Patent Application
20170044617
The present invention relates to methods for detecting brain cancer in a subject. The invention also relates to methods of predicting a clinical outcome in a patient with brain cancer; methods of monitoring the progression of brain cancer in a patient; and methods of grading a patient's brain cancer.
In 2010, there were 9,156 new cases of brain cancer in the UK alone (Cancer Research UK). Worldwide it is estimated that there are 445,000 new cases of brain cancer every year (Cancer Research UK). As the population grows every year, so the incidence of brain cancer will follow, highlighting the need for improved diagnosis, prognosis and prediction of response to treatment. This invention has the potential to fulfil this need both in the UK and worldwide.
Current diagnosis of glioma involves imaging with MRI and histological analysis by neuropathology. In some cases MRI scans are not accurate enough to definitively diagnose an individual, following this histological analysis is required. Histological analysis can only be performed following removal of tumour tissue during surgery and it is extremely subjective depending on the interpretations of individual pathologists. A risky and invasive procedure for patients, especially as there is a high incidence of glioma in older individuals who present a higher risk when undergoing surgery.
MicroRNAs (miRNA) are small non-coding RNAs which play a role in post-transcriptional regulation of gene and protein expression. MiRNAs exhibit disease specific expression, which can be used to provide information about a particular biological state, such as glioma. Changes in miRNA expression in gliomas can be measured following the isolation of glioma specific exosomes released into the circulation. The aim of this study is to identify a panel of miRNAs which have an altered expression in glioma and can be used for diagnosis, prognosis and the prediction of response to treatment.
In a first aspect, the invention provides a method of detecting brain cancer in a subject, the method comprising:
assaying a sample from the subject to determine the amount of at least one miRNA, selected from the group consisting of: Hsa-miR-20a-5p; Hsa-miR-34a-5p; Hsa-miR-92a-3p hsa-miR-15b; hsa-miR-181b; hsa-miR-19a; hsa-miR-210; hsa-miR-23a; hsa-miR-15a; hsa-miR-181a; hsa-miR-21; hsa-miR-222; hsa-miR-26a; hsa-miR-29c; hsa-miR-101-3p; hsa-miR-29b-3p; hsa-miR-328; hsa-miR-9-5p; Hsa-miR-106b-5p; Hsa-miR-107; Hsa-miR-125a-5p; Hsa-miR-128; Hsa-miR-130b-3p; Hsa-miR-132-3p; Hsa-miR-138-5p; Hsa-miR-141-3p; Hsa-miR-146a-5p; Hsa-miR-148a-3p; Hsa-miR-16-5p; Hsa-miR-17-5p; Hsa-miR-17-3p; Hsa-miR-182-5p; Hsa-miR-183-5p; Hsa-miR-187-3p; Hsa-miR-18a-5p; Hsa-miR-190a; Hsa-miR-19b-3p; Hsa-miR-200a-3p; Hsa-miR-203a; Hsa-miR-31-5p; Hsa-miR-326; Hsa-miR-425-5p; Hsa-miR-7-5p; Hsa-miR-93-5p; Hsa-miR-96-5p; Hsa-let-7b-5p; Hsa-miR-106b-5p; Hsa-miR-191-5p; Hsa-miR-24-3p; Hsa-miR-25-3p; Hsa-miR-320a; Hsa-miR-486-5p; and Hsa-miR-451a;, present in the sample;
comparing the amount of the at least one miRNA present in the sample with a reference value;
wherein a difference in the amount of at the least one miRNA in the sample, as compared to the reference value, indicates that the subject has brain cancer.
This first aspect of the present invention is based upon the inventors' finding that the miRNAs referred to above have a change in abundance in samples that are representative of brain cancer (either being taken from individuals that have brain cancers, or from cell culture models of brain cancer) as compared to subjects without brain cancer (or models using non-cancerous brain cells). Indeed, as discussed in more detail elsewhere in the present disclosure, the inventors have found that the miRNAs referred to are present in quantities that are multiple times (“fold” increases) higher or lower than those found in non-cancerous reference samples.
In a second aspect of the invention, there is provided a method of predicting a clinical outcome in a patient with brain cancer, the method comprising:
assaying a sample from the patient for the presence of at least one miRNA selected from the group consisting of: Hsa-miR-20a-5p; Hsa-miR-34a-5p; Hsa-miR-92a-3p hsa-miR-15b; hsa-miR-181b; hsa-miR-19a; hsa-miR-210; hsa-miR-23a; hsa-miR-15a; hsa-miR-181a; hsa-miR-21; hsa-miR-222; hsa-miR-26a; hsa-miR-29c; hsa-miR-101-3p; hsa-miR-29b-3p; hsa-miR-328; hsa-miR-9-5p; Hsa-miR-106b-5p; Hsa-miR-107; Hsa-miR-125a-5p; Hsa-miR-128; Hsa-miR-130b-3p; Hsa-miR-132-3p; Hsa-miR-138-5p; Hsa-miR-141-3p; Hsa-miR-146a-5p; Hsa-miR-148a-3p; Hsa-miR-16-5p; Hsa-miR-17-5p; Hsa-miR-17-3p ; Hsa-miR-182-5p; Hsa-miR-183-5p; Hsa-miR-187-3p; Hsa-miR-18a-5p; Hsa-miR-190a; Hsa-miR-19b-3p; Hsa-miR-200a-3p; Hsa-miR-203a; Hsa-miR-31-5p; Hsa-miR-326; Hsa-miR-425-5p; Hsa-miR-7-5p; Hsa-miR-93-5p; Hsa-miR-96-5p; Hsa-let-7b-5p; Hsa-miR-106b-5p; Hsa-miR-191-5p; Hsa-miR-24-3p; Hsa-miR-25-3p; Hsa-miR-320a; Hsa-miR-486-5p; and Hsa-miR-451a;
comparing the amount of the at least one miRNA present in the sample with a reference value;
wherein a difference in the amount of at the least one miRNA in the sample, as compared to the reference value, indicates a negative outcome in respect of the patient's brain cancer.
This second aspect of the present invention is based upon the inventors' finding of the link between the miRNAs referred and the presence of brain cancer. This finding allows the investigation of the miRNAs to above provide an indication as to the likely progression of a patient's brain cancer, and accordingly the clinical outcome that may be expected. In particular, the inventors have found that changes in the abundance of these miRNA markers in the manners set out below are generally associated with a negative outcome in respect of the patient's brain cancer.
Techniques for use in the diagnosis, prognosis and monitoring of brain cancers currently typically use an approach of imaging, such as MRI techniques, followed by confirmatory histological analysis.
The inventors believe that the panel of miRNA biomarkers identified herein may be of benefit in the grading of brain cancers such as gliomas.
In a third aspect the invention provides a method of monitoring the progression of brain cancer in a patient, the method comprising:
assaying a first sample from the patient, indicative of miRNA in the patient at a first timepoint, for the presence of at least one miRNA selected from the group consisting of: hsa-Hsa-miR-20a-5p; Hsa-miR-34a-5p; Hsa-miR-92a-3p hsa-miR-15b; hsa-miR-181b; hsa-miR-19a; hsa-miR-210; hsa-miR-23a; hsa-miR-15a; hsa-miR-181a; hsa-miR-21; hsa-miR-222; hsa-miR-26a; hsa-miR-29c; miR-101-3p; hsa-miR-29b-3p; hsa-miR-328; hsa-miR-9-5p; Hsa-miR-106b-5p; Hsa-miR-107; Hsa-miR-125a-5p; Hsa-miR-128; Hsa-miR-130b-3p; Hsa-miR-132-3p; Hsa-miR-138-5p; Hsa-miR-141-3p; Hsa-miR-146a-5p; Hsa-miR-148a-3p; Hsa-miR-16-5p; Hsa-miR-17-5p; Hsa-miR-17-3p ; Hsa-miR-182-5p; Hsa-miR-183-5p; Hsa-miR-187-3p; Hsa-miR-18a-5p; Hsa-miR-190a; Hsa-miR-19b-3p; Hsa-miR-200a-3p; Hsa-miR-203a; Hsa-miR-31-5p; Hsa-miR-326; Hsa-miR-425-5p; Hsa-miR-7-5p; Hsa-miR-93-5p; Hsa-miR-96-5p; Hsa-let-7b-5p; Hsa-miR-106b-5p; Hsa-miR-191-5p; Hsa-miR-24-3p; Hsa-miR-25-3p; Hsa-miR-320a; Hsa-miR-486-5p; and Hsa-miR-451a; to determine a first value for the abundance of the at least one miRNA present in the sample;
and assaying a second sample from the patient, indicative of miRNA in the patient at a second timepoint, for the presence of the same at least one miRNA to determine a second value for the abundance of the at least one miRNA present in the second sample; and
comparing the first and second values for the abundance of the at least one miRNA;
wherein a difference between the first and second values indicates that there has been progression in respect of the patient's brain cancer.
When the miRNA investigated is one that is up-regulated in cancer as compared to reference values, then an increase in the second value as compared to the first value indicates that the progression of the brain cancer has been to worsen between the first and second timepoints.
When the miRNA investigated is one that is down-regulated in cancer as compared to reference values, then decrease in the second value as compared to the first value also indicates that the progression of the brain cancer has been to worsen between the first and second timepoints.
In contrast, when the miRNA investigated is one that is up-regulated in cancer as compared to reference values, then a decrease in the second value as compared to the first value indicates that the progression of the brain cancer has been to improve between the first and second timepoints.
Similarly, when the miRNA investigated is one that is down-regulated in cancer as compared to reference values, then a increase in the second value as compared to the first value indicates that the progression of the brain cancer has been to improve between the first and second timepoints.
The monitoring methods of the invention may make use of further samples representative of miRNA in the patient at further timepoints (for example a third sample representative of miRNA in the patient at a third timepoint, in addition to the first and second samples).
The first, second (and any subsequent) timepoints may be separated by any period of interest during which it is wished to monitor progression of the patient's brain cancer.
The patient may be subject to treatment that is intended to alter the status of the cancer between the first and second timepoints. For example, the patient may be subject to clinical treatment, or treatment with a putative therapeutic agent. In this case the monitoring of the progression of the patient's cancer may provide an indication as to whether the clinical treatment, or putative therapeutic agent, is proving successful.
Monitoring of cancer progression in this manner may also be beneficial in determining when cancer treatment should be initiated. Merely by way of example, the initiation of treatment may be indicated when a cancer worsens (e.g. a low grade tumour progressing to a high grade tumour). Similarly, a decision as to whether to begin or end treatment regimens, such as chemotherapy regimens, may be taken with a view to monitored advancement and/or regression of the tumour.
It will be appreciated that multiple miRNAs from the recited list may be assayed for in respect of the two samples, and that different miRNAs may be assayed for, so long as at least one of the miRNAs assayed for is in common between the two samples (thus allowing a comparison to be performed in respect of the abundance of that miRNA in the samples).
In a fourth aspect, there is provided a method of grading a patient's brain cancer, the method comprising:
assaying a sample from the patient to determine the amount of at least one miRNA, selected from the group consisting of: Hsa-miR-20a-5p; Hsa-miR-34a-5p; Hsa-miR-92a-3p hsa-miR-15b; hsa-miR-181b; hsa-miR-19a; hsa-miR-210; hsa-miR-23a; hsa-miR-15a; hsa-miR-181a; hsa-miR-21; hsa-miR-222; hsa-miR-26a; hsa-miR-29c; hsa-miR-101-3p; hsa-miR-29b-3p; hsa-miR-328; hsa-miR-9-5p; Hsa-miR-106b-5p; Hsa-miR-107; Hsa-miR-125a-5p; Hsa-miR-128; Hsa-miR-130b-3p; Hsa-miR-132-3p; Hsa-miR-138-5p; Hsa-miR-141-3p; Hsa-miR-146a-5p; Hsa-miR-148a-3p; Hsa-miR-16-5p; Hsa-miR-17-5p; Hsa-miR-17-3p ; Hsa-miR-182-5p; Hsa-miR-183-5p; Hsa-miR-187-3p; Hsa-miR-18a-5p; Hsa-miR-190a; Hsa-miR-19b-3p; Hsa-miR-200a-3p; Hsa-miR-203a; Hsa-miR-31-5p; Hsa-miR-326; Hsa-miR-425-5p; Hsa-miR-7-5p; Hsa-miR-93-5p; Hsa-miR-96-5p; Hsa-let-7b-5p; Hsa-miR-106b-5p; Hsa-miR-191-5p; Hsa-miR-24-3p; Hsa-miR-25-3p; Hsa-miR-320a; Hsa-miR-486-5p; and Hsa-miR-451a, present in the sample;
comparing the amount of the at least one miRNA present in the sample with reference values for miRNA expression obtained from a cancers of known clinical grades; and
allocating the patient's brain cancer to the clinical grade to which the amount of the at least one miRNA present in the sample most closely resembles.
The methods of each of the first, second, third and fourth aspects may, for the sake of brevity, be referred to herein as “methods of the invention”. The following pages will provide more details of suitable embodiments of these, and other, aspects of the invention. Except for where the context requires otherwise embodiments described with reference to one aspect of the invention may also be applied to other aspects of the invention.
The methods of the invention are able to provide many advantages over those techniques known from the prior art. The methods of the first aspect of the invention are able to be used as a diagnostic test for brain tumours, especially glioma. Through a non-invasive process of blood sampling, serum can be isolated from patients and tested to identify changes in a select panel of microRNAs to determine the presence of a brain tumour without the need for surgery. A simple test when the patient initially presents with neurological symptoms could lead to earlier diagnosis allowing for prompt treatment and giving the patient the best chance at a positive outcome.
The methods of the fourth aspect of the invention can also be used to distinguish between different grades of brain tumour. If such methods are performed at diagnosis; this could be useful in selecting the correct treatment for the patient, again giving them the best chance at a positive outcome without the need for an invasive procedure.
A major benefit of the methods of the invention is that they can be performed without the need for surgery as with histological techniques. They are also able to improve the accuracy of diagnosis, compared to MRI. There is also potential for earlier diagnosis when the tumour may be present but not identifiable by imaging, allowing for prompt treatment and potentially an improved prognosis.
The measurement of the microRNA expression in the serum and/or CSF could overcome the limitations of current diagnostic techniques. By improving accuracy through the analysis of microRNAs but at the same time being non-invasive by the taking of a blood samples rather than surgery.
Analysis of microRNA expression in tumour tissue, when surgery is necessary again, improves accuracy in comparison to current techniques.
The analysis performed by the inventors provides further insight into the manner in which the various biomarker miRNAs herein identified may be used to practice the methods of the invention.
A selection of the miRNAs referred to above show their diagnostic utility when they are up-regulated as compared to reference values. Accordingly, finding an increased abundance of one or more of these diagnostic up-regulated miRNAs in a sample of a subject, who may be of unknown brain cancer status indicates that the subject in question has brain cancer. miRNAs suitable for use in such embodiments may be selected from the group consisting of:
Has-miR-20a-5p; Hsa-miR-34a-5p; Hsa-miR-92a-3p; hsa-miR-101-3p; hsa-miR-148a; hsa-miR-29b-3p; Hsa-let-7b-5p; Hsa-miR-106b-5p; Hsa-miR-24-3p; Hsa-miR-25-3p; Hsa-miR-320a; Hsa-miR-486-5p; Hsa-miR-15b; Hsa-miR-17-5p; Hsa-miR-17-3p; Hsa-miR-181b; Hsa-miR-19a; Hsa-miR-210; and Hsa-miR-23a. Suitable embodiments may utilise one, more, or all of such miRNAs. A particularly useful selection of these miRNAs up-regulated in incidences of cancer may comprise one or more selected from the group consisting of: Has-miR-20a-5p; Hsa-miR-34a-5p; Hsa-miR-92a-3p; hsa-miR-101-3p; hsa-miR-148a; hsa-miR-29b-3p; Hsa-miR-320a; Hsa-miR-486-5p; Hsa-miR-15b; Hsa-miR-17-5p; Hsa-miR-17-3p; Hsa-miR-181b; Hsa-miR-19a; Hsa-miR-210; and Hsa-miR-23a.
In contrast to the up-regulated miRNA biomarkers referred to above, the inventors have also identified a panel of markers that are down-regulated in cancerous cells as compared to reference values. Accordingly, finding decreased abundance of one or more of these diagnostic down-regulated miRNAs in a sample from a subject, who may otherwise be of unknown brain cancer status, indicates that the subject in question has brain cancer. Thus, in an alternative embodiment a method of the invention may involve assaying a sample from a subject to determine the amount of at least one miRNA selected from the group consisting of: Hsa-miR-191-5p; Hsa-miR-451a; hsa-miR-328; hsa-miR-9-5p; Hsa-miR-106b-5p; Hsa-miR-107; Hsa-miR-125a-5p; Hsa-miR-128; Hsa-miR-130b-3p; Hsa-miR-132-3p; Hsa-miR-138-5p; Hsa-miR-141-3p; Hsa-miR-146a-5p; Hsa-miR-148a-3p; Hsa-miR-16-5p; ; Hsa-miR-182-5p; Hsa-miR-183-5p; Hsa-miR-187-3p; Hsa-miR-18a-5p; Hsa-miR-190a; Hsa-miR-19b-3p; Hsa-miR-200a-3p; Hsa-miR-203a; Hsa-miR-31-5p; Hsa-miR-326; Hsa-miR-425-5p; Hsa-miR-7-5p; Hsa-miR-93-5p; Hsa-miR-15a; Hsa-miR-181a; Hsa-miR-21; Hsa-miR-222; Hsa-miR-26a; Hsa-miR-Hsa-miR-29c; and Hsa-miR-96-5p; and comparing the amount found in the sample to a reference value, wherein a decrease of the amount present in the sample as compared to the reference value indicates the presence of cancer. Suitable embodiments may utilise one, more, or all of such miRNAs. A particularly useful selection of these miRNAs down-regulated in incidences of cancer may comprise one or more selected from the group consisting of: Hsa-miR-191-5p; Hsa-miR-451a; hsa-miR-328; hsa-miR-9-5p; Hsa-miR-138-5p; Hsa-miR-16-5p; Hsa-miR-19b-3p; Hsa-miR-15a; Hsa-miR-181a; Hsa-miR-21; Hsa-miR-222; Hsa-miR-26a; Hsa-miR-29c; and Hsa-miR-93.
As referred to above, the methods of the second aspect of the invention are useful in the prediction of a clinical outcome in a patient with brain cancer. These methods are able to provide an indication as to the patient's expected length of survival with the brain cancer.
In a suitable embodiment of such a method et the second aspect of the invention, the at least one miRNA is selected from the group consisting of: hsa-miR-101-3p; hsa-miR-29b-3p; hsa-miR-328; hsa-miR-9-5p; Hsa-let-7b-5p; Hsa-miR-106b-5p; Hsa-miR-191-5p; Hsa-miR-24-3p; Hsa-miR-25-3p; Hsa-miR-320a; Hsa-miR-486-5p; Hsa-miR-451a; Hsa-miR-34a-5p; and Hsa-miR-92a-3p, and wherein an increase in the amount of the at least one miRNA present in the sample as compared to the reference value indicates a negative outcome in respect of the patient's brain cancer.
In another suitable embodiment of a method of the second aspect of the invention, the at least one miRNA is selected from the group consisting of: Hsa-miR-106b-5p; Hsa-miR-107; Hsa-miR-125a-5p; Hsa-miR-128; Hsa-miR-130b-3p; Hsa-miR-132-3p; Hsa-miR-138-5p; Hsa-miR-141-3p; Hsa-miR-146a-5p; Hsa-miR-148a-3p; Hsa-miR-16-5p;; Hsa-miR-182-5p; Hsa-miR-183-5p; Hsa-miR-187-3p; Hsa-miR-18a-5p; Hsa-miR-190a; Hsa-miR-19b-3p; Hsa-miR-200a-3p; Hsa-miR-203a; Hsa-miR-20a-5p; Hsa-miR-31-5p; Hsa-miR-326; Hsa-miR-425-5p; Hsa-miR-7-5p; Hsa-miR-93-5p; and Hsa-miR-96-5p; and a decrease in the amount of the at least one miRNA present in the sample as compared to the reference value indicates a negative outcome in respect of the patient's brain cancer.
As discussed further below, in the case of a method of the preceding paragraph in which the amount of Hsa-miR-20a-5p present is assessed, a suitable reference value may be a two-fold increase as compared to a suitable control (for example a sex and age matched control).
In the case of those microRNAs found to be up-regulated in serum of cancer patients, it may generally be expected that the greater the elevation of regulation, the worse the prognosis for the patient. Similarly, it may be expected that in cases of microRNAs down-regulated in serum of patients with cancer, the more down-regulated the microRNA, the worse the likelihood of clinical outcome for the patient. However, the inventors have found a group of microRNAs that constitute useful indicators of clinical outcome, but which do not follow the pattern set out above.
Hsa-miR-20a-5p; Hsa-miR-92a-3p; and Hsa-miR-34a-5p, are all up-regulated in serum patients with glioma brain cancer, as compared to controls. Surprisingly, the inventors have found that, when the levels of these miRNAs are compared to suitable controls, a higher level of up-regulation is associated with better clinical outcome.
Thus in a suitable embodiment of a method of the second aspect of the invention, the method involves assaying a sample from the patient for at least one miRNA selected from the group consisting of: Hsa-miR-20a-5p; Hsa-miR-92a-3p; and Hsa-miR-34a-5p,
comparing the amount of the at least one miRNA present in the sample with a reference value reflecting the level of the same at least ore miRNA present in a control subject without cancer;
wherein an decrease in the amount of at the least one miRNA in the sample, as compared to the reference value, indicates a negative outcome in respect of the patient's brain cancer.
In the case of such a method utilising Hsa-miR-20a-5p, a suitable reference value reflecting the level of this miRNA in a control subject without cancer may be a value twice the level of this miRNA in a control subject without cancer. A patient in whom the level of Hsa-miR-20a-5p is greater than the value twice the level in a control subject will be expected to have a positive outcome in respect of their cancer. A patient in whom the level of Hsa-miR-20a-5p is elevated as compared to the level in a control subject, but is not greater than twice the value in a control subject, will be expected to have a negative outcome in respect of their cancer.
In the case of such methods utilising Hsa-miR-34a-5p and/or Hsa-miR-92a-3p, a suitable reference value reflecting the level of this miRNA in a control subject without cancer may be a value twice, three times, or more the level of the miRNA in question in a control subject without cancer. A patient in whom the level of Hsa-miR-34a-5p and/or Hsa-miR-92a-3p is greater than the selected value in a control subject will be expected to have a positive outcome in respect of their cancer. A patient in whom the level of Hsa-miR-34a-5p and/or Hsa-miR-92a-3p is elevated as compared to the level in a control subject, but is not greater than the selected value in a control subject, will be expected to have a negative outcome in respect of their cancer.
Suitably the sample from the patient is a body fluid sample, such as a serum sample.
In suitable embodiments, the methods of the invention may further comprise steps involving the selection, and optionally implementation, of an appropriate therapeutic regimen. Thus, for example, a method of detecting brain cancer in accordance with the first aspect of the invention may further comprise selecting an appropriate treatment regimen for a subject identified as having brain cancer, and optionally providing said treatment regimen.
In the case of methods of the second aspect of the invention, for predicting a clinical outcome in a patient with brain cancer, the method may further comprise selecting an appropriate treatment regimen for a subject identified as at risk of a negative outcome in respect of their brain cancer, and may optionally further involve providing said treatment regimen. Suitable treatments in this context may include more radical treatments than those that would be deemed clinically appropriate in respect of a patient viewed as likely to have a positive clinical outcome.
In the case of methods of the third aspect of the invention, for monitoring the progression of brain cancer in a patient, the method may further comprise making the decision to initiate treatment for brain cancer in the event that the method indicates a worsening in respect of the patient's brain cancer. The method may optionally comprise the initiation of the selected treatment. If the patient is already undergoing treatment, but the method indicates that the patient's brain cancer is still worsening, then the further step may involve a decision to select a more radical treatment regimen, and optionally the provision of the selected more radical treatment regimen. In the event that a method in accordance with the third aspect of the invention indicates an improvement in respect of the patient's brain cancer, a suitable further step of the method may involve reducing or ceasing any ongoing treatment.
In the case of methods in accordance with the fourth aspect of the invention, in which a patient's brain cancer is graded, the method may further comprise selecting, and optionally providing, a treatment regimen appropriate to the clinical grade that has been allocated to the patient's brain cancer.
Suitable treatments for brain cancer, that may be provided as further steps of the methods of the invention, including more or less radical treatments for brain cancer, will be known to those skilled in the art.
For the avoidance of doubt, and in order to clarify the way in which the present disclosure is to be interpreted, certain terms used in accordance with the present invention will now be defined further.
Samples Suitable for Use in the Methods of the Invention
The methods of the invention make use of samples that provide useful biological information regarding the presence of miRNA biomarkers within the subject undergoing investigation.
i) Tissue Samples
In a suitable embodiment, the sample may be a tissue sample. Merely by way of example, the sample may be a biopsy sample, such as a brain biopsy sample.
Although the collection of tissue samples, such as biopsy samples, is generally more invasive than the collection of body fluid samples (discussed below), it may still represent a commonly used procedure in many clinical contexts. In such cases the tissue sample from the subject may suitably be assayed to determine the amount of at least one miRNA of interest in the sample.
Any of the down-regulated miRNAs discussed above may be used in methods of the invention practiced on tissue samples.
While the inventors believe that all of the biomarker miRNAs referred to in the preceding paragraph have diagnostic utility when down-regulated in a sample (as compared to a reference value) certain of these markers show particularly marked changes in their abundance. Thus, in a preferred embodiment, a method of the invention may involve comparing the level of at least one miRNA selected from the group consisting of Hsa-miR-141-3p; Hsa-miR-148a-3p; Hsa-miR-16-5p; Hsa-miR-182-5p; Hsa-miR-18a-5p; Hsa-miR-200a-3p; Hsa-miR-203a; Hsa-miR-31-5p; Hsa-miR-326; and Hsa-miR-425-5p with a reference value, wherein a decrease in the amount of said at least one miRNA in the sample, as compared to the reference value, is indicative of cancer.
The inventors have also found that the certain of the up-regulated miRNAs described above are particularly increased in brain cancer cells, and so may be of notable diagnostic utility in embodiments in which the sample is a tissue sample. Accordingly, in such embodiments the methods may involve assaying a tissue sample for the level of at least one miRNA selected from the group consisting of: hsa-miR-101-3p; hsa-miR-29b-3p; hsa-miR-328; and hsa-miR-9-5p, wherein increased abundance of the at least one selected miRNA in said sample, as compared to a reference value, is indicative of the presence of cancer.
ii) Body Fluid Samples
In an alternative embodiment the sample is a body fluid sample. In a suitable embodiment the body fluid sample is selected from the group consisting of: a cerebrospinal fluid (CSF) sample; a blood sample; and a serum sample.
The skilled person will appreciate that under normal circumstances it can be difficult to obtain detailed information regarding biological processes, such as the presence or progression of cancer, occurring within the brain. The brain is separated from much of the body by the blood brain barrier, and is physically enclosed and protected within the skull. These considerations, and the difficulties that they impose upon the diagnosis or monitoring of brain cancer, have already been discussed elsewhere in the specification.
In light of these known difficulties, it will be appreciated that body fluid samples may represent particularly useful examples of samples that can be used in the methods of the invention, since they may generally be obtained by less invasive procedures than tend to be necessary in order to obtain tissue samples, such as biopsy samples, from the brain. In particular, samples such as serum samples are especially easy and safe to obtain, since they merely the taking of a blood sample. It is both highly advantageous and surprising that the methods of the invention are able to provide information, such as about the presence or progression of cancer in the brain, using serum which (as a constituent of blood) is usually separated from the brain by the blood brain barrier.
The use of biological fluids as a means of monitoring the diagnosis of the disease state and prognosis is a relatively non-invasive procedure. It circumvents the need for risky surgery and offers a definitive diagnosis thus eliminating subjective interpretation in histopathological sections.
For individuals which surgery is necessary, microRNA expression of tumour tissue again provides improved accuracy for diagnosis, prognostic information and predicting response to treatment.
In an embodiment in which the sample is bodily fluid, such as a serum sample, the presence of cancer may be indicated by an increase in the abundance of at least one miRNA selected from the group consisting of: Hsa-let-7b-5p; Hsa-miR-106b-5p; Hsa-miR-191-5p; Hsa-miR-24-3p; Hsa-miR-25-3p; Hsa-miR-320a; Hsa-miR-486-5p; Hsa-miR-451a; Hsa-miR-34a-5p; and Hsa-miR-92a-3p; as compared to a reference value.
In an embodiment in which the sample is a serum sample, and the subject is male, the presence of cancer may be indicated by an increase in the abundance of at least one miRNA selected from the group consisting of: hsa-let-7b-5p; Hsa-miR-106b-5p; Hsa-miR-191-5p; Hsa-miR-24-3p; Hsa-miR-25-3p; Hsa-miR-320a; and Hsa-miR-486-5p as compared to a reference value.
In a preferred embodiment in which the sample is a serum sample, and the subject is male, the inventors have found that a subset of the miRNA markers referred to above undergo particularly marked increases in abundance. Accordingly, in such an embodiment the presence of cancer may be indicated by an increase in the abundance of at least one miRNA selected from the group consisting of: Hsa-miR-191-5p; Hsa-miR-486; Hsa-let-7b-5p; and Hsa-miR-25-3p as compared to a reference value. The inventors consider these markers to have particular diagnostic value in such embodiments of the invention.
In an embodiment of a method of the invention in which the sample is a serum sample, and the subject is female, the presence of cancer may be indicated by an increase in the abundance of at least one miRNA selected from the group consisting of: Hsa-miR-451a; Hsa-miR-486-5p; Hsa-miR-92a-3p; and Hsa-miR-25-3p as compared to a reference value.
In a preferred embodiment of the methods of the invention using serum samples from female subjects, the presence of cancer may be indicated by an increase in the abundance of at least one miRNA selected from the group consisting of: Hsa-miR-486-5p; and Hsa-miR-25-3p as compared to a reference value. These miRNAs represent biomarkers that are particularly strongly up-regulated in the serum of female subjects with brain cancer, and so are considered to be of notable diagnostic utility.
In a suitable embodiment of the methods of the invention in which the sample is a serum sample, and the subject is aged 60 years, or over, the presence of cancer may be indicated by an increase in the abundance of Hsa-miR-34a-5p as compared to control values. Suitable controls may be appropriately age-matched. The inventors have found that Hsa-miR-34a is a biomarker that is up-regulated in the serum of subjects aged 60 or over with brain cancer, and so Hsa-miR-34a-5p is considered to be of particular diagnostic utility in serum samples from individuals of this age.
“Comparing”
The step of comparing the amounts of the miRNAs in a sample with those in a reference value will generally merely require that sufficient information be available to determine whether the abundance of the miRNA present in the sample is increased or decreased as compared to the reference value. In preferred embodiments the information available may be sufficient to allow the identification of fold-changes in the abundance of the miRNA as compared to the reference value.
“Difference” Between Amounts of miRNA in a Sample and the Reference Value
The difference between the amount of the miRNA present in the sample and the reference value may be either a relative increase in the abundance of the miRNA in the sample as compared to the reference value, or a relative decrease in the abundance of the miRNA in the sample as compared to the reference value. The nature of the “difference” that is relevant to the use of different miRNA markers (e.g. whether a particular marker has diagnostic utility if increased or decreased as compared to a reference valued) is discussed elsewhere in the present disclosure
“Reference Value”
The methods of the invention make use of comparison between the amount of a miRNA of interest that is present in a sample, and a suitable reference value. This comparison with the reference value allows an assessment to be made as to whether the abundance of the miRNA in question is increased or decreased as compared to a suitable control.
It will be appreciated that in a simple embodiment a reference value may be determined by parallel processing of a suitable control sample in the same manner as the sample of interest. However this need not be the case, and the methods of the invention can be practice making use of standardised information as to the levels of the miRNAs of interest in suitable control samples.
Some of these miRNAs of interest are secreted, while others are not. This distinction allows sub-selections of miRNAs to be detected with reference to the type of sample available.
The recognition that certain of the miRNAs that may be utilised in the methods of the invention are secreted also has a significant impact upon the selection of appropriate reference values. If a miRNA indicative of brain cancer is secreted into body fluids then suitable reference values must be determined from subjects known not to have cancer, since otherwse there is a risk that at least some contamination from an unknown cancer may occur, even in samples collected from a site distant from the brain cancer.
Similarly, the recognition that certain miRNAs useful in the methods of the invention are not secreted also has a significant impact upon the selection of suitable samples and reference values for use in embodiments in which these miRNAs are to be assessed. In contrast to the secreted miRNAs, these non-secreted miRNAs are not suitable for assessment in body fluid samples. Suitable reference values may be determined from non-cancerous tissue samples. Alternatively, suitable reference values may be determined from cultured cells known to be non-cancerous.
In embodiments in which the sample is a tissue sample the presence and amount of miRNAs in the sample may be assayed by techniques in which the miRNAs in question are extracted from the sample. Such methods may make use of many of the assay techniques suitable for use in methods where the sample is a body fluid sample.
Alternatively, methods of the invention in which the sample is a tissue sample may employ assays in which the presence and amount of miRNAs is determined while the miRNAs remain in situ. A range of histological techniques known to the skilled person may be employed in embodiments of this sort. Merely by way of example, the presence and location of miRNAs within a tissue sample may be determined by techniques using in situ hybridisation. Without wishing to be bound by any hypothesis, the inventors believe that at least some of the miRNAs referred to above may be involved in tumourigenesis, and so the ability to determine their location in situ may be advantageous monitoring the progression of brain cancer.
“Assaying”
The methods of the invention involve assaying samples from a subject in order to determine the amount of selected miRNAs that are found in the sample. Generally, the assays used to detect the miRNAs may be of any sort known to those skilled in the art as suitable for the detection of nucleic acids (such assays allowing a simple assessment that “some amount” or “no amount” of the miRNA in question is present), and preferably may allow quantification of the selected miRNA(s).
The assaying methods of the invention may involve the formation of complexes between naturally occurring miRNA molecules in a patient sample and non-natural agents. The non-natural agents may incorporate moieties or other suitable means that allow their detection when complexed with the miRNAs from the patient sample. Assaying for the miRNA in the methods of the invention may involve detection of these complexes formed between miRNA and a non-naturally occurring agent, such as a synthetic oligonucleotide, labelled antibody, or the like.
The assays used in the methods of the invention may determine the amount of the miRNA present in the sample directly. Suitable assays may, for example, involve labelling only to the native miRNA present in the sample.
Alternatively, the assays used in the methods of the invention may indirectly determine the amount of the miRNA present in the sample. By this is meant that an assay may be used in which a proxy for the miRNA is produced, and the amount of this proxy produced determined, thereby indirectly allowing quantification of the miRNA.
By way of example, in a suitable embodiment, the assay used to determine the presence of the miRNA may comprise an amplification step in which miRNA in the patient sample is used as a template for the generation of artificial nucleic acid molecules, and the presence and quantity of the artificial nucleic acid molecules present assessed, thus allowing the amount of the at least one miRNA present in the sample to be determined.
Suitable examples of assays using such amplification steps will be known to those skilled in the art. In a suitable embodiment, the amplification step utilises quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). It will be appreciated that many such techniques, including the example of qRT-PCR referred to above, will bring about the production of complementary DNA (cDNA) molecules—artificial nucleic acid sequences that are not found in nature. Such artificial nucleic acid sequences may be isolated from naturally occurring sequences as part of the assay.
“Brain Cancer”
The inventors believe that the methods of the invention are applicable in respect of a wide variety of brain cancers. Merely by way of example, the brain cancer referred to in conjunction with the methods of the invention may be selected from the group consisting of: gliomas; meningiomas; pituitary adenomas; and nerve sheath tumours. As will be appreciated from consideration of the experimental results described herein, in particularly suitable embodiments, the methods of the invention may be ones in which the brain cancer referred to is glioma.
The invention will now be further described with reference to the following experimental results and accompanying Figures, in which:
R2=0.23, p=2.26e−8.
Comparison to normal reveals that miR-92a is increased in GBM as compared to normal. Log fold change=1.21, p=5.6e−9 (adjusted for multiple testing).
Table 1 summarises results of changes in miRNA levels in serum samples from cancer patients as compared to controls
Table 2 summarises biomarker validation with respect to power analysis
Experimental Results
Study 1
Introduction
MicroRNAs (miRNA) are small non-coding RNAs which play a role in post-transcriptional regulation of gene and protein expression. MiRNAs exhibit disease specific expression, which can be used to provide information about a particular biological state, such as glioma. Changes in miRNA expression in gliomas can be measured following the isolation of glioma specific exosomes released into the circulation.
Aim: To identify a panel of miRNAs isolated from the circulation for diagnosis, prognosis and prediction of response to treatment of glioma.
Samples
Patient samples: Serum was obtained post-operatively from male and female patients aged over 60 years, with a diagnosis of glioblastoma. Non-cancerous serum was obtained from age and sex matched patients undergoing elective surgery, postoperatively. Information on the type of medication being used by these patients was also obtained to account for any effects these drugs may have on miRNA expression.
Levels of miRNAs in tissue samples from patients with cancer, such a glioblastoma, were assessed with reference to the cancer genorre atlas (TCGA) is an online bioinformatics repository containing data such as miRNA expression in patient tissues.
Cell lines: U87MG, grade IV glioma and SVGp12, non-cancerous astrocyte, cell lines (ECACC) were cultured as a monolayer in standard conditions until 80% confluent. Cells were then harvested and miRNA isolated.
Methods
MiRNA was extracted using a spin column method (
MicroRNA Extraction of Serum Samples
100 μl per sample of RNase DEPC treated water was heated in a heat block to 95° C.
Trizol LS Protocol
750 μl of Trizol LS (invitrogen) was added to 250 μl serum and homogenised by pipetting up and down.
The sample was centrifuged at 4° C., 12,000×g for 10 minutes to remove high molecular weight DNA and protein.
The sample was transferred to a new tube and 3.5 μl of cel-miR-39 spike in was added and the sample incubated for five minutes at room temperature.
200 μl of chloroform was added and shook vigorously by hand for 15 seconds and incubated at room temperature for 10 minutes.
The sample was then centrifuged at 4° C., 12,000×g for 15 minutes to separate the phases, the aqueous phase was removed and transferred to a fresh tube, noting the volume removed.
Continue with miRVana Protocol
1.25 volumes of ethanol were added to the samples and pipetted onto mirVana spin columns, 700 μl at a time and spun at 10,000×g for 15 seconds.
500 μl of wash solution 1 was added to the filter and centrifuged at 10,000×g for 10 seconds. 500 μl of wash solution 2/3 was added to the filter and centrifuged at 10,000×g for 10 seconds. 500 μl of wash solution 2/3 was added and centrifuged at 10,000×g for 10 seconds.
The spin column was then centrifuged for one minute at 10,000×g to remove residual fluid from the filter. The filter was transferred to a new tube and 100 μl of the RNase free DEPC treated water was added to the filter and spun for 30 seconds at 10,000×g.
Reverse Transcription
Reverse transcription was performed using the qiagen miscript 11 RT kit. 12.5 ng/μl of total RNA was used in the reverse transcription reaction.
The kit components were thawed on ice and prepared as below and gently mixed.
The reaction was incubated at 37° C. for 60 minutes followed by 5 minutes at 95° C. Following reverse transcription, 20 μl of the cDNA was diluted in 200 μl of RNase free, DEPC treated water.
qPCR Reaction
Miscript human brain cancer miRNA PCR arrays (MIHZ-108Z) were used for the qPCR reaction. The qPCR master mix was prepared using the miScript SYBR green PCR kit.
The kit components were thawed and prepared as below.
25 μl of master mix was pipetted into the miscript miRNA array. The plate was centrifuged for 1 minute at 1000×g. The qPCR reaction was performed using the parameters below for 40 cycles using the ABI 7500 qPCR machine. Dissociation analysis was performed following the qPCR reaction.
Data analysis was performed using the SABiosciences miScript miRNA PCR Data Analysis web portal. Data was normalised to cel-miR-39 spike in.
Results
Cell Lines: Profiling of the U87MG cell line identified 26 miRNAs whose expression were down-regulated compared to SVGp12 (
Serum: Seven miRNAs exhibited a 3-fold increase in expression in male serum compared to the control (
Discussion
MiRNA expression of both cell lines showed no similarity to the circulatory miRNAs isolated from serum. Inherent differences between immortalised cells and glioma expression in vivo could account for the contrast in miRNA expression. A study which profiled cancerous and non-cancerous tissue found a general down-regulation of miRNA expression in tumours, similar to that seen in the U87MG profile obtained in this study3.
Conclusion and Future Work
A panel of circulatory miRNAs with altered expression in the serum of glioma patients was identified and will be tested on a larger sample set. In conclusion, the use of circulatory miRNA biomarkers could vastly improve the diagnosis of gliomas as well as provide invaluable prognostic information. In addition to improving clinical aspects of gliomas, these results will contribute to our understanding of the role of miRNAs in the pathology of glioma.
Study 2
The aim of this second study was to identify circulating microRNA for use as biomarkers for glioma.
MicroRNA was isolated from serum of glioblastoma (n=26) and control patients (n=23), using phenol-chloroform extraction. Relative expression of microRNA was determined using qRT-PCR. Data were normalised using a synthetic spike in and analysed using the 2−ΔΔCt method. Statistical significance was determined using a Mann-Whitney t-test and a p-value of <0.05 was considered significant.
Three microRNAs were identified as being differentially expressed in the serum of glioblastoma patients when compared to control serum. In confirmation of the results reported above, microRNA-20a was up-regulated in the serum of glioblastoma patients as compared to controls. Furthermore, individuals with a two fold increase in microRNA-20a had a better survival time than those with only a one fold increase shown by Kaplan-Meier survival analysis. Levels of miRNAs in tissue samples from patients with cancer, such a glioblastoma, were assessed with reference to the cancer genome atlas (TCGA), and this analysis indicated that, in 558 patient tissues, high levels of expression of micro-RNA-20a also correlated with better prognosis.
miRNA20a is a particularly promising prognostic biomarker. The level of miRNA20a in cancer patients is inversely correlated with age, but analysis using age and sex matched patients with glioblastoma multiforme (GBM) and controls has shown that a >2 fold increase in expression in GBM patients is correlated with a better prognosis. These results are illustrated in
An additional finding was that microRNA-34a-5p (Hsa-miR-34a-5p) was found to be statistically significantly up-regulated in the serum of patients over the age of 60 when compared to age matched controls. This finding is surprising, since microRNA-34a-5p has previously been reported to be down-regulated in glioblastoma tissue. The present study represented the first occasion on which the abundance of this marker has been measured in the serum of glioblastoma patients. In serum samples from GBM patients the level of miRNA 34a correlated with increasing age. The results provided here show that miRNA34 is overexpressed in 60+ glioma patients and the higher the expression, the better the prognosis (
Sequence Information
The present disclosure refers to various miRNAs using standard designations that will be recognised by those skilled in the art. For the avoidance of doubt, details of the sequences of various miRNAs referred to herein are set out below.
| Number | Date | Country | Kind |
|---|---|---|---|
| 1312336.9 | Jul 2013 | GB | national |
| 1400436.0 | Jan 2014 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/GB2014/000280 | 7/9/2014 | WO | 00 |
