WO2005124353A1 - Utilisation de pyrophosphatases inorganiques comme marqueur pour le cancer colorectal - Google Patents

Utilisation de pyrophosphatases inorganiques comme marqueur pour le cancer colorectal Download PDF

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Publication number
WO2005124353A1
WO2005124353A1 PCT/EP2005/006520 EP2005006520W WO2005124353A1 WO 2005124353 A1 WO2005124353 A1 WO 2005124353A1 EP 2005006520 W EP2005006520 W EP 2005006520W WO 2005124353 A1 WO2005124353 A1 WO 2005124353A1
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WIPO (PCT)
Prior art keywords
ipyr
marker
colorectal cancer
crc
cea
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PCT/EP2005/006520
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English (en)
Inventor
Michael Tacke
Herbert Andres
Marie-Luise Hagmann
Johann Karl
Michael Pfeffer
Michael Thierolf
Norbert Wild
Werner Zolg
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Roch Diagnostics Gmbh
F. Hoffmann-La Roche Ag
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Application filed by Roch Diagnostics Gmbh, F. Hoffmann-La Roche Ag filed Critical Roch Diagnostics Gmbh
Priority to EP05753595A priority Critical patent/EP1761780A1/fr
Priority to JP2007515890A priority patent/JP2008502889A/ja
Priority to CA002567157A priority patent/CA2567157A1/fr
Publication of WO2005124353A1 publication Critical patent/WO2005124353A1/fr

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57419—Specifically defined cancers of colon
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/90—Enzymes; Proenzymes
    • G01N2333/914—Hydrolases (3)
    • G01N2333/916—Hydrolases (3) acting on ester bonds (3.1), e.g. phosphatases (3.1.3), phospholipases C or phospholipases D (3.1.4)

Definitions

  • CRC colorectal cancer
  • the staging of cancer is the classification of the disease in terms of extent, progression, and severity. It groups cancer patients so that generalizations can be made about prognosis and the choice of therapy.
  • TNM the most widely used classification of the anatomical extent of cancer. It represents an internationally accepted, uniform staging system. There are three basic variables: T (the extent of the primary tumor), N (the status of regional lymph nodes) and M (the presence or absence of distant metastases).
  • TNM criteria are published by the UICC (International Union against Cancer), edition, 1997 (Sobin, L.H., and Fleming, I.D., TNM 80 (1997) 1803-4).
  • early diagnosis of CRC refers to a diagnosis at a pre-malignant state (adenoma) or at a tumor stage where no metastases at all (neither proximal nor distal), i.e., adenoma, T; s , NO, MO or Tl-4; NO; MO are present.
  • T; s denotes carcinoma in situ.
  • the earlier cancer can be detected/diagnosed, the better is the overall survival rate. This is especially true for CRC.
  • the prognosis in advanced stages of tumor is poor.
  • More than one third of the patients will die from progressive disease within five years after diagnosis, corresponding to a survival rate of about 40% for five years.
  • Current treatment is only curing a fraction of the patients and clearly has the best effect on those patients diagnosed in an early stage of disease.
  • CRC colorectal cancer
  • a new diagnostic marker as a single marker should be at least as good as the best single marker known in the art. Or, a new. marker should lead to a progress in diagnostic sensitivity and/or specificity either if used alone or in combination with one or more other markers, respectively.
  • the diagnostic sensitivity and/or specificity of a test is best assessed by its receiver- operating characteristics, which will be described in detail below.
  • CEA carcinoembryonic antigen
  • serum CEA determination possesses neither the sensitivity nor the specificity to enable its use as a screening test for colorectal cancer in the asymptomatic population (Reynoso, G., et al, JAMA 220 (1972) 361- 365; Sturgeon, C, Clinical Chemistry 48 (2002) 1151-1159).
  • the present invention therefore relates to a method for assessing colorectal cancer in vitro by biochemical markers comprising measuring in a sample the concentration of a) IPYR, and b) using the concentration determined in step (a) in the assessment of colorectal cancer.
  • Another preferred embodiment of the invention is a method for assessing colorectal cancer comprising the steps of a) contacting a liquid sample obtained from an individual with a speci c binding agent for IPYR under conditions appropriate for formation of a complex between said binding agent and IPYR, and b) correlating the amount of complex formed in (a) to the assessment of colorectal cancer.
  • Yet another preferred embodiment of the invention relates to a method for assessing colorectal cancer in vitro by biochemical markers, comprising measuring in a sample the concentration of IPYR and of one or more other marker of colorectal cancer and using the concentrations determined in the assessment of colorectal cancer.
  • the present invention also relates to the use of a marker panel comprising at least IPYR and CYFRA 21-1 in the assessment of CRC.
  • the present invention also relates to the use of a marker panel comprising at least IPYR and NSE in the assessment of CRC.
  • the present invention also relates to the use of a marker panel comprising at least IPYR and CEA in the assessment of CRC.
  • the present invention also relates to the use of a marker panel comprising at least
  • IPYR and NNMT in the assessment of CRC.
  • the present invention also relates to the use of a marker panel comprising at least IPYR and CA 19-9 in the assessment of CRC.
  • the present invention also relates to the use of a marker panel comprising at least IPYR and CA 72-4 in the assessment of CRC.
  • the present invention also provides a kit for performing the method according to the present invention comprising at least the reagents required to specifically measure IPYR and CYFRA 21-1, respectively, and optionally auxiliary reagents for performing the measurement.
  • the present invention also provides a kit for performing the method according to the present invention comprising at least the reagents required to specifically measure IPYR and NSE, respectively, and optionally auxiliary reagents for performing the measurement.
  • the present invention relates to a method for assessing colorectal cancer in vitro comprising measuring in a sample the concentration of a) IPYR, b) optionally one or more other marker of colorectal cancer, and c) using the concentrations determined in step (a) and optionally step (b) in the assessment of colorectal cancer.
  • a marker means one marker or more than one marker.
  • marker refers to a molecules to be used as a target for analyzing patient test samples.
  • molecular targets are proteins or polypeptides themselves as well as antibodies present in a sample.
  • Proteins or polypeptides used as a marker in the present invention are contemplated to include any variants of said protein as well as fragments of said protein or said variant, in particular, immunologically detectable fragments.
  • proteins which are released by cells or present in the extracellular matrix which become damaged, e.g., during inflammation could become degraded or cleaved into such fragments.
  • Certain markers are synthesized in an inactive form, which may be subsequently activated by proteolysis.
  • proteins or fragments thereof may also be present as part of a complex.
  • Such complex also may be used as a marker in the sense of the present invention.
  • Variants of a marker polypeptide are encoded by the same gene, but differ in their PI or MW, or both (e.g., as a result of alternative mRNA or pre- mRNA processing, e.g. alternative splicing or limited proteolysis) and in addition, or in the alternative, may arise from differential post-translational modification (e.g., glycosylation, acylation, and/or phosphorylation).
  • assessing colorectal cancer is used to indicate that the method according to the present invention will (alone or together with other markers or variables, e.g., the criteria set forth by the UICC (UICC (International Union against Cancer), Sobin, L.H., Wittekind, Ch. (eds), TNM Classification of Malignant Tumours, fifth edition, 1997)) e.g., aid the physician to establish or confirm the absence or presence of CRC or aid the physician in the prognosis, the detection of recurrence (follow-up of patients after surgery) and/or the monitoring of treatment, especially of chemotherapy.
  • UICC International Union against Cancer
  • Sobin L.H., Wittekind, Ch. (eds), TNM Classification of Malignant Tumours, fifth edition, 1997)
  • aid the physician to establish or confirm the absence or presence of CRC or aid the physician in the prognosis, the detection of recurrence (follow-up of patients after surgery) and/or the monitoring of treatment, especially of chemotherapy.
  • sample refers to a biological sample obtained for the purpose of evaluation in vitro.
  • the sample or patient sample preferably may comprise any body fluid.
  • Preferred test samples include blood, serum, plasma, urine, saliva, and synovial fluid.
  • Preferred samples are whole blood, serum, plasma or synovial fluid, with plasma or serum being most preferred.
  • any such assessment is made in vitro.
  • the patient sample is discarded afterwards.
  • the patient sample is solely used for the in vitro method of the invention and the material of the patient sample is not transferred back into the patient's body.
  • the sample is a liquid sample, e.g., whole blood, serum, or plasma.
  • the present invention relates to a method for assessing CRC in vitro by biochemical markers, comprising measuring in a sample the concentration of IPYR and using the concentration determined in the assessment of CRC.
  • the protein IPYR inorganic pyrophosphatase, also known as pyrophosphate phospho-hydrolase (PPase); HSPC124; MGC49850; PPA2; PPase; SID6 306) is characterized by the sequences given SEQ ID NO:l, SEQ ID NO:2 or an isoform.
  • the protein inorganic pyrophosphatase is essential for the catalytic activity of PPase.
  • PPases catalyze the hydrolysis of pyrophosphate to inorganic phosphate, which is important for the phosphate metabolism of cells.
  • the present invention shall not be construed to be limited to the full-length protein IPYR of SEQ ID NO: 1.
  • Physiological or artificial fragments of IPYR, secondary modifications of IPYR, as well as allelic variants of IPYR are also encompassed by the present invention.
  • Artificial fragments preferably encompass a peptide produced synthetically or by recombinant techniques, which at least comprises one epitope of diagnostic interest consisting of at least 6 contiguous amino acids as derived from the sequence disclosed in SEQ ID NO:l. Such fragment may advantageously be used for generation of antibodies or as a standard in an immunoassay. More preferred the artificial fragment comprises at least two epitopes of interest appropriate for setting up a sandwich immunoassay.
  • full-length IPYR or a physiological variant of this marker is detected in a method according to the present invention.
  • the assessment method according to the present invention is based on a liquid sample which is derived from an individual. Unlike to methods known from the art
  • IPYR is specifically measured from this liquid sample by use of a specific binding agent.
  • a specific binding agent is, e.g., a receptor for IPYR, a lectin binding to IPYR or an antibody to IPYR.
  • a specific binding agent has at least an affinity of 10 7 1/mol for its corresponding target molecule.
  • the specific binding agent preferably has an affinity of 10 8 1/mol or even more preferred of 10 9 1/mol for its target molecule.
  • specific is used to indicate that other biomolecules present in the sample do not significantly bind to the binding agent specific for IPYR.
  • the level of binding to a biomolecule other than the target molecule results in a binding affinity which is only 10%, more preferably only 5% of the affinity of the target molecule or less.
  • a most preferred specific binding agent will fulfill both the above minimum criteria for affinity as well as for specificity.
  • a specific binding agent preferably is an antibody binding to IPYR.
  • the term antibody refers to a polyclonal antibody, a monoclonal antibody, fragments of such antibodies, as well as to genetic constructs comprising the binding domain of an antibody.
  • Antibodies are generated by state of the art procedures, e.g., as described in Tijssen (Tijssen, P., Practice and theory of enzyme immunoassays 11 (1990) the whole book, especially pages 43-78; Elsevier, Amsterdam).
  • Tijssen Tejssen, P., Practice and theory of enzyme immunoassays 11 (1990) the whole book, especially pages 43-78; Elsevier, Amsterdam.
  • the skilled artisan is well aware of methods based on immunosorbents that can be used for the specific isolation of antibodies. By these means the quality of polyclonal antibodies and hence their performance in immunoassays can be enhanced (Tijssen, P., supra, pages 108-115).
  • IPYR has been identified as a marker which is useful in the diagnosis of CRC
  • alternative ways may be used to reach a result comparable to the achievements of the present invention.
  • alternative strategies to generate antibodies may be used.
  • Such strategies comprise amongst others the use of synthetic peptides, representing an epitope of IPYR for immunization.
  • DNA Immunization also known as DNA vaccination may be used.
  • the liquid sample obtained from an individual is incubated with the specific binding agent for IPYR under conditions appropriate for formation of a binding agent IPYR-complex.
  • Such conditions need not be specified, since the skilled artisan without any inventive effort can easily identify such appropriate incubation conditions.
  • the amount of complex is measured and correlated to the diagnosis of CRC.
  • the skilled artisan will appreciate there are numerous methods to measure the amount of the specific binding agent IPYR-complex all described in detail in relevant textbooks (cf., e.g., Tijssen P., supra, or Diamandis, et al., eds. (1996) Immunoassay, Academic Press, Boston).
  • IPYR is detected in a sandwich type assay format.
  • a first specific binding agent is used to capture IPYR on the one side and a second specific binding agent, which is labeled to be directly or indirectly detectable is used on the other side.
  • IPYR can be measured from a liquid sample obtained from an individual sample. No tissue and no biopsy sample is required to apply the marker IPYR in the assessment of CRC.
  • the method according to the present invention is practiced with serum as liquid sample material. In a further preferred embodiment the method according to the present invention is practiced with plasma as liquid sample material. In a further preferred embodiment the method according to the present invention is practiced with whole blood as liquid sample material.
  • stool can be prepared in various ways known to the skilled artisan to result in a liquid sample as well.
  • sample liquid derived from stool also represents a preferred embodiment according to the present invention.
  • the inventors of the present invention have surprisingly been able to detect protein IPYR in a bodily fluid sample. Even more surprising they have been able to demonstrate that the presence of IPYR in such liquid sample obtained from an individual can be correlated to the assessment of colorectal cancer.
  • an antibody to IPYR is used in a qualitative (IPYR present or absent) or quantitative (IPYR amount is determined) immunoassay. Measuring the level of protein IPYR has proven very advantageous in the field of CRC. Therefore, in a further preferred embodiment, the present invention relates to use of protein IPYR as a marker molecule in the assessment of colorectal cancer from a liquid sample obtained from an individual.
  • the ideal scenario for diagnosis would be a situation wherein a single event or process would cause the respective disease as, e.g., in infectious diseases. In all other cases correct diagnosis can be very difficult, especially when the etiology of the disease is not fully understood as is the case of CRC.
  • no biochemical marker for example in the field of CRC, is diagnostic with 100% specificity and at the same time 100% sensitivity for a given disease.
  • biochemical markers are used to assess with a certain likelihood or predictive value the presence or absence of a disease. Therefore, in routine clinical diagnosis various clinical symptoms and biological markers are generally considered together in the diagnosis, treatment, and management of the underlying disease.
  • Biochemical markers can either be determined individually or, in a preferred embodiment of the invention, they can be measured simultaneously using a chip- or a bead-based array technology. The concentrations of the biomarkers are then interpreted independently using an individual cut-off for each marker or they are combined for interpretation.
  • the assessment of colorectal cancer according to the present invention is performed in a method comprising measuring in a sample the concentration of a) IPYR, b) optionally one or more other marker of colorectal cancer, and c) using the concentration determined in step (a) and optionally step (b) in the assessment of colorectal cancer.
  • the method for assessment of CRC is performed by measuring the concentration of IPYR and of one or more other marker and by using the concentration of IPYR and of the one or more other marker in the assessment of CRC.
  • the present invention is also directed to a method for assessing CRC in vitro by biochemical markers, comprising measuring in a sample the concentration of IPYR and of one or more other marker of CRC and using the concentrations determined in the assessment of CRC.
  • the marker IPYR in the univariate analysis has (at a specificity of about 90%) a sensitivity for CRC of 54.7%.
  • the marker IPYR will be of advantage in one or more of the following aspects: screening; diagnostic aid; prognosis; monitoring of chemotherapy, and follow-up.
  • CRC is the second most common malignancy of both males and females in developed countries. Because of its high prevalence, its long asymptomatic phase and the presence of premalignant lesions, CRC meets many of the criteria for screening. Clearly, a serum tumour marker which has acceptable sensitivity and specificity would be more suitable for screening than either FOB testing or endoscopy.
  • IPYR will form an integral part of a marker panel appropriate for screening purposes.
  • the present invention therefore relates to the use of IPYR as one marker of a CRC marker panel for CRC screening purposes.
  • the present data further indicate that certain combinations of markers will be advantageous in the screening for CRC.
  • the present invention also relates to the use of a marker panel comprising IPYR and CYFRA 21-1, or of a marker panel comprising IPYR and NSE, or of a marker panel comprising IPYR and CYFRA 21-1 and NSE for the purpose of screening for CRC.
  • IPYR as a single marker according to the data of the present invention might be at least as good a single marker as CEA or even superior it has to be expected that IPYR will be used as a diagnostic aid, especially by establishing a baseline value before surgery.
  • the present invention thus also relates to the use of IPYR for establishing a baseline value before surgery for CRC.
  • the gold standard for determining prognosis in patients with CRC is the extend of disease as defined by the Dukes', TNM or other staging systems, If a marker such as
  • CEA is to be used for predicting outcome, it must: provide stronger prognostic information than that offered by existing staging systems, provide information independent of the existing systems or provide prognostic data within specific subgroups defined by existing criteria, e.g. in Dukes' B or node-negative patients.
  • CEA should be added to the TNM staging system for colorectal cancer.
  • the CEA level should be designated as follows: CX, CEA cannot be assessed; CO, CEA not elevated ( ⁇ 5 ⁇ g/l) or CEA1, CEA elevated (> 5 ⁇ g/1) (Compton, C, et al, Cancer 88 (2000) 1739-1757).
  • IPYR IP-based prognosis .
  • the level of preoperative IPYR will most likely be combined with one or more other marker for CRC and/or the TNM staging system, as recommended for CEA by the AJCC.
  • IPYR is used in the prognosis of patients with CRC.
  • IPYR will be at least as good a marker for monitoring of chemotherapy as CEA.
  • the present invention therefore also relates to the use of IPYR in the monitoring of CRC patients under chemotherapy.
  • CEA Serial monitoring with CEA has been shown to detect recurrent/metastatic disease with a sensitivity of approximately of 80 %, specificity of approximately 70 % and provides an average lead-time of 5 months (for review, see Duffy, M.J., et al., supra and Fletcher, R.H., supra). Furthermore, CEA was the most frequent indicator of recurrence in asymptomatic patients (Pietra, N., et al, Dis. Colon Rectum 41 (1998) 1127-1133 and Graham, R.A., et al., Ann. Surg. 228 (1998) 59-63) and was more cost-effective than radiology for the detection of potentially curable recurrent disease.
  • CEA was most sensitive (almost 100%) for the detection of liver metastasis.
  • CEA was less reliable for diagnosing locoregional recurrences, the sensitivity being only approximately 60 % (Moertel, C.G., et al., JAMA 270 (1993)943-7)
  • the EGTM Panel like the IPYRO Panel (Anonymous, J. Clin. Oncol. 14 (1996) 2843-2877) suggests that CEA testing be carried out every 2-3 months for at least 3 years after the initial diagnosis. After 3 years, testing could be carried out less frequently, e.g. every 6 months. No evidence exists, however, to support this frequency of testing.
  • the present invention discloses and therefore in a preferred embodiment relates to the use of IPYR in the diagnostic field of CRC or in the assessment of CRC, respectively.
  • the present invention relates to the use of IPYR as a marker molecule for colorectal cancer in combination with one or more marker molecules for colorectal cancer in the assessment of colorectal cancer from a liquid sample obtained from an individual.
  • IPYR as a marker molecule for colorectal cancer in combination with one or more marker molecules for colorectal cancer in the assessment of colorectal cancer from a liquid sample obtained from an individual.
  • the expression "one or more” denotes 1 to 20, preferably 1 to 10, preferably 1 to 5, more preferred 3 or 4.
  • IPYR and the one or more other marker form a CRC marker panel.
  • a preferred embodiment of the present invention is the use of IPYR as a marker molecule for colorectal cancer in combination with one or more marker molecules for colorectal cancer in the assessment of colorectal cancer from a liquid sample obtained from an individual.
  • Preferred selected other CRC markers with which the measurement of IPYR maybe combined are NSE, CYFRA 21-1, NMMT, CA 19-9, CA 72-4, and/or CEA.
  • the marker panel used in the assessment of CRC comprises IPYR and at least one other marker molecule selected from the group consisting of NSE, CYFRA 21-1 and NMMT. The markers which preferably are combined with IPYR or which form part of the CRC marker panel comprising IPYR, respectively, are discussed in more detail below.
  • NSE neuro-specific enolase
  • glycolytic enzyme enolase (2-phospho-D-glycerate hydrolase, EC 4.2.1.11, molecular weight approx. 80 kD) occurs in a variety of dimeric isoforms comprising three immunologically different subunits termed ⁇ , ⁇ , and ⁇ .
  • the ⁇ - subunit of enolase occurs in numerous types of tissue in mammals, whereas the ⁇ - subunitis found mainly in the heart and in striated musculature.
  • the enolase isoforms ⁇ and ⁇ which are referred to as neuron-specific enolase (NSE) or ⁇ - enolase, are primarily detectable in high concentrations in neurons and neuro- endocrine cells as well as in tumors originating from them (Lamerz, R., NSE (Neuronen-spezifische Enolase), ⁇ -Enolase, In: Thomas L (ed) Clinical Laboratory Diagnosis, TH-Books, Frankfurt, 1 st English Edition 1998: 979-981, 5. yer Auflage 1998:1000-1003).
  • NSE Neuron-specific enolase
  • ⁇ -Enolase In: Thomas L (ed) Clinical Laboratory Diagnosis, TH-Books, Frankfurt, 1 st English Edition 1998: 979-981, 5. yer Auflage 1998:1000-1003).
  • NSE is described as the marker of first choice in the monitoring of small cell bronchial carcinoma (Lamerz, R., supra), whereas CYFRA 21-1 is superior to NSE for non-small cell bronchial carcinoma (Ebert, W., et al., Eur. J. Clin. Chem. Clin. Biochem 32 (1994) 189-199).
  • Elevated NSE concentrations are found in 60-81 % of cases of small cell bronchial carcinoma.
  • NSE In response to chemotherapy there is a temporary rise in the NSE level 24-72 hours after the first therapy cycle as a result of cytolysis of the tumor cells. This is followed within a week or by the end of the first therapy cycle by a rapid fall in the serum values (which were elevated prior to therapy). By contrast, non-responders to therapy display levels which are constantly elevated or fail to fall into the reference range. During remission, 80-96 % of the patients have normal values. Rising NSE values are found in cases of relapse. The rise occurs in some cases with a latent period of 1-4 months, is often exponential (with a doubling time of 10-94 days) and correlates with the survival period. NSE is useful as a single prognostic factor and activity marker during the monitoring of therapy and the course of the disease in small cell bronchial carcinoma: diagnostic sensitivity 93 %, positive predictive value 92% (Lamerz, R., supra).
  • NSE serum values above 30 ng/ml are found in 62 % of the affected children.
  • the medians rise in accordance with the stage of the disease.
  • NSE has also been measured in other tumors: Non-pulmonary malignant diseases show values above 25 ng/ml in 22 % of the cases (carcinomas in all stages). Brain tumors such as glioma, miningioma, neurofibroma, and neurinoma are only occasionally accompanied by elevated serum NSE values. In primary brain tumors or brain metastasis and in malignant melanoma and phaeochromocytoma, elevated NSE- values can occur in the CSF (cerebrospinal fluid). Increased NSE concentrations have been reported for 14 % of organ-restricted and 46 % of metastasizing renal carcinomas, with a correlation to the grade as an independent prognosis factor.
  • the CA 19-9 values measured are defined by the use of the monoclonal antibody 1116-NS-19-9.
  • the 1116-NS-19-9-reactive determinants on a glycolipid having a molecular weight of approx. 10,000 daltons are measured.
  • This mucin corresponds to a hapten of Lewis-a blood group determinants and is a component of a number of mucous membrane cells (Koprowski, H., et al., Somatic Cell Genet 5 (1979) 957- 971).
  • 3-7 % of the population have the Lewis a-negative/b-negative blood group configuration and are unable to express the mucin with the reactive determinant CA 19-9. This must be taken into account when interpreting the findings.
  • Mucin occurs in fetal gastric, intestinal and pancreatic epithelia. Low concentrations can also be found in adult tissue in the liver, lungs, and pancreas (Stieber, P., and Fateh-Moghadam, A., Boeringer Mannheim, Cat. No. 1536869 (engl), 1320947 (dtsch), ISBN 3-926725-07-9 dtsch/engl. Juergen Hartmann Verlag Marloffstein-Rathsberg (1993); Herlyn, M., et al, J. Clin. Immunol 2 (1982) 135-
  • CA 19-9 assay values can assist in the differential diagnosis and monitoring of patients with pancreatic carcinoma (sensitivity 70-87 %) (Ritts, R.E., Jr., et al, Int. J. Cancer 33 (1984) 339-345). There is no correlation between tumor mass and the CA 19-9 assay values. However, patients with CA 19-9 serum levels above 10,000
  • CA 19-9 cannot be used for the early detection of pancreatic carcinoma (Steinberg, W.M., et al., Gastroenterology 90 (1986) 343-349).
  • CA 19-9 values provide a sensitivity of 50-75 %.
  • the concomitant determination of CA 72-4 and CEA is recommended in case of gastric carcinoma.
  • determination of CEA alone is adequate; only in rare CEA-negative cases the determination of CA 19-9 can be useful.
  • CA 19-9 has been measured on an Elecsys® analyzer using Roche product number 11776193 according to the manufacturers instructions.
  • CEA is a monomeric glycoprotein (molecular weight approx. 180.000 dalton) with a variable carbohydrate component of approx. 45-60 % (Gold, P., and Freedman, S.O., J. Exp. Med. 121 (1965) 439-462).
  • CEA like AFP, belongs to the group of carcinofetal antigens that are produced during the embryonic and fetal period.
  • the CEA gene family consists of about 17 active genes in two subgroups. The first group contains CEA and the Non-specific Cross-reacting Antigens (NCA); the second group contains the Pregnancy-Specific Glycoproteins (PSG).
  • NCA Non-specific Cross-reacting Antigens
  • PSG Pregnancy-Specific Glycoproteins
  • CEA is mainly found in the fetal gastrointestinal tract and in fetal serum. It also occurs in slight quantities in intestinal, pancreatic, and hepatic tissue of healthy adults. The formation of CEA is repressed after birth, and accordingly serum CEA values are hardly measurable in healthy adults.
  • High CEA concentrations are frequently found in cases of colorectal adenocarcinoma (Stieber, P., and Fateh-Moghadam, A., supra).
  • Slight to moderate CEA elevations occur in 20-50 % of benign diseases of the intestine, the pancreas, the liver, and the lungs (e.g. liver cirrhosis, chronic hepatitis, pancreatitis, ulcerative colitis, Crohn's Disease, emphysema) (Stieber, P., and Fateh-Moghadam, A., supra).
  • Smokers also have elevated CEA values.
  • the main indication for CEA determinations is the follow-up and therapy management of colorectal carcinoma.
  • CEA determinations are not recommended for cancer-screening in the general population.
  • CEA concentrations within the normal range do not exclude the possible presence of a malignant disease.
  • the antibodies in assay manufactured by Roche Diagnostics react with CEA and (as with almost all CEA methods) with the meconium antigen (NCA2).
  • Cross- reactivity with NCA1 is 0.7 % (Hammarstrom, S., et al., Cancer Research 49 (1989) 4852-4858 and Bormer, O.P., Tumor Biol. 12 (1991) 9-15).
  • CEA has been measured on an Elecsys® analyzer using Roche product number
  • CYFRA 21-1 specifically measures a soluble fragment of cytokeratin 19 as present in the circulation.
  • the measurement of CYFRA 21-1 is typically based upon two monoclonal antibodies (Bodenmueller, H., et al., Int. J. Biol. Markers 9
  • cytokeratin 19 having a molecular weight of approx. 30,000 daltons is measured.
  • Cytokeratins are structural proteins forming the subunits of epithelial intermediary filaments. Twenty different cytokeratin polypeptides have so far been identified. Due to their specific distribution patterns they are eminently suitable for use as differentiation markers in tumor pathology. Intact cytokeratin polypeptides are poorly soluble, but soluble fragments can be detected in serum (Bodenmueller, H., et al., supra).
  • CYFRA 21-1 is a well-established marker for Non-Small-Cell Lung Carcinoma (NSCLC).
  • NSCLC Non-Small-Cell Lung Carcinoma
  • the main indication for CYFRA 21-1 is monitoring the course of non- small cell lung cancer (NSCLC) (Sturgeon, C, Clinical Chemistry 48 (2002) 1151- 1159).
  • CYFRA 21-1 serum levels indicate an advanced tumor stage and a poor prognosis in patients with non-small-cell lung cancer (van der Gaast A. et al., Br. J. Cancer 69 (1994) 525-528).
  • a normal or only slightly elevated value does not rule out the presence of a tumor.
  • Successful therapy is documented by a rapid fall in the CYFRA 21-1 serum level into the normal range.
  • a constant CYFRA 21-1 value or a slight or only slow decrease in the CYFRA 21-1 value indicates incomplete removal of a tumor or the presence of multiple tumors with corresponding therapeutic and prognostic consequences. Progression of the disease is often shown earlier by increasing
  • CYFRA 21-1 values than by clinical symptomatology and imaging procedures.
  • CYFRA 21-1 is also suitable for course-monitoring in myoinvasive cancer of the bladder. Good specificity is shown by CYFRA 21-1 relative to benign lung diseases (pneumonia, sarcoidosis, tuberculosis, chronic bronchitis, bronchial asthma, emphysema).
  • CYFRA 21-1 also is of use in detecting disease relapse and assessing treatment efficacy in the field of breast cancer (Nakata, B., et al, British J. of Cancer (2004) 1-6).
  • CYFRA 21-1 has been measured on an Elecsys ® analyzer using Roche product number 11820966 according to the manufacturers instructions.
  • CYFRA 21-1 is an established marker in the field of NSCLC.
  • NSCLC non- malignant disease controls derived from patients with certain lung non-malignant diseases have been used. This has been considered important to differentiate benign from malign lung diseases (H. Bodenm ⁇ ller, et al., supra).' Since only recently it is possible to detect the marker CYFRA 21-1 in a significant percentage of samples derived from patients with CRC.
  • the presence of CYFRA 21-1 in such liquid sample obtained from an individual can be used in the assessment of colorectal cancer. Particularly in combination with other markers CYFRA 21 - 1 is considered to be a very useful marker in the field of CRC.
  • the protein nicotinamide N-methyltransferase (NNMT; Swiss-PROT: P40261) has an apparent molecular weight of 29.6 kDa and an isoelectric point of 5.56.
  • NNMT catalyzes the N-methylation of nicotinamide and other pyridines. This activity is important for biotransformation of many drugs and xenobiotic compounds.
  • the protein has been reported to be predominantly expressed in liver and is located in the cytoplasm.
  • NNMT has been cloned from cDNA from human liver and contained a 792-nucleotide open reading frame that encoded a 264-amino acid protein with a calculated molecular mass of 29.6 kDa (Akso , S., et al., J. Biol. Chem. 269 (1994) 14835-14840). Little is known in the literature about a potential role of the enzyme in human cancer.
  • markers are used in order to improve the diagnostic question under investigation.
  • a positive result is assumed if a sample is positive for at least one of the markers investigated. This may e.g. the case when diagnosing an infectious disease, like AIDS. Frequently, however, the combination of markers is evaluated.
  • the values measured for markers of a marker panel e.g. for IPYR, CYFRA 21-1 and NSE, are mathematically combined and the combined value is correlated to the underlying diagnostic question. Marker values may be combined by any appropriate state of the art mathematical method.
  • DA discriminant analysis
  • SVM Kernel Methods
  • Nonparametric Methods i.e. k-Nearest-Neighbor Classifiers
  • PLS Partial Least Squares
  • Tree-Based Methods i.e. Logic Regression, CART, Random Forest Methods, Boosting/Bagging Methods
  • Generalized Linear Models i.e. Logistic
  • the method used in correlating the marker combination of the invention e.g. to the absence or presence of CRC is selected from DA (i.e. Linear-, Quadratic-, Regularized Discriminant Analysis), Kernel Methods (i.e. SVM), Nonparametric Methods (i.e. k-Nearest-Neighbor Classifiers), PLS (Partial Least Squares), Tree- Based Methods (i.e.
  • DA i.e. Linear-, Quadratic-, Regularized Discriminant Analysis
  • Kernel Methods i.e. SVM
  • Nonparametric Methods i.e. k-Nearest-Neighbor Classifiers
  • PLS Partial Least Squares
  • Tree- Based Methods i.e.
  • state A e.g. diseased from healthy.
  • the markers are no longer independent but form a marker panel. It could be established that combining the measurements of IPYR, NSE and CYFRA 21-1, does particularly improve the diagnostic accuracy for CRC as compared to either healthy controls or, as also assessed, as compared to healthy controls plus non-malignant disease controls. Especially the later finding is of great importance, because a patient with a non-malignant disease may require quite a different treatment as a patient with CRC.
  • ROC receiver-operating characteristics
  • the clinical performance of a laboratory test depends on its diagnostic accuracy, or the ability to correctly classify subjects into clinically relevant subgroups. Diagnostic accuracy measures the test's ability to correctly distinguish two different conditions of the subjects investigated. Such conditions are for example health and disease or benign versus malignant disease.
  • the ROC plot depicts the overlap between the two distributions by plotting the sensitivity versus 1 - specificity for the complete range of decision thresholds.
  • sensitivity or the true-positive fraction [defined as (number of true-positive test results) (number of true-positive + number of false- negative test results)].
  • This has also been referred to as positivity in the presence of a disease or condition. It is calculated solely from the affected subgroup.
  • the false-positive fraction or 1 - specificity [defined as (number of false- positive results) / (number of true-negative + number of false-positive results)]. It is an index of specificity and is calculated entirely from the unaffected subgroup.
  • the ROC plot is independent of the prevalence of disease in the sample.
  • Each point on the ROC plot represents a sensitivity/ 1 -specificity pair corresponding to a particular decision threshold.
  • a test with perfect discrimination has an ROC plot that passes through the upper left corner, where the true-positive fraction is 1.0, or 100% (perfect sensitivity), and the false-positive fraction is 0 (perfect specificity).
  • the theoretical plot for a test with no discrimination is a 45° diagonal line from the lower left corner to the upper right corner. Most plots fall in between these two extremes.
  • One convenient goal to quantify the diagnostic accuracy of a laboratory test is to express its performance by a single number.
  • tissue specimen from 10 patients suffering from colorectal cancer are analyzed. From each patient three different tissue types are collected from therapeutic resections: tumor tissue (>80% tumor) (T), adjacent healthy tissue (N) and stripped mucosa from adjacent healthy mucosa (M). The latter two tissue types serve as matched healthy control samples. Tissues are immediately snap frozen after resection and stored at -80°C before processing. Tumors are diagnosed by histopathological criteria. Tissue preparation
  • 0.8-1.2 g of frozen tissue are put into a mortar and completely frozen by liquid nitrogen.
  • the tissue is pulverized in the mortar, dissolved in the 10-fold volume (w/v) of lysis buffer (40 mM Na-citrate, 5 mM MgCl 2 , 1% Genapol X-080, 0.02% Na-azide, Complete ® EDTA-free [Roche Diagnostics GmbH, Mannheim,
  • the protein concentration of the soluble protein fraction is determined using Bio- Rad® protein assay (Cat.No. 500-0006; Bio-Rad Laboratories GmbH, M ⁇ nchen, Germany) following the instructions of the supplier's manual.
  • Bio- Rad® protein assay Cat.No. 500-0006; Bio-Rad Laboratories GmbH, M ⁇ nchen, Germany
  • the concentrated solution is diluted to 2.5 M urea and incubated with 4 ⁇ g trypsin (Proteomics grade, Roche Diagnostics GmbH, Mannheim, Germany) over night. The digestion is stopped by adding 1 ml 1% formic acid and analyzed.
  • the tryptic digest (500 ⁇ l) is separated on a two-dimensional Nano-HPLC-System
  • the protein IPYR is identified with the sequences given in Table 1.
  • IPYR as a potential marker for colorectal cancer
  • protein IPYR is found to be specifically expressed or strongly overexpressed in tumor tissue and not or less detectable or less strongly expressed in healthy control tissue. It therefore - amongst many other proteins - qualifies as a candidate marker for use in the diagnosis of colorectal cancer.
  • the protein IPYR is strongly over-represented in tumor tissue from patients suffering from colorectal cancer.
  • the peptide sequences of the protein IPYR listed in Table 1 has been identified with Bioworks 3.1 form LCQ-MS2-data in tumor tissue:
  • IPYR colorectal cancer marker protein
  • recombinant expression of the protein is performed for obtaining immunogens.
  • the expression is done applying a combination of the RTS 100 expression system and E.coli.
  • the DNA sequence is analyzed and recommendations for high yield cDNA silent mutational variants and respective PCR-primer sequences are obtained using the "ProteoExpert RTS E.coli HY” system. This is a commercial web based service (www.proteoexpert.com).
  • the "RTS 100 E. coli Linear Template Generation Set, His-tag” (Roche Diagnostics GmbH, Mannheim, Germany, Cat.No.
  • His-IPYR fusion protein Purification of His-IPYR fusion protein is done following standard procedures on a Ni-chelate column. Briefly, 1 1 of bacteria culture containing the expression vector for the His-IPYR fusion protein is pelleted by centrifugation. The cell pellet is resuspended in lysis buffer, containing phosphate, pH 8.0, 7 M guanidium chloride, imidazole and thioglycerole, followed by homogenization using a Ultra-Turrax . Insoluble material is pelleted by high speed centrifugation and the supernatant is applied to a Ni-chelate chromatographic column. The column is washed with several bed volumes of lysis buffer followed by washes with buffer, containing phosphate, pH 8,0 and urea. Finally, bound antigen is eluted using a phosphate buffer containing SDS under acid conditions.
  • Spleen cells of the mice immunized according to a) are fused with myeloma cells according to Galfre, G., and Milstein, C, Methods in Enzymology 73 (1981) 3-46. In this process ca. 1* 10 8 spleen cells of the immunized mouse are mixed with 2xl0 7 myeloma cells (P3X63-Ag8-653, ATCC CRL1580) and centrifuged (10 min at
  • the cells are then washed once with RPMI 1640 medium without fetal calf serum (FCS) and centrifuged again at 400 x g in a 50 ml conical tube. The supernatant is discarded, the cell sediment is gently loosened by tapping, 1 ml PEG (molecular weight 4,000, Merck, Darmstadt) is added and mixed by pipetting. After 1 min in a water-bath at 37°C, 5 ml RPMI 1640 without FCS is added drop-wise at room temperature within a period of 4-5 min. Afterwards 5 ml RPMI 1640 containing 10% FCS is added drop-wise within ca.
  • FCS fetal calf serum
  • IPYR-positive primary cultures are cloned in 96-well cell culture plates by means of a fluorescence activated cell sorter. In this process again interleukin 6 at 100 U/ml is added to the medium as a growth additive.
  • the hybridoma cells obtained are sown at a density of lxl 0 5 cells per ml in RPMI 1640 medium containing 10% FCS and proliferated for 7 days in a fermenter (Thermodux Co., Wertheim/Main, Model MCS-104XL, Order No. 144-050). On average concentrations of 100 ⁇ g monoclonal antibody per ml are obtained in the culture supernatant. Purification of this antibody from the culture supernatant is carried out by conventional methods in protein chemistry (e.g. according to Bruck, C, et al., Methods Enzymol. 121 (1986) 587-695). Generation of polyclonal antibodies
  • a fresh emulsion of the protein solution (100 ⁇ g/ml protein IPYR) and complete Freund's adjuvant at the ratio of 1:1 is prepared.
  • Each rabbit is immunized with 1 ml of the emulsion at days 1, 7, 14 and 30, 60 and 90. Blood is drawn and resulting anti-IPYR serum used for further experiments as described in examples 3 and 4.
  • IgG immunoglobulin G
  • rabbit serum is diluted with 4 volumes of acetate buffer (60 mM, pH 4.0). The pH is adjusted to 4.5 with 2 M Tris-base. Caprylic acid (25 ⁇ l/ml of diluted sample) is added drop-wise under vigorous stirring. After 30 min the sample is centrifuged (13,000 x g, 30 min, 4°C), the pellet discarded and the supernatant collected. The pH of the supernatant is adjusted to 7.5 by the addition of 2 M Tris-base and filtered (0.2 ⁇ m).
  • the immunoglobulin in the supernatant is precipitated under vigorous stirring by the drop-wise addition of a 4 M ammonium sulfate solution to a final concentration of 2 M.
  • the precipitated immunoglobulins are collected by centrifugation (8,000 x g, 15 min, 4°C).
  • the supernatant is discarded.
  • the pellet is dissolved in 10 mM NaH 2 PO 4 /NaOH, pH 7.5, 30 mM NaCl and exhaustively dialyzed.
  • the dialysate is centrifuged (13,000 x g, 15 min, 4°C) and filtered (0.2 ⁇ m).
  • Polyclonal rabbit IgG is brought to 10 mg/ml in 10 mM NaH 2 PO 4 /NaOH, pH 7.5, 30 mM NaCl. Per ml IgG solution 50 ⁇ l Biotin-N-hydroxysuccinimide (3.6 mg/ml in DMSO) are added. After 30 min at room temperature, the sample is chromatographed on Superdex 200 (10 mM NaH 2 PO 4 /NaOH, pH 7.5, 30 mM NaCl). The fraction containing biotinylated IgG are collected. Monoclonal antibodies are biotinylated according to the same procedure.
  • Polyclonal rabbit IgG is brought to 10 mg/ml in 10 mM NaH 2 PO /NaOH, 30 mM NaCl, pH 7.5.
  • Per ml IgG solution 50 ⁇ l digoxigenin-3-O-methylcarbonyl- ⁇ - aminocaproic acid-N-hydroxysuccinimide ester (Roche Diagnostics, Mannheim, Germany, Cat. No. 1 333 054) (3.8 mg/ml in DMSO) are added. After 30 min at room temperature, the sample is chromatographed on Superdex® 200 (10 mM NaH 2 PO 4 /NaOH, pH 7.5, 30 mM NaCl). The fractions containing digoxigenylated IgG are collected. Monoclonal antibodies are labeled with digoxigenin according to the same procedure.
  • Tissue lysates from tumor samples and healthy control samples are prepared as described in Example 1, "Tissue preparation”.
  • the gel-separated protein mixture is blotted onto nitrocellulose membranes using the Invitrogen XCell II Blot Module (Invitrogen) and the NuPAGE ® transfer buffer system.
  • the membranes are washed 3 times in PBS/0.05% Tween-20 and blocked with Roti ® -Block blocking buffer (A151.1; Carl Roth GmbH, Düsseldorf, Germany) for 2 h.
  • the primary antibody, polyclonal rabbit anti-IPYR serum (generation described in Example 2), is diluted 1:10,000 in Roti ® - Block blocking buffer and incubated with the membrane for 1 h.
  • the membranes are washed 6 times in PBS/0.05% Tween-20.
  • the specifically bound primary rabbit antibody is labeled with an POD-conjugated polyclonal sheep anti-rabbit IgG antibody, diluted to 10 mU/ml in 0.5 x Roti ® -Block blocking buffer. After incubation for 1 h, the membranes are washed 6 times in PBS/0.05% Tween-20. For detection of the bound POD-conjugated anti-rabbit antibody, the membrane is incubated with the Lumi-Light PLUS Western Blotting Substrate (Order-No. 2015196, Roche Diagnostics GmbH, Mannheim, Germany) and exposed to an autoradiographic film.
  • the Lumi-Light PLUS Western Blotting Substrate Order-No. 2015196, Roche Diagnostics GmbH, Mannheim, Germany
  • IPYR IPYR-specific ELISA
  • aliquots of the anti-IPYR polyclonal antibody are conjugated with biotin and digoxygenin, respectively.
  • Streptavidin- coated 96-well microwell plates are incubated with 100 ⁇ l biotinylated anti-IPYR polyclonal antibody for 60 min at 10 ⁇ g/ml in 10 mM phosphate, pH 7.4, 1% BSA, 0.9% NaCl and 0.1% Tween 20. After incubation, plates are washed three times with 0.9% NaCl , 0.1% Tween 20. Wells are then incubated for 2 h with either a serial dilution of the recombinant protein (see Example 2) as standard antigen or with diluted liquid samples obtained from patients. After binding of IPYR, plates are washed three times with 0.9% NaCl, 0.1% Tween 20.
  • wells are incubated with 100 ⁇ l of digoxygenylated anti-IPYR polyclonal antibody for 60 min at 10 ⁇ g/ml in 10 mM phosphate, pH 7.4, 1% BSA, 0.9% NaCl and 0.1% Tween 20. Thereafter, plates are washed three times to remove unbound antibody.
  • wells are incubated with 20 mU/ml anti- digoxigenin-POD conjugates (Roche Diagnostics GmbH, Mannheim, Germany, Catalog No. 1633716) for 60 min in 10 mM phosphate, pH 7.4, 1% BSA, 0.9% NaCl and 0.1% Tween 20. Plates are subsequently washed three times with the same buffer.
  • wells are incubated with 100 ⁇ l ABTS solution (Roche Diagnostics GmbH, Mannheim, Germany, Catalog
  • Accuracy is assessed by analyzing individual liquid samples obtained from well- characterized patient cohorts, i.e., 50 patients having undergone colonoscopy and found to be free of adenoma or CRC, 50 patients diagnosed and staged as Tj s -3, NO, MO of CRC, and 50 patients diagnosed with progressed CRC, having at least tumor infiltration in at least one proximal lymph node or more severe forms of metastasis, respectively.
  • CEA as measured by a commercially available assay (Roche Diagnostics, CEA-assay (Cat. No. 1 173 1629 for Elecsys ® Systems immunoassay analyzer) and IPYR measured as described above are quantified in a serum obtained from each of these individuals.
  • ROC-analysis is performed according to Zweig, M. H., and Campbell, supra. Discriminatory power for differentiating patients in the group Ti S -3, NO, MO from healthy individuals for the combination of RCN1 with the established marker CEA is calculated by regularized discriminant analysis
  • IPYR may also be very helpful in the follow-up of patients after surgery.

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Abstract

La présente invention a trait au diagnostic de cancer colorectal. L'invention a trait à l'utilisation d'une protéine (la pyrophosphatase inorganique) dans le diagnostic de cancer colorectal. L'invention a également trait à un procédé pour le diagnostic de cancer colorectal à partir d'un échantillon liquide, dérivé d'un sujet par la mesure de la pyrophosphatase inorganique dans ledit échantillon. La mesure de la pyrophosphatase inorganique peut, par exemple, être utilisé dans la détection précoce ou le diagnostic de cancer colorectal.
PCT/EP2005/006520 2004-06-18 2005-06-17 Utilisation de pyrophosphatases inorganiques comme marqueur pour le cancer colorectal WO2005124353A1 (fr)

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EP2818479A1 (fr) * 2005-05-09 2014-12-31 Siemens Healthcare Diagnostics Products GmbH Partenaires de liaison du facteur de croissance placentaire, notamment des anticorps dirigés contre le facteur de croissance placentaire, leur production et leur utilisation
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