WO2013164787A1

WO2013164787A1 - Assay methods for diagnosing and monitoring cancer

Info

Publication number: WO2013164787A1
Application number: PCT/IB2013/053487
Authority: WO
Inventors: Oddmund NORDGÅRD
Original assignee: Helse Stavanger As
Priority date: 2012-05-02
Filing date: 2013-05-02
Publication date: 2013-11-07

Abstract

The present invention relates to methods for the detection and/or diagnosis of a cancer, for example colorectal, gut, stomach and/or pancreatic cancer, in a biological sample obtained from a subject. Preferably, biological sample is a lymph tissue sample or a blood sample.

Description

ASSAY METHOD

Cancer of the gut, for example of the stomach and colon, are major killers and if detected late may require extensive and at least partially disabling surgery. As with many cancers, a particular risk is of metastasis whereby dislocated cancerous cells establish themselves in other organs, frequently resulting in inoperable and fatal tumours.

There is a need for assay methods whereby the presence of tumour cells outside the original tumour site of a gut or pancreatic cancer may be detected, either to alert the physician and enable diagnosis and treatment, or to allow the physician to monitor progress of treatment.

Numerous tumour associated antigens are known in the art, e.g.

US2010/0203040. One of the many tumour associated antigens which is disclosed in US2010/0203040 is identified therein as PCSC (SEQ ID NOs: 63 and 64).

Specific mRNA expression of this gene was said to be found in normal colon and in colon carcinomas, but in all other tissues the mRNA was said to be transcriptionally repressed. PCSC was said to be "a differentiation antigen for normal colon epithelia which is also expressed in colorectal tumours" (Example 8). There is no indication that this antigen could be detected in either lymph tissue or in blood. In fact, both lymph node tissue and PMBCs were tested in US2010/0203040 and found to be negative for the expression of PCSC.

It has now been found that an antigen which is related to, but distinct from, PCSC may be used as a marker for cancer and that this antigen may be detected in lymph node tissue and in blood. Whilst the PCSC protein (SEQ ID NO: 64 of US2010/0203040) and the protein of the invention (PHGR1 , SEQ ID NO: 2 herein) share a similar N-terminal sequence, the C-terminal sequences are completely different. Hence the protein of the invention, PHGR1 , is not disclosed in

US2010/0203040 perse or in the context of cancer diagnosis. The invention now provides the use of PHGR1 nucleic acid and polypeptides, and fragments, thereof as biomarkers for cancer, particularly for colorectal, gut, stomach and/or pancreatic cancer.

In one aspect, the invention provides a method of detecting and/or diagnosing a cancer in a subject, the method comprising:

(a) assaying for the presence of PHGR1 polypeptide or PHGR1 mRNA in a biological sample obtained from the subject,

wherein the presence of PHGR1 polypeptide or PHGR1 mRNA in the biological sample is indicative of the presence of a cancer in the subject.

In another aspect, the invention provides a method of detecting and/or diagnosing a cancer in a subject, the method comprising the steps:

(a) measuring the level of PHGR1 polypeptide or PHGR1 mRNA in a biological sample obtained from the subject,

(b) comparing the measured level of PHGR1 polypeptide or PHGR1 mRNA with the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in a biological sample obtained from a control,

wherein an increase in the level of PHGR1 polypeptide or PHGR1 mRNA in the biological sample obtained from the subject compared to the level of PHGR1 polypeptide or PHGR1 mRNA in the control sample is indicative of a cancer in the subject.

In another aspect, the invention provides a method of monitoring the development of a cancer in a subject, the method comprising the steps:

(a) measuring the level of PHGR1 polypeptide or PHGR1 mRNA in first and second biological samples which have been obtained from the subject at first and second time points,

(b) comparing the levels of PHGR1 polypeptide or PHGR1 mRNA in the first and second biological samples,

wherein an increase in the level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the later time point compared to the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the earlier time point is indicative of an increase in tumour growth in the patient, and

wherein a decrease in the level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the later time point compared the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the earlier time point is indicative of a decrease in tumour growth in the patient. In another aspect, the invention provides a method of monitoring the metastasis of a cancer in a subject, the method comprising the steps:

wherein an increase in the level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the later time point compared to the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the earlier time point is indicative of an increase in the number of circulating cancer cells in the patient, and wherein a decrease in the level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the later time point compared the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the earlier time point is indicative of a decrease in the number of circulating cancer cells in the patient.

In yet a further aspect, the invention provides a method of monitoring the effectiveness of an anti-cancer therapy in a subject, the method comprising the steps:

wherein the subject has been treated with an anti-cancer therapy before the two time points or in the interval between the first and second time points, and (b) comparing the levels of PHGR1 polypeptide or PHGR1 mRNA in the first and second biological samples,

wherein a decrease in the level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the later time point compared the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the earlier time point is indicative of the anti-cancer therapy being efficacious, and

wherein an increase in the level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the later time point compared the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the earlier time point is indicative of the anti-cancer therapy being non-efficacious. The anti-cancer therapy may, for example, be chemo-therapy (e.g. an anticancer drug) or radio-therapy (e.g. x-ray treatment).

The invention further provides a method of assaying for the presence of a biomarker which is indicative of cancer cells in a biological sample, the method comprising the step:

(a) assaying for the presence of PHGR1 polypeptide or PHGR1 mRNA in the biological sample,

wherein presence of PHGR1 polypeptide or PHGR1 mRNA in the biological sample is indicative of cancer cells being present in the biological sample.

The invention further provides a method of assaying for the presence of a biomarker which is indicative of metastatic cancer cells in a biological sample, preferably blood, the method comprising the step:

wherein presence of PHGR1 polypeptide or PHGR1 mRNA in the biological sample is indicative of metastatic cancer cells being present in the biological sample.

Viewed from a further aspect the invention provides a method of assaying for an analyte which is indicative of colorectal, gut, stomach or pancreatic cancer, which method comprises

(a) contacting a biological sample with a binding agent capable of selectively binding to a PHGR1 polypeptide, and

(b) detecting conjugates formed by said binding agent.

In some aspects of the invention, the term "method of detecting and/or diagnosing cancer in a subject" means a method for detecting probable cancer in a subject or a method of determining an increased likelihood of cancer in the subject.

The cancer is preferably a gastrointestinal cancer (e.g. gut or stomach cancer) or pancreatic cancer. The gut cancer may, for example, be colorectal cancer, colon cancer or rectal cancer. The cancer may also be in the caecum or appendix. In some embodiments, the cancer is a metastatic cancer or a

metastasizing cancer.

As used herein, the term "cancer" also encompasses "cancer cells". The cancers or the cells of the invention may be benign or malignant. The cancer or cancer cells may be circulating cells, e.g. circulating metastatic or metastasizing cancer cells.

The subject is preferably a mammalian subject, most preferably a human. As used herein, the term "PHGR1" refers to the proline/histidine/glycine-rich 1 polypeptide and encoding nucleic acids e.g. mRNA and cDNA.

The invention relates primarily to a mammalian PHGR1 , e.g. a sequence obtained from mouse, rat or human. Preferably, the PHGR1 is a human sequence or a variant thereof.

The human mRNA and polypeptide sequences of PHGR1 are given in Genebank accession number NM_001145643.1 and NP_001139115.1 and are included herein as SEQ ID NOs: 1 and 2, respectively.

The term "PHGR1 mRNA" includes cDNA which has been reverse- transcribed from PHGR1 mRNA.

Since there may of course be non-disabling individual-to-individual variations in the PHGR1 amino acid sequence and in the corresponding PHGR1 mRNA sequence, the terms mammalian PHGR1 polypeptide and mammalian PHGR1 mRNA as used herein shall be understood to include SEQ ID NO: 2, and a nucleotide sequence encoding SEQ ID NO: 2 or SEQ ID NO: 1, respectively, and homologous sequences, derivatives and functional equivalents thereof, e.g. having a sequence homology of at least 90%, preferably at least 95%, and most preferably at least 96%, 97%, 98% or 99% sequence homology thereto.

Sequence alignments and percent identity or similarity calculations may be determined using a variety of comparison methods designed to detect homologous sequences including, but not limited to, the MegAlign(TM) program of the

LASARGENE bioinformatics computing suite (DNASTAR Inc., Madison, Wl). Multiple alignment of the sequences may be performed using the Clustal V method of alignment (Higgins, D.G. and Sharp, P.M. (1989) Comput. Appl. Biosci. 5:151-153; Higgins, D.G. et al. (1992) Comput. Appl. Biosci. 8:189-191) with the default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Default parameters for pairwise alignments and calculation of percent identity of protein sequences using the Clustal method are KTUPLE=1 , GAP PENALTY=3, WINDOW=5 and

DIAGONALS SAVED=5. For nucleic acids these parameters are KTUPLE=2, GAP PENALTY=5, WINDOW=4 and DIAGONALS SAVED=4.

Whilst the cellular function of PHGR1 is not presently known, the inventor's studies have found that it is most concentrated in mature colonocytes. The PHGR1 nucleic acids of the invention encode a polypeptide which is expressed at high levels in normal colon and rectum, and to some extent in normal stomach and pancreas, but not in other tissues. (The term "normal" is used in this context to denote tissue which is not cancerous.)

The methods of the invention will in general be carried out in vitro or ex vivo. In particular, the references to the term "biological sample" are intended to indicate that the methods are not in general carried out on the human or animal body, unless otherwise indicated.

In particular, the term "obtained from" may comprise receiving a sample from an agent acting on behalf of the subject, e.g. receiving a sample from a doctor, nurse, hospital, medical centre, etc., either directly or indirectly, e.g. via a courier or postal service.

In some embodiments of the methods disclosed herein, however, the method additionally comprises the step of obtaining a biological sample (directly) from the subject and/or directly from one or more control subjects.

The biological sample used in the methods of the invention may be or derive from any body fluid or tissue into which metastatic colorectal, gut, stomach or pancreatic cells may distribute. The sample (apart from some controls) will not be a sample of healthy colorectum, gut, stomach or pancreatic tissue or healthy exudates therefrom, e.g. colorectum, gut or stomach contents or the contents of pancreatic ducts.

The sample may be of or derive from lymph nodes in these organs or elsewhere; however such lymph nodes will normally only serve as sample sources where they are separated from tissue removed during a biopsy or surgery. More normally the sample will be or will derive from blood, lymph fluid, from lymph nodes remote from the colorectum, gut or stomach or pancreas, or from tissue removed from other organs during a biopsy or surgery, e.g. liver tissue. Hence in some embodiments the sample will be from a non-colorectum, non-gut, non-stomach or non-pancreatic tissue. In yet other embodiments, the sample is from lymph nodes from the colonic mesentery (which may be removed together with the tumour during surgery).

The samples tested in the method of the invention may be of body tissue or fluids themselves, or of materials derived therefrom, e.g. following removal of extracellular fluid, cell fixation, cell lysis, cell separation, cell cleavage, cell porosification, protein denaturation and other conventional histological sample preparation techniques. In the detection method of the invention, where, as is preferred, the tissue sample section comprises colon or colorectal tissue, the sample preferably includes lymph nodes and cancer or metastasis presence is signalled by conjugate formation in lymph nodes. Conjugate formation in colon or colorectal tissue other than lymph nodes should not be viewed as indicating the presence of cancer or metastases.

In some preferred embodiments, the biological sample is blood or a fraction derived therefrom, e.g. blood plasma, blood serum, white blood cells, red blood cells or the cell-containing fraction of blood.

In some preferred embodiments, the biological sample comprises or consists essentially of the mononuclear cell fraction of blood or the plasma fraction.

In an especially preferred embodiment, the methods of the invention comprise separating cells from a blood sample from a mammalian subject from extracellular fluid; lysing, porosifying or cleaving the cells; contacting the resulting composition with a selective binding agent for a PHGR1 protein; and detecting conjugates of said selective binding agent and PHGR1 protein.

In some embodiments, certain cells in the sample (e.g. a blood sample) have previously been enriched. Enrichment may be by any suitable process, for example by centrifugation (e.g. density centrifugation) or by immunological means (e.g. by antibodies or immuno-magnetic beads). The cells to be enriched may, for example, be mononuclear cells and/or tumour cells (e.g. circulating tumour cells).

In some aspects, a method of the invention additionally comprises the step of treating the subject with an appropriate anti-cancer therapy, e.g. chemo-therapy and/or radio-therapy or surgery.

In yet other embodiments of the invention, the method additionally comprises the step of administering to the subject a medicament, preferably one which is appropriate for the diagnosis, i.e. a medicament for the treatment of a cancer as defined herein.

As used herein, the term "control" refers to a sample obtained from a healthy subject, i.e. one in which cancer cells expressing PHGR1 are not present, or from a healthy tissue in the subject which is non-adjacent to the primary tumour.

The PHGR1 polypeptide or mRNA levels in the control may, for example, be available from published charts, computer databases, look-up tables, etc. In other embodiments, the term "control" encompasses a level which has previously been determined. Thus the method of the invention is not limited to methods which comprise the step of physically testing the level of PHGR1 obtained from a control. Levels for control samples from healthy subjects may be established by prospective and/or retrospective statistical studies. Healthy subjects who have no clinically evident disease or abnormalities may be selected for statistical studies. Diagnosis may be made by the finding of statistically significant different levels of PHGR1 polypeptide or mRNA compared to a control sample or previous levels quantified for the same subject.

Preferably, the changes in the levels of the PHGR1 polypeptide or mRNA (between the subject and the control samples or between the samples taken at different time intervals from the subject) are significant changes.

In some embodiments of the present invention, a significant increase is one where the level of measured polypeptide or mRNA in the biological sample obtained from the subject is more than a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 100% increase compared to the corresponding level in the biological sample obtained from a control or in the biological sample obtained from the subject at an earlier time point. In other embodiments of the invention, a significant increase means that the increase is significant using the criteria p<0.05, 2-tailed test.

In other embodiments of the present invention, a significant decrease is one where the level of measured polypeptide or mRNA in the biological sample obtained from the subject is more than a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 100% decrease compared to the corresponding level in the biological sample obtained from a control or in the biological sample obtained from the subject at an earlier time point. In other embodiments of the invention, a significant decrease means that the decrease is significant using the criteria p<0.05, 2-tailed test.

As used herein, the term "control" relates to an individual or group of individuals of the same species as the subject being tested. For example, if the subject is a human, the control will also be a human.

With regard to binding agents which "selectively" bind to a PHGR1

polypeptide, in this context it is meant that binding occurs preferentially to the PHGR1 polypeptide rather than to other endogenous sample components, unless such components are naturally present in the healthy tissue or fluid at such low levels as to provide a background (noise) signal over which the signal from the PHGR1 polypeptide, when present, is distinguishable. Satisfactory specificity may readily be ensured by determining cross-reactivity with comparable samples from healthy subjects and rejecting candidate specific binding agents which give too high a background (noise) signal. The detection means or binding agent is preferably an immuno-affinity reagent, e.g. an antibody. The antibody may for example be an isolated monoclonal antibody, polyclonal antibody or an antibody mimetic. The antibody may be a whole antibody, an antigen-binding fragment, a humanised antibody, a single chain antibody or an immuno-conjugate. Most preferably, the antibody is a monoclonal antibody or a polyclonal antibody.

In some embodiments, the binding agent may comprise or may be conjugated to a therapeutic moiety or to a detectable label, e.g. a cytotoxic moiety, a drug moiety, a chromophore or a radioactive moiety. The binding agent (e.g. an antibody) may be immobilised on a substrate

Such binding agents and their production, maturation and selection are well known in the art.

Specific binding agents may be raised and maturated against full length PHGR1 polypeptide or a fragment thereof, typically an 8- to 35-mer, especially a 12- to 20- mer, more especially a 14- to 18-mer. Since PHGR1 is a naturally occurring protein, if antibodies are to be raised in a mammal, e.g. a mouse, rabbit or sheep, the protein or protein fragment will generally be coupled in known fashion to an immunogenic entity, e.g. keyhole limpet haemocyanin, blue carrier protein, bovine serum albumin, tetanus toxoid, diphtheria toxoid, soybean trypsin inhibitor, etc, before being injected into the antibody-producing animal. Where phage display is to be used to select a specific binding partner, for example for subsequent affinity maturation and single chain antibody production, no immunogenic carrier is required.

Where a PHGR1 polypeptide fragment is to be used for antibody production, appropriate fragments may be selected by taking appropriately-lengthed fragments from along the length of the protein of SEQ ID NO 2, raising antibodies, and selecting those with the best balance of affinity and selectivity. However it is convenient to use an oligopeptide string containing at least two PPP units, particularly with at least 90% sequence homology with a corresponding string from amino acids 60 to 82 of SEQ ID NO 2. Particularly preferably, the oligopeptide fragment used is of SEQ ID NO 3:

Hence in a further aspect, the invention provides a binding agent (e.g. an antibody) which is capable of immunospecific binding to a PHGR1 polypeptide, wherein the binding agent is not a polyclonal antibody. Preferably, the binding agent is a monoclonal antibody.

The invention further provides a binding agent (e.g. an antibody) which is capable of immuno-specific binding to a peptide defined by SEQ ID NO: 3. Preferably, the binding agent is not capable of binding to a peptide defined by SEQ ID NO: 6.

The invention further provides a monoclonal antibody which is capable of immuno-specific binding to a peptide defined by SEQ ID NO: 2 or 3.

The invention further provides a pharmaceutical composition comprising a binding agent of the invention, optionally together with one or more pharmaceutically acceptable diluents, carriers or excipients.

The oligopeptide fragments used may be constructed by conventional solid state peptide synthesis techniques.

The conjugates of PHGR1 polypeptides with specific binding agents, e.g. antibodies, antibody fragments or antibody constructs, may be detected directly or indirectly using any of the techniques conventional in immunochemistry and molecular diagnostics. Thus, for example, the specific binding agent may be immobilised on a substrate, contacted with the sample and subsequently contacted with a labelled competitively binding agent (e.g. a radio- or chromo-labelled PHGR1 fragment), or gold micro beads carrying the specific binding agent may be contacted with the sample and then with a filter which retains analyte conjugated beads but not unconjugated beads, etc. Many such techniques are known and conventional in the field of molecular diagnostics.

Preferably, the detection assay is an immunoassay. Most preferably, the detection method uses antibodies against PHGR1 polypeptide.

PHGR1 mRNA may be detected by any suitable means. Examples include Northern blots and PCR-based amplification methods. Preferably, the PHGR1 mRNA is detected by a PCR-based amplification method, e.g. RT-PCR.

In one embodiment, PHGR1 mRNA is detected by a method comprising the steps of (a) reverse-transcribing PHGR1 mRNA into cDNA, followed by (b) amplification of all or part of the cDNA using nucleotide primers.

The invention further provides a kit comprising:

(a) a first nucleotide primer capable of binding to the complement of SEQ ID NO: 1 , and

(b) a second nucleotide primer capable of binding to SEQ ID NO: 1 , either in admixture or in separate containers,

wherein the first and second primers are capable of being used in an exponential amplification procedure to amplify a fragment of a nucleotide molecule of SEQ ID NO: 1. The primers used may be any suitable primers for PHGR1 mRNA

amplification. Preferably a primer of SEQ ID NO: 4 is used as a forward primer and one of SEQ ID NO: 5 as a reverse primer.

The invention further provides a composition comprising a nucleotide primer of SEQ ID NO: 4 and/or SEQ ID NO: 5; or a kit comprising nucleotide primers of SEQ ID NOs: 4 and 5, either in admixture or in separate containers. Such compositions and kits may be used to detect PHGR1 mRNA and/or cDNA.

The assay methods of the invention may conveniently be calibrated against comparable samples of healthy tissue or body fluid to establish signal values indicative of background and against samples of PHGR1 producing cells (e.g. Caco- 2 cells, LS174T cells, cells from healthy colon crypts, or cells from blood or colonic lymph nodes in colon cancer patients) to establish signal levels indicative of gut or pancreatic cancer metastasis. The assay methods may then be run to give a quantitative, semi quantitative or qualitative output value indicative of analyte concentration, e.g. "clear", "of concern" or "positive". The choice of output signal type will generally be dependent on the purpose for which the assay is run, e.g. to monitor the progress of cancer therapy (i.e. to detect a reduction or increase in dislocated PHGR1 -producing cells) or to screen undiagnosed patients for dislocated PHGR1 -producing cells and hence the possibility of metastatic cancer. For screening purposes, the threshold value for "at risk" may be set within or slightly above the values recorded for healthy individuals, as further investigation of false positives is preferable to the overlooking of false negatives. Where efficacy of cancer therapy is being monitored, failure of detected analyte levels to fall as therapy progresses may be used as an indicator that alternative or more aggressive therapy should be tried.

Viewed from a still further aspect the invention provides a kit for the performance of a method according to the invention comprising a binding agent according to the invention, optionally together with at least one of detectors, and conjugate binders or retainers (e.g. filters), and optionally together with calibration charts or standards and/or instructions for the performance of the method.

In yet another embodiment, the invention provides a kit comprising one or more binding agents of the invention. Preferably, the kit is for use in the detection or diagnosis of cancer, e.g. in one or more of the methods of the invention. Also provided is the use of a kit of the invention for the diagnosis or detection of a cancer as defined herein. By way of example, the kit may contain antibodies specific for PHGR1 , antibodies against the antibodies labelled with an enzyme; and a substrate for the enzyme. The kit may also contain one or more of microtiter plate wells, standards, assay diluent, wash buffer, adhesive plate covers, and/or instructions for carrying out a method of the invention using the kit.

In yet a further aspect, the invention provides a pharmaceutical composition comprising a polypeptide of SEQ ID NO: 2 or 3, together with one or more pharmaceutically acceptable carriers, diluents or excipients.

The invention further provides a vaccine comprising a PHGR1 polypeptide or immunogenic fragment thereof, optionally coupled to a protein carrier, together with one or more pharmaceutically acceptable adjuvants. Preferably, the PHGR1 polypeptide or immunogenic fragment thereof is a polypeptide whose amino acid sequence comprises or consists of SEQ ID NO: 2 or 3.

The pharmaceutical composition or vaccine may be used for the prevention, prophylaxis or treatment of a cancer described herein.

The invention further provides a method for the treatment or prophylaxis of cancer or for preventing or reducing a cancer or the metastasis of a cancer, the method comprising administering an effective amount of a binding agent of the invention to a subject in need thereof.

The invention further provides a binding agent of the invention for use in a method for the treatment or prophylaxis of cancer or for preventing or reducing the metastasis of a cancer.

The invention also provides the use a binding agent of the invention in the manufacture of a medicament for the treatment or prophylaxis of cancer or for preventing or reducing the metastasis of a cancer.

The invention further provides a vector comprising a nucleic acid encoding a PHGR1 polypeptide or a variant thereof, the vector optionally additionally comprising one or more expression control sequences (e.g. a promoter sequence, a termination sequence). Preferably, the nucleic acid encoding a PHGR1 polypeptide comprises the sequence of SEQ ID NO: 1 or a variant thereof. The invention further provides a host cell comprising such a vector.

FIGURE LEGENDS

Figure 1 is a box-plot graph showing the relative PHGR1 mRNA levels in lymph nodes with known metastases (HES+ LNs), lymph nodes without known metastases (HES- LNs), and normal lymph nodes (Normal LNs), as determined by quantitative RT-PCR.

Figure 2 is a graph showing relative PHGR1 mRNA concentrations in blood samples spiked with LS174T colon cancer cells.

Figure 3 shows PHGR1 immunostaining of four different lymph node metastases. Continuous single arrows indicates PHGR1 staining of metastases.

Dashed double arrows indicate the blue nuclear counterstaining of normal lymphatic tissue.

Figure 4 shows PHGR1 immuno-fluorescent staining of LS174T colon cancer cells spiked into peripheral blood leukocytes.

A) A single cancer cell is seen (indicated by the arrow) among numerous leukocytes.

B) Inverted colour version of the same picture.

Figures 5A and 5B: Multicolor immucytochemical detection of CTCs. PHGR1 are stained green, CD45 red and nucleus blue. A) Patient blood sample. Detected green- stained CTC is indicated by a white arrow. B) Patient blood sample stained with negative control (isotype-specific control) antibody. C) Negative control sample from healthy donor. The left image (Figure 5A) shows the original image in greyscale, whereas the right image (Figure 5B) is an inverted colour copy in greyscale.

Fig. 6: PHGR1 mRNA levels in PB samples from mCRC patients and healthy control persons. Samples with PHGR1 levels below the limit of detection (LOD) are indicated below the dashed line.

EXAMPLES

The present invention is further illustrated by the following Examples. It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions. Thus, various modifications of the invention in addition to those shown and described herein will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims.

The disclosure of each reference set forth herein is incorporated herein by reference in its entirety. Example 1: DNA Primers

DNA primers of SEQ ID NO: 4 and SEQ ID NO: 5 were prepared

conventionally. Example 2: PHGR1 Antibodies

Anti-PHGR1 antibodies were prepared in rabbits using immunogenic conjugates of an oligopeptide of SEQ ID NO: 3. Non-cross reactive antibodies were selected for use in the assay method of the invention. Example 3: PHGR1 mRNA quantification in colonic lymph nodes

Fresh-frozen lymph nodes (LNs) from surgically removed colonic mesentery were transferred frozen to RLT lysis buffer (Qiagen, Hilden, Germany) and homogenized immediately with an Ultra-Turrax T8 (IKA Works, Staufen, Germany) rotor-stator homogenizer. RNA was isolated by the Allprep DNA RNA isolation kit (Qiagen) according to the protocol of the manufacturer.

RNA concentrations were determined by ultraviolet (260 nm)

spectrophotometry.

RNA was DNase-treated by incubating 1 μ g total RNA from each sample with one unit RQ1 RNase-free DNase (Promega, Madison, Wl, USA) in a total volume of 10 u I 1x First Strand Synthesis buffer (Invitrogen, Carlsbad, CA, USA) containing 10 units RNaseOUT RNase inhibitor (Invitrogen). The reaction mixture was incubated at 37°C for 30 minutes and the DNAse was inactivated by adding 1 μΙ RQ1 stop solution and incubating 10 minutes at 65°C. Complementary DNA was synthesized by M-MLV reverse transcriptase in a total volume of 20 μΙ according to the protocol of the manufacturer (Invitrogen), using random primers.

The forward and reverse PCR primers were designed to bind to different exons to avoid amplification of genomic DNA. The sequences were: PHGR1-F: SEQ ID NO: 4, and PHGR1-R: SEQ ID NO: 5.

PCR amplifications were performed with the SYBR Green Core Kit

(Eurogentec, Seraing, Belgium) according to the manufacturer's recommendations. Twenty nanograms of reverse-transcribed RNA was amplified in a total volume of 25 μΙ 1x reaction buffer containing 0.2 mM dNTP; 0.15 μΜ forward and reverse primers; 0.75 μ1 1 :200 SYBR Green I diluted in DMSO; and 1.3 mM MgCI₂. Thermocycling and real-time fluorescence measurements were performed in an MX3000P real-time PCR instrument (Stratagene), incubating 10 min at 95°C and then 40 cycles of 30 s at 95°C and 60 s at 60°C. Subsequently the reaction products were analyzed by melting curves. All melting curves revealed well-defined peaks with the expected melting temperatures, confirming the specificity of the primers at the reaction conditions. Amplicon identities were also confirmed by sequencing. No-template controls were included in every run to monitor potential contamination.

Relative PHGR1 transcript concentration was determined by normalizing against a reference (house-keeping) transcript. Threshold level for positivity of the PHGR1 mRNA marker was based on the highest levels in normal colonic lymph nodes.

PHGR1 mRNA was quantitated in the snap-frozen part of 48 bisected regional LNs in which metastases had been detected in the other half by routine HES staining (HES+ LNs, Fig. 1) and in 52 normal LNs from patients undergoing surgery for benign bowel diseases (Normal LNs, Fig. 1). The PHGR1 mRNA level was also determined in 625 LNs without known metastases in the other half (HES- LNs, Fig. 1 ). A threshold for marker positivity that was significantly higher than the highest normal LN mRNA levels determined was established. With this threshold, 42 of the 48 LNs with known metastases were positive (88 % sensitivity for known metastases in the other half). Of the LNs without known metastases by routine analysis, 138 (22 %) were positive for PHGR1 mRNA according to the threshold, suggesting the presence of occult metastases not detected by routine histological analysis.

The results, and the threshold level, are shown in the box-plot of Figure 1.

Example 4: PHGR1 mRNA detection in blood samples

The leukocyte fraction (containing potential tumor cells) was isolated from peripheral blood samples by Lymphoprep density centrifugation (Axis-Shield,

Dundee, UK). RNA was isolated from the lymphocyte fraction, DNase-treated, and reverse-transcribed as described above (in Example 3). The relative level of PHGR1 mRNA was determined by quantitative RT-PCR as described above (in Example 3). The highest level of PHGR1 mRNA in blood from healthy donors was used as a threshold to indicate detection of tumor cells in the blood samples.

Increasing numbers of LS174T colon cancer cells were spiked into 1 E7 normal lymphocytes, and PHGR1 mRNA levels were determined by quantitative RT- PCR as described above (Example 3). As can be seen from Figure 2, it was possible to detect as few as 10 cancer cells in 1 E7 normal lymphocytes. Example 5: PHGR1 immunostaining of lymph nodes with known metastases

Paraffin sections of lymph nodes with known metastases were mounted onto Superfrost Plus slides (Menzel, Braunschweig, Germany) and dried overnight at 37°C followed by 1 h at 60°C. Sections were deparaffinized in xylene and rehydrated in decreasing concentrations of alcohol. Antigen was retrieved with a highly stabilized retrieval system (ImmunoPrep, Instrumec, Oslo, Norway) using 10 mM TRIS/1 mM EDTA (pH 9.0) as the retrieval buffer. Sections were heated for 3 min at 110°C followed by 10 min at 95°C and cooled to 20° C.

The sections were incubated with a rabbit polyclonal PHGR1 antibody (raised against a synthetic subpeptide of PHGR1 , SEQ ID NO 3 above). The primary antibody were diluted to a final dilution of 1 :20 0000 using Dako antibody diluent (S0809). The EnVisionTMFlex detection system (Dako, K8000) were used for visualization. Sections were incubated for 30 min. with the primary antibody, 5 min. with peroxydase-blocking reagent (SM801), 20 min with the EnVision™ FLEX /HRP Detection Reagent (SM802), 10 min with EnVision™ FLEX DAB+ Chromogen (DM827)/ EnVision™ FLEX Substrate Buffer (SM803) mix and 5 min. with

EnVision™ FLEX Hematoxylin (K8008). The slides were dehydrated and mounted.

All Immunohistochemical stainings were performed using a Dako Autostainer Link 48 instrument and EnVision™ FLEX Wash Buffer (DM831).

Figure 3 shows PHGR1 immostaining of four lymph nodes (A to D) with known metastases. The metastases are easily observed by intense brown staining (the dark areas, examples of which in each image are labelled by single continuous arrows, whereas the normal lymphatic tissue only shows the blue nuclear

counterstain (hematoxylin) (the pale grey areas, examples of which in each image are labelled by dashed double arrows)).

Example 6: PHGR1 immunofluorescent staining of tumour cells in peripheral blood

The leukocyte fraction was isolated from peripheral blood samples (from healthy volunteers) by Lymphoprep density centrifugation (Axis-Shield, Dundee, UK). LS174T colon tumour cells were added to the cell fraction leukocytes to a final relative concentration of 1%. Cytospins of the spiked leukocyte suspension were prepared. The cells were fixed by 4% paraformaldehyde in PBS and permeabilized by 0.2% Triton X-100 in PBS. Subsequently, the cytospins were incubated with blocking solution (PBS w/0.1% Tween-20 and 1 % goat serum), followed by the PHGR1 antibody described above, diluted 1 :1000 in blocking solution. After washing, the spins were incubated with a 1 :500 dilution of FITC-labelled secondary antibody, washed and incubated with DAPI nuclear stain. Pictures were obtained by fluorescence microscopy, showing strong green fluorescent labelling of the colon tumour cells and almost no staining of the leukocytes (Fig. 4). This technique may be used for detection of circulating tumour cells in patient blood.

Example 7: Multicolour immunofluorescence assay for CTCs in patient blood samples

A multicolour immunofluorescense assay for the detection of circulating tumour cells (CTCs) in blood samples from CRC patients was established. This assay was based on the anti-PHGR1 antibody described in Example 2.

It was not known whether levels of CTCs could be detected in blood and initial tests on patient blood failed to detect any CTCs. It was considered that this might be due to the presence of only low levels of CTCs in patient blood samples. Hence various enrichment steps were tried. A number of different immunological assays were evaluated, including Dynabeads (Invitrogen) and Rosettesep (Stem Cell Research), but none were adequate.

An immunomagnetic enrichment system from Miltenyi Biotech was then evaluated and eventually optimised to produce positive results, by using CD326 (EpCAM) MicroBeads, human, (130-061-101), FcR blocking solution (130-059-901) and MS columns (130-042-201) according to the protocol of the manufacturer. Mononuclear cells and tumor cells were first enriched by Lymphoprep (Axis-Shield) density centrifugation. Subsequently, Epcam-expressing cells were enriched by incubation with immunomagnetic beads and washing on MS columns. Eluted cells were moderately fixated by incubation in 2 % paraformaldehyde in PBS for 10 minutes at room temperatur, washed and cytospun.

A multicolour immunofluorescense assay for detecting CTCs from patient blood samples was then established in cytospins (Fig. 5). PHGR1 (green), cytokeratins (red), CD45 (far red) and DNA (blue) were stained. Cytokeratin staining was done as a reference staining, as this is the most common staining of CTCs, for example in the CellSearch system. CD45 protein is located on the surface of leukocytes. The staining protocol was as described in Example 6, with an additional incubation step with CD45 (CD45-Alexa647; Abd Serotec) and cytokeratin (AE1/AE3-eFluor570; eBioscience) antibodies, diluted 1:200 in blocking solution. PHGR1 antibody was now diluted 1 :500 and secondary antibody 1 :2000 in blocking solution. Fluorescence microscopy and autoated image analysis software were used to identify CTCs (PHGR1 positive, DAPI positive, CD45 negative). Figures 5A and 5B shows example images from analysis of a CRC patient blood sample and a normal control sample. Example 8: PHGR1 mRNA detection in patient blood samples

This example describes the detection of PHGR1 mRNA in peripheral blood samples from patients with metastatic CRC (mCRC), indicating the presence of CTCs. Peripheral blood (PB) samples (n=28) were collected from 20 mCRC patients; 19 samples before starting new chemotherapy and from 9 samples after more than two weeks of chemotherapy. In addition, PB samples were collected from seven healthy control persons. All samples were collected in EDTA-tubes. Blood samples were handled as described in Example 4 and PHGR1 mRNA was measured as described in Example 3. PHGR1 mRNA was not detectable in any of the normal control samples, whereas 5 (18%) of the 28 patient samples had detectable PHGR1 mRNA levels (Figure 6). Preliminary survival data suggests that the 5 patients with PHGR1 -positive PB samples have poorer prognosis compared with the other patients.

SEQUENCES

SEQ ID NO: 1

1 agacttcctg cccctgctct gcactctcag gtattccctg ctcttactcc aaaaagatgg 61 acccaggtcc gaaggggcac tgccactgtg gggggcatgg ccatcctcca ggtcactgcg 121 ggccaccccc tggccatggc ccagggccct gcgggccacc cccccaccat ggtccagggc 181 cctgcgggcc accccctggc catggcccag ggccctgcgg gccacccccc caccatggtc 241 cagggccctg cgggcctccc cctggccatg gcccaggtca cccaccccct ggtccacatc 301 actgaggaag tagaagaaaa caggacacaa gatggcaagc ctgagagaat tgcccagctg 361 acctggaatg aggcctaaac cacaatcttc tcttcctaat aaacagcctc ctagaggcca 421 cattctattc tttaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaa

SEQ ID NO: 2

MDPGP KGHCH CGGHG HPPGH CGPPP GHGPG

1

PCGPP PHHGP GPCGP PPGHG PGPCG PPPHH

31

GPGPC GPPPG HGPGH PPPGP HH

61

SEQ ID NO: 3

CGPPP GHGPG HPPPG P SEQ ID NO: 4

5'-CCCTG CTCTG CACTC TCAG-3'

SEQ ID NO: 5

5^*-CGCAG TGACC TGGAG GAT-3'

SEQ ID NO: 6 (from US2010/0203040, SEQ ID NO: 112)

GHGPG HPPPG PHH

Claims

1. A method of detecting and/or diagnosing colorectal cancer in a subject, the method comprising:

(a) assaying for the presence of PHGR1 polypeptide in a blood sample obtained from the subject,

wherein the presence of PHGR1 polypeptide in the blood sample is indicative of the presence of colorectal cancer in the subject.

2. A method of detecting and/or diagnosing a cancer in a subject, the method comprising:

3. A method of detecting and/or diagnosing a cancer in a subject, the method comprising the steps:

4. A method of monitoring the development of a cancer in a subject,

the method comprising the steps:

(b) comparing the levels of PHGR1 polypeptide or PHGR1 mRNA in the first and second biological samples, wherein an increase in the level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the later time point compared to the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the earlier time point is indicative of an increase in tumour growth in the patient, and

wherein a decrease in the level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the later time point compared the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the earlier time point is indicative of a decrease in tumour growth in the patient.

5. A method of monitoring the metastasis of a cancer in a subject, the method comprising the steps:

6. A method of monitoring the effectiveness of an anti-cancer therapy in a subject, the method comprising the steps:

wherein the subject has been treated with an anti-cancer therapy before the two time points or in the interval between the first and second time points, and

(b) comparing the levels of PHGR1 polypeptide or PHGR1 mRNA in the first and second biological samples, wherein a decrease in the level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the later time point compared the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the earlier time point is indicative of the anti-cancer therapy being efficacious, and

wherein an increase in the level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the later time point compared the corresponding level of PHGR1 polypeptide or PHGR1 mRNA in the sample taken at the earlier time point is indicative of the anti-cancer therapy being non-efficacious.

7. A method of assaying for the presence of a biomarker which is indicative of cancer cells in a biological sample, the method comprising the step:

8. A method of assaying for an analyte which is indicative of colorectal, gut, stomach or pancreatic cancer, which method comprises:

(b) detecting conjugates formed by said binding agent.

9. A method as claimed in any one of claims 2 to 8, wherein the cancer is a metastatic cancer.

10. A method as claimed in any one of claims 2 to 9, wherein the cancer is colorectal, gut, stomach or pancreatic cancer, preferably a metastatic colorectal, gut, stomach or pancreatic cancer

11. A method as claimed in any one of claims 2 to 10, wherein the biological sample is blood or is derived from blood.

12. A method as claimed in any one of claims 2 to 10, wherein the biological sample is lymph node tissue or lymph fluid or is derived from lymph node tissue or fluid.

13. A method as claimed in any one of claims 2 to 12, wherein the PHGR1 polypeptide is assayed, measured or detected using a binding agent which specifically binds to PHGR1 polypeptide.

14. A method as claimed in claim 13, wherein the binding agent is an immuno- affinity reagent, preferably an antibody.

15. A method as claimed in any one of claims 2 to 7 or 9 to 12, wherein the PHGR1 mRNA is assayed, measured or detected by a method comprising the steps of:

(a) reverse-transcribing PHGR1 mRNA into cDNA, followed by

(b) amplifying all or part of the cDNA using nucleotide primers.

16. A pharmaceutical composition comprising:

(a) a binding agent which is capable of immuno-specific binding to a PHGR1 polypeptide, wherein the binding agent is not a polyclonal antibody, or

(b) a binding agent which is capable of immuno-specific binding to a peptide defined by SEQ ID NO: 3,

wherein the binding agent optionally comprises or is conjugated to a therapeutic moiety or a detectable label, and

wherein the composition optionally additionally comprises one or more

pharmaceutically-acceptable diluents, carriers or excipients.

17. A kit comprising:

wherein the first and second primers are capable of being used in an exponential amplification procedure to amplify a fragment of a nucleotide molecule of SEQ ID NO: 1.

18. A kit comprising:

(a) a nucleotide primer of SEQ ID NO: 4, and/or

(b) a nucleotide primer of SEQ ID NO: 5,

either in admixture or in separate containers.

19. A method for the treatment or prophylaxis of cancer or for preventing or reducing the growth and/or metastasis of a cancer, the method comprising administering an effective amount of a composition as defined in claim 16 to a subject in need thereof.

20. A method as claimed in claim 19, wherein the cancer is colorectal, gut, stomach or pancreatic cancer, preferably metastatic colorectal, gut, stomach or pancreatic cancer.