WO2018143896A1 - Ovarian cancer biomarker - Google Patents

Abstract

Described herein is a method of detecting ovarian cancer and monitoring, prognosing, choosing a therapy and determining the likelihood of success of a particular therapy in an individual suffering from ovarian cancer. The methods comprise detecting the level of expression, activity or amount of MMP9 polypeptide (GenBank Accession Number: NP_004985-2) in an Annexin V binding microparticle in a sample of or from an individual suspected to be suffering or is suffering from ovarian cancer, wherein the microparticle comprises microvesicles, exosomes, ectosomes or apoptotic bodies.

Description

OVARIAN CANCER BIOMARKER

FIELD

This invention relates to the fields of medicine, cell biology, molecular biology and genetics. This invention relates to the field of medicine.

BACKGROUND

Ovarian cancer is the most lethal gynaecologic malignancies. Part of the reason for the lethality of ovarian cancer is that it is relatively asymptomatic in its early stages, and is diagnosed only when the cancer is in an advanced stage with a poor prognosis. Early detection of ovarian cancer is currently hampered by the lack of adequate screening and diagnostic tools [1]·

SUMMARY

According to a 1^st aspect of the present invention, we provide a method of detecting ovarian cancer in an individual. The method may comprise detecting the level of expression, activity or amount of a MMP9 polypeptide (GenBank Accession Number: NP_004985-2) in an Annexin V binding microparticle. The detection may be conduction in a sample of or from an individual suspected to be suffering from ovarian cancer.

The method may further comprise comparing the level of expression, activity or amount of a MMP9 polypeptide in an Annexin V binding microparticle in a sample of or from an individual known not to be suffering from ovarian cancer or an individual who has benign ovarian cyst.

The method may be such that a higher level of expression, activity or amount of MMP9 polypeptide indicates that the individual is suffering from, or is likely to be suffering from, ovarian cancer.

The method may comprise detecting a level of expression, activity or amount of a MMP9 polypeptide in an Annexin V binding microparticle of 650 picogram per ml plasma or more.

The method may be such that the level of expression, amount or activity of the MMP9 polypeptide in an Annexin V binding microparticle is increased by 5% or more, 10% or more, 15% or more, 20% or more, 25% or more, 30% or more, 35% or more, 40% or more, 45% or more, 50% or more, 55% or more, 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more or 100% or more.

The method may further comprise a step of normalising the level, concentration or amount of the selected polypeptide between two or more samples. The normalisation may be conducted with reference to beta actin polypeptide (GenBank Accession Number:

NP_001092; NCBI reference sequence: NM_001101.4).

The method may further comprise a step of selecting microparticles by size, for example, by size exclusion chromatography. The method may be such that the microparticles comprise CD9+ microparticles. The method may be such that a sample is selected from the group consisting of: urine, blood, tears, saliva, bronchoaveolar fluid, tumoral effusions, amniotic fluid and milk. The method may be such that the microparticles comprise

microvesicles, exosomes, ectosomes or apoptotic bodies.

We provide, according to a 3^rd aspect of the present invention, a method of monitoring the progress of an individual suffering from ovarian cancer. The method may comprise monitoring the modulation of expression of a MMP9 polypeptide in a cell, tissue or organ of the individual by a method as set out above.

As a 4^th aspect of the present invention, there is provided a method of prognosis of an individual suffering from ovarian cancer. The method may comprise detecting modulation of expression of a MMP9 polypeptide in a cell, tissue or organ of the individual by a method as set out above.

We provide, according to a 5^th aspect of the present invention, a method of choosing a therapy for an individual suffering from ovarian cancer. The method may comprise detecting modulation of expression of MMP9 polypeptide in a cell, tissue or organ of the individual by a method as set out above. An appropriate therapy may then be chosen based on the severity of the ovarian cancer.

The present invention, in a 6^th aspect, provides a method of determining the likelihood of success of a particular therapy in an individual suffering from ovarian cancer. The method may comprise comparing the therapy with a therapy determined by such a method.

The method may be such that the therapy comprises: (a) a chemotherapeutic drug such as Albumin bound paclitaxel (nab-paclitaxel, Abraxane®), Altretamine (Hexalen®), Capecitabine (Xeloda®), Cyclophosphamide (Cytoxan®), Etoposide (VP- 16), Gemcitabine (Gemzar®), Ifosfamide (Ifex®), Irinotecan (CPT-11, Camptosar®), Liposomal doxorubicin (Doxil®), Melphalan, Pemetrexed (Alimta®), Topotecan, Vinorelbine (Navelbine®); (b) radiation therapy, such as external beam radiation therapy; (c) surgery, such as debulking, total abdominal hysterectomy (TAH) and bilateral salpingo oophorectomy (BSO); (d) hormone therapy or hormone blocking therapy such as Luteinizing-hormone-releasing hormone (LHRH) agonists; or (e) targeted therapy such as Bevacizumab (Avastin®) or Olaparib (Lynparza™).

In a 7^th aspect of the present invention, there is provided a kit for detecting ovarian cancer in an individual or susceptibility of the individual to ovarian cancer comprising means for detection of MMP9 polypeptide expression, activity or amount in a microparticle of or from the individual or a sample taken from him or her, preferably further comprising a therapeutic drug for treatment, prophylaxis or alleviation of ovarian cancer, such as a chemotherapeutic drug such as Albumin bound paclitaxel (nab-paclitaxel, Abraxane®), Altretamine (Hexalen®), Capecitabine (Xeloda®), Cyclophosphamide (Cytoxan®), Etoposide (VP-16), Gemcitabine (Gemzar®), Ifosfamide (Ifex®), Irinotecan (CPT-11, Camptosar®), Liposomal doxorubicin (Doxil®), Melphalan, Pemetrexed (Alimta®), Topotecan, Vinorelbine (Navelbine®); a hormone therapy or hormone blocking therapy such as Luteinizing-hormone- releasing hormone (LHRH) agonists; or a targeted therapy such as Bevacizumab (Avastin®) or Olaparib (Lynparza™)

The practice of this invention will employ, unless otherwise indicated, conventional techniques of chemistry, molecular biology, microbiology, recombinant DNA and

immunology, which are within the capabilities of a person of ordinary skill in the art. Such techniques are explained in the literature. See, for example, J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Books 1-3, Cold Spring Harbor Laboratory Press; Ausubel, F. M. et al. (1995 and periodic supplements;

Current Protocols in Molecular Biology, ch. 9, 13, and 16, John Wiley & Sons, New York, N.Y.); B. Roe, J. Crabtree, and A. Kahn, 1996, DNA Isolation and Sequencing: Essential Techniques, John Wiley & Sons; J. M. Polak and James O'D. McGee, 1990, In Situ

Hybridization: Principles and Practice; Oxford University Press; M. J. Gait (Editor), 1984,

Oligonucleotide Synthesis: A Practical Approach, Irl Press; D. M. J. Lilley and J. E. Dahlberg, 1992, Methods ofEnzymology: DNA Structure Part A: Synthesis and Physical Analysis of DNA Methods in Enzymology, Academic Press; Using Antibodies: A Laboratory Manual: Portable Protocol NO. I by Edward Harlow, David Lane, Ed Harlow (1999, Cold Spring Harbor Laboratory Press, ISBN 0-87969-544-7); Antibodies: A Laboratory Manual by Ed Harlow (Editor), David Lane (Editor) (1988, Cold Spring Harbor Laboratory Press, ISBN 0- 87969-314-2), 1855. Handbook of Drug Screening, edited by Ramakrishna Seethala,

Prabhavathi B. Fernandes (2001, New York, NY, Marcel Dekker, ISBN 0-8247-0562-9); and Lab Ref: A Handbook of Recipes, Reagents, and Other Reference Tools for Use at the Bench, Edited Jane Roskams and Linda Rodgers, 2002, Cold Spring Harbor Laboratory, ISBN 0- 87969-630-3. Each of these general texts is herein incorporated by reference. BRIEF DESCRIPTION OF THE FIGURES

Figure 1 is a drawing showing the distribution of MMP9 concentration in the plasma, AV-EV and CTB-EV of patients with ovarian cyst and ovarian cancer.

DETAILED DESCRIPTION

We test if the plasma MMP9 which is widely associated with cancers in general could be a more accurate biomarker for ovarian cancers if it is associated in a plasma EVs such as CTB- or AV-binding EVs (i.e. CTB-EVs and AV-EVs, respectively).

We show that MMP9 in AV-EVs is more significantly associated with ovarian cancer than those with benign ovarian cysts.

We have previously reported that the beta actin level is constant in different EV types secreted by cells (Lai et al (2016). MSC Secretes at Least 3 EV Types Each with a Unique

Permutation of Membrane Lipid, Protein andRNA. Journal of Extracellular Vesicles 2016, 5: 29828).

The method may therefore comprise a step of normalising the level, concentration or amount of the selected polypeptide between two or more samples. The normalisation s may be conducted with reference to beta actin polypeptide (GenBank Accession Number:

NP_001092; NCBI reference sequence: NM_001101.4).

DETECTION AND MONITORING OF CANCER STATES

We provide a method of monitoring the cancer state of a cell, tissue, organ or organism. The cancer may comprise an ovarian cancer. The method may comprise establishing, for a sample of microparticles from the cell, tissue, organ or organism, the amount of an MMP9 polypeptide in a subfraction of microparticles, such as an Annexin V binding fraction of microparticles.

The microparticle subfraction may comprise any subfraction of microparticles. They may be microparticles which comprise exposed phosphotidylserine. The microparticles may be capable of binding to Annexin V (referred to as "Annexin V microparticles" or "AV- microvesicles" for convenience).

For convenience, we refer to the presence, amount, mass or number etc of MMP9 polypeptide in the Annexin V microparticles as "Annexin V microparticle MMP9

polypeptide".

The method may be such that the microparticles comprise CD9+ microparticles. The method may be such that the microparticles comprise microvesicles, exosomes, ectosomes or apoptotic bodies.

In particular, we provide for a method of monitoring the cancer state of a cell, tissue, organ or organism, such as the ovarian cancer state, the method comprising establishing, for a sample of microparticles from the cell, tissue, organ or organism, the expression, amount, mass or number of MMP9 polypeptide in microparticles which comprise exposed

phosphotidylserine, preferably which bind to Annexin V; in which the amount, mass or number of MMP9 polypeptide in the Annexin V binding microparticle so established is indicative of the cancer, such as ovarian cancer, state of the cell, tissue, organ or organism.

We further provide a method for establishing that a cell, tissue, organ or organism is in a particular cancer state, such as an ovarian cancer state. The method may comprise comparing the expression, amount, mass or number, etc of MMP9 polypeptide in an Annexin V microparticle of the cell, tissue, organ or organism with that of a cell, tissue, organ or organism known to be in that particular state.

In addition to, or instead of, using a single polypeptide, combinations of selected polypeptides may also be used. Accordingly, where we refer to polypeptides, such reference should be taken to include reference to combinations of polypeptides, for example by establishing or comparing amounts of combinations of polypeptides. The measurement of MMP9 in the microparticles may be conducted by selecting microparticles in the sample which bind to Annexin V.

The method may further comprise a step of selecting microparticles by size. The size selection step may comprise size exclusion chromatography. Where this is done, the size selection step may be conducted prior to the first step, e.g., step (a) above.

Where determination of an "amount" of a polypeptide is referred, it should be understood to extend to the determination or establishment of the mass, number concentration etc of the polypeptide. Where reference is made to the amount of, being "higher" in a first state than a second state (or higher in a first sample than a second sample), this may be taken to mean that the amount is statistically different in the first state(or sample) compared to the second state (or sample) with a p value <0.01.

The amount or increase so established may be indicative of the state of the cell, tissue, organ or organism.

The method may be such that the cancer state of the cell, tissue, organ or organism comprises an oncogenic state, a cancerous state or a tumour state.

The method may be such that the state of the cell, tissue, organ or organism comprises a state of being sick, a state of poor prognosis, a state of recovery from sickness, a state of good prognosis or a healthy state.

The method may be such that the sample is selected from the group consisting of: sweat, urine, blood, tears, saliva, bronchoaveolar fluid, tumoral effusions, amniotic fluid and milk.

Where the sample is of an organism, the organism may comprise any animal. The organism may comprise a mammal, such as a human.

The method may be such that it comprises any combination of the above.

DETECTION OF EXPRESSION OF OVARIAN CANCER BIOMARKER MMP9

Expression of MMP9 ovarian cancer biomarker in individuals affected by ovarian cancer is modulated in Annexin V binding microparticles when compared to unaffected individuals. Accordingly, we provide for a method of diagnosis of ovarian cancer, comprising detecting modulation of expression of MMP9 as an ovarian cancer biomarker, in Annexin V binding microparticles, in a sample of an individual.

The method may comprise use of the anti-MMP9 antibodies described in this document. The anti-ovarian cancer biomarker antibodies may be used in immunoassays to detect and assay the quantity of MMP9 ovarian cancer biomarker in a biological sample, and hence provide an indication of the level of expression of MMP9 ovarian cancer biomarker in a cell, tissue, organ or individual from which the sample is derived. Immunoassays include ELISA, Western Blot, etc, and methods of employing these to assess MMP9 ovarian cancer biomarker expression are known to the skilled reader.

It will be appreciated that as the level of MMP9 ovarian cancer biomarker varies with the severity of the cancer, that detection of MMP9 ovarian cancer biomarker expression, amount or activity may also be used to predict a survival rate of an individual with ovarian cancer, i.e., high levels of MMP9 ovarian cancer biomarker indicating a lower survival rate or probability and low levels of MMP9 ovarian cancer biomarker indicating a higher survival rate or probability, both as compared to individuals or cognate populations with normal levels of MMP9 ovarian cancer biomarker, all in Annexin V binding microparticles. Detection of expression, amount or activity of MMP9 ovarian cancer biomarker may therefore be used as a method of prognosis of an individual with ovarian cancer. Detection of MMP9 ovarian cancer biomarker expression, amount or level may be used to determine the likelihood of success of a particular therapy in an individual with a ovarian cancer. Appropriate therapy may then be chosen for that individual (e.g., a more aggressive therapy may be indicated for a person suffering from a more aggressive ovarian cancer, while a less aggressive or milder therapy may be indicated for a person suffering from a less aggressive ovarian cancer).

The diagnostic methods described in this document may be combined with the therapeutic methods described. Thus, we provide for a method of treatment, prophylaxis or alleviation of ovarian cancer in an individual, the method comprising detecting modulation of expression, amount or activity of MMP9 ovarian cancer biomarker in a cell or sample of the individual and administering an appropriate therapy to the individual based on the severity of the ovarian cancer. If ovarian cancer is diagnosed or suspected, known therapies may be prescribed or administered to the affected individual. Ovarian cancer therapies include any one or more of the following:

(a) a chemotherapeutic drug such as Albumin bound paclitaxel (nab-paclitaxel, Abraxane®), Altretamine (Hexalen®), Capecitabine (Xeloda®),

Cyclophosphamide (Cytoxan®), Etoposide (VP- 16), Gemcitabine (Gemzar®), Ifosfamide (Ifex®), Irinotecan (CPT-11, Camptosar®), Liposomal doxorubicin (Doxil®), Melphalan, Pemetrexed (Alimta®), Topotecan, Vinorelbine (Navelbine®);

(b) radiation therapy, such as external beam radiation therapy;

(c) surgery, such as debulking, total abdominal hysterectomy (TAH) and bilateral salpingo oophorectomy (BSO);

(d) hormone therapy or hormone blocking therapy such as Luteinizing-hormone- releasing hormone (LHRH) agonists; or

(e) targeted therapy such as Bevacizumab (Avastin®) or Olaparib (Lynparza™).

Typically, physical examination of the patient and laboratory analysis are used for the detection of ovarian cancer.

Detection of MMP9 ovarian cancer biomarker expression, amount or activity in Annexin V binding microparticles may be combined with other means of detecting and diagnosing ovarian cancer.

Main symptoms of ovarian cancer include feeling constantly bloated; a swollen stomach; discomfort in stomach or pelvic area; feeling full quickly when eating, or loss of appetite and needing to urinate more often or more urgently than normal.

Other symptoms of ovarian cancer can include persistent indigestion or nausea, pain during sex, change in bowel habits, back pain, vaginal bleeding, particularly bleeding after menopause, feeling tired all the time and unintentional weight loss.

Common laboratory tests for ovarian cancer include RT-PCR and serological tests. Blood tests for CA125, which is produced by some ovarian cancer cells, may be conducted. Ultrasound scans may be conducted, including abdominal ultrasound or transvaginal ultrasound. CT scans, X-rays, biopsies and laparoscopy may be conducted as well to diagnose ovarian cancer.

Detection of ovarian cancer biomarker expression, amount or activity can be used to diagnose, or further confirm the diagnosis of, ovarian cancer, along with the standard procedures described above. This may be especially useful when the analysis does not yield a clear result.

The presence and quantity of MMP9 ovarian cancer biomarker polypeptides may be detected in a sample as described in further detail below. Thus, ovarian cancer can be diagnosed by methods comprising determining from a sample derived from a subject an abnormally increased expression, amount or activity, such as a increased expression, amount or activity, of the MMP9 ovarian cancer biomarker polypeptide in Annexin V binding microparticles.

The sample may comprise a cell or tissue sample from an organism or individual suffering or suspected to be suffering from a disease associated with increased, reduced or otherwise abnormal MMP9 ovarian cancer biomarker expression, amount or activity, including spatial or temporal changes in level or pattern of expression, amount or activity. The level or pattern of expression, amount or activity of MMP9 ovarian cancer biomarker in an organism suffering from or suspected to be suffering from such a disease may be usefully compared with the level or pattern of expression, amount or activity in a normal organism as a means of diagnosis of disease.

The sample may comprise a cell or tissue sample from an individual suffering or suspected to be suffering from ovarian cancer, such as a relevant tissue or cell sample.

In some embodiments, an increased level of expression, amount or activity of MMP9 ovarian cancer biomarker is detected in the sample. The level of MMP9 ovarian cancer biomarker may be increased to a significant extent when compared to normal cells, or cells known not to be from individuals infected with ovarian cancer. Such cells may be obtained from the individual being tested, or another individual, such as those matched to the tested individual by age, weight, lifestyle, etc.

In some embodiments, the level of expression, amount or activity of MMP9 ovarian cancer biomarker is increased by 10%, 20%, 30% or 40% or more. In some embodiments, the level of expression, amount or activity of ovarian cancer biomarker is increased by 45% or more, such as 50% or more, as judged by immunoassay.

The expression, amount or activity of MMP9 ovarian cancer biomarker may be detected in a number of ways, as known in the art, and as described in further detail below. Typically, the amount of MMP9 ovarian cancer biomarker in Annexin V binding

microparticles in a sample of tissue from an individual is measured, and compared with a sample from an unaffected individual.

Detection of the amount, activity or expression of MMP9 ovarian cancer biomarker may be used to grade the ovarian cancer. For example, a high level of amount, activity or expression of ovarian cancer biomarker (not MMP9) may indicate an aggressive ovarian cancer. Similarly, a low level of amount, activity or expression of MMP9 may indicate a non- aggressive ovarian cancer. Such a grading system may be used in conjunction with established grading systems.

Levels of MMP9 ovarian cancer biomarker gene expression may be determined using a number of different techniques, as described elsewhere in this document.

MMP9

MMP9 polypeptide (GenBank Accession Number: NP 004985-2)

MSLWQPLVLV LLVLGCCFAA PRQRQSTLVL FPGDLRTNLT DRQLAEEYLY RYGYTRVAEM

RGES SLGPA LLLLQ QLSL PETGELDSAT L AMRTPRCG VPDLGRFQTF EGDL WHHHN

ITYWIQNYSE DLPRAVIDDA FARAFALWSA VTPLTFTRVY SRDADIVIQF GVAEHGDGYP

FDG DGLLAH AFPPGPGIQG DAHFDDDELW SLG GVWPT RFGNADGAAC HFPFIFEGRS

YSACTTDGRS DGLPWCSTTA NYDTDDRFGF CPSERLYTQD GNADG PCQF PFIFQGQSYS

ACTTDGRSDG YRWCATTANY DRD LFGFCP TRADSTVMGG NSAGELCVFP FTFLG EYST

CTSEGRGDGR LWCATTSNFD SD WGFCPD QGYSLFLVAA HEFGHALGLD HSSVPEALMY

PMYRFTEGPP LH DDVNGIR HLYGPRPEPE PRPPTTTTPQ PTAPPTVCPT GPPTVHPSER

PTAGPTGPPS AGPTGPPTAG PSTATTVPLS PVDDACNV I FDAIAEIGNQ LYLF DG YW

RFSEGRGSRP QGPFLIAD W PALPR LDSV FEERLS LF FFSGRQVWVY TGASVLGPRR

LD LGLGADV AQVTGALRSG RG MLLFSGR RLWRFDVKAQ MVDPRSASEV DRMFPGVPLD

THDVFQYRE AYFCQDRFYW RVSSRSELNQ VDQVGYVTYD ILQCPED DETECTION OF MMP9 POLYPEPTIDE

The method may comprise determining the presence, amount, mass or number etc of MMP9 polypeptide.

Such determination may be conducted by any suitable means as known in the art, depending on the protein or polypeptide. Examples of such determination methods include mass spectrometry, spectrophotometry, UV absorption, etc.

Normalisation

The method may further comprise a step of normalisation. Such a step may comprise determining or ensuring that the quantity or concentration of any one or more proteins or polypeptides is the same across different samples.

A normalisation step, as applied to the methods and compositions described here, may make use of a polypeptide whose concentration is known to be the same across any two samples.

Accordingly, the methods described here may comprise a normalisation step. The normalisation step may comprise adjusting the level, concentration or amount of a particular polypeptide in one or more samples. The normalisation step may be conducted on two or more samples in which the level, concentration or amount of a particular polypeptide (prior to normalisation) are substantially different from each other. The normalisation step may be such that, following normalisation, the level, concentration or amount of a particular polypeptide in two or more samples are substantially the same.

The normalisation step may comprise diluting or concentrating one or other of the two samples, to increase or decrease the level, concentration or amount of a particular polypeptide in one or both samples.

Alternatively, or in addition, the normalisation step may comprise determining, for a selected two or more samples, the ratio of the levels concentration or amount of a particular polypeptide between the samples. This may be achieved by reference to a reference polypeptide which is known to have the same level, concentration or amount in each of a group of samples of interest. The reference polypeptide may comprise for example beta actin polypeptide (GenBank Accession Number: NP_001092; NCBI reference sequence:

NM 001101.4). It will be appreciated that, where the normalisation step comprises such determination of ratios, concentration or dilution of samples may not be needed.

Normalisation Using Beta Actin Polypeptide

We have established that levels of beta actin polypeptide in Annexin V microparticles in a cell, tissue, organ or organism that is suffering (or is at risk of suffering) from ovarian cancer is not statically different from levels of beta actin polypeptide in a cell, tissue, organ or organism that is not suffering (or is at risk of suffering) from ovarian cancer, e.g., from healthy individuals.

Accordingly, the level or concentration or quantity of beta actin proteins or polypeptides in in Annexin V microparticles in a cell, tissue, organ or organism may be used to normalise any of the markers usable in the method described here, e.g., MMP9 levels.

Detection of protein expression in extracellular vesicles (EVs) subfractions, such as Annexin V binding microparticles, including normalisation, is described in detail in Lai et al (2016) MSC secretes at least 3 EV types each with a unique permutation of membrane lipid, protein and RNA. Journal of Extracellular Vesicles, 5: 1, 29828.

Beta Actin Polypeptide (GenBank Accession Number: NP 001092; NCBI reference sequence: NM 001101.4)

MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRG ILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFET FNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYL MKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGN ERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQK EITALAPSTMKIKI IAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

MICROPARTICLES

The microparticle may in particular comprise a vesicle such as a microvesicle. The microparticle may comprise an exosome.

The microparticle may comprise a vesicle or a flattened sphere limited by a lipid bilayer. The microparticle may comprise a diameter of 40-100 nm. The microparticle may be formed by inward budding of the endosomal membrane. The microparticle may have a density of -1.13 - 1.19 g/ml and may float on sucrose gradients. The microparticle may be enriched in cholesterol and sphingomyelin, and lipid raft markers such as GM1, GM3, flotillin and the src protein kinase Lyn. Methods of isolating microparticles are known in the art and are described in detail in the Examples below, as well as in documents such as International Patent Publication WO 2009/105044.

We describe in particular a technology to rapidly isolate different lipid microparticles found in plasma that could be used to identify and/or stratify biomarkers in different microparticle sub-populations to enhance their diagnostic, prognostic or theranostic value.

We therefore provide a method of treating a sample containing microparticles, the method comprising selecting microparticles in the sample which comprise exposed phosphotidylserine and establishing the expression, amount, etc of MMP9 in the selected microparticles.

ANNEXIN V BINDING MICROPARTICLES

The method may be such that it comprises selecting microparticles in the sample which bind to Annexin V. The microparticles may be such that they are capable of binding to Annexin V but not to cholera toxin B (CTB). The method may be such that it further comprises a step of selecting microparticles by size, for example, by size exclusion chromatography.

The method may be such that the microparticles comprise CD9+ microparticles.

Specifically, we provide a method to rapidly isolate an annexin V- binding subfraction of lipid microparticles from plasma for the detection of microparticle-associated proteins such as MMP9.

The method may further comprise the step of detecting and/or quantitating a membrane protein or a luminal protein, or both, such as MMP9 in a fractionated sample of microparticles.

BIOLOGICAL SAMPLE

The methods and compositions described here involve detecting a elevated level of expression, amount or activity of a MMP9 polypeptide in an Annexin V binding microparticle for the detection of ovarian cancer in an individual.

Conveniently, the level or levels may be determined by taking a biological sample comprising secretions of a cell. Where the cell is comprised in an organism, the sample may comprise any number of things, including, but not limited to, bodily fluids (including, but not limited to, blood, nasopharyngeal secretions, urine, serum, lymph, saliva, anal and vaginal secretions and perspiration, of virtually any organism. PREPARATION OF ANNEXIN V BINDING MICROPARTICLES

Annexin V binding microparticles may be prepared from plasma (or other fluids) using the following protocol:

10 μΐ, plasma were incubated with 0.1 μg biotinylated Annexin V (AV) (BioVision) in ΙΟΟμΙ, PBS pH 7.4 for 1 hour at 37 °C with shaking at 800 rpm. In the meantime, ΙΟΟμΙ. of Dynabeads® M-280 Streptavidin (Invitrogen) was washed three times with l00μL· PBS.

After the last wash, the plasma-AV reaction mix was added to the washed beads and incubated with shaking at 800 rpm for 30 minutes. The beads were immobilised with a magnet and the supernatant was removed. The beads were then washed thrice with 200μ1 PBS and the washes were removed each time after immobilizing the beads with a magnet.

MEASURING EXPRESSION OF MMP9 OVARIAN CANCER BIOMARKER AT THE POLYPEPTIDE LEVEL

MMP9 ovarian cancer biomarker expression can be detected at the polypeptide level in Annexin V binding microparticles.

In a further embodiment, therefore, MMP9 ovarian cancer biomarker expression, amount or activity in Annexin V binding microparticles may be detected by detecting the presence or amount of MMP9 ovarian cancer biomarker polypeptide in Annexin V binding microparticles in a sample. This may be achieved by using molecules which bind to MMP9 ovarian cancer biomarker polypeptide. Suitable molecules/agents which bind either directly or indirectly to the MMP9 ovarian cancer biomarker polypeptide in order to detect its presence include naturally occurring molecules such as peptides and proteins, for example antibodies, or they may be synthetic molecules. Thus, we disclose a method of detecting the presence of a MMP9 ovarian cancer biomarker polypeptide in Annexin V binding microparticles by contacting a cell sample with an antibody capable of binding the polypeptide and monitoring said sample for the presence of the polypeptide.

For example, the MMP9 ovarian cancer biomarker polypeptide may be detected using an anti-MMP9 ovarian cancer biomarker antibody as described here. Such antibodies may be made by means described in detail in this document.

In a specific example, an anti-MMP9 antibody may comprise an antibody with catalogue number ELH-MMP9-1, obtainable from RayBiotech, Inc. (Georgia, USA).

The assay may conveniently be achieved by monitoring the presence of a complex formed between the antibody and the polypeptide, or monitoring the binding between the polypeptide and the antibody. Methods of detecting binding between two entities are known in the art, and include FRET (fluorescence resonance energy transfer), surface plasmon resonance, etc.

Standard laboratory techniques such as immunoblotting as described above can be used to detect altered levels of MMP9 ovarian cancer biomarker protein in Annexin V binding microparticles, as compared with untreated cells in the same cell population.

Gene expression may also be determined by detecting changes in post-translational processing of MMP9 ovarian cancer biomarker polypeptides or post-transcriptional modification of MMP9 ovarian cancer biomarker nucleic acids. For example, differential phosphorylation of MMP9 ovarian cancer biomarker polypeptides, the cleavage of MMP9 ovarian cancer biomarker polypeptides or alternative splicing of MMP9 ovarian cancer biomarker RNA, and the like may be measured. Levels of expression of gene products such as MMP9 ovarian cancer biomarker polypeptides, as well as their post-translational

modification, may be detected using proprietary protein assays or techniques such as 2D polyacrylamide gel electrophoresis.

Assay techniques that can be used to determine levels of MMP9 ovarian cancer biomarker protein in Annexin V binding microparticles in a sample derived from a host are well-known to those of skill in the art. Antibodies can be assayed for immunospecific binding by any method known in the art. The immunoassays which can be used include but are not limited to competitive and non-competitive assay systems using techniques such as western blots, radioimmunoassays, ELISA, sandwich immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement- fixation assays, immunoradiometric assays, fluorescent immunoassays and protein A immunoassays. Such assays are routine in the art (see, for example, Ausubel et al, eds, 1994, Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New York, which is incorporated by reference herein in its entirety).

The specimen may be assayed for polypeptides/proteins by immunohistochemical and immunocytochemical staining (see generally Stites and Terr, Basic and Clinical Immunology, Appleton and Lange, 1994), ELISA, RIA, immunoblots, Western blotting,

immunoprecipitation, functional assays and protein truncation test. Other assay methods include radioimmunoassays, competitive-binding assays, Western Blot analysis and ELISA assays. ELISA assays are well known to those skilled in the art. Both polyclonal and monoclonal antibodies may be used in the assays. Where appropriate other immunoassays, such as radioimmunoassays (RIA) may be used as are known to those in the art. Available immunoassays are extensively described in the patent and scientific literature. See, for example, U.S. Pat. Nos. 3,791,932; 3,839, 153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521 as well as Sambrook et al, 1992.

DIAGNOSTIC KITS

We also provide diagnostic kits for detecting ovarian cancer in an individual, or susceptibility to such in an individual. The diagnostic kit may comprise means for detecting expression, amount or activity of any of the MMP9 ovarian cancer biomarkers disclosed above in Annexin V binding microparticles, by any means as described in this document. The diagnostic kit may therefore comprise an anti-MMP9 ovarian cancer biomarker antibody, which may comprise a monoclonal antibody. It may comprise a probe capable of specifically binding to a MMP9 ovarian cancer biomarker. The antibody or probe may be labelled for detection. The diagnostic kit may comprise instructions for use, or other indicia. The diagnostic kit may further comprise means for treatment or prophylaxis of ovarian cancer, such as any of the compositions described in this document, or any means known in the art for treating ovarian cancer. ANTI-MMP9 OVARIAN CANCER BIOMARKER ANTIBODY PRODUCTION

Anti-MMP9 ovarian cancer biomarker antibody can be produced by recombinant DNA methods or synthetic peptide chemical methods that are well known to those of ordinary skill in the art.

By way of example, the anti-MMP9 ovarian cancer biomarker antibody may be synthesized by techniques well known in the art, as exemplified by "Solid Phase Peptide Synthesis: A Practical Approach" E. Atherton and R. C. Sheppard, IRL Press, Oxford England. Similarly, multiple fragments can be synthesized which are subsequently linked together to form larger fragments. These synthetic peptide fragments can also be made with amino acid substitutions at specific locations in order to test for activity in vitro and in vivo.

The anti-MMP9 ovarian cancer biomarker antibody can be synthesized in a standard microchemical facility and purity checked with HPLC and mass spectrophotometry. Methods of peptide synthesis, HPLC purification and mass spectrophotometry are commonly known to those skilled in these arts.

The anti-MMP9 ovarian cancer biomarker antibody may also be expressed under in vitro and in vivo conditions in a transformed host cell into which has been incorporated the DNA sequences described here (such as variable sequences) or allelic variations thereof and which can be used in the prevention and/or treatment of ovarian cancer.

The term "vector" includes expression vectors and transformation vectors. The term "expression vector" means a construct capable of in vivo or in vitro expression. The term "transformation vector" means a construct capable of being transferred from one species to another.

Vectors which may be used for expression include recombinant viral vectors, in particular recombinant retroviral vectors (RRV) such as lentiviral vectors, adenoviral vectors including a combination of retroviral vectors. The term 'recombinant retroviral vector" (RRV) refers to a vector with sufficient retroviral genetic information to allow packaging of an RNA genome, in the presence of packaging components, into a viral particle capable of infecting a target cell. Infection of the target cell includes reverse transcription and integration into the target cell genome. The RRV carries non-viral coding sequences which are to be delivered by the vector to the target cell. An RRV is incapable of independent replication to produce infectious retroviral particles within the final target cell. Usually the RRV lacks a functional gag pol and/or env gene and/or other genes essential for replication. Vectors which may be used include recombinant pox viral vectors such as fowl pox virus (FPV), entomopox virus, vaccinia virus such as NYVAC, canarypox virus, MVA or other non-replicating viral vector systems such as those described for example in WO9530018.

Pox viruses may be engineered for recombinant gene expression and for the use as recombinant live vaccines in a dual immunotherapeutic approach. The principal rationale for using live attenuated viruses, such as viruses, as delivery vehicles and/or vector based vaccine candidates, stems from their ability to elicit cell mediated immune responses. The viral vectors, as outlined above, are capable of being employed as delivery vehicles and as vector based vaccine candidates because of the immunogenicity of their constitutive proteins, which act as adjuvants to enhance the immune response, thus rendering a nucleotide sequence of interest (NOI) such as a nucleotide sequence encoding an anti-MMP9 ovarian cancer biomarker antibody more immunogenic.

The pox virus vaccination strategies have used recombinant techniques to introduce NOIs into the genome of the pox virus. If the NOI is integrated at a site in the viral DNA which is non-essential for the life cycle of the virus, it is possible for the newly produced recombinant pox virus to be infectious, that is to say to infect foreign cells and thus to express the integrated NOI. The recombinant pox virus prepared in this way can be used as live vaccines for the prophylaxis and/or treatment of ovarian cancer.

Other requirements for pox viral vector delivery systems include good

immunogenicity and safety. MVA is a replication-impaired vaccinia strain with a good safety record. In most cell types and normal human tissue, MVA does not replicate. Limited replication of MVA is observed in a few transformed cell types such as BHK21 cells. Carroll et al (1997 Vaccinel5 : 387-394) have shown that the recombinant MVA is equally as good as conventional recombinant vaccinia vectors at generating a protective CD8+T cell response and is an efficacious alternative to the more commonly used replication competent vaccinia virus. The vaccinia virus strains derived from MVA, or independently developed strains having the features of MVA which make MVA particularly suitable for use in a vaccine, are also suitable for use as a delivery vehicle. The nucleotide sequence of interest, and of which expression is desired, may operably linked to a transcription unit. The term "transcription unit" as described herein are regions of nucleic acid containing coding sequences and the signals for achieving expression of those coding sequences independently of any other coding sequences. Thus, each transcription unit generally comprises at least a promoter, an optional enhancer and a polyadenylation signal. The term "promoter" is used in the normal sense of the art, e. g. an RNA polymerase binding site. The promoter may contain an enhancer element. The term "enhancer" includes a DNA sequence which binds to other protein components of the transcription initiation complex and thus facilitates the initiation of transcription directed by its associated promoter. The term "cell" includes any suitable organism. The cell may comprise a mammalian cell, such as a human cell.

The term "transformed cell" means a cell having a modified genetic structure. For example, as described here, a cell has a modified genetic structure when a vector such as an expression vector has been introduced into the cell. The term "organism" includes any suitable organism. The organism may comprise a mammal such as a human. Here the term "transgenic organism" means an organism comprising a modified genetic structure. For example, the organism may have a modified genetic structure if a vector such as an expression vector has been introduced into the organism.

ANTIBODY EXPRESSION

We further describe a method comprising transforming a host cell with a nucleic acid sequence capable of expressing an anti-MMP9 ovarian cancer biomarker antibody.

We also provide a method comprising culturing a transformed host cell-which cell has been transformed with a or the such nucleotide sequences under conditions suitable for the expression of the anti-MMP9 ovarian cancer biomarker antibody encoded by said nucleotide sequences. We further provide a method comprising culturing a transformed host cell-which cell has been transformed with a or the such nucleotide sequences under conditions suitable for the expression of the anti-MMP9 ovarian cancer biomarker antibody encoded by said nucleotide sequences; and then recovering said anti-MMP9 ovarian cancer biomarker antibody from the transformed host cell culture.

Thus, anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences, fusion proteins or functional equivalents thereof, may be used to generate recombinant DNA molecules that direct the expression thereof in appropriate host cells.

By way of example, anti-MMP9 ovarian cancer biomarker antibody may be produced in recombinant E. coli, yeast or mammalian expression systems, and purified with column chromatography.

In certain circumstances there are advantages of using antibody fragments, rather than whole antibodies. The smaller size of the fragments allows for rapid clearance, and may lead to improve tumour to non-tumour ratios. Fab, Fv, ScFv antibody fragments can all be expressed in and secreted from E. coli, thus allowing the production of large amounts of the such fragments.

The nucleotide sequences encoding the anti-MMP9 ovarian cancer biomarker antibody may be operably linked to a promoter sequence capable of directing expression of the anti- MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences in a suitable host cell. When inserted into the host cell, the transformed host cell may be cultured under suitable conditions until sufficient levels of the anti-MMP9 ovarian cancer biomarker antibody are achieved after which the cells may be lysed and the anti-MMP9 ovarian cancer biomarker antibody is isolated.

Host cells transformed with the anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences may be cultured under conditions suitable for the expression and recovery of the anti-MMP9 ovarian cancer biomarker antibody from cell culture. The protein produced by a recombinant cell may be secreted or may be contained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing the Anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences can be designed with signal sequences which direct secretion of the anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences through a particular prokaryotic or eukaryotic cell membrane. Other recombinant constructions may join the anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequence to a nucleotide sequence encoding a polypeptide domain which will facilitate purification of soluble proteins (Kroll DJ et al(1993) DNA Cell Biol 12:441- 5 3', see also the discussion below on vectors containing fusion proteins).

The anti-MMP9 ovarian cancer biomarker antibody may also be expressed as a recombinant protein with one or more additional polypeptide domains added to facilitate protein purification. Such purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals (Porath J (1992) Protein Expr Purif 3-26328 1), protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex Corp, Seattle, WA). The inclusion of a cleavable linker sequence such as Factor XA or enterokinase (Invitrogen, San Diego, CA) between the purification domain and the anti-MMP9 ovarian cancer biomarker antibody is useful to facilitate purification.

The nucleotide sequences described here may be engineered in order to alter a the anti- MMP9 ovarian cancer biomarker antibody encoding sequences for a variety of reasons, including but not limited to alterations which modify the cloning, processing and/or expression of the gene product. For example, mutations may be introduced using techniques which are well known in the art, e.g., site-directed mutagenesis to insert new restriction sites, to alter glycosylation patterns or to change codon preference. In another embodiment, a or the natural, modified or recombinant anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences may be ligated to a heterologous sequence to encode a fusion protein. By way of example, fusion proteins comprising the anti- MMP9 ovarian cancer biomarker antibody or an enzymatically active fragment or derivative thereof linked to an affinity tag such as glutathione-S-transferase (GST), biotin, His6, ac-myc tag (see Emrich etal 1993 BiocemBiophys Res Commun 197(1): 21220), hemagglutinin (HA) (as described in Wilson et al (1984 Cell 37 767) or a FLAG epitope (Ford etal 1991 Protein Expr Purif Apr; 2 (2):95-107). May be produced The fused recombinant protein may comprise an antigenic coprotein such as GST, b eta-gal acto si dase or the lipoprotein D from Haemophilus influenzae which are relatively large co-proteins, which solubilise and facilitate production and purification thereof.

Alternatively, the fused protein may comprise a carrier protein such as bovine serum albumin (BSA) or keyhole limpet haemocyanin (KLH). In certain embodiments, the marker sequence may comprise a hexa-histidine peptide, as provided in the pQE vector (Qiagen Inc) and described in Gentz et al (1989 PNAS 86: 821-824). Such fusion proteins are readily expressable in yeast culture (as described in Mitchell et al 1993 Yeast 5:715-723) and are easily purified by affinity chromatography. A fusion protein may also be engineered to contain a cleavage site located between the nucleotide sequence encoding the anti-MMP9 ovarian cancer biomarker antibody and the heterologous protein sequence, so that the anti- MMP9 ovarian cancer biomarker antibody may be cleaved and purified away from the heterologous moiety. In another embodiment, an assay for the target protein may be conducted using the entire, bound fusion protein. Alternatively, the co-protein may act as an adjuvant in the sense of providing a generalised stimulation of the immune system. The co-protein may be attached to either the amino or carboxy terminus of the first protein.

Although the presence/absence of marker gene expression suggests that the nucleotide sequence for anti-MMP9 ovarian cancer biomarker antibody is also present, its presence and expression should be confirmed. For example, if the anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequence is inserted within a marker gene sequence, recombinant cells containing the anti-MMP9 ovarian cancer biomarker antibody coding regions may be identified by the absence of the marker gene function. Alternatively, a marker gene may be placed in tandem with a anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequence under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the anti-MMP9 ovarian cancer biomarker antibody as well.

Additional methods to quantitate the expression of a particular molecule include radiolabeling (Melby PC etal 1993 J Immunol Methods 159:235-44) or biotinylating (Duplaa C et al 1993 Anal Biochem229-36) nucleotides, co amplification of a control nucleic acid, and standard curves onto which the experimental results are interpolated. Quantitation of multiple samples may be speeded up by running the assay in an ELISA format where the anti-MMP9 ovarian cancer biomarker antibody of interest is presented in various dilutions and a spectrophotometric or calorimetric response gives rapid quantitation.

Altered anti-MMP9 ovarian cancer biomarker antibody nucleotide sequences which may be made or used include deletions, insertions or substitutions of different nucleotide residues resulting in a nucleotide sequence that encodes the same or a functionally equivalent anti-MMP9 ovarian cancer biomarker antibody. By way of example, the expressed anti- MMP9 ovarian cancer biomarker antibody may also have deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent anti-MMP9 ovarian cancer biomarker antibody. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity. and/or the amphipathic nature of the residues as long as the binding affinity of the anti-MMP9 ovarian cancer biomarker antibody is retained. For example, negatively charged amino acids include aspartic acid and glutamic acid: positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine, valine, glycine, alanine, asparagine, glutamine, serine, threonine, phenylalanine, and tvrosine.

Gene therapy whereby the anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences as described here is regulated in vivo may also be employed. For example, expression regulation may be accomplished by administering compounds that bind to the anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences, or control regions associated with the anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequence or its corresponding RNA transcript to modify the rate of transcription or translation.

By way of example, the anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences described here may be under the expression control of an expression regulatory element, usually a promoter or a promoter and enhancer. The enhancer and/or promoter may be preferentially active in a hypoxic or ischaemic or low glucose environment, such that the anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences is preferentially expressed in the particular tissues of interest, such as in the environment of a tumour cell or mass. Thus, any significant biological effect or deleterious effect of the anti- MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences on the individual being treated may be reduced or eliminated. The enhancer element or other elements conferring regulated expression may be present in multiple copies.

The promoter and/or enhancer may be constitutively efficient, or may be tissue or temporally restricted in their activity. Examples of suitable tissue restricted

promoters/enhancers are those which are highly active in tumour cells such as a

promoter/enhancer from a MUC1 gene, a CEA gene or a STV antigen gene. Examples of temporally restricted promoters/enhancers are those which are responsive to ischaemia and/or hypoxia, such as hypoxia response elements or the promoter/enhancer of agrp78 or agrp94 gene. The alpha fetoprotein (AFP) promoter is also a tumour-specific promoter. Another promoter-enhancer combination is a human cytomegalovirus (hCMV) major immediate early (MIE) promoter/enhancer combination.

The promoters may be tissue specific. That is, they may be capable of driving transcription of a anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences in one tissue while remaining largely "silent" in other tissue types. The term "tissue specific" means a promoter which is not restricted in activity to a single tissue type but which nevertheless shows selectivity in that they may be active in one group of tissues and less active or silent in another group. A desirable characteristic of such promoters is that they possess a relatively low activity in the absence of activated hypoxia- regulated enhancer elements, even in the target tissue. One means of achieving this is to use "silencer" elements which suppress the activity of a selected promoter in the absence of hypoxia.

The term "hypoxia" means a condition under which a particular organ or tissue receives an inadequate supply of oxygen.

The level of expression of a or the anti-MMP9 ovarian cancer biomarker antibody encoding nucleotide sequences under the control of a particular promoter may be modulated by manipulating the promoter region. For example, different domains within a promoter region may possess different gene regulatory activities. The roles of these different regions are typically assessed using vector constructs having different variants of the promoter with specific regions deleted (that is, deletion analysis). This approach may be used to identify, for example, the smallest region capable of conferring tissue specificity or the smallest region conferring hypoxia sensitivity. A number of tissue specific promoters, described above, may be used. In most instances, these promoters may be isolated as convenient restriction digestion fragments suitable for cloning in a selected vector. Alternatively, promoter fragments may be isolated using the polymerase chain reaction. Cloning of the amplified fragments may be facilitated by incorporating restriction sites at the 5' end of the primers.

EXAMPLES

Example 1. Materials and Methods

Women aged 21 to 85 who have pre-op ultrasound, CT or MRI suggestive of an ovarian tumour or cyst and did not have chemotherapy or surgery yet were recruited over a period of 12 months at KK Gynaecological Cancer Centre (GCC) and Gynaecol ogical- oncology wards of KK Women's & Children's Hospital (KKH), Singapore.

Patients who had physiological, simple, corpus luteum or endometrioid cyst, or cancer recurrence, previous treatment with chemotherapy, radiation and/or surgery were excluded.

The recruitment and enrolment of the patients was approved by the SingHealth Centralized Institutional Review Board (ref no: CIRB 2014/708/D).

A total of 37 patients were recruited: 15 patients with benign cyst and 22 patients with cancer. Peripheral blood from each patient was collected in EDTA vacutainer tubes, centrifuged and the plasma was stored at -80°C until analysis.

Table El. Age distribution of study cohort (37 patients).

For analysis of MMP9, the plasma was first extracted for CTB-EVs or AV-EVs. Then plasma, CTB-EVs and AV-EVs were analysed by sandwich Enzyme Link Immunosorbent Assay (ELISA) for MMP9.

CTB-EVs and AV-EVs were extracted as previously described[2]. Briefly, 30 μΐ. plasma sample was incubated with 150 ng biotinylated CTB or 150 ng biotinylated AV in l00μL· Binding Buffer (0.1M Hepes, 1.4M NaCl, and 25 mM CaCl₂) at room for 30 minutes and then with 20 μΐ. of PBS-washed Streptavidin Coated Polystyrene Particles (Spherotech) for another 30 minutes at room temperature.

The beads were removed, washed thrice with 200 μΐ PBS and then incubated with 200 μΐ. of Lysis Buffer (Biovision) for another 30 minutes at room temperature.

The plasma, CTB-EVs and AV-EVs are then assayed for MMP9 sandwich ELISA kits (catalogue number ELH-MMP9-1, RayBiotech, Inc., Georgia, USA) as per manufacturer's instructions. Statistical analysis were performed using Mann-Whitney U test.

Example 2. Results

The results are shown in Figure 1.

The level of MMP9 in plasma and CTB-EVs in patients with benign ovarian cysts was not significantly different from those with ovarian cancers.

However, MMP9 level in AV-EVs from patients with ovarian cancer was significantly higher than that in patients with benign ovarian cyst (1134.6 ± 174.6 versus 699.8 ± 69.9pg/ml plasma, respectively p=0.0051).

REFERENCES

1. Bast, R.C., B. Hennessy, and G.B. Mills, The biology of ovarian cancer: new opportunities for translation. Nat Rev Cancer, 2009. 9(6): p. 415-428.

2. Tan, K.H., et al., Plasma biomarker discovery in preeclampsia using a novel differential isolation technology for circulating extracellular vesicles. Am J Obstet Gynecol, 2014. 211(4): p. 380 el-13.

Lai et al (2016). MSC Secretes at Least 3 EV Types Each with a Unique Permutation of Membrane Lipid, Protein andRNA. Journal of Extracellular Vesicles 2016, 5: 29828.

In this document and in its claims, the verb "to comprise" and its conjugations is used in its non-limiting sense to mean that items following the word are included, but items not specifically mentioned are not excluded. In addition, reference to an element by the indefinite article "a" or "an" does not exclude the possibility that more than one of the element is present, unless the context clearly requires that there be one and only one of the elements. The indefinite article "a" or "an" thus usually means "at least one".

Each of the applications and patents mentioned in this document, and each document cited or referenced in each of the above applications and patents, including during the prosecution of each of the applications and patents ("application cited documents") and any manufacturer's instructions or catalogues for any products cited or mentioned in each of the applications and patents and in any of the application cited documents, are hereby

incorporated herein by reference. Furthermore, all documents cited in this text, and all documents cited or referenced in documents cited in this text, and any manufacturer's instructions or catalogues for any products cited or mentioned in this text, are hereby incorporated herein by reference.

Various modifications and variations of the described methods and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in molecular biology or related fields are intended to be within the scope of the claims.

Claims

1. A method of detecting ovarian cancer in an individual, the method comprising detecting the level of expression, activity or amount of a MMP9 polypeptide (GenBank Accession Number: NP_004985-2) in an Annexin V binding microparticle in a sample of or from an individual suspected to be suffering from ovarian cancer.

2. A method according to Claim 1, further comprising comparing the level of expression, activity or amount of a MMP9 polypeptide in an Annexin V binding microparticle in a sample of or from an individual known not to be suffering from ovarian cancer or an individual who has benign ovarian cyst.

3. A method according to Claim 1 or 2, in which a higher level of expression, activity or amount of MMP9 polypeptide indicates that the individual is suffering from, or is likely to be suffering from, ovarian cancer.

4. A method according to Claim 1, 2 or 3, comprising detecting a level of expression, activity or amount of a MMP9 polypeptide in an Annexin V binding microparticle of 650 picogram per ml plasma or more.

5. A method according to any preceding claim, in which the level of expression, amount or activity of the MMP9 polypeptide in an Annexin V binding microparticle is increased by 5% or more, 10% or more, 15% or more, 20% or more, 25% or more, 30% or more, 35% or more, 40% or more, 45% or more, 50% or more, 55% or more, 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more or 100% or more.

6. A method according to any preceding claim, which further comprises a step of normalising the level, concentration or amount of the selected polypeptide between two or more samples, in which the normalisation is preferably conducted with reference to beta actin polypeptide (GenBank Accession Number: NP_001092; NCBI reference sequence:

NM_001101.4).

7. A method according to any preceding claim: (a) which further comprises a step of selecting microparticles by size, for example, by size exclusion chromatography; (b) in which the microparticles comprise CD9+ microparticles; (c) in which the sample is selected from the group consisting of: urine, blood, tears, saliva, bronchoaveolar fluid, tumoral effusions, amniotic fluid and milk; or (d) in which the microparticles comprise microvesicles, exosomes, ectosomes or apoptotic bodies.

8. A method of monitoring the progress of an individual suffering from ovarian cancer, the method comprising monitoring the modulation of expression of a MMP9 polypeptide in a cell, tissue or organ of the individual by a method according to any preceding claim.

9. A method of prognosis of an individual suffering from ovarian cancer, the method comprising detecting modulation of expression of a MMP9 polypeptide in a cell, tissue or organ of the individual by a method according to any of Claims 1 to 7.

10. A method of choosing a therapy for an individual suffering from ovarian cancer, the method comprising detecting modulation of expression of MMP9 polypeptide in a cell, tissue or organ of the individual by a method according to any of Claims 1 to 7 and choosing an appropriate therapy based on the severity of the ovarian cancer.

11. A method of determining the likelihood of success of a particular therapy in an individual suffering from ovarian cancer, the method comprising comparing the therapy with a therapy determined by a method according to Claim 10.

12. A method according to Claim 10 or 11, in which the therapy comprises:

(a) a chemotherapeutic drug such as Albumin bound paclitaxel (nab-paclitaxel,

Abraxane®), Altretamine (Hexalen®), Capecitabine (Xeloda®),

Cyclophosphamide (Cytoxan®), Etoposide (VP- 16), Gemcitabine (Gemzar®), Ifosfamide (If ex®), Irinotecan (CPT-11, Camptosar®), Liposomal doxorubicin

(Doxil®), Melphalan, Pemetrexed (Alimta®), Topotecan, Vinorelbine (Navelbine®);

(b) radiation therapy, such as external beam radiation therapy;

(c) surgery, such as debulking, total abdominal hysterectomy (TAH) and bilateral salpingo oophorectomy (BSO);

(d) hormone therapy or hormone blocking therapy such as Luteinizing-hormone- releasing hormone (LHRH) agonists; or

(e) targeted therapy such as Bevacizumab (Avastin®) or Olaparib (Lynparza™).

13. A kit for detecting ovarian cancer in an individual or susceptibility of the individual to ovarian cancer comprising means for detection of MMP9 polypeptide expression, activity or amount in a microparticle of or from the individual or a sample taken from him or her, preferably further comprising a therapeutic drug for treatment, prophylaxis or alleviation of ovarian cancer, such as a chemotherapeutic drug such as Albumin bound paclitaxel (nab- paclitaxel, Abraxane®), Altretamine (Hexalen®), Capecitabine (Xeloda®),

Cyclophosphamide (Cytoxan®), Etoposide (VP- 16), Gemcitabine (Gemzar®), Ifosfamide (Ifex®), Irinotecan (CPT-11, Camptosar®), Liposomal doxorubicin (Doxil®), Melphalan, Pemetrexed (Alimta®), Topotecan, Vinorelbine (Navelbine®); a hormone therapy or hormone blocking therapy such as Luteinizing-hormone-releasing hormone (LHRH) agonists; or a targeted therapy such as Bevacizumab (Avastin®) or Olaparib (Lynparza™).