US20160355889A1

US20160355889A1 - Method to assess prognosis and to predict therapeutic success in cancer by determining hormone receptor expression levels

Info

Publication number: US20160355889A1
Application number: US15/178,660
Authority: US
Inventors: Ralph Wirtz
Original assignee: Individual
Current assignee: Individual
Priority date: 2009-04-29
Filing date: 2016-06-10
Publication date: 2016-12-08
Also published as: WO2010125117A2; WO2010125117A3; EP2425015B1; EP2425015A2; US20120157542A1; US9376720B2

Abstract

The present invention is related to a method of classifying a sample of a patient who suffers from or being at risk of developing cancer, said method comprising the steps of determining in said sample from said patient, on a non protein basis, the expression level of at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor in said sample; comparing the one or more expression level(s) determined with one or more expression level(s) of one or more reference genes, and classifying the sample of said patient from the outcome of the comparison into one of at least two classifications.

Description

CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority to International Application No. PCT/EP2010/055745 filed on 28 Apr. 2010, which, in turn, claims priority from Patent Application No. EP 09159005.9, filed on 29 Apr. 2009, each of which is incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to a method to assess the prognosis of cancer and to predict therapeutic outcome in cancer treatment. The invention has been tested to be useful for different cancer diseases such as but not limited to lung, ovarian, breast and prostate cancer.

BACKGROUND OF THE INVENTION

Cancer is a class of diseases in which a group of cells display uncontrolled growth (division beyond the normal limits), invasion (intrusion on and destruction of adjacent tissues), and sometimes metastasis (spread to other locations in the body via lymph or blood).
Lung cancer is a cancerous disease of uncontrolled cell growth in tissues of the lung. This growth may lead to metastasis, which is the infiltration and invasion of adjacent tissue and infiltration beyond the lungs. The vast majority of primary lung cancers are carcinomas of the lung, derived from epithelial cells.
Response to chemotherapy in lung cancer is comparatively low with about 10%-30% of patients having benefit from treatment, while having serious side effects and being costly for the national health systems. Despite responsiveness towards chemotherapy, the survival of lung cancer patients is still very poor. Lung cancer is the most lethal cancer in the world with estimated 215,000 new cases and 162,000 deaths per year in the US (Jemal, et al. 2008; 5 year overall survival: Stage I 50%, Stage IV 3%) in part due to the fact that most cases are detected in the later stages.
It is a well-established fact, that systemic treatment after surgery reduces the risk of disease relapse and death in patients with primary operable cancer. However, there still are a great number of patients who do not benefit from systemic therapy.
Prognostic factors in lung cancer include presence or absence of pulmonary symptoms, tumor size, cell type (histology), degree of spread (stage) and metastases to multiple lymph nodes, and vascular invasion.
There are only few data addressing the molecular prediction of response to therapy in lung cancer. Endocrine therapies have not been considered for early treatment of lung cancer so far mostly for several reasons: lung cancer is not a gynecologic tumor site, estrogens do not play a major role in lung development, significant (initial) response to chemotherapy and lack of stratification marker for endocrine therapies. This is in part due to the fact that the determination of hormone receptors and particularly ESR1 by immunohistochemistry failed to have prognostic value for lung cancer, while ESR2 determined on protein level may have some relevance in the comparatively small group of EGFR mutated tumors (Nose N, Sugio K, Oyama T, Nozoe T, Uramoto H, Iwata T, Onitsuka T, Yasumoto K.: Association between estrogen receptor-beta expression and epidermal growth factor receptor mutation in the postoperative prognosis of adenocarcinoma of the lung. J Clin Oncol. 2009 Jan. 20; 27(3):411-7. Epub 2008 Dec. 8.).
This all is in sharp contrast to breast cancer, where the role of ESR1 mRNA and ER protein expression is well established as a stratification marker for endocrine treatment options.
In sharp contrast to, e.g., Nose, et al. (2009), who have not found any prognostic role of ER protein expression in 447 resected primary lung adenocarcinoma, we have surprisingly found significant results obtained by using the RNA extraction and target gene determination approach described below.
Markers predicting tumor response can function as sensitive short-term surrogates of long term outcome. Response to primary chemotherapy is an excellent experimental model to study the efficacy of anticancer therapy in a relatively short period of time. Moreover, the molecular analysis of pre- and post-chemotherapy tumor specimen enables the identification of chemotherapy resistant tumor cell subpopulation and thereby leads to adapted treatment options. However the identification of relevant resistance mechanisms in such settings and development of tests that could be used to detect these underlying resistance mechanisms for patient selection before therapy in clinical routine tissue have not succeeded so far. The use of such markers can make therapeutic strategies more effective for the individual patient and will allow changing regimen early in the case of non-responding tumors. Moreover, the identification of such markers has the potential to identify new drug targets and develop new and more effective treatments.
Lung cancer is commonly treated by chemotherapy, radiotherapy, or surgery with adjuvant chemotherapy. While hormonal therapies are commonly used in the treatment of endocrine organ-associated malignancies such as breast and prostate cancer, at present they are not indicated for lung cancer cases.
Ovarian cancer is the most lethal gynecologic cancer with 20,000 new cases per year and 15,000 deaths per year in the US (5 year overall survival: Stage I 80%, Stage IV 20%) in part due to the fact that most cases are detected in the late stages III and IV). Chemotherapy is standard of care for early and advanced ovarian cancer, while endocrine therapy is given only after failure of chemotherapy regimens. Response to chemotherapy is comparatively low with about 10%-30% of patients having benefit from treatment, while having serious side effects and being costly for the national health systems. Despite prominent responses towards chemotherapy, the survival of particularly ovarian cancer patients is still very poor. To date there are no reliable response markers to predict response to chemotherapy or endocrine therapy in ovarian cancer based on immunohistochemistry, FISH or expression profiling analysis. However, there are only few data addressing the molecular prediction of response to therapy in ovarian cancer.
Prostate cancer is the most frequent male cancer with approximately 190,000 new cases per year in the United States. However, in contrast to the situation in lung and ovarian cancer, most tumors are identified in an early and yet good prognostic stage. Compared to the high incidence rate the annual death rate is therefore comparably low with approximately 30,000 deaths. For most prostate cancer patients “watchful waiting”, i.e., sparing patients surgery, radiation and systemic treatment would be the most appropriate way to treat prostate cancer patients, as the individual risk of distant metastasis and death is very low (=“progression risk”). This is of particular importance given the higher age and comorbidities of prostate cancer patients. Moreover, therapeutic approaches to treat prostate cancer all bear a high risk of developing significant and persistent side effects, such as incontinence and impotence in about 80% of the cases. However, there are no reliable markers that might be useful to reliably identify patients of low progression risk and be useful for tailored treatment approaches. A particular problem is the high heterogeneity and dispersed growth of prostate cancer. Biopsying and subsequent tissue analysis is therefore only of limited efficacy and prognostic value.
Despite state of the art chemo- and endocrine therapy, more than 15% of all breast cancer patients metastasize early and die within the first three to five years after initial surgery. Multiple studies have demonstrated that adjuvant therapy for early-stage breast cancer produces a 23% or greater improvement in disease-free survival and a 15% or greater increase in overall survival rates. However, 30% of breast cancer patients suffer from recurring disease even after harsh chemotherapeutic and endocrine treatment and 15% of the patients die within four years after primary surgery.
In general, all patients of a given cohort do receive the same treatment, even though many will fail in treatment success. Markers predicting tumor response can function as sensitive short-term surrogates of long-term outcome. The use of such markers can make chemotherapy more effective for the individual patient and will allow changing regimen early in the case of non-responding tumors.
Although much effort has been devoted in developing an optimal clinical treatment course for individual patients with cancer, very little progress has been made in predicting the individual's response to a certain treatment. Currently, the probability of response of patients to a certain cancer treatment is usually determined by measuring the status of a marker on protein-level by immunohistochemistry (IHC). Assays based on protein-level measurements exhibit only limited quantitative performance and comparatively high inter- and intra-assay variabilities. Especially immunohistochemistry often yields different results in different laboratories. IHC assays have the added drawback that they often need to be evaluated by trained pathologists or other personnel, thus adding a subjective component to the determination of assay results.
Other approaches, as FISH (Fluorescence In Situ Hybridization) or expression profiling analysis, suffer of drawbacks as low sensitivity, restriction of sample preparation and restricted multiplexing capabilities.
Chemotherapy is standard of care for early and advanced lung cancer, while endocrine therapies have not been tested in this cancer indication. To date there are no reliable response markers to predict response to chemotherapy or endocrine therapy in lung cancer based on immunohistochem-istry, FISH or expression profiling analysis. So, it is yet difficult to determine those patients suffering of lung cancer who will respond to a certain therapy.
Similarly, in ovarian cancer endocrine therapies have not been tested in early treatment stages. Lack of reliable response markers and failure of immunohistochemical methods to determine the prognostic value of hormone receptors has corrupted these developments. In contrast in breast and prostate cancer the endocrine treatment options are standard of care as being one of the most effective treatment options. Here, the reasons for failure of endocrine treatment, is still not well understood.
The present invention surprisingly opens a new approach to diagnostic assessment of cancer and also suggests the possibility of endocrine therapy for cancer patients. Moreover it enables a new kind of cancer tumor classification into the principle underlying biological activities and therefore a general risk categorization resembling to some extent the current situation in breast cancer.

BASIS OF THE INVENTION

In several cancer diseases, the determination of hormone receptors by immunohistochemistry so far has failed to have prognostic value. Surprisingly, even in cancers that have been recalcitrant to hormone-based therapies thus far, the inventor of the present invention has found methods by which the determination of hormone receptor status can have prognostic significance.
The significance of hormone receptor status in cancers of the female breast or reproductive organs, including uterus, ovaries, cervix, fallopian tubes, vulva, vagina, prostate and testes, is well known. In some of these cancers, e.g., breast cancer, the determination of hormone receptor status is standard medical practice. Lung tissues, however, unlike tissues of the reproductive organs, are not generally known to be growth regulated by steroid hormones. It is particularly surprising and unexpected that hormone receptor status should have a prognostic value in such types of cancer.
Moreover, it is new that hormone receptor status of female cancer patients determined according to said methods should be taken into account, when intending to administrate hormone replacement therapy (HRT) to peri- or postmenopausal women. Here, elevated hormone receptor levels, such as, e.g., estrogen receptor ESR1, and/or low levels of snail factors, such as, e.g., SNAI2, indicate not to administer hormones, as this could force aggressiveness and progression of an otherwise comparably less harmful or low risk tumor.
Determining the expression levels of hormone receptors and counteracting transcription factors involved in epithelial-mesenchymal-transition (“EMT”), that directly and negatively affect the hormone receptor expression level, improves said method with regard to higher robustness and lower technical complexity. By generating a two gene ratio between hormone receptors (e.g., ESR1) and EMT-transcription factors (e.g., SNAIL2), the hormone receptor status becomes more precise and robust. Surprisingly this two gene ratio not only performed in lung cancer, but also in ovarian, prostate and breast cancer, indicating that the balance between hormone receptors and EMT markers is generally critical with regard to survival and response to treatment in cancer.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Kaplan-Meier-Analysis of overall survival (OAS) of patients suffering from lung cancer based on i ESR1 (ER) determination. The overall survival (OAS) is depicted in months. Patients are stratified according to ESR1 expression above or below the median ESR1 expression.

FIG. 2: Kaplan-Meier-Analysis of overall survival (OAS) of patients suffering from lung cancer based on i ESR1 (ER) determination. The overall survival (OAS) is depicted in months. Patients are stratified according to ESR1 expression above or below the third quartile of ESR1 expression.

FIG. 3: Spearman correlation analysis between affected metastatic sites and ESR1 mRNA expression level in NSCLC patients. Patients are depicted according to ESR1 expression above and below the median (i.e., “1” vs “0” respectively). Metastatic site being affected is depicted as “1” or “0” depending on whether metastatic lesions were found before first line treatment.

FIG. 4: Spearman correlation analysis between candidate genes (ESR1, SNAI2, CDH1, CDH11). Spearman correlation coefficients and p-values are depicted.

FIG. 5: Kaplan-Meier-Analysis of Recurrence Free Survival (RFS) of patients suffering from ovarian cancer based on combined SNAI2 and ESR1 determination. The Recurrence Free Survival (RFS) is depicted in months. Patients are stratified according to SNAI2/ESR1 two gene ratios.

FIG. 6: Kaplan-Meier-Analysis of Recurrence Free Survival (RFS) of patients suffering from lung cancer based on combined SNAI2 and ESR1 determination. The Recurrence Free Survival (RFS) is depicted in months. Patients are stratified according to SNAI2/ESR1 two gene ratios.

FIG. 7: Kaplan-Meier-Analysis of Recurrence Free Survival (RFS) of patients suffering from lung cancer based PGR expression determination. The Recurrence Free Survival (RFS) is depicted in months. Patients are stratified according to PGR expression levels above or below the cut-off vale of 2.28 dividing the cohort in ˜65% Low Risk patients and ˜35% High Risk patients.

FIGS. 8-16: SEQ ID NOs 1-9, respectively.

DEFINITIONS

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.
The term “prediction” as used herein relates to the likelihood that a patient will respond either favorably or unfavorably to a given therapy. Especially, the term “prediction”, as used herein, relates to an individual assessment of the malignancy of a tumor, or to the expected survival rate (DFS, disease free survival) of a patient, if the tumor is treated with a given therapy. In contrast thereto, the term “prognosis” relates to an individual assessment of the malignancy of a tumor, or to the expected survival rate (DFS, disease free survival) of a patient, if the tumor remains untreated.
The term “predicting an outcome” of a disease, as used herein, is meant to include both a prediction of an outcome of a patient undergoing a given therapy and a prognosis of a patient who is not treated. The term “predicting an outcome” may, in particular, relate to the risk of a patient suffering an event, such as metastasis or death, preferably within a given time frame.
The term “classification of a sample” of a patient, as used herein, relates to the association of said sample with at least one of at least two categories. These categories may be for example “high risk” and “low risk”, high, intermediate and low risk, wherein risk is the probability of a certain event occurring in a certain time period, e.g., occurrence of metastasis, disease free survival, and the like. It can further mean a category of favorable or unfavorable clinical outcome of disease, responsiveness or non-responsiveness to a given treatment or the like. Classification may be performed by use of an algorithm, in particular a discriminant function. A simple example of an algorithm is classification according to a first quantitative parameter, e.g., expression level of a gene of interest, being above or below a certain threshold value. Classification of a sample of a patient may be used to predict an outcome of disease. Instead of using the expression level of a single gene of interest, a combined score of several genes of interest may be used. Further, additional data may be used in combination with the first quantitative parameter. Such additional data may be clinical data from the patient, such as sex, age, weight of the patient, tumor grading or stage, and the like.
A “discriminant function” is a function of a set of variables used to classify an object or event. A discriminant function thus allows classification of a patient, sample or event into a category or a plurality of categories according to data or parameters available from said patient, sample or event. Such classification is a standard instrument of statistical analysis well known to the skilled person. For example, a patient may be classified as “high risk” or “low risk”, “high probability of metastasis” or “low probability of metastasis”, “in need of treatment” or “not in need of treatment” according to data obtained from said patient, sample or event. Classification is not limited to “high vs. low”, but may be performed into a plurality of categories, grading or the like. Examples for discriminant functions which allow a classification include, but are not limited to discriminant functions defined by support vector machines (SVM), k-nearest neighbors (kNN), (naive) Bayes models, or piece-wise defined functions such as, for example, in subgroup discovery, in decision trees, in logical analysis of data (LAD) and the like.
The term “response marker” relates to a marker which can be used to predict the clinical response of a patient towards a given treatment. Response includes direct observation of tumor shrinkage upon neoadjuvant or palliative treatment as evident by, e.g., CT-Scans and/or serum biomarkers as well as effects on Disease Free Survival (DFS), Overall Survival (OAS), Metastasis Specific Survival (MSS), Disease Specific Survival and related assessments.
The term “clinical response” of a patient, as used herein, relates to the effectiveness of a certain therapy in a patient, meaning an improvement in any measure of patient status, including those measures ordinarily used in the art, such as overall survival, progression free survival, recurrence-free survival, and distant recurrence-free survival. Recurrence-free survival (RFS) refers to the time (in years) from surgery to the first local, regional, or distant recurrence. Distant recurrence-free survival (DFRS) refers to the time (in years) from surgery and/or initial diagnosis to the first anatomically distant recurrence. The calculation of these measures in practice may vary from study to study depending on the definition of events to be either censored or not considered. The term “response marker” relates to a marker which can be used to predict the clinical response of a patient towards a given treatment.
The term “neoplastic disease” refers to a cancerous tissue this includes carcinomas, e.g., carcinoma in situ, invasive carcinoma, metastatic carcinoma, and pre-malignant conditions, neomorphic changes independent of their histological origin. The term “adenocarcinoma” refers to a malignant tumor originating in glandular tissue. The terms “cancer” and “cancerous” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. The term “cancer” is not limited to any stage, grade, histomorphological feature, invasiveness, aggressiveness or malignancy of an affected tissue or cell aggregation. In particular stage 0 cancer, stage I cancer, stage II cancer, stage III cancer, stage IV cancer, grade I cancer, grade II cancer, grade III cancer, malignant cancer, primary carcinomas, and all other types of cancers, malignancies and transformations specially associated with gynecologic cancer are included. The terms “neoplastic disease” or “cancer” are not limited to any tissue or cell type they also include primary, secondary or metastatic lesions of cancer patients, and also comprise lymph nodes affected by cancer cells or minimal residual disease cells either locally deposited or freely floating throughout the patient's body.
As used herein, the term “lung cancers” refers to cancer or malignancies which are diagnosed in the lung and is meant to include all cancers, neoplastic growths and cancerous transformations of lung tissue. Examples of lung cancers include, but are not limited to: small cell lung carcinoma (SCLC), and non-small cell lung carcinoma (NSCLC), in particular squamous cell lung carcinoma, adenocarcinoma, bronchioloalveolar carcinoma, large cell lung carcinoma, and others, such as pleuropulmonary blastoma and carcinoid tumors.
The term “tumor” as used herein, refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues.
The term “neoplastic cells” refer to abnormal cells that grow by increased cellular proliferation, altered cell division symmetry or decreased cell death mechanisms more rapidly than normal. As such, neoplastic cells of the invention may be cells of a benign neoplasm or may be cells of a malignant neoplasm.
Furthermore, the term “characterizing the state” of a neoplastic disease or cancer is related to, but not limited to, measurements and assessment of one or more of the following conditions: Type of tumor, histomorphological appearance, dependence on external signal (e.g., hormones, growth factors), invasiveness, motility, state by TNM Classification of Malignant Tumors (TNM), a cancer staging system developed and maintained by the International Union Against Cancer, or similar, agressivity, malignancy, metastatic potential, and responsiveness to a given therapy.
The terms “therapy modality”, “therapy mode”, “regimen”, “chemo regimen”, and “therapy regimen” each refer to a timely sequential or simultaneous administration of anti-tumor, and/or anti-vascular, and/or immune stimulating, and/or blood cell proliferative agents, and/or radiation therapy, and/or hyperthermia, and/or hypothermia—any and all approaches for cancer therapy. The administration of these approaches can be performed in an adjuvant and/or neoadjuvant mode. The composition of any such “protocol” may vary in the dose of the single agent, timeframe of application and frequency of administration within a defined therapy window. Currently various combinations of various drugs and/or physical methods, and various schedules are under investigation.
The term “endocrine treatment” refers to various treatment modalities known as hormonal therapy or anti-hormonal therapy that produce the desired therapeutic effect by means of change of hormone/hormones level. The treatment may include administration of hormones or hormone analogs, synthetic hormones or other drugs to the patient, or decreasing the level of hormones in the body by using hormone antagonists, hormone receptor antagonists or hormone ablation therapy either by surgical resection of ovaries or by chemical suppression of hormone synthesis. Endocrine therapy shall be taken to include hormonal therapies such as selective estrogen reuptake inhibitors, selective estrogen receptor downregulators, aromatase inhibitors and ovarian ablation. Said endocrine treatment may include administration of hormones or hormone analogs, synthetic hormones or other drugs to the patient, e.g., tamoxifen, raloxifen and/or gosereline (tradename Zoladex®). In one embodiment, the said endocrine treatment comprises the administration of tamoxifen or of tamoxifen and gosereline. Further, said endocrine treatment may comprise the administration of an antiestrogen drug selected from the group comprising anastrozole, letrozole, exemestane, fulvestrant, toremifene and megasterol acetate. Said endocrine treatment may also comprise the administration of estrogen, progestin and/or gestagen.
The term “determining the expression level of a gene on a nonprotein basis” relates to methods which are not focused on the secondary gene translation products, i.e., proteins, but on other levels of the gene expression, based on RNA and DNA analysis. In one embodiment of this invention the analysis uses mRNA including its precursor forms. An exemplary determinable property is the amount of the estrogen receptor or progesterone receptor mRNA, i.e., of the ESR1, ESR2 and/or PGR gene. It may also include the detection of DNA amplification of the respective gene.
The term “expression level” refers, e.g., to a determined level of gene expression. The term “pattern of expression levels” refers to a determined level of gene expression compared either to a reference gene, e.g., housekeeper, or inversely regulated genes, or to a computed average expression value, e.g., in DNA-chip analyses. A pattern is not limited to the comparison of two genes but is more related to multiple comparisons of genes to reference genes or samples. A certain “pattern of expression levels” may also result and be determined by comparison and measurement of several genes disclosed hereafter and display the relative abundance of these transcripts to each other. Expression levels may also be assessed relative to expression in different tissues, e.g., expression of a gene in cancerous tissue vs. noncancerous tissue.
Alternatively, a differentially expressed gene disclosed herein may be used in methods for identifying reagents and compounds and uses of these reagents and compounds for the treatment of cancer as well as methods of treatment. The differential regulation of the gene is not limited to a specific cancer cell type or clone, but rather displays the interplay of cancer cells, muscle cells, stromal cells, connective tissue cells, other epithelial cells, fat cells, endothelial cells of blood vessels as well as cells of the immune system, e.g., lymphocytes, macrophages, killer cells.
The term “RNA expression level” refers to a determined level of the converted DNA gene sequence information into transcribed RNA, the initial unspliced RNA transcript or the mature mRNA. RNA expression can be monitored by measuring the levels of either the entire RNA of the gene or subsequences.
The term “pattern of RNA expression” refers to a determined level of RNA expression compared either to a reference RNA or to a computed average expression value. A pattern is not limited to the comparison of two RNAs but is more related to multiple comparisons of RNAs to reference RNAs or samples. A certain “pattern of expression levels” may also result and be determined by comparison and measurement of several RNAs and display the relative abundance of these transcripts to each other. A “reference pattern of expression levels”, within the meaning of the invention shall be understood as being any pattern of expression levels that can be used for the comparison to another pattern of expression levels. In an embodiment of the invention, a reference pattern of expression levels is, e.g., an average pattern of expression levels observed in a group of healthy or diseased individuals, serving as a reference group.
The term “comparing the one or more expression levels(s)” expression levels” refers to the comparison of the expression levels, e.g., by arithmetical means, such as but not limited to the ratio of the expression levels of two or more genes.
The terms “sample”, “biological sample”, or “clinical sample”, as used herein, refer to a sample obtained from a patient. The sample may be of any biological tissue or fluid. Such samples include, but are not limited to, sputum, blood, serum, plasma, blood cells (e.g., white cells), tissue, core or fine needle biopsy samples, cell-containing body fluids, free floating nucleic acids, urine, peritoneal fluid, and pleural fluid, liquor cerebrospinalis, tear fluid, or cells there from. Biological samples may also include sections of tissues such as frozen or fixed sections taken for histological purposes or microdissected cells or extracellular parts thereof. A biological sample to be analyzed is tissue material from a neoplastic lesion taken by aspiration or punctuation, excision or by any other surgical method leading to biopsy or resected cellular material. Such a biological sample may comprise cells obtained from a patient. The cells may be found in a cell “smear” in solid tumor material, in a lavage fluid, or in a body fluid. The sample may be a processed sample, e.g., a sample, which has been frozen, fixed, embedded or the like. A sample that is usefully employed in the context of the present invention is a formaline fixed paraffin embedded (FFPE) sample. Preparation of FFPE samples are standard medical practice and these samples can be conserved for long periods of time.
By “array” is meant an arrangement of addressable locations or “addresses” on a device. The locations can be arranged in two dimensional arrays, three dimensional arrays, or other matrix formats. The number of locations can range from several to at least hundreds of thousands. Most importantly, each location represents an independent reaction site. Arrays include but are not limited to nucleic acid arrays, protein arrays and antibody arrays. A “nucleic acid array” refers to an array containing nucleic acid probes, such as oligonucleotides, polynucleotides or larger portions of genes. The nucleic acid on the array can be rendered single stranded. Arrays wherein the probes are oligonucleotides are referred to as “oligonucleotide arrays” or “oligonucleotide chips.” A “microarray,” herein also refers to a “biochip” or “biological chip”, an array of regions having a density of discrete regions of at least about 100/cm, and can be usefully employed as well having at least about 1000/cm, as well-understood by those skilled in the art. The regions in a microarray have typical dimensions, e.g., diameters, in the range of between about 10-250 μm, and are separated from other regions in the array by about the same distance.
The term “oligonucleotide” refers to a relatively short polynucleotide, including, without limitation, single-stranded deoxyribonucleotides, single- or double-stranded ribonucleotides, RNA:DNA hybrids and double-stranded DNAs. Oligonucleotides can be single-stranded DNA probe oligonucleotides. Moreover, in context of applicable detection methodologies, the term “oligonucleotide” also refers to nucleotide analogues such as PNAs and morpholinos.
The terms “modulated” or “modulation” or “regulated” or “regulation” and “differentially regulated” as used herein refer to both upregulation, i.e., activation or stimulation, e.g., by agonizing or potentiating, and down regulation, i.e., inhibition or suppression, e.g., by antagonizing, decreasing or inhibiting.
The terms “primer”, “amplification primer”, “probes” and “labeled probes”, within the meaning of the invention, shall have the ordinary meaning of each term as is well known to the person skilled in the art of molecular biology. In the context of many embodiments of the present invention, these terms shall be understood as being polynucleotide molecules having a sequence identical, complementary, homologous, or homologous to the complement of regions of a target polynucleotide which is to be detected or quantified. In yet another embodiment, nucleotide analogues are also comprised for usage as primers and/or probes. Probe technologies used for kinetic or real time PCR applications include, e.g., PCR systems generally, such as TaqMan® systems obtainable at Roche Molecular Diagnostics, extension probes such as Scorpion® Primers, Dual Hybridisation Probes, Amplifluor® obtainable at Chemicon International, Inc, or Minor Groove Binders. Probes can be surface bound, either on a chip or on beads, and then be used as a microarray.
The phrase “response”, “therapeutic success”, or “response to therapy” refers in the neoadjuvant, adjuvant and palliative chemotherapeutic setting to the observation of a defined tumor free or recurrence free or progression free survival time (e.g., two years, four years, five years, ten years). This time period of disease-free, recurrence-free or progression-free survival may vary among the different tumor entities but is sufficiently longer than the average time period in which most of the recurrences appear. In a neoadjuvant and palliative therapy modality, response may additionally be monitored by measurement of tumor shrinkage and regression due to apoptosis and necrosis of the tumor mass or reduced blood supply due to altered angiogenic events.
The term “recurrence” or “recurrent disease” includes distant metastasis that can appear even many years after the initial diagnosis and therapy of a tumor, or local events such as infiltration of tumor cells into regional lymph nodes, or occurrence of tumor cells at the same site and organ of origin within an appropriate time.
“Prediction of recurrence” or “prediction of therapeutic success” does refer to the methods described in this invention, wherein a tumor specimen is analyzed for, e.g., its gene expression, genomic status and/or histopathological parameters (such as TNM and Grade) and/or imaging data and furthermore classified based on correlation of the expression pattern to known ones from reference samples. This classification may either result in the statement that such given tumor will develop recurrence and therefore is considered as a “non-responding” tumor to the given therapy, or may result in a classification as a tumor with a prolonged disease free post therapy time.
The term “marker” or “biomarker” refers to a biological molecule, e.g., a nucleic acid, peptide, protein, hormone, etc., whose presence or concentration can be detected and correlated with a known condition, such as a disease state or a combination of these, e.g., by a mathematical algorithm.
The term “marker gene” as used herein, refers to a differentially expressed gene whose expression pattern may be utilized as part of a predictive, prognostic or diagnostic process in malignant neoplasia or cancer evaluation, or which, alternatively, may be used in methods for identifying compounds useful for the treatment or prevention of malignant neoplasia and gynecological cancer in particular. A marker gene may also have the characteristics of a target gene.
“Target gene”, as used herein, refers to a differentially expressed gene involved in cancer, e.g., lung cancer, in a manner in which modulation of the level of the target gene expression or of the target gene product activity may act to ameliorate symptoms of malignant neoplasia. A target gene may also have the characteristics of a marker gene.
The term “receptor”, as used herein, relates to a protein on the cell membrane or within the cytoplasm or cell nucleus that binds to a specific molecule (a ligand), such as a neurotransmitter, hormone, or other substance, especially a hormone as estrogen, and initiates the cellular response. Ligand-induced changes in the behavior of receptor proteins result in physiological changes that constitute the biological actions of the ligands.
The term “signaling pathway” is related to any intra- or intercellular process by which cells converts one kind of signal or stimulus into another, most often involving ordered sequences of biochemical reactions out- and inside the cell, that are carried out by enzymes and linked through hormones and growth factors (intercellular), as well as second messengers (intracellular), the latter resulting in what is thought of as a “second messenger pathway”. In many signaling pathways, the number of proteins and other molecules participating in these events increases as the process emanates from the initial stimulus, resulting in a “signal cascade” and often results in a relatively small stimulus eliciting a large response. In particular, the term “signaling pathways” relates to processes located upstream or downstream of a hormone receptor, e.g., a ligand binding said receptor, or an intracellular signaling cascade activated by said receptor.
The term “small molecule”, as used herein, is meant to refer to a compound which has a molecular weight of less than about 5 kD; not uncommonly, the small molecule employed in the context of the present invention is less than about 4 kD. Small molecules can be nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids or other organic (carbon-containing) or inorganic molecules. Many pharmaceutical companies have extensive libraries of chemical and/or biological mixtures, often fungal, bacterial, or algal extracts, which can be screened with any of the assays of the invention to identify compounds that modulate a bioactivity.
When used in reference to a single-stranded nucleic acid sequence, the term “substantially homologous” refers to any probe that can hybridize (i.e., it is the complement of) the single-stranded nucleic acid sequence under conditions of low stringency as described above.
As used herein, the term “hybridization” is used in reference to the pairing of complementary nucleic acids.
The term “hybridization based method”, as used herein, refers to methods imparting a process of combining complementary, single-stranded nucleic acids or nucleotide analogues into a single double stranded molecule. Nucleotides or nucleotide analogues will bind to their complement under normal conditions, so two perfectly complementary strands will bind to each other readily. In bioanalytics, very often labeled, single stranded probes are in order to find complementary target sequences. If such sequences exist in the sample, the probes will hybridize to said sequences which can then be detected due to the label. Other hybridization based methods comprise microarray and/or biochip methods. Therein, probes are immobilized on a solid phase, which is then exposed to a sample. If complementary nucleic acids exist in the sample, these will hybridize to the probes and can thus be detected. These approaches are also known as “array based methods”. Yet another hybridization based method is PCR, which is described below. When it comes to the determination of expression levels, hybridization based methods may for example be used to determine the amount of mRNA for a given gene.
The term “a PCR based method” as used herein refers to methods comprising a polymerase chain reaction (PCR). This is an approach for exponentially amplifying nucleic acids, like DNA or RNA, via enzymatic replication, without using a living organism. As PCR is an in vitro technique, it can be performed without restrictions on the form of DNA, and it can be extensively modified to perform a wide array of genetic manipulations. When it comes to the determination of expression levels, a PCR based method may for example be used to detect the presence of a given mRNA by (1) reverse transcription of the complete mRNA pool (the so called transcriptome) into cDNA with help of a reverse transcriptase enzyme, and (2) detecting the presence of a given cDNA with help of respective primers. This approach is commonly known as reverse transcriptase PCR (rtPCR). The term “PCR based method” comprises both end-point PCR applications as well as kinetic/real time PCR techniques applying special fluorophors or intercalating dyes which emit fluorescent signals as a function of amplified target and allow monitoring and quantification of the target. Quantification methods could be either absolute by external standard curves or relative to a comparative internal standard.
The term “method based on the electrochemical detection of molecules” relates to methods which make use of an electrode system to which molecules, particularly biomolecules like proteins, nucleic acids, antigens, antibodies and the like, bind under creation of a detectable signal. Such methods are for example disclosed in WO0242759, WO0241992 and WO02097413 filed by the applicant of the present invention, the content of which is incorporated by reference herein. These detectors comprise a substrate with a planar surface which is formed, for example, by the crystallo-graphic surface of a silicon chip, and electrical detectors which may adopt, for example, the shape of inter digital electrodes or a two dimensional electrode array. These electrodes carry probe molecules, e.g., nucleic acid probes, capable of binding specifically to target molecules, e.g., target nucleic acid molecules. The probe molecules are for example immobilized by a Thiol-Gold-binding. For this purpose, the probe is modified at its 5′- or 3′-end with a thiol group which binds to the electrode comprising a gold surface. These target nucleic acid molecules may carry, for example, an enzyme label, like horseradish peroxidase (HRP) or alkaline phosphatase. After the target molecules have bound to the probes, a substrate is then added (e.g., α-naphthyl phosphate or 3.3′ 5.5′-tetramethylbenzidine which is converted by said enzyme, particularly in a redox-reaction. The product of said reaction, or a current generated in said reaction due to an exchange of electrons, can then be detected with help of the electrical detector in a site specific manner.
The term “nucleic acid molecule” is intended to indicate any single- or double stranded nucleic acid and/or analogous molecules comprising DNA, cDNA and/or genomic DNA, RNA, such as, for example, mRNA, peptide nucleic acid (PNA), locked nucleic acid (LNA) and/or Morpholino.
The term “stringent conditions” relates to conditions under which a probe will hybridize to its target subsequence, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength, pH and nucleic acid concentration) at which 50% of the probes complementary to the target sequence hybridize to the target sequence at equilibrium. (As the target sequences are generally present in excess, at Tm, 50% of the probes are occupied at equilibrium). Typically, stringent conditions will be those in which the salt concentration is less than about 1.0 M Na ion, typically about 0.01 to 1.0 M Na ion (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for longer probes. Stringent conditions may also be achieved with the addition of destabilizing agents, such as formamide and the like.
The term “fragment of the nucleic acid molecule” is intended to indicate a nucleic acid comprising a subset of a nucleic acid molecule according to one of the claimed sequences. The same is applicable to the term “fraction of the nucleic acid molecule”.
The term “variant of the nucleic acid molecule” refers herein to a nucleic acid molecule which is substantially similar in structure and biological activity to a nucleic acid molecule according to one of the claimed sequences.
The term “homologue of the nucleic acid molecule” refers to a nucleic acid molecule the sequence of which has one or more nucleotides added, deleted, substituted or otherwise chemically modified in comparison to a nucleic acid molecule according to one of the claimed sequences, provided always that the homologue retains substantially the same binding properties as the latter.
The term “derivative” as used herein, refers to a nucleic acid molecule that has similar binding characteristics to a target nucleic acid sequence as a nucleic acid molecule according to one of the claimed sequences
The term “hybridizing counterparts” as used herein, refers to a nucleic acid molecule that is capable of hybridizing to a nucleic acid molecules under stringent conditions.
The term “anamnesis” relates to patient data gained by a physician or other healthcare professional by asking specific questions, either of the patient or of other people who know the person and can give suitable information (in this case, it is sometimes called heteroanamnesis), with the aim of obtaining information useful in formulating a diagnosis and providing medical care to the patient.
This kind of information is called the symptoms, in contrast with clinical signs, which are ascertained by direct examination.
The term “etiopathology” relates to the course of a disease, that is its duration, its clinical symptoms, and its outcome.
As used herein, the term “repair mechanisms related therewith” refers to cellular repair enzymes the expression of which correlates with the expression of at least one of said hormone receptors selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor. A low ratio of hormone receptor versus EMT marker is generally correlated to an unfavorable outcome. Further, an decreased or downregulated expression of said hormone receptor indicates that the patient has lower PARP1 expression levels and higher angiogenic activities and therefore benefit from a specific mode of therapy, in particular treatments comprising targeting repair mechanisms and angiogenic activities selected from the group comprising PARP1, VEGFRs, PDGFRs, and/or their ligands and/or their respective signaling pathways.

OBJECT OF THE INVENTION

It is one object of the present invention to provide biological markers allowing one skilled in the medical arts to predict outcome of cancer patients by providing prognostic and/or predictive information concerning the therapeutic outcome of a given treatment including surgery, systemic and/or local application of chemotherapeutic and/or endocrine agents as well as antibody based, nucleic acid based and/or small molecule based strategies.
It is another object of the present invention to provide a method for predicting a clinical response of cancer to a given treatment based on tissue analysis before, during or after therapy.
These objects are met with the methods and means according to the independent claims of the present invention.

SUMMARY OF THE INVENTION

Before the invention is described in detail, it is to be understood that this invention is not limited to the particular component parts of the process steps of the methods described as such methods may vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting. It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include singular and/or plural referents unless the context clearly dictates otherwise. It is also to be understood that plural forms include singular and/or plural referents unless the context clearly dictates otherwise. It is moreover to be understood that, in case parameter ranges are given which are delimited by numeric values, the ranges are deemed to include these limitation values.
In its most general term, the invention relates to a method of classifying a sample of a patient who suffers from or is at risk of developing cancer, said method comprising the steps of determining in said sample from said patient, on a non-protein basis, the expression level of at least one gene in said sample encoding for a hormone receptor selected from the group consisting of an estrogen receptor, a progesterone receptor, and an androgen receptor, comparing the one or more expression level(s) determined with one or more expression level(s) of one or more reference genes and thereby forming a pattern of expression level(s); and classifying the sample of said patient from the outcome of the comparison into one of at least two classifications.
The method thus allows predicting a clinical response towards a given mode of treatment. An increased or upregulated expression of said hormone receptor is generally correlated to a favorable outcome. Further, an increased or upregulated expression of said hormone receptor indicates that the patient can benefit from a specific mode of therapy, in particular a treatment targeting at least one hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor, or targeting their respective signaling pathways, and/or a treatment targeting repair mechanisms related therewith.
As used herein, the term “signaling pathways” relates to processes located upstream or downstream of the said receptor, e.g., a ligand binding said receptor, or an intracellular signaling cascade activated by said receptor.
In a more specific term, the invention relates to a method of predicting an outcome of disease in a patient suffering from cancer wherein the expression level of at least one gene encoding for a hormone receptor selected from the group consisting of an estrogen receptor, a progesterone receptor, and an androgen receptor is determined on a nonprotein basis and one gene selected from the group of Epithelial-Mesenchymal-Transition factors comprising SNAI1, SNAI2 and/or SNAI3. The expression levels are set into a ratio thereby abrogating the need of housekeeping or reference genes. This enables single well detection of all relevant genes by multiplexing and eliminates problems arising from variations (pipetting, enzyme reaction, fluorescence scanning, etc.). Moreover, it lowers costs and increases throughput of the diagnostic workflow with finite resources (sample amount, reagent costs, capacity utilization). A high ratio of hormone receptor versus EMT marker is generally correlated to a favorable outcome. Further, an increased or upregulated expression of said hormone receptor indicates that the patient can benefit from a specific mode of therapy, in particular treatment comprising targeting hormone receptors selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor or targeting the respective hormones and/or their respective signaling pathways.
As used herein, the term “repair mechanisms related therewith” refers to cellular repair enzymes the expression of which correlates with the expression of at least one of said hormone receptors selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor. A low ratio of hormone receptor versus EMT marker is generally correlated to an unfavorable outcome. Further, an decreased or downregulated expression of said hormone receptor indicates that the patient has lower PARP1 expression levels and higher angiogenic activities and therefore benefit from a specific mode of therapy, in particular treatments comprising targeting repair mechanisms and angiogenic activities selected from the group comprising PARP1, VEGFRs, PDGFRs, and/or their ligands and/or their respective signaling pathways.
By way of illustration and not by way of limitation said signaling activities comprise receptor tyrosine kinase signaling, e.g., via epidermal growth factor receptor (EGFR) family members, vascular endothelial growth factor receptor (VEGFR) signaling, Fibroblast Growth Factor Receptor (FGFR) family members, Platelet Derived Growth Factor Receptor (PDGFR) family members, c-KIT, a proto-oncogene encoding a receptor tyrosine kinase, or Mesenchymal epithelial transition factor (c-Met); WNT signaling; Notch signaling; Hedgehog signaling; Transforming growth factor-beta (TGF-beta)/SMAD signaling and nuclear factor-kappa B (NFkB) signaling.
In particular, the invention relates to the method and kit specified in the claims. As specific embodiments of the invention, herein disclosed are the invention according to the following embodiments:
A first aspect of the invention is directed to a method of classifying a sample of a patient suffering from or at risk of developing a lung cancer, said method comprising the steps of:

- a. determining in said sample from said patient, on a non protein basis, the expression level of at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor in said sample;
- b. comparing the pattern of expression level(s) determined in step (a) with one or several reference pattern(s) of expression levels; and
- c. classifying the sample of said patient from the outcome of the comparison in step (b) into one of at least two classifications.

A second aspect of the invention is directed to a method for predicting a clinical response of a patient suffering from or at risk of developing a lung cancer towards a given mode of treatment, said method comprising the steps of:

- a. determining in a sample from said patient, on a non protein basis, the expression level of at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor in said sample;
- b. comparing the pattern of expression level(s) determined in step (a) with one or several reference pattern(s) of expression levels; and
- c. predicting therapeutic success for said given mode of treatment in said patient from the outcome of the comparison in step (b).

A third aspect the invention is directed to a method of predicting a clinical response towards a given mode of cancer treatment or classifying a sample of a patient who suffers from or being at risk of developing cancer, said method comprising the steps of:

- a. determining in said sample from said patient, on a non protein basis, the expression level of at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor in said sample;
- b. comparing the one or more expression level(s) determined in step (a) with one or more expression level(s) of one or more reference genes and thereby forming a pattern of expression level(s); and
- c. classifying the sample of said patient from the outcome of the comparison in step (b) into one of at least two classifications.

In one embodiment, the mode of treatment based on the classification in step (c) comprises an endocrine treatment by targeting hormone receptors selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor or their respective signaling pathways and/or a treatment targeting repair mechanisms related therewith.
In another embodiment, said endocrine treatment is a hormonal treatment and/or antihormonal treatment. In yet another embodiment, said endocrine treatment comprises the administration of tamoxifen. In another embodiment, said endocrine treatment is intended to be given as hormone replacement therapy (HRT) in peri- or postmenopausal women. In yet another embodiment, the gene encoding for the estrogen receptor is ESR1.
In another embodiment, the upregulated expression of said at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor determined in step (a) is indicative of a promising prediction as regards therapeutic success for said given mode of treatment.
In yet another embodiment, it is an intermediate upregulated expression of said at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor determined in step (b) which is indicative of a promising prediction as regards therapeutic success for a therapeutic regimen targeting hormone receptors selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor. In an embodiment, said one or more reference gene(s) is at least one housekeeping gene and/or at least one EMT marker gene.
In another embodiment, the at least one housekeeping gene is selected from the group comprising RPL37A, GAPDH, RPL13 and/or HPRT1; and the at least one EMT marker gene is selected from the group comprising SNAI1, SNAI2 and/or SNAI3.
In another embodiment, the comparison in step (b) of the method is a two gene ratio between the expression level of a hormone receptor and an EMT marker gene, such as, for example, a ratio of ESR1 to SNAI2.
In another embodiment, said given mode of treatment acts on recruitment of lymphatic vessels, angiogenesis, cell proliferation, cell survival and/or cell motility, and/or comprises administration of a chemotherapeutic agent.
In a further embodiment said given mode of treatment is selected from the group comprising chemotherapy, administration of small molecule inhibitors, antibody based regimen, anti-proliferation regimen, pro-apoptotic regimen, pro-differentiation regimen, radiation and/or surgical therapy.
The invention is also directed to a method of selecting a therapy modality for a patient afflicted with a lung cancer, said method comprising the steps of:

- a. predicting from a biological sample from said patient, by the method according to any one of the aforementioned numbered paragraphs, therapeutic success for a plurality of individual modes of treatment; and
- b. selecting a mode of treatment which is predicted to be successful in step (a).

And the invention is further directed to a method for adapting therapeutic regimen based on individualized risk assessment for a patient suffering from or at risk of developing a lung cancer, comprising the steps of:

- a. determining in a biological sample from said patient, on a non protein basis, the expression level of at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor in said sample;
- b. comparing the pattern of expression level(s) determined in step (a) with one or several reference pattern(s) of expression levels; and
- c. implementing therapeutic regimen targeting hormone receptors selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor or signaling pathways in said patient from the outcome of the comparison in step (b).

In a number of the recited embodiments, said expression level(s) is determined by

- a. a hybridization based method;
- b. a PCR based method;
- c. a method based on the electrochemical detection of particular molecules, and/or
- d. an array based method.

In another embodiment said expression level is determined by reverse transcriptase polymerase chain reaction of RNA transcripts.
In yet another embodiment said expression level is determined in formalin and/or paraffin fixed tissue samples of the RNA transcripts.
In a further embodiment, the sample is treated with silica-coated magnetic particles and a chaotropic salt, for purification of the nucleic acids contained in said sample prior to the determination in step (a).
In another embodiment, the upregulated expression level of said at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor is related to a favorable outcome, in particular to prolonged survival.
In yet another embodiment, said cancer displays characteristics of or is an adenocarcinoma.
It yet another embodiment, it could also be a non-carcinogen neoplastic disease. In another embodiment, the cancer is selected from the group consisting of a lung cancer, a non-small cell lung cancer (NSCLC), an ovarian cancer, a breast cancer, and a prostate cancer.
In another embodiment, the pattern of expression level(s) determined in step (a) is correlated with said patient's data, said data being selected from the group consisting of etiopathology data, clinical symptoms, anamnesis data and/or data concerning the therapeutic regimen.
The invention is further directed to a kit useful for carrying out a method of any one of the aforementioned numbered paragraphs, comprising at least a pair of gene specific primers and/or probes each having a sequence sufficiently complementary to at least one gene or gene fragments or genomic nucleic acid sequence encoding for a at least one gene coding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor for quantifying the expression of said at least one gene or gene fragment or genomic nucleic acid sequence, and/or their fractions, variants, homologues, derivatives, fragments, complements, hybridizing counterparts, or molecules sharing a sequence identity of at least about 70%, of at least about 75%, of at least about 80%, of at least about 85%, of at least about 90%, of at least about 95%, of at least about 97%.
It is again pointed out that all details of the methods and kits described are not limited to their application in lung cancer but also to other types of cancer. Thus, lung cancer is only the example of choice. Up to now the prognostic and predictive role of hormone receptors in lung cancer selected from the group comprising estrogen receptor (ESR), progesterone receptor (PGR) and/or androgen receptor (AR) in lung cancer has not been shown. Accordingly no endocrine treatment options are offered to lung cancer patients in the neoadjuvant or adjuvant setting.
The hormone receptor RNA expression of ESR1, ESR2, PGR, AR in fresh and fixed tissue biopsy samples and tumor resectates of stage III and IV small cell and non-small cell lung cancer patients from a non-stratified, population based cohort treated with chemotherapy were analyzed.
Surprisingly, it was found that the expression level of a gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor has prognostic and/or predictive value in lung cancer.
In this regard it is to be understood, that the analysis of estrogen receptor and progesterone receptor status on protein basis has turned out to be inferior to the detection of genes coding for estrogen receptor on RNA basis, as the determination of estrogen receptor by immune histochemistry fails to have prognostic value for lung cancer. This has been experimentally confirmed by the inventors in a very same cohort of patients, where the diagnostic value of estrogen and/or progesterone receptor expression determination by kinetic PCR (kPCR) methods has been proven.
The validity of these findings have been shown by independent measurements of fresh tissue biopsies and resectates by array analysis and also by PCR based analysis of clinical routine material, i.e., formalin fixed and paraffin embedded (=FFPE) tissues.
Moreover, it was established, for the first time, to use the expression level of a gene encoding for hormone receptors selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor for the decision whether a given therapy is the most promising therapy for the respective patient having lung cancer or if treatment modalities should be altered. In particular, the method disclosed herein is highly prognostic in the identical samples of a patient cohort where the state of the art technology, i.e., immunohistochemistry (=IHC), clearly fails to have any prognostic information.
The prediction of therapeutic success or the investigation of the response to a treatment can be performed at time of first biopsy or after surgery, at a stage in which other methods cannot provide the required information on the patient's response to chemotherapy. Hence the current invention also provides means to decide even shortly after tumor surgery whether or not a certain mode of chemo-therapy is likely to be beneficial to the patient's health and/or whether to maintain or change the applied mode of chemotherapy treatment. This is of particular importance as the decision which systemic therapy to apply first is of outmost importance for survival, development of resistance and therefore also for subsequent treatment strategies. Also the overall status of patients is usually best at initial diagnosis and therefore allows to apply more complex and/or aggressive treatment options at intended. This not only holds true for chemotherapeutic strategies but is also of importance for generally less toxic strategies, such as anti-angiogenic treatments as exemplified by application of Bevacizumab (tradename Avastin®), Sunitinib (tradename Sutent®) or Sorafenib (tradename Nexavar®). The reason for this is in part the extensive surgery being necessary for lung cancer, which inter alias increases the risk of bleeding and intraoperative or postoperative death.
According to the superiority of non-protein based determination of hormone receptor status selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor status, the method should substitute currently available measurements, or used in addition to currently available tests or histopathological parameter to make diagnosis more accurate.
Furthermore, the method according to the invention may be applied in neoadjuvant, adjuvant and metastatic settings. Importantly, the inventors have found that hormone receptors such as estrogen, progesterone and/or androgen receptor are useful for prediction based on untreated tumor samples but also prognostic for treated tumor samples.
The inventor suggests, for the first time, to use the expression level of at least one gene encoding for estrogen receptor for the decision whether a therapeutic regimen targeting a hormone receptor, e.g., estrogen receptor, in other words, an endocrine therapy, could be beneficial in a lung cancer patient. This particularly not only comprises different kinds of hormone antagonists or enzyme inhibitors blocking steps of the estrogen biosynthesis but also the usage of hormone agonists, e.g., estrogen, as this could accelerate hormonal control of deregulated cancer cell activities and/or sensitize towards other therapeutic options such as chemotherapy.
It is yet another embodiment of the invention to combine the information of the mRNA expression level of at least one gene encoding for hormone receptors such as estrogen, progesterone and/or androgen receptor with the level of microRNAs regulating the stability and/or translation of respective mRNAs. By way of illustration and not by way of limitation this may mean that tumors expressing intermediate levels of ESR1 mRNA do worse, when higher levels of microRNAs downregulate ESR1 protein expression, compared to tumors expressing intermediate levels of ESR1 mRNA that do not display microRNA expression of respective microRNAs.
It is yet another embodiment of the invention to combine the information of the mRNA expression level of at least one gene encoding for hormone receptors such as estrogen, progesterone and/or androgen receptor with the expression level of CYP19A1, which is responsible for the conversion of androgens to estrogens is expressed not only in gonads and adrenals but also in many other tissues, including normal lungs and lung cancers and therefore produces hormone receptor ligands in proximity to the neoplastic tissue. This contributes to the finding being part of this invention, that the determination of hormone receptors is not only useful in women but also in men and therefore of diagnostic and therapeutic importance in both genders.
It is yet another embodiment of the present invention to provide a method for predicting the development of resistance to therapeutic intervention of a patient suffering from lung cancer to a given treatment.
In this context it is of note that it is part of this invention to use the described method to stratify patients, which may benefit from hormonal treatments.
It is yet another embodiment that it is part of this invention to use the described method to stratify patients, which may benefit from PARP Inhibition.
Another embodiment of the present invention provides a method to stratify patients for systemic treatments other than chemotherapy in a neoadjuvant, adjuvant or palliative setting. In one embodiment, these alternative treatment options comprise antibody based or small molecule based treatment. Notably, treatment in the context of the present invention includes endocrine treatment options.
Moreover, the method according to the invention may help to detect those tumors which are probably more susceptible to endocrine treatment than to a chemotherapeutic regimen. These tumors have so far remained undetected with methods from the state of the art. Particularly the determination of ESR1 status by IHC is not part of the current standard of care as it does not provide any prognostic information. Thereby the endocrine options have been neglected for treatment of lung cancer and ovarian cancer.
The present inventive method includes the step of assessing the expression level of at least one gene encoding for an estrogen receptor that is selected from the group consisting of ESR1, ESR2, progesterone receptor, PGR, and androgen receptor. This assessment is usefully employed in the context of the present invention for deciding whether a therapeutic regimen targeting signaling pathways, as specified above or otherwise, could be beneficial in that patient.
The inventor suggests moreover to use the expression level of at least one gene encoding for an estrogen receptor, such as, for example, one that is selected from the group consisting of ESR1, ESR2, a progesterone receptor, PGR, and an androgen receptor for the decision whether a therapeutic regimen targeting matrix metalloproteinases could be beneficial in that patient. These regimens comprise therapeutics blocking the protease activity of MMP1, MMP2, MMP7, MMP9 and/or MMPlO.
The inventor suggests moreover to use the expression level of at least one gene encoding for an estrogen receptor, such as one selected from the group consisting of ESR1, ESR2, a progesterone receptor, PGR, and an androgen receptor for the decision whether a therapeutic regimen targeting repair mechanism could be beneficial in that patient. These regimen comprise therapeutics blocking the PARP1 gene product.
The inventor suggests moreover to use the expression level of at least one gene encoding for an estrogen receptor, such as, for example, and without limitation intended, one selected from the group consisting of ESR1, ESR2, a progesterone receptor, PGR, and an androgen receptor for the decision whether a therapeutic regimen affecting bone metabolism, such as bisphosphonates, and/or antibody regimen having similar properties by attacking the RANKL system, such a denosumab, could be beneficial in that patient.
The inventor has found that the balance between hormone receptors and stem cell activities or SNAI factors is indicative of tumor outcome in lung cancer. However the inventors suggests that this balance is not limited to lung cancer but rather a general tumor principle. The present invention moreover sets forth a method to use the expression level of at least one gene encoding for an estrogen receptor, such as, for example, and without limitation intended, one selected from the group consisting of ESR1, ESR2, a progesterone receptor, PGR, and an androgen receptor for the decision whether targeted therapy such as an anti-tyrosine kinase regimen may be effective. This relates to the finding, that the absence or low activity of hormone receptors relates to more aggressive tumors characterized by, e.g., elevated EGFR family and VEGFR family activities. The inventor suggests moreover to use the expression level of at least one gene encoding for an estrogen receptor, such as one selected from the group consisting of ESR1, ESR2, a progesterone receptor, PGR, and an androgen receptor for the decision whether a tyrosine kinase inhibitor could be beneficial in a patient suffering an adenocarcinoma bearing mutated tyrosine kinase expression. The mutated tyrosine kinase in the patient that may be benefited by the present invention is EGFR of c-Met.
In one embodiment of the invention, said given mode of chemotherapy is targeted therapy such as small molecule inhibitors like Sunitinib (tradename Sutent®), Sorafenib (tradename Nexavar®), Lapatinib (tradename Tykerb®) and/or therapeutic antibodies, e.g., Bevacizumab (tradename Avastin®) or cetuximab (tradename Erbitux®).
However, other treatments related to signaling pathways which fall under the scope of the present invention comprise the administration of BAY 43-9005, target receptors are VEGFR-2, VEGFR-3, c-KIT, PDGFR-B, RET and Raf-Kinase), BAY 57-9352 (target receptor is VEGFR-2), Sunitinib (tradename Sutent®, target receptors are VEGFR-I, VEGFR-2 and PDGFR), AG13925 (target receptors are VEGFR-I and VEGFR-2), AGO 13736 (target receptors are VEGFR-I and VEGFR-2), AZD2171 (target receptors are VEGFR-I and VEGFR-2), ZD6474 (target receptors are VEGFR-I, VEGFR-2 and VEGFR-3), PTK-787/ZK-222584 (target receptors are VEGFR-I and VEGFR-2), CEP-7055 (target receptors are VEGFR-I, VEGFR-2 and VEGFR-3), CP-547 (target receptors are VEGFR-I and VEGFR-2), CP-632 (target receptors are VEGFR-I and VEGFR-2), GW786024 (target receptors are VEGFR-I, VEGFR-2 and VEGFR-3), AMG706 (target receptors are VEGFR-I, VEGFR-2 and VEGFR-3), Imatinib mesylate (tradename Glivec®/Gleevec®, target receptors are bcr-abl and c-KIT), BMS-214662 (target enzyme is Ras farnesyl transferase), CCI-779 (target enzyme is mTOR), RADOOO1 (tradename Everolismus®, target enzyme is mTOR), CI-1040 (target enzyme is MEK), SU6668 (target receptors are VEGFR-2, PDGFR-B and FGFR-I), AZD6126, CP547632 (target receptors are VEGFRs), CP868596 GW786034 (target receptors are PDGFRs), ABT-869 (target receptors are VEGFRs and PDGFRs), AEE788 (target receptors are VEGFRs and PDGFRs), AZD0530 (target enzymes are src and abl), and CEP7055.
In another embodiment, the genes encoding for estrogen receptor are selected from the group consisting of ESR1 and ESR2. In one embodiment, the gene encoding for the estrogen receptor is ESR1.
Surprisingly, the inventors have found that the expression level of ESR1 has good prognostic and/or diagnostic value in lung cancer when tested before treatment, which resembles the de novo hormone activity of the tumor tissue. More surprisingly, the inventors have found that the benefit from chemotherapy was particularly striking in high grade and/or higher size tumors expressing estrogen and progesterone receptors, while the response of estrogen or progesterone receptor negative tumors remained to be poor. The prognostic value of hormone receptor activity was particularly prominent in NSCLC and in women suffering lung cancer, thereby contributing to the known better prognosis of the tumors in these lung cancer subgroups.
Therefore, the inventor suggests for the first time, to use the expression level of ESR1 and/or ESR2 for the decision whether a given therapy is the most promising therapy for lung cancer, or if treatment modalities should be altered. As the inventor does show by comparing with the current standard techniques, these decisions cannot be drawn with, e.g., IHC, as these techniques fail to determine the prognostic value of hormone receptors.
In another embodiment, the gene encoding for the progesterone receptor is PGR. In yet another embodiment, PGR is used for to decide on treatment modalities.
Moreover surprisingly, the inventor has found that the expression level of PGR has good prognostic and/or diagnostic value in lung cancer.
The inventor suggests for the first time, to use the expression level of PGR for the decision whether a given therapy is the most promising therapy for lung cancer or if treatment modalities should be altered.
In another embodiment, the gene encoding for the androgene receptor is AR. In yet another embodiment, AR is used for to decide on treatment modalities.
Moreover surprisingly, the inventor has found that the expression level of AR has prognostic and/or diagnostic value in lung cancer.
The inventors suggest for the first time, to use the expression level of AR for the decision whether a given therapy is the most promising therapy for lung cancer or if treatment modalities should be altered.
In another embodiment the gene encoding for the aromatase is CYP19. In yet another embodiment CYP19 is used for to decide on treatment modalities.
Moreover surprisingly, the inventors have found that the expression level of CYP19 has prognostic and/or diagnostic value in lung cancer, particularly when combined with the expression level of hormone receptors and, as one example, ESR1. The inventors suggest for the first time, to use the expression level of CYP19 and/or ESR1 for the decision whether a given therapy is the most promising therapy for lung cancer or if treatment modalities should be altered.
In another embodiment, the microRNA affecting the ESR1 expression is 206, 221 and/or 222. In yet another embodiment, microRNA is used for to decide on treatment modalities.
Moreover surprisingly, the inventor has found that the microRNA has prognostic and/or diagnostic value in lung cancer, particularly when combined with the expression level of hormone receptors and, as one useful example, ESR1.
The inventors suggest for the first time, to use the expression level of microRNA and/or ESR1 for the decision whether a given therapy is the most promising therapy for lung cancer or if treatment modalities should be altered.
Importantly, the decision when to use altered treatment modalities such as endocrine options can be influenced. These treatment modalities may be applied before, during or after chemotherapy and/or surgery.
In another embodiment of the present invention, the methods of the present invention comprise comparing the level of mRNA expression of ESR1 and/or ESR2 and/or PGR and/or AR in a patient sample, and the average level of expression of ESR1 and/or ESR2 and/or PGR and/or AR in a sample from a control subject, e.g., a human subject without cancer. Comparison of the pattern of expression levels of ESR1 and/or ESR2 and/or PGR and/or AR can also be performed on any other reference.
In another embodiment of the present invention, the methods of the present invention also comprise comparing the pattern of expression levels of mRNA of ESR1 and/or ESR2 and/or PGR and/or AR in an unclassified patient sample, and the pattern of expression levels of ESR1 and/or ESR2 and/or PGR and/or AR in a sample cohort comprising patients responding in different intensity to an administered neoadjuvant, adjuvant and/or palliative cancer therapy.
In another embodiment of this invention, the expression of ESR1 and/or ESR2 and/or PGR and/or AR can be utilized for discrimination of responders and non-responders to a given treatment, especially a chemotherapeutic and/or endocrine intervention.
In another embodiment of the present invention, it is provided that upregulated expression of said at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor, especially of the RNA transcripts of ESR1, determined in step (b) is indicative of a promising prediction as regards therapeutic success for a given mode of treatment.
Moreover, the combined analysis of estrogen, progesterone and androgen receptors improved the diagnostic value of the single marker evaluation, i.e., just based on estrogen, progesterone or androgen receptor.
By correlation analysis, the inventors have found that overexpression of ESR1 in untreated tumor samples that are, for example, assessed by PCR analysis, is an indicator for a good prognosis of lung cancer patients treated by standard chemotherapy as indicated by prolonged disease free and overall survival. Especially a high expression of ESR1 was found to provide a good overall survival prognosis upon standard adjuvant chemotherapy. Also in the palliative chemotherapeutic setting the elevated expression level of estrogen receptors and progesterone receptors was associated with increased response to endocrine treatments. This indicates the direct link between treatment and directly related response, i.e., tumor shrinkage, whose assumption is difficult to draw in the adjuvant setting. In other embodiments, intermediate expression of ESR1, for example assessed by PCR analysis, indicates poor prognosis of lung cancer patients treated by standard chemotherapy.
In another embodiment of the present invention, it is provided that highly or intermediately upregulated expression of said at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor determined in step (b) is indicative of a promising prediction as regards therapeutic success for a therapeutic regimen targeting hormone receptors selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor especially endocrine treatment.
In another embodiment of the present invention, it is provided that highly or intermediately upregulated expression of said at least one gene encoding for the estrogen receptor especially ESR1 determined in step (b) is indicative of a promising prediction as regards therapeutic success for a therapeutic regimen targeting the estrogen receptor, especially endocrine treatment.
In yet another embodiment of the present invention, it is provided that highly or intermediately upregulated expression of said at least one gene encoding for the estrogen receptor especially ESR1 determined in step (b) is indicative of increased risk of bone metastasis a promising prediction as regards therapeutic success for a therapeutic regimen targeting the bone metabolism (such as bisphosphonates, denosumab).
In another embodiment of the present invention, it is provided that highly or intermediately upregulated expression of said at least one gene encoding for the estrogen receptor especially ESR1 and downregulated expression of said at least one gene encoding EMT markers especially SNAIL2 simultaneous determined in step (b) is indicative of a promising prediction as regards therapeutic success for a therapeutic regimen targeting the estrogen receptor, especially endocrine treatment.
In another embodiment of the present invention, it is provided that downregulated expression of said at least one gene encoding EMT markers especially SNAIL2 determined in step (b) is indicative of a promising prediction as regards therapeutic success for a therapeutic regimen targeting the estrogen receptor, especially endocrine treatment.
For example, in the case of highly upregulated expression of said at least one gene encoding for the estrogen receptor especially ESR1 determined in step (b) the nodal status may provide additional information with regard to outcome. In particular, if node negative the outcome of patients with high expression of, e.g., ESR1 may be very good (i.e., above 95% survival), whereas if node positive, the outcome may be inferior (i.e., at about 80% survival), while still being clearly superior to bad prognosis at low expression of, e.g., ESR1 (i.e., at 22% survival). This means that patients with tumors exhibiting high expression of, e.g., ESR1 still may have a benefit from additional endocrine treatment.
In yet another embodiment of the present invention, it is provided that low expression of said at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor especially ESR1 indicates poor prognosis of lung cancer patients treated by standard chemotherapy.
Moreover this finding also enables to decide which patients should receive other treatment options targeting signaling pathways, e.g., small molecules.
In another embodiment of the present invention, it is provided that the pattern of expression level(s) determined in step (b) refers to a level of gene expression compared to a reference selected from the group comprising RPL37A, GAPDH, CALM2, OAZ1 RPL13, and/or HPRT1. In another embodiment these reference genes are RPL37A, GAPDH and HPRT1. In yet another embodiment, the reference genes are RPL37A and HPRT1. In another embodiment of the present invention, it is provided that said reference or housekeeping gene is RPL37A.
Normalization to a housekeeping gene selected from the group comprising RPL37A, GAPDH, RPL13, and/or HPRT1 can provide the advantage of a highly reliable comparison. In another embodiment of the present invention, it is provided that the pattern of expression level(s) determined in step (b) refers to a level of gene expression compared to an anticorrelated gene reference selected from the group comprising SNAIL1, SNAIL2, CDH11, MMP2. In an embodiment, these reference genes are SNAIL1.
In yet another embodiment of the present invention, it is provided that said given mode of treatment acts on recruitment of lymphatic vessels, angiogenesis, cell proliferation, cell survival and/or cell motility, and/or comprises administration of a chemotherapeutic agent.
Furthermore, it is provided in an another embodiment of the present invention that said given mode of treatment is selected from the group comprising chemotherapy, administration of small molecule inhibitors, antibody based regimen, anti-proliferation regimen, pro-apoptotic regimen, pro-differentiation regimen, radiation and/or surgical therapy. In yet other embodiments said given mode of treatment may include administration of cis-Platin (tradename Cisplatin®).
Said chemotherapy may comprise the administration of at least one agent selected from the group comprising Cyclophosphamid (Endoxan®, Cyclostin®). Adriamycin (Doxorubicin) (Adriblastin®), BCNU (Carmustin) (Carmubris®), Busulfan (Myleran®), Bleomycin (Bleomycin®), Carboplatin (Carboplat®), Chlorambucil (Leukeran®), Cis-Platin (Cisplatin®), Platinex (Platib-Lastin®), Dacarbazin (DTIC®; Detimedac®), Docetaxel (Taxotere®), Epirubicin (Farmorubicin®), Etoposid (Vepesid®), 5-Fluorouracil (Fluroblastin®, Fluorouracil®), Gemcitabin (Gemzar®), Ifosfamid (Holoxan®), Interferon alpha (Roferon®), Irinotecan (CPT 11, Campto®), Melphalan (Alkeran®), Methotrexat (Methotrexat®, Farmitrexat®), Mitomycin C (Mitomycin®), Mitoxantron (Novantron®), Oxaliplatin (Eloxatine®), Paclitaxel (Taxol®), Prednimustin (Sterecyt®), Procarbazin (Natulan®), Pemetrexed (Alimta®), Ralitrexed (Tomudex®), Topotecan (Hycantin®), Trofosfamid (Ixoten®), Vinblastin (Velbe®), Vincristin (Vincristin®), Vindesin (Eldisine®) and/or Vinorelbin (Navelbine®).
In other embodiments said given mode of treatment may be endocrine treatment.
In a further aspect, the present invention provides a method of selecting a therapy modality for a patient afflicted with lung cancer, said method comprising the steps of:

- a. obtaining a biological sample from said patient;
- b. predicting from said sample, by the described before, therapeutic success for a plurality of individual modes of treatment; and
- c. selecting a mode of treatment which is predicted to be successful in step (b).

It is of note, that the inventors have proven the validity of the disclosed method in fresh tissue as well as fixed tissues. Also the inventors have shown the validity of the disclosed method in biopsies as well as tumor resectates.
On the basis of the findings of the present invention a therapy can be selected, which is most promising for the individual patient.
In a further aspect, the present invention provides a method of selecting a modality for a patient afflicted with lung cancer, said method comprising the steps of:

- a. obtaining a biological sample from said patient;
- b. predicting from said sample, by the method described before, diagnostic success for a plurality of individual modes of imaging; and
- c. selecting a mode of imaging which is predicted to be successful in step (b).

On the basis of the findings of the present invention an imaging modality can be selected, which is most promising for the individual patient.
Here the inventor has shown for the first time that high or intermediate expression of ESR1 is predictive for increased risk of bone metastasis in lung cancer patients.
Based on the ESR1, PGR, AR and or snail mRNA determination in the primary tumor the subsequent imaging modality can be chosen for more precise staging and tailored treatment choice. Higher ESR1 expression indicates a bone scan or application of labeled estrogen receptor ligands (e.g., fluoridinated estradiol “[18F]FES”). Higher PGR expression indicates a bone scan or application of labeled progesteron receptor ligands (e.g., fluoridinated progrestin. Higher AR expression indicates a bone scan or application of labeled androgen receptor ligands (e.g., fluoridinated testosterone). Higher snail expression indicates application of labeled Matrix-Metallo-Proteinase (=MMP) ligands (e.g., labeled MMP inhibitors, particularly for MMP2).
Higher risk of bone involvement in disease progression may indicate altered treatment, e.g., by including bisphosphonates or antibodies against RANKL (such as denosumab “Prolia®”) to treat metastatic spread and recruitment of bone marrow derived precursor cells early on. This is thought to prevent disease progression and potentially prolong life.
In addition the inventor suggests, for the first time, to use the expression level of a gene encoding for the estrogen receptor and/or progesterone receptor, especially ESR1, for the decision whether or not chemotherapeutic treatment should be kept as treatment or if endocrine treatment or treatment options targeting signaling pathways should be included as a treatment options. In yet another addition the inventor suggests, for the first time, to use the expression level of a gene encoding for the estrogen receptor and/or progesterone receptor, especially ESR1, for the decision whether or not bone preserving treatments should be included as a therapeutic option in lung cancer.
In this regard, the accurate detection of the expression level of ESR1 enables to identify a subpopulation of tumors that overexpress ESR1 in an intermediate or slightly higher fashion, yet having a comparatively low overexpression of ESR1 that cannot be resolved by immunohistochemical techniques. This subpopulation may be particularly sensitive to endocrine treatment.
The methods of the invention maybe used to evaluate a patient before, during and after therapy, for example to evaluate the reduction in tumor burden.
In the method of the present invention the determination of gene expression or the determination of the pattern of expression level is not limited to any specific method, or to the detection of mRNA.
In the method according to the invention, said expression level determined in step (b) can be determined by

The above mentioned methods have in common that they are focused on the detection of nucleic acids, particularly on the detection of mRNA, DNA, peptide nucleic acid (PNA), locked nucleic acid (LNA) and/or Morpholino.
Moreover, these methods provide the option that high quality determinations can be done as multiplex assays in one reaction based on the high specificity of the reagent design and performance.
Another advantage is that the method requires only small amounts of biological sample.
In yet another embodiment of the present invention, it is provided that said expression level of the RNA transcripts is determined by reverse transcriptase polymerase chain reaction (RT-PCR).
The method according to the invention has the advantage that it works on paraffin embedded tissues. In yet another embodiment of the present invention, it is provided that said expression level of the RNA transcripts is determined in formalin and/or paraffin fixed tissue samples.
For this purpose, at least one fixative may be used in an embodiment which is selected from the group consisting of Neutral Buffered Formaline, Unbuffered Formaline, Glutaraldehyde, Ethanol, Acetone, Methanol, Methacarn, Carnoy's fixative, AFA-Fixative (Formaldehyde, Ethanol and acetic acid), Pen-Fix (alcoholic formalin fixative), Glyo-Fixx (glyoxal-based fixative), Hope (Hepes-glutamic acid buffer mediated organic solvent fixative), and/or Zinc Formal-Fixx (Formaldehyde fixative which contains zinc).
In yet another embodiment of the present invention, it is provided, that the information of the method disclosed herein is combines with standard histopathological data, such as TNM status, Grade, Location, Cell Type, Inflammatory status, to improve the validity of the result and/or adopt to the clinical situation.
In yet another embodiment of the present invention, it is provided, that the results are adjusted to tumor cell content or sublocalization of the tissue material within the malignant tissue, e.g., invasive front, central oarts, angiogenic subregion, inflammatory region, etc.
Routinely, in tumor diagnosis tissue samples are taken as biopsies from a patient and undergo diagnostic procedures. For this purpose, the samples are fixed in formaline, embedded in paraffine and are then examined with immunohistochemistry methods. The formaline treatment leads to the inactivation of enzymes, as for example the ubiquitous RNA-digesting enzymes (RNAses). For this reason, the mRNA status of the tissue (the so called transcriptome), remains unaffected.
However, the formaline treatment leads to partial depolymerization of the individual mRNA molecules. Same applies for other fixatives, as for example mentioned in the above enumeration.
For this reason, it is provided in an embodiment of the present invention that after lysis, the sample is treated with silica-coated magnetic particles and a chaotropic salt, for purification of the nucleic acids contained in said sample for further determination.
However, the isolation method may alternatively also be silica column based with or without chaotropic agents.
Collaborators of the inventor of the present invention have developed an approach which however allows successful purification of mRNA out of tissue samples fixed in such manner, and which is disclosed, among others, in WO03058649, WO2006136314A1 and DE10201084A1, the content of which is incorporated herein by reference. Said method comprises the use of magnetic particles coated with silica (SiO₂). The silica layer is closed and tight and is characterized by having an extremely small thickness on the scale of a few nanometers. These particles are produced by an improved method that leads to a product having a closed silica layer and thus entail a highly improved purity. The said method prevents an uncontrolled formation of aggregates and clusters of silicates on the magnetite surface whereby positively influencing the additional cited properties and biological applications. The said magnetic particles exhibit an optimized magnetization and suspension behavior as well as a very advantageous run-off behavior from plastic surfaces. These highly pure magnetic particles coated with silicon dioxide are used for isolating nucleic acids, including DNA and RNA, from cell and tissue samples, the separating out from a sample matrix ensuing by means of magnetic fields. These particles are particularly well-suited for the automatic purification of nucleic acids, mostly from biological body samples for the purpose of detecting them with different amplification methods.
The selective binding of these nucleic acids to the surface of said particles is due to the affinity of negatively charged nucleic acids to silica containing media in the presence of chaotropic salts like guanidinisothiocyanate. Said binding properties are known as the so called “boom principle”. They are described in the European Patent EP819696, the content of which is incorporated herein by reference.
The said approach is particularly useful for the purification of mRNA out of formaline and/or paraffine fixed tissue samples. In contrast to most other approaches, which leave very small fragments behind that are not suitable for later determination by PCR and/or hybridization technologies, the said approach creates mRNA fragments which are large enough to allow specific primer hybridization and/or specific probe hybridization. A minimal size of at least about 50 base pairs, or at least about 100 base pairs, or at least about 200 base pairs is needed for specific and robust detection of target gene expression. Moreover it is also necessary to not have too many inter-sample variations with regard to the size of the RNA fragments to guarantee comparability of gene expression results. Other issues of perturbance of expression data by sample preparation problems relate to the contamination level with DNA, which is lower compared to other bead or column based technologies.
The said approach thus allows a highly specific determination of the status of hormone receptors selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor with one of the above introduced methods, particularly with hybridization based methods, PCR based methods and/or array based methods, even in fixed routine tissue samples, and is thus extremely beneficial in the context of the present invention, as it allows the use of tissue samples fixed with formaline and/or paraffine, which are available in tissue banks and connected to clinical databases of sufficient follow-up to allow retrospective analysis. Another important aspect is that the said approach allows the simultaneous determination of more than one analyte (multiplexing), and is thus ideally suited for the determination of hormone receptors selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor especially ESR1, ESR2, PGR and/or of one or more housekeeping genes in said sample. Alternatively to housekeeping genes, which are per definition being expressed in virtually all cells to similar amounts, tumor specific, endothelial cell specific and or stroma specific genes may be included to further increase the diagnostic precision of said method. By this approach one can derive a calibration factor in order to normalize the expression values of the target genes in samples which have different shares of tumor tissue and nontumor tissue.
In yet another embodiment of the present invention, it is provided that said endocrine treatment is a hormonal treatment and/or antihormonal treatment.
Said endocrine treatment may comprises the administration of antagonists of estrogen binding to the estrogen receptor, estrogen reuptake inhibitors, selective estrogen receptor downregulators, or as inhibitors of estrogen biosynthesis, such as aromatase inhibitors. Said endocrine treatment may also comprise similar approaches to target progesterone and/or androgen receptors.
In yet another embodiment of the invention a method for correlating the clinical outcome of a patient suffering from or at risk of developing a lung cancer with the presence or non-presence of a defect in expression levels of the RNA transcripts of at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor is provided, said method comprising the steps of:

- a. obtaining a fixed biological sample from said patient;
- b. determining the expression levels of the RNA transcripts of at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor, and
- c. correlating the pattern of expression level(s) determined in (b) with said patient's data, said data being selected from the group consisting of etiopathology data, clinical symptoms, anamnesis data and/or data concerning the therapeutic regimen.

The said method is particularly beneficial for epidemiological studies. These studies profit from the fact that large tissue databases exist comprising paraffin and/or formalin fixed tissue samples together with an extensive documentation of the patient's history, including etiopathology data, clinical symptoms, anamnesis data and/or data concerning the therapeutic regimen. The said methods advantageously allows for large scale studies.
In another embodiment of the present invention, a kit useful for carrying out a method of the invention, comprising at least a pair of gene specific primers and/or probes each having a sequence sufficiently complementary to at least one gene or gene fragments or genomic nucleic acid sequence encoding for a at least one gene coding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor for quantifying the expression of said at least one gene or gene fragment or genomic nucleic acid sequence, and/or their fractions, variants, homologues, derivatives, fragments, complements, hybridizing counterparts, or molecules sharing a sequence identity of at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 97%.
These nucleic acids can be used either as primers for a polymerase chain reaction protocol, or as detectable probes for monitoring the said process.
Furthermore, it is provided that the said nucleic acid or nucleic acid homologue is selected from the group consisting of DNA, RNA, PNA, LNA and/or morpholino. The nucleic acid may, in a given embodiment, be labeled with at least one detectable marker. This feature is applicable particularly for those nucleic acids which serve as detectable probes for monitoring the polymerase chain reaction process.
Such detectable markers may for example comprise at least one label selected from the group consisting of fluorescent molecules, luminescent molecules, radioactive molecules, enzymatic molecules and/or quenching molecules.
In another embodiment, the said detectable probes are labeled with a fluorescent marker at one end and a quencher of fluorescence at the opposite end of the probe. The close proximity of the reporter to the quencher prevents detection of its fluorescence; breakdown of the probe by the 5′ to 3′ exonuclease activity of the taq polymerase breaks the reporter-quencher proximity and thus allows unquenched emission of fluorescence, which can be detected. An increase in the product targeted by the reporter probe at each PCR cycle therefore causes a proportional increase in fluorescence due to the breakdown of the probe and release of the reporter.
The oligonucleotide in one embodiment of the invention comprises a nucleotide sequence which is a fragment, a fraction, a variant, a homologue, a derivative of, or a complementary to, any of the nucleic acid molecules set forth as SEQ ID NOs 1-9, or which is capable of hybridizing to a fragment, a fraction, a variant, a homologue, or a derivative of any of the nucleic acid molecules set forth as SEQ ID NOs 1-9.

DISCLAIMER

To provide a comprehensive disclosure without unduly lengthening the specification, the applicant hereby incorporates by reference each of the patents and patent applications referenced above.
The particular combinations of elements and features in the above-detailed embodiments are exemplary only; the interchanging and substitution of these teachings with other teachings in this and the patents/applications incorporated by reference are also expressly contemplated. As those skilled in the art will recognize, variations, modifications, and other implementations of what is described herein can occur to those of ordinary skill in the art without departing from the spirit and the scope of the invention as claimed. Accordingly, the foregoing description is by way of example only and is not intended as limiting. The invention's scope is defined in the following claims and the equivalents thereto. Furthermore, reference signs used in the description and claims do not limit the scope of the invention as claimed.

TABLE 1

Genes of interest

Gene_Symbol	Ref. Sequences	Ref. Sequences	Unigene_ID
[A]	Description [A]	[A]	[A]

ESR1	Estrogen receptor	NM 000125.2	Hs.208124
ESR2	Estrogen receptor	NM	001040276+1	Hs.525392;
			HS660607
PGR	Progesterone	NM 000926.4	Hs.368072
	receptor
AR	Androgen receptor	NM	000044+2	Hs.496240
AR	Androgen receptor	NM	001011645+1	Hs.496240
CYP19	Aromatase	NM 000103.3
miRNA 205
miRNA 221
miRNA 222
SNAI1	Snail homolog	1	NM 005985.2	Hs.48029
SNAI2	SLUG; Snail	NM 003068.3	Hs.360174
	homolog 2
SNAI3	SMUC; Snail	NM 17810.3	Hs.673548
	homolog 3

The terms “Ref. Sequences” and “Unigene ID” relate to databases in which the respective proteins are listed under the given access number. These databases can be accessed over the NCBI server.
Additional details, features, characteristics and advantages of the invention are disclosed in the following examples that, in an exemplary fashion, show embodiments of the present invention. However, these examples should by no means be understood as to limit the scope of the invention.

Example 1

Measurement of ESR1 by RT PCR

Molecular Methods
RNA was isolated from formalin-fixed paraffin-embedded (“FFPE”) tumor tissue samples employing an experimental method based on proprietary magnetic beads from Siemens Medical Solutions Diagnostics. In short, the FFPE slide were lysed and treated with Proteinase K for 2 hours 55° C. with shaking After adding a binding buffer and the magnetic particles (Siemens Medical Solutions Diagnostic GmbH, Leverkusen, Germany) nucleic acids were bound to the particles within 15 minutes at room temperature. On a magnetic stand the supernatant was taken away and beads were washed several times with washing buffer. After adding elution buffer and incubating for 10 min at 70° C. the supernatant was taken away on a magnetic stand without touching the beads. After normal DNAse I treatment for 30 minutes at 37° C. and inactivation of DNAse I the solution was used for reverse transcription-polymerase chain reaction (RT-PCR).
RT-PCR was run as standard kinetic one-step Reverse Transcriptase TaqMan™ polymerase chain reaction (RT-PCR) analysis on a ABI7900 (Applied Biosystems) PCR system for assessment of mRNA expression. Raw data of the RT-PCR were normalized to one or combinations of the housekeeping genes RPL37A, GAPDH, RPL13, and HPRT1 by using the comparative ΔΔCT method, known to those skilled in the art. In brief, a total of 40 cycles of RNA amplification were applied and the cycle threshold (CT) of the target genes was set as being 0.5. CT scores were normalized by subtracting the CT score of the housekeeping gene RPL37A or the mean of the combinations from the CT score of the target gene (Delta CT). RNA results were then reported as 40-Delta CT or 2^{((40-(CT Target Gene-CT Housekeeping Gene)*(−1)))}(2̂(40−(CT Target Gene−CT Housekeeping Gene)*(−1))) scores, which would correlate proportionally to the mRNA expression level of the target gene. For each gene specific Primer/Probe were designed by Primer Express® software v2.0 (Applied Biosystems) according to manufactures instructions.
Statistics
The statistical analysis was performed with Graph Pad Prism Version 4 (Graph Pad Prism Software, Inc).
The clinical and biological variables were categorized into normal and pathological values according to standard norms. The Chi-square test was used to compare different groups for categorical variables. To examine correlations between different molecular factors, the Spearman rank correlation coefficient test was used.
For univariate analysis, logistic regression models with one covariate were used when looking at categorical outcomes. Survival curves were estimated by the method of Kaplan and Meier, and the curves were compared according to one factor by the log rank test. For the estimation of multivariate models, all parameters which were significant at the univariate analysis (p<0.05) were fitted to a Cox regression model using a backward forward stepwise method for the selection of covariates. Confidence intervals (CI) at 95% for hazard rates (HR) were calculated. All the probabilities that were calculated were two-tailed.
Experiments have repeatedly shown that determination of hormone receptor status by RT PCR consistently yielded better results than analysis by immunohistochemistry (IHC), i.e., while no stratification of patients could be achieved by analysis of IHC data, analysis of gene expression data obtained by PCR based methods consistently yielded significant results allowing a reliable stratification of patients in to high risk and low risk groups.

Example 2

Determination of ESR1 Expression Using RT-PCR in a Lung Cancer Patient Cohort

Hormone receptor RNA expression of ESR1, ESR2, PGR, AR was analyzed by Affymetrix array technologies and kPCR technologies by employing a standardized RNA-extraction method based on proprietary magnetic beads from Siemens Healthcare Diagnostics and using standard Taqman® PCR Methodology on the ABI7900 PCR system. Fresh tissue biopsy samples and tumor resectates of stage III and IV small cell and non small cell lung cancer patients kPCR from a non-stratified, population based cohort treated with chemotherapy (n=83) were analyzed.
By correlation analysis, it was surprisingly found that overexpression of ESR1 as assessed by Affymetrix and kPCR analysis indicates good prognosis of lung cancer patients treated by standard chemotherapy as indicated by prolonged disease free and overall survival. ESR1 expression displayed a broad range of relative copy number (2.5 logs) as determined by standard kPCR technologies after normalization to various housekeeping genes (RPL37A, GAPDH, RPL13, HPRT1, CALM2) in the populations based cohort (n=83) of patients with both SCLC and NSCLC. By taking technical cut-offs like the median and tertiles, it was shown that high expression is related to prolonged survival. Importantly, the ESR1 and AR expressing tumor group may benefit most from endocrine treatment options. The test could be used for stratification of lung cancer patients towards endocrine treatments in the late and also earlier setting. As the median expression of ESR1 and AR was lower than in breast cancer and there is need for quantitative assessment of ESR1 and AR expression to reliably select patients, it is reasonable to expect a technical superiority of the present approach over standard technologies (i.e., immunohistochemistry) will also persist also in lung cancer.

Example 3

Determination of ESR Expression Using RT-PCR in NSCLC Patient Cohort

By correlation analysis, it was surprisingly found that overexpression of ESR1 as kPCR analysis indicates good prognosis of non small cell lung cancer (NSCLC) patients (male and female Caucasian patients) treated by standard chemotherapy as indicated by prolonged disease free and overall survival. ESR1 expression displayed a broad range of relative copy number (2.5 logs) as determined by standard kPCR technologies after normalization to various housekeeping genes (RPL37A, GAPDH, RPL13, HPRT1, CALM2) in the populations based cohort (n=35) of patients with NSCLC. By taking technical cut-offs like the median and tertiles, it was shown that high expression is related to prolonged survival. Results for ESR1 expression greater or lower than median are shown in FIG. 1. Patients stratified according to ESR1 expression above or below the third quartile of ESR1 expression are shown in FIG. 2. The majority of patients were treated with a platinum-based regimen. Samples were FFPE tissue analyzed with RT-kPCR. The median follow up 9 month; 82% Stage IV; patient number was n=35.

Example 4

Correlation of ESR1 Expression Determined by Using RT-PCR with Site of Initial Metastasis in NSCLC Patient Cohort

By correlation analysis, it was surprisingly found that high ESR1 expression positively correlates with development of bone metastasis also in NSCLC patients as depicted in FIG. 3. In addition, metastasis to the adrenal gland trends to be significantly associated with adrenal metastasis, which is in females the major source of androgens. Tropism of hormone receptor positive NSCLC cells towards the endocrine gland has not been described before but is in line with the surprising finding that a subtype of NSCLC cells derives growth advantage from hormones such as androgens or its derivatives (estrogen).

Example 5

Spearman Correlation of ESR1, SNAI2, CDH1, CDH11 Expression Determined by Using RT-PCR with Site of Initial Metastasis in NSCLC Patient Cohort

In view of the extreme effect of hormone receptors on patient survival in NSCLC, the inventor has analyzed the promoter sites regulating the expression of hormone receptor RNA expression, i.e., ESR1, ESR2, PGR, AR to identify candidate genes that oppose the effect of ESR1 and contribute to more aggressive and hormone insensitive tumor subtypes. Thereby he had the idea to first analyze the isoform specific expression of ESR1 in cancer and then analyze the respective isoform specific promoter sites in molecular detail. Surprisingly, he has identified tumor specific ESR1 isoforms, whose promoter region in turn exhibited several snail transcription factor binding sites (i.e., bindings sites for SNAI1, SNAI2 and SNAI3). The interaction of hormone receptors and snail factors was then analyzed in diverse Affymetrix data sets. As one example, fresh tissue biopsy samples (laparoscopy; pre-treatment) and tumor resectates (surgery; post-treatment) of stage III and IV ovarian cancer patients (n=40) neoadjuvantly treated with chemotherapy (6×AUC) were analyzed by Affymetrix expression profiling. By Spearman correlation analysis and as depicted in FIG. 4, it could be proven that the transcription factor SNAI2 indeed strongly and negatively correlated with ESR1 (r=−0.56; p=0.0004) followed by E-Cadherin (“CDH1”; r=−0.36; p=0.03), both of which are associated with epithelial and good prognosis phenotype. Conversely, SNAI2 positively correlated with MMP2 (r=0.86; p<0.0001), Spon2 (r=0.80; p<0.0001), ADAM12 (r=0.72; p<0.0001) and OB-Cadherin (“CDH11”; r=0.66; p=0.03). Surprisingly the dramatic switch of cell-cell-adhesion from E-Cadherin to OB-Cadherin further illustrated the Epithelial-Mesenchymal transition, which might be associated with highly invasive behavior of tumor cells. However, the presence of OB-Cadherin might also indicate successful recruitment of osteoblast-like bone marrow cells into the primary tumor site further indicating the more aggressive phenotype of ESR1 low expressing and simultaneously SNAI2 overexpressing tumors.

Example 6

Determination of ESR1 in Combination with SNAI2 Expression Using Array Profiling in Ovarian Cancer Patient Cohort

A two gene-ratio was generated by dividing SNAI2 by ESR1. As depicted in FIG. 5, Kaplan-Meier-Analysis revealed that ovarian cancer patients having high two-gene-ratio values (Cut-Off 0.21), indicating high SNAI2 expression and simultaneously low ESR1 expression, which accounts for approximately one third of the ovarian cancer patients, have a worse overall survival than patients having high ESR1 expression and low SNAI2 expression. The latter exhibited 100% overall survival at three years within this stage IV neoadjuvantly treated ovarian cancer cohort (Hazard ratio 0.00; p=0.0021; Median Recurrence free Survival not reached versus 24, 8 months; 100% Overall Survival versus 20% Overall Survival at three years of follow-up). By generating a two gene ratio of SNAI2 and ESR1 the test can be performed without using any housekeeping gene, which further limits the number of required genes and reduces complexity and costs for performing the assay. The test could be used for stratification of cancer patients towards targeted treatments in the late and also earlier setting. Particularly SNAI2 negatively correlates with PARP1 (r=−0.54; p=0.0004) meaning that high expression of SNAI2 is associated with low expression of PARP 1. PARP1 is the target of PARP Inhibitors. Lower expression of PARP1 (and/or BRCA1) indicates responsiveness towards this regimen. However, the expression of PARP1 is very difficult to determine on protein and mRNA level, due to comparably low general expression and low dynamic range. However patients responding to PARP Inhibitors could be more easily detected by determining the balance between hormone receptors and SNAI factors.

Example 7

Determination of ESR1 in Combination with SNAI2 Expression Using Array Profiling in Non-Small Cell Lung Cancer Patient Cohort

To further validate, that the two gene-ratio generated by dividing SNAI2 by ESR1 is also prognostic in other cancer indications and particularly in lung cancer, the public available whole genome Affymetrix gene expression data from Jinkook Kim (GSE8894; Lee E S et al. (2008): Prediction of Recurrence-free survival in postoperative non-small cell lung cancer patients by using an integrated model of clinical and gene expression. Clin Cancer Res. 14(22): 7397-404) was retrieved from the GEO database. In brief, a total of 253 fresh frozen non-small lung cancer tumor samples from patients who underwent curative resection of NSCLC at Samsung Medical Center in Seoul (South Korea) between January 1995 and December 2005 were selected and acceptable RNA quality for microarray analysis was achieved from 138 tumors.
The first validation focused on female NSCLC patients (n=34; Adenocarcinoma and Squamous Cell Carcinoma). The two-gene ratio was constructed by dividing SNAI2 by ESR1 expression values. According to this invention low gene-ratio values reflect lower expression of ESR1 and simultaneously higher expression of ESR1 and are associated with lower risk of recurrence. By using a two gene-ratio cut-off at 2.32 a low risk was predicted for approximately 30% of the women (i.e., 11/34 patients). As depicted in FIG. 6, the Kaplan-Meier analysis validated that the low-risk prediction by using the SNAI2 and ESR1 expression ratio have a lower risk of recurrence (Hazard ratio 0.25; p=0.0012; Median Recurrence free Survival not reached versus 9.8 months; 70% Recurrence Free Survival versus 20% Recurrence Free Survival at two years of follow-up). This validates the prognostic significance of SNAI2 and ESR1 in independent patients. Importantly, this indicates that the invention not only works for metastatic, Caucasian NSCLC patients treated within a first-line chemotherapy protocol as depicted in Example 3, but also works in non-metastatic, Asian NSCLC patients after curative resection of the tumor mass. This means, that the invention is suitable for NSCLC patients at different disease and treatment stages. Importantly, as estrogen receptor is capable of triggering tumor growth, the determination of hormone receptors (particularly ESR1) and/or Snail factors (particularly SNAI2) is important for peri- or post-menopausal women, to evaluate possible risks associated with hormone replacement therapy, as treatment with hormones could force tumor growth and aggressiveness particularly in ESR1 high expressors and/or SNAI2 low expressors.

Example 8

Determination of PGR Using Array Profiling in Non-Small Cell Lung Cancer Patient Cohort

The second validation focused on male NSCLC patients (n=100; Adenocarcinoma and Squamous Cell Carcinoma). As depicted in FIG. 7 the Kaplan-Meier analysis validated that high PGR expression indicates lower risk of recurrence (Hazard ratio 0.46; p=0.0056; Median Recurrence free Survival not reached versus 23 months; 65% Recurrence Free Survival versus 40% Recurrence Free Survival at three years of follow-up). This validates that hormone receptor expression is significant also for male NSCLC in Asian patients having undergone curative resection of the primary tumor (see above).

Claims

What is claimed is:

1. A method of classifying a sample of a patient who suffers from or being at risk of developing cancer, said method comprising the steps of:

a. determining in said sample from said patient, on a non protein basis, the expression level of at least one gene encoding for a hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor in said sample;

b. comparing the one or more expression level(s) determined in step (a) with one or more expression level(s) of one or more reference genes; and

c. classifying the sample of said patient from the outcome of the comparison in step (b) into one of at least two classifications.

2. The method according to claim 1, wherein a mode of treatment based on the classification in step (c) comprises a treatment targeting at least one hormone receptor selected from the group comprising estrogen receptor, progesterone receptor and/or androgen receptor, or targeting their respective signaling pathways, and/or a treatment targeting repair mechanisms related therewith.

3. The method according to claim 1 or 2, characterized in that said treatment comprises the administration of tamoxifen.

4. The method according to any of the aforementioned numbered paragraphs, characterized in that said treatment is intended to be given as hormone replacement therapy (HRT) in peri- or postmenopausal women.

5. The method according to claim any of the aforementioned claims, characterized in that the gene encoding for the estrogen receptor is ESR1.

6. A method according any of the aforementioned claims, characterized in that said one or more reference gene(s) is at least one housekeeping gene and/or at least one EMT marker gene.

7. The method according to claim 6, wherein the at least one housekeeping gene is selected from the group comprising RPL37A, GAPDH, RPL 13 and/or HPRT1; and the at least one EMT marker gene is selected from the group comprising SNAI1, SNAI2 and/or SNAI3.

8. The method according to any of the aforementioned claims, wherein the comparing step (b) is a ratio between the expression level of at least one hormone receptor and at least one EMT marker gene.

9. The method according to any of the aforementioned claims, wherein the comparing step (b) is a ratio of ESR1 to SNAI2.

10. The method according to any one of the aforementioned claims, wherein said expression level(s) is determined by

a. a hybridization based method;

b. a PCR based method;

c. a method based on the electrochemical detection of particular molecules, and/or

d. an array based method.

11. The method according to any one of the aforementioned claims, characterized in that said expression level is determined by reverse transcriptase polymerase chain reaction of RNA transcripts.

12. The method according to claim 10, characterized in that said expression level is determined in formalin and/or paraffin fixed tissue samples of the RNA transcripts.

13. The method according to any one of the aforementioned claims, wherein, after lysis, the sample is treated with silica-coated magnetic particles and a chaotropic salt, for purification of the nucleic acids contained in said sample prior to the determination in step (a).

14. The method according to any one of the aforementioned claims, characterized in that said cancer displays characteristics of, or is, an adenocarcinoma.

15. The method according to any one of the aforementioned claims, characterized in that said cancer is selected from the group comprising lung cancer, a non-small cell lung cancer (NSCLC), ovarian cancer; breast cancer and/or prostate cancer.

16. The method according to any one of the aforementioned claims, wherein the expression level(s) determined in step (a) is/are correlated with said patient's data, said data being selected from the group consisting of etiopathology data, clinical symptoms, anamnesis data and/or data concerning the therapeutic regimen.

17. An oligonucleotide comprising a nucleotide sequence which is a fragment, a fraction, a variant, a homologue, a derivative of, or a complementary to, any of the nucleic acid molecules set forth as SEQ ID NOs 1-9, or which is capable of hybridizing to a fragment, a fraction, a variant, a homologue, or a derivative of any of the nucleic acid molecules set forth as SEQ ID NOs 1-9.

18. The oligonucleotide according to claim 17, wherein said oligonucleotide is selected from the group consisting of

a. an amplification primer

b. a labeled probe, and/or

c. a substrate bound probe.

19. A kit useful for carrying out a method of any one of the aforementioned claims, comprising at least one oligonucleotide according to claim 17 and/or 18.