US20130065233A1 - Detection of dna methylation - Google Patents

Detection of dna methylation Download PDF

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US20130065233A1
US20130065233A1 US13/581,971 US201113581971A US2013065233A1 US 20130065233 A1 US20130065233 A1 US 20130065233A1 US 201113581971 A US201113581971 A US 201113581971A US 2013065233 A1 US2013065233 A1 US 2013065233A1
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dna
methylation
mse
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Xiyu Jia
Onyinyechi Chimaokereke
Lam Nguyen
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Zymo Research Corp
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  • the present invention generally relates to molecular biology. More specifically, the invention relates to methods and compositions for genomic DNA methylation analysis.
  • DNA methylation one such modification, plays crucial roles in widespread biological phenomena including host defense in bacteria and cell cycle regulation, gene imprinting, embryonic development and X-chromosome inactivation in mammals.
  • Aberrant DNA methylation patterns in gene promoters are closely associated with perturbations in gene expression and have recently been indicated as leading cause of human cancers (Jones and Laird, 1999).
  • DNA methylation involves the chemical addition of a methyl group to the 5′ carbon position on the cytosine pyrimidine ring. Most DNA methylation occurs within CpG islands which are commonly found in the promoter region of a gene. Thus, this form of post modification of DNA acts as communicative signal for activation or inactivation of certain gene expression throughout various cell types.
  • the invention provides a method for detecting methylation status of a DNA sequence in a DNA sample comprising (i) contacting a DNA sample with a reaction mixture comprising a methylation-sensitive endonuclease (MSE), a DNA polymerase, oligonucleotide primers flanking the DNA sequence and a buffer formulated to facilitate activity of the MSE and the DNA polymerase; (ii) incubating the sample under conditions permissive for DNA cleavage by the MSE; (iii) incubating the sample under conditions permissive for DNA polymerization (i.e., conditions permissive for polymerase chain reaction (PCR)); and (iv) detecting DNA amplification wherein DNA amplification is indicative of methylation status of the DNA sequence in the DNA sample.
  • MSE methylation-sensitive endonuclease
  • PCR polymerase chain reaction
  • the reaction mixture volume is not adjusted during steps (ii)-(iii) of the method (e.g., no additional components are added to the reaction mixture).
  • the incubation steps (ii-iii) are automated, such as by the use of a thermal cycler.
  • a method according to the invention may be defined as method for quantitating the proportion of DNA methylation in a DNA sequence or at a specific DNA position.
  • the step (iii) comprises incubating the sample in conditions permissive for quantitative PCR (qPCR). Following qPCR the amount to amplified DNA can be determined and used to determine the proportion of methylation in the DNA sequence of the sample.
  • quantitating methylation in the DNA sample may comprise comparing the amount of DNA amplification to an amplification standard.
  • An amplification standard may, for example, be a DNA sample with a known proportion of methylation.
  • the amplification standard is obtained by subjecting a portion of a DNA sample to a method according to the invention wherein the MSE is substantially absent or inactive, thereby determining the amount of DNA amplification that occurs when no methylation-sensitive DNA cleavage occurs.
  • the proportion of DNA methylation is determined from a change in the cycle threshold (Ct) value obtained from the DNA amplification as compared to an amplification standard.
  • Ct cycle threshold
  • a method for quantifying site-specific DNA methylation prevalence in a genomic DNA sample comprises (a) digesting a portion (e.g., half) of the DNA sample with MSE to specifically cleave methylated or non-methylated DNA; (b) incubating another portion (e.g., the second half) of the DNA sample with inactivated MSE; (c) amplifying the MSE-treated DNA from both samples using a DNA polymerase and oligonucleotide primers in the presence of an oligonucleotide probe or dye to produce amplified samples; and (d) determining the methylation status be measuring Ct values for the amplified samples. Quantification of site-specific DNA methylation may be accomplished, for example, by comparing the Ct values obtained from the samples to established Ct values correlated to percent DNA methylation.
  • the invention provides a reaction mixture comprising at least one MSE, a DNA polymerase and a buffer formulated to facilitate activity of the methylation-sensitive DNA endonuclease and the DNA polymerase.
  • a reaction mixture is formulated such that the MSE and polymerase may be frozen without substantial loss of activity.
  • the reaction mixture is provided as a kit of separately packaged components along with instructions for formulating a complete reaction mixture from the components.
  • reaction mixture according to the invention may further comprise one or more additional MSEs, free nucleotides, salts, preservatives, one or more oligonucleotide probes, one or more oligonucleotide primers and/or appropriate labels and dyes.
  • kits comprising one or more vials comprising a reaction mixture according to the invention.
  • a kit may further comprise one more additional components such as a reaction mixture wherein the MSE component is absent or inactive, an instruction pamphlet for methylation analysis, one or more oligonucleotide primers, a DNA sample or a DNA amplification standard.
  • a reaction mixture comprises an oligonucleotide probe that binds to a DNA sequence in a sample (e.g., in a region flanked by oligonucleotide primers).
  • oligonucleotide primers or probes comprise a label.
  • a reaction mixture may comprise a label that binds to double stranded DNA, such as SYBR® Green, a SYTO dye (e.g., SYTO® 9) or free nucleotides that are labeled.
  • Useful labels include, but are not limited to, fluorescent labels, radioactive labels, sequence labels, enzymatic labels and affinity labels. The presence of labeled (e.g., fluorescent labeled) continuants in the reaction mixture may be used to facilitate detection and quantification of DNA amplification.
  • a MSE comprises an enzyme having reduced activity on methylated DNA substrates.
  • Such enzymes may be naturally occurring or an engineered recombinant enzyme.
  • MSEs for use according to the invention include, but are not limited to, AccII, AciI, HpaII, HinP1I, HpyCH4IV, AatII, AclI, AfeI, AgeI, AscI, AsiSI, AvaI, BmgBI, BsaAI, BsaHI, BsiEI, BsiWI, BsmBI, BspDI, BstBI, ClaI, EagI, FauI, FnuDII, FseI, FspI, HaeII, HgaI, HhaI, Hpy99I, KasI, MluI, NaeI, NarI, NgoMIV, NotI, NruI, PaeR7I, PmlI, PvuI, RsrII,
  • the MSE is an endonuclease which recognizes a 4-base-pair sequence (e.g., a 4-based pair sequence comprising a CpG dinucleotide sequence).
  • a 4-base-pair sequence e.g., a 4-based pair sequence comprising a CpG dinucleotide sequence.
  • an AciI, AccII, HpaII, Hinp1I or HpyCH4IV enzyme or a combination thereof can be used.
  • a MSE comprises an enzyme having increased activity on methylated DNA substrates (e.g., a methylation-dependent endonuclease).
  • methylated DNA substrates e.g., a methylation-dependent endonuclease
  • Such enzymes may be naturally occurring or an engineered recombinant enzyme.
  • Examples of such MSEs for use according to the invention include, but are not limited to, BisI, GlaI, McrBC or a mixture thereof.
  • reaction mixtures may comprise 2, 3, 4 or more MSEs.
  • a MSE for use according to the invention is an MSE that can be heat inactivated, such as an enzyme that retains less than about 10%, 5%, 2% or 1% of its activity after heat inactivation.
  • methods and compositions according to the invention involve DNA polymerase enzymes.
  • the DNA polymerase enzyme is an enzyme that thermal stable, such as taq.
  • Methods and reaction mixtures disclosed here may further comprise molecules that modulate DNA polymerase activity or DNA polymerase enzymes that have been modified for “hot start” activity.
  • a reaction mixture may comprise a molecule (e.g., a DNA polymerase-binding antibody) that inhibits DNA polymerase activity during MSE cleavage of a DNA sample.
  • a molecule e.g., a DNA polymerase-binding antibody
  • Such DNA polymerase systems are also commonly referred to as “hot start” systems.
  • a DNA sample for use according to the invention may be any sample that comprises DNA that is potentially methylated.
  • the sample may comprise genomic DNA (e.g., mammalian genomic DNA), such as human genomic DNA.
  • genomic DNA e.g., mammalian genomic DNA
  • a DNA sample can be obtained from a variety of sources such as from a human subject or from a cell line or tissue bank. DNA from a patient or subject may be isolated from, for example, a blood sample, a tissue biopsy sample, a urine sample or a saliva sample.
  • Embodiments discussed in the context of a methods and/or composition of the invention may be employed with respect to any other method or composition described herein. Thus, an embodiment pertaining to one method or composition may be applied to other methods and compositions of the invention as well.
  • FIG. 1 One-step MSE-qPCR selectively amplifies methylated DNA. 5 ng of fully methylated and non-methylated pUC19 was subjected to one-step MSE-qPCR. Methylated pUC19 (top two curves) and non-methylated pUC19 (bottom line) were differentially amplified.
  • FIG. 2A-B Exemplary genomic loci for methylation analysis.
  • the hMSH2 locus includes three Hinp1I sites and two HpaII sites. Forward primers hybridize to a Hinp1I site, the probe to a HpaII site and the reverse primers to a Hinp1I site.
  • FIG. 2B the DAPK1 locus encompasses one HpyCH41V and one HpaII site.
  • FIG. 3A-B Digestion of fully and non-methylated DNA by one-step MSE-qPCR master mix is comparable to optimal buffer conditions.
  • Fully methylated and non-methylated human DNA were digested in either 5 U AciI, Hinp1I or HpyCH41V or 25 U HpaII for 2 hrs at 37° C. either under standard MSE buffer conditions ( FIG. 3A ) or using the one-step MSE-qPCR master mix ( FIG. 3B ).
  • FIG. 4 Comparison of qAMP methylation values to one-step MSE-qPCR values. Fully methylated and non-methylated human genomic DNA was subjected to Hinp1I digestion and qPCR using either qAMP or the one-step MSE-qPCR method to ascertain the hMSH2 locus methylation status. Methylation percent values were calculated by applying ⁇ Ct values to the established relationship.
  • FIG. 5 Methylation values of standards using one-step quantification method coincide with actual methylation values.
  • Human DNA standards with known methylation percentages were MSE-digested and amplified using the one-step MSE-qPCR method.
  • Methylation percent values of all CpGs in the hMSH2 locus (diamonds) and DAPK1 locus (squares) were calculated by applying ⁇ Ct values to the established relationship.
  • FIG. 6 One-step methylation quantification method accurately determines methylation profiles of blind controls.
  • Two blind controls prepared by mixing fully methylated or non-methylated human DNA with known methylation percentages were subjected to one-step MSE qPCR method.
  • ⁇ Ct values were used to determine methylation values by use of the established relationship. Error bars represent standard deviation.
  • FIG. 7 Amplification curve for a one-step methylation quantification reaction.
  • a non-methylated human DNA standard was subjected to the one-step methylation quantification method using Mgmt I and II (SEQ ID NOs: 7-8) primers for qPCR amplification.
  • the amplification curve revealed significant differences in Ct value between test (*) and control reactions (c), demonstrating not only the efficiency of the test reaction to specifically cleave non-methylated DNA but also the robust real-time amplification that ensues within test and control reactions.
  • FIG. 8 A schematic diagram illustrating one-step methylation quantification method in a control and test (digest) reaction mix.
  • DNA methylation plays a central role in widespread biological phenomena.
  • Current methods used to evaluate DNA methylation such as bisulfite sequencing and Methylation Specific PCR present a number of problems as they are expensive, lengthy and involve multiple steps that increase chances of contamination.
  • the invention provides single reaction system for rapid and accurate DNA methylation quantification.
  • the method exploits the specificity of MSE to digest methylated or unmethylated CpG dinucleotides juxtaposed to real-time PCR for the selective amplification of methylated DNA.
  • multiple steps and reactions are integrated into one simple step.
  • Advantages offered by this new system include decreased opportunity for contamination and rapid and accurate DNA methylation percentage quantification.
  • the disclosed method is demonstrated to selectively amplify methylated DNA and accurately measure methylation profiles of known DNA methylated standards when MSEs that have decreased activity at methylated DNA positions are used. Methylation percentages of blind controls determined by the method closely coincided with actual methylation percentages. The assay has also proven to be a cost-effective for accurate region-specific methylation status quantification and will be a valuable tool in research and diagnostics.
  • the proportion of DNA methylation is determined from the change in the cycle threshold (Ct) value obtained from the DNA amplification.
  • Ct cycle threshold
  • a reaction mixture may be formulated with a MSE, a DNA polymerase (e.g., a thermophilic DNA polymerase or a hot-start DNA polymerase system), oligonucleotide primers flanking the DNA sequence, dNTPs and a buffer formulated to facilitate activity of the MSE and the DNA polymerase.
  • Reaction mixtures may additionally comprise a DNA binding label that can be used to detect the presence of dsDNA such as SYTO 9TM. Salt concentrations in the reaction mixture will vary depending upon the MSE and polymerase used. For example, a 2 ⁇ reaction mixture may comprise about 7.5 mM MgCl 2 .
  • An MSE for use in the reaction mixture may be a naturally occurring or engineered enzyme.
  • the MSE can be an enzyme blocked by DNA methylation, such as one or more of AatII, AccIII, AciI, AfaI, AgeI, AhaII, Alw26I, Alw44I, ApaLI, ApyI, Ascl, Asp718I, AvaI, AvaII, Bme216I, BsaAI, BsaHI, BscFI, BsiMI, BsmAI, BsiEI, BsiWI, BsoFI, Bsp105I, Bsp119I, BspDI, BspEI, BspHI, BspKT6I, BspMII, BspRI, BspT104I, BsrFI, BssHII, BstBI, BstEIII, BstUI, BsuFI, BsuRI, CacI, CboI, Cbr
  • the MSE can be an enzyme that cleaves DNA only in the presence methylation such as BisI, GlaI, or McrBC (see, e.g., Chernukin et al., 2006; Russian Patent No. 2322494; and Sutherland et al., 1992, each incorporated herein by reference).
  • DNA samples may be obtained from a variety of sources, as further detailed herein.
  • a plurality of DNA samples are analyzed in parallel.
  • Samples for parallel analysis may include a DNA standard having a known level of methylation.
  • a plurality of different oligonucleotide probes may be employed to determine methylation status at multiple regions within a DNA sample.
  • the buffer and temperature conditions for MSE cleavage may be adjusted based on the specific MSE enzymes used and as further detailed herein. For example, using AccII, HpaII and/or HpyCH41V involves an incubation at 37° C. In the case of a McrBC and/or GlaI the incubation would also be at about 37° C.
  • samples are incubated in thermocycler and subjected to 25-40 rounds of amplification using temperatures to facilitate denaturation of the primers; annealing of the primers to sample DNA and elongation of intact sample DNA.
  • a fluorescent dye that binds to dsDNA can be detected.
  • an increase in fluorescence is indicative of DNA amplification.
  • labeled DNA probes may be used to detect amplification.
  • multiple labels or dyes may be included in single reaction.
  • Exemplary eukaryotic genomic DNA that can be used in a method of the invention includes, without limitation, mammal DNA such as a rodent, mouse, rat, rabbit, guinea pig, ungulate, horse, sheep, pig, goat, cow, cat, dog, primate, human or non-human primate.
  • Plant DNA may also be analyzed according to the invention. For example, DNA from Arabidopsis thaliana , maize, sorghum, oat, wheat, rice, canola, or soybean may be analyzed.
  • genomic DNA from other organisms such as algae, a nematodes, insects (e.g., Drosophila melanogaster , mosquito, fruit fly, honey bee or spider), fish, reptiles, amphibians and yeast may be analyzed.
  • insects e.g., Drosophila melanogaster , mosquito, fruit fly, honey bee or spider
  • fish e.g., reptiles, amphibians and yeast
  • genomic DNA can be isolated from one or more cells, bodily fluids or tissues.
  • An array of methods can be used to isolate genomic DNA from samples such as blood, sweat, tears, lymph, urine, saliva, semen, cerebrospinal fluid, feces or amniotic fluid.
  • Genomic DNA can also be obtained from one or more cell or tissue in primary culture, in a propagated cell line, a fixed archival sample, forensic sample or archeological sample. Methods for isolating genomic DNA from a cell, fluid or tissue are well known in the art (see, e.g., Sambrook et al., 2001).
  • Exemplary cell types from which genomic DNA can be obtained in a method of the invention include, a blood cell such as a B lymphocyte, T lymphocyte, leukocyte, erythrocyte, macrophage, or neutrophil; a muscle cell such as a skeletal cell, smooth muscle cell or cardiac muscle cell; germ cell such as a sperm or egg; epithelial cell; connective tissue cell such as an adipocyte, fibroblast or osteoblast; neuron; astrocyte; stromal cell; kidney cell; pancreatic cell; liver cell; or keratinocyte.
  • a blood cell such as a B lymphocyte, T lymphocyte, leukocyte, erythrocyte, macrophage, or neutrophil
  • a muscle cell such as a skeletal cell, smooth muscle cell or cardiac muscle cell
  • germ cell such as a sperm or egg
  • epithelial cell such as an adipocyte, fibroblast or osteoblast
  • neuron astrocyte
  • stromal cell kidney cell
  • pancreatic cell liver cell
  • a cell from which genomic DNA is obtained can be at a particular developmental level including, for example, a hematopoietic stem cell or a cell that arises from a hematopoietic stem cell such as a red blood cell, B lymphocyte, T lymphocyte, natural killer cell, neutrophil, basophil, eosinophil, monocyte, macrophage, or platelet.
  • a hematopoietic stem cell or a cell that arises from a hematopoietic stem cell such as a red blood cell, B lymphocyte, T lymphocyte, natural killer cell, neutrophil, basophil, eosinophil, monocyte, macrophage, or platelet.
  • Other cells include a bone marrow stromal cell (mesenchymal stem cell) or a cell that develops therefrom such as a bone cell (osteocyte), cartilage cells (chondrocyte), fat cell (adipocyte), or other kinds of connective tissue cells such as one found in tendons; neural stem cell or a cell it gives rise to including, for example, a nerve cells (neuron), astrocyte or oligodendrocyte; epithelial stem cell or a cell that arises from an epithelial stem cell such as an absorptive cell, goblet cell, Paneth cell, or enteroendocrine cell; skin stem cell; epidermal stem cell; or follicular stem cell.
  • stem cell can be used including, without limitation, an embryonic stem cell, adult stem cell, totipotent stem cell or pluripotent stem cell.
  • a cell from which a genomic DNA sample is obtained for use in the invention can be a normal cell or a cell displaying one or more symptom of a particular disease or condition.
  • a genomic DNA used in a method of the invention can be obtained from a cancer cell, neoplastic cell, apoptotic cell, senescent cell, necrotic cell, an autoimmune cell, a call comprising a heritable genetic disease or the like.
  • DNA for use according to the invention may be a standard or reference DNA sample.
  • Such reference samples may comprise a known level of DNA methylation.
  • reference DNA samples may be DNA extracted from cells that lack one of more DNA methyltransferase enzyme and are essentially devoid of CpG methylation.
  • a reference DNA sample may be treated with a DNA methyltransferase (e.g., M.SsssI methyltransferase) and therefore comprise methylation at essentially all CpG sites that can be methylated.
  • a standard DNA may be DNA isolated from the human cell line such as the HCT116 DKO cell line.
  • methods according to the invention involve the use of two for more standard DNA samples, such as DNA samples comprising essentially no CpG methylation and essentially complete CpG methylation.
  • kits may comprise suitably aliquoted reagents of the present invention, such as a control premix (comprising one or more inactivated MSE(s)) and test premix (comprising one or more active MSE(s)).
  • Control and test premix reagents comprise all of the components required for efficient MSE DNA cleavage and for qPCR.
  • the premix may comprise one, two, three or more MSEs, a DNA polymerase, free nucleotides, and salt/buffer system formulated to maximize activity of the polymerase and MSE enzymes.
  • Premix reagents may also comprise a label that can be used to quantify PCR amplification in the sample.
  • the label may be a fluorescent label that binds to amplified dsDNA or a nucleic acid probe that specifically binds to amplified DNA.
  • Dyes for used in reagents include for example a SYTO nucleic acid binding dye available from Life Technologies Corporation. See e.g., U.S. Pat. Nos. 5,436,134 and 5,658,751, incorporated herein by reference.
  • a premix reaction may also comprise oligonucleotide primers; however, such primers may also be packaged separately. Premix reactions must be carefully formulated to ensure that they are free of unwanted DNA as well as nonspecific DNase activity.
  • kits include, but are not limited to, oligonucleotide primers, reference DNA samples (e.g., methylated and non-methylated reference samples), distilled water, probes, dyes, sample vials and instructions for performing methylation assays.
  • reagents for DNA isolation, DNA purification and/or DNA clean-up may also be included in a kit.
  • kits may be packaged either in aqueous media or in lyophilized form.
  • the container means of the kits will generally include at least one vial, test tube, flask, bottle, syringe or other container means, into which a component may be placed, and preferably, suitably aliquoted. Where there is more than one component in the kit, the kit also will generally contain a second, third or other additional container into which the additional components may be separately placed. However, various combinations of components may be comprised in a vial.
  • the kits of the present invention also will typically include a means for containing reagent containers in close confinement for commercial sale. Such containers may include cardboard containers or injection or blow-molded plastic containers into which the desired vials are retained.
  • the liquid solution is an aqueous solution, with a sterile aqueous solution being preferred.
  • the components of the kit may be provided as dried powder(s).
  • the powder can be reconstituted by the addition of a suitable solvent. It is envisioned that the solvent may also be provided in another container means.
  • endonuclease refers to an enzyme that cleaves nucleic acid molecules at an internal position.
  • the terms “endonuclease” and “restriction endonuclease” are used interchangeably. Accordingly, the term “methylation-sensitive endonuclease (MSE)” is used interchangeably with ““methylation-sensitive restriction enzyme (MSRE).”
  • Methylation-sensitive endonuclease refers to endonuclease enzymes that have increased or decreased activity at DNA sites that include one or more methylated positions. Accordingly, in one embodiment, an MSE comprises reduced or blocked activity when DNA methylation is present. In a second embodiment, a MSE comprises increased activity when methylation is present (e.g., a methylation-dependent endonuclease).
  • Genomic DNA used in the study was from Zymo Research's Human Methylated and Non-methylated DNA set derived from HCT116 DKO cells.
  • the DNA has a low level of DNA methylation ( ⁇ 5%) and can be used as a negative control for DNA methylation analysis.
  • the Human HCT116 DKO methylated DNA is purified HCT116 DKO DNA that has been enzymatically methylated at all cytosine positions comprising CG dinucleotides by M.SssI methyltransferase 2 (EC 2.1.1.37;) and can be used as a positive control for DNA methylation analysis.
  • Primers were designed to flank MSE restriction sites and generate amplicons in the range of from about 50 to about 200 bp.
  • the forward primer, reverse primer and probe for HMSH2 locus respectively were 5′-GCTTCGTGCGCTTCTTTCAG-3′ (SEQ ID NO: 1), 5′-CCGTGCGCCGTATAGAAGTC-3′ (SEQ ID NO: 2) and 5′FAM-CATGCCGGAGAAGCCGACCAC-BHQ3′ (SEQ ID NO: 3).
  • the forward primer, reverse primer and probe for DAPK1 locus were; 5′-TCATGACCGTGTTCAGGCAGG-3′ (SEQ ID NO: 4), 5′-ATGCATTTCCACAATCCAGGAGG-3′ (SEQ ID NO: 5) and 5′FAM-ATTACTACGACACCGGCGAGGAACT-BHQ3′ (SEQ ID NO: 6).
  • PCR amplification was initially performed on input DNA to determine optimum annealing temperature and minimal primer dimers.
  • MSE digest and qPCR were integrated into carried a single step. Twenty nanograms of input DNA was added to the one-step MSE-qPCR master mix (1 ⁇ ZymoTaq reaction buffer (commercially available from Zymo Research Corp.), 0.25 mM dNTPs, 0.04 U/mL ZymoTaq, 2 mM MgCl 2 , 0.4 ⁇ M forward and reverse primers, 0.2 ⁇ M probe, 0.025 U/ ⁇ l Hinp1I and 0.05 U/ ⁇ l HpaII, AciI and HpyCH41V) in a reaction volume of 25 The samples were digested for 2 hr at 37° C.
  • Cycle threshold (Ct) values were obtained from real-time PCR amplification.
  • Each qPCR was performed in triplicate.
  • a negative control was prepared by the use of inactivated MSEs (65° C. for 20 minutes) instead of active MSEs.
  • Percent DNA methylation was determined from the change in Ct value by using the principle that each successive round of PCR amplification results in approximately a 2-fold increase in the amount of product. Thus, a ⁇ Ct of 1 indicates that 50% template has been cleaved.
  • the single-step MSE-qPCR procedure was further evaluated by comparing its measured methylation levels with methylation levels determined by traditional qAMP (Oakes et al., 2009). Percent methylation assessment of the hMSH2 locus ( FIG. 2A ) with fully and non-methylated human DNA by qAMP and the one-step master mix generated similar percent methylation values in both procedures ( FIG. 4 ). Thus, region-specific, rapid DNA methylation quantification by the one-step MSE method is as accurate as the two day qAMP procedure.
  • the one-step system was further validated by identifying methylation percentages of two blind controls prepared by mixing fully methylated or non-methylated human DNA with known methylation percentages. Methylation percentages in the hMSH2 locus determined by the one-step system corresponded closely with the actual methylation percentages ( FIG. 6 ). Together, these data provide a compelling argument for the application of the one-step MSE-qPCR system a cost-efficient, rapid tool for accurately assessing methylation profiles of specific DNA loci.
  • the present study clearly demonstrates that the one-step MSE-qPCR system accurately quantifies percent methylation. Unmethylated DNA was efficiently digested and allowed for the selective methylated DNA amplification. Further evaluation of the system revealed that it is comparable to qAMP, a procedure which is less time-efficient and involves two separate steps that increase the risk of contamination.
  • An additional advantage of the one-step method over qAMP is that, in a single buffer system, an environment conducive for efficient digestion by multiple MSEs is created. This remarkable hallmark of the one-step system allows for the simultaneous evaluation of CpG dinucleotides within different MSE's cognate sequences. Conversely, employment of a typical buffer system by qAMP restricts which MSEs may be digested within the same reaction tube. Methylation values of standard and blind control samples using one-step quantification method coincided closely with actual methylation values. Thus, this study establishes the value of the one-step MSE-qPCR method in rapid and accurate methylation profiling.
  • the following example protocol uses methylated and non-methylated human DNA standards to demonstrate one-step quantification of methylation using the One-Step qMethylTM PCR procedure. To determine percent DNA methylation for a given locus, both a test reaction and control reaction are prepared.
  • Control Reaction 37.5 ⁇ l 2 ⁇ Control PreMix (5 mM Syto9, 7.5 mM MgCl 2 , 0.08 U/ ⁇ l ZymoTaq DNA Polymerase, 2 mM dNTP mix, 0.25 U/ ⁇ l HpaII, 0.05 U/ ⁇ l HpyCH4IV, 0.04 U/ ⁇ l AccII) 3 ⁇ l 10 ⁇ M Mgmt Primer I (5′-GGTGTGAAAACTTTGAAGGA-3′; SEQ ID NO: 7) 3 ⁇ l 10 ⁇ M Mgmt Primer II (5′-CACTATTCAAATTCCAACCC-3′; SEQ ID NO: 8) 3 ⁇ l human methylated/non-methylated DNA standard (20 ng/ ⁇ l) 28.5 ⁇ l ddH 2 O 75 ⁇ l total volume* Test Reaction 37.5 ⁇ l 2 ⁇ test PreMix 3 ⁇ l 10 ⁇ M Mgmt Primer I 3 ⁇ l 10 ⁇ M Mg
  • Human non-methylated DNA standard was purified from HCT116 DKO cells (DNMT1 ( ⁇ / ⁇ )/DNMT3b ( ⁇ / ⁇ )).
  • Human methylated DNA standard was purified from HCT116 DKO cells (DNMT1 ( ⁇ / ⁇ )/DNMT3b ( ⁇ / ⁇ )) and enzymatically methylated with M.SssI methyltransferase (EC 2.1.1.37).
  • Both standards were formulated at a concentration of 20 ng/ ⁇ l in buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) and stored at ⁇ 20° C.
  • the following parameters for qPCR have been optimized for digestion and amplification of methylated and non-methylated human DNA standards and can be used as a guideline when setting up qPCR.
  • the expected amplicon should be 186 bp in length and have the sequence (SEQ ID NO: 9) shown below:
  • the annealing temperature and extension time for test DNA samples can be adjusted according to primer melting temperatures (Tms) and amplicon size, respectively. Between 35-40 cycles amplification cycles are used for most DNA templates. Typically primers are designed to span a DNA region of 120 bp to 350 bp that comprises at least two sites of potential methylation.
  • the percent methylation for the amplified locus can be determined by applying the following equation:
  • non-methylated DNA samples provided the following results and the amplification curves shown in FIG. 7 .
  • the actual methylation level of the non-methylated DNA standard was determined to be 13.4%. The actual value has been shown to be around 5%.
  • Using one-step PCR to detect methylation percentages of multiple loci can be accomplished by formulating reactions mixtures indicated below.

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US10801060B2 (en) 2015-02-24 2020-10-13 Zymo Research Corporation Assays to determine DNA methylation and DNA methylation markers of cancer
TWI717547B (zh) * 2016-08-15 2021-02-01 中央研究院 以表觀遺傳區分dna
US11965157B2 (en) 2017-04-19 2024-04-23 Singlera Genomics, Inc. Compositions and methods for library construction and sequence analysis

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EP2968606B1 (fr) 2013-03-15 2020-10-07 Loma Linda University Traitement de maladies auto-immunes
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WO2023175434A1 (fr) * 2022-03-15 2023-09-21 Diagenode S.A. Détection de l'état de méthylation d'un échantillon d'adn

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US10801060B2 (en) 2015-02-24 2020-10-13 Zymo Research Corporation Assays to determine DNA methylation and DNA methylation markers of cancer
CN113186288A (zh) * 2015-02-24 2021-07-30 兹莫研究公司 测定dna甲基化的分析法和癌症的dna甲基化标记
TWI717547B (zh) * 2016-08-15 2021-02-01 中央研究院 以表觀遺傳區分dna
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US11965157B2 (en) 2017-04-19 2024-04-23 Singlera Genomics, Inc. Compositions and methods for library construction and sequence analysis

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