WO2014006160A1 - A mirna oncologic biomarker of breast cancer - Google Patents

A mirna oncologic biomarker of breast cancer Download PDF

Info

Publication number
WO2014006160A1
WO2014006160A1 PCT/EP2013/064188 EP2013064188W WO2014006160A1 WO 2014006160 A1 WO2014006160 A1 WO 2014006160A1 EP 2013064188 W EP2013064188 W EP 2013064188W WO 2014006160 A1 WO2014006160 A1 WO 2014006160A1
Authority
WO
WIPO (PCT)
Prior art keywords
mir
breast cancer
sample
kit
assay
Prior art date
Application number
PCT/EP2013/064188
Other languages
French (fr)
Inventor
Michael J. Kerin
Nicola Miller
Ailbhe McDermott
Original Assignee
National University Of Ireland, Galway
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by National University Of Ireland, Galway filed Critical National University Of Ireland, Galway
Priority to EP13733332.4A priority Critical patent/EP2870259B1/en
Priority to US14/412,174 priority patent/US20150141280A1/en
Publication of WO2014006160A1 publication Critical patent/WO2014006160A1/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/178—Oligonucleotides characterized by their use miRNA, siRNA or ncRNA

Definitions

  • the present invention relates to the diagnosis of breast cancers, in determining the prognosis of a breast cancer patient and prediction of a response to cancer treatment.
  • the goal of the invention is to allow early detection and diagnosis of breast cancers as well as individualised treatment for patients.
  • the markers are particularly suitable for the detection and assessment of Luminal A breast cancer.
  • Breast cancer is an extremely important disease in Irish Society. It is the most commonly diagnosed malignancy in Irish women (with over 2,600 new diagnoses annually), and accounts for the greatest number of cancer related deaths in women. With 1 in 8 Irish women being diagnosed with breast cancer, it is a disease which impacts, in some way, most peoples lives. Breast cancer is an extremely prevalent disease accounting for the greatest number of cancers diagnosed and the greatest number of deaths from cancer in women in Ireland. When diagnosed and treated early, breast cancer is a highly curable disease, and the past decade has witnessed major advances in its management. However, many women continue to die from this disease process as a consequence of late diagnosis, with incurable metastases at the time of presentation.
  • the focus of the invention is on the development of sensitive, specific, minimally invasive biomarkers for breast cancer that can be utilised to detect early tumours, as well as being applied to monitoring the response to treatment, and detecting disease recurrence.
  • MiR are a class of small, non-coding R A fragments that have captured the attention and innovation of the scientific community since their discovery almost twenty years ago. The discovery that MiRNAs are dysregulated in several disease processes, including carcinogenesis, has unveiled their putative role as disease-specific biomarkers and therapeutic targets.
  • MicroRNAs are a class of small non-coding RNA fragments that are ideal biomarker candidates and therapeutic targets.
  • MiRNAs have been demonstrated to play a key role in practically all aspects of the cell cycle. They function at a post-transcriptional level to cause either transcriptional cleavage or transcriptional repression. MiRNAs are abberently expressed in almost all pathological conditions, including carcinogenesis and have a putative role as oncogenes or tumour suppressor genes.
  • MiRNAs have the advantage that they can be detected in the systemic circulation, and thus diagnostic assay is based on miRNAs are not invasive.
  • Luminal A is the most common sub-type of breast cancer with over 70% of breast tumours falling into this category. Luminal A tumours are characterised by hormone receptor positivity (oestrogen receptor and progesterone receptor) and HERl/neu negativity. Women diagnosed with Luminal A tumours typically have a good prognosis, with a five year survival over 90%. However, with most breast tumours being Luminal A, it forms a good starting point on which to base a diagnostic test.
  • hormone receptor positivity oestrogen receptor and progesterone receptor
  • HERl/neu negativity Women diagnosed with Luminal A tumours typically have a good prognosis, with a five year survival over 90%. However, with most breast tumours being Luminal A, it forms a good starting point on which to base a diagnostic test.
  • kits comprising probes capable of binding to a combination of microR As which combination comprises all detectable
  • microRNAs stably existing in the serum or plasma of a patient.
  • Miyamoto and Ushijima XP002686872 describes an in vitro analysis of breast cancer cell lines to determine a global expression profile for a number of microRNAs.
  • MiRNA expression in cell lines cannot be directly correlated with expression in the bloodstream of a patient.
  • this paper shows over expression of miR-652 in the cell line whereas the present study shows under-expression of the same marker in whole blood.
  • Pigati et al PLOS ONE, vol. 5, issue 10, el3 15
  • report that released miRNAs do not necessarily reflect the abundance of miRNA in the cell of origin.
  • a diagnostic kit for the detection of breast cancer or to assist prognosis, or determine the efficacy of a treatment regime for breast cancer comprising at least one oligonucleotide probe capable of binding to at least a portion of a circulating miR A selected from the group comprising miR-181a and miR-652 biomarkers, and a receptacle for containing blood.
  • the receptacle may contain an anti-coagulant.
  • the kit may comprise an oligonucleotide probe capable of binding to at least a portion of a circulating miR-181a and an oligonucleotide probe capable of binding to at least a portion of the circulating miR-652.
  • the kit may be adapted for performance of an assay selected from a real-time PCR assay, a micro-array assay, histochemistry assay or an immunological assay.
  • the kit is particularly suited for use in Luminal A breast cancer detection or assessment.
  • the invention also provides a method of identifying a therapeutic agent capable of preventing or treating cancers, including breast cancer, comprising testing the ability of the potential therapeutic agent to enhance the expression of at least one circulating miRNA selected from the group comprising miR-181a and miR-652.
  • the invention provides for use of a circulating miRNA selected from miR-181a and miR-652 to detect breast cancer, to stratify patients according to expected prognosis or to assess the efficacy of a medical treatment.
  • the detection may be carried out in a blood sample or a sample derived from blood.
  • the invention also provides a method of detecting or screening for early stage breast cancers comprising analysing a sample of blood taken from a patient for the presence of one or more biomarkers selected from the group comprising miR-181a and miR-652, the presence of at least one of these miRNAs in the sample indicating the presence of breast cancer.
  • Figure 1 The validation cohort of the study. A group of forty-seven cancer patients were compared with a control group of forty-seven normal subjects.
  • Figure 2 Circulating miRNA Expression level showing there was no significant difference in expression levels between the two groups in 5 of the 7 miRNAs studied.
  • Figure 3 Circulating miR-181a Expression showing miR-181a was significantly down- regulated in the blood of women with breast cancer compared to those who do not have cancer.
  • Figure 4 Circulating miR-652 Expression showing miR-652 was significantly down- regulated in the blood of women with breast cancer compared to those who do not have cancer.
  • Figure 5 Circulating miR-181a and miR-652 Expression level Stage of Disease - An important trait in any biomarker is the ability to detect both early and late stage disease, both miR As were down-regulated in early and late stage disease.
  • Figure 7 Binary logistics regression analysis of a combination of miR-181a and miR- 652. Area under the curve is AUC 0.77 with a Sensitivity of 70% and a Specificity of 65%.
  • FISH fluorescence in situ hybridization
  • RNA concentration and integrity were analyzed respectively by conducting NanoDrop Spectrophotometry to evaluate the 260/280 ratio (NanoDrop ND-1000 Technologies Inc., DE, USA) and using the Agilent Bioanalyzer (Agilent Technologies, Germany).
  • Taqman miRNA assays were purchased from ABI (Applied Biosystems, Foster City, CA, USA) for each of the 7 miRNAs: miR-19b, miR-93, miR-181a, miR-182, miRSOla, miR-423-5p and miR-652.
  • Each RNA sample was reverse transcribed for each specific miRNA target primer, and real time quantitative polymerase chain reaction (RT-qPCR) was then conducted using the appropriate TaqMan miRNA primers and probes, as described by the manufacturer.
  • RT-qPCR real time quantitative polymerase chain reaction
  • lOOng of total RNA was reverse transcribed using MultiScribe, followed by RT-qPCR on a 7900 HR Fast Real-Time PCR System (Applied Biosystems).
  • RT-qPCR was performed in triplicate for each target miRNA, and for each RNA sample. Inter-assay controls and intra-assay controls were used throughout.
  • the cycle thresholds (Ct) for each sample in this cohort were normalized to miR-16, a validated endogenous control for use in breast cancer. MiRNA expression levels were determined using QBase Plus software. A group of forty-seven cancer patients were compared with a control group of forty- seven normal subjects. The validation cohort is shown in Figure 1.
  • the data generated from the validation phase was analysed using Minitab 16.0 for Windows. A log transformation of the miRNA expression level was performed, given the wide range of expression values. The t-test and ANOVA were used to compare miRNA expression levels between groups. Results with a p ⁇ 0.05 were considered to be statistically significant.
  • the expression profiles of miR-181a and miR-652 were used to generate a Receiver Operating Characteristic (ROC) curve.
  • Circulating miRNA expression level was determined as outlined above for 47 Luminal A samples and 47 control samples.
  • the patient demographic details are summarised in Figure 1.
  • Binary logistics regression analysis was performed in order to determine the accuracy of a combination of both miR-181a and miR-652 in predicting women with Luminal A breast cancer from controls, as shown in Figure 7.
  • the area under the curve (AUC) was 0.77, which models a combination of the sensitivity and specificity.
  • the sensitivity and specificity of the combination of miR-181a and miR-652 for distinguishing between those with cancer and the controls was 70% and 65%, respectively.
  • the two novel biomarkers identified in the present application provide a sensitivity and specificity profile which exceeds that of several current clinical biomarkers.
  • the words "comprises/comprising” and the words “having/including” when used herein with reference to the present invention are used to specify the presence of stated features, integers, steps or components but does not preclude the presence or addition of one or more other features, integers, steps, components or groups thereof. It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination.

Abstract

The invention provides methods of and diagnostic kits for the detection of breast cancer, in particular luminal A breast cancer, or to assist in assessing the prognosis, or determine the efficacy of a treatment regimen for breast cancer comprising at least one oligonucleotide probe capable of binding to at least a portion of a circulating miRNA selected from the group comprising the miR-181a and miR-652 biomarkers. The invention also provides methods of identifying a therapeutic agent capable of preventing or treating cancers, including breast cancer, comprising testing the ability of the potential therapeutic agent to enhance the expression of at least one protein selected from the group comprising miR-181a and miR-652.

Description

Title
A MIRNA ONCOLOGIC BIOMARKER OF BREAST CANCER
Field of the Invention
The present invention relates to the diagnosis of breast cancers, in determining the prognosis of a breast cancer patient and prediction of a response to cancer treatment. The goal of the invention is to allow early detection and diagnosis of breast cancers as well as individualised treatment for patients. The markers are particularly suitable for the detection and assessment of Luminal A breast cancer.
Background to the Invention
Breast cancer is an extremely important disease in Irish Society. It is the most commonly diagnosed malignancy in Irish women (with over 2,600 new diagnoses annually), and accounts for the greatest number of cancer related deaths in women. With 1 in 8 Irish women being diagnosed with breast cancer, it is a disease which impacts, in some way, most peoples lives. Breast cancer is an extremely prevalent disease accounting for the greatest number of cancers diagnosed and the greatest number of deaths from cancer in women in Ireland. When diagnosed and treated early, breast cancer is a highly curable disease, and the past decade has witnessed major advances in its management. However, many women continue to die from this disease process as a consequence of late diagnosis, with incurable metastases at the time of presentation. The focus of the invention is on the development of sensitive, specific, minimally invasive biomarkers for breast cancer that can be utilised to detect early tumours, as well as being applied to monitoring the response to treatment, and detecting disease recurrence. MiR As are a class of small, non-coding R A fragments that have captured the attention and innovation of the scientific community since their discovery almost twenty years ago. The discovery that MiRNAs are dysregulated in several disease processes, including carcinogenesis, has unveiled their putative role as disease-specific biomarkers and therapeutic targets.
Currently diagnosis of breast cancer involves a combination of clinical examination, radiological imaging and an invasive tissue biopsy, to provide histological confirmation. Mammography is currently considered the gold standard for diagnosis, yet it is not without its constraints, with both ionisation exposure and a false positive rate of up to 10%. Small curable early cancers can potentially be missed. When diagnosed promptly, women are more likely to have early stage disease, confined to the breast. These cases are amenable to breast conserving surgery. In cases where tumour cells have
metastasised to the lymph nodes at the time of diagnosis more extensive local surgery and auxiliary surgery (an auxiliary lymph node clearance is often required). This procedure carries the potential for severe complications, including lymphoedema, which impacts extensively on one's quality of life. More over, tumour cells in the lymph nodes may be an indicator of distant metastases elsewhere, that are undetectable by current strategies. Current practice demands that the majority of these women receive adjunct chemotherapy and/or hormonal therapies. The decision to commence such regiments should not be taken lightly as each of these treatment modalities has an associate cluster of adverse effects. The appropriateness of adjunct therapy is usually based on a culmination of histological and patient factors. Only two predicted markers are validated and routinely assessed in the management of breast cancer. One of these is Oestrogen Receptor (ER) status and the other is Her2/neureceptor status. These markers indicate that there is a likely benefit to be achieved from treatment with hormonal therapies or Trastuzumab, respectively.
MicroRNAs are a class of small non-coding RNA fragments that are ideal biomarker candidates and therapeutic targets. MiRNAs have been demonstrated to play a key role in practically all aspects of the cell cycle. They function at a post-transcriptional level to cause either transcriptional cleavage or transcriptional repression. MiRNAs are abberently expressed in almost all pathological conditions, including carcinogenesis and have a putative role as oncogenes or tumour suppressor genes. MiRNAs have the advantage that they can be detected in the systemic circulation, and thus diagnostic assay is based on miRNAs are not invasive.
The concept of breast screening is now accepted internationally and is associated with an improved outcome from breast cancer due to its earlier diagnosis. However, it is not without its drawbacks; a high proportion of lobular carcinomas are mammographically occult dense breasts make the interpretation of the mammogram difficult and there are high false negative rates. Therefore, the development of a blood based diagnostic tool would be a significant advantage as it would permit screening to begin at a younger age and could potentially successfully diagnose tumours which are not detectable by mammography. Over the past decade our understanding of breast cancer has advanced remarkably. It is a heterogeneous disease, with distinct molecular subtypes (Luminal A, Luminal B, HER2/neu over-expressing and Basal). Luminal A is the most common sub-type of breast cancer with over 70% of breast tumours falling into this category. Luminal A tumours are characterised by hormone receptor positivity (oestrogen receptor and progesterone receptor) and HERl/neu negativity. Women diagnosed with Luminal A tumours typically have a good prognosis, with a five year survival over 90%. However, with most breast tumours being Luminal A, it forms a good starting point on which to base a diagnostic test.
US patent application 2010/173288 describes kits comprising probes capable of binding to a combination of microR As which combination comprises all detectable
microRNAs stably existing in the serum or plasma of a patient.
Guo, Li- Juan et al, International Journal of Molecular Medecine, Spandidos
Publications, Gr, vol 30, no. 3, p680m to 686, describes a reduction in serum miR-181a in early stage breast cancer patients.
Miyamoto and Ushijima, XP002686872, describes an in vitro analysis of breast cancer cell lines to determine a global expression profile for a number of microRNAs. MiRNA expression in cell lines cannot be directly correlated with expression in the bloodstream of a patient. In particular, this paper shows over expression of miR-652 in the cell line whereas the present study shows under-expression of the same marker in whole blood. Furthermore, Pigati et al (PLOS ONE, vol. 5, issue 10, el3 15) report that released miRNAs do not necessarily reflect the abundance of miRNA in the cell of origin.
Object of the Invention
It is an objective of the present invention to identify novel biomarkers which could be used in the diagnosis, prognosis or prediction of response to medical treatment of breast cancer. It is a further objective to identify a minimally invasive marker for use as an adjunct in breast cancer diagnosis and/or assessment of response to treatment.
Summary of the Invention
According to the present invention there is provided a A diagnostic kit for the detection of breast cancer or to assist prognosis, or determine the efficacy of a treatment regime for breast cancer comprising at least one oligonucleotide probe capable of binding to at least a portion of a circulating miR A selected from the group comprising miR-181a and miR-652 biomarkers, and a receptacle for containing blood.
The receptacle may contain an anti-coagulant. The kit may comprise an oligonucleotide probe capable of binding to at least a portion of a circulating miR-181a and an oligonucleotide probe capable of binding to at least a portion of the circulating miR-652. The kit may be adapted for performance of an assay selected from a real-time PCR assay, a micro-array assay, histochemistry assay or an immunological assay.
The kit is particularly suited for use in Luminal A breast cancer detection or assessment. The invention also provides a method of identifying a therapeutic agent capable of preventing or treating cancers, including breast cancer, comprising testing the ability of the potential therapeutic agent to enhance the expression of at least one circulating miRNA selected from the group comprising miR-181a and miR-652.
In a still further aspect the invention provides for use of a circulating miRNA selected from miR-181a and miR-652 to detect breast cancer, to stratify patients according to expected prognosis or to assess the efficacy of a medical treatment.
In this use the detection may be carried out in a blood sample or a sample derived from blood.
The invention also provides a method of detecting or screening for early stage breast cancers comprising analysing a sample of blood taken from a patient for the presence of one or more biomarkers selected from the group comprising miR-181a and miR-652, the presence of at least one of these miRNAs in the sample indicating the presence of breast cancer.
Brief Description of the Drawings
Figure 1 - The validation cohort of the study. A group of forty-seven cancer patients were compared with a control group of forty-seven normal subjects.
Figure 2 - Circulating miRNA Expression level showing there was no significant difference in expression levels between the two groups in 5 of the 7 miRNAs studied. Figure 3 - Circulating miR-181a Expression showing miR-181a was significantly down- regulated in the blood of women with breast cancer compared to those who do not have cancer. Figure 4 - Circulating miR-652 Expression showing miR-652 was significantly down- regulated in the blood of women with breast cancer compared to those who do not have cancer.
Figure 5 -Circulating miR-181a and miR-652 Expression level Stage of Disease - An important trait in any biomarker is the ability to detect both early and late stage disease, both miR As were down-regulated in early and late stage disease.
Figure 6 - Correlation between
Figure imgf000006_0001
level and Invasive Tumour Size
Figure 7 - Binary logistics regression analysis of a combination of miR-181a and miR- 652. Area under the curve is AUC 0.77 with a Sensitivity of 70% and a Specificity of 65%.
Figure 8 - The two novel biomarkers of the present invention, in combination, provide a sensitivity and specificity profile which exceeds that of several current clinically used biomarkers. Detailed Description of the Invention
Seven miRNAs were evaluated for their utility as oncological biomarkers. These candidate markers were miR-181a, miRSOla, miR-182, miR-423-5p, miR-93, miR-652 and miR-19b. Ethical approval was obtained and written informed consent was obtained from all study participants in advance of blood sampling. Women with breast cancer were identified at the Symptomatic Breast Unit where they were referred by their General Practitioner for investigation of a newly palpable breast lesion, or other symptoms suggestive of malignancy. All women in the cancer group had Luminal A breast cancer which was confirmed by histology, immunohistochemistry and
fluorescence in situ hybridization (FISH). Demographic details and clinicopathological parameters were prospectively collected. Whole blood samples were prospectively collected from women with a new diagnosis of Luminal A breast cancer, at the time of diagnosis. Whole blood samples were also collected from healthy female volunteers who served as the control group. Venous non- fasting whole blood was collected in BD Vacutainer K2E blood bottles containing 18mg EDTA as an anticoagulant (BD- Plymouth), immediately transferred to the surgical laboratory and stored at minus 4°C until required. Total RNA was extracted from 1ml of room temperature whole blood using TRI Reagent BD technique (Molecular Research Centre, Inc). RNA concentration and integrity were analyzed respectively by conducting NanoDrop Spectrophotometry to evaluate the 260/280 ratio (NanoDrop ND-1000 Technologies Inc., DE, USA) and using the Agilent Bioanalyzer (Agilent Technologies, Germany).
Taqman miRNA assays were purchased from ABI (Applied Biosystems, Foster City, CA, USA) for each of the 7 miRNAs: miR-19b, miR-93, miR-181a, miR-182, miRSOla, miR-423-5p and miR-652. Each RNA sample was reverse transcribed for each specific miRNA target primer, and real time quantitative polymerase chain reaction (RT-qPCR) was then conducted using the appropriate TaqMan miRNA primers and probes, as described by the manufacturer. In brief, lOOng of total RNA was reverse transcribed using MultiScribe, followed by RT-qPCR on a 7900 HR Fast Real-Time PCR System (Applied Biosystems). RT-qPCR was performed in triplicate for each target miRNA, and for each RNA sample. Inter-assay controls and intra-assay controls were used throughout. The cycle thresholds (Ct) for each sample in this cohort were normalized to miR-16, a validated endogenous control for use in breast cancer. MiRNA expression levels were determined using QBase Plus software. A group of forty-seven cancer patients were compared with a control group of forty- seven normal subjects. The validation cohort is shown in Figure 1.
Validation Study Statistical Analysis
The data generated from the validation phase was analysed using Minitab 16.0 for Windows. A log transformation of the miRNA expression level was performed, given the wide range of expression values. The t-test and ANOVA were used to compare miRNA expression levels between groups. Results with a p<0.05 were considered to be statistically significant. The expression profiles of miR-181a and miR-652 were used to generate a Receiver Operating Characteristic (ROC) curve.
Results
Circulating miRNA expression level was determined as outlined above for 47 Luminal A samples and 47 control samples. The patient demographic details are summarised in Figure 1. There was no significant difference in expression levels between the two groups in five of the seven miRNAs; namely miRSOla miR-182, miR-423-5p, miR-93 and miR-19b, as shown in Figure 2. However, as shown in Figure 3, circulating miR- 181a was significantly down-regulated in the blood of women with breast cancer, compared to those who did not have cancer (p=0.005). Similarly, as shown in Figure 4, miR-652 was significantly down-regulated in the blood of women with breast cancer compared to those normal patients (p=0.001).
It is an important attribute of any biomarker that it is able to detect both early and late stage disease. As shown in figure 5, both miR-181a and miR-652 were down-regulated in both early and late stage disease. Figure 6 also shows that there is a correlation between the circulating expression level of miR-181a and invasive tumour size.
Binary logistics regression analysis was performed in order to determine the accuracy of a combination of both miR-181a and miR-652 in predicting women with Luminal A breast cancer from controls, as shown in Figure 7. The area under the curve (AUC) was 0.77, which models a combination of the sensitivity and specificity. The sensitivity and specificity of the combination of miR-181a and miR-652 for distinguishing between those with cancer and the controls was 70% and 65%, respectively.
As shown in Figure 8, the two novel biomarkers identified in the present application, in combination, provide a sensitivity and specificity profile which exceeds that of several current clinical biomarkers. The words "comprises/comprising" and the words "having/including" when used herein with reference to the present invention are used to specify the presence of stated features, integers, steps or components but does not preclude the presence or addition of one or more other features, integers, steps, components or groups thereof. It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination.

Claims

Claims
1. A diagnostic kit for the detection of breast cancer or to assist prognosis, or
determine the efficacy of a treatment regime for breast cancer comprising at least one oligonucleotide probe capable of binding to at least a portion of a circulating miRNA selected from the group comprising miR-181a and miR-652 biomarkers, and a receptacle for containing blood.
2. A kit as claimed in Claim 1 , wherein the receptacle contains an anti-coagulant.
3. A kit as claimed in any preceding claim comprising an oligonucleotide probe
capable of binding to at least a portion of a circulating miRNA-181a and an oligonucleotide probe capable of binding to at least a portion of the circulating miR-652.
4. A kit as claimed in any preceding claim adapted for performance of an assay
selected from a real-time PCR assay, a micro-array assay, histochemical assay or an immunological assay.
5. A kit as claimed in any preceding claim for use in detecting Luminal A breast cancer.
6. A method of identifying a therapeutic agent capable of preventing or treating cancers, including breast cancer, comprising testing the ability of the potential therapeutic agent to enhance the expression of at least one circulating miRNA selected from the group comprising miR-181a and miR-652.
7. Use of a circulating miRNA selected from miR-181a and miR-652 to detect breast cancer in a whole blood sample, to stratify patients according to expected prognosis or to assess the efficacy of a medical treatment.
8. Use of the circulating miRNA miR-652 to detect breast cancer, to stratify patients according to expected prognosis or to assess the efficacy of a medical treatment.
9. Use as claimed in Claim 8, wherein the detection is carried out in a blood sample or a sample derived from blood.
10. A method of detecting or screening for early stage breast cancers comprising analysing a sample of whole blood taken from a patient for the presence of one or more biomarkers selected from the group comprising miR-181a and miR-652, a decreased level of miR-181a or miR-652 in the sample, when compared to a control, indicating the presence of breast cancer in a patient.
11. A method of detecting or screening for luminal A breast cancer comprising
analysing a sample of whole blood taken from a patient for the presence of the combination of the biomarkers miR-181a and miR-652, a decreased level of miR- 181a and miR-652 in the sample, when compared to a control, indicating the presence of luminal A breast cancer in the patient.
PCT/EP2013/064188 2012-07-06 2013-07-04 A mirna oncologic biomarker of breast cancer WO2014006160A1 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP13733332.4A EP2870259B1 (en) 2012-07-06 2013-07-04 A mirna oncologic biomarker of breast cancer
US14/412,174 US20150141280A1 (en) 2012-07-06 2013-07-04 Mirna oncologic biomarker of breast cancer

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
EP12175354.5 2012-07-06
EP12175354.5A EP2682477A1 (en) 2012-07-06 2012-07-06 miR-181a and miR652 as oncologic biomarker of breast cancer

Publications (1)

Publication Number Publication Date
WO2014006160A1 true WO2014006160A1 (en) 2014-01-09

Family

ID=48745978

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2013/064188 WO2014006160A1 (en) 2012-07-06 2013-07-04 A mirna oncologic biomarker of breast cancer

Country Status (3)

Country Link
US (1) US20150141280A1 (en)
EP (2) EP2682477A1 (en)
WO (1) WO2014006160A1 (en)

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2016135168A1 (en) * 2015-02-24 2016-09-01 Ruprecht-Karls-Universität Heidelberg Biomarker panel for the detection of cancer
US9623040B2 (en) 2014-07-14 2017-04-18 The Board Of Trustees Of The Leland Stanford Junior University Immunomodulation by controlling expression levels of microRNAs in dendritic cells
EP3144395A4 (en) * 2014-03-13 2018-01-03 Universidad de Málaga Microrna signature as an indicator of the risk of early recurrence in patients with breast cancer
WO2018055093A1 (en) * 2016-09-22 2018-03-29 Hummingbird Diagnostics Gmbh Mirnas as non-invasive biomarkers for breast cancer

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN115762801B (en) * 2022-05-13 2024-01-23 中国医学科学院肿瘤医院 Peripheral blood lipid metabolism biomarker for predicting new adjuvant therapy response of breast cancer and application

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100173288A1 (en) 2007-11-02 2010-07-08 Chenyu Zhang Serum/plasma micronas and uses thereof
CN101921760A (en) * 2010-09-08 2010-12-22 南京医科大学 Serum/plasma miRNA marker associated with breast cancer and application thereof
US20120040353A1 (en) * 2010-03-11 2012-02-16 National University Of Ireland, Gaway Detection and quantification of microRNAs in the circulation and the use of circulating microRNAs as biomarkers in cancer
US20120115929A1 (en) * 2009-04-29 2012-05-10 Esther Elisa Johanna Maria Creemers Means And Methods For Counteracting, Preventing And/Or Determining Heart Failure, Or A Risk Of Heart Failure

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2354246A1 (en) * 2010-02-05 2011-08-10 febit holding GmbH miRNA in the diagnosis of ovarian cancer

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100173288A1 (en) 2007-11-02 2010-07-08 Chenyu Zhang Serum/plasma micronas and uses thereof
US20120115929A1 (en) * 2009-04-29 2012-05-10 Esther Elisa Johanna Maria Creemers Means And Methods For Counteracting, Preventing And/Or Determining Heart Failure, Or A Risk Of Heart Failure
US20120040353A1 (en) * 2010-03-11 2012-02-16 National University Of Ireland, Gaway Detection and quantification of microRNAs in the circulation and the use of circulating microRNAs as biomarkers in cancer
CN101921760A (en) * 2010-09-08 2010-12-22 南京医科大学 Serum/plasma miRNA marker associated with breast cancer and application thereof

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
GUO LI-JUAN ET AL: "Decreased serum miR-181a is a potential new tool for breast cancer screening", INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE, SPANDIDOS PUBLICATIONS, GR, vol. 30, no. 3, 11 June 2012 (2012-06-11), pages 680 - 686, XP009164422, ISSN: 1107-3756 *
GUO, LI-JUAN ET AL.: "International Journal of Molecular Medecine", vol. 30, SPANDIDOS PUBLICATIONS, pages: 680M - 686
K MIYAMOTO AND T USHIJIMA: "MicroRNAs and epigenetics in human breast cancer", 2009, XP002686872, Retrieved from the Internet <URL:http://hwmaint.cancerres.aacrjournals.org/cgi/content/meeting_abstract/69/2_MeetingAbstracts/4051> [retrieved on 20121112] *
PIGATI ET AL., PLOS ONE, vol. 5, no. 10, pages E13515
PIGATI LUCY ET AL: "Selective release of microRNA species from normal and malignant mammary epithelial cells.", PLOS ONE, vol. 5, no. 10, E13515, 20 October 2010 (2010-10-20), pages 1 - 13, XP002686873, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0013515 *

Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3144395A4 (en) * 2014-03-13 2018-01-03 Universidad de Málaga Microrna signature as an indicator of the risk of early recurrence in patients with breast cancer
US9623040B2 (en) 2014-07-14 2017-04-18 The Board Of Trustees Of The Leland Stanford Junior University Immunomodulation by controlling expression levels of microRNAs in dendritic cells
WO2016135168A1 (en) * 2015-02-24 2016-09-01 Ruprecht-Karls-Universität Heidelberg Biomarker panel for the detection of cancer
US10941451B2 (en) 2015-02-24 2021-03-09 Ruprecht-Karls-Universitat Heidelberg Biomarker panel for the detection of cancer
EA037995B1 (en) * 2015-02-24 2021-06-21 Рупрехт-Карлс-Университет Гейдельберг Biomarker panel for the detection of cancer
WO2018055093A1 (en) * 2016-09-22 2018-03-29 Hummingbird Diagnostics Gmbh Mirnas as non-invasive biomarkers for breast cancer

Also Published As

Publication number Publication date
EP2870259A1 (en) 2015-05-13
EP2682477A1 (en) 2014-01-08
EP2870259B1 (en) 2017-12-27
US20150141280A1 (en) 2015-05-21

Similar Documents

Publication Publication Date Title
JP6246845B2 (en) Methods for quantifying prostate cancer prognosis using gene expression
Agell et al. A 12-gene expression signature is associated with aggressive histological in prostate cancer: SEC14L1 and TCEB1 genes are potential markers of progression
EP2870259B1 (en) A mirna oncologic biomarker of breast cancer
Brand et al. A microRNA-based test improves endoscopic ultrasound–guided cytologic diagnosis of pancreatic cancer
Wu et al. The analysis of cell-free DNA concentrations and integrity in serum of initial and treated of lymphoma patients
CN115094141A (en) Compositions and methods for determining prognosis of endometrial cancer
Lasham et al. A predictor of early disease recurrence in patients with breast cancer using a cell-free RNA and protein liquid biopsy
Constâncio et al. MiRNA biomarkers in cancers of the male reproductive system: are we approaching clinical application?
Syed et al. Current management strategy for active surveillance in prostate cancer
Lerebours et al. Hemoglobin overexpression and splice signature as new features of inflammatory breast cancer?
Yadav et al. Identification of suitable reference genes in blood samples of carcinoma lung patients using quantitative real-time polymerase chain reaction
Pavlov et al. Circulating miRNAs in patients with Barrett’s esophagus, high-grade dysplasia and esophageal adenocarcinoma
CN108424962B (en) MiRNA detection marker for mesangial proliferative glomerulonephritis and diagnostic kit thereof
Chavarriaga et al. miRNAs for testicular germ cell tumours: Contemporary indications for diagnosis, surveillance and follow‐up
EP3548631A1 (en) Risk scores based on human phosphodiesterase 4d variant 7 expression
US9777334B2 (en) Cancer blood test using BC200 RNA isolated from peripheral blood for diagnosis and treatment of invasive breast cancer
WO2019245587A1 (en) Methods and compositions for the analysis of cancer biomarkers
US20120184452A1 (en) Methods for diagnosing follicular thyroid cancer
CN110592223B (en) Application of diagnostic and prognostic marker hsa _ circRNA _012515 for NSCLC
Lyle et al. Molecular grading of tumors of the upper urothelial tract using FGFR3 mutation status identifies patients with favorable prognosis
US20160194719A1 (en) A biomarker of breast cancer
CN110951865B (en) Placenta-implanted disease marker
CN110951863B (en) Placenta-implanted disease marker
Hall et al. Role of Liquid Biopsy in Clinical Decision-Making for Breast Cancer
US20210269883A1 (en) PREDICTIVE AND PROGNOSTIC USE OF A miRNA FOR HIGH GRADE SEROUS OVARIAN CARCINOMA THERAPEUTIC CARE

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 13733332

Country of ref document: EP

Kind code of ref document: A1

WWE Wipo information: entry into national phase

Ref document number: 2013733332

Country of ref document: EP

WWE Wipo information: entry into national phase

Ref document number: 14412174

Country of ref document: US

NENP Non-entry into the national phase

Ref country code: DE