# Patent

## Title
Method for detecting methylation status by using methylation-independent primers

## Abstract

A reliable and highly sensitive method is provided for detecting methylation status of CpG-containing nucleic acids by nucleic acid amplification and melting curve analysis of amplification products. The methods and compositions employs a novel design of primers, CpG-containing methylation-independent oligonucleotide primers, wherein both unmethylated and methylated alleles of a CpG-containing nucleic acid can be detected by use of only one set of primers after the CpG-containing nucleic acid has been subjected to cytosine to thymine conversion of unmethylated Cytosine. The method is useful for detection of methylation status in for example cancer genes and other disease related genes, wherein methylation influences gene expression.

## Background
All patent and non-patent references cited in the application, or in the present application, are also hereby incorporated by reference in their entirety.
FIELD OF INVENTION
The present invention relates to a method of detecting methylated CpG-containing nucleic acids by nucleic acid amplification and melting curve analysis of amplification products.
BACKGROUND OF INVENTION
The modification of DNA in eukaryotes by methylation has regulatory effects on gene regulation.
Cancer treatments, in general, have a higher rate of success if the cancer is diagnosed early and treatment is started earlier in the disease process. The relationship between improved prognosis and stage of disease at diagnosis hold across all forms of cancer for the most part. Therefore, there is an important need to develop early assays of general tumorigenesis through marker assays that measure general tumorigenesis without regard to the tissue source or cell type that is the source of a primary tumor. Moreover, there is a need to address distinct genetic alteration patterns that can serve as a platform associated with general tumorigenesis for early detection and prognostic monitoring of many forms of cancer.
Importance of DNA Methylation
Methylation of DNA is a mechanism for changing the sequence of DNA without altering its coding function. DNA methylation is a heritable, reversible and epigenetic change. DNA methylation harbours the potential to alter gene expression which in turn affects developmental and genetic processes. The methylation reaction involves flipping a target cytosine out of an intact double helix thereby allowing the transfer of a methyl group from S-adenosylmethionine in a cleft of the enzyme DNA (cytosine-5)-methyltransferase (Klimasauskas et al., Cell 76:357-369, 1994) to form 5-methylcytosine (5-mCyt). This enzymatic conversion is the only epigenetic modification of DNA known to exist in vertebrates and is essential for normal embryonic development (Bird, Cell 70:5-8, 1992; Laird and Jaenisch, Human Mol. Genet. 3:1487-1495, 1994; and Bestor and Jaenisch, Cell 69:915-926, 1992).
CpG-rich sequences are known as CpG islands (1). CpG islands are distributed across the human genome and often span the promoter region as well as the first exon of protein coding genes. Methylation of individual promoter region CpG islands usually turns off or reduce the rate of transcription by recruiting histone deacetylases, which supports the formation of inactive chromatin (2). CpG islands are typically between 0.2 to about 1 kb in length and are located upstream of many housekeeping and tissue-specific genes, but may also extend into gene coding regions. Therefore, it is the methylation of cytosine residues within CpG islands in somatic tissues, which is believed to affect gene function by altering transcription (Cedar, Cell 53:3-4, 1988).
Abnormal methylation of CpG islands associated with tumor suppressor genes may also cause decreased gene expression. Increased methylation of such regions may lead to progressive reduction of normal gene expression giving abnormal cells a growth advantage (i.e., a malignancy).
Methylation promoter regions, particularly in tumour suppressor genes, and genes involved in apoptosis and DNA repair, is one of the hallmarks of cancer (2). Changes in the methylation status of these genes are an early event in cancer and continue throughout the different stages of the cancer. Specifically, distinct tumour types often have characteristic patterns of methylation, which can be used as markers for early detection and/or monitoring the progression of carcinogenesis (3, 4). For therapeutic purposes, the methylation of certain genes, particularly DNA repair genes, can cause sensitivity to specific chemotherapeutics and methylation of those genes can thereby act as a predictive marker if those chemotherapeutic agents are used (5).
A number of current methodologies for methylation studies already exist (9). Sequencing of bisulphite-treated DNA is the gold standard for methylation studies as it reveals directly the status of each CpG dinucleotide. The technique is, however, both time consuming and cost inefficient, and therefore not immediately applicable for large scale analysis such as screening programmes.
Another technique is the methylation specific PCR (MSP) (21). U.S. Pat. No. 5,786,146 discloses a method of methylation specific PCR (MSP) for identifying DNA methylation patterns in a CpG containing nucleic acid. The method uses agents to modify unmethylated cytosine in the nucleic acid. CpG specific oligonucleotide primers are used to distinguish between modified methylated and unmethylated nucleic acid. The identification of the methylated nucleic acid is based on the presence or absence of amplification product resulting from the amplification and distinguishing modified methylated and non-methylated nucleic acids. However, methylation-specific PCR (MSP) is prone to false positive results and may result in overestimation of the number of methylated samples. Furthermore, MSP mainly offers a qualitative result of the methylation status of the target nucleic acid. The results are not easily quantified.
An alternative methodology for determination of methylation status is methylation-sensitive melting curve analysis (MS-MCA) or high resolution melting curve analysis (HRMS-MCA), which is rapid and relatively inexpensive (27). MS-MCA is a reliable technique, and the results do not need to be verified by other techniques, such as is required for example for positive MSP results. The MS-MCA technique is based on the fact that the melting temperature of methylated and unmethylated alleles are different after modification of unmethylated cytosine and amplification, which converts methylated C:G base pairs to A:T base pairs with a lower melting temperature. The standard protocol for determination of methylation status MS-MCA stipulates that the oligonucleotide primers used to amplify the target nucleic acid are devoid of CpG dinucleotides to ensure that the primers does not discriminate between methylated an unmethylated target alleles. This constraint limits the primer binding sites to regions of the template without CpG dinucleotides, which can be very difficult or impossible to find within a CpG cluster in the region of interest. Furthermore, the unmethylated and methylated alleles are not equally efficient amplified. There is a significant bias towards the unmethylated allele in the PCR amplification (23).
Currently, no methylation detection method has been established for reliable, fast and cost-effective locus specific methylation testing that is readily applicable for both research and diagnostic settings. The research-based methods have various limitations and pitfalls and contradictory results can be obtained using different protocols, therefore none of them have found ready applicability in diagnostics (9).
A new more reliable method for promoter methylation analyses in clinical samples is needed.
The present invention offers a method for the determination of methylation status of a CpG-containing nucleic acid by nucleic acid amplification employing a novel design of primers, methylation-independent oligonucleotide primers, that allows for the use of only one set of primers to detect both alleles of a CpG-containing nucleic acid after it has been subjected to C to T conversion by conventional techniques.
SUMMARY OF INVENTION
The present invention relates to methods and compositions for detection of methylated CpG-containing nucleic acids by nucleic acid amplification and subsequent analysis of amplification products.
In one aspect, the present invention relates to a method for detecting methylation status of a CpG-containing nucleic acid in a sample comprising the steps of a) modifying said CpG-containing nucleic acid using an agent which modifies at least one unmethylated cytosine in said methylated CpG-containing nucleic acid, and b) amplifying said CpG-containing nucleic acid by means of at least one methylation-independent oligonucleotide primer.
Another aspect of the present invention relates to a kit for the detection of methylation status of a CpG-containing nucleic acid in a sample, said kit comprising at least one methylation-independent oligonucleotide primer, which comprises at least one CpG dinucleotide.
In a third aspect, the present invention relates to a use of at least one methylation-independent oligonucleotide primer for detecting methylation status of a CpG-containing nucleic acid.
In all aspects of the present invention, embodiments of the methylation-independent oligonucleotide primer comprise primers which comprise at least one CpG dinucleotide, preferably in the 5′ end.



DESCRIPTION OF DRAWINGS
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee.
FIG. 1. In-tube DNA methylation-sensitive melting curve analyses (MS-MCAs) performed on five different template mixes consisting of varying ratios of fully methylated and unmethylated DNA.
The melting peaks were obtained by plotting the negative derivative of fluorescence (−dF/dT) over temperature versus temperature (T). (A) The melting profiles for the PCR product performed with primers designed according to Reference 6. The melting profiles after amplification with the redesigned primers according to the present invention containing one CpG dinucleotide each at Ta (B) 62° C. and (C) 69° C.
FIG. 2. The promoter sequence of PPP3CC (NM—005605) spanning 22,355,033-22,355,131 bp on chromosome 8p21.3. F1, R1 and F2, R2 are the primer sets used in the methylation sensitive melting curve analysis (MS-MCA) experiments. From Genome Browser, May 2004, UCSC.
FIG. 3. Annealing temperature (Ta) dependent amplification of methylated and unmethylated variants of the sequence. Melting profiles of the PCR products amplified from the promoters of two putative tumor suppressor genes. Panels A and B sequence one amplified at Ta 61° or 68° C., respectively, and panels C and D sequence two amplified at Ta 60° and 64° C., respectively.
FIG. 4. The effect of annealing temperature on the sensitivity of the MS-HRM assay. The MGMT MS-HRM1 assay was run at the following annealing temperatures. (A) 60° C., (B) 62° C. and (C) 63° C.
FIG. 5. The sensitivity of different MS-HRM assays for MGMT methylation. (A) MGMT MS-HRM1, (B) MGMT MS-HRM2 and (C) MGMT MS-HRM3. All the assays were run at the annealing temperature of 64° C. which enables the highest sensitivity of methylation detection. The results from the 0.1% methylation dilution for MGMT MS-HRM1 were not reproducible between replicates and this dilution was excluded from the figure.
FIG. 6. Validation of the MGMT MS-HRM1 assay by the MGMT MethylLight assay. The samples are the series of dilution standards and three of the cell lines (MDA MB 468, SW480 and HS578T). Panel A shows the MGMT MS-HRM1 assay and panel B shows the MethylLight assay. The MS-HRM assay was run at an annealing temperature of 61° C.
FIG. 7. The MS-HRM assay for BNIP3 methylation. Results of the BNIP3-MS-HRM assay for five clinical samples compared to the dilution standards. Samples 1-5 show different methylation levels. The samples have been distributed over three panels to help distinguish the individual samples.
FIG. 8-40. Different embodiments of the present invention. Different primer sets are disclosed for detection of methylation status in respect of specific genes. The preferred annealing temperature in respect of each primer set is indicated in each figure. The performance of the MS-HRM assay tested on the mixes on methylated template (percentage indicated in the legend and replicates in the same colour) in unmethylated template background. The examined gene name is indicated below in the legend of each figure.
FIG. 8. APC
FIG. 9. ATM
FIG. 10. BIN1
FIG. 11. BRCA1
FIG. 12. BIRC5
FIG. 13. BSG
FIG. 14. CCND2
FIG. 15. CDH1
FIG. 16. CDKN2A/p16
FIG. 17. CST6
FIG. 18. DAPK1
FIG. 19. ESR1
FIG. 20. FANCF
FIG. 21. GSTP1
FIG. 22. HIC1
FIG. 23. HIN1
FIG. 24. KL
FIG. 25. LAT52
FIG. 26. MLH1
FIG. 27. PITX2
FIG. 28. RAR beta2
FIG. 29. RASSF1A
FIG. 30. TMS1
FIG. 31. TWIST
FIG. 32. UPA
FIG. 33. ABO
FIG. 34. p15/CDKN2B
FIG. 35. RASSF1A
FIG. 36. SDHA
FIG. 37. SDHB
FIG. 38. SDHC
FIG. 39. SDHD
FIG. 40. Assay for LIT1 involved in imprinting disorders. The performance of the MS-HRM assay tested on the mixes on methylated template in unmethylated template background. Normal tissue—dotted line, Fully methylated control—solid line
FIG. 41. The example of primer design for MS-HRM assay targeting the promoter of the MGMT gene (chr10:131, 155,538-131, 155,631 by UCSC Genome Browser, March 2006). The primers were designed to include a limited number of CpGs that allowed the control of PCR bias during PCR amplification. Bold print—primer binding sites, underlined—CpGs.
FIG. 42. Melting peak analyses (first derivative of the melting curves) of the MGMT gene. Details of the MS-HRM assay are given in (6) and Note 7. The melting curves were derived from samples with known methylated to unmethylated template ratios (ranging from 100% to 0.1%) of fully methylated template diluted in unmethylated template. The experiments were performed on the LC480.
FIG. 43. a. An example of “Gene Scan” analyses (see 3.8.1.) of melting curves of the MGMT MSHRM assay (see Note 7), in which melting curves derived from mixtures of methylated and unmethylated template were normalized for input fluorescence. The use of normalization allows similarly shaped curves to be grouped together. b. An example of the estimation of the methylation levels of an unknown sample (red) on the basis of the similarity of its normalized melting profile to normalized melting profiles of standards of known methylated to unmethylated template ratios. The unknown sample shows methylation level at around 10% as its normalized melting profile is similar to the melting profile of the standard with 10% methylated template.
FIG. 44. AML samples analysed using conventional MS-HRM. MS-HRM can distinguish homogeneous from heterogeneous DNA methylation as each have characteristic melting profiles. The fully methylated DNA control is indicated by a solid black line (M ctrl), and the WGA control by a broken grey line (UM ctrl). The six AML samples are indicated by unbroken coloured lines. A. shows the normalised melting curves, and B. shows the negative first derivative (or Tm) curves. Apart from 4276, the AML samples do not fit into the range set by the controls. They begin melting before the controls, with three continuing to melt into the region normally indicative of methylation. All five show broad melting ranges, in direct contrast to the controls.
FIG. 45. MS-HRM and dMS-HRM profiles for AML samples. Negative first derivative (or Tm) curves are shown. The MS-HRM curves for the controls are shown. The fully methylated DNA control is indicated by a solid black line (M ctrl), and the WGA control by a broken grey line (UM ctrl). Digital MS-HRM peaks seen in each AML sample are shown in grey. Only one representative of each variant peak is shown for clarity.
FIG. 46. Sequencing of dMS-HRM products. A: Digital MS-HRM of sample 9164 exhibits alleles appearing to contain differing levels of methylation. The cyan peak indicated with an asterisk (*) falls beyond the upper limit of the expected region of results, and was found to contain a non-CpG cytosine that failed to be converted. B: Methylation pattern obtained by direct sequencing of the dMS-HRM products from A, shown as lollipops, where unmethylated CpG sites are filled, and unmethylated sites are open. Open and filled circles represent unmethylated and methylated CpG sites, respectively. Those denoted with a ‘c’ are control samples C: One dMSHRM product (number 69, indicated by an asterisk (*) in A) shows one incompletely converted cytosine (highlighted in red), shown in comparison to unmethylated control (above) and fully methylated control (below).



DETAILED DESCRIPTION OF THE INVENTION
The present invention provides methods, oligonucleotide primers and kits for the identification of DNA methylation patterns in a biological sample comprising CpG containing nucleic acids. Determination of methylation status of promoter regions of a number of genes is applicable for diagnosis of various diseases including hyperproliferative disorder such as cancer, imprinting disorders, environmental and age related methylation changes based disorders.
Definitions
Amplification according to the present invention is the process wherein a plurality of exact copies of one or more starting molecule (template) is synthesised, without employing knowledge of the exact composition of the starting molecule. Hence a template may be amplified even though the exact composition of said template is unknown. In one preferred embodiment of the present invention, amplification of a template comprises the process wherein a template is copied by a nucleic acid polymerase or polymerase homologue, for example a DNA polymerase or an RNA polymerase. For example, templates may be amplified using reverse transcription, the polymerase chain reaction (PCR), ligase chain reaction (LCR), in vivo amplification of cloned DNA, and similar procedures capable of generating a complementing nucleic acid sequence.
A double stranded polynucleotide contains two strands that are complementary in sequence and capable of hybridizing to one another. In general, a gene is defined in terms of its coding strand, but in the context of the present invention, an oligonucleotide primer, which hybridize to a gene as defined by the sequence of its coding strand, also comprise oligonucleotide primers, which hybridize to the complement thereof.
A nucleotide is herein defined as a monomer of RNA or DNA. A nucleotide is a ribose or a deoxyribose ring attached to both a base and a phosphate group. Both mono-, di-, and tri-phosphate nucleosides are referred to as nucleotides.
The term ‘nucleotides’ as used herein refers to both natural nucleotides and non-natural nucleotides capable of being incorporated—in a template-directed manner—into an oligonucleotide, preferably by means of an enzyme comprising DNA or RNA dependent DNA or RNA polymerase activity, including variants and functional equivalents of natural or recombinant DNA or RNA polymerases. Corresponding binding partners in the form of coding elements and complementing elements comprising a nucleotide part are capable of interacting with each other by means of hydrogen bonds. The interaction is generally termed “base-pairing”. Nucleotides may differ from natural nucleotides by having a different phosphate moiety, sugar moiety and/or base moiety. Nucleotides may accordingly be bound to their respective neighbour(s) in a template or a complementing template by a natural bond in the form of a phosphodiester bond, or in the form of a non-natural bond, such as e.g. a peptide bond as in the case of PNA (peptide nucleic acids). Nucleotides according to the invention includes ribonucleotides comprising a nucleobase selected from the group consisting of adenine (A), uracil (U), guanine (G), and cytosine (C), and deoxyribonucleotide comprising a nucleobase selected from the group consisting of adenine (A), thymine (T), guanine (G), and cytosine (C). Nucleobases are capable of associating specifically with one or more other nucleobases via hydrogen bonds. Thus it is an important feature of a nucleobase that it can only form stable hydrogen bonds with one or a few other nucleobases, but that it can not form stable hydrogen bonds with most other nucleobases usually including itself. The specific interaction of one nucleobase with another nucleobase is generally termed “base-pairing”. The base pairing results in a specific hybridisation between predetermined and complementary nucleotides. Complementary nucleotides according to the present invention are nucleotides that comprise nucleobases that are capable of base-pairing. Of the naturally occurring nucleobases adenine (A) pairs with thymine (T) or uracil (U); and guanine (G) pairs with cytosine (C). Accordingly, e.g. a nucleotide comprising A is complementary to a nucleotide comprising either T or U, and a nucleotide comprising G is complementary to a nucleotide comprising C.
The term ‘oligonucleotide’ is used herein interchangebly with polynucleotide. The term oligonucleotide comprises oligonucleotides of both natural and/or non-natural nucleotides, including any combination thereof. The natural and/or non-natural nucleotides may be linked by natural phosphodiester bonds or by non-natural bonds. Preferred oligonucleotides comprises only natural nucleotides linked by phosphodiester bonds. Oligonucleotide is used interchangeably with polynucleotide. The oligomer or polymer sequences of the present invention are formed from the chemical or enzymatic addition of monomer subunits. The term “oligonucleotide” as used herein includes linear oligomers of natural or modified monomers or linkages, including deoxyribonucleotides, ribonucleotides, anomeric forms thereof, peptide nucleic acid monomers (PNAs), locked nucleotide acid monomers (LNA), and the like, capable of specifically binding to a single stranded polynucleotide tag by way of a regular pattern of monomer-to-monomer interactions, such as Watson-Crick type of base pairing, base stacking, Hoogsteen or reverse Hoogsteen types of base pairing, or the like. Usually monomers are linked by phosphodiester bonds or analogs thereof to form oligonucleotides ranging in size from a few monomeric units, e.g. 3-4, to several tens of monomeric units, e.g. 40-60. Whenever an oligonucleotide is represented by a sequence of letters, such as “ATGCCTG,” it will be understood that the nucleotides are in 5′→3′ order from left to right and the “A” denotes deoxyadenosine, “C” denotes deoxycytidine, “G” denotes deoxyguanosine, and “T” denotes thymidine, unless otherwise noted. Usually oligonucleotides of the invention comprise the four natural nucleotides; however, they may also comprise methylated or non-natural nucleotide analogs. Suitable oligonucleotides may be prepared by the phosphoramidite method described by Beaucage and Carruthers (Tetrahedron Lett., 22, 1859-1862, 1981), or by the triester method according to Matteucci, et al. (J. Am. Chem. Soc., 103, 3185, 1981), both incorporated herein by reference, or by other chemical methods using either a commercial automated oligonucleotide synthesizer or VLSIPS.TM. technology. When oligonucleotides are referred to as “double-stranded,” it is understood by those of skill in the art that a pair of oligonucleotides exist in a hydrogen-bonded, helical configuration typically associated with, for example, DNA. In addition to the 100% complementary form of double-stranded oligonucleotides, the term “double-stranded” as used herein is also meant to refer to those forms which include such structural features as bulges and loops. For example as described in U.S. Pat. No. 5,770,722 for a unimolecular double-stranded DNA. It is clear to those skilled in the art when oligonucleotides having natural or non-natural nucleotides may be employed, e.g. where processing by enzymes is called for, usually oligonucleotides consisting of natural nucleotides are required. When nucleotides are conjugated together in a string using synthetic procedures, they are always referred to as oligonucleotides.
A plurality of individual nucleotides linked together in a single molecule may form a polynucleotide. Polynucleotide covers any derivatized nucleotides such as DNA, RNA, PNA, LNA etc. Any oligonucleotide is also a polynucleotide, but every polynucleotide is not an oligonucleotide.
The term “dinucleotide” as used herein refers to two sequential nucleotides. The dinucleotide may be comprised in an oligonucleotide or a polynucleotide. In particular, the dinucleotide CpG, which denotes a cytosine linked to a guanine by a phosphodiester bond, may be comprised in an oligonucleotide according to the present invention. A CpG dinucleotide is also herein referred to as a CpG site.
Methylation status: the term “methylation status” as used herein, refers to the presence or absence of methylation. In particular, the present invention relates to detection of methylated cytosine (5-methylcytosine). A nucleic acid sequence may comprise one or more methylation sites. The nucleic acid sequence may be methylated on all methylation sites (i.e. 100% methylated), or unmethylated on all methylation sites (i.e. 0% methylated). However, the nucleic acid sequence may also be methylated on a subset of its methylation sites, such as on at least 50%, such as on at least 60%, such as on at least 70%, for example on at least 80%, such as on at least 90%, such as on at least 95%, for example on at least 99%, such as least 99.9% of its methylation sites. The term “methylation status” as used herein reflects any relative or absolute amount of methylation of a nucleic acid sequence.
Thus, methylation may be heterogeneous and the present invention is suitable to detect sequence heterogeneity. This is because heteroduplexes created from sequence heterogeneity broaden the shape of the melting curves. The CpG position relative to the position within the amplicon can also affect shape. Both melting temperature as well as curve shape can be used in combination for epigenetic studies.
The term “PCR bias” as used herein refers to conditions, wherein PCR more efficiently amplifies a specific nucleic acid allele. In the present invention, PCR bias often relates to the fact that unmethylated nucleic acid template is more efficiently amplified than methylated nucleic acid template.
Samples
According to the present invention the nucleic acid to be analysed with respect to its methylation status as described in the present invention is obtained from a sample of any source. Thus, detection of methylated CpG may be performed on samples selected from the group consisting of breast tissue, ovarian tissue, uterine tissue, colon tissue, prostate tissue, lung tissue, renal tissue, thymus tissue, testis tissue, hematopoietic tissue, bone marrow, urogenital tissue, expiration air, stem cells, including cancer stem cell, and body fluids, such as sputum, urine, blood and sweat.
In preferred embodiments the sample is selected from the group consisting of breast tissue, ovarian tissue, uterine tissue, colon tissue, prostate tissue, lung tissue, renal tissue, thymus tissue, testis tissue, hematopoietic tissue, bone marrow, urogenital tissue, expiration air, stem cells, including cancer stem cell, and body fluids, such as sputum, urine, blood and sweat.
In another embodiment the sample is selected from the group consisting of breast tissue, ovarian tissue, uterine tissue, colon tissue, prostate tissue, lung tissue, urogenital tissue, stem cells, including cancer stem cell, and body fluids, such as sputum, urine, blood and sweat.
In even another embodiment the sample is selected from the group consisting of breast tissue, ovarian tissue, uterine tissue, colon tissue, prostate tissue and lung tissue. In yet another embodiment the sample is selected from the group consisting of stem cells and cancer stem cells.
In an even other embodiment the sample is selected from the group consisting of body fluids, sputum, urine, blood and sweat.
In an even further embodiment the sample is selected from the group consisting of ovarian tissue, uterine tissue, colon tissue, and urogenital tissue
In an especially preferred embodiment the sample is breast tissue. In another especially preferred embodiment the sample is bladder tissue. In another especially preferred embodiment the sample is colon tissue. In another especially preferred embodiment the sample is blood tissue. In another especially preferred embodiment the sample is lung tissue. In another especially preferred embodiment the sample is skin tissue. In another especially preferred embodiment the sample is prostate tissue. In another especially preferred embodiment the sample is ovarian tissue.
The nucleic acid to be analysed for the presence of methylated CpG may be extracted from the samples by a variety of techniques such as that described by Maniatis, et al (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y., pp 280, 281, 1982). However, the sample may be used directly.
Any nucleic acid, in purified or nonpurified form, can be utilized as the starting nucleic acid or acids, provided it contains, or is suspected of containing, the specific nucleic acid sequence containing the target site (e.g., CpG).
Therefore, for example, DNA or RNA, including messenger RNA, microRNA, siRNA, shRNA, rRNA, snoRNA, tRNA and SNRNA, wherein DNA or RNA may be single stranded or double stranded may be used as target material. Where RNA is to be used as a template, enzymes, and/or conditions optimal for reverse transcribing the template to DNA would be utilized as known to a person skilled in the art. A DNA-RNA hybrid which contains one strand of each may also be utilized. A mixture of nucleic acids may also be employed, or the nucleic acids produced in a previous amplification reaction herein, using the same or different primers may be so utilized.
The specific nucleic acid sequence which is to be amplified may be a part of a larger molecule or is present initially as a discrete molecule. The nucleic acid sequence to be amplified need not to be present in a pure form, it may for example be a fraction of a complex mixture of other DNA molecules, and/or RNA. In one example, the nucleic acid sequence is a fraction of a genomic nucleic acid preparation.
The amount of the nucleic acid used as target sequence according to the method of the present invention is in the range of micrograms to nanograms. It is appreciated by the person skilled in the art that in practical terms no upper limit for the amount of nucleic acid to be analysed exists. The problem that the skilled person encounters is that the amount of sample to be analysed is limited. Therefore, it is beneficial that the method of the present invention can be performed on a small amount of sample and thus a limited amount of nucleic acid in said sample. The amount of the nucleic acid to be analysed is thus at least 0.01 ng, such as 0.1 ng, such as 0.5 ng, for example 1 ng, such as at least 10 ng, for example at least 25 ng, such as at least 50 ng, for example at least 75 ng, such as at least 100 ng, for example at least 125 ng, such as at least 150 ng, for example at least 200 ng, such as at least 225 ng, for example at least 250 ng, such as at least 275 ng, for example at least 300 ng, 400 ng, for example at least 500 ng, such as at least 600 ng, for example at least 700 ng, such as at least 800, ng, for example at least 900 ng or such as at least 1000 ng.
In one preferred embodiment the amount of nucleic acid as the starting material for the method of the present invention is 50 ng, alternatively 100 ng or 200 ng.
The sample may be from any mammal including a human. For example the sample may be from mouse, hamster, rat, rabbit, cow, dog, pig, cat, sheep, goat, monkey, ape or humans. In a preferred embodiment the sample is from a human.
Modification of DNA
The method of the present invention for detecting methylation status of CpG-containing nucleic acids in a sample comprises a step of modifying the CpG-containing nucleic acids using an agent which modifies unmethylated cytosine in the CpG-containing nucleic acid. As used herein the term “modifies” refers to the conversion of an unmethylated cytosine to another nucleotide which will distinguish an unmethylated cytosine from a methylated cytosine. In one preferred embodiment, an agent modifies unmethylated cytosine to uracil. Such an agent may be any agent conferring said conversion, wherein unmethylated cytosine is modified, but not methylated cytosine. In one preferred embodiment the agent for modifying unmethylated cytosine is sodium bisulfite. Sodium bisulfite (NaHSO3) reacts readily with the 5,6-double bond of cytosine, but only poorly with methylated cytosine. The cytosine reacts with the bisulfite ion, forming a reaction intermediate in the form of a sulfonated cytosine which is prone to deamination, eventually resulting in a sulfonated uracil. Uracil can subsequently be formed under alkaline conditions which removes the sulfonate group.
During a nucleic acid amplification process uracil will by the Taq polymerase be recognised as a thymidine. The product upon PCR amplification of a Sodium bisulfite modified nucleic acid contains cytosine at the position where a methylated cytosine (5-methylcytosine) occurred in the starting template DNA of the sample. Moreover, the product upon PCR amplification of a Sodium bisulfite modified nucleic acid contains thymidine at the position where an unmethylated cytosine (5-methylcytosine) occurred in the starting template DNA of the sample. Thus, an unmethylated cytosine in converted into a thymidine residue upon amplification of a bisulfite modified nucleic acid.
In a preferred embodiment of the present invention, the CpG-containing nucleic acid are modified using an agent which modifies methylated cytosine in the CpG-containing nucleic acid. In a specific embodiment, such an agent is bisulfite.
Methylation-independent Primer
The term “methylation-independent primer” refers to the oligonucleotide primers of the present invention. A methylation-independent primer is capable of hybridizing to both methylated and unmethylated nucleic acid alleles and modified as well as unmodified alleles. The oligonucleotide primers of the present invention are capable of being employed in amplification reactions, wherein the primers are used in amplification of template DNA originating from either a methylated or an unmethylated strand. The preferred methylation-independent primers of the present invention comprise a CpG dinucleotide, as described below. Accordingly, in a methylated and bisulfite modified nucleic acid target sequence, the primer sequence will anneal to the nucleic acid template with a perfect match, wherein all of the nucleotides in a consecutive region of the primer forms base pairs with a complementary region in the nucleic acid target. However, in an unmethylated nucleic acid target after bisulfite modification, the methylation-independent primers of the present invention will anneal to the nucleic acid template with an imperfect match, wherein the primer sequence comprise a mis-match (i.e. the primer and template does not form base pairs) at the position of the unmethylated Cytosine at a CpG site in the nucleic acid template. Nonetheless, as the primers of the present invention are methylation-independent, the primers will hybridize to both unmethylated and methylated nucleic-acid sequences after bisulfite modification, and the primers will form a perfect match with the target sequence of a methylated nucleic acid target and an imperfect match, where the primers and target nucleic acid sequence does not form base pairing at the positions of unmethylated Cytosine (which is converted by bisulfite to Uracil) at CpG sites.
The methylation-independent primers of the present invention will, due to the mis-match after bisulfite modification at positions of unmethylated cytosine of a CpG-site in the nucleic acid target sequence, hybridize less efficiently to an unmethylated nucleic acid sequence. However, by reducing the stringency of hybridization, the methylation-independent primers of the present invention are able to anneal to the nucleic acid target, also when the nucleic acid target comprise unmethylated CpG-sites, which have been modified by for example bisulfite treatment. In one example, the stringency is reduced by reducing the annealing temperature as described elsewhere herein.
The design of oligonucleotide primers suitable for nucleic acid amplification techniques, such as PCR, is known to people skilled within the art. The design of such primers involves analysis of the primer's melting temperatures and ability to form duplexes, hairpins or other secondary structures. Both the sequence and the length of the oligonucleotide primers are relevant in this context. The oligonucleotide primers according to the present invention comprise between 10 and 200 consecutive nucleotides, such as at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 100, at least 110, at least 120, at least 130, at least 140, at least 150, at least 160, at least 180 or at least 200 nucleotides. In a specific embodiment, the oligonucleotide primers comprise between 15 and 60 consecutive nucleotides, such as 15, 16, 17, 18, 19, 20, preferably 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, such as 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, alternatively at least 41, at least 42, at least 44, at least 46, at least 48, at least 50, at least 52, at least 54, at least 56, at least 58, or at least 60 consecutive nucleotides.
The present invention relates to a method for determining the methylation status of a CpG-containing nucleic acid, said method comprising amplification of the CpG-containing nucleic acid by use of a methylation independent oligonucleotide primer of the present invention. In one embodiment, the oligonucleotide primers of the present invention are able to hybridize to a nucleic acid sequence comprising CpG islands. In a preferred embodiment, at least one of the oligonucleotide primers according to the present invention comprises at least one CpG dinucleotide. In another embodiment of the present invention, the oligonucleotide primers comprise 2, alternatively 3, 4, 5, 6, 7, 8, 9 or 10 CpG dinucleotides. In even further embodiments, the oligonucleotide primers of the present invention comprise at least 10 CpG dinucleotides. In one preferred embodiment the at least one methylation-independent oligonucleotide primer comprises one CpG dinucleotide at the 5′-end of the primer.
The CpG dinucleotide may be located anywhere within the oligonucleotide primer sequence. However, in a preferred embodiment of the present invention, the at least one CpG dinucleotide is located in the 5′-end of the oligonucleotide primer. In another preferred embodiment, the at least one CpG dinucleotide constitute the first two nucleotides of the 5′-end. In an even further preferred embodiments of the present invention, the at least one CpG dinucleotide is located within the first 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides of the 5′-terminus. In alternative embodiments, the at least one CpG dinucleotide is located within the first 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or 120 nucleotides of the 5′-terminus.
The primers of the present invention comprises at least one CpG site, whereby annealing with a higher efficiency to a methylated than to an unmethylated template upon modification of unmethylated cytosine is achieved. The primers of the present invention comprise at least one CpG site. However, the primers comprise also for example two CpG sites.
The at least one CpG site is positioned in the 5′ end of the primer. For example within the first 10 nucleotides in the 5′ end of the primer, within the first 9 nucleotides in the 5′ end of the primer, within the first 8 nucleotides in the 5′ end of the primer, within the first 7 nucleotides in the 5′ end of the primer, within the first 6 nucleotides in the 5′ end of the primer, within the first 5 nucleotides in the 5′ end of the primer, within the first 4 nucleotides in the 5′ end of the primer or within the first 3 nucleotides in the 5′ end of the primer. In a preferred embodiment the CpG site is introduced immediately after the first nucleotide of the 5′ end of the primer.
Specific hybridization typically is accomplished by a primer having at least 10, for example at least 12, such as at least 14, for example at least 16, such as at least 18, for example at least 20, such as at least 22, for example at least 24, such as at least 26, for example at least 28, or such as at least 30 contiguous nucleotides, which are complementary to the target template. Often the primer will be close to 100% identical to the target template. However, the primer may also be 98% identical to the target template or for example at least 97%, such as at least 96%, for example at least 95%, such as at least 94%, for example at least 93%, such as at least 92%, for example at least 91%, such as at least 90%, for example at least 89%, such as at least 88%, for example at least 87%, such as at least 86%, for example at least 85%, such as at least 84%, for example at least 83%, such as at least 82%, for example at least 81%, such as at least 80%, for example at least 79%, such as at least 78%, for example at least 77%, such as at least 76%, for example at least 75%, such as at least 74%, for example at least 73%, such as at least 72%, for example at least 71%, such as at least 70%, for example at least 68%, such as at least 66%, for example at least 64%, such as at least 62% or for example at least 60% identical to the target template. If there is a sufficient region of complementary nucleotides, e.g., at least 10, such as at least 12, for example at least 15, such as at least 18, or for example at least 20, for example at least 30, such as at least 40, for example at least 50, such as at least 60, for example at least 70 nucleotides, then the primer may also contain additional nucleotide residues that do not interfere with hybridization but may be useful for other manipulations. Examples of such other residues may be sites for restriction endonuclease cleavage, for ligand binding or for factor binding or linkers.
The methylation-independent oligonucleotide primer of the present invention is designed to hybridize to CpG-containing nucleic acids in a sample. Importantly, the CpG-containing nucleic acids in that sample are treated with an agent which modifies unmethylated cytosine in said CpG-containing nucleic acid. Thereby, any unmethylated Cytosine of CpG dinucleotides comprised in the CpG-containing nucleic acid are converted to Uracil as explained elsewhere herein. Consequently, in primers comprising a CpG dinucleotide, designed to hybridize with the complementary CpG dinucleotide of the CpG-containing nucleic acid of the sample, the CpG dinucleotide will only hybridize to the methylated CpG dinucleotide fraction of the CpG-containing nucleic acid. In the unmethylated fraction of CpG dinucleotides comprised in the CpG-containing nucleic acid of the sample, Cytosine are modified to uracil which does not hybridize with the CpG dinucleotide of the CpG-containing oligonucleotide primer.
The methylation-independent oligonucleotide primers according to the present invention are designed to comprise sufficient nucleotides for specific hybridization to the target CpG-containing nucleic acid sequence regardless of its original methylation status. In some embodiments the oligonucleotide primers also comprise one or more CpG dinucleotides, as specified elsewhere herein. These CpG dinucleotides only hybridize with the originally methylated alleles of the CpG-containing nucleic acids. Nevertheless, the oligonucleotide primers can still be functionally used for amplification of both originally methylated and unmethylated nucleic acids. The CpG dinucleotides are typically comprised in the 5′-terminus of the oligonucleotide primers, as described elsewhere herein. A primer-template mismatch within the 5′-terminus of the primer usually allow the primers to hybridize with the target CpG-containing nucleic acid, and still function as primers in an amplification reaction.
The presence of one or more mismatches between the primer and template affects the optimal annealing temperature of said oligonucleotide primer for use in amplification reactions. The more hybridizing nucleotides comprised on the oligonucleotide primers, the higher is the optimal annealing temperature. Consequently, amplification of methylated alleles of CpG-containing nucleic acids by CpG-containing oligonucleotide primers according to the present invention is favoured by increased annealing temperature. Conversely, amplification of unmethylated alleles is favoured by decreased annealing temperature. In the present invention, the PCR bias towards amplification of unmethylated alleles of a nucleic acid template is reversed by amplification of said nucleic acid template at a relatively higher annealing temperature, which favours oligonucleotide primer binding and priming of the methylated allele. By modulation of the primer annealing temperature, the priming of either the unmethylated modified allele or the methylated allele of the nucleic acid can be favoured. By increasing the annealing temperature below the theoretical optimum, the amplification of the methylated allele is favoured, while a decrease of the annealing temperature will tend to favour amplification of the unmethylated allele.
Other factors than annealing temperature also affect hybridisation to a CpG-containing target sequence of a methylation-independent primer according to the present invention. At highly stringent conditions, hybridization between perfect matching primer and target sequences are favoured, such as hybridization between a methylation-independent primer according to the present invention and a methylated target sequence upon cytosine modification. Less stringent conditions will tend to favour oligonucleotide primer binding, priming and amplification of the unmethylated allele. Modulation of temperature is one way of adjusting the stringency of hybridization, but the stringency of hybridization may also be modulated by adjusting buffer composition, and/or salt concentrations in the hybridization mixture, which is known to those of skill within the art. The present invention comprises any such method of modulating hybridization stringency to balance the PCR bias towards amplification of unmethylated template. However, modulation of temperature is preferred.
In one embodiment, the methylation-independent oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 46 to 151. In another embodiment, the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 185 to 250.
In a preferred embodiment the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 132 to 139. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 138 and 139.
In another preferred embodiment the oligonucleotide primers of the present invention are selected from the group consisting of SEQ ID NO.: 142 and 143.
In another preferred embodiment the oligonucleotide primers of the present invention are selected from the group consisting of SEQ ID NO.: 144 to 151.
In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 128 and 129. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 130 and 131. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 132 and 133. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 134 and 135. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 136 and 137. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 138 and 139. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 140 and 141. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 142 and 143. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 144 and 145. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 146 and 147. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 148 and 149. In another preferred embodiment the oligonucleotide primers of the present invention are SEQ ID NO.: 150 and 151.
In yet another preferred embodiment the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 46 to 53. In another preferred embodiment the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 54 to 61. In another preferred embodiment the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 62 to 71. In another preferred embodiment the oligonucleotide primers of the present invention are selected from the group consisting of SEQ ID NO.: 72 to 79. In another preferred embodiment the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 80 to 85. In another preferred embodiment the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 86 to 97. In another preferred embodiment the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 98 to 107. In another preferred embodiment the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 108 to 115. In another preferred embodiment the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 116 to 127. In another preferred embodiment the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 128 to 151.
In one embodiment, the methylation-independent oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 185 to 200. In another embodiment, the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 201 to 210. In a further embodiment, the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 211 to 220. In another embodiment, the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 221 to 230. In yet another embodiment, the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 231 to 240. In yet another embodiment, the oligonucleotide primer of the present invention is selected from the group consisting of SEQ ID NO.: 241 to 250.
In one embodiment, present invention relates oligonucleotide primers which specifically hybridize to regions within 1 kb of the transcription start sites of genes. In particular, the present invention relates to oligonucleotide primers, which specifically hybridize to regions within 1 kb of the transcription start sites of genes, which comprise at least one CpG dinucleotide. In a specific embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of PPP3CC, BNIP3, MGMT, SNRPN, GSTP1, RARB2, RASSF1A, TIMP3, APC, beta-Actin, PTGS2, 14-3-3 sigma, TNFRSF10B tumor necrosis factor receptor superfamily (member 10b), RUNX3 runt-related transcription factor 3, CGI-38 brain specific protein, SMPD2 sphingomyelin phosphodiesterase 2 (neutral membrane; neutral sphingomyelinase), MYBL2 v-myb myeloblastosis viral oncogene homolog (avian)-like 2, BARD1 BRCA1 associated RING domain 1,NDP Norrie disease (pseudoglioma), TM4SF11 transmembrane 4 superfamily member 11 (plasmolipin) DEKDEK oncogene (DNA binding), ASK activator of S phase kinase, HEC highly expressed in cancer, rich in leucine heptad repeats, ACTN1 actinin (alpha 1), FANCG Fanconi anemia (complementation group G), and HDGF hepatoma-derived growth factor (high-mobility group protein 1-like), or the complement thereof.
In another embodiment of the present invention the methylation-independent oligonucleotide primer hybridize to a target polynucleotide sequence of a gene selected from the group consisting of PPP3CC, BNIP3, MGMT, SNRPN, GSTP1, RARB2, RASSF1A, TIMP3, APC, beta-Actin, PTGS2 and 14-3-3 sigma, or the complement thereof.
In a further embodiment of the present invention, the methylation-independent oligonucleotide primer hybridize to a target polynucleotide sequence of a gene selected from the group consisting of TNFRSF10B tumor necrosis factor receptor superfamily (member 10b), RUNX3 runt-related transcription factor 3, TM4SF11 transmembrane 4 superfamily member 11 (plasmolipin), ACTN1 actinin (alpha 1), and FANCG Fanconi anemia (complementation group G), or the complement thereof.
In a preferred embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of CHD1, COX2, PRSS3, PYCARD, BIN1, BRCA1, LATS2, PITX2, BCL2, EYA4, GSK3B, MLH1, TIMP-3, MSH6, MTHFR, PTEN, SFN, CD109, ERS1, PCDH10, DAPK1, FHIT, P16ink4a, PRSS3, RASSF1, TMS1, CAGE-1, GPR150, ITGA8, PRDX2, SYK, ALX3, HOXD11, PTPRO, WWOX, ABHD9, CAV9, GPR78, GSTP1, HIC1, PTGS2, CSMD1, C10orf59, MGMT, BNIP3, PPP3CC CSMD1, MAP3k7, C10orf59 and GRIFK2, or the complement thereof.
In another preferred embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of BNIP3, APC, ATM, BIN1, BRCA1, BIRC5, BSG, CCND2, CDH1, CDKN2A/p16, CST6, DAPK1, ESR1, FANCF, GSTP1, HIC1, HIN1, KL, LAT52, MLH1, PITX2, RAR beta2, RASSF1A, TMS1, TWIST, UPA, ABO, CDKN2B/p15, RASSF1A, SDHA, SDHB, SDHC, SDHD and LIT1, or the complement thereof.
In a preferred embodiment of the present invention the at least one oligonucleotide primer hybridizes to a target polynucleotide sequence selected from the group consisting of SEQ ID NO.: 1-45 and 152-184, or the complement thereof.
In another embodiment of the present invention the methylation-independent oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of CHD1, COX2, PRSS3 and PYCARD, as defined in SEQ ID NO.: 1-4, or the complement thereof.
In another embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of BIN1, BRCA1, LATS2 and PITX2, as defined in SEQ ID NO.: 5-8, or the complement thereof.
In another embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of BCL2, EYA4, GSK3B, MLH1 and TIMP-3, as defined in SEQ ID NO.: 9-13, or the complement thereof.
In another embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of MSH6, MTHFR, PTEN and SFN, as defined in SEQ ID NO.: 14-17, or the complement thereof.
In another embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of CD109, ERS1 and PCDH10, as defined in SEQ ID NO.: 18-20, or the complement thereof.
In another embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of DAPK1, FHIT, P16ink4a, PRSS3, RASSF1 and TMS1, as defined in SEQ ID NO.: 21-26, or the complement thereof.
In another embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of CAGE-1, GPR150, ITGA8, PRDX2 and SYK, as defined in SEQ ID NO.: 27-31, or the complement thereof.
In another embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of ALX3, HOXD11, PTPRO and WWOX, as defined in SEQ ID NO.: 32-35, or the complement thereof.
In another embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of ABHD9, CAV9, GPR78, GSTP1, HIC1 and PTGS2, as defined in SEQ ID NO.: 36-41, or the complement thereof.
In another embodiment of the present invention the oligonucleotide primers hybridize to a target polynucleotide sequence of a gene selected from the group consisting of CSMD1 (SEQ ID NO.: 42), C10orf59 (SEQ ID NO.: 43), MGMT, BNIP3, PPP3CC CSMD1, MAP3k7, C10orf59 and GRIFK2, or the complement thereof.
In a specific embodiment of the present invention the oligonucleotide primer hybridize to a target polynucleotide sequence of a gene selected from the group consisting of APC, ATM, BIN1, BRCA1, BIRC5, BSG, CCND2, CDH1, CDKN2A/p16, CST6, DAPK1, ESR1, FANCF, GSTP1, HIC1, HIN1, KL, LAT52, MLH1, PITX2, RAR beta2, RASSF1A, TMS1, TWIST, UPA, ABO, CDKN2B/p15, RASSF1A, SDHA, SDHB, SDHC, SDHD and LIT1, as defined in SEQ ID NO.: 152-184, or the complement thereof.
In a preferred embodiment, the methods and kits of the present invention comprise oligonucleotide primers that hybridize to PPP3CC, as defined in SEQ ID NO.: 45 or 45
In another preferred embodiment, the methods and kits of the present invention comprise oligonucleotide primers that hybridize to the BNIP3 gene.
In yet another preferred embodiment, the methods and kits of the present invention comprise oligonucleotide primers that hybridize to the MGMT gene. The methylation status of the MGMT gene is predictive of various cancers (6-8). The MGMT protein removes methyl/alkyl adducts from the O6-position of guanine and thereby acts to protect the cell from undergoing transition mutations. The tumour-specific methylation of the MGMT promoter and subsequent elimination of MGMT protein activity will render tumour cells susceptible to alkylating agents used in cancer chemotherapy.
Consistently, patients whose tumour was methylated at the MGMT promoter displayed significantly higher survival rates than patients with tumours that did not show methylation of MGMT when treated with alkylating agents (6-8).
However in another embodiment, the oligonucleotide primers of the present invention hybridize to regions within exons of genes.
Amplifying Step
The method of the present invention comprises an amplifying step, wherein the CpG-containing nucleic acid is amplified by means of at least one methylation-independent oligonucleotide primer. In a preferred embodiment the amplifying step is achieved by means of two methylation-independent oligonucleotide primers. The at least one methylation-independent primer preferably comprise at least one CpG dinucleotide as described elsewhere herein.
The amplifying step is a polymerisation reaction wherein an agent for polymerisation is involved, effecting an oligonucleotide primer extension. The agent for polymerization may be any compound or system which will function to accomplish the synthesis of primer extension products, including enzymes. Enzymes that are suitable for this purpose include, for example, E. coli DNA polymerase I, Klenow fragment of E. coli DNA polymerase I, T4 DNA polymerase, other available DNA polymerases, polymerase muteins, reverse transcriptase, and other enzymes, including heat-stable enzymes (i.e., those enzymes which perform primer extension after being subjected to temperatures sufficiently elevated to cause denaturation also known as Taq polymerases). Suitable enzymes will facilitate combination of the nucleotides in the proper manner to form the primer extension products which are complementary to each locus nucleic acid strand. Generally, the synthesis will be initiated at the 3′ end of each primer and proceed in the 5′ direction along the template strand, until synthesis terminates, producing molecules of different lengths. There may be agents for polymerization, however, which initiate synthesis at the 5′ end and proceed in the other direction, using the same process as described above.
A preferred method for amplifying the CpG-containing nucleic acid by means of at least one methylation-independent oligonucleotide primer is by the polymerase chain reaction (PCR), as described herein and as is commonly used by those skilled in the art.
It is appreciated that PCR amplification requires a set of oligonucleotide primers, one forward primer and one reverse primer. According to the present invention, the forward primer is a methylation independent primer. The reverse primer is in another embodiment a methylation independent primer. However, both reverse and forward primer may be methylation independent oligonucleotide primers according to the definitions herein.
The amplification product may be of any length, however in one preferred embodiment, the amplification product comprise between 15 and 1000 nucleotides, such as between 15 and 500 nucleotides, such as between 50 and 120 nucleotides, preferably between 80 and 100 nucleotides.
The PCR reaction is characterised by three steps a) melting a CpG-containing nucleic acid template, b) annealing at least one methylation-independent oligonucleotide primer to said CpG-containing nucleic acid template, and c) elongating said at least one methylation-independent oligonucleotide primer.
Melting
The melting of a CpG-containing nucleic acid template may also be referred to as strand separation. Melting is necessary where the target nucleic acid (a CpG-containing nucleic acid) contains two complementary strands bound together by hydrogen bonds. This strand separation can be accomplished using various suitable denaturing conditions, including physical, chemical, or enzymatic means. One physical method of separating nucleic acid strands involves heating the nucleic acid until it is denatured. The denaturation by heating is the preferred procedure for melting in the present invention. Typical heat denaturation involves temperatures ranging from about 85 degrees Celsius to 102 degrees Celsius for times ranging from about 1 to 10 minutes.
The melting temperature is typically between 90 and 98 degrees Celsius, such as at least 91, for example at least 92, such as at least 94, preferably at least 95, at least 96, such as at least 97, for example at least 98 degrees Celsius. The PCR reaction mixture is incubated at the melting temperature for at least 5 seconds, alternatively at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, or at least 100 seconds.
Annealing
Separated strands are used as a template for the synthesis of additional nucleic acid strands. It is understood that the separated strands may result from the separation of complementary strands in an originally double stranded nucleic acid. However, separated strands originally single stranded are also used as templates according to the present invention. The synthesis of additional nucleic acid strands is performed under conditions that allow the hybridisation of oligonucleotide primers to templates. Such a step is herein referred to as annealing. The oligonucleotide primers form hydrogen bonds with the template.
The annealing temperature is between 40 and 75 degrees Celsius, such as at least 40, at least 45, for example at least 50, at least 52, at least 54, at least 56, at least 57, at least 58, at least 59 preferably at least 60, at least 61, at least 62, at least 63, at least 64, at least 65, at least 66, at least 67, for example at least 68, at least 69, at least 70, at least 72, at least 73, at least 75 degrees Celsius. The PCR reaction mixture is incubated at the annealing temperature for 1 to 100 seconds, such as at least 1, at least 2, at least 3, at least 4, preferably at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, alternatively at least 11, at least 13, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, or at least 100 seconds.
In a specific embodiment of the present invention, the annealing temperature is between at least 15 degrees Celsius above the optimal annealing temperature, such as at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15 degrees Celsius above the optimal annealing temperature.
The optimal annealing temperature can be calculated by standard algorithms, as known to people skilled within the art. In one embodiment, the optimal primer annealing temperature (Tm) is calculated as: Tm=4(G+C)+2(A+T), wherein G, C, A, T designates the number of the respective nucleotides. In another embodiment, the optimal primer annealing temperature (Tm) is calculated as: Tm=64.9° C.+41° C.×(number of G's and C's in the primer−16.4)/N, where N is the length of the primer. However, the annealing temperature should be empirically determined in respect of each specific primer. The modulation of the annealing temperature is used to adjust hybridization stringency as described elsewhere herein. Thus, the optimal annealing temperature should be set at a level, wherein the PCR bias towards amplification of unmethylated nucleic acid template is balanced by the less efficient annealing of methylation-independent oligonucleotide primer according to the present invention to unmethylated nucleic acid target sequence. Preferred annealing temperature in respect of a number of methylation-independent oligonucleotide primer according to the present invention are specified elsewhere herein.
Elongation
The oligonucleotide primers annealed to the template is elongated to form an amplification product. The elongating temperature depends on optimum temperature for the polymerase, and is usually between 30 and 80 degrees Celsius. Typically, the elongating temperature is between 60 and 80 degrees Celsius, such as at least 60, at least 65, at least 68, at least 69, at least 70, preferably at least 71, at least 72, at least 73, at least 74, alternatively at least 75, at least 76, at least 77, at least 78, at least 79, at least 80 degrees Celsius. The PRC reaction mixture is incubated at the elongating temperature for 1 to 100 seconds, such as at least 1, at least 2, at least 3, at least 4, preferably at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, alternatively at least 11, at least 13, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, or at least 100 seconds.
Elongation occurs in a buffered aqueous solution, preferably at a pH of 7-9.
The two oligonucleotide primers are added to the reaction mixture in a molar excess of primer: template especially when the template is genomic DNA which will ensure an improved efficiency. Deoxyribonucleoside triphosphates dATP, dCTP, dGTP, and dTTP are added to the reaction mixture, either separately or together with the primers.
An appropriate agent for effecting the primer extension reaction, referred to and described elsewhere herein as an agent for polymerization is added to the reaction mixture. It is appreciated by a person skilled in the art that for PCR the agent for polymerisation preferable is a heat-stable polymerase enzyme, such as Taq polymerase.
Cycling
The PCR method comprises incubating the nucleic acid at a cycle of different specific temperatures in order to control the steps of amplification. The amplification buffer and polymerase required for PCR are well known to people of skill within the art.
The PCR reaction mixture is incubated sequentially at the melting temperature, the annealing temperature and the elongating temperature, respectively, for a number of cycles. The PCR reaction may run between 10 and 70 cycles. Typically, the PCR reaction run between 25 and 55 cycles, such as at least 25, at least 30, at least 35, at least 40, preferably at least 45, at least 50 or at least 55 cycles.
PCR can be performed on a PCR machine, which is also known as a thermal cycler. Specifically, the thermal cycler may be coupled to a fluorometer, thus allowing the monitoring of the nucleic acid amplification in real time by use of intercalating fluorescent dyes, or other fluorescent probes. Applicable dyes according to the present invention include any DNA-intercalating dye.
Suitable dyes include ethidium bromide, EvaGreen, LC Green, Syto9, SYBR Green, SensiMix HRMTM kit dye.
Real-time PCR allows for easy performance of quantitative PCR (qPCR), which is usually aided by algorithms comprised in the software, which is usually supplied with the PCR machines.
The fluorometer can furthermore be equipped with software that will allow interpretation of the results. Such software for data analyses may also be supplied with the kit of the present invention.
Another variant of the PCR technique, multiplex PCR, enables the simultaneous amplification of many targets of interest in one reaction by using more than one pair of primers.
PCR according to the present invention comprise all known variants of the PCR technique known to people of skill within the art. Thus, the PCR technology comprise real-time PCR, qPCR, multiplex PCR.
Analysis of Amplified CpG-containing Nucleic Acids
According to the present invention the nucleic acid (target) sample is subjected to an agent that converts an unmethylated cytosine to another nucleotide which will distinguish the unmethylated from the methylated cytosine. In a preferred embodiment the agent modifies unmethylated cytosine to uracil. The modifying agent can be sodium bisulphite. During the amplification process uracil will be converted to thymidine.
Thus, after conversion of unmethylated cytosines to uracils in the nucleic acid (target) sample, the subsequent PCR amplification converts uracils to thymine. As a consequence of the sodium bisulfite and PCR-mediated specific conversion of unmethylated cytosines to thymines, G:C base pairs are converted to A:T base pairs at positions, where the cytosine was methylated.
The difference in nucleic acid sequence at previously methylated or unmethylated cytosines allows for the analysis of methylation status in a sample.
By this method, analysis of the amplified nucleic acid after treatment with a modifying agent such as sodium bisulphite and subsequent PCR amplification can reveal the methylation status of the target nucleic acid sequence. Thus, in one embodiment, the method for detection of methylation status of a CpG-containing nucleic acid according to the present invention further comprises a step of analyzing the amplified CpG-containing nucleic acids.
Specifically, the subsequent analysis of the amplified CpG-containing nucleic acid is selected from the group consisting of melting curve analysis, high resolution melting analysis, nucleic acid sequencing, primer extension, denaturing gradient gel electrophoresis, southern blotting, restriction enzyme digestion, methylation-sensitive single-strand conformation analysis (MS-SSCA) and denaturing high performance liquid chromatography (DHPLC).
In a preferred embodiment of the present invention, the analysis of the amplified CpG-containing nucleic acid is melting curve analysis. In another preferred embodiment of the present invention, the analysis of the amplified CpG-containing nucleic acid is high resolution melting analysis (HRM), as disclosed in the co-pending application entitled “analysis of methylation status by high resolution melting analysis”, hereby incorporated by reference.
Melting Curve Analysis
Melting curve analysis or high resolution melting analysis exploits the fact that methylated and unmethylated alleles are predicted to differ in thermal stability because of the difference in GC contents after bisulphite treatment and PCR-mediated conversion of methylated C:G base pairs to A:T base pairs. The melting temperature of an amplification product according to the present invention is determined by the composition of methylated and unmethylated alleles in the nucleic acid sample. If the nucleic acid is completely unmethylated, all cytosines are converted to thymines, and the resulting PCR product will have a relatively low melting temperature compared to a methylated nucleic acid. If on the other hand, the nucleic acids comprised in the sample contain methylated cytosines at all CpG dinucleotides, the melting temperature of the PCR product will be relatively higher. If the nucleic acid sample comprises a mixture of methylated and unmethylated alleles, bisulphite treatment followed by amplification will result in two distinct amplification products. The unmethylated alleles will display a low melting temperature and the methylated alleles a high melting temperature. If only a subset of the CpG dinucleotides of the target sequence contain a methylated cytosine, the amplification product represents a pool of molecules with different melting temperatures, which leads to an overall intermediate melting temperature.
Melting curve analysis is performed by incubating the nucleic acid amplification product at a range of increasing temperatures. The temperature is increased from a starting temperature of at least 50 degrees Celsius, alternatively at least 55, at least 60, at least 62, at least 64, preferably at least 65, at least 66, at least 67, at least 68, at least 69, at least 70, at least 71, at least 72, at least 73, at least 74, at least 75, for example at least 76, at least 78, at least 80, at least 82, at least 84 degrees Celsius. The temperature is then increased to a final temperature of at least 70, at least 72, at least 74, at least 76, at least 78, at least 80, at least 82, at least 84, at least 86, preferably at least 88, at least 89, at least 90, at least 91, at least 92, at least 93, at least 94, at least 95, at least 96, at least 97, at least 98, at least 99, at least 100 degrees Celsius. In one embodiment, the temperature transitions from the starting temperature to the final temperature are a linear function of time. In a specific embodiment of the present invention, the linear transitions are at least 0.05 degrees Celsius per second, alternatively at least 0.01, at least 0.02, at least 0.03, at least 0.04, at least 0.06, at least 0.07, at least 0.08, at least 0.09, at least 0.1, at least 0.2, at least 0.3, at least 0.4, at least 0.5, at least 0.6, at least 0.7, at least 0.8, at least 0.9, at least 1.0, at least 1.1, at least 1.2, at least 1.3, at least 1.4, at least 1.5, at least 1.6, at least 1.7, at least 1.8, at least 1.9, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10 degrees Celsius per second. In a preferred embodiment, the melting curve analysis is performed by incubating the nucleic acid amplification product at increasing temperatures, from 70 to 95 degrees Celsius, wherein the temperature increases by 0.05 degrees per second.
The melting of the nucleic acid can be measured by a number of methods, which are known to people within skill of the art. One method involves use of agents, which fluoresce when bound to a nucleic acid in its double stranded conformation. Such agents include fluorescent probes or dyes, such as ethidium bromide, EvaGreen, LC Green, Syto9, SYBR Green, SensiMix HRMTM kit dye. Thus, in one embodiment, the melting curve analysis is performed by measurement of fluorescence. The melting of the nucleic acid amplification product according to the present invention can then be monitored as a decrease in the level of fluorescence from the sample. After measurement of the fluorescence the melting curves can be generated by plotting fluorescence as a function of temperature.
For direct comparison of melting curves from samples that have different starting fluorescence levels, the melting curves for data collected in HRM can be normalized, as described in the examples of the present invention. Such normalization methods are known to people of skill in the art. One preferred means of normalization include calculation of the ‘line of best fit’ in between two normalization regions before and after the major fluorescence decrease representing the melting of the amplification product.
The ‘line of best fit’ is a statistical measure, designating a line plotted on a scatter plot of data (using a least-squares method) which is closest to most points of the plot. Calculation of the line of best fit is performed differentially on LightCycler and LightScanner, as illustrated in the examples of the present invention.
A platform with a combined thermal cycler and a fluorescence detector is ideal to perform intube melting analyses. Thus, in one embodiment, the melting curve analysis is performed on a thermal cycler coupled to a fluorometer, such as the Ligthcycler, LC480 (Roche) or the Rotorgene 6000 (Corbett Research). Thereby, the measurement of fluorescence, corresponding to the melting of the double stranded nucleic acid template, can be monitored in real time. In a specific embodiment, the melting curve analysis is performed immediately after amplification. This allows an in-tube methylation assay, wherein the amplification and melting curve analysis is performed sequentially without transferring the sample from the tube. This procedure reduces the risk of contamination of the sample as a result from handling during the methylation assay.
Melting curve analysis allows the determination of the relative amount of methylated CpG-containing nucleic acid in a sample. By comparison of the melting curve of an unknown sample with the melting curve of at least one standard sample comprising said CpG-containing nucleic acid, the relative amount of methylated CpG-containing nucleic acid can be estimated. Thus, the present invention relates to a method, wherein the relative amount of methylated CpG-containing nucleic acid is estimated by comparison the melting curve of at least one standard sample comprising said CpG-containing nucleic acid. In one embodiment of the present invention, said standard sample comprise any combination of methylated and unmethylated CpG-containing nucleic acid. In a specific embodiment, said standard sample comprise 100% methylated CpG-containing nucleic acid. In another specific embodiment, said standard sample comprise 100% unmethylated CpG-containing nucleic acid. In yet another specific embodiment, said standard sample comprise 50% methylated nucleic acid and 50% unmethylated CpG-containing nucleic acid. In even another specific embodiment, said standard sample comprise 0.1% 0.5%, 1%, 2%, 3%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% methylated CpG-containing nucleic acid.
In one embodiment of the present invention, wherein the relative amount of methylated CpG-containing nucleic acid in the nucleic acid sample is between 40-60%. In another embodiment, the relative amount of methylated CpG-containing nucleic acid in the nucleic acid sample is below 50%. In yet another embodiment, the relative amount of methylated CpG-containing nucleic acid in the nucleic acid sample is below 10%, below 1% or below 0.1%. Thus, the term “presence of methylation” as used herein refers to a relative amount of methylated CpG-containing nucleic acid in the nucleic acid sample of at least 0.1%, such as at least 1%, for example at least 10%, such as at least 20%, for example at least 30%, such as at least 50%, for example at least 70%, such as at least 90%, or for example at least 99%.
If the melting temperature (as measured by the melting curve) of an unknown sample is higher than the melting temperature of a standard sample, then the relative amount of methylated CpG-containing nucleic acid in said unknown sample is also higher than the relative amount of methylated CpG-containing nucleic acid in the standard sample.
Conversely, if the melting curve of an unknown sample is lower, i.e. the melting temperature is lower, than the melting temperature of a standard sample, then the relative amount of methylated CpG-containing nucleic acid in said unknown sample is also lower than the relative amount of methylated CpG-containing nucleic acid in the standard sample. The amount of standard samples included in the melting curve analysis, thus determines the precision of the determination of methylation status. The more standard samples, the more precise can the relative amount of nucleic acids be determined.
Thus, in one embodiment of the present invention a higher melting temperature of the amplified nucleic acid sample than of the standard sample is indicative of a higher relative amount of methylated nucleic acid of that sample than of the standard sample.
Conversely, a lower melting temperature of the amplified nucleic acid sample than of the standard is indicative of a lower relative amount of methylated nucleic acid of that sample than of the standard sample.
Peak Melting Temperature.
The term “peak melting temperature” as used herein, refers to the temperature at which the largest discrete melting step occurs. The nature of nucleic acid melting is explained elsewhere herein. The top of the peak corresponds to the major drop in fluorescence on melting curve
The peak melting temperature corresponds to the highest level of the negative derivative of fluorescence (−dF/dT) over temperature versus temperature (T). (−dF/dT) versus temperature (T) is graphically illustrated in FIG. 1 and FIG. 3 for different nucleic acid targets. A nucleic acid sample subjected to melting curve analysis may display more than one peak melting temperature. In a preferred embodiment of the present invention, the melting curve analysis display at least 1, 2 or 3 peak melting temperatures.
Nucleic Acid Sequencing
In another embodiment of the present invention, the method for analysis of the amplified nucleic acid is sequencing of the nucleic acid. By nucleic acid sequencing the order of nucleotides (base sequences) in the nucleic acid is determined. Sequencing is usually performed by extending a primer, which anneals to the nucleic acid sequence of interest. The primer is extended by a polymerase in the presence of deoxynucleonucleotides.
In the dideoxy sequencing method 2,3-Dideoxyribose—a deoxyribose sugar lacking the 3 hydroxyl group is incorporated into the extended polynucleotide chain. When 2,3-Dideoxyribose is incorporated into a polynucleotide chain, it blocks further chain elongation. This method is also known as the Sanger method or chain termination method. The primer is extended in the presence of the normal dNTPs (A, T, G, C) and a small amount of 2,3-DideoxyriboseNTPs (ddNTP). The reactions are either performed in four separate reactions, one for each of the ddNTPs (ddATP, ddTTP, ddCTP, ddGTP), or in a joint reaction, wherein ddATP, ddTTP, ddCTP and ddGTP are coupled to different fluorescent dyes. The primers are then extended to variable lengths, each transcript being terminated upon incorporation of a ddNTP. The sequence of the nucleic acid of interest can then by read after denaturing polyacrylamide gel electrophoresis. Such sequencing techniques are known to people skilled within the art. Additionally, a number of different commercial kits are available for sequencing of nucleic acids.
Primer Extension
In yet another embodiment of the present invention, the method for analysis of the amplified nucleic acid is primer extension. The primer extension method uses primers designed to hybridize with a target. The primers may end one base upstream of the position of the putative single nucleotide polymorphism, in this method, the C of a CpG dinucleotide. In the single nucleotide primer extension technique a single chain-ending nucleotide, such as a ddNTP, is added. The only one of the four nucleotides that will extend the primer is the one that is complementary. The identity of the added nucleotide is determined in a variety of ways known to people of general skill within the art. For example, the chain-ending nucleotide may be radioactively labelled or coupled to a fluorescent dye, which can subsequently be identified.
Restriction Enzyme Digestion
In a further embodiment, the method according to the present invention for analysis of the amplified nucleic acid is restriction enzyme digestion. Restriction enzymes can be divided into exonucelases and endonucleases. In a specific embodiment, the analysis of the amplified nucleic acid is restriction endonuclease digestion.
The method of the present invention results in the specific conversion of unmethylated cytosines to thymines, i.e. G:C base pairs are converted to A:T base pairs at positions, where a cytosine was methylated. This means that the nucleic acid sequence is changed, which may lead to disruption of a restriction endonuclease site or the change of a site specific for one restriction endonuclease to another restriction endonuclease.
In a preferred embodiment of the present invention, the modified and amplified nucleic acid is analyzed for disruption of a site specific for the endonuclease AciI, BstUI, HhaI, HinP1I, HpaII, HpyCH4IV, MspI, TaqαI, Fnu4HI, Hpy188I, HpyCH4III, NciI, ScrFI, BssKI, Hpy99I, Nt.CviPII. StyD4I, AatII, AccI, AcI, AfeI, AflIII, AgeI, AvaI, BanI, BmgBI, BsaAI, BsaHI, BsaJI, BsaWI, BsiEI, BsiWI, BsoBI, BspDI, BspEI, Barbie, Bari, Bessie, Byssi, Bestir, Begin, Scab 8I, Clay, Eerie, Eagan, Sip, Haiti, Hindi, Hpy188III, Kais, Mule, Slab 1I, NaeI, NarI, NgoMIV, NlaIV, Brui, Pear 7I, PmlI, PvuI, SacII, SalI, SfoI, SmaI, SmlI, SnaBI, TliI, TspMI, XhoI, XmaI, ZraI, RsrII, AscI, AsiSI, FseI, NotI, PspXI, SgrAI, AlwNI, DraIII, PflFI, Tth111I, AleI, BsaBI, MslI, PshAI, XmnI, AhdI, BglI, BslI, BstAPI, EcoNI, MwoI, PfIMI, BsmBI, FauI, BstXI, DrdI, SfiI, XcmI, HgaI, EciI, BceAI, BtgZI, MmeI, NmeAIII, BsaXI, BcgI, CspCI, BaeI, AccII, AspLEI, Bsh1236I, BsiSI, BstFNI, BstHHI, CfoI, HapII, Hin6I, HspAI or MaeII. The digested nucleic acid sample is subsequently analysed by for example gel electrophoresis.
Denaturing Gradient Gel Electrophoresis
In another embodiment of the present invention, the method for analysis of the amplified nucleic acid is denaturing gradient gel electrophoresis (DGGE). In this technique, the modified and amplified nucleic acid is loaded on a denaturing gel. This techniques allows the resolution of nucleic acids with different melting temperatures, which is based on the conversion of C:G base pairs to A:T base pairs, explained elsewhere herein. For DGGE analysis the nucleic acid is subjected to denaturing polyacrylamide gel electrophoresis, wherein the gel contain an increasing gradient of denaturants, such as for example a combination of urea and formamide. The increasing denaturant concentration corresponds to increased temperature, and therefore, a gradient of denaturants mimics a temperature gradient within the gel. The concentrations of denaturants alone, however, are not sufficient to induce DNA melting. Therefore, the gel is immersed in a electrophoresis buffer kept at 54-60 degrees Celsius. When a nucleic acid molecule reaches a level of denaturant that matches the melting temperature of the lowest melting domain, a partially melted intermediate will be formed that moves very slowly. Small shifts in the melting temperature of the low melting domain induced by differences in G:C content will cause the domain to unwind at different concentrations of denaturant. Accordingly, the modified and amplified nucleic acid of the present invention will bi retarded at different positions in the gel, providing the basis for physical separation between species with different G:C contents.
Southern Blotting
In another embodiment of the present invention, the method for analysis of the amplified nucleic acid is Southern blotting. In this procedure, the nucleic acid to be analysed are separated by gel electrophoresis and transferred to a nitrocellulose filter, whereto it is immobilized. After immobilization, the transferred nucleic acids can be identified by hybridization with specific probes comprising a complementary nucleic acid. After hybridization and removal of excess unbound probe, the amount of hybridized indicate whether the sequence of interest was represented in the nucleic acids immobilized on the nitrocellulose membrane. The probes are usually radioactively labelled for subsequent detection by radiography. The details of the southern blotting technique are well known to people of skill within the art.
Temperature increments or increasing concentration of denaturants result in a series of melting steps of the double-stranded DNA molecule. Each melting step represents the melting of a discrete segment also known as a melting domain. Several melting domains may be present in a double stranded DNA molecule. The interaction of a C on one DNA strand with a G on the other DNA strand of the double-stranded molecule, referred to as a G:C base pair, involves three hydrogen bonds. The interaction of an A on one strand DNA strand with a T on the other DNA strand of the double-stranded molecule, referred to as an A:T base pair, involves two hydrogen bonds. Therefore, the melting temperature of a melting domain increases with an increase in G:C content.]
Methylation-Sensitive, Single-Strand Conformation Analysis (MS-SSCA)
MS-SSCA is a method of screening for methylation changes. MS-SSCA uses single-strand conformation analysis for the screening of an amplified region of bisulfite-modified nucleic acid. The amplified products are denatured and electrophoresed on a nondenaturing polyacrylamide gel, whereby the sequence differences between unmethylated and methylated sequences lead to the formation of different secondary structures (conformers) with different mobilities. Once the normal mobility pattern is established, any variation would indicate some degree of methylation.
Denaturing High Performance Liquid Chromatography (DHPLC)
DHPLC is yet another technique for methylation screening of bisulfite-modified PCR products. As for other techniques mentioned herein, DHPLC identifies single nucleotide polymorphisms, which are arise after bisulfite treatment of unmethylated alleles of the CpG containing nucleic acid. The optimum temperature for DHPLC can be predicted by the sequence of the fully methylated product. Subsequently, the temperature is verified to obtain tight peaks. The retention time of the peak reflects methylation status, because the more unmethylated the target is, the less GC rich the PCR product is and the lower the retention time is.
Disorders
The method of the present invention can by applied for the diagnosis of disorders, of which the presence or absence of CpG methylation is indicative of the disorder. In the case of protooncogenes, the absence of CpG methylation is usually indicative of an increased risk of developing cancer. Also, demethylation of transposable elements, such as retrotransposons may be indicative of an increased risk of developing cancer. Conversely, for tumour suppressor genes, the presence of CpG methylation is usually indicative of an increased risk of developing cancer.
In one embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence or absence of methylated CpG-containing nucleic acid is indicative of a disorder selected from the group consisting of Alzheimer's disease, atherosclerosis, breast cancer, bladder cancer, ovarian cancer, melanoma, prostate cancer, lung cancer, renal cancer, colon cancer, gastric cancer, cervical cancer, leukaemia, low grade astrocytoma, anaplastic astrocytoma, glioblastoma, haematopoietic disorders, medulloblastoma, leukemia, metabolic disorders, endometrial cancer, neuroblastoma, diffuse large B-cell lymphoma, developmental disorders, Prader-Willi syndrome, Angelman syndrome and imprinting disorders.
In a preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of a disorder selected from the group consisting of breast cancer, bladder cancer, ovarian cancer, melanoma, prostate cancer, lung cancer, colon cancer, endometrial cancer and leukaemia.
In another preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of breast cancer.
In yet another preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of bladder cancer.
In another preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of ovarian cancer.
In another preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of melanoma.
In another preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of prostate cancer.
In another preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of lung cancer.
In another preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of colon cancer.
In another preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of endometrial cancer.
In another preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of leukaemia.
In another preferred embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of colon cancer.
In one embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of a disorder selected from the group consisting of gastric cancer and cervical cancer.
In one embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the presence of methylated CpG-containing nucleic acid is indicative of imprinting disorders.
In one embodiment, the methods and kits of the present invention can be used for the detection of methylation status of CpG-containing nucleic acids in a sample, wherein the absence of methylated CpG-containing nucleic acid is indicative of imprinting disorders.
In a specific embodiment the methods and kits of the present invention comprise the primers according to SEQ ID NO.: 46 and 47 for the detection of methylation status of CHD1 as defined in SEQ ID NO.: 1, wherein the primer annealing temperature during amplification is 59 degrees Celsius, and the presence of methylation is indicative of Bladder cancer.
In another specific embodiment the methods and kits of the present invention comprise the primers according to SEQ ID NO.: 60 and 61 for the detection of methylation status of PITX2 as defined in SEQ ID NO.: 8, wherein the primer annealing temperature during amplification is 60 degrees Celsius, and the presence of methylation is indicative of Breast cancer.
In another specific embodiment the methods and kits of the present invention comprise the primers according to SEQ ID NO.: 68 and 69 for the detection of methylation status of MLH1 as defined in SEQ ID NO.: 12, wherein the primer annealing temperature during amplification is 62 degrees Celsius, and the presence of methylation is indicative of Colon cancer.
In another specific embodiment the methods and kits of the present invention comprise the primers according to SEQ ID NO.: 72 and 73 for the detection of methylation status of MSH6 as defined in SEQ ID NO.: 14, wherein the primer annealing temperature during amplification is 59 degrees Celsius, and the presence of methylation is indicative of Endometrial cancer.
In another specific embodiment the methods and kits of the present invention comprise the primers according to SEQ ID NO.: 80 and 81 for the detection of methylation status of CD109 as defined in SEQ ID NO.: 18, wherein the primer annealing temperature during amplification is 60 degrees Celsius, and the presence of methylation is indicative of Leukemia.
In another specific embodiment the methods and kits of the present invention comprise the primers according to SEQ ID NO.: 92 and 93 for the detection of methylation status of PRSS3 as defined in SEQ ID NO.: 24, wherein the primer annealing temperature during amplification is 59 degrees Celsius, and the presence of methylation is indicative of Lung cancer.
In another specific embodiment the methods and kits of the present invention comprise the primers according to SEQ ID NO.: 104 and 105 for the detection of methylation status of PRDX2 as defined in SEQ ID NO.: 30, wherein the primer annealing temperature during amplification is 61 degrees Celsius, and the presence of methylation is indicative of Melanoma.
In another specific embodiment the methods and kits of the present invention comprise the primers according to SEQ ID NO.: 114 and 115 for the detection of methylation status of WWOX as defined in SEQ ID NO.: 35, wherein the primer annealing temperature during amplification is 62 degrees Celsius, and the presence of methylation is indicative of Ovarian cancer.
In another specific embodiment the methods and kits of the present invention comprise the primers according to SEQ ID NO.: 116 and 117 for the detection of methylation status of ABHD9 as defined in SEQ ID NO.: 36, wherein the primer annealing temperature during amplification is 60 degrees Celsius, and the presence of methylation is indicative of Prostate cancer.
Kit
One aspect of the present invention relates to Another aspect of the present invention relates to a kit for the detection of methylation status of a CpG-containing nucleic acid in a sample, said kit comprising at least one methylation-independent oligonucleotide primer, which comprises at least one CpG dinucleotide. A kit will typically comprise both a forward and a reverse primer to be used in the amplifying step of the present invention. The forward primer, the reverse primer or both may be a methylation-independent oligonucleotide primer as described herein.
In one embodiment the kit further comprises at least one reference sample comprising control CpG-containing nucleic acid. Such a control CpG-containing nucleic acid is at least 97% identical to the target CpG-containing nucleic acid which is the object for detecting the methylation status. The target CpG-containing sequence may be any sequence prone to methylation or demethylation, for example tumor suppressor genes, oncogenes, retrotransposons as described elsewhere herein. For example, the at least one reference sample comprises 100% methylated CpG-containing nucleic acid, and/or 100% unmethylated CpG-containing nucleic acid. In a preferred embodiment the kit comprises at least two reference samples, wherein one of said reference samples comprises 100% methylated CpG-containing nucleic acid and a second reference sample comprises 100% unmethylated CpG-containing nucleic acid. The methylated and unmethylated CpG-containing nucleic acids may be mixed, by a person employing the kit, in ratios that are suitable for the detection of methylation in a particular sample.
It is understood that control samples in different ratios of methylated to unmethylated CpG-containing nucleic acids may be comprised in the kit. For example the kit may comprise, at least one reference sample comprising 50% methylated and 50% non-methylated nucleic acid.
The kit may also comprise additional reagents used in the amplifying step of the detection method as disclosed herein. Thus, the kit may further comprise deoxyribonucleoside triphosphates, DNA polymerase enzyme and/or nucleic acid amplification buffer. In another embodiment the kit further comprises an agent that modifies unmethylated cytosine nucleotides. Such an agent may for example be bisulfite.
The kit may in preferred embodiments further comprise instructions for the performance of the detection method of the kit and for the interpretation of the results. The kit involves the method of detecting the methylation status of a CpG-containing nucleic acid, wherein said CpG-containing nucleic acids is modified using an agent which modifies at least one unmethylated cytosine in said methylated CpG-containing nucleic acid and amplifying said CpG-containing nucleic acid by means of at least one methylation-independent oligonucleotide primer. The instructions for performing the method of the kit comprises for example information of particular annealing temperatures to be used for the at least one methylation-independent primers, as well as for example information on cycling parameters. The kit may further comprise instructions for the interpretation of the results obtained by the method. For example how to interpret the amplified products subsequently analysed by melting curve analysis or methods as described elsewhere herein. Information of the interpretation of melting curve analysis is described elsewhere herein.
The kit may in preferred embodiments further comprise software comprising an algorithm for calculation of primer annealing temperature and interpretation of results.
Preferred embodiments for the CpG-containing nucleic acid for which the methylation status is determined are CpG-containing nucleic acids having a sequence, which is at least 97% identical to the sequence selected from the group consisting of SEQ ID NO.: 1-45 and SEQ ID NO: 152-184.
The at least one methylation-independent oligonucleotide primer of the kit is selected from the group consisting of SEQ ID NO.: 46-151 and SEQ ID NO: 185-250.
It is appreciated that the kit may be used for the diagnosis of a disorder as specified elsewhere herein. The specific embodiments are described elsewhere herein.
Use
In one aspect, the present invention relates to the use of a methylation-independent oligonucleotide primer for detecting methylation status of a CpG-containing nucleic acid. Embodiments of that use comprise any methylation-independent oligonucleotide primer as described elsewhere herein. In a preferred embodiment, the primer comprises at least one CpG dinucleotide, such as at least two CpG dinucleotide. The CpG dinucleotide is preferably located in the 5′ end region of the primer. In one example, the methylation-independent oligonucleotide primer for the use according to the present invention is any such primer, however in a preferred embodiment, the primer is selected from the group consisting of SEQ ID NOs: 46-150 and SEQ ID NOs: 185-250. In another embodiment, the primer is as described elsewhere herein
Moreover, the use according to the present invention comprises detecting methylation status of any CpG-containing nucleic acid. In a preferred embodiment, the CpG-containing nucleic acid is selected from the group consisting of SEQ ID NOs: 1-45 and SEQ ID NOs: 151-184. In another embodiment, the CpG-containing nucleic acid is as defined elsewhere herein.
EXAMPLES
Example 1
Modification of CpG Containing Nucleic Acid in Sample
For bisulfite conversion the following reagents were used: 3 M sodium bisulfite, 10 mM hydroquinone, 3 M NaOH and 0.3 M NaOH.
200 ng of sample DNA is mixed with water up to final volume 18 μL. The DNA is denatured by adding 2 μL 3 M NaOH and incubating for 10 min at 37° C. followed by 5 min at 95° C. and directly placing the mixture on ice.
208 μL freshly prepared 3 M sodium bisulfite is added (final concentration 2.6 M) and 12 μL hydroquinone solution (final concentration 0.5 mM). The mixture is mixed with pipet, and incubated for 16 h (overnight) at 55° C.
The bisulfite reaction is diluted with water up to volume of 350-400 μL and the resulting solution transferred to an assembled Microcon YM-100 centrifugal filter unit.
The solution is subjected to centrifugation at 2800 rpm using a Model 5417R centrifuge (Eppendorf, Westbury, N.Y., USA) for 10 min. The filtrate is discarded, and 250 μL water is added to upper chamber, and centrifuged for 12 min at 2800 rpm. This filtration step is repeated. Again the filtrate is discarded and 300 μL 0.3 M NaOH is added to the upper chamber, incubated at 37° C. for 15 min, and centrifuged for 6 min at 2800 rpm. The resulting filtrate is discarded and 250 μL water is added to the upper chamber, and centrifuged at 2800 rpm for 15 min.
The sample is eluted by adding 50 μL Tris-EDTA (TE) buffer, mixed by use of a pipet, and allowed to stand for 15 min. The device is inverted and the TE solution of the bisulfite-converted DNA is transferred to a clean tube. The bilsulfite-converted DNA is kept overnight at −20° C. before use for analyses.
Amplification of Modified CpG Containing Nucleic Acids
The PCR amplifications were performed using the LightCycler® System (Roche Applied Science, Indianapolis, Ind., USA). The reaction mixture consisted of 10 pmol of each primer, 3 mM MgCl2, 1× LightCycler FastStart DNA Master SYBR® Green I (Roche Applied Science), and 1 μL bisulfite-treated DNA stock in a final volume 10 μL. The PCR amplification was initiated by heating to 95° C. for 10 min, followed by 45 cycles comprising 95° C. for 10 s, Ta (depending on primer set) for 10 s, and 72° C. for 10 s. Melting analyses were performed immediately after amplification, and the fluorescence of LightCycler FastStart DNA Master SYBR Green I was measured during linear temperature transition from 70°-95° C. at 0.05° C./s. The melting peaks were obtained by plotting the negative derivative of fluorescence (−dF/dT) over temperature versus temperature (T). FIG. 1 (A) The melting profiles for the PCR product performed with primers designed according to Reference 6. The melting profiles after amplification with the redesigned primers containing one CpG dinucleotide each at Ta (B) 62° C. and (C) 69° C.
The PCR bias toward the unmethylated allele due to the difference in CG content after bisulfite treatment was tested using different ratios of methylated and unmethylated DNA [CpGenomeTM Universal Methylated DNA (Chemicon, Temecula, Calif., USA) and peripheral blood DNA as methylated and unmethylated control, respectively]. The majority of assays showed a positive methylation specific signal only in samples containing >50% methylated template. Representative results are shown in FIG. 1A, in which the target is a portion of the putative tumor suppressor gene PPP3CC.
Two changes were introduced in an attempt to address these limitations. First, the primers were redesigned to contain a limited number of CpG sites, thereby to anneal with a higher efficiency to the methylated than to the unmethylated template. FIG. 2 shows the original and redesigned primers for methylation screening experiments of PPP3CC. The new primer sets efficiently amplified both methylated and unmethylated alleles (FIG. 1B). Moreover, depending on the primer annealing temperature (Ta) during PCR, we were able to control the bias of the PCR amplification. At a relatively low Ta, both the methylated and unmethylated templates were amplified with comparable efficiency (FIG. 1B), whereas elevating the Ta resulted in a significantly more efficient amplification of the methylated template (FIG. 1C). In summary, by adjusting the Ta of the PCR amplification we were able to improve the sensitivity of our assay.
Example 2
Validation of our approach was performed using four assays previously designed according to Reference 26. The assays were developed to screen for methylation of putative tumor suppressor genes in prostate cancer samples, and two of them showed methylation in <15% of samples in our panel. The redesigned primers according to the present invention were tested using templates containing defined mixtures of methylated and unmethylated DNA in experiments analogous to those shown in FIG. 1. In all cases, the assays followed the pattern shown here for PPP3CC gene (i.e., depending on Ta, the same primer set was able to amplify the methylated allele of the gene of interest with higher efficiency; see FIG. 3). In panels A and B of FIG. 3 the promoter region of the CSMD1 gene (SEQ ID NO.:42) is amplified at annealing temperatures 61° or 68° C., respectively, by use of the primers identified by SEQ ID NO.: 144 and 145. In panels C and D a CpG rich region of the MAP3k7 gene is amplified at annealing temperatures Ta 60° and 64° C., respectively by use of the primers identified by SEQ ID NO.: 146 and 147.
For the two assays that previously had been used to detect methylation in clinical samples, the modified procedure allowed detection of 40%-50% more methylated samples from the same sample panel (unpublished data). The observed differences in methylation detection levels most likely result from increased sensitivity of the redesigned assays.
Analyses of primer sequences used during these experiments showed that more than two CpG sites in the sequence of a single primer resulted in no amplification of unmethylated template (data not shown) and that the primer CpG sites should be kept as close as possible to the 5′ end of the primer sequence.
The primer design approach of the present invention—allowing CpG nucleotides into the primer sequences—significantly increases the flexibility in selection of amplification targets suitable for analyses, which is crucial for the experiment as the sequences subjected to MS-MCAs ideally should contain only one melting domain to ensure unambiguous results in the post-PCR melting analysis (29). Furthermore, the use of one primer set that is able to amplify both the methylated and unmethylated templates overcomes the problem of heterogeneous methylation of the primer binding sites, as primers always amplify the sequence of interest, no matter the methylation status of CpG sites included in primer binding sites.
This modified MS-MCA methodology serves as an alternative to other qualitative techniques currently used in methylation studies. By allowing users to control for the bias of PCR amplification, this method has potential in semiquantitative applications. The use of intercalating dyes reduces the costs of the experiments, as there is no need for the use of expensive probes. The method is characterized by high sensitivity; in our experiments we used a DNA bisulfite treatment protocol requiring only 200 ng genomic DNA, as described herein. This feature is especially relevant for diagnostics and cancer research experiments, which are frequently limited by a low quantity of tumor DNA.
Example 3
Methylation-sensitive High Resolution Melting (MS-HRM): a New Approach for Sensitive and High-throughput Assessment of Methylation
This example illustrates that high resolution melting analysis (HRM) is a sensitive and specific method for the detection of methylation. Methylated DNA and unmethylated DNA acquire different sequences after bisulphite treatment resulting in PCR products with markedly different melting profiles. We used PCR to amplify both methylated and unmethylated sequences and assessed HRM for the determination of the methylation status of the MGMT promoter region. Reconstruction experiments showed that MGMT methylation could be detected at levels as low as 0.1%. Moreover, MS-HRM allows for estimation of the methylation level by comparing the melting profiles of unknown PCR products to the melting profiles of PCR products derived from standards with a known unmethylated to methylated template ratio. Here, MS-HRM is used for the analysis of eight cell lines of known methylation status and a panel of colorectal cancer specimens. The simplicity and high reproducibility of the MS-HRM protocol makes MS-HRM the method of choice for methylation assessment in many diagnostic and research applications.
DNA Samples and Controls
Colorectal cancer samples were provided by the Peter MacCallum Cancer Centre Tissue Bank. DNA was extracted from those samples by using the DNeasy Tissue Extraction Kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. DNA from cell lines was purified by using the salting out method (11). As a positive/methylated control in our experiments, we used CpGenomeTM Universal Methylated DNA (Chemicon, Millipore, Billerica, Mass.). DNA from peripheral blood mononuclear cells was used as a negative/unmethylated reference. To create the range of methylated and unmethylated allele dilutions, the above two controls were mixed in 0.1, 1, 10 and 50% methylated to unmethylated template ratios. Each of our experimental runs included the range of methylated/unmethylated standards.
Bisulphite Modification
We used the MethylEasyTM Kit (Human Genetic Signatures, Sydney, Australia) for bisulphite modification of the DNA. The starting amount of DNA for all the bisulphite modifications was 1 mg and all the modification reactions were performed according to the manufacturer's protocol with the exclusion of the second 70% ethanol wash.
High Resolution Melting Analysis (HRM)
PCR amplification and high resolution melting analysis were carried out sequentially on a Rotor-GeneTM 6000 (Corbett Research, Mortlake, Australia). PCR was carried out in a 20 ml total volume containing: 1× Buffer, 4mM Mgb2,200 mM of each of the four dNTPs, 250 nM of each primer, 5 mM Syto9 dye (Invitrogen, Carlsbad, Calif.), 1U HotStarTaq polymerase (Qiagen) and 1 ml of bisulphite modified template (theoretical concentration 20 ng/ml). The amplification consisted of 15 min at 95° C., followed by 50 cycles of 5 s 95° C., 5 s at the primer annealing temperature (Ta) and 10 s at 72° C. High resolution melting analyses were performed at the temperature ramping and florescence acquisition setting recommended by the manufacturer i.e. temperature ramping from 70-95° C., rising by 0.1° C. /2 s. All the reactions were performed in triplicate. The melting curves were normalized by calculation of the ‘line of best fit’ in between two normalization regions before and after the major fluorescence decrease representing the melting of the PCR product using the software provided with the Rotor-GeneTM 6000. This algorithm allows the direct comparison of the samples that have different starting fluorescence levels.
MGMT MethylLight Assay
The MGMT MethylLight assay used for validation of our experiments was as previously reported (12). The reaction consisted of: 1× Buffer, 4 mM Mgb2, 200 mM of each of the four dNTPs, 500 nM of each primer, 200 nM of probe, 1 U HotStarTaq polymerase and 1 ml of bisulphite modified template (theoretical concentration 20 ng/ml). The real-time amplifications were carried over and analysed on a Rotor-GeneTM 3000 machine (Corbett Research). After 15 min at 95° C., 50 cycles of 95° C. for 15 s and 60° C. for 30 s were performed. The assay was optimized on the same range of methylated/unmethylated template mixes as in MS-HRM analyses. All the PCR amplifications were performed in triplicate. MGMTMS-HRM and BNIP3 MS-HRM assays The primer sets for all MS-HRM assays were designed according to the principles recently set out to compensate for PCR bias (13). The primers were designed to amplify both methylated and unmethylated template. The primers used and the amplified sequences are disclosed in the co-pending application entitled “Method for detecting methylation status by using methylation-independent primers”, hereby incorporated by reference.
The Sensitivity of the MS-HRM Assay
The sensitivity of the MGMT MS-HRM assay was tested by using dilutions of fully methylated control DNA into peripheral blood DNA. The inclusion of CpGs in the primer sequence gave us the possibility to direct the PCR bias towards the methylated templates by manipulating the annealing temperature of PCR amplification and, therefore, making our assays more sensitive for methylation detection. All assays showed annealing temperature dependent sensitivity (FIG. 4). The first assay that we designed (MGMT MS-HRM1) targeted a 175-bp long fragment of the MGMT promoter.
This assay did not give reproducible methylation signals at the 0.1% methylation measurement point. We addressed this by redesigning the primers to amplify shorter fragments of the template. Two new assays MGMT MS-HRM2 and MGMT MS-HRM3 amplified fragments of 109 and 94 bp, respectively. Both MGMT MS-HRM2 and MGMT MS-HRM3, when run at the annealing temperature that significantly favoured amplification of methylated template, were able to reproducibly detect methylation in the samples containing 0.1% methylated template shown in FIGS. 5B and C.
Profiling of Methylation Content of the Samples by MS-HRM
The consistency of normalized melting profiles derived from samples with different ratios of methylated and unmethylated template was tested. The normalized melting profiles of the PCR product amplified from the same mix of methylated and unmethylated template were consistent between replicates and between different runs (data not shown). Furthermore, the shapes of normalized melting profiles were amplification independent as samples with different starting amount of template displayed very similar profiles. The consistency of HRM profiles allows the design of MS-HRM for estimation of the methylation content of unknown samples on the basis of similarities of normalized HRM profiles. Nevertheless, when designing MS-HRM the length and the number of differences between methylated and unmethylated PCR products need to be taken into account. A short product will give high sensitivity but limited resolution between different levels of methylation because of the smaller differences in melting profiles between methylated and unmethylated products (FIG. 5 and unpublished data). On the other hand, a longer product will give readily distinguishable HRM profiles for PCR products derived from samples with different ratios of methylated and unmethylated template which will allow for the estimation of the methylated proportion of an unknown sample on the basis of similarities of HRM profiles of standards and unknown (FIGS. 4, 6A and 7). However, the annealing temperature at which the PCR amplification is in equilibrium between methylated and unmethylated product has to be empirically determined prior to analyses.
Validation of MS-HRM Results Against the MethylLight Assay
We validated the performance of the MGMT MS-HRM1 assay against a previously described MethylLight assay for the MGMT promoter region (12). In our hands, the performance of the MGMT MS-HRM1 assay for the detection of MGMT promoter region methylation was equivalent to the MethylLight assay as both of the assays gave reproducible results until the 0.1% methylation dilution (data not shown). However, the sensitivity of the MGMT MS-HRM2 and MS-HRM3 assays were superior to that observed for the MethylLight MGMT assay (12). MGMT MS-HRM2 as well as MGMT MS-HRM3 gave fully reproducible methylation signals from the standard sample containing 0.1% methylated template in the background of unmethylated DNA (data not shown).
Application of the MGMT MS-HRM Assay to Cell Lines
We also tested DNA from eight cell lines (MDA-MB-468, HS578T, SW480, MDA-MB-435, MDA-MB-231, PC3, T47D and SW48) for which the methylation status of the MGMT promoter had been previously reported (14) by using the MGMT MS-HRM1, MGMT MS-HRM3 and MethylLight assays. Four of the eight cell lines studied (SW480, MDA-MB-435, MDA-MB-231 and SW48) showed complete (100%) methylation (FIG. 6).
HS578T displayed a less characteristic melting profile which we interpreted as being due to heterogeneous methylation. Whereas there was no evidence for heteroduplex formation between PCR products arising from unmethylated and fully methylated templates, heteroduplexes could form if the individual PCR products differed at only a few bases. Therefore, the curve was differently shaped as a consequence of complex melting pattern of multiple heteroduplexes (FIG. 6). The results from MGMT MS-HRM were consistent with MethylLight data for the cell lines (FIG. 6B).
Application of the MGMT MS-HRM Assay to Clinical Specimens
The diagnostic applicability of MS-HRM assay was tested on a panel of 19 colorectal cancer samples. The MGMT MS-HRM3 assay was used in those experiments and we also validated the MS-HRM results against the MethylLight assay (12). MS-HRM assays detected MGMT methylation in 8 of the 19 samples (42%). However, two of the above samples showed a very low methylation level (less than the 0.1% standard).
Methylation of one of the above samples was only detectable by the MGMT-MS-HRM3 assay. We repeated all the runs to test the reproducibility of our results in between two different experiments and obtained identical results.
Verification of Accuracy of MS-HRM Approach: BNIP3 MS-HRM Assay
To verify that the MS-HRM approach is widely applicable in methylation studies, an MS-HRM assay was developed for the promoter region of BNIP3. The BNIP3 specific oligonucleotide primers are disclosed in the co-pending application entitled “Method for detecting methylation status by using methylation-independent primers”, hereby incorporated by reference. BNIP3 has been reported to undergo aberrant methylation in various cancer types (15-17). As with the MGMT MS-HRM assay, we used the range of methylated/unmethylated mixes at different PCR annealing temperatures to determine the best conditions. In this model system, the BNIP3 MS-HRM assay was able to unambiguously detect methylation at the 0.1% level (FIG. 7). During evaluation of this assay, we performed the BNIP3 MS-HRM assay for the eight cell lines used in the MGMT methylation study. Three of the cell lines SW480, MDA-MB-435 and SW48 were methylated at the BNIP3 promoter (data not shown). The assay was also used to test for methylation of the panel of 19 colorectal cancer samples. Methylation of the BNIP3 promoter sequence was detected in 12 out of 19 (63%) of colorectal cancer samples. The methylation levels of 8 of these samples (42%) were less than 10% with 3 of them displaying 0.1% or less methylation (FIG. 7). All the results were reproducible between replicates (data not shown).
Discussion
There are many methods for the analysis of methylation at individual loci, each with their characteristic strengths and weaknesses (9). However, only a few protocols have gained widespread use. Genomic sequencing can be considered the gold standard (18,19). It provides the most detailed information but its sensitivity is relatively low (about 20%) and it is generally unsuitable for screening because it is expensive to run, particularly when individual clones are analysed. Pyrosequencing, which has been recently introduced, is more sensitive (about 5%) but is dependent on the availability of the proprietary instrumentation (20). The most widely used method is methylation-specific PCR (MSP) that uses primers specific for methylated, bisulphite-modified DNA (21). Unmethylated sequences are not normally amplified unless primers specific for unmethylated bisulphite modified DNA are designed. Despite its widespread use, MSP has a number of important limitations (9,22). As with other techniques that rely on PCR primer 30 mismatching to give specificity, false positives can arise if primers are badly designed or used at too low a temperature. MSP is very sensitive but is not quantitative. This can lead to the classification of a tumour as being methylated for a gene when a small minority of cells only is positive, or more seriously, if the bisulphite conversion of the DNA is incomplete. Consistent with these reservations, in the recent trial of temozolomide in glioblastoma, it was reported that testing for MGMT methylation using MSP gave ‘highly variable and centre-dependent’ results (8). The majority of applications in methylation studies utilize methylation-independent PCR (MIP) where the primers are designed to amplify the bisulphite-modified sequence regardless of its methylation status. However, the standard algorithms for the design of MIP primers and the protocols used do not always lead to the proportional amplification of methylated and unmethylated sequences (13,20,23). As it is often difficult to avoid CpG dinucleotides in primers designed to amplify CpG islands, some authors have suggested that the Cs in CpG sequences in primers get replaced by a mismatched base (19). Other authors have suggested that since the purpose of these assays is to detect methylation, some bias towards methylated sequences is acceptable and that a limited number of CpGs can be included in the primers, particularly if they are placed away from the 30 end (24). More recently, it has been shown that some CpGs are necessary in the primer sequence, otherwise PCR bias can lead to a significant underestimate of the degree of methylation (13). We have accordingly adopted the strategy of using primers containing limited numbers of CpGs and manipulating the annealing temperature to control the bias of PCR amplification in the design of MS-HRM assays. At lower annealing temperatures, the primers bind both methylated and unmethylated templates and PCR bias will favour the amplification of unmethylated sequences. At higher annealing temperatures, primer binding will favour methylated sequences, and thus at the optimal annealing temperature, amplification is effectively independent of methylation status. Therefore, MS-HRM can be used to estimate the proportion of methylation of a sample when run with standards. This is especially important when assessing clinical cancer samples for predictive markers such as MGMT where discrimination between tumour specimens that are methylated in all cells of the tumour from those that only show methylation in a small subset of their cells may have prognostic value. In the ideal situation, an estimate of the proportion of tumour cells in the sample will be given by pathological examination of the tissue and this can be compared with the estimated proportion of DNA that is methylated. Furthermore, if the tumour samples are of high purity, they can be used to determine whether the tumour is homozygously or heterozygously methylated. The technique would also be applicable to the diagnosis of imprinting disorders that are characterized by the abnormal methylation of imprinted genes. High resolution melting relies on the use of high sensitivity florescence detection instrumentation, fully saturating intercalating dyes and software allowing the analysis of the melting profiles of PCR products. We developed HRM for discrimination between methylated and unmethylated sequences after bisulphite modification of the target DNA. Sodium bisulphite converts unmethylated cytosines to uracil and leaves methylated cytosines intact. Therefore, the PCR product derived from a methylated template will have a higher melting temperature than that from an unmethylated template and those differences can be resolved by melting analysis. We have shown that HRM is applicable for the very sensitive detection of methylation in an unmethylated background. With MS-HRM, we were able to unambiguously detect the methylated fraction of DNA in samples containing as little as 0.1-1.0% of methylated DNA, the same range as seen for the MethylLight assay (25). MS-HRM is an in-tube method meaning that the analysis takes place without the PCR product leaving the tube that it was amplified in. This is of importance for diagnostic laboratories not only because of the rapidity that it affords, but also the elimination of PCR product contamination which has proven to be a major problem both in research and the diagnostic settings. An in-tube strategy based on the analysis of derivative peaks of melting curves of PCR products to assess methylation has already been reported (26,27). This has not become widely used presumably because of the difficulty of the suggested guidelines for assay design and the technical limitations of reagents, instrumentation and data analysis software which have now been overcome since the development of HRM methodology. MethylLight, the other in-tube method, is used by a greater number of laboratories. It is a quantitative adaptation of MSP that uses TaqMan probes. Whereas MethylLight assays methylation of CpG sites covered by the primers and probe, MS-HRM scans all of the CpGs flanked by the primers-binding to the target sequence, regardless of the methylation status of CpGs in the primer binding side. Thus, the results of MS-HRM are not compromised by heterogeneous methylation of a particular CpG dinucleotide or incomplete conversion of some of CpGs within the template, as the latter will fall below the limits of resolution.
Heterogeneous methylation can readily be distinguished from homogeneous methylation by the shape of the curves as seen for HS678T. Moreover, the use of probes in MethylLight complicates the design and increases the costs of experiments.
Also quantitative MethylLight requires normalization against a reference assay which needs to be run for each sample (24). By contrast, MS-HRM does not require a reference assay for normalization. All of the above make MethylLight experiments relatively complex and expensive. In summary, MS-HRM is a new approach that can be readily applied to the methylation analysis of MGMT. It can also be readily extended to other loci as we have shown for the BNIP3 locus. The sensitivity of MSHRM allows for detection of even a very small fraction of methylated material which is of importance as tumour samples may contain a low proportion of methylated sequences due to the presence of significant amounts of normal tissue or heterogeneity of the tumour. Furthermore, the high reproducibility and cost effectiveness of HRM makes this method suitable for both research and diagnostic applications.
References


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Example 4
Melting Curve Assays for DNA Methylation Analysis
The ability of sodium bisulfite to modify cytosines in a methylation-dependent manner allows the conservation of DNA methylation information during PCR amplification. PCR products amplified from bisulfite modified DNA have significantly different base compositions according to whether they originate from methylated or unmethylated variants of the target template. Different base compositions give rise to different thermal properties of the PCR products. Hence, melting analysis of amplification products in methylation studies allows the determination of whether the PCR products originate from methylated or unmethylated templates. Here, we briefly review recent advances in methodologies based on melting analyses of PCR products derived from bisulfite modified templates and provide a methodology for methylation-sensitive high resolution melting.
1. Introduction
The introduction of bisulfite modification of genomic DNA enabled the general use of PCR amplification in methylation studies (1). Sodium bisulfite deaminates unmethylated cytosines to uracils leaving 5-methylcytosines intact. As a consequence, methylated cytosines are amplified during the subsequent polymerase chain reaction (PCR) as cytosines whereas unmethylated cytosines are amplified as thymines. Hence, the base composition of the PCR product depends on the 5-methylcytosine content of the template. The two complementary strands of DNA are held together by hydrogen bonds and stacking interactions. Dissociation of double-stranded DNA is known as DNA melting or denaturation and can be induced either by increased temperature or denaturing chemicals. The dissociation of the triple hydrogen bond between C and G requires more energy than the dissociation of the double hydrogen bond between T and A, therefore GC rich sequences melt at relatively higher temperatures compared to AT rich sequences. The melting of a DNA amplicon often consists of a series of progressive dissociations of shorter domains within the sequence, which due to their local GC content have different melting temperatures.
The sequence dependent melting of an amplicon across a denaturing gradient is described as a ‘melting profile’. The melting profile of an amplicon can be determined by subjecting it to a gradually increasing temperature in the presence of an intercalating fluorescent dye, which emit fluorescence when bound (intercalated) to double-stranded DNA. At temperatures below the initiation of the melting process, the intercalating dye saturates the PCR product resulting in high levels of fluorescence. As the temperature rises, the fluorescence levels are stable until the point at which the double-stranded amplicon begins to separate into single strands, and a marked drop in fluorescence is observed as the dye is released from the double-stranded DNA. Thus, by monitoring the fluorescence during the increase of the temperature, it is possible to determine the melting profile of a PCR amplicon. The melting profiles of PCR products originating from methylated and unmethylated variants of the same template are significantly different due to their different GC content. Therefore the methylation status of an unknown sample can be determined by comparing the melting profile of the PCR product with the melting profiles of PCR products obtained from the amplification of methylated and unmethylated control templates. The first application of melting curve analysis to the profiling of DNA methylation was reported in 2001 (2). This methodology was not generally adopted as SYBR Green I, the principal fluorescent dye used at that time, could not be used at concentrations that fully saturated the PCR products, thereby blunting the resolution of the methodology. Current advances in fluorescence detection technology, new algorithms for data calculation, and the use of novel dyes have allowed the development of high resolution melting analysis (HRM) (3). We applied HRM to methylation analysis in the methodology that we called Methylation-Sensitive High Resolution Melting (MS-HRM). Together with a novel approach to primer design (see section 3.1), which allows the control of PCR bias and hence highly sensitive detection of low-level methylation, MS-HRM is proving to be a powerful new methodology for methylation analysis.
2. Materials
2.1. Bisulfite Modification of Genomic DNA
As an alternative to the procedure described in this chapter, some users may prefer to use one of the kits currently available from commercial suppliers.

    1. 3 M sodium bisulfite (Sigma S9000): Dissolve 0.57 g of sodium bisulfite dilute in 1 mL of water (this step may take several minutes as sodium bisulfite does not easily dissolve).
    2. 10 mM hydroquinone (Merck 8.22.333.0250): Prepare a 40 mM solution of hydroquinone: by dissolving 0.132 g of hydroquinone in 30 mL of water, and dilute it to 10 mM solution (10 mL of 40 mM hydroquinone solution plus 40 mL of water). Note that hydroquinone should be handled with care.
    3. 3 M NaOH and 0.1 M NaOH: The 0.1 M NaOH should be made from the 3 M NaOH stock on the day of the procedure. Discard the 3 M NaOH stock when it becomes cloudy.
    4. Microcon YM-100 centrifugal filter unit (Millipore).
    5. Eppendorf microcentrifuge 5417R
    6. TE buffer (10 mM Tris, 1 mM EDTA, pH 8)

2.2. Instrumentation



A platform with a combined thermal cycler and a fluorescence detector is ideal to perform intube melting analyses. PCR amplification of bisulfite modified template could be performed prior to melting analyses on any thermocycler but real-time monitoring of PCR amplification constitutes an important quality control step in the experiments allowing the elimination of samples where amplification failed with no need to run gel electrophoresis. The first experiments using melting profiles to differentiate methylated and unmethylated PCR product were performed on the LightCycler (Roche) (2).
Recently, a new generation of instruments capable of high resolution melting (HRM) analyses has been developed with superior data capture abilities and improved software. In our laboratory, we have used two HRM systems: the Roche LC480 and the Corbett RG600 as their real time PCR capacity allows the monitoring of the amplification which is invaluable for quality control.
2.3. DNA saturating dyes The very first intercalating dye reported to be suitable for melting based analyses of methylation was SYBR Green I (2). However, SYBR Green I at the concentration allowing saturation of PCR product was toxic to all polymerases we have tested (unpublished data). PCR amplifications in the presence of SYBR Green I were not robust and the very low yield of PCR products for post PCR melting analyses compromised our experiments. The new generation of saturating dyes includes the LC Green family (Idaho Technology Inc., Salt Lake City, Utah), Syto®9 (Invitrogen, Carlsbad, Calif.), ResoLight (Roche) and Eva Green (Biotium Inc., Hayward, Calif.). These dyes fully saturate the PCR product at concentrations that do not inhibit PCR amplification and allow for both real time monitoring of PCR amplification and subsequent in-tube melting analyses. These dyes can be used with most of the commercially available polymerases as an additive to the PCR reaction mix. The rapid development of High Resolution Melting has resulted in the introduction of two high resolution melting master mixes: LightCycler□ 480 High Resolution Melting Master (Roche) and SensiMixHRM□ (Quantace Ltd., London, UK). We routinely use 5 μM Syto®9 and or 1×LC Green (as recommended by the supplier).

3. Methods

3.1 Sodium Bisulfite Treatment of Genomic DNA

Bisulfite conversion of genomic DNA consists of 3 steps: sulfonation of cytosines, hydrolytic deamination of the cytosine sulfonates to uracil sulfonates, and alkaline desulfonation of the uracil sulfonates. Many parameters have to be taken in to account during the performance of the above steps and therefore many protocols have been published with different conditions for each step of conversion. In our experience, the most important parameters of the conversion are initial (sufficient) denaturation of the DNA template, incubation time with sodium bisulfite mixture (we have observed few problems with incomplete conversion when overnight incubation was used) the method used to recover bisulfite modified DNA that gives the highest yield possible. A protocol utilizing a column based recovery procedure (4) showed the highest recovery rates in our hands. Our modified version of that protocol was published in (5) and is described below. This operation should preferably be carried out in a safety cabinet or fume hood.

    1. Mix 0.1-1 g of genomic DNA with water to a final volume of 16 μL.
    2. Add 1.1 μL of 3M NaOH to denature the DNA, and incubate at 37° C. for at least 15 min. Then place directly on ice and proceed promptly with the remainder of the protocol.
    3. Add 173 μL of freshly prepared 3 M sodium bisulfite and 10 μL of the hydroquinone solution, mix with the pipette and incubate in the dark for 16 hours (overnight) at 50° C.
    4. Dilute the bisulfite reaction with water to a total volume of 350-400 μL.
    5. Transfer this solution to an assembled Microcon YM-100 centrifugal filter unit (Millipore).
    6. Centrifuge at 2800 700 g for 10 min (Eppendorf microcentrifuge 5417R)
    7. Discard the filtrate and add 300 μL of water to the upper chamber and centrifuge for 10 min at 700 g.
    8. Repeat step 7.
    9. Discard the filtrate, add 350 μL of 0.1 M NaOH to the upper chamber and centrifuge for 6 min at 700 g.
    10. Discard the filtrate, add 350 μL of water to the upper chamber, and centrifuge at 700 g for 8 min.
    11. Elute the sample by adding 50 μL of TE buffer; use the pipette for mixing of TE with the sample on the column membrane and let stand for 15 min.
    12. Invert the device, and collect the bisulfite converted DNA in a clean tube

3.2. Primer Design for PCR Amplification



The primers for amplification of bisulfite modified DNA for MS-HRM studies have to amplify the sequence of interest regardless of its methylation status (MIP—methylation independent primers) (6). It is important to note that when using one primer set for the amplification of two templates with different GC content, the PCR will be biased towards the template with lower GC content (FIG. 41) (5,7). The most commonly followed rules in primer design advise not to include any CG nucleotides into the primer sequence and, if this is not possible, to mismatch the C from CG with T (8). In our experience, following the above rules led to amplifications which showed strong bias towards the unmethylated sequence (5). We proposed new guidelines for MIP primer design where inclusion of a limited number of CGs towards the 5′ end of the sequence allowed us to manipulate PCR bias (5,6, FIG. 41). When primers containing a limited number of CpGs are used, their relative binding affinity for methylated and unmethylated templates is annealing temperature dependent. Hence by manipulating the annealing temperature of the PCR amplification with MIP primers, one can shift the PCR bias from the unmethylated to the methylated sequence and make the assay highly sensitive for methylation detection. If there is no methylated template available, the primers with limited CpGs will amplify unmethylated sequence even at high annealing temperature. That allows not only the determination of the methylation status of the sample but at the same time to the confirmation of the unmethylated status of the template. Apart from this point, good practice for primer design such as matching primer melting temperatures, selection against unconverted sequences (inclusion of a T derived from a non-CpG at or near the 3′ end of the primer) and prediction of primer dimer formation should be followed for the design of MIP primers. The melting temperature of MIP primers should be around 65° C. (e.g. using Oligonucleotide properties calculator for calculation of the melting temperature of the primers) allowing an annealing temperature of 60° C., which is an empirical value at which our primer design gives good results in our hands. Each primer set should be extensively tested on the mixes of methylated and unmethylated controls for the performance and the extent of PCR bias (see Note 2).
3.3. Predicting the Melting Behavior of the Sequence of Interest
Long sequences can have very complex melting profiles due to the fact that they consist of multiple small melting domains. Ideally, the melting profile of the sequence of interest should consist of a single melting domain that gives only one drop in the fluorescence and makes melting results easy to interpret. Amplicons of 100 bp or less often comprise only one major melting domain and therefore the recommended size of the PCR amplicon for melting analyses is around this size. A rough estimate of the melting profile of the sequence of interest can be made on freely available tools like POLAND, or the MELT94 algorithm. The complex melting of a PCR product containing more than one melting domain may complicate melting analyses as drops in fluorescence observed for short melting domains within the sequence can mask the fluorescence changes specific for the methylated/unmethylated alleles.
3.4. Predicting the Melting Temperature of Methylated/Unmethylated PCR Amplicons
The tools described in 3.3. can also be used to estimate the melting temperature of methylated and unmethylated variants of the template. Sequences originating from methylated allele where the C within CpG dinucleotides has not been changed will have a higher melting temperature in comparison to the sequence originating from unmethylated allele where all the C were changed into Ts. The difference in melting temperature of unmethylated and methylated templates depends on the number and density of CpGs in the amplicon. It is important to make sure that the difference in melting temperature between methylated and unmethylated version of the sequence is large enough to unambiguously distinguish both alleles during melting. When low-resolution fluorescence detection systems are used the melting temperature differences between methylated and unmethylated PCR product has to be significant. With HRM systems, very small differences in melting temperature can be unambiguously resolved as the specification of the systems allow for highly sensitive fluorescence acquisition and precise control of temperature ramp rates (see Note 3).
3.5. PCR Amplification
PCR reagents from different suppliers differ in their ability to amplify bisulfite modified DNA (unpublished data). The differences tend to be polymerase dependent and good quality polymerases are necessary for successful PCR amplification of bisulfite-modified template. Hot Start protocols give superior results to regular amplification techniques when bisulfite modified DNA is used as a template (see Note 4), (unpublished data). 0.5-1 U polymerase with standard dNTP concentration (200 μM each) is sufficient in most of applications. The role of Mg+2 concentration and input template amount will be discussed separately 3.5.1. Mg+2 concentration The amplification of bisulfite modified DNA is rarely as robust as amplification of genomic DNA presumably due to the extensive degradation of DNA during incubation with bisulfite. As a consequence, the use of high concentrations of Mg+2 to enhance PCR amplification is essential in many cases. The Mg+2 concentration in polymerase buffers is generally insufficient to give a high yield of PCR product from bisulfite modified DNA. In our hands, most amplifications for melting analyses required a Mg+2 concentration of 2.5-3.5 mM. In general, the concentration of Mg+2 in amplifications of bisulfite-modified template has to be empirically adjusted for each assay and is dependent on the bisulfite modification protocol, the PCR reagents used and input of bisulfite-modified template. 3.5.2. Bisulfite template input for PCR amplification The main problem in methylation studies is the degradation of DNA during bisulfite modification. As high as 90% degradation of the template has been reported (9). Our practice shows that the greater the quantity of DNA that is subjected to bisulfite modification, the less the extent of degradation and more template available for PCR amplifications. In cancer research especially, the amount of available sample DNA is generally a limiting factor in methylation studies (see Note 5). The use of carrier DNA (e.g. herring or salmon sperm DNA) can partly solve the problem allowing for higher recovery rates when small amounts of genomic DNA are subjected to bisulfite modification. The sensitivity of the melting assay is directly correlated to the input DNA for bisulfite modification. With MS-HRM, we were able to reproducibly detect 1-0.1% methylated sequence in unmethylated background when 1 g genomic DNA was used for bisulfite modification. Post modification DNA recovery rates also depend on the system used to purify DNA. In our experience, procedures using purification columns are superior to precipitation protocols, especially when an inexperienced person performed the bisulfite modification. 3.5.3. PCR amplification parameters The PCR amplification of bisulfite modified DNA may require up to 50-60 cycles of amplification to obtain a sufficient yield of PCR product for melting analyses. The number of cycles depends on the assay and real time monitoring of the amplification allows for the adjustment of the cycles number. The PCR should be stopped where possible just before amplification reaches the plateau phase. When amplification is carried on too long, the byproducts of PCR may disturb the melting profile of the sequence of interest (see Note 6). For an example, see Note 7.
3.6. Re-annealing of PCR product and the design of temperature gradient for melting analyses Before subjecting PCR products to temperature gradients, the PCR product should be reannealed. The protocol for re-annealing of the PCR product should consist of a denaturation step at 95° C. for one minute and fast cool down and hold for one minute (to allow reannealing of all the DNA strands) at the temperature from which acquisition of the fluorescence for melting procedure starts. The range of temperatures for temperature gradient has to be investigated empirically and it depends on the melting temperatures of unmethylated and methylated PCR product The gradient has to fully cover the melting temperatures of methylated and unmethylated PCR product (see Notes 3, 6 and 7).
3.7. Acquisition of the fluorescence The precise and accurate acquisition of fluorescence, and small temperature transition rates are the foundations of high resolution melting analysis. On the first generation of LightCyclers, the temperature ramp rates could be as low as 0.05° C./s. This allowed in combination with continuous fluorescence acquisition the attainment of detailed melting curves. Fluorescence acquisition systems in the new generation of the instruments have even higher specifications allowing collection of higher quality data. We have tested two of the HRM instruments available on the market, the LC480 (Roche) and the Rotor-Gene 6000 (Corbett). The settings for data collection in melting experiments giving us satisfactory results for the LC480 system were 50 fluorescence acquisition points per ° C. The corresponding temperature ramp rate for 50 acquisitions per degree was calculated automatically by the instrument by taking into account the time needed at each degree for sufficient acquisition of fluorescence. For the RG-6000 the HRM default settings were used consisting of the continuous acquisition of the fluorescence with a temperature ramp rate of 0.1° C. and a 2 s hold on each step. The parameters of the melting gradient can be adjusted individually for each melting assay on both the LC480 and the RG-6000 (see Note 7).
3.8. Analysis of the Results
3.8.1. Derivative peak Melting curves are generated by continuous acquisition of fluorescence from the samples subjected to the linear temperature gradient. For basic analyses, the melting curves can be converted to peaks by plotting the negative derivative of fluorescence over the temperature (−dF/dT) versus temperature (FIG. 42). The top of the peak represents the highest drop of fluorescence during melting and can be interpreted as the melting temperature of the PCR product (Tm). In methylation studies, two peaks, one for unmethylated (lower Tm) and one for methylated (higher Tm), are obtained from the control samples. Comparing the peaks of an unknown sample with controls scores the methylation status of the unknown sample (see Note 1). Heterogeneously methylated templates give a broader peak due to the formation of heteroduplexes (see Note 8).
3.8.2. Direct visualization of melting The high resolution data collected on HRM instruments allowed the development of new algorithms for melting curve analyses. After PCR amplification, even replicates of the same sample can differ in the amount of PCR product amplified and therefore display different fluorescence levels. The differences between samples are especially pronounced when HRM detection is used which does not allow for direct comparison of the curves as the HRM curves have to be normalized for starting and ending levels of fluorescence to make them comparable (FIG. 43a). The new algorithms supplied with HRM instruments allow for normalization of the starting levels of fluorescence. After normalization, similarly shaped curves, which before were visually not readily comparable, group together. If unknown samples are run with standards of known methylated to unmethylated template ratios, the level of methylation in screened samples can be estimated by comparison of their melting curves to the melting curves of standards (FIG. 43b, see Notes 2 and 6).
4. Notes


    1. Bisulfite modified DNA should be used up as soon as possible after modification. For longer storage: aliquot the stock DNA into small amounts that are thawed for each run. Repetitive freezing and thawing of the bisulfite DNA hastens its degradation.
    2. Standards for MS-HRM analyses/primers optimization can be obtained by mixing of bisulfite modified methylated and unmethylated controls. The equal amount of DNA has to be used for bisulfite modification of controls. Unmethylated control can be DNA from any tissue where the locus of interest is not methylated. The methylation status of the locus of interest in control DNA has to be investigated prior to analyses as some loci have different methylation status in different tissues. We routinely use CpGenomeTM Universal Methylated DNA (Millipore Co.) for the methylated-control. SssI treated DNA is an alternative to CpGenomeTM Universal Methylated DNA, but complete methylation of the genomic DNA by SssI enzyme can be difficult to achieve.
    3. The numerical calculations of the melting temperatures of the methylated and unmethylated PCR products are a good estimate, nevertheless the range of the temperatures for melting experiments has to be adjusted/corrected after the first run of the experiments.
    4. A 3 step PCR amplification protocol including an extension step was superior to a two step protocol. When a two step set up is used, some polymerases may generate by products and/or incompletely elongated amplicons that interfered with melting analyses.
    5. MS-HRM analysis can also be performed on formalin fixed tissues. As many of these will be extensively degraded, the success rate will be increased here by using relatively small (less than 100 base pairs) amplicons.
    6. In MS-HRM, the sensitivity of detection of lower levels of methylation depends on the extent of PCR bias during PCR amplification. As the PCR bias can be adjusted by annealing temperature, the range of the standards has to be designed to each experiment individually and depending on the goals of the user.
    7. The MS-HRM protocol used in the methylation screening experiments of MGMT gene performed on the LC 480. Primers: F-CGTTTGCGATTTGGTGAGTGTT (SEQ ID NO: 136) and R-ACCCCGCCCTACCCTATAAATTC (SEQ ID NO: 139). PCR cycling and HRM analysis conditions were as follows: initial activation 10 min at 95° C. and 50 cycles of 5 s 95° C., 5 s at 63° C. and 5 s at 72° C. Subsequently the product was denatured for 1 min at 95° C., re annealed by fast cooling and held for 1 minute at 75° C. The HRM analyses were performed in the temperature interval 70-95° C. With 50 acquisitions per ° C. and the default fluorescence temperature gradient parameters selected by the instrument see paragraph 3.7 and FIG. 42 and FIG. 43 for an example of the analysis of the results.


8. Heterogeneously methylated templates can be observed in many amplifications. On derivative curves, these are characterized by a broader melting peak typically starting before the unmethylated peak and extending into the methylated peak area. This is due to the formation of heteroduplexes, between heterogeneously methylated templates. An important advantage of MS-HRM is that, unlike many other methods, it allows the detection of heterogeneous methylation.
6. References


    1 Wang, R. Y., Gehrke, C. W., and Ehrlich, M. (1980) Comparison of bisulfite modification of 5-methyldeoxycytidine and deoxycytidine residues Nucleic Acids Res. 8, 4777-4790.
    2 Worm, J., Aggerholm, A., and Guldberg, P. (2001) In-tube DNA methylation profiling by fluorescence melting curve analysis Clin. Chem. 47, 1183-1189.
    3 Wittwer, C. T., Reed, G. H., Gundry, C. N., Vandersteen, J. G., and Pryor, R. J. (2003) High-resolution genotyping by amplicon melting analysis using LCGreen Clin. Chem. 49, 853-860.
    4 Boyd, V. L., and Zon, G. (2004) Bisulfite conversion of genomic DNA for methylation analysis: protocol simplification with higher recovery applicable to limited samples and increased throughput Anal. Biochem. 326, 278-280.
    5 Wojdacz, T. K., and Hansen, L. L. (2006) Reversal of PCR bias for improved sensitivity of the DNA methylation melting curve assay Biotechniques 41, 274-278.
    6 Wojdacz, T. K., and Dobrovic, A. (2007) Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation Nucleic Acids Res. 35, e41.
    7. Warnecke, P. M., Stirzaker, C., Melki, J. R., Millar, D. S., Paul, C. L., and Clark, S. J. (1997) Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA Nucleic Acids Res. 25, 4422-4426.
    8 Clark, S. J., Harrison, J., Paul, C. L., and Frommer, M. (1994) High sensitivity mapping of methylated cytosines Nucleic Acids Res. 22, 2990-2997.
    9 Warnecke, P. M., Stirzaker, C., Song, J., Grunau, C., Melki, J. R., and Clark, S. J. (2002) Identification and resolution of artifacts in bisulfite sequencing Methods 27, 101-107.


Example 5
Methylation Sensitive High Resolution Melting (MS-HRM)
PCR products derived from sodium bisulfite modified templates have methylation dependent base compositions. Hence, they show different melting profiles when subjected to thermal denaturation. The Methylation Sensitive High Resolution Melting (MS-HRM) protocol is based on the comparison of the melting profiles of PCR products from unknown samples with profiles specific for PCR products derived from methylated and unmethylated references. The protocol consists of the PCR amplification of bisulfite modified DNA templates with primers designed to proportionally amplify both methylated and unmethylated templates at the same time and subsequent high resolution analysis of the PCR product. The MS-HRM protocol allows investigation of the methylation status of the locus of interest in less than 3 hours. Here we provide the methodology for highly sensitive, labor and cost efficient single locus methylation studies based on DNA high resolution melting technology.
Design of Primers Allowing Correction for PCR Bias (BOX1)
The proportional amplification of bisulfite modified methylated and unmethylated templates can be compromised by PCR bias due to the fact that they have different base compositions. PCR bias is described as the preferential amplification of one DNA template. The PCR bias in methylation studies has long been recognized and is principally directed towards the unmethylated (GC-poor) strand 16. The relative disproportionate amplification of the unmethylated strand may result in misinterpretation of the final results and the underestimation of methylation levels. The extent of PCR bias is sequence specific and can be compensated by optimizing the annealing temperature of PCR amplification 18. The widely adopted primer design guidelines for post amplification methylation analyses protocols advise not to include any CpG nucleotides into the primer sequence and if not possible to do so, to use a mismatched C from CpG dinucleotide with T to avoid the preferential binding of the primer to methylated template 11. We have shown that in some most cases, inclusion of limited number of CpGs into the primer sequence is necessary to compensate for PCR bias 15,17. Our primer design system is thus based upon the inclusion of a limited number of CpG dinucleotides into the primer sequence enabling the conditionally selective binding of the primer to the methylated sequence and therefore enables compensation of PCR bias that would otherwise normally favor the amplification of the unmethylated template. Furthermore, reversal of PCR bias to favor methylated sequences increases the sensitivity of the melting assays allowing detecting methylation levels as low as 1-0.1%, which is the level of sensitivity similar to MSP. Our primer design guidelines are outlined below (for examples see Table 1).

    1. Primers should usually contain one or two CpGs dinucleotides each.
    2. The CpGs should be placed as close as possible to the 5′ end of the primer
    3. The melting temperature of the primers should be matched, preferably within one degree.
    4. The 3′ end of the primer should contain one or more Ts specific to non-CpG Cs, to ensure amplification of only bisulfite converted template.
    5. The primers should meet standard parameters for primer design e.g. secondary structure, primer dimer formation.
    6. The preferred length of the amplified sequence should be around 100 bp to reduce the complexity of the melting profile.

Materials

Reagents
    
        Bisulfite modification kit
        EpiTect Bisulfite Kit, Qiagen cat. no. 59104
        Human Genetic Signatures, MethylEasyTM cat. no. ME001
        Zymo, EZ DNA Methylation KitTM cat. no. D5001
        ABI, methylSSEQrTM cat. no. 4374710
        DNA intercalating dye
        LCGreen I and LCGreen plus (Idaho Technology Inc., cat. no. BCHM-ASY-0003 and BCHM-ASY-0005 respectively)
        Syto®9 (Invitrogen, cat. no. S-34854)
        LightCycler®480 ResoLight Dye (Roche, cat. no. 04909640001)
        Eva Green (Biotium Inc., cat. no. 00013)
        Taq polymerase
        Master mixes with PCR reagents and intercalating dye
        LightCycler□ 480 High Resolution Melting Master (Roche cat. no. 04909631001)
        SensiMixHRM□ (Quantace Ltd., cat. no. QT805-02)
        Mg+2
        Methylated reference
        Unmethylated reference
        Dilution series of methylated in unmethylated controls
        DNA primers

Equipment

        High Resolution Melting fluorimeter ideally coupled with a real time PCR cycler
        LightCycler® 480 System (Roche cat. no. 04545885001)
        Rotor-GeneTM 6000 (Corbett Research cat. no. 6600)
        LightScanner and HR-1 instrument (Idaho Technologies cat. no. LSCN-ASY-0011 and HR01-ASY-0001 respectively).

Reagents

    
    


Bisulfite modification of genomic DNA can be performed as described 8. Nevertheless, currently commercially available kits for bisulfite modification ensure highly efficient template conversion, reduction of the time needed for conversion and high bisulfite modified template recovery rates. CAUTION Bisulfite modified template is susceptible to rapid degradation. The bisulfite-modified sample should be used up soon after bisulfite modification or if required for a longer period of time, the DNA should be stored at −80° C. Freezing and thawing of the template should also be avoided.
DNA saturating dyes can be used as PCR additives as they do not interfere with the polymerase performance in saturating concentrations. High resolution PCR Master mixes containing all PCR reagents and saturating dye can be used for increased convenience of the setup. Extensive evaluation of HRM dyes has been described 21. Mg+2 the concentration of Mg+2 supplied in the PCR buffers is normally not sufficient to ensure efficient amplification of bisulfite modified template. An increase concentration of Mg+2 to 2.5-3.0 mM significantly enhances the amplification. CAUTION increased Mg+2 concentration enhances non-specific amplification and therefore has to be optimized for each primer set.
Methylated reference fully methylated reference for melting experiments can be obtained by subjecting genomic DNA to SSS1 enzyme treatment (NEB, Ipswich, Mass., cat. no. M0226L). Nevertheless complete methylation of DNA is hard to achieve without repeated rounds of incubation. Fully methylated genomic DNA can be also purchased from commercial suppliers (e.g. Millipore, CpGenomeTM Universal Methylated DNA cat. no. S7821).
Unmethylated reference DNA from the tissue in which the sequence of interest does not show methylation can be used as a source of unmethylated reference. CAUTION Many genes show low level methylation in certain tissues. The methylation status of the DNA chosen as the unmethylated control has to be investigated prior to analyses. Unmethylated genomic DNA can be also purchased from commercial suppliers. Dilution series of methylated in unmethylated controls The dilution series of methylated template in unmethylated background has to be obtained to estimate the PCR bias extent and methylation levels in screened samples.
Equipment
A real time PCR thermocycler coupled with a High Resolution Melting capable fluorimeter is the ideal platform for MS-HRM experiments. To date, 4 HRM systems are available: the LightCycler480 (Roche), the RotorGene6000 (Corbett Research), the LightScanner® System and the HR-1 instrument (Idaho Technologies). The LightScanner® and HR-1 instruments contain only a HRM module.
Procedure


    1. DNA template extraction via any “good practice” method. CAUTION Column based systems are preferred for the extraction of the DNA for HRM analyses as the impurities from the extraction procedure can interfere with melting analyses.
    2. Sodium bisulfite modification of the DNA 11. When a commercially available kit is chosen follow the supplier's protocol. TROUBLESHOOTING (3).
    3. Amplification of bisulfite modified DNA


Bisulfite converted template (3-10 ng) 2 μl
Primers 250 nM of each forward and reverse 0.5 μl
Mg+2 (3 mM final concentration) 2.4 μl
LightCycler□ 480 High Resolution Melting Master 10 μl
H2O 5.1 μl
Cycling
10 min 95° C. (depends on the type of polymerase used and HotStart protocols are advised here)
50 cycles of:
5 s 95° C.
5 s primer specific annealing temperature
5 s 72° C.
CAUTION The amplification of sufficient amount of PCR product from bisulfite modified template normally requires more cycles than a standard PCR amplification. Initial experiments should be run with 50 cycles and the number of the cycles should subsequently be adjusted. TROUBLESHOOTING (1,2)

    4. Re-annealing of the PCR products


1 min at 95° C. (to denature all amplified PCR product)
cool down to 70° C.
1 min at 70° C. (to allow all PCR product to hybridize)

    5. HRM scans: The default settings of fluorescence acquisition and the temperature ramp rates suggested by the equipment supplier should be used during the initial experiments. A temperature gradient from 70° C. to 95° C. in advised. The ranges of the temperatures can subsequently be adjusted for each assay to cover the melting of temperatures of the methylated and unmethylated products TROUBLESHOOTING (3,4,5)
    6. Investigation of equal amplification of the methylated and unmethylated template for primers without CpGs. To test CpG free primers for the extent of PCR bias the reaction mix from STEP 3 should be run with the 50:50 methylated and unmethylated template mix. An equal amount of the PCR product has to be seen for originating from each template to rule out the presence of preferential amplification of unmethylated sequence (see ANTICIPATED RESULTS section) TROUBLESHOOTING (6)
    7. Optimization of the annealing temperature of PCR amplification for primers containing CpGs. To test the annealing temperature at which the primers are able to compensate for PCR bias, run the PCR mix on the range of the temperatures and the mixes of the methylated in unmethylated template. The analysis of the HRM scans will show at which annealing temperature the preferential amplification is eliminated. We advise to run the initial PCR amplification at the annealing temperature at 5° C. below the melting temperature of the primers.


TIMING
Bisulfite modification 5-16 h depending on the protocol used
PCR amplification 3 h
HRM analyses 30 min
Data analysis 30 min
Troubleshooting


    1a. Problem: Low efficiency PCR amplification
    1b. Solution: Test the primers on control methylated/unmethylated control template, optimize the PCR chemistry and parameters, repeat PCR with new reagents, test bisulfite conversion protocol for losses of the template during purification step, when no HRM master mixes used decrease dye concentration.
    2a. Problem: primer dimers in PCR product
    2b. Solution: decrease the primer and/or the Mg+2 concentration, increase the annealing temperature of PCR amplification.
    3a. Problem: non-reproducible results
    3b. Solution: repeat bisulfite modification of the sample (the problem may arise from incomplete bisulfite conversion of the template), decrease the DNA input for bisulfite modification.
    redesign the primers to contain 5′ CpGs BOX1
    4a. Problem: No unambiguous peaks are obtained in HRM analyses
    4b. Solution: redesign primers to include more CpGs into the amplified sequence, and to include only one melting domain.
    5a Problem: presence of non-specific peaks on the HRM scans
    5b. Solution: redesign the primers, optimize the PCR chemistry, increase the annealing temperature of PCR amplification.
    6a. Problem: amplification using primers without CpGs shows PCR bias towards unmethylated sequence.
    6b. Solution: Optimize annealing temperature and Mg+2 concentration of the PCR amplification.

Anticipated Results

Derivative Peaks



The melting curves data can be transformed into peaks by plotting the negative derivative of fluorescence over temperature. After this transformation, the top of the peak represents the sharpest drop in the florescence from the melting curve slope and therefore indicates the melting temperature of the amplicon. For each of the unmethylated and methylated reference samples, an unambiguous peak should be obtained. The unknown sample can be scored on the bases of the similarities to one of the two reference profiles. The samples containing PCR product derived from both methylated and unmethylated templates will display two peaks similar to the methylated and unmethylated references.
Normalized melting curves and estimation of methylation levels
The replicates of a sample after amplification display different amounts of PCR product. The algorithms developed for analyses of HRM data (the software packages are supplied with the machines) allow the normalization of the raw data and therefore direct comparison of the melting curves. If the unknown samples are run along with the standards representing different mixes of methylated and unmethylated templates the methylation levels of an unknown sample can be estimate by comparing it to the controls 15.
Heterogeneously Methylated Samples
A number of loci in the human genome do not undergo full methylation but altered methylation of single CpGs, which is known as heterogeneous methylation. Therefore the sequences that are heterogeneously methylated give rise to a mixture of PCR products with Ts at some CpG sites and Cs at others. The PCR products with minor differences in the sequence can cross-hybridize and form heteroduplexes. Heteroduplexes are less stable then homoduplexes in denaturing conditions and therefore display different melting temperature from the fully methylated and unmethylated references. The HRM melting profiles of the PCR products derived from the samples with heterogenously methylated templates show a characteristic complex melting pattern, which allows for their ready identification, especially when first derivative curves are analysed. The heterogeneous pattern of methylation can be investigated in detail by sequencing based methodologies.
Example 6
Rapid Analysis of Heterogeneously Methylated DNA Using Digital Methylation Sensitive High Resolution Melting (dMS-HRM)
List of abbreviations used
AML Acute Myeloid Leukaemia
dMS-HRM digital Methylation Sensitive High Resolution Melting
dPCR digital Polymerase Chain Reaction
FFPE Formalin-Fixed Paraffin-Embedded
MDS Myelodysplastic Syndrome
MS-HRM Methylation Sensitive High Resolution Melting
PCR Polymerase Chain Reaction
WGA Whole Genome Amplification
Material and Methods
DNA Samples
Acute myeloid leukemia (AML) samples were obtained from patients referred to the Department of Hematology, Aarhus University Hospital. DNA was redissolved in TE Buffer (1×) with a final concentration of 5 ng/μL. Genomic DNA was extracted from peripheral blood of healthy controls using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The investigation was approved by the Peter MacCallum Cancer Centre Ethics of Human Research Committee (Approval number 02/26).
Whole-Genome Amplification (WGA)
Whole genome amplification was performed as described previously [14].
Bisulfite Modification
Two hundred ng of genomic DNA of the AML samples was subjected to bisulfite modification by using the EpiTect Bisulfite Kit (Qiagen) according to the manufacturer's instructions. DNA was eluted once in 20 μL of buffer EB. For the control DNA, Universal Methylated DNA (Chemicon, Millipore, Billerica, USA), and WGA, 500 ng of genomic DNA and WGA product, respectively, was modified and eluted twice, the second elution being in 30 μL of buffer EB.
Methylation Sensitive High Resolution Melting
PCR cycling and (d)MS-HRM analysis were performed on the Rotor-Gene 6000 (Corbett Research, Sydney, Australia). Each sample was analysed in duplicate for MS-HRM, and sixty times for dMS-HRM. Primers were designed according to the principles outlined in Wojdacz and Hansen [15] and subsequently in Wojdacz and Dobrovic [13]. The primers used to amplify bisulfite-treated DNA were CDKN2B-F, 5'-GTTAGGCGTTTTTTTTTAGAAGTAATTTAGG-3′(SEQ ID NO:237) and CDKN2B-R, 5′-TACGACTTAAAACCCCGTACAATAACC-3′ (SEQ ID NO:238) and do not amplify unmodified genomic DNA (data not shown). The amplified region corresponds to [GenBank: AL449423] nucleotides 99845 to 99958, and encompasses nine CpG dinucleotides. PCR was performed in a 100 μL PCR tube (Corbett Research) with a final volume of 20 μL, containing 200 nmol/L of each primer, 200 μmol/L of each dNTP, 0.5 U of HotStarTaq DNA polymerase (Qiagen) in the supplied PCR-buffer containing 2.5 mmol/L MgCl12, 5 μmol/L SYTO9 (Invitrogen, Carlsbad, USA), and different dilutions of bisulfite-treated DNA as template (see Results). The initial denaturation (95° C., 15 minutes) was followed by 50 cycles for MS-HRM (60 cycles for dMS-HRM) of 10 seconds at 95° C., 30 seconds at 59° C., 30 seconds at 72° C.; one cycle of 1 minute at 95° C., 72° C. for 1.5 minutes and a HRM step from 65° C. to 90° C. rising at 0.2° C. per second, and holding for 1 second after each stepwise increment.
Direct Sequencing
dMS-HRM products were cleaned up with the PCR-M clean up kit (Viogene, Taipei, Taiwan), according to the manufacturer's instructions, further processed with ExoSapIT (GE Healthcare, Little Chalfont, England), followed by the sequencing reaction using Big Dye Terminator v3.1 chemistry (Applied Biosystems, Foster City, Calif.) according to the manufacture's instructions. Sequencing was performed in both directions using the PCR primers given above as sequencing primers. The initial denaturation (95° C., 1 minute) was followed by 30 cycles of 10 seconds at 95° C., 30 seconds at 59° C. and 3 minutes at 72° C. The sequencing products were purified by ethanol precipitation and separated on a 3100 Genetic Analyser (Applied Biosystems). The sequencing data obtained were analysed independently by two scientists (IC and TM) in a blinded manner. The methylation pattern of single dMS-HRM products were visualized using the BiQ Analyzer software (Max-Planck-Institut für Informatik, Saarbrücken, Germany) [16].
Results and Discussion
MS-HRM of AML Samples
FIG. 1 shows the melting profiles of the CDKN2B promoter region in acute myeloid leukemia (AML) samples analysed using MS-HRM. The amplicons derived from fully methylated DNA and the fully unmethylated WGA product defines the range of methylation. Due to the homogeneity of the DNA methylation pattern within these control samples, their melting profiles reflect the melting behaviour of homoduplexes only.
Heterogeneously methylated DNA samples result in multiple products after PCR. Not only will there be many different homoduplexes, but heteroduplexes will also form between similarly methylated sequences, giving rise to complex melting curves that often will not lie within the range defined by fully methylated and unmethylated DNA due to the earlier melting of heteroduplexes relative to homoduplexes. Dependent on the amount of DNA methylation (and the amount of normal cells present in the tumour sample), the resulting melting curve is flattened and exhibits a complex melting pattern. Detection of DNA methylation at the CDKN2B promoter has relied upon the sensitivity of the method used. However, this may have lead to an overestimation of methylation, as normal background levels of methylation can confound interpretation of results [9]. Whilst this can be resolved using bisulfite sequencing of individual clones [7,8], a cost- and time effective method, which separates individuals based on biological relevance and clinical significance is necessary. Cameron et al. state that about 40% of the CpG sites within the CDKN2B CpG island need to be methylated to achieve complete silencing of the gene, regardless of the CpG methylation pattern [7]. Methylation Sensitive High Resolution Melting (MS-HRM) [13] shows great sensitivity when the samples contains a mixture of fully methylated and fully unmethylated templates as it has been empirically observed that the sequence differences between these are too great for heteroduplexes to form.
However, its sensitivity is considerably diminished for heterogeneously methylated samples due to the PCR products forming heteroduplexes, resulting in an overall melting profile that cannot be correlated against fully methylated, unmethylated or normal controls. It is possible that samples from normal healthy individuals can give rise to profiles suggestive of heteroduplex formation, as underlying low-level methylation may be present in some cases.
Applying digital PCR (dPCR) to MS-HRM isolates single-copy templates, removing the possibility of heteroduplex formation and therefore allowing its resultant profile to lie within the fully methylated and whole genome amplified product (WGA, fully unmethylated) standards.
To use a PCR-based technique, potential PCR bias needs to be eliminated or at least minimised. Given that the DNA methylation pattern in the entire interrogated sequence and not just the primer binding sites influence bias [17], eliminating a PCR bias in a heterogeneous population of alleles becomes nearly impossible. Isolating single templates is desirable [18]. However cloning from a heterogeneous pool may introduce a cloning bias [11, 19].
Digital PCR addresses all of the problems above. HRM after dPCR is able to quantify the portion of methylation at each allele, and the number of alleles present at each level of methylation [20]. Proceeding onto sequencing of dMS-HRM products opens up the possibility to map the position of methylated CpG sites in the discrete amplicon, but this would rarely be necessary for prognostic information [5, 7, 21].
The dMS-HRM Approach
The basis of this approach is the PCR amplification of single molecules, which is readily attained by limiting dilution [22, 23]. The Poisson distribution can then be used to determine the expected distribution of templates. For example, if the sample is diluted such that one amplifiable template is found on average in the volume of template used per reaction, 36.8% of reactions will have no templates, 36.8% will have one template, and 26.4% will have more than one template. Amplification will occur, when one or more template molecules are present in the PCR reaction.
From a practical point of view, for a given sample the DNA concentration is determined and appropriately diluted. Dependent on the starting concentration, a reasonable dilution (in our cases in the order of 1:1000 to 1:2000) series should be applied. Another important point is the quality of the DNA. In general we observed that high-quality DNA (e.g. extracted from snapfrozen samples or cell lines) had to be more diluted than low-quality DNA (e.g. extracted from formalin-fixed paraffin-embedded (FFPE) samples), as would be expected.
The dilution which seems to perform best is empirically chosen and used for the final experimental setup. Amplifications from single molecules can be readily identified when the melting curves are analysed. They show a smooth and sharp single signal (FIG. 2), whereas melting curves from two or more molecules often result in signals showing two peaks or more complex patterns, resembling those seen before diluting.
dMS-HRM of AML Samples
FIG. 2 shows the digital melting profiles of the AML samples 4383, 4156, 4276, 3224, and 730-06. Sample 4276 does not show any methylated alleles. Sample 4156 shows mainly profiles which correspond either to fully unmethylated products or have only few CpG positions methylated. Sample 3224, 730-06 and 9164 covers a broad range of various heterogeneously methylated alleles.
Sequencing of the dMS-HRM products of sample 9164 confirms the broad range of various methylated alleles with different CpG sites being affected (FIG. 3A). There appears to be an even distribution between the melting peaks and the number of CpGs positions methylated, which vary only in the CpG positions being methylated.
In dMS-HRM, a slight increase in the melting temperature of the products relative to the controls can be seen (FIG. 3A). Sequencing of digital ‘clones’ obtained from the controls showed that the sequences were comparable to those from sample 9164 (FIG. 3B). dMS-HRM analysis of control DNA was replicated with the template DNA being diluted into an equivalent amount of background DNA used for MS-HRM (fish sperm and not bisulfite-treated, genomic control DNA), and the same result was obtained (data not shown). The shift may be due to a relative increase in the effective magnesium concentration around each amplicon [24, 25].
Incomplete conversion was encountered on one occasion in replicate 69 (FIG. 3), and confirmed by direct sequencing (FIG. 3C). This was detected using dMS-HRM, as the peak was slightly right-shifted beyond the fully methylated signal (FIG. 3A). Previous reports show that conversion of cytosine to uracil is 97.0 to 99.7% complete, whilst still leaving 5-methylcytosines intact [26, 27]. Such a low non-conversion rate is not expected to be a major problem with dMS-HRM, as the number of replicates required to achieve digital PCR will move non-converted cytosines into the background.
Conclusions
dMS-HRM is a powerful tool for analysis of heterogeneous DNA methylation. It is readily performed by limiting dilution and the results are directly visualised by the melting profile. It can be used for counting methylated sequences and for estimating the extent of their methylation, all within a single-tube format. dMS-HRM can rapidly generate clonal templates ready for sequencing, eliminating the need for cloning into a vector. Used in combination with standard MS-HRM, it rapidly gives detailed information regarding the nature of the observed methylation, both at the individual allele and entire molecular population levels.

## Claims

1. A method for detecting the methylation status of a CpG-containing nucleic acid in a sample comprising the steps of:
a) providing said sample comprising a CpG-containing nucleic acid,
b) denaturing said CpG-containing nucleic acid, thereby producing denatured CpG-containing nucleic acid,
c) treating said denatured CpG-containing nucleic acid with bisulphite which modifies at least one unmethylated cytosine in said CpG-containing nucleic acid, thereby producing treated CpG-containing nucleic acid,
d) amplifying said treated CpG-containing nucleic acid by means of at least one methylation-independent oligonucleotide primer, which comprises within the first 10 nucleotides of the 5′-end, at least one CpG dinucleotide in a region which hybridizes to the CpG-containing nucleic acid, wherein said at least one methylation-independent oligonucleotide primer hybridizes to both methylated and unmethylated CpG-containing nucleic acids after modification, and
e) analyzing the amplified CpG-containing nucleic acid by melting curve analysis.

2. The method according to claim 1, wherein said at least one methylation-independent oligonucleotide primer comprises at least two CpG dinucleotides.

3. The method according to claim 1, wherein said at least one CpG dinucleotide is located immediately after the first nucleotide of the 5′-end of said at least one methylation-independent oligonucleotide primer.

4. The method according to claim 1, wherein said unmethylated cytosine is modified to uracil.

5. The method according to claim 1, wherein said amplifying step is performed by a polymerisation reaction.

6. The method according to claim 5, wherein said polymerisation reaction is a polymerase chain reaction (PCR).

7. The method according to claim 6, wherein said PCR comprises the steps of:
a) melting a CpG-containing nucleic acid template,
b) annealing at least one methylation-independent oligonucleotide primer to said CpG-containing nucleic acid template, and
c) elongating said at least one methylation-independent oligonucleotide primer.

8. The method according to claim 1, wherein said amplifying step is achieved by means of at least two methylation-independent oligonucleotide primers.

9. The method according to claim 1, wherein said sample is selected from the group consisting of breast tissue, ovarian tissue, uterine tissue, colon tissue, prostate tissue, lung tissue, renal tissue, thymus tissue, testis tissue, hematopoietic tissue, bone marrow, urogenital tissue, expiration air, stem cells, body fluids, sputum, urine, blood and sweat.

10. The method according to claim 1, wherein said sample is selected from the group consisting of breast tissue, ovarian tissue, uterine tissue, colon tissue, prostate tissue and lung tissue.

11. The method according to claim 1, wherein the at least one methylation-independent oligonucleotide primer comprises between 10 and 200 nucleotides.

12. The method according to claim 1, wherein the at least one methylation-independent oligonucleotide primer comprises between 15 and 60 nucleotides.

13. The method according to claim 1, wherein said CpG-containing nucleic acid is amplified using a first oligonucleotide primer and a second oligonucleotide primer of a primer pair wherein the first primer is the at least one methylation-independent oligonucleotide primer which comprises within the first 10 nucleotides of the 5′-end at least one CpG dinucleotide in a region which hybridizes to the CpG-containing nucleic acid, and wherein the second primer comprises at least one CpG dinucleotide in a region which hybridizes to the CpG-containing nucleic acid and wherein the first and second primers are selected from the group consisting of SEQ ID NO.: 46-151.

14. The method according to claim 1, wherein said at least one methylation-independent oligonucleotide primer is selected from the group consisting of SEQ ID NO.: 185-250.

15. The method according to claim 13, wherein said first oligonucleotide primer is SEQ ID NO.: 136 and said second oligonucleotide primer is SEQ ID NO: 137.

16. The method according to claim 1, wherein said at least one methylation-independent oligonucleotide primers is SEQ ID NO.: 138 and 139.

17. The method according to claim 8, wherein said at least two methylation-independent oligonucleotide primers is SEQ ID NO.: 142 and 143.

18. The method according to claim 8, wherein said at least two methylation-independent oligonucleotide primers is SEQ ID NO.: 144 and 145.

19. The method according to claim 8, wherein said at least two methylation-independent oligonucleotide primers is SEQ ID NO.: 146 and 147.

20. The method according to claim 7, wherein the primer annealing temperature during amplification of said CpG-containing nucleic acid is between 40 and 75 degrees Celsius.

21. The method according to claim 7, wherein the primer annealing temperature during amplification of said CpG-containing nucleic acid is 60 degrees Celsius.

22. The method according to claim 7, wherein the primer annealing temperature during amplification of said CpG-containing nucleic acid is 64 degrees Celsius.

23. The method according to claim 1, wherein the presence of methylated CpG-containing nucleic acid is indicative of a disorder.

24. The method according to claim 1, wherein the absence of methylated CpG-containing nucleic acid is indicative of a disorder.

25. The method according to claim 23, wherein said disorder is selected from the group consisting of Alzheimer's disease, atherosclerosis, breast cancer, bladder cancer, ovarian cancer, melanoma, prostate cancer, lung cancer, renal cancer, colon cancer, gastric cancer, cervical cancer, leukaemia, low grade astrocytoma, anaplastic astrocytoma, glioblastoma, haematopoietic disorders, medulloblastoma, leukemia, metabolic disorders, endometrial cancer, neuroblastoma, diffuse large B-cell lymphoma, developmental disorders, Prader-Willi syndrome, Angelman syndrome and imprinting disorders.

26. The method according to claim 23, wherein said disorder is selected from the group consisting of breast cancer, bladder cancer, ovarian cancer, melanoma, prostate cancer, lung cancer, colon cancer, endometrial cancer and leukaemia.

27. The method according to claim 23, wherein said disorder is colon cancer.

28. The method according to claim 23, wherein said disorder is breast cancer

29. The method according to claim 1, wherein said at least one methylation-independent oligonucleotide primer hybridizes to a target CpG-containing nucleic acid sequence, wherein methylation of said target sequence is indicative of the presence of a disorder.

30. The method according to claim 1, wherein said at least one methylation-independent oligonucleotide primer hybridizes to a target CpG-containing nucleic acid sequence of a gene selected from the group consisting of PPP3CC, BNIP3, Methylguanine-DNA Methyltransferase (MGMT), SNRPN, GSTP1, RARB2, RASSF1A, TIMP3, APC, beta-Actin, PTGS2 and 14-3-3 sigma.

31. The method according to claim 1, wherein said at least one oligonucleotide primer hybridizes to a target CpG-containing nucleic acid sequence of a gene selected from the group consisting of CHD1, COX2, PRSS3, PYCARD, BIN1, BRCA1, LATS2, PITX2, BCL2, EYA4, GSK3B, MLH1, TIMP-3, MSH6, MTHFR, PTEN, SFN, CD109, ERS1, PCDH10, DAPK1, FHIT, P16ink4a, PRSS3, RASSF1,TMS1, CAGE-1, GPR150, ITGA8, PRDX2, SYK, ALX3, HOXD11, PTPRO, WWOX, ABHD9, CAV9, GPR78, GSTP1, HIC1, PTGS2, CSMD1, C10orf59, MGMT, BNIP3, PPP3CC CSMD1, MAP3k7, C10orf59 and GRIFK2.

32. The method according to claim 1, wherein said at least one oligonucleotide primer hybridizes to a target CpG-containing nucleic acid sequence of a gene selected from the group consisting of SEQ ID NO.: 1-45, or the complement thereof.

33. The method according to claim 1, wherein said at least one oligonucleotide primer hybridizes to a target CpG-containing nucleic acid sequence of a gene selected from the group consisting of SEQ ID NO.: 9-13, or the complement thereof.

34. The method according to claim 1, wherein said at least one oligonucleotide primer hybridizes to a target CpG-containing nucleic acid sequence of a gene selected from the group consisting of SEQ ID NO.: 5-8, or the complement thereof.

35. The method according to claim 1, wherein said at least one oligonucleotide primer hybridizes to a target CpG-containing nucleic acid sequence of a gene selected from the group consisting of SEQ ID NO.: 21-26, or the complement thereof.

36. The method according to claim 1, wherein said at least one oligonucleotide primer hybridizes to a target CpG-containing nucleic acid sequence as defined by SEQ ID NO.: 44 or 45, or the complement thereof.

37. The method according to claim 1, wherein said at least one oligonucleotide primer hybridizes to a target CpG-containing nucleic acid sequence as defined by SEQ ID NO.: 42, or the complement thereof.

38. The method according to claim 1, wherein said at least one methylation-independent oligonucleotide primer hybridizes with a CpG-containing nucleic acid sequence, which is at least 97% identical to the target sequence, or the complement thereof.

39. The method according to claim 1, wherein the relative amount of methylated CpG-containing nucleic acid in said sample is between 40-60%.

40. The method according to claim 1, wherein the relative amount of methylated CpG-containing nucleic acid in said sample is below 50%.

41. The method according to claim 1, wherein the relative amount of methylated CpG-containing nucleic acid in said sample is below 1%.

42. The method according to claim 1, wherein the relative amount of methylated CpG-containing nucleic acid in said sample is below 0.1%.

43. The method according to claim 1, comprising the primers according to SEQ ID NO.: 46 and 47 for the detection of methylation status of CHD1 as defined in SEQ ID NO.: 1, wherein the primer annealing temperature during amplification is 59 degrees Celsius and the presence of methylation is indicative of Bladder cancer.

44. The method according to claim 1, comprising the primers according to SEQ ID NO.: 60 and 61 for the detection of methylation status of PITX2 as defined in SEQ ID NO.: 8, wherein the primer annealing temperature during amplification is 60 degrees Celsius and the presence of methylation is indicative of Breast cancer.

45. The method according to claim 1, comprising the primers according to SEQ ID NO.: 68 and 69 for the detection of methylation status of MLH1 as defined in SEQ ID NO.: 12, wherein the primer annealing temperature during amplification is 62 degrees Celsius and the presence of methylation is indicative of Colon cancer.

46. The method according to claim 1, comprising the primers according to SEQ ID NO.: 72 and 73 for the detection of methylation status of MSH6 as defined in SEQ ID NO.: 14, wherein the primer annealing temperature during amplification is 59 degrees Celsius and the presence of methylation is indicative of Endometrial cancer.

47. The method according to claim 1, wherein said melting curve analysis comprise normalization of melting curves by calculation of the ‘line of best fit’ in between two normalization regions before and after a major fluorescence decrease.

48. The method according to claim 1, wherein a melting profile displays at least one peak melting temperature.

49. The method according to claim 1, wherein a melting profile displays at least two peak melting temperatures.

50. The method according to claim 1, wherein the relative amount of methylated CpG-containing nucleic acid is estimated by comparison with melting curve analysis of at least one standard sample comprising said CpG-containing nucleic acid.

51. The method according to claim 50, wherein a higher melting Temperature of the amplified nucleic acid sample than of the standard sample is indicative of a higher relative amount of methylated nucleic acid of that sample than of the standard sample.

52. The method according to claim 50, wherein a lower melting Temperature of the amplified nucleic acid sample than of the standard sample is indicative of a lower relative amount of methylated nucleic acid of that sample than of the standard sample.

53. The method according to claim 50, wherein said at least one standard sample comprise any combination of methylated and unmethylated CpG-containing nucleic acid.

54. The method according to claim 50, wherein said at least one standard sample comprise 100% methylated CpG-containing nucleic acid.

55. The method according to claim 50, wherein said at least one standard sample comprise 100% unmethylated CpG-containing nucleic acid.

56. The method according to claim 50, wherein said at least one standard sample comprise 50% methylated nucleic acid and 50% unmethylated CpG-containing nucleic acid.

57. The method according to claim 1, wherein said melting curve analysis is performed by measurement of fluorescence.

58. The method according to claim 57, wherein said fluorescence is Measured immediately after amplification.

59. The method according to claim 57, wherein said peak melting temperature corresponds to the highest level of the negative derivative of fluorescence (−dF/dT) over temperature versus temperature (T).

60. The method according to claim 1, wherein said melting curve analysis is performed by using a thermal cycler coupled to a fluorometer.

61. The method according to claim 1, wherein said melting curve analysis is performed by incubating the nucleic acid amplification product at increasing temperatures, from 70 to 95 degrees Celsius, wherein the temperature increases by 0.05 degrees per second.