PBMC samples, a group of probe sets changed over 2-fold towards the control phenotype as a consequence of successful treatment. The upregulated (A) and down-regulated (B) probe sets are presented as compared to the average expression of these probe sets in all patient samples. The changes in gene expression correlated with the clinical phenotype of the patient before (C) and after (D) treatment. The percentage of Sezary cells of blood lymphocytes is indicated in the inserts.
FIGS. 6A-D show immunohistochemical detection of CD52 and IL7R, found upregulated at RNA level, in lesional mycosis fungoides and Sezary syndrome skin samples before therapy. A) Abundant expression of CD52 protein in the skin-infiltrating lymphocytes of CTCL (Patient P2). Magnification, ×15. B) Only few CD52+ lymphocytes were found in inflammatory lesions (case C14). Magnification, ×40. C) IL7R is expressed by  ̃30% of lesional lymphocytes in CTCL (patient P15). Magnification, ×60. D) Only few cells are positive for IL7R in the inflammatory control samples.



DETAILED DESCRIPTION OF THE INVENTION
Novel targets for CTCL or CTCL subtype diagnosis as well as for prevention, amelioration and therapy have been revealed.
Aberrant regulation of one or several genes or gene products, specifically MS4A4A, NKG7 (also known as GIG1), IL7R (also known as IL7R-ALPHA or CD127), CD52, TBX21 (also known as TBET), SCYA5 (also known as CCL5 or TCP228), and LIR9 (also known as ILT11 or CD85F), is associated with CTCL. The genes have been described in the prior art.
The present invention is based on a method of detecting CTCL or susceptibility to CTCL by determining differential regulation of one or more genes or gene products selected from the group comprising MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9.
Specifically, CTCL or CTCL subtype is mycosis fungoides (MF) or Sezary syndrome (SzS).
In one specific embodiment of the method of the invention over- or underexpression of one or several of the genes is characteristic of Th1 or Th2 polarization.
In one specific embodiment of the method of the invention over-expression of LIR9 is characteristic of Th2 polarization.
In one specific embodiment of the method of the invention under-expression of NKG7, TBX21 or SCYA5 is characteristic of Th2 polarization.
In one specific embodiment of the method of the invention under- or overexpression indicates the early stage of CTCL.
In one specific embodiment of the method of the invention under- or overexpression indicates the late stage of CTCL.
In one specific embodiment of the method of the invention expression of genes, gene fragments or gene products that is one or several genes, gene fragments or gene products listed in Tables 2 or 3, is determined.
The present invention is also based on a diagnostic kit comprising the necessary means for detecting one or more genes, gene fragments or gene products selected from the group comprising MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9.
In one specific embodiment of the kit of the invention the test kit comprises the necessary means for detecting genes MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9 or gene fragments or gene products thereof.
As used herein the expression “gene product” refers to a mRNA, protein or to any product achieved directly or indirectly from the gene.
As used herein the expression “gene fragment” refers to any part of a gene or an incomplete or isolated portion of a gene, which is detectable in the methods of the invention.
As used herein the expressions “over- and underexpression” refer to up- or down-regulation of a gene or gene products, correspondingly.
As used herein the expression “biological sample” refers to any suitable tissue sample, such as whole blood or biopsy from the tissue or lymph node. The biological sample can be, if necessary, pretreated in a suitable manner known to those skilled in the art.
As used herein the expression “subtype” refers to a restricted type of disease, functional disorder or defect such as mycosis fungoides or Sezary syndrome.
As used herein the expression “Th1 or Th2 polarization” refers to a path, where pre-Th cells begin to proliferate, become activated, and depending on the stimulation gain characteristics of Th1 or Th2 cells and develop to Th1 or Th2 cells.
As used herein the expression “by screening agents” refers to any in vitro or in vivo method known by the man skilled in the art, which method can be used in evaluating or measuring the effect of an agent on genes or gene products.
As used herein the expression “necessary means for detecting genes, gene fragments or gene products” refers for example to any markers, probes, primers, antibodies as well as standards, labels, buffers, diluents, and washing solutions suitable for detection. The expression also refers to compositions or diagnostic kits, which are provided for example in the form of an ELISA, protein chip, nucleic acid chip or a membrane loaded with DNA, RNA or protein, or any other composition known by the man skilled in the art. Optionally, diagnostic kits comprise instructions to carry out the methods for detecting genes, gene fragments or gene products.
In the present invention, information on the poorly understood pathogenesis of CTCL was obtained by microarray gene expression analysis with Affymetrix oligonucleotide array containing over 22 000 transcripts and by combining the data with results obtained with CGH. Real-time quantitative PCR and immunohistochemistry were used to validate the microarray data.
Th1-specific genes such as SCYA5, NKG7, and TBX21 were found to be downregulated in SzS samples (FIG. 1E) and genes e.g. LIR9 and MS4A4A were found upregulated in both MF and SzS samples (Table 3). In lesional MF skin samples IL7R and CD52 were upregulated. Chromosomal arms 1q, 3p, 3q, 4q, 12q, 16p and 16q revealed amplified chromosomal areas and overexpressed genes. Chromosomal areas 4q and 12q also contain down-regulated genes and deleted areas.
After successful therapy of one SzS patient a group of 57 probe sets was changed towards the control PBMC phenotype. The therapy-responsive genes included e.g. S100P, CCR10, BCL2, VAV3 and GZMB.
Differential regulation of genes, gene fragments or gene products can be caused by various events or mechanisms such as point mutations, polymorphisms, translocations, genetic or chromosomal deletions, insertions, gene or chromosomal amplifications, gene conversions and any other defects. Silencing of genes or chromosomal areas can be caused for example by epigenetic mechanisms such as methylation.
According to the method of the present invention, expression of genes, gene fragments, and gene products can be detected in a biological sample by any known suitable detection method. These methods comprise detecting a gene expression or methods based on detecting the copy number of the gene, DNA or chromosome and/or those based on detecting the gene expression products (mRNA or protein). Such methods are easily recognized by those skilled in the art and include for example enzymatic methods, electrophoretic methods or physical methods such as conventional polymerase chain reaction (PCR)-methods, RT-PCR, real time quantitative PCR, single strand conformation polymorphism (SSCP), heteroduplex analysis, fragment analysis, DNA sequencing, minisequencing, primer extension methods, microarrays, mass spectrometry and denaturing high performance liquid chromatography (DHPLC). In addition, suitable methods include conventional G-banding techniques, comparative genomic hybridization (CGH), in situ hybridisations, such as FISH, mRNA in situ hybridization, Northern analysis, and Southern as well as Western analyses, immunohistochemistry, and other immunoassays, such as ELISA. Epigenetic assays such as methylation assays may also be used.
Any markers suitable for detecting differential gene regulation, include any biological markers such as microsatellite markers, SNP-markers, any probes, primers or antibodies associated with genes or gene products.
The current finding of up- and downregulation of specific genes can be used in the field of CTCL diagnostics. Diagnostic tests, based on the current findings, may also have implications in the tests for screening patients for eventual subclinical forms of CTCL. Such screening tests may be based on the detection of secretory proteins upregulated in CTCL. Furthermore, any diagnostic test developed on basis of the currently revealed genetic alterations in CTCL may be used to monitor or predict the disease outcome, to predict the drug responsiveness of the patients and in clinical follow-up.
The current finding of up- and downregulation of specific genes in CTCL can also be used in the field of therapy, when restoration of the normal function of genes can be used. This may be reached by enhancing the expression of functionally homologous genes, by introducing an intact gene or by using an altered form of the gene or antisense oligonucleotide or small inhibitory RNA against the gene or gene product in any technique presently available for gene therapy to prevent the progression of a proliferating disease. Such techniques include the in vivo, ex vivo and in situ therapy methods comprising transducing or transfecting an intact or altered gene (or its functional domains) in a recombinant or peptide form or as antisense oligonucleotides or in an expression vector to the patient or inserting the altered gene or oligonucleotide into a carrier, which is then introduced into the patient. It is noteworthy that the delivery of those genes, which are hoped to be expressed in a therapeutic manner can be achieved by epicutaneous delivery of naked DNA vectors expressing the gene of interest. One possible way to express a therapeutic gene would be to use viral vectors, especially ones with a preferential homing to skin and dermis. Alternatively, monoclonal or humanized antibodies, modified antibodies or peptides binding to the protein or to the fusion gene generated can be used to suppress the function of the altered protein. Antibodies against the protein could also be used to carry and target other agents, such as cytotoxic substances, to specific cells. In particular, a transient or a permanent cure of CTCL may be achieved by above-mentioned methods.
Observed genetic changes as well as consequent alteration in the expression profile in CTCL and SzS are useful to design novel drugs for these malignancies. Such drugs may be monoclonal antibodies targeted against membrane proteins that are expressed on the malignant cells or against secretory proteins that in turn affect the host regulatory processed, such as immune response against the malignant cells. Furthermore, monoclonal antibodies or other response modifiers may be targeted against secretory products of the malignant cells that favor the spread of the tumor. An important group of target molecules for therapeutic approaches for CTCL are the genes and gene products involved in immune regulation.
To identify shared expression profile to the most common forms of CTCL and to mask the effect of reactive T-cells, likely to influence the results, our sample material consisted of several cell subpopulations of both SzS and MF patients. Despite the difference in the quantity of malignant T-cells in SzS and MF blood, we identified a common gene expression pattern. Our findings provide basis for previous findings of a preferential Th2 type cytokine profile in SzS, since we identified a panel of Th1-specific genes (Szabo S J et al. Cell 100:655-669, 2000, Hamalainen H et al. Genome Biol 2:RESEARCH0022, 2001, Rogge L et al. Nat Genet 25:96-101, 2000, Lund R et al. Eur J Immunol 35:3307-3319, 2005, Nagai S et al. Int Immunol 13:367-376, 2001, and Kashi-wakura J et al. J Exp Med 190:1147-1154, 1999), e.g. TBX21, SCYA5, NKG7, XCL1, TXK, and GZMB, to be down-regulated in SzS samples.
Of the Th1-specific genes downregulated in SzS, TBX21 and TXK represent transcription factors essential for Th commitment to Th1 phenotype. They both regulate IFNγ expression, the expression of which we have previously shown to be absent from the chromosomally clonal, i.e. true malignant cells in SzS (Karenko L et al. J Invest Dermatol 116:188-193, 2001). Also, they belong to a positive feedback loop promoting Th1 cytokine secretion leading to Th1 development (Szabo S J et al. Cell 100:655-669, 2000, Takeba Y et al. J Immunol 168:2365-2370, 2002). The expression of TBX21 was very low also in one MF patient, but the overall variation among MF patients, representing various stages, was greater than among the leukaemic SzS patients. Recently, TBX21 has also been shown to regulate the CD4+ cell trafficking to inflammatory sites, by regulating e.g. the expression of the chemokine ligand CXCR3 (Lord G et al. Blood 106:3432-3439, 2005), but TBX21 has not been linked to CTCL before. Our finding of TBX21 downregulation in SzS thus explains the previous observation of the loss of CXCR3 expression along the progression of MF (Appay V and Rowland-Jones SL. Trends Immunol 22:83-87, 2001). Furthermore, the expression of SCYA5 (RANTES), a chemokine mediating the trafficking and homing of T-cells (Turman M A et al. Hum Immunol 36:34-40, 1993), and that of NKG7 (Vowels B R et al. J Invest Dermatol 99:90-94, 1992) was downregulated in our SzS PBMC samples. These genes have also been linked to Th cell differentiation, and they are more abundantly expressed in cells polarized to Th1 than to Th2 direction (Hamalainen H et al. Genome Biol 2:RESEARCH0022, 2001, Rogge L et al. Nat Genet 25:96-101, 2000, Lund R et al. Eur J Immunol 35:3307-3319, 2005, Nagai S et al. Int Immunol 13:367-376, 2001).
Other genes, which were upregulated during the early polarization of T-helper cells into Th2-direction (Lund R et al. Eur J Immunol 35:3307-3319, 2005) and were upregulated in both our SzS and MF PBMC samples, included the SLOOP gene. S100P has a role in cell cycle progression and differentiation, and its upregulation has been found in various malignancies (Vowels B R et al. J Invest Dermatol 103:669-673, 1994, Dummer R et al. Blood 88:1383-1389, 1996, Cairns C M et al. J Immunol 167:57-65, 2001, and Dohring C et al. Immunogenetics 44:227-230, 1996). Since an expression bias for S100P was found in MF blood samples, too, S100P may have a role in the early oncogenesis of CTCL. Also, we found membrane-bound LIR9 (215838_at) to be overexpressed in SzS PBMC, MF PBMC and MF CD4+ samples compared to controls. LIR9 is a member of leukocyte immunoglobulin-like receptor family mostly expressed on monocytes and neutrophils but not on normal T cells. In monocytes, activation of LIR9 has been shown to induce calcium mobilization and secretion of IL-1β, TNF-α and IL-6 (Gardiner C M et al. J Immunol 166:2992-3001, 2001). Of the latter, dysregulation of TNF signalling pathway has been linked to both SzS and MF pathogenesis (Tracey L et al. Blood 102:1042-1050, 2003 and Guerreiro Da Silva I D et al. Int J Oncol 16:231-240, 2000), and IL-6 has been shown to be a marker of SzS tumor burden and to correlate with clinical stage in non-leukemic CTCL (Sato N et al. Oncogene 23:1531-1538, 2004). IL-6 is an important cytokine for Th2 cell differentiation (Hammacher A et al. Int J Biochem Cell Biol 37:442-450, 2005), but also induces S100P (Cairns C M et al. J Immunol 167:57-65, 2001).
Taking together the above knowledge (Table 3), our findings seem to explain the occurrence of a functional bias towards Th2 in Sezary syndrome (Mousses S et al. Cancer Res 62:1256-1260, 2002, Diederichs S et al. Cancer Res 64:5564-5569, 2004, and Sheibani K et al. Am J Pathol 127:27-37, 1987). Our findings also indicate that a bias towards Th2 takes place already in the MF stage, prior to progression to the leukaemic phase. Such a skewing is likely to influence the progressive immune dysregulation in CTCL and would thus provide a growth advantage for the malignant cell clone(s).
Of the cytotoxicity-associated genes, we found downregulation of XCL1 (lymphotactin), previously shown to augment antitumor responses (Boehncke W H. Arch Dermatol Res 285:127-130, 1993), and GZMB (granzymeB). We have previously shown, with the combination of immunihisto-chemistry and FISH, that granzymeB is absent from the clonal cells in skin and lymph node samples of SzS (Karenko L et al. J Invest Dermatol 116:188-193, 2001). KIR3DL2, a member of the killer cell immunoglobulin-like receptors, has previously been suggested as a phenotypic marker for Sezary cells (Poszepczynska-Guigne E et al. J Invest Dermatol 122:820-823, 2004) and has been found upregulated in SzS (van Doorn R et al. Cancer Res 64:5578-5586, 2004). Contradictory, we found KIR3DL2 gene to be downregulated in SzS. However, the LIR9 gene, located in the same leukocyte receptor cluster as KIR3DL2 was overexpressed. This discrepancy of observations may be due to the considerable polymorphism of the KIR3DL2 gene (Jones D et al. Clin Cancer Res 10:5587-5594, 2004, Duvic M et al. Am J Hematol 58:87-90, 1998). Thus, our data provide evidence for the downregulation of several cytotoxicity-associated genes in SzS.
We found IL2Rβ to be downregulated in SzS blood samples, which is of interest since IL2 is the major cytokine for T-cell activation and proliferation. IL2R consists of three subunits, of which IL2Rβ and IL2Rγ are expressed on resting T-cells and upregulated by e.g. IL-2. Previously, the high/intermediate affinity IL2R (α/p55/CD25+β/p75/CD122+γ/p64/CD132 chains/β+γ chains) has been reported to be expressed on about 50% of CTCL cells (Olsen E et al. J Clin Oncol 19:376-388, 2001, Duvic M. Algorithms. Clin Lymphoma 1 Suppl 1:S51-5, 2000, and Foss F et al. Blood 106:454-457, 2005). Consequently, IL2-targeted therapy has been used for CTCL, most recently with a fusion protein denileukin diftitox (ONTAK) (Borges L et al. Blood 101:1484-1486, 2003). Interestingly, the retinoid X receptor (RXR) retinoid, bexarotene, a new therapeutic agent for MF (French L E et al. Blood 105:219-225, 2005), has been shown to upregulate both the p55 and p75 subunits of IL-2R. This upregulation, in turn, enhances the susceptibility of the malignant cells to denileukin diftitox, resulting in overall response rates of 67% in relapsed CTCL patients (Hassel J C et al. Dermatology 209:296-300, 2004).
We also observed, for instance, that one member of the MS4A superfamily (Liang Y and Tedder T F. Genomics 72:119-27, 2001), MS4A4A was upregulated on SzS cells. Another member of this superfamily, CD20, is already now the target of monoclonal antibody mediated therapy in large B-cell lymphomas (Press O W et al. Blood 69:584-91, 1987). We therefore propose, that the MS4A4A is useful as a target molecule for therapy of SzS.
Another potential target membrane protein is LIR9 (215838_at) found to be over expressed on SzS. Similarly to MS4A4A, specific monoclonal antibodies against LIR9 (215838_at), preferentially humanized or hybrid forms, are useful as a therapeutic principle. However, several other potential forms of drug acting on membrane proteins can be designed, based on the findings in this patent application, such forms being for example aptomeres or agonistic peptides. Furthermore, genetically altered natural ligands for the membrane protein that inhibits or strengthens the action of the natural ligand may be used as a therapeutic principle.
Another potential target molecule for therapeutic approaches is the S100P gene, which has a role in cell cycle progression and differentiation. Its upregulation has been found in various malignancies (Vowels B R et al. J Invest Dermatol 103:669-673, 1994, Dummer R et al. Blood 88:1383-1389, 1996, Cairns C M et al. J Immunol 167:57-65, 2001, and Dohring C et al. Immunogenetics 44:227-230, 1996) and its expression is regulated by steroid hormones, notably by androgens and progestins. We propose therefore that similar principles are useful for therapy of CTCL.
Several expression alterations of the invention tended to skew the Th1/Th2 balance. Furthermore, genes that would be involved in the activation of cytotoxic T-cells (CTL) were down regulated. Although it is not clear how a chance in the immunological profile of the T-cells in CTCL will lead to malignancy, it is noteworthy that the effective therapy with bexarotene and ONTAK leads to a Th1 favoured balance. Therefore, it can be assumed that any therapeutic principle leading to the same but involving those genes and gene products noticed in the current work can be employed.
In addition to the genes involved in immune regulation, two genes, commonly upregulated in our samples, were of interest. The SNCA gene, mapping to chromosome 4q21, was upregulated in all studied tissue or cell types of MF and SzS patients. Amplifications of 4q are frequent in CTCL (Diehl S and Rincon M. Mol Immunol 39:531-536, 2002) and in our integrated analysis, 4q turned out to be one of the areas with overexpressed genes and DNA copy number amplifications. SNCA is a major component of protein aggregates present in Parkinson's disease (Mao X et al. Br J Dermatol 147:464-475, 2002). Although some genes linked to Parkinson's disease may also have aberrant expression levels in cancers (Kim S et al. Parkinsonism Relat Disord 10 Suppl 1:S9-13, 2004), such a connection has not been found for SNCA so far. However, overexpression of SNCA has been shown to cause increased cell proliferation (West A B et al. Trends Neurosci 28:348-352, 2005). The matrix metalloproteinase MMP-9 was overexpressed in SzS and MF PBMC samples. This provides new aspects for the pathogenesis of CTCL since MMPs, in addition to their role in facilitating tumor cell invasion and metastasis (Lee S S et al. Neurobiol Aging 24:687-696, 2003 and Klein G et al. Crit Rev Oncol Hematol 50:87-100, 2004), are involved in cancer initiation, possibly by activating intracellular mediators that are inducers of genomic damage and may cause genomic instability (Overall C M and Lopez-Otin C. Nat Rev Cancer 2:657-672, 2002, Demers M et al. Cancer Res 65:5205-5210, 2005, and Sakata K et al. Acta Cytol 46:697-703, 2002). Concordant to our finding, MMP-9 overexpression has been previously observed in MF in relation to an advancing stage (Egeblad M and Werb Z. Nat Rev Cancer 2:161-174, 2002). Thus, our observation suggests that the role of MMPs should be studied further at the early stages of CTCL carcinogenesis.
Previously, several studies on CTCL have pointed out chromosomal instability as a hallmark of the disease. In SzS samples, we observed down-regulation of VAV3, which has structural similarities with the NAV3 gene, frequently deleted in CTCL (Karenko L et al. Cancer Res 65:8101-8110, 2005). The DLG5 tumor suppressor gene (Karenko L et al. J Invest Dermatol 108:22-29, 1997), also downregulated in SzS samples, is located in 10q23, a chromosomal area often deleted in CTCL (Diehl S and Rincon M. Mol Immunol 39:531-536, 2002 and Kaltoft K et al. Dermatol Clin 12:295-304, 1994). In this study, we have for the first time correlated the chromosomal changes with aberrations observed in gene expression level in the same patient subset. We identified seven chromosome arms, namely 1q, 3p, 3q, 4q, 12q, 16p and 16q, where both gene expression and DNA copy number was changed to the same direction. All these arms contain overexpressed genes and amplified chromosomal areas in our data set. Areas 4q and 12q also contain down-regulated genes and deleted areas. Previously, it has been shown with breast cancer samples by using array CGH, that a 2-fold change in DNA copy number is associated with an analogous 1.5-fold change in mRNA expression and at least 12% of the differences seen at transcription level were due to the variation in gene copy number (Pollack J R et al. Proc Natl Acad Sci USA 99:12963-12968, 2002).
In summary, detection of differential regulation of genes or gene products during CTCL initiation and progression will contribute to early diagnosis of disease and treatment of patients. The present invention discloses for the first time the role of at least one or several of the genes MS4A4A, NKG7, IL7R, CD52, TBX21, SCYA5, and LIR9 in CTCL. The present invention also discloses that detection of up- or down-regulation of these genes or gene products allows identification of CTCL patients or patients with an increased risk to develop CTCL. Discoveries of novel diagnostics and follow-up methods reveal new possibilities in the field of CTCL medicine.
The following examples are given for further illustration of the invention.
It will be obvious to a person skilled in the art that, as the technology advances, the inventive concept can be implemented in various ways. The invention and its embodiments are not limited to the examples described above but may vary within the scope of the claims.
Example 1
Genes expressed differentially among CTCL patients and Controls
a) Patient and Control Samples
Altogether, 30 samples obtained from 18 patients volunteering to the study were analyzed (Table 1). Peripheral blood mononuclear cell (PBMC) samples were obtained from 12 Sezary syndrome and mycosis fungoides patients and lesional skin biopsies from 9 mycosis fungoides patients (stage IA-IVB; defined according to the WHO-European Organization for Research and Treatment of Cancer classification for cutaneous lymphomas; Willemze R et al. Blood 105:3768-3785, 2005). More precisely, Affymetrix (Santa Clara, Calif.) analysis was done for 6 PBMC or CD4+-enriched cell samples of four Sezary syndrome patients and for 11 PBMC, CD4+, or skin lesion samples of five mycosis fungoides patients (Table 1). The percentage of Sezary cells (medium-sized lymphoid cell with a highly cleaved “cerebriform” nucleus and darkly clumped chromatin) among peripheral blood lymphocytes of Sezary syndrome patients ranged from 16% to 70%. None of the Sezary syndrome patients had received any anticancer therapy before sampling. Real-time quantitative PCR (qPCR) analysis was done for PBMC samples of six Sezary syndrome patients and for 12 PBMC, CD4+, or lesional skin samples of seven mycosis fungoides patients. In addition, skin lesion samples of two Sezary syndrome and seven mycosis fungoides patients were studied immunohistologically (Table 1). For reference material, blood samples were obtained from 5 healthy volunteers and skin biopsies were obtained from 10 voluntary patients with nonmalignant, lymphoid skin infiltrates (Table 1). The study was approved by the Ethical Re-view Board of the Skin and allergy hospital, Helsinki University Hospital.
b) RNA Isolation
Peripheral blood mononuclear cells (PBMC) from patients and healthy controls were collected by Ficoll Paque density gradient centrifugation (Ficoll-Paque PLUS, Amersham Biosciences, Uppsala Sweden), and CD4 positive cells were enriched with magnetic beads (CD4+ T-cell isolation kit #130-053-101, or CD4+ MicroBeads #130-045-101, Miltenyi Biotec, Bergisch Gladbach, Germany). Total RNA was isolated with Trizol Reagent (Invitrogen, Life Technologies, Grand Island, N.Y.). Fresh skin biopsies were immediately placed in RNA Later buffer (Ambion, Austin, Tex.), and RNA was collected by homogenizing the tissue in Trizol Reagent, whereafter RNA isolation was performed with Qiagen RNeasy kit according to manufacturer's instructions.
c) Analysis of Gene Expression Microarray Data
100 ng of purified (RNeasy Mini, Qiagen, Valencia, Calif.) RNA was prepared for hybridization according to Affymetrix small sample protocol (Affymetrix Technical note, GeneChip® Eucaryotic Small Sample Target Labelling Assay Version II). cDNA was hybridized against Affymetrix HG-U133A chip (Affymetrix, Santa Clara, Calif.). Gene expression estimates were calculated using the GC-RMA procedure (Wu Z et al. Journal of the American Statistical Association 99:909-917, 2004). In each two-group comparison, the statistical significance of the difference in gene expression levels between the groups was assessed with a modified t-test (Smyth GK. Statistical Applications in Genetics and Molecular Biology 3:Article 3, 2004). A gene was considered changed if the p-value of the test was less than 0.05 and there was at least a 2-fold change in the mean expression levels. The statistical analyses were carried out with R (cran.r-project.org) packages Affy and Limma and visualization with the TreeView software (Eisen M B et al. Proc Natl Acad Sci USA 95:14863-14868, 1998).
d) Identification of Regional Biases in Gene Expression
Patient-specific gene expression profiles were constructed by calculating gene expression ratios between each patient and the average of the matched controls. To assess regional biases in the expression profiles, the microarray probe sets were mapped along the chromosomes using the Bio-conductor annotation package hgu133a. To determine whether the set of expression ratios that map to a particular chromosomal arm exhibit upward or downward bias, a sign test was applied (Crawley J J and Furge K A. Genome Biol 3:RESEARCH0075, 2002). The algorithm scores a gene as up- or down-regulated if the expression change is at least 1.8-fold, and the sign test determines whether the corresponding chromosomal arm contains a statistically significant number of genes that change in the same relative direction. An expression bias was considered significant if the p-value of the sign test was less than 0.05. Of the acrocentric chromosomes only q-arms were included in the analysis.
e) Genes Expressed Differentially Among CTCL Patients and Controls
We identified altogether 168 probe sets (fold change>2, p-value<0.05) to be differentially regulated in SzS PBMC samples compared to control PBMC samples (FIG. 1A; FIG. 1 shows differentially regulated genes in all studied cell populations with fold change exceeding the value 3) and substantial variation of gene expression between control and MF skin samples (FIG. 1B). Since the number of malignant cells in SzS patient blood samples is considerably greater than that in MF patient blood samples, the gene expression profiles varied remarkably between SzS and MF PBMC samples (FIG. 2A). However, a subset of genes was found to change in a similar manner both in SzS and MF PBMC samples (FIG. 2B). To mask the effect of reactive or regulatory T-cells, commonly present in the samples of CTCL (Wood G S et al. J Cutan Pathol 21(2):151-156, 1994, Bagot M et al. Blood 91:43314341, 1998, and Berger C L et al. Blood 105:1640-1647, 2005), comparison of microarray data from different cell populations was performed, and changes common to different cell sources of MF patients (PBMC, CD4+ lymphocytes, lesional skin) as well as for SzS PBMC samples were identified (Table 2).
Two Th1-specific genes (SCYA5 and NKG7), and IL-2Rβ, VAV3, DLG5, and KIR3DL2 were found to be over 2-fold downregulated in SzS samples (FIG. 1E). Genes upregulated in both MF and SzS blood samples included e.g. S100P and MMP-9. In lesional MF skin samples, compared to inflammatory dermatoses, IL7R and CD52 were upregulated. SNCA and LIR9 genes were upregulated in several cell populations of SzS and MF patients (Table 2). In addition, TBX21 was selected for further analysis based on its crucial role in Th1 differentiation.
Example 2
Real-Time Quantitative PCR and Immunohistochemistry
The key findings of gene expression data were confirmed with real-time quantitative PCR (qPCR). RNA samples were treated with Deoxyribonuclease 1, Amplification grade (Invitrogen Life Technologies, Carlsbad, Calif.) to eliminate possible genomic DNA and the purity of RNA was checked with RT run. The cDNA was prepared with Superscript II kit (Gibco BRL, Life Technologies, Paisley, Scotland). TBX21, NKG7, SCYA5, SLOOP, and house keeping gene EF1α were run with FAM (reporter) and TAMRA (quencher) duallabeled probes and other genes with ProbeLibrary probes (Exiqon A/S, Vedbaek, Denmark). Primer and probe sequences are listed in table 4. Linearity of amplification was confirmed by running standard curves for each amplicon and specificity of the reagents was verified by gel electrophoresis. The PCR reactions were carried out using ABsolute QPCR ROX mix (ABgene, Epsom, UK) with 300 nM primers and 200 nM probe. Detection was done with Applied Bio-systems's ABI Prism 7700 sequence detector (15 min 95° C. followed by 40 cycles of 15 s 95° C. and 1 min 60° C.). The results were normalized against EF1a detection value (Hamalainen HK et al. Anal Biochem. 299: 63-70, 2001).
Immunostainings for CD52 (Abcam, Cambridge, UK, diluted in 1:100), IL7R (R&D Systems, MN, USA, 1:10), IL7 (R&D Systems, 1:20), and KLK10 (R&D Systems, 1:30) were performed with Vectastain Elite Mouse kit (Vector Laboratories, Burlingame, Calif.), according to manufacturer's instructions. The immunostainings were carried out on frozen tissue sections of four CTCL patients included in the Affymetrix study, of 5 additional CTCL patients, and of 5 controls with eczema or lichen planus. MMP9 immunostaining was performed on formalin fixed paraffin embedded tissue sections of six CTCL patients included in the Affymetrix study and on controls with lichen planus and psoriasis using a mouse monoclonal antihuman MMP9 antibody (Research Diagnostics Inc, Flanders, N.J.; diluted in 1:50) as previously described by Saarialho-Kere and coworkers 1993.
Quantitative PCR, performed on 10 genes (FIG. 3), and immunohistochemistry, performed on four gene products (CD52, IL7R, IL7, MMP-9), validated the microarray data (FIGS. 6A-D). Especially, we wanted to make sure that our array results on KIR3DL2, previously reported to be a marker gene of CTCL (Poszepczynska-Guigne E et al. J Invest Dermatol 122:820-823, 2004), and now found downregulated in our SzS patients, were not due to differences in target sequence. Therefore, the KIR3DL2 result was confirmed by using qPCR reagents detecting the same sequence as the Affymetrix probe set (207314_x_at) and region previously reported (Uhrberg M et al. Immuno-genetics 54:221-229, 2002). Both sets of reagents for KIR3DL2 inevitably showed that the expression of this gene was downregulated in our sample set. Interestingly, we also show the downregulation of TBX21 (T-bet) gene in PBMC samples of both SzS and MF patients (FIG. 3B). Downregulation in the expression of SCYA5 (RANTES), and NKG7 were observed also in MF PBMC samples (FIG. 3A).
In immunohistochemistry (FIG. 6), CD52 protein was expressed by the majority (in average, 3 of 4) of skin-infiltrating lymphocytes of all CTCL patients when compared with inflammatory dermatoses with sparse expression. IL7R was expressed in basal keratinocytes (focally) but also in skin-infiltrating lymphocytes of all CTCL biopsies. The number of lymphocytes or keratinocytes expressing IL7R was, in average, thrice higher than in control samples. No difference in the expression levels of IL7 protein was found between CTCL patients and controls. MMP-9 protein was demonstrable in 25% to 50% of infiltrating lymphocytes in Sezary syndrome samples, whereas MMP-9 expression in mycosis fungoides samples was variable. In inflammatory dermatoses, the lymphocytes did not express MMP-9.
Example 3
Chromosomal regions showing both gene expression and Gene Copy Number Changes
a) Comparative Genomic Hybridization (CGH) and Multifluor Fluorescent In Situ Hybridization (mFISH)
CGH was performed as previously reported (Karenko L et al. J Invest Dermatol 112:392-395, 1999) from the DNA of three SzS and three MF patients (Table 1). Nine to twelve metaphases were included in the analysis for each case. As an internal control, normal male and female DNA were cohybridized and only differences in sex chromosomes were identified. MFISH of metaphase preparations from cases 1-3, 5, 7, and 8, was performed as described previously (Karenko L et al. Cancer Res 65:8101-8110, 2005). At least 50 metaphases were analyzed for each case.
Finally, we examined the gene expression profiles by chromosome arms in four SzS PBMC and three MF skin samples. Five chromosomal arms showed consistently significant upward bias in gene expression in at least four of the seven patients: 1q, 3p, 3q, 16p, and 16q. Also, in chromosomes 4q and 12q, both an upward and a downward bias was detected (FIG. 4A). As an example, FIG. 4B illustrates the gene expression ratios mapped to chromosome 12q. Clusters of differentially expressed genes can be visualized especially in the areas 12q13 and 12q23-q24.
To integrate the chromosomal and transcriptomic data, the chromosomal regions identified with the sign test were compared to the chromosomal aberrations detected by CGH. In three of the identified seven chromosomal arms, 1q, 4q, and 16q, a significant gain was detected also by the CGH analysis in at least four of the MF skin and SzS blood samples. For example, the SNCA gene found to be upregulated locates to cytoband 4q21. In chromosomes 3p, 3q, and 12q, a significant gain was detected in at least two of the samples, and in 16p, in one sample. In chromosomes 4q and 12q, where also downward expression bias was identified, a loss was detected by CGH in one and two of the samples, respectively (FIG. 4C).
Example 4
A Subset of Genes was Found to Change Following Therapy (Example of One Patient)
A follow-up PBMC sample of one of the Sezary syndrome patients (case 2, described in Example 1a, Table 1) was obtained 19 months after a continuous therapy resulting in clinical response. Among the probe sets differentially regulated in SzS PBMC samples, when compared to control PBMC samples, a group of 57 probe sets was changed towards the control phenotype after successful therapy (FIG. 5). The therapy-responsive genes included e.g. S100P, CCR10, BCL2, VAV3 and GZMB.







TABLE 1







Characteristics of patient and reference samples included into the study

















Sex and




Chromosomal
Prior





Age
Diagnosis
Array
QPCR
IHC
clone*
therapy
SzS
Other




















Patients











P1 §
M52
SzS
PBMC
PBMC
skin
t(1; 5), del (9)
nil
40%
DOD


P2 §
M63
SzS
PBMC
PBMC
skin
t(2; 5)
nil
70%



M65
SzS,
PBMC, CD4+


t(2; 5)
C + P, B
31%




follow-up sample


P3 §
M72
SzS
PBMC
PBMC

none
nil
16%
DOD


P4
M72
SzS
PBMC
PBMC


nil
33%


P5 ∥
M58
MF IB
PBMC, CD4+,
PBMC, CD4+,
skin
del (12q21-22) †,
nil





skin
skin








NAV3 deletion ‡


P6
F69
MFIB
PBMC
PBMC


PUVA,

DOD









chemotherapy


P7 ∥
M71
MF IB, CD30+
PBMC, CD4+,
PBMC, CD4+
skin
NAV3 deletion ‡
PUVA





skin


P8 ∥
F79
MF IA
PBMC, CD4+,
PBMC, CD4+,

none
nil





skin
skin


P9
F45
MF IVB
PBMC
PBMC


PUVA, UVB,









retinoids


P10
F73
MF

skin

ND
PUVA


P11 (MF1)
F59
MF

PBMC

ND
electron beam


P12 (SzS1)
M58
SzS

PBMC

ND
nil


P13 (SzS2)
M74
SzS

PBMC

ND
methotrexate


P14
M62
MF


skin
NAV3 deletion ‡


P15
M76
MF


skin
NAV3 deletion ‡


P16
F56
MF


skin
NAV3 deletion ‡


P17
M42
MF


skin
NAV3 deletion ‡


P18
M55
MF


skin
NAV3 deletion ‡


P19
M58
SzS


skin


P20
M62
SzS


skin


Controls


C1
M27
Control
PBMC, CD4+
PBMC, CD4+


C2
M49
Control
PBMC, CD4+
PBMC, CD4+


C3
F52
Control
PBMC, CD4+
PBMC, CD4+


C4
M67
Control
PBMC, CD4+
PBMC, CD4+


C5
F66
Control
PBMC, CD4+
PBMC, CD4+


C6
F51
Infiltr.
skin
skin




lymphocytica


C7
F68
Lichen planus
skin
skin


C8
M77
Eczema
skin
skin


C9
F63
Eczema
skin
skin


C10
F72
Lichen planus


skin


C11
M62
Lichen planus


skin


C12
F74
Lichen planus


skin


C13
F76
Lichen planus


skin


C14
M59
Eczema


skin


C15
F69
Eczema


skin





Array = samples studied with Affymetrix microarray


QPCR = samples studied with real-time quantitative PCR


IHC = samples studied immunohistologically


SzS = percentage of morphological Sezary cells of lymphocytes


*detected with MFISH


† detected with G-banding or


‡ FISH as described in Karenko et al. 2005


§ CGH from PBMC


∥ CGH from lesional skin


C + P = chlorambusil + prednison, B = bexarotene, PUVA = psoralen + UVA photochemotherapy


DOD = died of disease


ND = not done













TABLE 2





Genes showing similar expression profiles in all CTCL subtypes and in different


tissue samples (fold change of at least 2, p-value less than 0.05)



















Gene
GO*
Probe ID
UniGene ID
Locus





ZBTB16
nucleid acid binding
205883_at
Hs.171299
11q23.1


CD160
receptor activity
207840_at
Hs.488237
1q21.1


HIST2H2AA
—
218280_x_at
Hs.530461
1q21.2


HIST2H2AA
—
214290_s_at
Hs.530461
1q21.2


HBD
oxygen transporter activity
206834_at
Hs.36977
11p15.5


MMP9
gelatinase B actvity
203936_s_at
Hs.297413
20q11.2-q13.1


SNCA
protein binding
204466_s_at
Hs.271771
4q21


YWHAE
protein domain specific binding
213655_at
Hs.513851
17p13.3


LIR9
—
215838_at
Hs.512233
19q13.4


TOP1
DNA topoisomerase type I activity
208900_s_at
Hs.472737
20q12-q13.1


S100P
calcium ion binding
204351_at
Hs.2962
4p16


STAT1
trancription factor activity
209969_s_at
Hs.470943
2q32.2


TRIB1
protein kinase activity
202241_at
Hs.444947
8q24.13


GLIPR1
—
204221_x_at
Hs.553516
12q21.1


GLIPR1
—
214085_x_at
Hs.553516
12q21.1


GLUL
glutamate-ammonia ligase activity
217202_s_at
Hs.518525
1q31


MS4A4A
receptor activity
219607_s_at
Hs.325960
11q12


PSMB3
threonine endopeptidase activity
201400_at
Hs.82793
17q12


ITM2A
—
202747_s_at
Hs.17109
Xq13.3-Xq21.2


ETHE1
—
204034_at
Hs.7486
19q13.31


BARD1
ubiquitin-protein ligase activity
205345_at
Hs.54089
2q34-q35


RECQL
nucleotide binding
212918_at
Hs.235069
12p12


HIST2H2BE
DNA binding
202708_s_at
Hs.2178
1q21-q23


CDC42
nucleotide binding
208727_s_at
Hs.467637
1p36.1


RPL31
structural constituent of ribosome
200962_at
Hs.469473
2q11.2


LOC55831
—
217882_at
Hs.475392
3p25.3


G0S2
—
213524_s_at
Hs.432132
1q32.2-q41


ARPC1A
—
200950_at
Hs.124126
7q22.1


C1QBP
—
208910_s_at
Hs.553487
17p13.3


C1QBP
—
214214_s_at
Hs.553487
17p13.3















SzS PBMC
MF PBMC
MF CD4+
MF Skin















Gene
M
P
M
P
M
P
M
P


















ZBTB16
−1.84
0.0001
−1.07
0.0014
—
—
—
—


CD160
−3.51
0.0000
−1.64
0.0290
—
—
—
—


HIST2H2AA
1.32
0.0021
1.43
0.0063
2.09
0.0180
—
—


HIST2H2AA
1.39
0.0008
1.19
0.0250
2.36
0.0220
—
—


HBD
3.45
0.0057
1.86
0.0065
—
—
—
—


MMP9
1.98
0.0083
1.17
0.0070
—
—
—
—


SNCA
2.08
0.0120
1.48
0.0079
†
†
1.19
0.0250


YWHAE
1.25
0.0033
1.06
0.0340
—
—
—
—


LIR9
1.10
0.0065
1.09
0.0360
1.91
0.0001
—
—


TOP1
1.18
0.0026
1.29
0.0480
—
—
‡
‡


S100P
2.21
0.0230
2.12
0.0220
—
—
—
—


STAT1
1.24
0.0270
1.10
0.0410
—
—
—
—


TRIB1
1.07
0.0390
—
—
3.36
0.0240
—
—


GLIPR1
1.14
0.0180
—
—
1.01
0.0083
—
—


GLIPR1
1.20
0.0270
—
—
1.05
0.0090
—
—


GLUL
1.54
0.0078
—
—
1.57
0.0260
—
—


MS4A4A
1.96
0.0140
—
—
1.52
0.0370
—
—


PSMB3
1.15
0.0059
—
—
—
—
1.26
0.0047


ITM2A
1.17
0.0350
—
—
—
—
1.75
0.0200


ETHE1
1.29
0.0260
—
—
—
—
1.40
0.0340


BARD1
1.03
0.0220
—
—
—
—
1.28
0.0320


RECQL
1.06
0.0085
—
—
—
—
1.00
0.0440


HIST2H2BE
—
—
1.73
0.0270
2.46
0.0490
—
—


CDC42
—
—
−1.00
0.0058
−1.36
0.0220
†
†


RPL31
—
—
−1.14
0.0470
−2.27
0.0008
—
—


LOC55831
—
—
1.06
0.0091
1.13
0.0440
—
—


G0S2
—
—
1.55
0.0360
3.73
0.0200
—
—


ARPC1A
—
—
—
—
1.06
0.0230
1.28
0.0072


C1QBP
—
—
—
—
−1.39
0.0008
−1.20
0.0420


C1QBP
—
—
—
—
−1.22
0.0012
−1.30
0.0110





*GO Molecular function


† Statistically significant change to the same direction


‡ Statistically significant change to the opposite direction













TABLE 3







Genes found to be differentially expressed and relevant to CTCL pathogenesis.













Presumed function





or expected functional


Gene designation
Finding
Molecular function
consequence





TBX21 (T-bet)
Downregulated
Transcription factor
Th1 down


SCYA5 (Rantes)
Downregulated
Chemokine
Th1 down


NKG7
Downregulated
Th differentiation
Th1 down


XCL1
Downregulated
Chemokine,
Th1 down, lack of CTL


(lymphotactin)

T-cell cytotoxicity (CTL)
activity


TXK
Downregulated
Transcription factor
Th1 down


GZMB (granzymeB)
Downregulated
T-cell cytotoxicity
Th1 down, lack of CTL





activity


S100P
Upregulated
Th2 polarisation, cell cycle
Th2 up




and differentition


LIR9
Upregulated
Membrane receptor,
Th2 up




induces IL-1β, TNF-α




and IL-6


KIR3DL2
Downregulated
Membrane receptor
Lack of CTL activity


IL2Rβ
Downregulated
Cytokine receptor
Impaired immune





response


VAV3
Downregulated
Signal transduction,
Disturbed T cell




activates e.g. Rho family
activation


DLG5
Downregulated
Tumor suppressor
Increases cell





proliferation


MMP-9
Upregulated
Matrix metalloproteinase
Carcinogenesis and





tumour spread


IL7R
Upregulated
Cytokine receptor
Lymphocyte activation



(basal

and homing to



keratinocytes)

epidermis


CD52
Upregulated
Membrane antigen
(target molecule of





alemtuzumab)


MS4A4A
Upregulated
Membrane antigen
Signal transduction in





haematopoietic cells
















TABLE 4







Real-time RT-PCR reagents












1) 5′-F primer-3′




Target
2) 5′-R primer-3′
Sequence


Probe ID
gene
3) 5′-Probe-3′
identifier





201681_s_at
DLG5
1) GGGGTAGGGGCTGTTTTCTA
SEQ ID NO: 1




2) TGTGCACACTGTACCATCTCAG
SEQ ID NO: 2




3) Probelibrary Human#13



 



EF1a
1) CTGAACCATCCAGGCCAAAT
SEQ ID NO: 3




2) GCCGTGTGGCAATCCAAT
SEQ ID NO: 4




3) AGCGCCGGCTATGCCCCTG
SEQ ID NO: 5


 


205291_at
IL2Rb
1) CCCAATACAAAAATACCTACTGCTG
SEQ ID NO: 6




2) TTTGGATATAAAGGCAACAGGAA
SEQ ID NO: 7




3) Probelibrary Human#66



 


207314_x_at
KIR3DL2_1
1) CTGAGCCCAGATCCAAAGTT
SEQ ID NO: 8




2) AACCCCCTCAAGACCTGACT
SEQ ID NO: 9




3) Probelibrary Human#51



 



KIR3DL2_2
1) CAGTGACGCCCTGGACAT
SEQ ID NO: 10




2) GAGCTACAGGACAAGGTCACG
SEQ ID NO: 11




3) Probelibrary Human#51



 


215838_at
LIR9
1) TCCTGCAGGTATGGTCAGAA
SEQ ID NO: 12




2) ACTGAGGTTATCAGCTGCTCCT
SEQ ID NO: 13




3) Probelibrary Human#79



 


203936_s_at
MMP9
1) GTGCCATGTAAATCCCCACT
SEQ ID NO: 14




2) TTTGTATCCGGCAAACTGG
SEQ ID NO: 15




3) Probelibrary Human#60



 


213915_at
NKG7
1) TCCCTGGGCCTGATGTTCT
SEQ ID NO: 16




2) TGGGACCCACAGCCTCAA
SEQ ID NO: 17




3) CCTGATTGCTTTGAGCACCGATTTCTG
SEQ ID NO: 18


 


204351_at
S100P
1) CATTTGAGTCCTGCCTTCTCAAA
SEQ ID NO: 19




2) CCGTGGATAAATTGCTCAAGGA
SEQ ID NO: 20




3) CATTTGAGTCCTGCCTTCTCAAA
SEQ ID NO: 21


 


203408_s_at
SATB1
1) CCGTAAGCATGAAACCAGTG
SEQ ID NO: 22




2) GATCAGTGTGGAGTGCTACAGAA
SEQ ID NO: 23




3) Probelibrary Human#55



 


204655_at
SCYA5
1) TCCCGAACCCATTTCTTCTCT
SEQ ID NO: 24




2) CCCAGCAGTCGTCTTTGTCA
SEQ ID NO: 25




3) TTGGCACACACTTGGCGGTTCTTTC
SEQ ID NO: 26


 


204466_s_at
SNCA
1) TGTTCCATCCTGTACAAGTGCT
SEQ ID NO: 27




2) CGAGATACACTGTAAAAACTTTGAGAA
SEQ ID NO: 28




3) Probelibrary Mouse#80



 


220684_at
TBX21
1) ACAGCTATGAGGCTGAGTTTCGA
SEQ ID NO: 29




2) GGCCTCGGTAGTAGGACATGGT
SEQ ID NO: 30




3) TCAGCATGAAGCCTGCATTGTTGCC
SEQ ID NO: 31


 


218807_at
VAV3
1) CGTCAGCCGAACTTTGTTATG
SEQ ID NO: 32




2) TCCACAGGAGTGTTTCTGCTT
SEQ ID NO: 33




3) Probelibrary Human#80

## Claims

1. A method for detecting cutaneous T-cell lymphoma (CTCL) in a human subject, said method comprising:
measuring a first expression level of MS4A4A mRNA in a peripheral blood mononuclear cell (PBMC) sample taken from the human subject; and
comparing the first expression level of MS4A4A mRNA to an expression level of MS4A4A mRNA in PBMC samples from a control population of human subjects without CTCL;
wherein the first expression level of MS4A4A mRNA is statistically significantly greater than the expression level of MS4A4A mRNA in PBMC samples from a control population, and the statistically significantly greater expression of MS4A4A mRNA in the PBMC sample taken from the human subject is indicative of the presence of CTCL in the human subject.

2. The method of claim 1 further comprising measuring expression of mRNA of at least one gene selected from the group consisting of: ZBTB16, CD160, HIST2H2AA, HBD, MMP9, SNCA, YWHAE, LIR9, TOP1, S100P, STAT1, TRIB1, GLIPR1, GLUL, PSMB3, ITM2A, ETHE1, BARD1, RECQL, HIST2, H2BE, CDC42, RPL31, LOC55831, G0S2, ARPC1A, C1QBP, TBX21 (T-bet), SCYA5 (Rantes), NKG7, XCL1 (Iymphotactin), TXK, GZMB (granzymeB), KIR3DL2, IL2Rβ, VAV3, DLG5, IL7R, and CD52.

3. The method of claim 1 wherein the subject has been treated with a CTCL therapy.

4. The method of claim 1 wherein said CTCL is a CTCL subtype selected from the group consisting of: mycosis fungoides (MF) or Sezary syndrome (SzS).

5. The method of claim 1 further comprising detecting underexpression or overexpression of one or several genes characteristic of Th1 or Th2 polarization.

6. The method of claim 2, wherein overexpression of LIR9 is characteristic of Th2 polarization.

7. The method of claim 2, characterized in that wherein underexpression of NKG7, TBX21 or SCYA5 is characteristic of Th2 polarization.

8. The method of claim 1 wherein an early stage of CTCL is detected.

9. The method of claim 1 wherein a late stage of CTCL is detected.