Patent Application
20150105265
Patients with Barrett's esophagus (BE) have a substantially increased risk of progression to esophageal adenocarcinoma (EAC) compared to the general population (RR: 11.3, 95% CI: 8.8-14.4)1. The incidence of EAC has increased 7-fold in the past 30 years (3.6 to 25.6 cases per million)2 and the prognosis is poor with a median survival of about 11 months due to late presentation3. Due to the improved survival in those diagnosed when the disease is confined to mucosa or sub-mucosal layers; patients with BE are recommended to undergo endoscopic surveillance for the early detection of cancer4, 5. The cost-effectiveness and risk:benefit ratio to the patient of endoscopy has been questioned time and again since the annual (per year) risk of progression is relatively low1, 6, 7; around 0.3% according to the recent estimates8. The intermediate dysplastic stages between BE and EAC are the most reliable marker of progression; however the histological presence of dysplasia is subjective due to known sampling bias during endoscopy along with a high inter and intra-observer variability9, 10. The wide variation in progression rates in patients categorized as having low grade dysplasia has been highlighted by two recent studies. In a Dutch study the incidence rate of high grade dysplasia (HGD) or EAC in individuals with confirmed low grade dysplasia was high at 13.4% (95% CI 3.5-23.2) per patient per annum 11; whereas in patients in a US study the progression rate of this group was similar to that of non-dysplastic patients which is a 16-fold difference12. In patients with high grade dysplasia, data from a randomized radiofrequency ablation (RFA) intervention trial suggest a rate of progression of 19% in the non-treatment arm13. Hence there is a high need for biomarkers that can accurately detect prevalent dysplasia in flat Barrett's mucosa and predict those patients most likely to progress to cancer.
Aberrant DNA methylation is shown to be a characteristic of cancer and these changes are known to occur early during transformation 14. It has already been shown in a number of studies that DNA methylation changes occur during progression from BE to EAC and that these alterations have the potential to be used as biomarkers15-20. These studies have mostly employed a candidate approach based on known methylation targets in other cancers. However high-throughput array based platforms are now available to identify DNA methylation changes and we have employed this approach to find candidate biomarkers in Barrett's carcinogenesis. Imprinted genes and the X-chromosome are both epigenetically controlled by DNA methylation21, but have never been examined specifically in the context of biomarkers for EAC.
Jin et al (2009 Cancer Research v.69, pages 4112 to 4115) disclose a multicentre, double-blinded validation study of methylation biomarkers for progression prediction in Barrett's esophagus. The authors studied eight BE progression prediction methylation biomarkers. The authors studied methylation in 145 non-progressors and 50 progressors from Barrett's esophagus to neoplasia. The study was a retrospective study—the study took candidate genes and assessed them for methylation status a posteriori. The eight candidate genes assessed were p16, RUNX3, HPP1, NELL1, TAC1, SST, AKAP12 and CDH13. The authors suggest that their eight marker panel is more objective and quantifiable and possesses higher predictive sensitivity and specificity than assessment of clinical features such as age. The authors assert that their eight marker panel accurately predicted approximately half of HGDs and EACs at high specificity levels.
Kaz et al (2011 Epigenetics v.6, pages 1403 to 1412) disclose that DNA methylation profiling in Barrett's esophagus and esophagal adenocarcinoma reveals unique methylation signatures and molecular subclasses. The authors report the finding of distinct global methylation signatures, as well as differential methylation of specific genes. The authors claim that their signatures could discriminate between squamous, BE, HGD and EAC cells. The authors do not disclose any biomarkers. Indeed, the authors even concede this when they state “Additional validation of those CpG sites that distinguished BE from BE+HGD and EAC may lead to the discovery of useful biomarkers with potential clinical applications in the diagnosis and prognosis of BE and EAC”. Thus, this report is focused on a description of CpG methylation profiles. In particular, the methylation status of 1505 CpG sites spread across 807 genes was studied. No specific teachings of biomarkers or prognosis are provided in this document.
The present invention seeks to overcome problem (s) associated with the prior art.
The inventors addressed the key issue of endoscopic surveillance of Barrett's esophagus (BE) and suggest how DNA methylation alterations can improve detection of high grade dysplasia and early cancer in flat Barrett's mucosa alongside histopathology.
To do this we have conducted a high-throughput array based methylation scan and utilized rigorous statistical methods (signal-to-noise ratio and two sided Wilcoxon tests) to rank differentially methylated genes on the Illumina Infinium platform. In addition, we have specifically looked at imprinted and X-chromosome genes for any changes in methylation occurring during the course of cancer development since these genes may be ideal biomarkers as physiological inactivation of one allelic copy has already occurred due to imprinting and via X-inactivation in females. Once we had identified candidate genes as biomarkers we then performed robust validation using pyrosequencing on the same samples as well as in a large independent set of retrospectively collected samples. This led to the identification of a four gene methylation panel which could distinguish between patients with non-dysplastic compared with dysplastic Barrett's and early carcinoma. Finally, we took this forward to a prospective, multicenter study and demonstrated that this panel does have clinical utility. Hence, we have gone from discovery all the way through to prospective evaluation of our panel.
Endoscopic surveillance of Barrett's esophagus (BE) is problematic because dysplasia and early-stage neoplasia are frequently invisible and likely to be missed due to sampling bias. Molecular abnormalities may be more diffuse than dysplasia. The aim was therefore to test whether DNA methylation; especially on imprinted and X-chromosome genes; is able to detect dysplasia/early-stage neoplasia.
We describe a surprisingly robust panel of methylation markers which correlate with useful clinical indications. A key further advantage of the invention is the use of the field effect whereby the invention can help overcome sampling bias since the informative markers taught occur in the Barrett's lesion and not solely in the dysplastic/EAC region (if present). The invention is based on these surprising findings.
Thus in one aspect the invention provides a method for aiding assessment of the likelihood of dysplasia or esophagal adenocarcinoma being present in a subject, the method comprising
(a) providing an esophagal sample from said subject
(b) determining the methylation status of
In one embodiment suitably step (a) comprises extracting nucleic acid such as DNA from said sample.
In one embodiment suitably step (b) comprises contacting said sample with a primer and determining methylation. Determining methylation may be carried out for example by MSP or pyrosequencing.
Suitably the method further comprises determining the methylation status of (v) TCEAL7.
Suitably if said subject is male, the method further comprises determining the methylation status of (vi) RGN.
Suitably the dysplasia is high grade dysplasia (HGD).
In another aspect, the invention relates to a method of assessing the risk for a particular subject comprising performing the method as described above, wherein if 0 or 1 of said genes are methylated then low risk is determined, and if 2 of said genes are methylated then intermediate risk is determined, if 3 or more of said genes are methylated then high risk is determined.
Depending on the outcome of the methods of the invention, alternate treatments may be offered to the subject.
For example, when a subject is identified as low risk according to the present invention, they may be prescribed surveillance at a longer time interval, for example three to five years.
When a subject is classified as intermediate risk according to the present invention, they may be prescribed a more frequent follow-up (a more frequent surveillance). For example, they may be prescribed a surveillance at a shortened interval such as one to two years.
When a subject is classified as high risk according to the present invention, they may be prescribed an intervention. For example, the subject may be prescribed a radio frequency ablation. This procedure is far more minor and less invasive than oesophagectomy. Therefore, the invention enables a more minor and less invasive treatment to be dispensed to patients who present in the high risk category according to the invention.
For comparison, the current UK guidelines are that if a patient presents with a Barrett's esophagus segment of 3 cm or longer, they would be prescribed surveillance at approximately two to three year time intervals. Thus, it can be appreciated that the invention provides savings in surveillance costs by extending the time interval between surveillance for low risk patients, and also improves outcomes by allowing intervention at an earlier stage for high risk patients.
Suitably methylation status is determined by pyrosequencing.
Suitably said pyrosequencing is carried out using one or more sequencing primers selected from Supplementary Table 5.
Suitably the methylation status is scored by determining the percentage methylation of each of said genes and comparing the values to the following methylation cut off percentages:
wherein a value for a gene which exceeds the methylation cut off percentage for said gene is scored as ‘methylated’.
In another aspect, the invention relates to an apparatus or system which is
(a) configured to analyse an esophagal sample from a subject, wherein said analysis comprises
(b) determining the methylation status of
Suitably said sample comprises frozen biopsy material.
In another aspect, the invention relates to a method for aiding assessment of the likelihood of dysplasia or esophagal adenocarcinoma being present in a subject, the method comprising
(a) providing an esophagal sample from said subject
(b) determining the methylation status of
Suitably said reference standard is from a subject having Barrett's esophagus, but not having dysplasia or esophagal adenocarcinoma.
Suitably said reference standard is from a Barrett's esophagus segment, but not having dysplasia or esophagal adenocarcinoma.
Suitably said reference standard comprises columnar epithelium such as Barrett's esophagus or duodenum.
Suitably the method further comprises determining the methylation status of (v) TCEAL7. Suitably if said subject is male, the method further comprises determining the methylation status of (vi) RGN.
In another aspect, the invention relates to a computer program product operable, when executed on a computer, to perform the method steps as described above.
We teach that DNA methylation can detect inconspicuous dysplasia and early-stage neoplasia in Barrett's esophagus, ie. that DNA methylation detects dysplasia/cancer.
Methylation changes in particular genes may be ideal biomarkers since physiological inactivation of one allelic copy may already have occurred due to imprinting and via X-inactivation in females.
We performed DNA methylation screening of BE and EAC samples using arrays to determine candidate biomarkers. We analyzed imprinted and X-chromosome genes separately and purposefully separated males from females to allow meaningful conclusions to be drawn. We performed robust internal and external validation using pyrosequencing which is the current gold standard in DNA methylation analysis and from this determined a panel of biomarkers to discriminate between dysplastic and non-dysplastic BE. Finally we validated the biomarker panel in a prospective cohort with real-time analysis to stratify BE patients into low, intermediate and high risk groups based on their risk of having prevalent dysplasia/EAC.
This study has identified widespread changes in DNA methylation which distinguish between BE and EAC. Use of an array based strategy has enabled us to identify novel genes previously unknown to play a role in this disease. We hypothesized that methylation of imprinted and X-chromosome genes might provide candidate biomarkers since one copy is already inactivated. The analysis demonstrated almost 70% imprinted genes had altered methylation status in EAC and one of these, SLC22A18, was in the final stratification panel. Robust internal and external validation using pyrosequencing allowed us to select a four gene panel with an excellent receiver operating characteristic to distinguish between non-dysplastic BE and dysplastic BE/EAC samples (AUC=0.988). This panel enabled us to stratify patients into three (low, intermediate and high) risk groups based on the number of methylated genes identified from analysis of a limited number of biopsies by virtue of the field effect.
A number of previous studies have looked at DNA methylation changes in Barrett's carcinogenesis. However none of the genes such as p16, APC24 and MGMT19 and a previously identified eight gene panel 25 were shown in this current study to be differentially methylated in EAC vs. BE. One reason for this might be that most biomarker studies have used a candidate, rather than an array based approach, and compared the BE associated disease states (dysplasia and EAC) to the normal squamous epithelium of the esophagus whereas we have compared dysplasia/EAC to BE in our study17, 26, 27. Metaplastic BE resembles intestinal epithelium rather than the squamous esophagus; and there is the possibility that the differences in DNA methylation observed between the normal squamous esophageal epithelium and BE/dysplsia/EAC might purely reflect differences in tissue morphology rather than playing any role in carcinogenesis. For this reason we included two duodenum samples as control in our array based methylation scan. If the methylation level of a gene was similar in both BE and duodenum; it was deemed that gene was involved in the maintenance of the columnar intestinal type epithelium rather than in the development of cancer. There were also methodological differences in the assays used; previous studies have employed methylation specific PCR (MSP) whereas here we used pyrosequencing which is a more quantitative method that has gained widespread acceptance28.
More hypermethylation was seen in cancer compared to hypomethylation (Table 1), in keeping with the fact that promoter hypermethylation is a well-established phenomenon in cancer. We also observed greater methylation changes to occur within known CpG islands. However in a recent publication comparing the normal squamous mucosa with Barrett's mucosa in 3 patients, methylation changes were reported to occur more frequently outside of CpG islands29. It should however be noted that the majority of probes on the Illumina Infinium platform are positioned around promoter sites and 60% of human genes are associated with promoters spanning CpG islands. The recent availability of comprehensive genome wide coverage of methylation changes will enable further light to be shed on this.
For imprinted genes, as mentioned above almost 70% of genes showed statistically significant changes in methylation in EAC vs. BE (Wilcoxon P<0.05) (Table 1). Disruption of genomic imprinting is a well-established phenomenon in cancer. One imprinted gene, SLC22A18, met the criteria for validation. This gene is located in the 11p15.5 cluster which is an important tumor-suppressor gene region. Mutations, deletions and LOH of this gene have all been reported in different cancers highlighting its importance in tumorigenesis. Gain of imprinting of SLC22A18 has been documented in other cancers such as breast and hepatocarcinomas32 but we have shown for the first time that this can have a biomarker potential.
We looked at X-chromosome genes not only because DNA methylation plays a major role in X-inactivation in females but also because BE is more common in males who only have one copy of the X-chromosome and thus would theoretically only require one hit for the loss of the only functional allele. We were able to identify RGN, a putative tumor-suppressor gene33, 34 that shows a successive increase in DNA methylation in the Barrett's associated metaplasia-dysplasia-adenocarcinoma sequence in males but not in females (Supplementary
Our findings have potential clinical applications. For the detection of dysplasia a four quadrant biopsy sampling technique is employed since dysplastic lesions can be focally distributed within the Barrett's segment without any endoscopically visible lesion. Furthermore, there is substantial intra-observer disagreement among pathologists in differentiating between low and high grade dysplasia9, 10, 35. In the prospective study we observed using our four gene methylation panel that DNA methylation is able to detect dysplasia/early-stage neoplasia in endoscopic biopsies even when the biopsy itself does not contain any visible dysplasia/early-stage neoplasia. This suggests that there is a field effect of methylation alterations in keeping with other research in the area of colon cancer36, 37. The clonality of BE and evolving dysplastic lesions is still not clearly understood38, 39 but there do appear to be widespread molecular genetic changes prior to the emergence of phenotypical alteration visible by histopathology criteria40. Our methylation panel therefore has the potential to flag patients which do not show any visible signs of dysplasia/early-stage neoplasia but might still be at a high risk of progression. This needs validation in cohorts not skewed by referral bias in tertiary referral centers and is a promising area for further study.
It is an advantage of the invention that the particular biomarkers taught herein show the field effect. This means that any cells sampled within the Barrett's segment will show methylation according to the present invention if dysplasia or EAC is likely to be present somewhere within the Barrett's segment. Clinical practice is that the Barrett's segment is sampled at a number of places within the lesion. However, an area of dysplasia or EAC is typically smaller than the entire Barrett's lesion. Therefore, whether or not HGD/EAC is detected from a particular biopsy is largely affected by chance. If one or more of the samples taken from the Barrett's segment happens to be within the dysplasia/EAC, then positive results can be expected. However, due to sampling bias and/or laws of probability, it is quite possible to sample a Barrett's segment at a number of points, and yet none of those points happens to lie within a dysplastic or EAC area. In this situation, the patient would be returned a negative result. This would clearly be undesirable and potentially life-threatening for that patient. However, advantageously, according to the present invention, the markers which are assayed as indicative of risk of dysplasia/EAC are found throughout the Barrett's segment (not just in the dysplasia/EAC patch(es)). Therefore, by using the present invention the problem of “missing” the dysplasia/EAC due to sampling error is advantageously reduced or eliminated.
Another problem which can arise from sampling errors is a so-called “oscillating diagnosis”. This refers to a situation where a first biopsy from a patient shows a negative result, a later biopsy shows a positive result, a still later biopsy shows a negative result and so on. This phenomenon arises due to probabilistic factors as outlined above, when the lesion such as dysplasia/EAC is smaller than the Barrett's segment being biopsied. It is typically only possible to see the dysplasia when it is in an advanced state and presents as a nodule or ulcer. More typically, the Barrett's segment is “flat”, which means that no lumps/nodules or ulcers/holes are visible in the Barrett's segment. This means that when the endoscopist is collecting the biopsies, there is no way of focusing those biopsies on the possibly dysplastic lesion to be examined. The endoscopist then simply tries to collect samples across the whole surface of the Barrett's esophagus segment. However, as explained above, any such random sampling is prone to chance effects, and so in a certain proportion of cases a lesion may actually be present but will not be detected due to none of the samples having been taken from within the (invisible) dysplasia/EAC region. This presents problems for the physician when it looks like the dysplasia/EAC can be appearing or disappearing over time, which is of course extremely unlikely or impossible. However skilled the endoscopist is, marking or reproducing the sampling is extremely difficult. The only practical measure is using a graduated endoscope when the location of the samples is typically noted by distance from the incisors. It is problematic that this is a rather rough and unreliable estimate. For practical reasons, such as the markings on the endoscope being only every 10 cm, the distance measurement is typically only accurate to +/−1-2 cm. Moreover, in the case of repeat surveillance events, it is important to note that the taking of biopsies leaves no scarring or visible marker on the surface. Therefore, even if a patient is presenting for a repeat biopsy, the endoscopist has no opportunity to sample the same or different areas as were sampled in previous biopsies, since there is no marking or scarring visible from the earlier events. By using the present invention, these difficulties and drawbacks are advantageously overcome.
It should be noted that the invention is not concerned specifically with diagnosis. The invention is concerned with prediction and/or assessment of risk; in particular, the invention is useful in prediction of probability or risk of harbouring a lesion such as HGD or EAC. In particular the invention is useful in prediction of probability or risk of the subject harbouring EAC. In one embodiment dysplasia itself may be considered a risk factor for developing EAC. In one embodiment risk of EAC is the most important aspect to assess. The invention is suitably useful to aid in decisions about how a subject or patient should be treated or managed. The invention is most useful in ascribing a risk category to said subject or patient as described above.
The term ‘comprises’ (comprise, comprising) should be understood to have its normal meaning in the art, i.e. that the stated feature or group of features is included, but that the term does not exclude any other stated feature or group of features from also being present.
BE—Barrett's esophagus; BED—Barrett's esophagus with dysplasia; EAC—Esophageal adenocarcinoma; HGD—High grade dysplasia; LGD—Low grade dysplasia.
Supplementary Table 5 provides details of the sequences of the genes of interest in the invention. Also provided are the addresses of the methylation regions of interest.
Suitably the reference sequences are as defined in the following table:
As the skilled person knows, the accession numbers above are absolute (dated) accession numbers. The database entries can be amended over time. Suitably the current database entry is used. The accession numbers for the current database entry are the same as above, but omitting the decimal point and any subsequent digits e.g. for SLC22A18 the absolute/dated accession number is NM—183233.1; the current entry is obtained using NM—183233 and so on.
Suitably the database for reference sequences is GenBank (National Center for Biotechnology Information, U.S. National Library of Medicine 8600 Rockville Pike, Bethesda Md., 20894 USA) and accession numbers provided relate to this unless otherwise apparent.
Suitably the database release referred to is 15 Apr. 2013, NCBI-GenBank Release 195.0.
The sample may be from a subject. The subject is suitably a mammal, most suitably a human.
Suitably the methods do not involve actual collection of the sample. Suitably the sample is an in vitro sample.
Methods of the invention are suitably performed on an isolated sample from the subject being investigated. Thus, suitably the methods are methods which may be conducted in a laboratory setting without the need for the subject to be present. Suitably the methods are carried out in vitro i.e. suitably the methods are in vitro methods. Suitably the methods are extracorporeal methods.
Suitably the invention is applied to analysis of nucleic acids. Suitably, nucleic acid is prepared from the cells collected from the subject of interest. Suitably, the sample comprises nucleic acid. Suitably, the sample consists of nucleic acid. Suitably, the nucleic acid is DNA.
Suitably the sample comprises cells from the surface of a subject's upper intestinal tract.
Suitably the sample consists of cells from the surface of a subject's upper intestinal tract.
Suitably the sample comprises cells from the surface of a subject's oesophagus.
Suitably the sample consists of cells from the surface of a subject's oesophagus.
Suitably the sample is an in vitro sample.
Suitably the sample is an extracorporeal sample.
Suitably the sample is from a subject having Barrett's Esophagus.
Suitably the sample comprises material taken from the region of the Barrett's Esophagus. Suitably the sample comprises material taken from the Barrett's Esophagus segment itself.
Suitably the sample is a biopsy.
Suitably the sample does not comprise formalin fixed paraffin embedded (FFPE) material. Pyrosequencing can be problematic on this type of material. Thus suitably the sample is such that pyrosequencing is possible.
Suitably the sample comprises fresh, chilled or frozen biopsy material. Suitably the sample comprises frozen biopsy material.
Suitably the biopsy material is endoscopically collected. Suitably the biopsy is a standard ‘pinch-type’ biopsy. Suitably this is collected in a standard forceps-pinch technique.
In one embodiment sampling the cellular surface of the upper intestinal tract such as the oesophagus may comprise the steps of
(i) introducing a swallowable device comprising abrasive material capable of collecting cells from the surface of the oesophagus into the subject,
(ii) retrieving said device by withdrawal through the oesophagus, and
(iii) collecting the cells from the device.
Suitably step (i) comprises introducing a swallowable device comprising abrasive material capable of collecting cells from the surface of the oesophagus into the subject's stomach. Suitably said cell collection device comprises a capsule sponge. Suitably the device is a capsule sponge as described in WO2007/045896 and/or as described in WO2011/058316. These two documents are incorporated herein by reference specifically for the description of the structure and/or construction of the cell collection devices (capsule sponges). Suitably said cell collection device comprises withdrawal means such as string. In one embodiment, the invention involves the sampling of the cells from the surface of the oesophagus using a swallowable abrasive material, which material is retrieved from the patient and from which the cells are subsequently separated for analysis. Suitably the majority of the surface of the oesophagus is sampled, more suitably substantially the entire surface of the oesophagus is sampled, most suitably the entire surface. Suitably the whole internal surface of the oesophagus ie. the complete inner lumen is sampled. In this embodiment abrasive is meant that the material is capable of removing cells from the internal surface of the oesophagus. Clearly, since this is meant for use in a subject's oesophagus, ‘abrasive’ must be interpreted in the light of the application. In the context of the present invention the term ‘abrasive’ has the meaning given above, which can be tested by passing the material through the oesophagus in an appropriate amount/configuration and examining it to determine whether cells have been removed from the oesophagus. Suitably the swallowable abrasive material is expandable. In this embodiment, suitably the abrasive material is of a smaller size when swallowed than when withdrawn. An expandable material may be simply a resilient material compressed such that when released from compression it will expand again back to a size approximating its uncompressed size. Alternatively it may be a material which expands eg. upon taking up aqueous fluid to a final size exceeding its original size.
Any suitable technique known in the art may be used to assay methylation of the genes of interest.
For example pyrosequencing may be used. Further details are found in the examples section.
For example MSP (Methyl-specific PCR) may be used.
For example the MethyLight assay may be used (Eads, C. A. et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 28, E32 (2000)). Kits for this type of assay are commercially available such as from Qiagen Inc., Hilden, Germany.
Most suitably the technique is suitable for use on frozen sample material.
Methylation status is suitably scored.
Methylation status is suitably scored in a binary ‘present’ or ‘absent’ manner.
Methylation status is more suitably scored by determining the level of methylation in the gene of interest.
Methylation status is most suitably scored by comparing the level of methylation in the gene of interest with a reference standard.
Suitably the reference standard comprises an esophagal sample from a subject who does not have esophagal dysplasia such as esophagal high grade dysplasia.
Suitably the reference standard comprises an esophagal sample from a subject who does not have esophagal adenocarcinoma.
Suitably the reference standard comprises an esophagal sample from a subject who does not have esophagal dysplasia such as esophagal high grade dysplasia, and does not have esophagal adenocarcinoma.
As will be apparent from the disclosure herein, the skilled operator working the invention may choose different methylation cut-offs depending on the specificity/sensitivity desired. Broadly speaking, the higher the methylation cut-off, the more stringent the method (and the higher the specificity/sensitivity values).
Most suitably methylation status is scored by determining the level of methylation in the gene of interest and comparing the level of methylation in the gene of interest with a reference standard, which reference standard is most suitably as shown in supplementary table 7 as ‘methylation cut-off’. Suitably this is done on a gene-by-gene basis. Suitably a methylation level matching or exceeding the ‘methylation cut-off’ is scored as ‘methylated’. Suitably a methylation level lower than the ‘methylation cut-off’ is scored as ‘not methylated’.
In more detail, it is an advantage of the invention that the methylation cut-offs can be chosen to specifically provide for the needs of the operator regarding sensitivity and/or specificity. The table below presents alternatives.
The lower cut-off gives the higher sensitivity and vice versa. For example, choosing a cut-off of 35.91 for GJA12 provides maximum sensitivity of 99%. Choosing a cut-off of 62.37 for GJA12 provides maximum specificity of 97% and so on.
Intermediate values may be chosen according to need.
Examples of intermediate values which may be chosen are provided below.
Individual cut-offs/sensitivities/specificities may be chosen for each gene in combinations according to the 6 tables presented below (one table of options per gene).
Thus in one embodiment there is provided a method as described above wherein the methylation status is scored by determining the percentage methylation of each of said genes and comparing the values to methylation cut off percentages selected from the table(s) above
wherein a value for a gene which exceeds the methylation cut off percentage for said gene is scored as ‘methylated’.
Thus in one embodiment there is provided a method as described above wherein a sensitivity is selected and the methylation status is scored by determining the percentage methylation of each of said genes and comparing the values to the corresponding methylation cut off percentages for the selected sensitivity, the values selected from the table(s) above,
wherein a value for a gene which exceeds the methylation cut off percentage for said gene is scored as ‘methylated’.
Thus in one embodiment there is provided a method as described above wherein a specificity is selected and the methylation status is scored by determining the percentage methylation of each of said genes and comparing the values to the corresponding methylation cut off percentages for the selected specificity, the values selected from the table(s) above,
wherein a value for a gene which exceeds the methylation cut off percentage for said gene is scored as ‘methylated’.
Thus in one embodiment there is provided a method as described above wherein a specificity and sensitivity is selected and the methylation status is scored by determining the percentage methylation of each of said genes and comparing the values to the corresponding methylation cut off percentages for the selected specificity and sensitivity, the values selected from the table(s) above,
wherein a value for a gene which exceeds the methylation cut off percentage for said gene is scored as ‘methylated’.
The reference standard typically refers to a sample from a healthy individual i.e. one who does not have EAC. The reference standard may be from a healthy individual who has BE but does not have HGD/EAC, most suitably does not have EAC.
Moreover, controls may be chosen with greater precision depending on which marker is being considered. For example if considering AOL then it may be advantageous to choose a control of BE without dysplasia or EAC. For example if ploidy is being considered then it may be advantageous to choose a control of any normal tissue (normal squamous oesophagus for example).
The reference standard can an actual sample analysed in parallel. Alternatively the reference standard can be one or more values previously derived from a comparative sample e.g. a sample from a healthy subject. In such embodiments a mere numeric comparison may be made by comparing the value determined for the sample from the subject to the numeric value of a previously analysed reference sample. The advantage of this is not having to duplicate the analysis by determining concentrations in individual reference samples in parallel each time a sample from a subject is analysed.
Suitably the reference standard is matched to the subject being analysed e.g. by gender e.g. by age e.g. by ethnic background or other such criteria which are well known in the art. The reference standard may be a number such as an absolute concentration or percentage methylation value drawn up by one or more previous studies.
Reference standards may suitably be matched to specific patient sub-groups e.g. elderly subjects, or those with a previous relevant history such as acid reflux or BE.
Suitably the reference standard is matched to the sample type being analysed. For example the concentration of the biomarker polypeptide(s) or nucleic acid(s) being assayed may vary depending on the type or nature of the sample. It will be immediately apparent to the skilled worker that the concentration value(s) for the reference standard should be for the same or a comparable sample to that being tested in the method(s) of the invention. For example, if the sample being assayed is from the Barrett's segment then the reference standard value should be for Barrett's segment to ensure that it is capable of meaningful cross-comparison. Suitably the sample type for the reference standard and the sample type for the subject of interest are the same.
Jin et al disclose a validation study of methylation biomarkers. Jin et al's study was a candidate study. This means that genes already thought to be connected with Barrett's esophagus/neoplastic progression were studied for their methylation status. By contrast, the present inventors undertook a prospective study. The present inventors looked across the whole genome. The inventors were trying to find the very best biomarkers available. The study carried out by the inventors is unbiased. This study sought to find the very best biomarkers free of any history or prejudice present in the art.
In Jin et al, comparisons are repeatedly made to normal tissue, such as normal esophagal epithelial tissue. Normal esophagal epithelial tissue is a squamous epithelium. Jin et al consistently compared this squamous epithelium with BE, with dysplastic cells, and with EAC. By contrast, the present inventors advantageously chose a different comparator. In selecting their markers, the inventors compared dysplastic cells with Barrett's esophagus, or EAC with Barrett's esophagus. The etiology of dysplasia/EAC is that it arises from Barrett's esophagus, such as the Barrett's segment itself. Therefore, the inventors have the insight that the most relevant cells for comparison are cells from Barrett's esophagus. It is the difference between those cells and the dysplastic/EAC cells which would allow progression to be predicted/identified. Thus in one aspect the invention relates to a method of selecting a marker useful in predicting presence of or progression to dysplasia/EAC, comprising comparing markers in dysplastic cells with Barrett's esophagus, or in EAC with Barrett's esophagus, and selecting those which display differences between those cell types.
Moreover, the inventors go on to teach that duodenum is an excellent control tissue. This is because duodenum is a normal intestinal tissue closely related to the cells in a Barrett's esophagus segment. The cells in both these settings (i.e. Barrett's cells in a Barrett's segment and duodenum) are columnar epithelium. This is a very different tissue organisation to squamous epithelium. Therefore, by comparing possibly dysplastic or cancerous cells with Barrett's esophagus cells or with duodenal cells, a more accurate biomarker may be selected. Thus in one aspect the invention relates to a method of selecting a marker useful in predicting presence of or progression to dysplasia/EAC, comprising comparing markers in dysplastic cells with duodenum, or in EAC with duodenum, and selecting those which display differences between those cell types.
Biomarkers selected according to the present invention have the advantage of showing a difference between a more clinically relevant tissue and the lesion compared to prior art techniques which compare squamous epithelium with the lesion.
A summary of key advantages of the invention compared with certain publications is presented to aid understanding of the benefits of the invention.
In so far as the embodiments of the invention described above are implemented, at least in part, using software-controlled data processing apparatus, it will be appreciated that a computer program providing such software control, and a storage medium by which such a computer program is stored, are envisaged as aspects of the present invention. Clearly in several of the methods or processes of the invention, one step (typically step (a)) comprises providing an esophagal sample from the subject—clearly that step would not typically be performed using software-controlled data processing apparatus; suitably that step is manually executed, or omitted, in embodiments implemented using software-controlled data processing apparatus.
In another aspect, the invention relates to a method for aiding assessment of the likelihood of dysplasia or esophageal adenocarcinoma being present in a subject, comprising carrying out the method steps as described above, wherein if 2 or more of said genes are methylated then increased likelihood of dysplasia or esophageal adenocarcinoma being present is determined.
In another aspect, the invention relates to a method for predicting the presence of, or the likelihood of presence of, dysplasia or esophageal adenocarcinoma in a subject, comprising carrying out the method steps as described above, wherein if 2 or more of said genes are methylated then presence of, or increased likelihood of presence of dysplasia or esophageal adenocarcinoma is predicted.
In another aspect, the invention relates to a method for determining a probability of, or determining a risk of, dysplasia or esophageal adenocarcinoma being present in a subject, comprising carrying out the method steps as described above, wherein if 2 or more of said genes are methylated then an increased probability of, or increased risk of, dysplasia or esophageal adenocarcinoma being present is determined.
In another aspect, the invention relates to a method of assessing a subject for presence of dysplasia or esophageal adenocarcinoma, comprising carrying out the method steps as described above, wherein if 2 or more of said genes are methylated then increased likelihood of presence of dysplasia or esophageal adenocarcinoma is determined.
In another aspect, the invention relates to a method for aiding assessment of the likelihood of dysplasia or esophageal adenocarcinoma being present in a subject, the method comprising
(a) providing an oesophagal sample from said subject
(b) determining the methylation status of
(iii) GJA12 and
in said sample
wherein if 2 or more of said genes are methylated then an increased likelihood of presence of dysplasia or esophageal is determined.
Suitably the dysplasia is high grade dysplasia (HGD).
In another aspect, the invention relates to a method of assessing the risk for a particular subject comprising performing the method as described above, wherein if 0 or 1 of said genes are methylated then low risk is determined, and if 2 of said genes are methylated then intermediate risk is determined, if 2 or more of said genes are methylated then high risk is determined.
Suitably methylation status is determined by pyrosequencing.
In another aspect, the invention relates to an apparatus or system which is
(a) configured to analyse an oesophagal sample from a subject, wherein said analysis comprises
(b) determining the methylation status of
(iii) GJA12 and
in said sample,
said apparatus or system comprising an output module,
wherein if 2 or more of said genes are methylated then an increased likelihood of presence of dysplasia or esophageal is determined.
Suitably said sample comprises frozen biopsy material.
The invention does not relate to mental acts. Suitably mental acts are omitted from the invention. Suitably the invention finds application in provision of information useful in aiding a prognosis or risk to be assessed for the subject or patient under investigation. The actual medical decision may be made by a physician or doctor, making use of the information provided by the invention.
a: Genes selected from the array analysis showing the greatest difference in methylation between BE and EAC. Beta values from the array are plotted on the x-axis against the gene name and tissue type on y-axis. 2b: For genes on the X-chromosome, analyses were separated on the basis of gender to cater for the effects of X-inactivation in females. Since RGN lies on the region of X-chromosome that is inactivated, males and females have different levels of methylation. Females have higher methylation in both tissues (BE and EAC) compared to males. TCEAL7 does not appear to be affected by X-inactivation and males and females have similar levels of methylation in both BE and EAC. 2c: Methylation levels for RGN and TCEAL7 in the normal esophageal epithelium in males and females using pyrosequencing.
a: The four gene risk score (SLC22A18+PIGR+GJA12+RIN2) had the best AUC of 0.988 (P<0.01). 6b: Graphical representation of percentage of patients falling into each group. The probability of HDG/early EAC increases with an increase in the number of positive biomarkers.
The invention is now described by way of example. These examples are intended to be illustrative, and are not intended to limit the appended claims.
27K methylation arrays were used to find genes best able to differentiate between 22 BE and 24 esophageal adenocarcinoma (EAC) samples. These were validated using pyrosequencing on a retrospective cohort (60 BE, 36 dysplastic and 90 EAC) and then in a prospective multicenter study (100 BE patients, including 21 dysplastic and 5 early EAC) designed to utilize biomarkers to stratify patients according to their dysplasia/EAC status.
23% of all genes on the array, including 7% of X-linked and 69% of imprinted genes, demonstrated statistically significant changes in methylation in EAC vs. BE (Wilcoxon P<0.05). 6/7 selected candidate genes were successfully internally (Pearson's P<0.01) and externally validated (ANOVA P<0.001). Four genes (SLC22A18, PIGR, GJA12 and RIN2) were found to have the greatest area under curve (0.988) to distinguish between BE and dysplasia/EAC. This methylation panel was able to stratify patients from the prospective cohort into three risk groups based on the number of genes methylated (low risk: <2 genes, intermediate: 2 and high: >2).
Widespread DNA methylation changes were observed in Barrett's carcinogenesis including ≈70% of known imprinted genes. A four gene methylation panel stratified BE patients into three risk groups with potential clinical utility.
For the retrospective studies (methylation arrays and external validation) all patient samples (H&E slides, endoscopic biopsies and surgical resection specimens), were obtained from patients who had attended Cambridge University Hospitals NHS Trust and provided individual informed consent (ethics: 04/Q2006/28, 09/H0308/118). For the prospective study patients with BE undergoing surveillance or tertiary referral for further evaluation of HGD or early EAC were recruited after obtaining informed consent from Cambridge University Hospitals NHS Trust, Queens University Hospital Nottingham and Amsterdam Medical Centre (ethics: 10/H0305/52). Pathology was verified for all cases according to the Royal College of Pathologists UK guidelines by an experienced upper GI pathologist (Dr Maria O'Donovan) and for dysplasia and EAC a minimum of two experienced pathologists reviewed the cases (referring hospital+Dr Maria O'Donovan). All BE samples were confirmed to have intestinal metaplasia and all EACs for a cellularity of 70%. Patient demographics are available in Supplementary Tables 1, 2 and 3.
For the methylation arrays, high molecular weight DNA was isolated from fresh frozen tissue using standard proteinase-K phenol/chloroform extraction. Samples with A260/280 of <1.8 and a fragment size of <2 kb were discarded. Volume corresponding to 1 μg of DNA was measured using Quant-iT™ PicoGreen® dsDNA kit (Invitrogen Ltd, UK) according to the manufacturer's instructions. Bi-sulfite modification was done using EZ DNA Methylation-Gold™ Kit (Zymo Research Corporation, USA).
DNA extraction for pyrosequencing assays was also carried out using the above mentioned protocol. DNA extraction from formalin fixed paraffin embedded (FFPE) tissues was carried out using QIAamp DNA Micro Kit (Qiagen, UK) using the manufacturer's instructions. 1 μg of DNA was bi-sulfite modified and eluted in 30 μl of elution buffer.
The Infinium assay (Illumina, UK) was run using the automated protocol from Cambridge Genomic Services. The samples were denatured prior to whole genome amplification (WGA) using 0.1 N NaOH. Multi-sample amplification master mix (MSM) was then added to the DNA samples and incubated at 37° C. for 20 hours. The amplified DNA was fragmented by vortexing, precipitated using isopropanol and dispensed onto the BeadChips which were incubated at 48° C. for 20 hours in hybridization buffer to allow for the DNA to hybridize. Unhybridized DNA was washed off and single-base extension was carried out with extended primers and labeled nucleotides using the TECAN Freedom Evo liquid handling robot. The BeadArray Reader (Illumina) was used to read the signal and output files were generated using GenomeStudio Software (Illumina).
a. Signal-to-noise ratio ranking: BE and EAC samples were separated into two groups and ranking of genes was done using the ‘Signal2Noise’ metric (GSEA software, Broad Institute, USA). Signal2Noise uses the difference of means scaled by the standard deviation.
(μA−μB)/(σA+σB)
where μ is the mean and σ is the standard deviation. The larger the signal-to-noise ratio, the larger the difference of means (scaled by standard deviation); hence more distinct methylation is seen for each phenotype and more the gene acts as a ‘class marker’. Imprinted genes and those on the X-chromosome were analyzed separately. The final list of genes can be obtained from Supplementary Table 4.
b. Wilcoxon tests: As a further check to test for differential methylation, a two-sided Wilcoxon test was performed for each probe on the array. Variance of probes with low or high methylation is in general lower than variance of probes with medium methylation22. So tests for differential methylation tend to preferentially select probes whose values are confined to the extremes of the scale. To reduce this effect we performed a Gaussian normalization prior to the Wilcoxon tests to reduce heteroscedasticity. The values' ranks, normalized between 0 and 1, were taken to be probabilities from a Gaussian distribution and transformed to variables using the distribution's quantile function. The P-values were adjusted for multiple testing using the false discovery rate method of Benjamini & Hochberg23. We were interested in probes that had both statistically significant and large absolute differences in methylation. Therefore, for each probe we also calculated the difference between the median of the methylation values in the two phenotypes. A probe's rank in the ordered list of Wilcoxon P-values and its rank in the ordered list of absolute difference in medians were averaged. The probes were arranged in descending order of this average.
The purpose of using two different tests to look for targets was to avoid false positives and to ensure that the selected targets not only have a statistically significant but a large absolute difference in methylation that was reproducible using pyrosequencing which has an error margin of ±5%. The targets appearing high up in both these analyses were then selected for validation.
Genes were selected for validation based on the following criteria: present in both of the lists, biological importance in EAC and/or other cancers, proximity to the promoter and relatively low density of CpGs in the vicinity so that it would be possible to design robust pyrosequencing assays (
Pyrosequencing assays were designed using PSQ Assay Design Software (version 1.0.6, Biotage, Sweden) (Supplementary Table 5). Genomic DNA sequences were obtained from NCBI map viewer (build 36). All PCR reactions were carried out in volumes of 25 μl using IMMOLASE™ DNA Polymerase (Bioline, UK). 0.75 μl of bi-sulfite converted DNA was used as a template for each reaction. 20 μl of each PCR reaction was mixed with 60 μl of bead mix composed of 3 μl streptavidin-coated beads solution (GE Healthcare, UK), 20 ul nuclease free water and 37 μl PyroMark binding buffer (Qiagen) in a 96-well plate and left on a shaking platform for 10 min. The pyrosequencing reaction plate was prepared by adding 1.5 μl of 10 μM sequencing primer and 43.5 μl of PyroMark Annealing Buffer (Qiagen) into each of the wells. The pyrosequencing vacuum machine (Biotage) was used to wash and denature the DNA bound to streptavidin-coated beads before being released into the pyrosequencing reaction plate. The plate was heated to 80° C. for 3 min and then cooled down to room temperature to allow the sequencing primer to anneal onto the single-stranded DNA and the sequencing reaction was carried out according to the manufacturers' protocol.
0%, 50% and 100% methylated controls were prepared for all the assays and used with every run. DNA synthesized by PCR was used for this. Primers were designed using the NCBI Primer Designing Tool (http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi) in order to amplify a region greater than but containing the sequence to be analyzed by pyrosequencing (Supplementary Table 6). Genomic DNA isolated from normal squamous esophagus was used as a template. All PCRs were performed in 50 μl duplicates. One reaction was used for in-vitro methylation. Briefly 40 μl of the PCR reaction was mixed with 5 μl of 10× NEBuffer2, 2.5 μl of 3.2 mM S-adenosylmethionine (SAM), 4U (1 μl) of CpG Methyltransferase (M.Sssl) (NEB, UK) and incubated for 2 hours at 37° C. After 2 hours another 0.5 μl of 3.2 mM SAM, 2U (0.5 μl) of M.Sssl and 0.5 μl of water were added and incubated overnight at 37° C. Both reactions (in-vitro methylated and unmethylated) were then purified using QIAquick PCR purification Kit (Qiagen). These were then bi-sulfite converted as mentioned before and mixed to generate a 50% methylated control along with 0% and 100% methylated controls.
Illumina HumanMethylation27 BeadChips were used to assess and compare methylation levels of 27,578 individual CpG loci spanning 14,475 genes and 110 miRNA promoters in 22 BE and 24 EAC samples (GEO accession no: GSE32925). Signal-to-noise ratio and two-sided Wilcoxon tests were used to rank genes showing the greatest difference in methylation (both hypermethylation and hypomethylation) between the BE and EAC, and from this a ‘class marker’ gene set was identified that was able to clearly distinguish between the two phenotypes (
Targets were Identified to have a Statistically Significant and Large Absolute Difference in Methylation Between BE and EAC:
To ensure that the selected targets for validation would have a statistically significant and large absolute difference in methylation and hence be suitable as biomarkers, the results of signal-to-noise ratio ranking were compared to the results of the Wilcoxon tests. The top seven genes present in both the lists fulfilling the aforementioned selection criteria (see methods) were selected for validation (
These seven genes were first internally validated using pyrosequencing assays on the same samples that were run on the methylation arrays. The assays were designed to analyze the same DNA sequence which was probed by the arrays. Pearson's correlation was used to assess whether the results from pyrosequencing matched with the results from the arrays (
External validation by pyrosequencing was carried out on an independent set of 60 BE, 36 BE with dysplasia and 90 EAC samples (
Methylation can Distinguish Non-Dysplastic BE from Dysplastic BE and EAC:
Since an increase in DNA methylation was observed in EAC and dysplastic BE compared to non-dysplastic BE, ROC curves were used to detect the power of the 6 genes individually and then in combination to differentiate between dysplastic BE/EAC and non-dysplastic BE (
DNA Methylation can Stratify BE Patients into Three Risk Groups; Low, Intermediate and High Risk:
The methylation cut-offs selected for the four genes using ROC curves (SLC22A18, PIGR, GJA12, RIN2) were then tested on a prospective cohort of 100 patients (including 21 dysplastic and 5 EAC cases) undergoing BE surveillance endoscopy in three tertiary referral centers to enrich for dysplasia and EAC. Random quadrantic biopsies every 2 cm were taken according British Society of Gastroenterology guidelines (http://www.bsg.org.uk/pdf_word_docs/Barretts_Oes.pdf) along with 3 extra biopsies for DNA methylation taken randomly from within the BE segment. For the analysis, the biopsy with the highest methylation value per gene was selected taking advantage of the likely molecular field effect. A patient was categorized according to their highest histopathological diagnosis (LGD<HGD<EAC) on any surveillance biopsy taken at that endoscopy. The data demonstrated that the risk of both dysplasia and EAC increased with the number of genes methylated (
All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described aspects and embodiments of the present invention will be apparent to those skilled in the art without departing from the scope of the present invention. Although the present 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 apparent to those skilled in the art are intended to be within the scope of the following claims.
| Number | Date | Country | Kind |
|---|---|---|---|
| 1208874.6 | May 2012 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/GB2013/051278 | 5/17/2013 | WO | 00 |
