US20230120076A1 - Dual-probe digital droplet pcr strategy for specific detection of tissue-specific circulating dna molecules - Google Patents

Dual-probe digital droplet pcr strategy for specific detection of tissue-specific circulating dna molecules Download PDF

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US20230120076A1
US20230120076A1 US17/900,935 US202217900935A US2023120076A1 US 20230120076 A1 US20230120076 A1 US 20230120076A1 US 202217900935 A US202217900935 A US 202217900935A US 2023120076 A1 US2023120076 A1 US 2023120076A1
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methylation
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Yuval Dor
Ruth SHEMER
Benjamin Glaser
Judith MAGENHEIM
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Hadasit Medical Research Services and Development Co
Yissum Research Development Co of Hebrew University of Jerusalem
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    • C12Q2523/00—Reactions characterised by treatment of reaction samples
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    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
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    • C12Q2561/00—Nucleic acid detection characterised by assay method
    • C12Q2561/101—Taqman
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers

Definitions

  • cfDNA has been used to detect graft cell death after kidney, liver or heart transplantation, based on single nucleotide polymorphisms (SNPs) distinguishing the DNA of donor from that of recipients.
  • SNPs single nucleotide polymorphisms
  • cfDNA Blood levels of cfDNA are known to increase under multiple additional conditions such as traumatic brain injury, cardiovascular disease, sepsis and intensive exercise. However in these cases, the source of elevated cfDNA is unknown, greatly compromising the utility of cfDNA as a diagnostic or prognostic tool. For example, cfDNA could originate from parenchymal cells of the injured tissue, but also from dying inflammatory cells.
  • DNA of each cell type in the body carries unique epigenetic marks correlating with its gene expression profile.
  • DNA methylation serving to repress nontranscribed genes, is a fundamental aspect of tissue identity. Methylation patterns are unique to each cell type, conserved among cells of the same type in the same individual and between individuals, and are highly stable under physiologic or pathologic conditions. Therefore, it may be possible to use the DNA methylation pattern of cfDNA to determine its tissue of origin and hence to infer cell death in the source organ.
  • tissue of interest could identify the rate of cell death in a tissue of interest, taking into account the total amount of cfDNA, the fraction derived from a tissue of interest, and the estimated half life of cfDNA (15-120 minutes).
  • the approach relies on normal, stable markers of cell identity, it cannot identify the nature of the pathology (e.g. distinguishing cfDNA derived from dead tumor cells or dead wild type cells due to trauma or inflammation in the same tissue).
  • the potential uses of a highly sensitive, minimally invasive assay of tissue specific cell death include early, precise diagnosis as well as monitoring response to therapy in both a clinical and drug-development setting.
  • Droplet Digital PCR technology is a digital PCR method utilizing a water-oil emulsion droplet system. Droplets are formed in a water-oil emulsion to form the partitions that separate the template DNA molecules. The droplets serve essentially the same function as individual test tubes or wells in a plate in which the PCR reaction takes place, albeit in a much smaller format. The massive sample partitioning is a key aspect of the ddPCR technique.
  • the Droplet Digital PCR System partitions nucleic acid samples into thousands of nanoliter-sized droplets, and PCR amplification is carried out within each droplet. This technique has a smaller sample requirement than other commercially available digital PCR systems, reducing cost and preserving precious samples.
  • Sample partitioning is the key to droplet digital PCR. In traditional PCR, a single sample offers only a single measurement, but in Droplet Digital PCR, the sample is partitioned into 20,000 nanoliter-sized droplets. This partitioning enables the measurement of thousands of independent amplification events within a single sample.
  • ddPCR technology uses a combination of microfluidics and proprietary surfactant chemistries to divide PCR samples into water-in-oil droplets.
  • the droplets support PCR amplification of the template molecules they contain and use reagents and workflows similar to those used for most standard TaqManTM probe-based assays.
  • each droplet is analyzed or read in a flow cytometer to determine the fraction of PCR-positive droplets in the original sample. These data are then analyzed using Poisson statistics to determine the target DNA template concentration in the original sample.
  • a method of analyzing the methylation status of methylation sites of a double-stranded DNA molecule which comprises at least two methylation sites per single strand of the double-stranded DNA molecule, the double-stranded DNA molecule being comprised in a specimen comprising:
  • kits for analyzing methylation sites of a double-stranded DNA molecule comprising:
  • kits for analyzing methylation sites of a double-stranded DNA molecule comprising:
  • the double-stranded DNA molecule is no longer than 300 base pairs (bp).
  • the double-stranded DNA molecule is no longer than 150 bp.
  • the at least two methylation sites are not more than 300 bp apart.
  • the at least two methylation sites are not more than 150 bp apart.
  • each strand of the double-stranded DNA comprises at least four methylation sites.
  • the at least four methylation sites are not more than 300 bp apart.
  • the at least four methylation sites are not more than 150 bp apart.
  • the method further comprises contacting the single-stranded DNA with amplification primers under conditions that generate amplified DNA from the single-stranded DNA following step (b) and prior to step (c).
  • the determining is effected using at least two non-identical labels.
  • the determining is effected using a single label.
  • the determining comprises:
  • the determining comprises contacting the amplified DNA with:
  • the first probe hybridizes to the forward strand of the amplified DNA and the second probe hybridizes to the reverse strand of the amplified DNA.
  • the double-stranded DNA molecule is differentially methylated in a cell or tissue of interest.
  • the cell of interest is selected from the group consisting of a pancreatic beta cell, a pancreatic exocrine cell, a hepatocyte, a brain cell, a lung cell, a uterus cell, a kidney cell, a breast cell, an adipocyte, a colon cell, a rectum cell, a cardiomyocyte, a skeletal muscle cell, a prostate cell and a thyroid cell.
  • the tissue is selected from the group consisting of pancreatic tissue, liver tissue, lung tissue, brain tissue, uterus tissue, renal tissue, breast tissue, fat, colon tissue, rectum tissue, cardiac tissue, skeletal muscle tissue, prostate tissue and thyroid tissue.
  • the tissue is cardiac tissue.
  • the double-stranded DNA molecule is non-methylated in cells of cardiac tissue and methylated in leukocytes.
  • the double-stranded DNA molecule comprises at least a part of the sequence of human chromosome 12, between coordinates 124692462-124692551.
  • the double stranded DNA molecule comprises a sequence which is comprised in SEQ ID NOs: 56 or 57.
  • the tissue is liver tissue.
  • the double-stranded DNA molecule comprises a sequence which is comprised in SEQ ID NOs: 65 or 66.
  • the first probe comprises a sequence as set forth in SEQ ID NO: 118 and the second probe comprises a sequence as set forth in SEQ ID NO: 119.
  • the first probe comprises a sequence as set forth in SEQ ID NO: 128 and the second probe comprises a sequence as set forth in SEQ ID NO: 129.
  • the first probe comprises a sequence as set forth in SEQ ID NO: 125 and the second probe comprises a sequence as set forth in SEQ ID NO: 126.
  • the single label is comprised on a probe.
  • the probe comprises a sequence as set forth in SEQ ID NO: 130.
  • the sequence of the first probe is selected such that the first probe binds to the amplified DNA when the methylation site of the double-stranded DNA molecule is non-methylated.
  • the sequence of the second probe is selected such that the second probe binds to the amplified DNA when the methylation site of the double-stranded DNA molecule is non-methylated.
  • the detectable moiety is FAM or HEX.
  • the double-stranded DNA is cell-free DNA.
  • the double-stranded DNA is cellular DNA.
  • the method further comprises lysing the cells of the cellular DNA prior to the determining.
  • the specimen is a fluid specimen.
  • the fluid specimen is a body fluid specimen.
  • the body fluid is selected from the group consisting of blood, plasma, sperm, milk, urine, saliva and cerebral spinal fluid.
  • the specimen comprises DNA from a plurality of cell-types.
  • the specimen is blood.
  • the method further comprises quantitating the amount of DNA of the cell or tissue origin.
  • the kit further comprises a droplet forming oil.
  • FIGS. 1 A-E Identification of cardiomyocyte-specific DNA methylation markers.
  • FIG. 1 A Unmethylation levels of FAM101A locus in 27 human tissues, including left ventricle, right ventricle and right atrium (red). Data was extracted from the Roadmap Epigenomics Consortium browser.
  • FIG. 1 B Structure of the FAM101A locus, used as two independent markers: FAM101A and FAM101A AS. Lollipops represent CpG sites; arrows mark positions of PCR primers; S, sense marker; AS, antisense marker.
  • FIG. 1 C Unmethylation status of FAM101A and FAM101A AS in DNA from multiple tissues and from isolated cardiomyocytes (purchased from ScienCell Research Laboratories, San Diego, Calif.).
  • Targeted PCR yields a lower background in non cardiac tissues compared with the Roadmap browser in panel A, since the roadmap data includes molecules that contain only some of the cytosines in the FAM101A locus (e.g. only one or two), which can occasionally be demethylated in non-cardiac tissue.
  • the targeted PCR by definition amplifies only molecules containing all cytosines in the locus.
  • FIGS. 1 D-E Spike in experiments for FAM101A and FAM101A AS.
  • Human cardiomyocyte DNA was mixed with human leukocyte DNA in the indicated proportions (0-100%), and the percentage of fully unmethylated FAM101A molecules (in which all five CpG sites were converted by bisulfite) was determined.
  • FIGS. 2 A-F Cardiomyocyte-derived cfDNA in healthy subjects and in patients with myocardial infarction.
  • FIG. 2 D Comparison of unmethylated FAM101A levels in samples from healthy controls, MI patients with low levels of high-sensitive troponin T (hs-cTn) ( ⁇ 0.03), and MI patients with high levels of hs-cTn (>0.03).
  • FIG. 2 F XY Scatter plot for cardiac cfDNA levels vs. cardiac troponin. Quadrants indicate negative and positive hs-Tn, and negative and positive cardiac cfDNA. Numbers indicate the percentage of specimens in each quadrant.
  • FIGS. 3 A-C Cardiac cfDNA dynamics during MI and after angioplasty.
  • FIG. 3 A Cardiac cfDNA levels in MI patients before and after PCI.
  • FIG. 3 B ROC curve for cardiac cfDNA in healthy individuals versus MI patients prior to intervention.
  • FIG. 3 C Time course of cardiac cfDNA and troponin levels in five patients. Vertical dashed lines indicate PCI time.
  • FIGS. 4 A-C Cardiac cfDNA in sepsis.
  • FIG. 4 A Levels of cardiac cfDNA in healthy controls and patients with sepsis.
  • FIG. 4 B Lack of correlation between cardiac cfDNA and troponin. Curved line represents non linear (quadratic) fit.
  • FIG. 4 C Kaplan-Meier plot showing correlation of cardiac cfDNA to patient survival.
  • FIGS. 5 A-D An exemplary method for detecting cardiac cfDNA using digital droplet PCR, according to embodiments of the present invention.
  • FIG. 5 A Schematic of approach for ddPCR-based detection of methylation status of multiple adjacent cytosines.
  • a signal from two probes in the same droplet reflects lack of methylation in 5 adjacent cytosines in the same original DNA strand.
  • FIG. 5 B Signal from cardiomyocyte and leukocyte DNA based on individual or dual probes. Scoring only dual probe signals drastically reduces noise from leukocyte DNA.
  • FIG. 5 C Spike-in experiment assessing sensitivity and linearity of signal from cardiomyocyte DNA diluted in leukocyte DNA. The use of dual probe enhances linearity and reduces baseline signal.
  • FIG. 5 D Measurement of cardiac cfDNA in plasma of healthy adults and patients with myocardial infarction. The use of dual probes reduces the baseline signal in healthy plasma.
  • FIGS. 6 A-C methylation of individual and multiple adjacent cytosines within the FAM101A locus.
  • FIG. 6 A Methylation status of cytosines in the sense strand of FAM101A
  • FIG. 6 B Metylation status of cytosines in the antisense (AS) strand of FAM101A. Graphs show the percentage of unmethylated molecules in DNA from each tissue. The set of columns on the far right describes the percentage of molecules in which all CpG sites are unmethylated, demonstrating the higher signal-to-noise ratio afforded by interrogating all CpGs simultaneously.
  • FIG. 6 C Correlation between results of spike-in experiments using the sense and antisense FAM101A markers.
  • FIGS. 7 A-F additional correlations of cardiac and total cfDNA in MI patients.
  • FIG. 7 C Total cfDNA concentration in controls and MI patients.
  • FIG. 7 D Lack of correlation between total concentration of cfDNA (genome equivalents/ml) and either hs-Tn (blue) or CK (red) levels.
  • FIG. 7 E Lack of correlation between total cfDNA (genome equivalents/ml) and percentage of cardiac cfDNA.
  • FIG. 7 F Linear correlation between FAM101A sense (S) and antisense (AS) signal in the MI specimens.
  • FIGS. 8 A-B Dynamics of cardiac cfDNA and CPK in myocardial infarction.
  • FIG. 8 A Ratio of cardiac cfDNA before and after PCI in 15 individuals with MI. As expected, cardiac cfDNA levels increased after intervention.
  • FIG. 8 B Dynamics of cardiac cfDNA and CPK in individual patients. Time 0 is the beginning of chest pain. Vertical dashed line indicates time of PCI.
  • FIGS. 9 A-C Total and cardiac cfDNA levels in patients with sepsis.
  • FIG. 9 A Concentration of cfDNA in patients with sepsis.
  • FIG. 9 B Percentage of cardiac cfDNA in patients with sepsis.
  • FIG. 9 C Correlation between FAM101A sense and antisense signals in sepsis specimens.
  • FIG. 10 is a pictorial representation of ddPCR technology.
  • FIG. 11 is a pictorial representation of an assay according to embodiments of the present invention. The figure illustrates the use of two probes (red and green) to define methylation status of two clusters of CpGs on the same DNA molecule in the same droplet.
  • FIG. 12 is a table comparing the time it takes to analyse methylation status by sequencing and by ddPCR.
  • FIGS. 13 A-B are bar graphs illustrating how ddPCR may be used to diagnose patients with a myocardial infarction.
  • FIGS. 14 A-B illustrate digital droplet PCR for the identification of liver-derived cfDNA according to embodiments of the present invention.
  • FIGS. 15 A-B illustrate digital droplet PCR for the identification of colon-derived cfDNA in plasma samples. ddPCR using both amplicons showed no signal in pancreas, liver, cfDNA from healthy controls DNA and a strong signal in cfDNA of patients with colorectal cancer.
  • FIGS. 16 A-B illustrates digital droplet PCR for the identification of liver-derived cfDNA according to embodiments of the present invention.
  • the present invention contemplates using digital droplet PCR (ddPCR) for analyzing the methylation status of single DNA molecules.
  • ddPCR digital droplet PCR
  • the method can be used to detect tissue-specific methylation markers.
  • tissue-specific methylation patterns present in circulating DNA fragments were performed using massively parallel sequencing, requiring access to a next generation sequencer and the application of a bioinformatics pipeline to interpret sequencing results.
  • the present inventors have now simplified the method by alleviating the need for sequencing, whilst maintaining accuracy and reliability.
  • the novel method which relies on digital droplet polymerase chain reaction (ddPCR; an overview of which is presented in FIG. 10 ), reduced the level of false positives to such an extent that clinical utility can now be envisaged.
  • ddPCR digital droplet polymerase chain reaction
  • ddPCR digital droplet PCR
  • fluorescent probes that recognize blocks of unmethylated CpGs in the amplified marker regions
  • FIG. 11 illustrates the use of two probes (red and green) to define the methylation status of two clusters of CpGs on the same DNA molecule in the same droplet.
  • FIG. 5 B The increased specificity of the technique is illustrated in FIG. 5 B .
  • the number of droplets positive for each individual probe demonstrated that it is possible to discriminate between cardiac and blood DNA. But when scoring for droplets that are positive for both probes (that is, unmethylated in all 5 CpG sites tested), the noise from blood (red bar) was reduced dramatically and accuracy was increased dramatically.
  • the present inventors propose that ddPCR (as compared to sequencing) for identification of the methylation status of cfDNA will radically reduce the time from drawing blood to results, from ⁇ 36 hours today to 7 hours, and potentially much less if rapid PCR machines are used.
  • the present inventors Whilst further reducing the present invention to practice, the present inventors have shown that the ddPCR protocol could successfully diagnose myocardial infarction patients ( FIGS. 13 A-B ). In addition, the present inventors have shown that the ddPCR protocol could successfully diagnose liver damage ( FIGS. 14 A-B ) and colon cancer ( FIGS. 15 A-B ).
  • a method of analyzing the methylation status of methylation sites of a double-stranded DNA molecule which comprises at least two methylation sites per single strand of said double-stranded DNA molecule, the double-stranded DNA molecule being comprised in a specimen comprising:
  • methylation status refers to the status of a cytosine in a DNA sequence.
  • the cytosine may be methylated (and present as 5-methylcytosine) or non-methylated and present as cytosine.
  • methylation site refers to a cytosine residue adjacent to guanine residue (CpG site) that has a potential of being methylated.
  • the DNA molecule which is analyzed is preferably no longer than 300 nucleotides, 295 nucleotides, 290 nucleotides, 285 nucleotides, 280 nucleotides, 275 nucleotides, 270 nucleotides, 265 nucleotides, 260 nucleotides, 255 nucleotides, 250 nucleotides, 245 nucleotides, 240 nucleotides, 235 nucleotides, 230 nucleotides, 225 nucleotides, 220 nucleotides, 215 nucleotides, 210 nucleotides, 205 nucleotides, 200 nucleotides, 195 nucleotides, 190 nucleotides, 185 nucleotides, 180 nucleotides, 175 nucleotides, 170 nucleotides, 165 nucleotides, 160 nucleotides, 155 nucleotides, 150 nucleot
  • the DNA molecule is between 50-300 nucleotides, e.g. between 50-250, between 50-200, between 100-300 nucleotides, or between 100-250 nucleotides.
  • the methylation sites of a methylation signature which are analyzed on a double stranded molecule are no more than 300 nucleotides apart, 295 nucleotides apart, 290 nucleotides apart, 285 nucleotides apart, 280 nucleotides apart, 275 nucleotides apart, 270 nucleotides apart, 265 nucleotides apart, 260 nucleotides apart, 255 nucleotides apart, 250 nucleotides apart, 245 nucleotides apart, 240 nucleotides apart, 235 nucleotides apart, 230 nucleotides apart, 225 nucleotides apart, 220 nucleotides apart, 215 nucleotides apart, 210 nucleotides apart, 205 nucleotides apart, 200 nucleotides apart, 195 nucleotides apart, 190 nucleotides apart, 185 nucleotides apart, 180 nucleotides apart,
  • the sequence of the DNA may be of a coding or non-coding region.
  • the sequence is not derived from a gene which is differentially expressed in the cell of interest.
  • the DNA sequence is not part of a gene encoding insulin or another pancreatic beta cell protein.
  • the methylation pattern characterizes the normal cell of interest and is not a methylation pattern characterizing a diseased cell (is not for example a methylation pattern characterizing cancer cells of a specific type).
  • the method of the present invention contemplates analyzing at least 2, at least 3, at least 4, at least 5, at least 6, at least 7 at least 8, at least 9 or even at least 10 or more methylation sites of a double-stranded DNA molecule.
  • the methylation signature of a double-stranded DNA molecule may comprise at least 2, at least 3, at least 4 at least 5, at least 6, at least 7 at least 8, at least 9 or even at least 10 or more methylation sites.
  • each of the methylation sites of the signature on the DNA molecule should be differentially methylated in that cell of interest with respect to a second non-identical cell.
  • the methylation signature comprises the methylation status of at least two, at least three, at least four methylation sites of a particular DNA molecule.
  • the methylation sites may be on a single strand of the DNA molecule or distributed amongst both strands of the DNA molecule.
  • each of the at least two, three, four or more methylation sites of the signature are unmethylated in the cell of interest (the cell for which the methylation pattern is being determined) on the DNA molecule, whereas in the second non-identical cell each of the sites are methylated on the DNA molecule.
  • each of the at least two, three, four or more methylation sites of the signature are methylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell each of the sites are unmethylated on the DNA molecule.
  • At least one of the methylation sites of the signature is unmethylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell that site is methylated on the DNA molecule.
  • At least one of the methylation sites of the signature is methylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell that site is unmethylated on the DNA molecule.
  • At least two methylation sites of the signature are unmethylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are methylated on the DNA molecule.
  • At least two methylation sites of the signature are methylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are unmethylated on the DNA molecule.
  • At least three methylation sites of the signature are unmethylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are methylated on the DNA molecule.
  • At least three methylation sites of the signature are methylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are unmethylated on the DNA molecule.
  • At least four methylation sites of the signature are unmethylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are methylated on the DNA molecule.
  • At least four methylation sites of the signature are methylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are unmethylated on the DNA molecule.
  • the second, non-identical cell may be of any source including for example blood cells.
  • the non-identical cell is one which is comprised in the specimen/sample being analyzed.
  • the method can be used for identifying methylation signatures of any cell of interest, including but not limited to cardiac cells (e.g. cardiomyocytes), pancreatic cells (such as pancreatic beta cells, exocrine pancreatic cells (e.g. acinar cells), brain cells, oligodendrocytes, liver cells (hepatocytes), kidney cells, tongue cells, vascular endothelial cells, lymphocytes, neutrophils, melanocytes, T-regs, lung cells, a uterus cells, breast cells, adipocytes, colon cells, rectum cells, prostate cells, thyroid cells and skeletal muscle cells.
  • Specimens which may be analyzed are generally fluid specimens derived from mammalian subjects and include for example blood, plasma, sperm, milk, urine, saliva or cerebral spinal fluid.
  • the specimen is plasma or blood.
  • Specimens which are analyzed typically comprise DNA from at least one or at least two cell/tissue sources, as further described herein below.
  • the specimens may comprise cell-free DNA from a single cell type or at least two cell types.
  • a specimen of blood is obtained from a subject according to methods well known in the art.
  • Plasma or serum may be isolated according to methods known in the art.
  • DNA may be isolated from the blood immediately or within 1 hour, 2 hours, 3 hours, 4 hours, 5 hours or 6 hours.
  • the blood is stored at temperatures such as 4° C., or at ⁇ 20° C. prior to isolation of the DNA.
  • a portion of the blood specimen is used in accordance with the invention at a first instance of time whereas one or more remaining portions of the blood specimen (or fractions thereof) are stored for a period of time for later use.
  • the DNA molecule which is analyzed is cellular DNA (i.e. comprised in a cell).
  • the DNA molecule which is analyzed is comprised in a shedded cell or non-intact cell.
  • kits that can be used to extract DNA from tissues and bodily fluids and that are commercially available from, for example, BD Biosciences Clontech (Palo Alto, Calif.), Epicentre Technologies (Madison, Wis.), Gentra Systems, Inc. (Minneapolis, Minn.), MicroProbe Corp. (Bothell, Wash.), Organon Teknika (Durham, N.C.), and Qiagen Inc. (Valencia, Calif.).
  • User Guides that describe in great detail the protocol to be followed are usually included in all these kits. Sensitivity, processing time and cost may be different from one kit to another. One of ordinary skill in the art can easily select the kit(s) most appropriate for a particular situation.
  • the DNA which is analyzed is cell-free DNA.
  • cell lysis is not performed on the specimen.
  • Methods of isolating cell-free DNA from body fluids are also known in the art.
  • Qiaquick kit manufactured by Qiagen may be used to extract cell-free DNA from plasma or serum.
  • the specimen may be processed before the method is carried out, for example DNA purification may be carried out following the extraction procedure.
  • the DNA in the specimen may be cleaved either physically or chemically (e.g. using a suitable enzyme). Processing of the specimen may involve one or more of: filtration, distillation, centrifugation, extraction, concentration, dilution, purification, inactivation of interfering components, addition of reagents, and the like.
  • the DNA is treated with bisulfite which converts cytosine residues to uracil (which are converted to thymidine following PCR), but leaves 5-methylcytosine residues unaffected.
  • bisulfite treatment introduces specific changes in the DNA sequence that depend on the methylation status of individual cytosine residues, yielding single-nucleotide resolution information about the methylation status of a segment of DNA.
  • Bisulfite sequencing relies on the conversion of every single unmethylated cytosine residue to uracil. If conversion is incomplete, the subsequent analysis will incorrectly interpret the unconverted unmethylated cytosines as methylated cytosines, resulting in false positive results for methylation. Only cytosines in single-stranded DNA are susceptible to attack by bisulfite, therefore denaturation of the DNA undergoing analysis is critical. It is important to ensure that reaction parameters such as temperature and salt concentration are suitable to maintain the DNA in a single-stranded conformation and allow for complete conversion.
  • an oxidative bisulfite reaction is performed.
  • 5-methylcytosine and 5-hydroxymethylcytosine both read as a C in bisulfite sequencing.
  • Oxidative bisulfite reaction allows for the discrimination between 5-methylcytosine and 5-hydroxymethylcytosine at single base resolution.
  • the method employs a specific chemical oxidation of 5-hydroxymethylcytosine to 5-formylcytosine, which subsequently converts to uracil during bisulfite treatment.
  • the only base that then reads as a C is 5-methylcytosine, giving a map of the true methylation status in the DNA specimen.
  • Levels of 5-hydroxymethylcytosine can also be quantified by measuring the difference between bisulfite and oxidative bisulfite sequencing.
  • the bisulfite-treated DNA sequence is fractionated and then optionally subjected to an amplification reaction.
  • emulsification techniques can be used so as to create large numbers of aqueous droplets that function as independent reaction chambers for the PCR reactions.
  • an aqueous specimen e.g., 20 microliters
  • droplets e.g., 20,000 droplets of one nanoliter each
  • Aqueous droplets can be suspended in oil to create a water-in-oil emulsion (W/0).
  • the emulsion can be stabilized with a surfactant to reduce coalescence of droplets during heating, cooling, and transport, thereby enabling thermal cycling to be performed.
  • a specimen is partitioned into a set of droplets at a dilution that ensures that more than 40% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • a specimen is partitioned into a set of droplets at a dilution that ensures that more than 50% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • a specimen is partitioned into a set of droplets at a dilution that ensures that more than 60% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • a specimen is partitioned into a set of droplets at a dilution that ensures that more than 70% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • a specimen is partitioned into a set of droplets at a dilution that ensures that more than 80% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • a specimen is partitioned into a set of droplets at a dilution that ensures that more than 90% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • the single-stranded DNA may then optionally be amplified.
  • amplification refers to a process that increases the representation of a population of specific nucleic acid sequences in a specimen by producing multiple (i.e., at least 2) copies of the desired sequences.
  • Methods for nucleic acid amplification are known in the art and include, but are not limited to, polymerase chain reaction (PCR) and ligase chain reaction (LCR).
  • PCR polymerase chain reaction
  • LCR ligase chain reaction
  • a nucleic acid sequence of interest is often amplified at least fifty thousand fold in amount over its amount in the starting specimen.
  • a “copy” or “amplicon” does not necessarily mean perfect sequence complementarity or identity to the template sequence.
  • copies can include nucleotide analogs such as deoxyinosine, intentional sequence alterations (such as sequence alterations introduced through a primer comprising a sequence that is hybridizable but not complementary to the template), and/or sequence errors that occur during amplification.
  • nucleotide analogs such as deoxyinosine
  • intentional sequence alterations such as sequence alterations introduced through a primer comprising a sequence that is hybridizable but not complementary to the template
  • sequence errors that occur during amplification.
  • a typical amplification reaction is carried out by contacting a forward and reverse primer (a primer pair) to the specimen DNA together with any additional amplification reaction reagents under conditions which allow amplification of the target sequence.
  • the oligonucleotide amplification primers typically flank the target sequence—(i.e. the sequence comprising the at least two, three, four or five methylation sites (per single strand).
  • forward primer and “forward amplification primer” are used herein interchangeably, and refer to a primer that hybridizes (or anneals) to the target (template strand).
  • reverse primer and “reverse amplification primer” are used herein interchangeably, and refer to a primer that hybridizes (or anneals) to the complementary target strand. The forward primer hybridizes with the target sequence 5′ with respect to the reverse primer.
  • amplification conditions refers to conditions that promote annealing and/or extension of primer sequences. Such conditions are well-known in the art and depend on the amplification method selected. Thus, for example, in a PCR reaction, amplification conditions generally comprise thermal cycling, i.e., cycling of the reaction mixture between two or more temperatures. In isothermal amplification reactions, amplification occurs without thermal cycling although an initial temperature increase may be required to initiate the reaction. Amplification conditions encompass all reaction conditions including, but not limited to, temperature and temperature cycling, buffer, salt, ionic strength, and pH, and the like.
  • amplification reaction reagents refers to reagents used in nucleic acid amplification reactions and may include, but are not limited to, buffers, reagents, enzymes having reverse transcriptase and/or polymerase activity or exonuclease activity, enzyme cofactors such as magnesium or manganese, salts, nicotinamide adenine dinuclease (NAD) and deoxynucleoside triphosphates (dNTPs), such as deoxyadenosine triphospate, deoxyguanosine triphosphate, deoxycytidine triphosphate and thymidine triphosphate.
  • Amplification reaction reagents may readily be selected by one skilled in the art depending on the amplification method used.
  • the amplification reaction uses a single labeled oligonucleotide probe which hybridizes to one strand of the amplified DNA which comprises at least two, at least three, at least four, at least five methylation sites (for example as illustrated in FIG. 16 B ).
  • the amplification reaction uses at least two probes, one which hybridizes to the first strand of the amplified DNA and one which hybridizes to the second strand of the amplified DNA (for example as illustrated in FIG. 16 A ).
  • the two probes are labeled with non-identical labels i.e. detectable moieties.
  • the oligonucleotides of the invention need not reflect the exact sequence of the target nucleic acid sequence (i.e. need not be fully complementary), but must be sufficiently complementary so as to hybridize to the target site under the particular experimental conditions. Accordingly, the sequence of the oligonucleotide typically has at least 70% homology, preferably at least 80%, 90%, 95%, 97%, 99% or 100% homology, for example over a region of at least 13 or more contiguous nucleotides with the target sequence. The conditions are selected such that hybridization of the oligonucleotide to the target site is favored and hybridization to the non-target site is minimized.
  • the lower the homology of the oligonucleotide to the target sequence the lower the stringency of the assay conditions should be, although the stringency must not be too low to allow hybridization to non-specific nucleic acid sequences.
  • Oligonucleotides of the invention may be prepared by any of a variety of methods (see, for example, J. Sambrook et al., “Molecular Cloning: A Laboratory Manual”, 1989, 2. sup. nd Ed., Cold Spring Harbour Laboratory Press: New York, N.Y.; “PCR Protocols: A Guide to Methods and Applications”, 1990, M. A. Innis (Ed.), Academic Press: New York, N.Y.; P. Tijssen “Hybridization with Nucleic Acid Probes-Laboratory Techniques in Biochemistry and Molecular Biology (Parts I and II)”, 1993, Elsevier Science; “PCR Strategies”, 1995, M. A.
  • oligonucleotides may be prepared using any of a variety of chemical techniques well-known in the art, including, for example, chemical synthesis and polymerization based on a template as described, for example, in S. A. Narang et al., Meth. Enzymol. 1979, 68: 90-98; E. L. Brown et al., Meth. Enzymol. 1979, 68: 109-151; E. S.
  • oligonucleotides may be prepared using an automated, solid-phase procedure based on the phosphoramidite approach.
  • each nucleotide is individually added to the 5′-end of the growing oligonucleotide chain, which is attached at the 3′-end to a solid support.
  • the added nucleotides are in the form of trivalent 3′-phosphoramidites that are protected from polymerization by a dimethoxytriyl (or DMT) group at the 5′-position.
  • DMT dimethoxytriyl
  • oligonucleotides are then cleaved off the solid support, and the phosphodiester and exocyclic amino groups are deprotected with ammonium hydroxide.
  • These syntheses may be performed on oligo synthesizers such as those commercially available from Perkin Elmer/Applied Biosystems, Inc. (Foster City, Calif.), DuPont (Wilmington, Del.) or Milligen (Bedford, Mass.).
  • oligonucleotides can be custom made and ordered from a variety of commercial sources well-known in the art, including, for example, the Midland Certified Reagent Company (Midland, Tex.), ExpressGen, Inc. (Chicago, Ill.), Operon Technologies, Inc. (Huntsville, Ala.), and many others.
  • Purification of the oligonucleotides of the invention may be carried out by any of a variety of methods well-known in the art. Purification of oligonucleotides is typically performed either by native acrylamide gel electrophoresis, by anion-exchange HPLC as described, for example, by J. D. Pearson and F. E. Regnier (J. Chrom., 1983, 255: 137-149) or by reverse phase HPLC (G. D. McFarland and P. N. Borer, Nucleic Acids Res., 1979, 7: 1067-1080).
  • sequence of oligonucleotides can be verified using any suitable sequencing method including, but not limited to, chemical degradation (A. M. Maxam and W. Gilbert, Methods of Enzymology, 1980, 65: 499-560), matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (U. Pieles et al., Nucleic Acids Res., 1993, 21: 3191-3196), mass spectrometry following a combination of alkaline phosphatase and exonuclease digestions (H. Wu and H. Aboleneen, Anal. Biochem., 2001, 290: 347-352), and the like.
  • chemical degradation A. M. Maxam and W. Gilbert, Methods of Enzymology, 1980, 65: 499-560
  • MALDI-TOF matrix-assisted laser desorption ionization time-of-flight
  • mass spectrometry U. Pieles et al., Nucleic Acid
  • the detection probes or amplification primers are labeled with a detectable agent or moiety before being used in amplification/detection assays.
  • the detection probes are labeled with a detectable agent.
  • a detectable agent is selected such that it generates a signal which can be measured and whose intensity is related (e.g., proportional) to the amount of amplification products in the sample being analyzed.
  • Labeled detection probes can be prepared by incorporation of or conjugation to a detectable moiety. Labels can be attached directly to the nucleic acid sequence or indirectly (e.g., through a linker). Linkers or spacer arms of various lengths are known in the art and are commercially available, and can be selected to reduce steric hindrance, or to confer other useful or desired properties to the resulting labeled molecules (see, for example, E. S. Mansfield et al., Mol. Cell. Probes, 1995, 9: 145-156).
  • Standard nucleic acid labeling methods include: incorporation of radioactive agents, direct attachments of fluorescent dyes (L. M. Smith et al., Nucl. Acids Res., 1985, 13: 2399-2412) or of enzymes (B.
  • nucleic acid labeling systems include, but are not limited to: ULS (Universal Linkage System), which is based on the reaction of mono-reactive cisplatin derivatives with the N7 position of guanine moieties in DNA (R. J. Heetebrij et al., Cytogenet. Cell. Genet. 1999, 87: 47-52), psoralen-biotin, which intercalates into nucleic acids and upon UV irradiation becomes covalently bonded to the nucleotide bases (C. Levenson et al., Methods Enzymol. 1990, 184: 577-583; and C. Pfannschmidt et al., Nucleic Acids Res.
  • ULS Universal Linkage System
  • the probes of this aspect of the present invention hybridize to more than one methylation site, for example, two, three, or even four—see for example FIG. 16 B .
  • the sequence of the first and/or second probe may be selected such that it binds to the amplified DNA when the methylation site of the double-stranded DNA molecule is non-methylated.
  • the sequence of the first and/or second probe may be selected such that it binds to the amplified DNA when the methylation site of the double-stranded DNA molecule is methylated.
  • the inventive detection probes are fluorescently labeled.
  • fluorescent dyes include, but are not limited to, fluorescein and fluorescein dyes (e.g., fluorescein isothiocyanine or FITC, naphthofluorescein, 4′,5′-dichloro-2′,7′-dimethoxy-fluorescein, 6 carboxyfluorescein or FAM), carbocyanine, merocyanine, styryl dyes, oxonol dyes, phycoerythrin, erythrosin, eosin, rhodamine dyes (e.g., carboxytetramethylrhodamine or TAMRA, carboxyrhodamine 6G, carboxy-X-rhodamine (ROX), lissamine rhodamine B,
  • fluorescein and fluorescein dyes e.g., fluorescein isothiocyanine or FITC, naph
  • fluorescent dyes and methods for linking or incorporating fluorescent dyes to nucleic acid molecules see, for example, “The Handbook of Fluorescent Probes and Research Products”, 9th Ed., Molecular Probes, Inc., Eugene, Oreg. Fluorescent dyes as well as labeling kits are commercially available from, for example, Amersham Biosciences, Inc. (Piscataway, N.J.), Molecular Probes Inc. (Eugene, Oreg.), and New England Biolabs Inc. (Beverly, Mass.).Another contemplated method of analyzing the methylation status of the sequences is by analysis of the DNA following exposure to methylation-sensitive restriction enzymes—see for example US Application Nos. 20130084571 and 20120003634, the contents of which are incorporated herein.
  • Exemplary probes for detecting cardiac DNA are set forth in SEQ ID NOs: 118 and 119.
  • Exemplary probes for detecting colon DNA are set forth in SEQ ID NOs: 125 and 126.
  • Exemplary probes for detecting liver DNA are set forth in SEQ ID NOs: 128, 129 and 130.
  • the probes that are used are TaqManTM probes.
  • TaqManTM probes comprise a detectable moiety (e.g. fluorophore) covalently attached to the 5′-end of the oligonucleotide probe and a quencher at the 3′-end.
  • a detectable moiety e.g. fluorophore
  • FAM 6-carboxyfluorescein
  • TET tetrachlorofluorescein
  • TAMRA quenchers
  • the quencher molecule quenches the fluorescence emitted by the fluorophore when excited by the cycler's light source via FRET (Forster Resonance Energy Transfer). As long as the fluorophore and the quencher are in proximity, quenching inhibits any fluorescence signals.
  • FRET Form Resonance Energy Transfer
  • quenchers include, but are not limited to DabcylTM, TAMRATM, ECLIPSETM, DDQTM, QSYTM, Blackberry Quencher, Black Hole Quencher, Qxl, Iowa black FQTM, Iowa black RQTM, and IRDye QC-1TM.
  • TaqManTM probes are designed such that they anneal within a DNA region amplified by a specific set of primers.
  • the 5′ to 3′ exonuclease activity of the Taq polymerase degrades the probe that has annealed to the template. Degradation of the probe releases the detectable moiety from it and breaks the close proximity to the quencher, thus relieving the quenching effect and allowing for detection of the detectable moiety (e.g. it allow for fluorescence of the fluorophore).
  • the amount of detectable moiety is directly proportional to the amount of DNA template present in the PCR.
  • determining the methylation status is carried out as follows:
  • the bisulfite-treated DNA of the specimen is contacted with:
  • the first probe hybridizes to the forward strand of the amplified DNA and the second probe hybridizes to the reverse strand of the amplified DNA (see for example FIG. 5 A ).
  • the contacting is effected under conditions that separate the quenching moiety from the first probe and the second probe to generate a non-quenched first probe and a non-quenched second probe.
  • the conditions are those which are inductive for an amplification reaction—i.e. presence of a polymerase enzyme having 5′ to 3′ nuclease activity (e.g. TaqmanTM polymerase), dNTPs and buffer etc.
  • the amount of non-quenched first probe and non-quenched second probe in a single droplet can be measured—e.g. by using a fluorimeter.
  • the number of droplets containing a signal from both probes is scored
  • the target comprises at least a part of the sequence of human chromosome 12, between coordinates 124692462-124692551 (e.g. SEQ ID NOs: 56 or 57).
  • the target comprises at least a part of the ECH1 locus.
  • the target comprises at least a part of the IGF2R gene or the VTN gene (e.g. SEQ ID NOs: 65 or 66).
  • targets that may be analyzed are comprised in the sequences set forth in SEQ ID Nos: 2-117 or SEQ ID NOs: 135-191.
  • the target sequence comprises the nucleotides CG which are at position 250 and 251 of each of these sequences.
  • At least one of the methylation sites of the signature are the nucleotides CG which are at position 250 and 251 of each of these sequences.
  • kit comprises:
  • sequence of said first probe is selected so as to determine a methylation status at a first methylation site of the double-stranded DNA molecule and the sequence of said second probe is selected so as determine a methylation status at a second methylation site of the same double-stranded DNA molecule, wherein said first methylation site and said second methylation site are no more than 300 base pairs apart;
  • the kit includes:
  • kits include at least one of the following components: a droplet forming oil, bisulfite (and other reagents necessary for the bisulfite reaction), reagents for purification of DNA, MgCl 2 .
  • the kit may also comprise reaction components for sequencing the amplified or non-amplified sequences.
  • kits may also comprise DNA sequences which serve as controls.
  • the kit may comprise a DNA having the same sequence as the amplified sequence derived from a healthy subject (to serve as a negative control) and/or a DNA having the same sequence as the amplified sequence derived from a subject known to have the disease which is being investigated (to serve as a positive control).
  • kits may comprise known quantities of DNA such that calibration and quantification of the test DNA may be carried out.
  • the containers of the kits will generally include at least one vial, test tube, flask, bottle, syringe or other containers, 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 container.
  • the liquid solution can be an aqueous solution.
  • the components of the kit may be provided as dried powder(s).
  • the powder can be reconstituted by the addition of a suitable solvent.
  • kits will preferably include instructions for employing, the kit components as well the use of any other reagent not included in the kit. Instructions may include variations that can be implemented.
  • Pathological and disease conditions that involve cell death cause the release of degraded DNA from dying cells into body fluids (blood, plasma, urine, cerebrospinal fluid).
  • body fluids blood, plasma, urine, cerebrospinal fluid.
  • the methods described herein may be used to analyze the amount of cell death of a particular cell population in those body fluids.
  • the amount of cell death of a particular cell population can then be used to diagnose a particular pathological state (e.g. disease) or condition (e.g. trauma).
  • death of a particular cell type may be associated with a pathological state—e.g. disease or trauma.
  • the monitoring of the death of a particular cell type may also be used for monitoring the efficiency of a therapeutic regime expected to effect cell death of a specific cell type.
  • the determination of death of a specific cell type may also be used in the clinical or scientific study of various mechanism of healthy or diseased subjects.
  • pancreatic beta cell death is important in cases of diabetes, hyperinsulinism and islet cell tumors, and in order to monitor beta cell survival after islet transplantation, determining the efficacy of various treatment regimes used to protect beta cells from death, and determining the efficacy of treatments aimed at causing islet cell death in islet cell tumors.
  • the method allows the identification and quantification of DNA derived from dead kidney cells (indicative of kidney failure), dead neurons (indicative of traumatic brain injury, amyotrophic lateral sclerosis (ALS), stroke, Alzheimer's disease, Parkinson's disease or brain tumors, with or without treatment); dead pancreatic acinar cells (indicative of pancreatic cancer or pancreatitis); dead lung cells (indicative of lung pathologies including lung cancer); dead adipocytes (indicative of altered fat turnover), dead hepatocytes (indicative of liver failure, liver toxicity or liver cancer) dead cardiomyocytes (indicative of cardiac disease, or graft failure in the case of cardiac transplantation), dead skeletal muscle cells (indicative of muscle injury and myopathies), dead oligodendrocytes (indicative of relapsing multiple sclerosis, white matter damage in amyotrophic lateral sclerosis, or glioblastoma), dead colon cells is indicative of colorectal cancer.
  • diagnosis refers to determining the presence of a disease, classifying a disease, determining a severity of the disease (grade or stage), monitoring disease progression and response to therapy, forecasting an outcome of the disease and/or prospects of recovery.
  • the method comprises quantifying the amount of cell-free DNA which is comprised in a fluid sample (e.g. a blood sample or serum sample) of the subject which is derived from a cell type or tissue.
  • a fluid sample e.g. a blood sample or serum sample
  • the amount of cell free DNA derived from the cell type or tissue is above a predetermined level, it is indicative that there is a predetermined level of cell death.
  • the level of cell death is above a predetermined level, it is indicative that the subject has the disease or pathological state. Determining the predetermined level may be carried out by analyzing the amount of cell-free DNA present in a sample derived from a subject known not to have the disease/pathological state.
  • the level of the cell-free DNA derived from a cell type or tissue associated with the disease in the test sample is statistically significantly higher (e.g. at least two fold, at least three fold, or at least 4 fold) than the level of cell-free DNA derived from the same cell type or tissue in the sample obtained from the healthy (non-diseased subject), it is indicative that the subject has the disease.
  • determining the predetermined level may be carried out by analyzing the amount of cell-free DNA present in a sample derived from a subject known to have the disease.
  • the level of the cell-free DNA derived from a cell type or tissue associated with the disease in the test sample is statistically significantly similar to the level of the cell-free DNA derived from a cell type of tissue associated with the disease in the sample obtained from the diseased subject, it is indicative that the subject has the disease.
  • the method comprises determining the ratio of the amount of cell free DNA derived from a cell of interest in the sample: amount of overall cell free DNA.
  • the method comprises determining the ratio of the amount of cell free DNA derived from a cell of interest in the sample: amount of cell free DNA derived from a second cell of interest.
  • the methods described herein may also be used to determine the efficacy of a therapeutic agent or treatment, wherein when the amount of DNA associated with a cell population associated with the disease is decreased following administration of the therapeutic agent, it is indicative that the agent or treatment is therapeutic.
  • screening of the subject for a specific disease is followed by substantiation of the screen results using gold standard methods.
  • the method can also be used to predict prognosis of the subject with the disease.
  • the method further comprising informing the subject of the predicted disease and/or the predicted prognosis of the subject.
  • the phrase “informing the subject” refers to advising the subject that based on the cfDNA levels, the subject should seek a suitable treatment regimen.
  • the results can be recorded in the subject's medical file, which may assist in selecting a treatment regimen and/or determining prognosis of the subject.
  • the method further comprising recording the cfDNA levels of the subject in the subject's medical file.
  • the prediction can be used to select the treatment regimen of a subject and thereby treat the subject in need thereof.
  • compositions, method or structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure.
  • a compound or “at least one compound” may include a plurality of compounds, including mixtures thereof.
  • range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
  • a numerical range is indicated herein, it is meant to include any cited numeral (fractional or integral) within the indicated range.
  • the phrases “ranging/ranges between” a first indicate number and a second indicate number and “ranging/ranges from” a first indicate number “to” a second indicate number are used herein interchangeably and are meant to include the first and second indicated numbers and all the fractional and integral numerals therebetween.
  • method refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts.
  • treating includes abrogating, substantially inhibiting, slowing or reversing the progression of a condition, substantially ameliorating clinical or aesthetical symptoms of a condition or substantially preventing the appearance of clinical or aesthetical symptoms of a condition.
  • any Sequence Identification Number can refer to either a DNA sequence or a RNA sequence, depending on the context where that SEQ ID NO is mentioned, even if that SEQ ID NO is expressed only in a DNA sequence format or a RNA sequence format.
  • SEQ ID NO: XXX is expressed in a DNA sequence format (e.g., reciting T for thymine), but it can refer to either a DNA sequence that corresponds to an XXX nucleic acid sequence, or the RNA sequence of an RNA molecule nucleic acid sequence.
  • RNA sequence format e.g., reciting U for uracil
  • it can refer to either the sequence of a RNA molecule comprising a dsRNA, or the sequence of a DNA molecule that corresponds to the RNA sequence shown.
  • both DNA and RNA molecules having the sequences disclosed with any substitutes are envisioned.
  • Tissue-specific DNA methylation markers were selected after a comparison of publically available DNA methylation datasets generated by whole-genome bisulfite sequencing (Roadmap Epigenomics).
  • the fragment of FAM101A used as a cariomyocyte-specific marker is located in chromosome 12, coordinates 124692462-124692551.
  • cfDNA analysis Blood specimens were collected in EDTA tubes, and centrifuged within 2 hours to separate plasma from peripheral blood cells: first at 1500 g for 10 min, and then at 3000 g for 10 min to remove any remaining cells. Plasma was then stored at ⁇ 80° C.
  • cfDNA was extracted using the QIAsymphony SP instrument and its dedicated QIAsymphony Circulating DNA Kit (Qiagen) according to the manufacturer's instructions.
  • DNA concentration was measured using the QubitTM dsDNA HS Assay Kit.
  • cfDNA was treated with bisulfite using a kit (Zymo Research), and PCR amplified with primers specific for bisulfite-treated DNA but independent of methylation status at the monitored CpG sites.
  • Primers were bar-coded, allowing the mixing of specimens from different individuals when sequencing PCR products using MiSeq or NextSeq (Illumina). Sequenced reads were separated by barcode, aligned to the target sequence, and analyzed using custom scripts written and implemented in R. Reads were quality filtered based on Illumina quality scores, and identified by having at least 80% similarity to target sequences and containing all the expected CpGs in the sequence. CpGs were considered methylated if “CG” was read and were considered unmethylated if “TG” was read.
  • Digital Droplet PCR A procedure was established for digital droplet PCR, in which bisulfite-treated cfDNA is amplified using a methylation-sensitive TaqmanTM probe.
  • probes up to 30 bp dictated that they could cover only 2 or 3 informative CpG sites in the FAM101A locus, predicting a relatively high frequency of “noise” (positive droplets) in DNA from non-cardiac tissue.
  • this problem was addressed by documenting the methylation status of multiple adjacent cytosines ( FIGS. 1 A-E ), which greatly increased specificity.
  • 5 cytosines located adjacent to the FAM101A locus
  • 5′-TATGGTTTGGTAATTTATTTAGAG-3′ SEQ ID NO: 1; forward
  • 5′-AAATACAAATCCCACAAATAAA-3′ SEQ ID NO: 120; reverse
  • probes that detected lack of methylation on 3 and 2 cytosines respectively: 5′-AATGTATGGTGAAATGTAGTGTTGGG-3′ (SEQ ID NO: 118; FAM-forward probe) and 5′-AAAAATACTCAACTTCCATCTACAATT-3′ (SEQ ID NO: 119, HEX-reverse probe).
  • FIG. 5 A Assay design is shown in FIG. 5 A .
  • Each 20- ⁇ L volume reaction mix consisted of ddPCRTM Supermix for Probes (No dUTP) (Bio-Rad), 900 nM primer, 250 nM probe, and 2 ⁇ L of specimen.
  • the mixture and droplet generation oil were loaded onto a droplet generator (Bio-Rad). Droplets were transferred to a 96-well PCR plate and sealed.
  • the PCR was run on a thermal cycler as follows: 10 minutes of activation at 95° C., 47 cycles of a 2 step amplification protocol (30 s at 94° C. denaturation and 60 s at 53.7° C.), and a 10-minute inactivation step at 98° C.
  • the PCR plate was transferred to a QX100Droplet Reader (Bio-Rad), and products were analyzed with QuantaSoft (Bio-Rad) analysis software. Discrimination between droplets that contained the target (positives) and those which did not (negatives) was achieved by applying a fluorescence amplitude threshold based on the amplitude of reads from the negative template control.
  • methylomes of human heart chambers (right atrium, left and right ventricle) were compared with the methylomes of 23 other human tissues, all publicly available 12 .
  • Several differentially methylated loci were identified and a cluster of cytosines adjacent to the FAM101A locus was selected for further analysis ( FIGS. 1 A-B ).
  • PCR was used to amplify a 90 bp fragment around this cluster after bisulfite conversion of unmethylated cytosines, and the PCR product was sequenced to determine the methylation status of all 6 cytosines in the cluster.
  • leukocyte DNA was spiked with increasing amounts of cardiac DNA.
  • the fraction of cardiac DNA in the mixture was assessed using PCR amplification and massively parallel sequencing.
  • the assay was able to correctly determine the fraction of cardiac DNA, even when it was only 0.5% of the DNA in the mixture ( FIG. 1 D ).
  • each strand can be considered an independent biomarker.
  • the present inventors designed primers against the antisense strand of FAM101A post-bisulfite conversion.
  • the sense and antisense templates showed a similar sensitivity and specificity ( FIGS. 1 B-E and 6 A-C). It was reasoned that by testing both strands in a given specimen, both sensitivity and specificity of the assay will increase. For this reason further analysis of clinical specimens was performed using both sense and antisense specific primer sets.
  • the sense and antisense FAM101A markers were used to assess the concentration of cardiac cfDNA in the plasma of donors.
  • cfDNA was extracted from plasma and treated with bisulfite.
  • PCR and sequencing were performed, typically using material from 0.5 ml of plasma.
  • the fraction of PCR products carrying the cardiac-specific methylation pattern was multiplied by the total concentration of cfDNA, to obtain an estimation of cardiac cfDNA content in plasma.
  • MI myocardial infarction
  • Specimens from individuals that presented with chest pain, before and after they underwent angioplasty were used.
  • the levels of cardiac cfDNA as well as troponin and CPK were assessed.
  • ROC Receiver Operator Characteristic
  • the present inventors also compared cardiac cfDNA to standard cardiac damage markers CPK and troponin. Compared with healthy controls, cardiac cfDNA was significantly higher in MI patients that had CPK just above normal ( ⁇ 200), and was even higher in patients with high CPK (>200) ( FIG. 2 C ). Similarly, cardiac cfDNA was higher than normal in plasma specimens that had either low or high levels of troponin ( FIG. 2 D and FIGS. 7 A-F ). Among the 6 specimens that had troponin levels above baseline but ⁇ 0.03, there was no more cfDNA than in healthy controls ( FIG. 2 D ).
  • PCI Percutaneous Coronary Intervention
  • Cardiac cfDNA levels increased dramatically in most patients after PCI ( FIG. 3 A and supplemental FIGS. 8 A-B ), further supporting authenticity of the signal.
  • a more detailed time course on a smaller group of patients revealed that cardiac cfDNA levels rose quickly after PCI and returned to baseline after 1-2 days, showing similar kinetics to troponin and CPK ( FIG. 3 B and supplemental FIGS. 8 A-B ).
  • the present inventors determined the levels of cardiac cfDNA in a cohort of 100 patients with sepsis, for which 201 plasma specimens were available. Cardiac cfDNA was assessed blindly, and values were correlated to other biomarkers and to clinical parameters.
  • FIGS. 9 A-C Septic patients had high levels of total cfDNA, reflective of broad tissue damage ( FIGS. 9 A-C ), as reported 19 . Strikingly, many patients had high levels of cardiac cfDNA, similar in magnitude to the acute setting of MI ( FIG. 4 A ). These findings argue strongly that in many septic patients, massive cardiomyocyte death occurs. The sense and antisense markers of FAM101A correlated well, supporting specificity of the signal ( FIGS. 9 A-C ). Cardiac cfDNA and troponin levels did not correlate in the sepsis, unlike the situation in MI ( FIG. 4 B ). This is not surprising, given the chronic nature of tissue damage in sepsis, which is expected to involve a major contribution of clearance rates on the actual measurements of biomarkers. A dramatic elevation of cardiac cfDNA was seen also in septic patients with normal renal function (data not shown), supporting the idea that cardiac cfDNA reflects cell death and not altered clearance rate.
  • the present inventors attempted to correlate the levels of cardiac cfDNA with clinical parameters recorded for the sepsis patients.
  • the presence of cardiac cfDNA was strongly correlated with short-term mortality ( FIG. 4 C ).
  • patients with cardiac cfDNA were 4 times more likely to die within 90 days of hospitalization than patients with no cardiac cfDNA.
  • the correlation was stronger than the correlation between troponin and mortality or between total cfDNA and mortality, but weaker than the correlation between age and mortality.
  • ddPCR digital droplet PCR
  • ddPCR analysis of cardiomyocyte and leukocyte DNA revealed that each probe alone was able to discriminate between DNA from the two sources, with a signal to noise ratio of 50 to 58. However, when only droplets positive for both probes were scored, the cardiomyocyte:leukocyte signal ratio increased to 258, affording a 5 fold increase in specificity ( FIG. 5 B ).
  • ddPCR on cardiac DNA spiked with leukocyte DNA gave a signal that increased linearly with the amount of cardiac DNA; scoring only dual-labeled probes gave a lower baseline signal than scoring individual probes, better reflecting cardiomyocyte contribution to the mixture ( FIG. 5 C ).
  • ddPCR assay was tested on plasma specimens. ddPCR revealed a clear signal in the plasma of MI patients and was able to distinguish well between controls and patients. A lower baseline signal was observed in healthy individuals when scoring only dual-labeled probes, indicating increased specificity ( FIG. 5 D ). It can be concluded that the ddPCR assay for cardiac cfDNA provides a rapid and simple alternative to sequencing-based assays.
  • Each probe was labeled with a different fluorophore, such that it was possible to identify droplets in which both probes found a target. Such droplets would be interpreted as containing a VTN cfDNA fragment in which all 4 targeted cytosines were unmethylated. This resulted in a ddPCR assay with the improved specificity afforded by interrogating multiple cytosines on the same DNA molecule.
  • Each 20 ⁇ L volume reaction mix consisted of ddPCRTM Supermix for Probes (No dUTP) (Bio-Rad), 900 nM primer, 250 nM probe, and 2 ⁇ L of sample.
  • the mixture and droplet generation oil were loaded onto a droplet generator (Bio-Rad). Droplets were transferred to a 96-well PCR plate and sealed.
  • the PCR was run on a thermal cycler as follows: 10 minutes of activation at 95° C., 47 cycles of a 2 step amplification protocol (30 s at 94° C. denaturation and 60 s at 56° C.), and a 10-minute inactivation step at 98° C.
  • the PCR plate was transferred to a QX100 Droplet Reader (Bio-Rad), and products were analyzed with QuantaSoft (Bio-Rad) analysis software. Discrimination between droplets that contained the target (positives) and those that did not (negatives) was achieved by applying a fluorescence amplitude threshold based on the amplitude of reads from the negative template control.
  • VTN Probe 1—SEQ ID NO: 128
  • IGF2R Probe 1—SEQ ID NO: 130
  • Primers were designed for digital droplet PCR (ddPCR) after bisulfite conversion of cfDNA, and probes were designed that recognize blocks of unmethylated CpGs in the amplified marker regions.
  • ddPCR digital droplet PCR
  • the present inventors focused on the VTN and IGF2R markers, which had multiple CpGs in close proximity.
  • ddPCR using both amplicons showed no signal in leukocyte DNA and a strong signal in hepatocyte DNA ( FIG. 14 A ).
  • the present inventors examined 6 sets of plasma samples from 6 patients before and after liver transplantation.
  • the ddPCR assay revealed a strong and transient elevation of hepatocyte cfDNA in plasma shortly after transplantation, which declined thereafter, strongly suggesting validity of the assay ( FIG. 14 B ).
  • the sequences provided are 500 base pairs.
  • the target sequence (which is amplified which is less than all the 500 base pairs) comprises the nucleotides CG which are at position 250 and 251 of each of these sequences and additional nucleotides up and/or down-stream of this site.

Abstract

A digital droplet PCR method of analyzing the methylation status of methylation sites of a double-stranded DNA molecule which comprises at least two methylation sites per single strand of the double-stranded DNA molecule is disclosed.

Description

    REFERENCE TO AN ELECTRONIC SEQUENCE LISTING
  • The contents of the electronic sequence listing (HUJI-HDST-P-049-US1_SQL.xml; Size: 261,733 bytes; and Date of Creation: Nov. 20, 2022) is herein incorporated by reference in its entirety.
    • CROSS-REFERENCE TO RELATED APPLICATIONS
  • This application is a Continuation of U.S. patent application Ser. No. 16/630,593, filed Jan. 13, 2020, which is a National Phase of PCT Patent Application No PCT/IL2018/050772 having International filing date of Jul. 13, 2018, which claims the benefit of priority of U.S. Provisional Patent Application No. 62/531,983 filed Jul. 13, 2017.
    • FIELD AND BACKGROUND OF THE INVENTION
  • It has been known for decades that plasma contains small fragments of cell-free circulating DNA (cfDNA) derived from dead cells (on average 1000 genome equivalents per ml). While the mechanisms underlying the release and clearance of cfDNA remain obscure, the phenomenon is rapidly being exploited for a variety of applications with clinical relevance. The recognition that fragments of fetal DNA travel briefly in maternal circulation has opened the way for next generation sequencing (NGS)-based prenatal testing to identify fetal trisomies and other genetic aberrations, potentially replacing amniocentesis. In cancer biology, tumors are known to release DNA (including tumor-specific somatic mutations) into the circulation, providing means for liquid biopsies to monitor tumor dynamics and genomic evolution. In addition, cfDNA has been used to detect graft cell death after kidney, liver or heart transplantation, based on single nucleotide polymorphisms (SNPs) distinguishing the DNA of donor from that of recipients. In all these cases, genetic differences exist between the DNA sequence of the tissue of interest (fetus, tumor or graft) and that of the host, providing the basis for highly specific assays.
  • Blood levels of cfDNA are known to increase under multiple additional conditions such as traumatic brain injury, cardiovascular disease, sepsis and intensive exercise. However in these cases, the source of elevated cfDNA is unknown, greatly compromising the utility of cfDNA as a diagnostic or prognostic tool. For example, cfDNA could originate from parenchymal cells of the injured tissue, but also from dying inflammatory cells.
  • Despite having an identical nucleotide sequence, the DNA of each cell type in the body carries unique epigenetic marks correlating with its gene expression profile. In particular, DNA methylation, serving to repress nontranscribed genes, is a fundamental aspect of tissue identity. Methylation patterns are unique to each cell type, conserved among cells of the same type in the same individual and between individuals, and are highly stable under physiologic or pathologic conditions. Therefore, it may be possible to use the DNA methylation pattern of cfDNA to determine its tissue of origin and hence to infer cell death in the source organ.
  • Theoretically, such an approach could identify the rate of cell death in a tissue of interest, taking into account the total amount of cfDNA, the fraction derived from a tissue of interest, and the estimated half life of cfDNA (15-120 minutes). Note that since the approach relies on normal, stable markers of cell identity, it cannot identify the nature of the pathology (e.g. distinguishing cfDNA derived from dead tumor cells or dead wild type cells due to trauma or inflammation in the same tissue). The potential uses of a highly sensitive, minimally invasive assay of tissue specific cell death include early, precise diagnosis as well as monitoring response to therapy in both a clinical and drug-development setting.
  • A classic example of tissue-specific DNA methylation is provided by the insulin gene promoter, which is unmethylated in insulin-producing pancreatic p-cells and methylated elsewhere. Recent studies have identified unmethylated insulin promoter DNA in the circulation of newly diagnosed T1D patients as well as in islet graft recipients, likely reflecting both autoimmune and alloimmune destruction of β-cells (Akirav E. M. et al. Proceedings of the National Academy of Sciences of the United States of America, 108, 19018-19023 (2011); Lebastchi J et al., Diabetes 62, 1676-1680 (2013); Husseiny M. I. Plos one 9 e94591 (2014; and Herold K. C. et al., J Clin Invest. Doi:10.1172/jc178142 (2015)).
  • Droplet Digital PCR technology is a digital PCR method utilizing a water-oil emulsion droplet system. Droplets are formed in a water-oil emulsion to form the partitions that separate the template DNA molecules. The droplets serve essentially the same function as individual test tubes or wells in a plate in which the PCR reaction takes place, albeit in a much smaller format. The massive sample partitioning is a key aspect of the ddPCR technique.
  • The Droplet Digital PCR System partitions nucleic acid samples into thousands of nanoliter-sized droplets, and PCR amplification is carried out within each droplet. This technique has a smaller sample requirement than other commercially available digital PCR systems, reducing cost and preserving precious samples.
  • Sample partitioning is the key to droplet digital PCR. In traditional PCR, a single sample offers only a single measurement, but in Droplet Digital PCR, the sample is partitioned into 20,000 nanoliter-sized droplets. This partitioning enables the measurement of thousands of independent amplification events within a single sample.
  • ddPCR technology uses a combination of microfluidics and proprietary surfactant chemistries to divide PCR samples into water-in-oil droplets. The droplets support PCR amplification of the template molecules they contain and use reagents and workflows similar to those used for most standard TaqMan™ probe-based assays. Following PCR, each droplet is analyzed or read in a flow cytometer to determine the fraction of PCR-positive droplets in the original sample. These data are then analyzed using Poisson statistics to determine the target DNA template concentration in the original sample.
  • Additional background art includes Bidshahri et al., The Journal of Molecular Diagnostics, Vol. 18, No. 2, March 2016, Usmani-Brown et al., Endocrinology 155: 3694-3698, 2014; International PCT Publication No. WO2013131083, WO 2014138133, WO201101728, WO2015/159292 and WO2015169947.
  • Unless otherwise defined, all technical and/or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and/or materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.
    • SUMMARY OF THE INVENTION
  • According to an aspect of some embodiments of the present invention there is provided a method of analyzing the methylation status of methylation sites of a double-stranded DNA molecule which comprises at least two methylation sites per single strand of the double-stranded DNA molecule, the double-stranded DNA molecule being comprised in a specimen, the method comprising:
      • (a) contacting the double-stranded DNA with bisulfite to generate single-stranded DNA molecules of which demethylated cytosines of the single-stranded DNA molecules are converted to uracils;
      • (b) fractionating the specimen into a plurality of specimen fractions wherein more than 50% of the fractions contain no more than one single-stranded DNA molecule per specimen fraction; and
      • (c) determining the methylation status of the at least two methylation sites of the single-stranded DNA molecule in at least one of the specimen fractions, wherein a methylation status of each of the at least two methylation sites on the single-stranded DNA molecule is indicative of the methylation status of methylation sites of a double-stranded DNA molecule.
  • According to an aspect of some embodiments of the present invention there is provided a kit for analyzing methylation sites of a double-stranded DNA molecule, the kit comprising:
      • (i) a first oligonucleotide probe, wherein the 3′ end of the first probe comprises a quenching moiety and the 5′ end is labeled with a first detectable moiety;
      • (ii) a second oligonucleotide probe, wherein the 3′ end of the second probe comprises a quenching moiety and the 5′ end is labeled with a second detectable moiety; wherein the sequence of the first probe is selected so as to determine a methylation status at a first methylation site of the double-stranded DNA molecule and the sequence of the second probe is selected so as determine a methylation status at a second methylation site of the same double-stranded DNA molecule, wherein the first methylation site and the second methylation site are no more than 300 base pairs apart; and
      • (iii) a Taqman™ polymerase.
  • According to an aspect of some embodiments of the present invention there is provided a kit for analyzing methylation sites of a double-stranded DNA molecule, the kit comprising:
      • (i) at least two oligonucleotides, wherein the sequence of the first oligonucleotide of the at least two oligonucleotides is selected so as to determine a methylation status at a first methylation site of the double-stranded DNA molecule and the sequence of the second oligonucleotide of the at least two oligonucleotides is selected so as determine a methylation status at a second methylation site of the same double-stranded DNA molecule, wherein the first methylation site and the second methylation site are no more than 300 base pairs apart; and
      • (ii) a droplet forming oil.
  • According to some embodiments of the invention, the double-stranded DNA molecule is no longer than 300 base pairs (bp).
  • According to some embodiments of the invention, the double-stranded DNA molecule is no longer than 150 bp.
  • According to some embodiments of the invention, the at least two methylation sites are not more than 300 bp apart.
  • According to some embodiments of the invention, the at least two methylation sites are not more than 150 bp apart.
  • According to some embodiments of the invention, each strand of the double-stranded DNA comprises at least four methylation sites.
  • According to some embodiments of the invention, the at least four methylation sites are not more than 300 bp apart.
  • According to some embodiments of the invention, the at least four methylation sites are not more than 150 bp apart.
  • According to some embodiments of the invention, the method further comprises contacting the single-stranded DNA with amplification primers under conditions that generate amplified DNA from the single-stranded DNA following step (b) and prior to step (c).
  • According to some embodiments of the invention, the determining is effected using at least two non-identical labels.
  • According to some embodiments of the invention, the determining is effected using a single label.
  • According to some embodiments of the invention, the determining comprises:
      • (a) contacting the amplified DNA with:
        • (i) a first probe that hybridizes to the amplified DNA at a site which comprises the first of the at least two methylation sites; and
        • (ii) a second probe that hybridizes to the amplified DNA at a site which comprises a second of the at least two methylation sites, wherein the first probe and the second probe are labeled with non-identical detectable moieties, wherein the first probe and the second probe comprise a quenching moiety;
      • wherein the contacting is effected under conditions that separate the quenching moiety from the first probe and the second probe to generate a non-quenched first probe and a non-quenched second probe; and
      • (b) analyzing the amount of the non-quenched first probe and the non-quenched second probe in at least one specimen fraction of the plurality of specimen fractions.
  • According to some embodiments of the invention, the determining comprises contacting the amplified DNA with:
      • (i) a first probe that hybridizes to the amplified DNA at a site which comprises the first of the at least two methylation sites; and
      • (ii) a second probe that hybridizes to the amplified DNA at a site which comprises a second of the at least two methylation sites, wherein the first probe and the second probe are labeled with non-identical detectable moieties.
  • According to some embodiments of the invention, the first probe hybridizes to the forward strand of the amplified DNA and the second probe hybridizes to the reverse strand of the amplified DNA.
  • According to some embodiments of the invention, the double-stranded DNA molecule is differentially methylated in a cell or tissue of interest.
  • According to some embodiments of the invention, the cell of interest is selected from the group consisting of a pancreatic beta cell, a pancreatic exocrine cell, a hepatocyte, a brain cell, a lung cell, a uterus cell, a kidney cell, a breast cell, an adipocyte, a colon cell, a rectum cell, a cardiomyocyte, a skeletal muscle cell, a prostate cell and a thyroid cell.
  • According to some embodiments of the invention, the tissue is selected from the group consisting of pancreatic tissue, liver tissue, lung tissue, brain tissue, uterus tissue, renal tissue, breast tissue, fat, colon tissue, rectum tissue, cardiac tissue, skeletal muscle tissue, prostate tissue and thyroid tissue.
  • According to some embodiments of the invention, the tissue is cardiac tissue.
  • According to some embodiments of the invention, the double-stranded DNA molecule is non-methylated in cells of cardiac tissue and methylated in leukocytes.
  • According to some embodiments of the invention, the double-stranded DNA molecule comprises at least a part of the sequence of human chromosome 12, between coordinates 124692462-124692551.
  • According to some embodiments of the invention, the double stranded DNA molecule comprises a sequence which is comprised in SEQ ID NOs: 56 or 57.
  • According to some embodiments of the invention, the tissue is liver tissue.
  • According to some embodiments of the invention, the double-stranded DNA molecule comprises a sequence which is comprised in SEQ ID NOs: 65 or 66.
  • According to some embodiments of the invention, the first probe comprises a sequence as set forth in SEQ ID NO: 118 and the second probe comprises a sequence as set forth in SEQ ID NO: 119.
  • According to some embodiments of the invention, the first probe comprises a sequence as set forth in SEQ ID NO: 128 and the second probe comprises a sequence as set forth in SEQ ID NO: 129.
  • According to some embodiments of the invention, the first probe comprises a sequence as set forth in SEQ ID NO: 125 and the second probe comprises a sequence as set forth in SEQ ID NO: 126.
  • According to some embodiments of the invention, the single label is comprised on a probe.
  • According to some embodiments of the invention, the probe comprises a sequence as set forth in SEQ ID NO: 130.
  • According to some embodiments of the invention, the sequence of the first probe is selected such that the first probe binds to the amplified DNA when the methylation site of the double-stranded DNA molecule is non-methylated.
  • According to some embodiments of the invention, the sequence of the second probe is selected such that the second probe binds to the amplified DNA when the methylation site of the double-stranded DNA molecule is non-methylated.
  • According to some embodiments of the invention, the detectable moiety is FAM or HEX.
  • According to some embodiments of the invention, the double-stranded DNA is cell-free DNA.
  • According to some embodiments of the invention, the double-stranded DNA is cellular DNA.
  • According to some embodiments of the invention, the method further comprises lysing the cells of the cellular DNA prior to the determining.
  • According to some embodiments of the invention, the specimen is a fluid specimen.
  • According to some embodiments of the invention, the fluid specimen is a body fluid specimen.
  • According to some embodiments of the invention, the body fluid is selected from the group consisting of blood, plasma, sperm, milk, urine, saliva and cerebral spinal fluid.
  • According to some embodiments of the invention, the specimen comprises DNA from a plurality of cell-types.
  • According to some embodiments of the invention, the specimen is blood.
  • According to some embodiments of the invention, the method further comprises quantitating the amount of DNA of the cell or tissue origin.
  • According to some embodiments of the invention, the kit further comprises a droplet forming oil.
    • BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
  • The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
  • Some embodiments of the invention are herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of embodiments of the invention. In this regard, the description taken with the drawings makes apparent to those skilled in the art how embodiments of the invention may be practiced.
    • IN THE DRAWINGS
  • FIGS. 1A-E: Identification of cardiomyocyte-specific DNA methylation markers.
  • FIG. 1A. Unmethylation levels of FAM101A locus in 27 human tissues, including left ventricle, right ventricle and right atrium (red). Data was extracted from the Roadmap Epigenomics Consortium browser.
  • FIG. 1B. Structure of the FAM101A locus, used as two independent markers: FAM101A and FAM101A AS. Lollipops represent CpG sites; arrows mark positions of PCR primers; S, sense marker; AS, antisense marker.
  • FIG. 1C. Unmethylation status of FAM101A and FAM101A AS in DNA from multiple tissues and from isolated cardiomyocytes (purchased from ScienCell Research Laboratories, San Diego, Calif.). Targeted PCR yields a lower background in non cardiac tissues compared with the Roadmap browser in panel A, since the roadmap data includes molecules that contain only some of the cytosines in the FAM101A locus (e.g. only one or two), which can occasionally be demethylated in non-cardiac tissue. In contrast, the targeted PCR by definition amplifies only molecules containing all cytosines in the locus.
  • FIGS. 1D-E. Spike in experiments for FAM101A and FAM101A AS. Human cardiomyocyte DNA was mixed with human leukocyte DNA in the indicated proportions (0-100%), and the percentage of fully unmethylated FAM101A molecules (in which all five CpG sites were converted by bisulfite) was determined.
  • FIGS. 2A-F: Cardiomyocyte-derived cfDNA in healthy subjects and in patients with myocardial infarction.
  • FIG. 2A. Cardiac cfDNA (copies of fully unmethylated FAM101A/ml plasma) in specimens from healthy controls (n=61) and patients during MI (n=79). Mann-Whitney test for controls vs. patients, P<0.0001
  • FIG. 2B. Receiver operating characteristic (ROC) curve for unmethylated FAM101A levels in healthy controls and patients with MI. Area under the curve (AUC) 0.884 (95% CI=0.8925 to 0.9766)
  • FIG. 2C. Comparison of unmethylated FAM101A levels (copies/ml) in samples from healthy controls, MI patients with low Creatine Kinase (CPK <200) and MI patients with high CK (CK>200). Kruskal-Wallis test P value<0.0001. Dunn's multiple comparisons test adjusted P Value: Ctrls vs. low CK, p<0.001; Ctrls vs. high CK, P<0.0001; low CK vs. high CK, P=0.0064.
  • FIG. 2D. Comparison of unmethylated FAM101A levels in samples from healthy controls, MI patients with low levels of high-sensitive troponin T (hs-cTn) (<0.03), and MI patients with high levels of hs-cTn (>0.03). Dunn's multiple comparisons test adjusted P Value: Ctrls vs. low hs-cTn (<0.03), P=0.8645; Ctrls vs. high hs-cTn (>0.03), PV<0.0001; low hs-cTn (<0.03) vs. high hs-cTn (>0.03), P=0.0189.
  • FIG. 2E. Spearman correlation between cardiac cfDNA and troponin levels in n=57 specimens.
  • FIG. 2F. XY Scatter plot for cardiac cfDNA levels vs. cardiac troponin. Quadrants indicate negative and positive hs-Tn, and negative and positive cardiac cfDNA. Numbers indicate the percentage of specimens in each quadrant.
  • FIGS. 3A-C: Cardiac cfDNA dynamics during MI and after angioplasty.
  • FIG. 3A. Cardiac cfDNA levels in MI patients before and after PCI.
  • FIG. 3B. ROC curve for cardiac cfDNA in healthy individuals versus MI patients prior to intervention.
  • FIG. 3C. Time course of cardiac cfDNA and troponin levels in five patients. Vertical dashed lines indicate PCI time.
  • FIGS. 4A-C: Cardiac cfDNA in sepsis.
  • FIG. 4A. Levels of cardiac cfDNA in healthy controls and patients with sepsis.
  • FIG. 4B. Lack of correlation between cardiac cfDNA and troponin. Curved line represents non linear (quadratic) fit.
  • FIG. 4C. Kaplan-Meier plot showing correlation of cardiac cfDNA to patient survival.
  • FIGS. 5A-D: An exemplary method for detecting cardiac cfDNA using digital droplet PCR, according to embodiments of the present invention.
  • FIG. 5A. Schematic of approach for ddPCR-based detection of methylation status of multiple adjacent cytosines. A signal from two probes in the same droplet reflects lack of methylation in 5 adjacent cytosines in the same original DNA strand.
  • FIG. 5B. Signal from cardiomyocyte and leukocyte DNA based on individual or dual probes. Scoring only dual probe signals drastically reduces noise from leukocyte DNA.
  • FIG. 5C. Spike-in experiment assessing sensitivity and linearity of signal from cardiomyocyte DNA diluted in leukocyte DNA. The use of dual probe enhances linearity and reduces baseline signal.
  • FIG. 5D. Measurement of cardiac cfDNA in plasma of healthy adults and patients with myocardial infarction. The use of dual probes reduces the baseline signal in healthy plasma.
  • FIGS. 6A-C: methylation of individual and multiple adjacent cytosines within the FAM101A locus.
  • FIG. 6A. Methylation status of cytosines in the sense strand of FAM101A
  • FIG. 6B. Metylation status of cytosines in the antisense (AS) strand of FAM101A. Graphs show the percentage of unmethylated molecules in DNA from each tissue. The set of columns on the far right describes the percentage of molecules in which all CpG sites are unmethylated, demonstrating the higher signal-to-noise ratio afforded by interrogating all CpGs simultaneously.
  • FIG. 6C. Correlation between results of spike-in experiments using the sense and antisense FAM101A markers.
  • FIGS. 7A-F: additional correlations of cardiac and total cfDNA in MI patients.
  • FIG. 7A. Log scale presentation of unmethylated FAM101A levels in plasma specimens from healthy controls (n=83) and patients during MI (n=74). 54 values were zero, so are not shown in the graph.
  • FIG. 7B. Cardiac cfDNA levels in controls vs MI patients positive or negative for high sensitive troponin using 0.1 as a cutoff. Dunn's multiple comparisons test adjusted P value: Ctrls vs. Low hs-cTn (<0.1), P=0.0433; Ctrls vs. High hs-cTn (>0.1), P<0.0001; Low hs-cTn (<0.1) vs. High hs-cTn (>0.1), P=0.0003.
  • FIG. 7C. Total cfDNA concentration in controls and MI patients.
  • FIG. 7D. Lack of correlation between total concentration of cfDNA (genome equivalents/ml) and either hs-Tn (blue) or CK (red) levels.
  • FIG. 7E. Lack of correlation between total cfDNA (genome equivalents/ml) and percentage of cardiac cfDNA.
  • FIG. 7F. Linear correlation between FAM101A sense (S) and antisense (AS) signal in the MI specimens.
  • FIGS. 8A-B. Dynamics of cardiac cfDNA and CPK in myocardial infarction.
  • FIG. 8A. Ratio of cardiac cfDNA before and after PCI in 15 individuals with MI. As expected, cardiac cfDNA levels increased after intervention.
  • FIG. 8B. Dynamics of cardiac cfDNA and CPK in individual patients. Time 0 is the beginning of chest pain. Vertical dashed line indicates time of PCI.
  • FIGS. 9A-C: Total and cardiac cfDNA levels in patients with sepsis.
  • FIG. 9A. Concentration of cfDNA in patients with sepsis.
  • FIG. 9B. Percentage of cardiac cfDNA in patients with sepsis.
  • FIG. 9C. Correlation between FAM101A sense and antisense signals in sepsis specimens.
  • FIG. 10 is a pictorial representation of ddPCR technology.
  • FIG. 11 is a pictorial representation of an assay according to embodiments of the present invention. The figure illustrates the use of two probes (red and green) to define methylation status of two clusters of CpGs on the same DNA molecule in the same droplet.
  • FIG. 12 is a table comparing the time it takes to analyse methylation status by sequencing and by ddPCR.
  • FIGS. 13A-B are bar graphs illustrating how ddPCR may be used to diagnose patients with a myocardial infarction.
  • FIGS. 14A-B illustrate digital droplet PCR for the identification of liver-derived cfDNA according to embodiments of the present invention.
      • A. Hepatocyte and leukocyte DNA examined using ddPCR. B. Hepatocyte-derived DNA in the plasma of six liver transplant recipients. Each patient was sampled at four time points as indicated. Graph shows the average values of the two liver markers in each sample.
  • FIGS. 15A-B illustrate digital droplet PCR for the identification of colon-derived cfDNA in plasma samples. ddPCR using both amplicons showed no signal in pancreas, liver, cfDNA from healthy controls DNA and a strong signal in cfDNA of patients with colorectal cancer.
  • FIGS. 16A-B illustrates digital droplet PCR for the identification of liver-derived cfDNA according to embodiments of the present invention.
    •  DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION
  • The present invention contemplates using digital droplet PCR (ddPCR) for analyzing the methylation status of single DNA molecules. In particular, the method can be used to detect tissue-specific methylation markers.
  • Analysis of circulating DNA is beginning to revolutionize prenatal diagnosis, tumor diagnosis and the monitoring of graft rejection. However a major limitation of all applications is the dependence on the presence of identifiable genetic differences between the tissue of interest and the host.
  • Until presently, analysis of tissue-specific methylation patterns present in circulating DNA fragments were performed using massively parallel sequencing, requiring access to a next generation sequencer and the application of a bioinformatics pipeline to interpret sequencing results.
  • The present inventors have now simplified the method by alleviating the need for sequencing, whilst maintaining accuracy and reliability. The novel method which relies on digital droplet polymerase chain reaction (ddPCR; an overview of which is presented in FIG. 10 ), reduced the level of false positives to such an extent that clinical utility can now be envisaged.
  • Using primers for digital droplet PCR (ddPCR) after bisulfite conversion of cfDNA, and fluorescent probes that recognize blocks of unmethylated CpGs in the amplified marker regions, the present inventors have shown that methylation status of clusters of CpG sites (comprising at least two, and preferably at least three, or even at least four CpG sites) in the same molecule can be scored.
  • FIG. 11 illustrates the use of two probes (red and green) to define the methylation status of two clusters of CpGs on the same DNA molecule in the same droplet.
  • The increased specificity of the technique is illustrated in FIG. 5B. The number of droplets positive for each individual probe (HEX probe and FAM probe) demonstrated that it is possible to discriminate between cardiac and blood DNA. But when scoring for droplets that are positive for both probes (that is, unmethylated in all 5 CpG sites tested), the noise from blood (red bar) was reduced dramatically and accuracy was increased dramatically.
  • The present inventors propose that ddPCR (as compared to sequencing) for identification of the methylation status of cfDNA will radically reduce the time from drawing blood to results, from −36 hours today to 7 hours, and potentially much less if rapid PCR machines are used.
  • Comparison of the time needed to analyze methylation status by sequencing or by ddPCR is summarized in FIG. 12 .
  • Whilst further reducing the present invention to practice, the present inventors have shown that the ddPCR protocol could successfully diagnose myocardial infarction patients (FIGS. 13A-B). In addition, the present inventors have shown that the ddPCR protocol could successfully diagnose liver damage (FIGS. 14A-B) and colon cancer (FIGS. 15A-B).
  • Thus, according to a first aspect of the present invention there is provided a method of analyzing the methylation status of methylation sites of a double-stranded DNA molecule which comprises at least two methylation sites per single strand of said double-stranded DNA molecule, the double-stranded DNA molecule being comprised in a specimen, the method comprising:
      • (a) contacting the double-stranded DNA with bisulfite to generate single-stranded DNA molecules of which demethylated cytosines of said single-stranded DNA molecules are converted to uracils;
      • (b) fractionating the specimen into a plurality of specimen fractions wherein more than 50% of the fractions contain no more than one single-stranded DNA molecule per specimen fraction; and
      • (c) determining the methylation status of said at least two methylation sites of said single-stranded DNA molecule in at least one of said specimen fractions, wherein a methylation status of each of said at least two methylation sites on said single-stranded DNA molecule is indicative of the methylation status of methylation sites of a double-stranded DNA molecule.
  • As used herein, the term “methylation status” refers to the status of a cytosine in a DNA sequence. The cytosine may be methylated (and present as 5-methylcytosine) or non-methylated and present as cytosine.
  • As used herein, the term “methylation site” refers to a cytosine residue adjacent to guanine residue (CpG site) that has a potential of being methylated.
  • The DNA molecule which is analyzed is preferably no longer than 300 nucleotides, 295 nucleotides, 290 nucleotides, 285 nucleotides, 280 nucleotides, 275 nucleotides, 270 nucleotides, 265 nucleotides, 260 nucleotides, 255 nucleotides, 250 nucleotides, 245 nucleotides, 240 nucleotides, 235 nucleotides, 230 nucleotides, 225 nucleotides, 220 nucleotides, 215 nucleotides, 210 nucleotides, 205 nucleotides, 200 nucleotides, 195 nucleotides, 190 nucleotides, 185 nucleotides, 180 nucleotides, 175 nucleotides, 170 nucleotides, 165 nucleotides, 160 nucleotides, 155 nucleotides, 150 nucleotides, 145 nucleotides, 140 nucleotides, 135 nucleotides, 130 nucleotides, 125 nucleotides, 120 nucleotides, 115 nucleotides, 110 nucleotides, 105 nucleotides, 100 nucleotides, 95 nucleotides, 90 nucleotides, 85 nucleotides, 80 nucleotides, 75 nucleotides, 70 nucleotides, 65 nucleotides, 60 nucleotides, 55 nucleotides, or 50 nucleotides.
  • According to a particular embodiment, the DNA molecule is between 50-300 nucleotides, e.g. between 50-250, between 50-200, between 100-300 nucleotides, or between 100-250 nucleotides.
  • In another embodiment, the methylation sites of a methylation signature which are analyzed on a double stranded molecule are no more than 300 nucleotides apart, 295 nucleotides apart, 290 nucleotides apart, 285 nucleotides apart, 280 nucleotides apart, 275 nucleotides apart, 270 nucleotides apart, 265 nucleotides apart, 260 nucleotides apart, 255 nucleotides apart, 250 nucleotides apart, 245 nucleotides apart, 240 nucleotides apart, 235 nucleotides apart, 230 nucleotides apart, 225 nucleotides apart, 220 nucleotides apart, 215 nucleotides apart, 210 nucleotides apart, 205 nucleotides apart, 200 nucleotides apart, 195 nucleotides apart, 190 nucleotides apart, 185 nucleotides apart, 180 nucleotides apart, 175 nucleotides apart, 170 nucleotides apart, 165 nucleotides apart, 160 nucleotides apart, 155 nucleotides apart, 150 nucleotides apart, 145 nucleotides apart, 140 nucleotides apart, 135 nucleotides apart, 130 nucleotides apart, 125 nucleotides apart, 120 nucleotides apart, 115 nucleotides apart, 110 nucleotides apart, 105 nucleotides apart, 100 nucleotides apart, 95 nucleotides apart, 90 nucleotides apart, 85 nucleotides apart, 80 nucleotides apart, 75 nucleotides apart, 70 nucleotides apart, 65 nucleotides apart, 60 nucleotides apart, 55 nucleotides apart, or 50 nucleotides apart.
  • The sequence of the DNA may be of a coding or non-coding region.
  • According to a particular embodiment, the sequence is not derived from a gene which is differentially expressed in the cell of interest. Thus, for example in the case of identifying a methylation pattern for a pancreatic beta cell, it is preferable that the DNA sequence is not part of a gene encoding insulin or another pancreatic beta cell protein.
  • In accordance with another particular embodiment, the methylation pattern characterizes the normal cell of interest and is not a methylation pattern characterizing a diseased cell (is not for example a methylation pattern characterizing cancer cells of a specific type).
  • The method of the present invention contemplates analyzing at least 2, at least 3, at least 4, at least 5, at least 6, at least 7 at least 8, at least 9 or even at least 10 or more methylation sites of a double-stranded DNA molecule.
  • Thus, the methylation signature of a double-stranded DNA molecule may comprise at least 2, at least 3, at least 4 at least 5, at least 6, at least 7 at least 8, at least 9 or even at least 10 or more methylation sites.
  • In order to be considered a methylation signature for a particular cell of interest each of the methylation sites of the signature on the DNA molecule should be differentially methylated in that cell of interest with respect to a second non-identical cell. The methylation signature comprises the methylation status of at least two, at least three, at least four methylation sites of a particular DNA molecule. The methylation sites may be on a single strand of the DNA molecule or distributed amongst both strands of the DNA molecule.
  • According to a particular embodiment, each of the at least two, three, four or more methylation sites of the signature are unmethylated in the cell of interest (the cell for which the methylation pattern is being determined) on the DNA molecule, whereas in the second non-identical cell each of the sites are methylated on the DNA molecule.
  • According to another embodiment, each of the at least two, three, four or more methylation sites of the signature are methylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell each of the sites are unmethylated on the DNA molecule.
  • According to another embodiment, at least one of the methylation sites of the signature is unmethylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell that site is methylated on the DNA molecule.
  • According to another embodiment, at least one of the methylation sites of the signature is methylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell that site is unmethylated on the DNA molecule.
  • According to another embodiment, at least two methylation sites of the signature are unmethylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are methylated on the DNA molecule.
  • According to another embodiment, at least two methylation sites of the signature are methylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are unmethylated on the DNA molecule.
  • According to another embodiment, at least three methylation sites of the signature are unmethylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are methylated on the DNA molecule.
  • According to another embodiment, at least three methylation sites of the signature are methylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are unmethylated on the DNA molecule.
  • According to another embodiment, at least four methylation sites of the signature are unmethylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are methylated on the DNA molecule.
  • According to another embodiment, at least four methylation sites of the signature are methylated in the cell of interest on the DNA molecule, whereas in the second non-identical cell those sites are unmethylated on the DNA molecule.
  • The second, non-identical cell may be of any source including for example blood cells. Typically, the non-identical cell is one which is comprised in the specimen/sample being analyzed.
  • The method can be used for identifying methylation signatures of any cell of interest, including but not limited to cardiac cells (e.g. cardiomyocytes), pancreatic cells (such as pancreatic beta cells, exocrine pancreatic cells (e.g. acinar cells), brain cells, oligodendrocytes, liver cells (hepatocytes), kidney cells, tongue cells, vascular endothelial cells, lymphocytes, neutrophils, melanocytes, T-regs, lung cells, a uterus cells, breast cells, adipocytes, colon cells, rectum cells, prostate cells, thyroid cells and skeletal muscle cells. Specimens which may be analyzed are generally fluid specimens derived from mammalian subjects and include for example blood, plasma, sperm, milk, urine, saliva or cerebral spinal fluid.
  • According to a particular embodiment, the specimen is plasma or blood.
  • Specimens which are analyzed typically comprise DNA from at least one or at least two cell/tissue sources, as further described herein below. Thus for example the specimens may comprise cell-free DNA from a single cell type or at least two cell types.
  • According to one embodiment, a specimen of blood is obtained from a subject according to methods well known in the art. Plasma or serum may be isolated according to methods known in the art.
  • DNA may be isolated from the blood immediately or within 1 hour, 2 hours, 3 hours, 4 hours, 5 hours or 6 hours. Optionally the blood is stored at temperatures such as 4° C., or at −20° C. prior to isolation of the DNA. In some embodiments, a portion of the blood specimen is used in accordance with the invention at a first instance of time whereas one or more remaining portions of the blood specimen (or fractions thereof) are stored for a period of time for later use.
  • According to one embodiment, the DNA molecule which is analyzed is cellular DNA (i.e. comprised in a cell).
  • According to still another embodiment, the DNA molecule which is analyzed is comprised in a shedded cell or non-intact cell.
  • Methods of DNA extraction are well-known in the art. A classical DNA isolation protocol is based on extraction using organic solvents such as a mixture of phenol and chloroform, followed by precipitation with ethanol (J. Sambrook et al., “Molecular Cloning: A Laboratory Manual”, 1989, 2nd Ed., Cold Spring Harbour Laboratory Press: New York, N.Y.). Other methods include: salting out DNA extraction (P. Sunnucks et al., Genetics, 1996, 144: 747-756; S. M. Aljanabi and I. Martinez, Nucl. Acids Res. 1997, 25: 4692-4693), trimethylammonium bromide salts DNA extraction (S. Gustincich et al., BioTechniques, 1991, 11: 298-302) and guanidinium thiocyanate DNA extraction (J. B. W. Hammond et al., Biochemistry, 1996, 240: 298-300).
  • There are also numerous versatile kits that can be used to extract DNA from tissues and bodily fluids and that are commercially available from, for example, BD Biosciences Clontech (Palo Alto, Calif.), Epicentre Technologies (Madison, Wis.), Gentra Systems, Inc. (Minneapolis, Minn.), MicroProbe Corp. (Bothell, Wash.), Organon Teknika (Durham, N.C.), and Qiagen Inc. (Valencia, Calif.). User Guides that describe in great detail the protocol to be followed are usually included in all these kits. Sensitivity, processing time and cost may be different from one kit to another. One of ordinary skill in the art can easily select the kit(s) most appropriate for a particular situation.
  • According to another embodiment, the DNA which is analyzed is cell-free DNA. For this method, cell lysis is not performed on the specimen. Methods of isolating cell-free DNA from body fluids are also known in the art. For example Qiaquick kit, manufactured by Qiagen may be used to extract cell-free DNA from plasma or serum.
  • The specimen may be processed before the method is carried out, for example DNA purification may be carried out following the extraction procedure. The DNA in the specimen may be cleaved either physically or chemically (e.g. using a suitable enzyme). Processing of the specimen may involve one or more of: filtration, distillation, centrifugation, extraction, concentration, dilution, purification, inactivation of interfering components, addition of reagents, and the like.
  • To analyze methylation status according to this aspect of the present invention, the DNA is treated with bisulfite which converts cytosine residues to uracil (which are converted to thymidine following PCR), but leaves 5-methylcytosine residues unaffected. Thus, bisulfite treatment introduces specific changes in the DNA sequence that depend on the methylation status of individual cytosine residues, yielding single-nucleotide resolution information about the methylation status of a segment of DNA.
  • During the bisulfite reaction, care should be taken to minimize DNA degradation, such as cycling the incubation temperature.
  • Bisulfite sequencing relies on the conversion of every single unmethylated cytosine residue to uracil. If conversion is incomplete, the subsequent analysis will incorrectly interpret the unconverted unmethylated cytosines as methylated cytosines, resulting in false positive results for methylation. Only cytosines in single-stranded DNA are susceptible to attack by bisulfite, therefore denaturation of the DNA undergoing analysis is critical. It is important to ensure that reaction parameters such as temperature and salt concentration are suitable to maintain the DNA in a single-stranded conformation and allow for complete conversion.
  • According to a particular embodiment, an oxidative bisulfite reaction is performed. 5-methylcytosine and 5-hydroxymethylcytosine both read as a C in bisulfite sequencing. Oxidative bisulfite reaction allows for the discrimination between 5-methylcytosine and 5-hydroxymethylcytosine at single base resolution. The method employs a specific chemical oxidation of 5-hydroxymethylcytosine to 5-formylcytosine, which subsequently converts to uracil during bisulfite treatment. The only base that then reads as a C is 5-methylcytosine, giving a map of the true methylation status in the DNA specimen. Levels of 5-hydroxymethylcytosine can also be quantified by measuring the difference between bisulfite and oxidative bisulfite sequencing.
  • Following bisulfite treatment, the bisulfite-treated DNA sequence is fractionated and then optionally subjected to an amplification reaction.
  • To fractionate the DNA specimen, emulsification techniques can be used so as to create large numbers of aqueous droplets that function as independent reaction chambers for the PCR reactions. For example, an aqueous specimen (e.g., 20 microliters) can be partitioned into droplets (e.g., 20,000 droplets of one nanoliter each) to allow an individual test for the target to be performed with each of the droplets.
  • Aqueous droplets can be suspended in oil to create a water-in-oil emulsion (W/0). The emulsion can be stabilized with a surfactant to reduce coalescence of droplets during heating, cooling, and transport, thereby enabling thermal cycling to be performed.
  • In an exemplary droplet-based digital assay, a specimen is partitioned into a set of droplets at a dilution that ensures that more than 40% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • In an exemplary droplet-based digital assay, a specimen is partitioned into a set of droplets at a dilution that ensures that more than 50% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • In an exemplary droplet-based digital assay, a specimen is partitioned into a set of droplets at a dilution that ensures that more than 60% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • In an exemplary droplet-based digital assay, a specimen is partitioned into a set of droplets at a dilution that ensures that more than 70% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • In an exemplary droplet-based digital assay, a specimen is partitioned into a set of droplets at a dilution that ensures that more than 80% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • In an exemplary droplet-based digital assay, a specimen is partitioned into a set of droplets at a dilution that ensures that more than 90% of the droplets contain no more than one single-stranded DNA molecule per specimen fraction.
  • Once fractionation has taken place, the single-stranded DNA may then optionally be amplified.
  • As used herein, the term “amplification” refers to a process that increases the representation of a population of specific nucleic acid sequences in a specimen by producing multiple (i.e., at least 2) copies of the desired sequences. Methods for nucleic acid amplification are known in the art and include, but are not limited to, polymerase chain reaction (PCR) and ligase chain reaction (LCR). In a typical PCR amplification reaction, a nucleic acid sequence of interest is often amplified at least fifty thousand fold in amount over its amount in the starting specimen. A “copy” or “amplicon” does not necessarily mean perfect sequence complementarity or identity to the template sequence. For example, copies can include nucleotide analogs such as deoxyinosine, intentional sequence alterations (such as sequence alterations introduced through a primer comprising a sequence that is hybridizable but not complementary to the template), and/or sequence errors that occur during amplification.
  • A typical amplification reaction is carried out by contacting a forward and reverse primer (a primer pair) to the specimen DNA together with any additional amplification reaction reagents under conditions which allow amplification of the target sequence. The oligonucleotide amplification primers typically flank the target sequence—(i.e. the sequence comprising the at least two, three, four or five methylation sites (per single strand).
  • The terms “forward primer” and “forward amplification primer” are used herein interchangeably, and refer to a primer that hybridizes (or anneals) to the target (template strand). The terms “reverse primer” and “reverse amplification primer” are used herein interchangeably, and refer to a primer that hybridizes (or anneals) to the complementary target strand. The forward primer hybridizes with the target sequence 5′ with respect to the reverse primer.
  • The term “amplification conditions”, as used herein, refers to conditions that promote annealing and/or extension of primer sequences. Such conditions are well-known in the art and depend on the amplification method selected. Thus, for example, in a PCR reaction, amplification conditions generally comprise thermal cycling, i.e., cycling of the reaction mixture between two or more temperatures. In isothermal amplification reactions, amplification occurs without thermal cycling although an initial temperature increase may be required to initiate the reaction. Amplification conditions encompass all reaction conditions including, but not limited to, temperature and temperature cycling, buffer, salt, ionic strength, and pH, and the like.
  • As used herein, the term “amplification reaction reagents”, refers to reagents used in nucleic acid amplification reactions and may include, but are not limited to, buffers, reagents, enzymes having reverse transcriptase and/or polymerase activity or exonuclease activity, enzyme cofactors such as magnesium or manganese, salts, nicotinamide adenine dinuclease (NAD) and deoxynucleoside triphosphates (dNTPs), such as deoxyadenosine triphospate, deoxyguanosine triphosphate, deoxycytidine triphosphate and thymidine triphosphate. Amplification reaction reagents may readily be selected by one skilled in the art depending on the amplification method used.
  • In one embodiment, the amplification reaction uses a single labeled oligonucleotide probe which hybridizes to one strand of the amplified DNA which comprises at least two, at least three, at least four, at least five methylation sites (for example as illustrated in FIG. 16B).
  • In another embodiment, the amplification reaction uses at least two probes, one which hybridizes to the first strand of the amplified DNA and one which hybridizes to the second strand of the amplified DNA (for example as illustrated in FIG. 16A). Preferably the two probes are labeled with non-identical labels i.e. detectable moieties.
  • The oligonucleotides of the invention (e.g. primers or probes) need not reflect the exact sequence of the target nucleic acid sequence (i.e. need not be fully complementary), but must be sufficiently complementary so as to hybridize to the target site under the particular experimental conditions. Accordingly, the sequence of the oligonucleotide typically has at least 70% homology, preferably at least 80%, 90%, 95%, 97%, 99% or 100% homology, for example over a region of at least 13 or more contiguous nucleotides with the target sequence. The conditions are selected such that hybridization of the oligonucleotide to the target site is favored and hybridization to the non-target site is minimized.
  • Various considerations must be taken into account when selecting the stringency of the hybridization conditions. For example, the more closely the oligonucleotide (e.g. primer) reflects the target nucleic acid sequence, the higher the stringency of the assay conditions can be, although the stringency must not be too high so as to prevent hybridization of the oligonucleotides to the target sequence. Further, the lower the homology of the oligonucleotide to the target sequence, the lower the stringency of the assay conditions should be, although the stringency must not be too low to allow hybridization to non-specific nucleic acid sequences.
  • Oligonucleotides of the invention may be prepared by any of a variety of methods (see, for example, J. Sambrook et al., “Molecular Cloning: A Laboratory Manual”, 1989, 2. sup. nd Ed., Cold Spring Harbour Laboratory Press: New York, N.Y.; “PCR Protocols: A Guide to Methods and Applications”, 1990, M. A. Innis (Ed.), Academic Press: New York, N.Y.; P. Tijssen “Hybridization with Nucleic Acid Probes-Laboratory Techniques in Biochemistry and Molecular Biology (Parts I and II)”, 1993, Elsevier Science; “PCR Strategies”, 1995, M. A. Innis (Ed.), Academic Press: New York, N.Y.; and “Short Protocols in Molecular Biology”, 2002, F. M. Ausubel (Ed.), 5. sup. th Ed., John Wiley & Sons: Secaucus, N.J.). For example, oligonucleotides may be prepared using any of a variety of chemical techniques well-known in the art, including, for example, chemical synthesis and polymerization based on a template as described, for example, in S. A. Narang et al., Meth. Enzymol. 1979, 68: 90-98; E. L. Brown et al., Meth. Enzymol. 1979, 68: 109-151; E. S. Belousov et al., Nucleic Acids Res. 1997, 25: 3440-3444; D. Guschin et al., Anal. Biochem. 1997, 250: 203-211; M. J. Blommers et al., Biochemistry, 1994, 33: 7886-7896; and K. Frenkel et al., Free Radic. Biol. Med. 1995, 19: 373-380; and U.S. Pat. No. 4,458,066.
  • For example, oligonucleotides may be prepared using an automated, solid-phase procedure based on the phosphoramidite approach. In such a method, each nucleotide is individually added to the 5′-end of the growing oligonucleotide chain, which is attached at the 3′-end to a solid support. The added nucleotides are in the form of trivalent 3′-phosphoramidites that are protected from polymerization by a dimethoxytriyl (or DMT) group at the 5′-position. After base-induced phosphoramidite coupling, mild oxidation to give a pentavalent phosphotriester intermediate and DMT removal provides a new site for oligonucleotide elongation. The oligonucleotides are then cleaved off the solid support, and the phosphodiester and exocyclic amino groups are deprotected with ammonium hydroxide. These syntheses may be performed on oligo synthesizers such as those commercially available from Perkin Elmer/Applied Biosystems, Inc. (Foster City, Calif.), DuPont (Wilmington, Del.) or Milligen (Bedford, Mass.). Alternatively, oligonucleotides can be custom made and ordered from a variety of commercial sources well-known in the art, including, for example, the Midland Certified Reagent Company (Midland, Tex.), ExpressGen, Inc. (Chicago, Ill.), Operon Technologies, Inc. (Huntsville, Ala.), and many others.
  • Purification of the oligonucleotides of the invention, where necessary or desirable, may be carried out by any of a variety of methods well-known in the art. Purification of oligonucleotides is typically performed either by native acrylamide gel electrophoresis, by anion-exchange HPLC as described, for example, by J. D. Pearson and F. E. Regnier (J. Chrom., 1983, 255: 137-149) or by reverse phase HPLC (G. D. McFarland and P. N. Borer, Nucleic Acids Res., 1979, 7: 1067-1080).
  • The sequence of oligonucleotides can be verified using any suitable sequencing method including, but not limited to, chemical degradation (A. M. Maxam and W. Gilbert, Methods of Enzymology, 1980, 65: 499-560), matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (U. Pieles et al., Nucleic Acids Res., 1993, 21: 3191-3196), mass spectrometry following a combination of alkaline phosphatase and exonuclease digestions (H. Wu and H. Aboleneen, Anal. Biochem., 2001, 290: 347-352), and the like.
  • In certain embodiments, the detection probes or amplification primers (or both) are labeled with a detectable agent or moiety before being used in amplification/detection assays. In certain embodiments, the detection probes are labeled with a detectable agent. Preferably, a detectable agent is selected such that it generates a signal which can be measured and whose intensity is related (e.g., proportional) to the amount of amplification products in the sample being analyzed.
  • The association between the oligonucleotide and detectable agent can be covalent or non-covalent. Labeled detection probes can be prepared by incorporation of or conjugation to a detectable moiety. Labels can be attached directly to the nucleic acid sequence or indirectly (e.g., through a linker). Linkers or spacer arms of various lengths are known in the art and are commercially available, and can be selected to reduce steric hindrance, or to confer other useful or desired properties to the resulting labeled molecules (see, for example, E. S. Mansfield et al., Mol. Cell. Probes, 1995, 9: 145-156).
  • Methods for labeling nucleic acid molecules are well-known in the art. For a review of labeling protocols, label detection techniques, and recent developments in the field, see, for example, L. J. Kricka, Ann. Clin. Biochem. 2002, 39: 114-129; R. P. van Gijlswijk et al., Expert Rev. Mol. Diagn. 2001, 1: 81-91; and S. Joos et al., J. Biotechnol. 1994, 35: 135-153. Standard nucleic acid labeling methods include: incorporation of radioactive agents, direct attachments of fluorescent dyes (L. M. Smith et al., Nucl. Acids Res., 1985, 13: 2399-2412) or of enzymes (B. A. Connoly and O. Rider, Nucl. Acids. Res., 1985, 13: 4485-4502); chemical modifications of nucleic acid molecules making them detectable immunochemically or by other affinity reactions (T. R. Broker et al., Nucl. Acids Res. 1978, 5: 363-384; E. A. Bayer et al., Methods of Biochem. Analysis, 1980, 26: 1-45; R. Langer et al., Proc. Natl. Acad. Sci. USA, 1981, 78: 6633-6637; R. W. Richardson et al., Nucl. Acids Res. 1983, 11: 6167-6184; D. J. Brigati et al., Virol. 1983, 126: 32-50; P. Tchen et al., Proc. Natl. Acad. Sci. USA, 1984, 81: 3466-3470; J. E. Landegent et al., Exp. Cell Res. 1984, 15: 61-72; and A. H. Hopman et al., Exp. Cell Res. 1987, 169: 357-368); and enzyme-mediated labeling methods, such as random priming, nick translation, PCR and tailing with terminal transferase (for a review on enzymatic labeling, see, for example, J. Temsamani and S. Agrawal, Mol. Biotechnol. 1996, 5: 223-232). More recently developed nucleic acid labeling systems include, but are not limited to: ULS (Universal Linkage System), which is based on the reaction of mono-reactive cisplatin derivatives with the N7 position of guanine moieties in DNA (R. J. Heetebrij et al., Cytogenet. Cell. Genet. 1999, 87: 47-52), psoralen-biotin, which intercalates into nucleic acids and upon UV irradiation becomes covalently bonded to the nucleotide bases (C. Levenson et al., Methods Enzymol. 1990, 184: 577-583; and C. Pfannschmidt et al., Nucleic Acids Res. 1996, 24: 1702-1709), photoreactive azido derivatives (C. Neves et al., Bioconjugate Chem. 2000, 11: 51-55), and DNA alkylating agents (M. G. Sebestyen et al., Nat. Biotechnol. 1998, 16: 568-576).
  • If the methylation sites are close enough together on the DNA, it is conceivable that the probes of this aspect of the present invention hybridize to more than one methylation site, for example, two, three, or even four—see for example FIG. 16B.
  • The sequence of the first and/or second probe may be selected such that it binds to the amplified DNA when the methylation site of the double-stranded DNA molecule is non-methylated.
  • Alternatively, the sequence of the first and/or second probe may be selected such that it binds to the amplified DNA when the methylation site of the double-stranded DNA molecule is methylated.
  • In certain embodiments, the inventive detection probes are fluorescently labeled. Numerous known fluorescent labeling moieties of a wide variety of chemical structures and physical characteristics are suitable for use in the practice of this invention. Suitable fluorescent dyes include, but are not limited to, fluorescein and fluorescein dyes (e.g., fluorescein isothiocyanine or FITC, naphthofluorescein, 4′,5′-dichloro-2′,7′-dimethoxy-fluorescein, 6 carboxyfluorescein or FAM), carbocyanine, merocyanine, styryl dyes, oxonol dyes, phycoerythrin, erythrosin, eosin, rhodamine dyes (e.g., carboxytetramethylrhodamine or TAMRA, carboxyrhodamine 6G, carboxy-X-rhodamine (ROX), lissamine rhodamine B, rhodamine 6G, rhodamine Green, rhodamine Red, tetramethylrhodamine or TMR), coumarin and coumarin dyes (e.g., methoxycoumarin, dialkylaminocoumarin, hydroxycoumarin and aminomethylcoumarin or AMCA), Oregon Green Dyes (e.g., Oregon Green 488, Oregon Green 500, Oregon Green 514), Texas Red, Texas Red-X, Spectrum Red M, Spectrum Green™, cyanine dyes (e.g., Cy-3™, Cy-5™, Cy-3.5™, Cy-5.5™, Alexa Fluor dyes (e.g., Alexa Fluor 350, Alexa Fluor 488, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 633, Alexa Fluor 660 and Alexa Fluor 680), BODIPY dyes (e.g., BODIPY FL, BODIPY R6G, BODIPY TMR, BODIPY TR, BODIPY 530/550, BODIPY 558/568, BODIPY 564/570, BODIPY 576/589, BODIPY 581/591, BODIPY 630/650, BODIPY 650/665), IRDyes (e.g., IRD40, IRD 700, IRD 800), and the like. For more examples of suitable fluorescent dyes and methods for linking or incorporating fluorescent dyes to nucleic acid molecules see, for example, “The Handbook of Fluorescent Probes and Research Products”, 9th Ed., Molecular Probes, Inc., Eugene, Oreg. Fluorescent dyes as well as labeling kits are commercially available from, for example, Amersham Biosciences, Inc. (Piscataway, N.J.), Molecular Probes Inc. (Eugene, Oreg.), and New England Biolabs Inc. (Beverly, Mass.).Another contemplated method of analyzing the methylation status of the sequences is by analysis of the DNA following exposure to methylation-sensitive restriction enzymes—see for example US Application Nos. 20130084571 and 20120003634, the contents of which are incorporated herein.
  • Exemplary probes for detecting cardiac DNA are set forth in SEQ ID NOs: 118 and 119.
  • Exemplary probes for detecting colon DNA are set forth in SEQ ID NOs: 125 and 126.
  • Exemplary probes for detecting liver DNA are set forth in SEQ ID NOs: 128, 129 and 130.
  • In one embodiment, the probes that are used are TaqMan™ probes.
  • TaqMan™ probes comprise a detectable moiety (e.g. fluorophore) covalently attached to the 5′-end of the oligonucleotide probe and a quencher at the 3′-end. Several different fluorophores (e.g. 6-carboxyfluorescein, acronym: FAM, or tetrachlorofluorescein, acronym: TET) and quenchers (e.g. tetramethylrhodamine, acronym: TAMRA) are available. The quencher molecule quenches the fluorescence emitted by the fluorophore when excited by the cycler's light source via FRET (Forster Resonance Energy Transfer). As long as the fluorophore and the quencher are in proximity, quenching inhibits any fluorescence signals.
  • Other examples of quenchers include, but are not limited to Dabcyl™, TAMRA™, ECLIPSE™, DDQ™, QSY™, Blackberry Quencher, Black Hole Quencher, Qxl, Iowa black FQ™, Iowa black RQ™, and IRDye QC-1™.
  • TaqMan™ probes are designed such that they anneal within a DNA region amplified by a specific set of primers. As the Taq polymerase extends the primer and synthesizes the nascent strand, the 5′ to 3′ exonuclease activity of the Taq polymerase degrades the probe that has annealed to the template. Degradation of the probe releases the detectable moiety from it and breaks the close proximity to the quencher, thus relieving the quenching effect and allowing for detection of the detectable moiety (e.g. it allow for fluorescence of the fluorophore). Hence, the amount of detectable moiety is directly proportional to the amount of DNA template present in the PCR.
  • According to a particular embodiment, determining the methylation status is carried out as follows:
  • The bisulfite-treated DNA of the specimen is contacted with:
      • (i) a first probe that hybridizes to at least one methylation site of the amplified DNA; and
      • (ii) a second probe that hybridizes to at least one other methylation site of the amplified DNA, wherein the first probe and the second probe are labeled with non-identical detectable moieties, wherein the first probe and the second probe comprise a quenching moiety.
  • According to a particular embodiment, the first probe hybridizes to the forward strand of the amplified DNA and the second probe hybridizes to the reverse strand of the amplified DNA (see for example FIG. 5A).
  • The contacting is effected under conditions that separate the quenching moiety from the first probe and the second probe to generate a non-quenched first probe and a non-quenched second probe. The conditions are those which are inductive for an amplification reaction—i.e. presence of a polymerase enzyme having 5′ to 3′ nuclease activity (e.g. Taqman™ polymerase), dNTPs and buffer etc.
  • Once sufficient amplification has occurred, the amount of non-quenched first probe and non-quenched second probe in a single droplet can be measured—e.g. by using a fluorimeter.
  • In one embodiment, the number of droplets containing a signal from both probes is scored
  • Exemplary targets that may be analyzed according to this aspect of the present invention are provided in US Patent Application No. 20170121767, the contents of which are incorporated herein by reference.
  • According to a particular embodiment, the target comprises at least a part of the sequence of human chromosome 12, between coordinates 124692462-124692551 (e.g. SEQ ID NOs: 56 or 57).
  • According to another embodiment, the target comprises at least a part of the ECH1 locus.
  • According to still another embodiment, the target comprises at least a part of the IGF2R gene or the VTN gene (e.g. SEQ ID NOs: 65 or 66).
  • Other exemplary targets that may be analyzed are comprised in the sequences set forth in SEQ ID Nos: 2-117 or SEQ ID NOs: 135-191. According to a particular embodiment, the target sequence comprises the nucleotides CG which are at position 250 and 251 of each of these sequences.
  • According to another embodiment, at least one of the methylation sites of the signature are the nucleotides CG which are at position 250 and 251 of each of these sequences.
  • Kits
  • Any of the components described herein may be comprised in a kit. In a non-limiting example the kit comprises:
      • (i) a first oligonucleotide probe, wherein the 3′ end of said first probe comprises a quenching moiety and the 5′ end is labeled with a first detectable moiety;
      • (ii) a second oligonucleotide probe, wherein the 3′ end of said second probe comprises a quenching moiety and the 5′ end is labeled with a second detectable moiety;
  • wherein the sequence of said first probe is selected so as to determine a methylation status at a first methylation site of the double-stranded DNA molecule and the sequence of said second probe is selected so as determine a methylation status at a second methylation site of the same double-stranded DNA molecule, wherein said first methylation site and said second methylation site are no more than 300 base pairs apart; and
      • (iii) a polymerase enzyme having 5′ to 3′ nuclease activity (e.g. Taqman™ polymerase).
  • In another non-limiting example, the kit includes:
      • (i) at least two oligonucleotides, wherein the sequence of said first oligonucleotide of said at least two oligonucleotides is selected so as to determine a methylation status at a first methylation site of the double-stranded DNA molecule and the sequence of said second oligonucleotide of said at least two oligonucleotides is selected so as determine a methylation status at a second methylation site of the same double-stranded DNA molecule, wherein said first methylation site and said second methylation site are no more than 300 base pairs apart; and
      • (ii) a droplet forming oil.
  • Detectable moieties, quenching moieties and probes have been described herein above.
  • Additional components that may be included in any of the above described kits include at least one of the following components: a droplet forming oil, bisulfite (and other reagents necessary for the bisulfite reaction), reagents for purification of DNA, MgCl2. The kit may also comprise reaction components for sequencing the amplified or non-amplified sequences.
  • The kits may also comprise DNA sequences which serve as controls. Thus, for example, the kit may comprise a DNA having the same sequence as the amplified sequence derived from a healthy subject (to serve as a negative control) and/or a DNA having the same sequence as the amplified sequence derived from a subject known to have the disease which is being investigated (to serve as a positive control).
  • In addition, the kits may comprise known quantities of DNA such that calibration and quantification of the test DNA may be carried out.
  • The containers of the kits will generally include at least one vial, test tube, flask, bottle, syringe or other containers, 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 container.
  • When the components of the kit are provided in one or more liquid solutions, the liquid solution can be an aqueous solution. However, the components of the kit may be provided as dried powder(s). When reagents and/or components are provided as a dry powder, the powder can be reconstituted by the addition of a suitable solvent.
  • A kit will preferably include instructions for employing, the kit components as well the use of any other reagent not included in the kit. Instructions may include variations that can be implemented.
  • Diagnostics
  • It will be appreciated that analysis of the methylation status according to methods described herein allows for the accurate determination of cellular/tissue source of a DNA molecule, even when the majority of the DNA of the sample is derived from a different cellular source. The present inventors have shown that they are able to determine the cellular source of a particular DNA even when its contribution to the total amount of DNA in the population is less than 1:1000, less than 1:5,000, 1:10,000 or even 1:100,000.
  • Pathological and disease conditions that involve cell death cause the release of degraded DNA from dying cells into body fluids (blood, plasma, urine, cerebrospinal fluid). Thus, the methods described herein may be used to analyze the amount of cell death of a particular cell population in those body fluids. The amount of cell death of a particular cell population can then be used to diagnose a particular pathological state (e.g. disease) or condition (e.g. trauma).
  • It will be appreciated that death of a particular cell type may be associated with a pathological state—e.g. disease or trauma.
  • The monitoring of the death of a particular cell type may also be used for monitoring the efficiency of a therapeutic regime expected to effect cell death of a specific cell type.
  • The determination of death of a specific cell type may also be used in the clinical or scientific study of various mechanism of healthy or diseased subjects.
  • Thus, for example measurement of pancreatic beta cell death is important in cases of diabetes, hyperinsulinism and islet cell tumors, and in order to monitor beta cell survival after islet transplantation, determining the efficacy of various treatment regimes used to protect beta cells from death, and determining the efficacy of treatments aimed at causing islet cell death in islet cell tumors. Similarly, the method allows the identification and quantification of DNA derived from dead kidney cells (indicative of kidney failure), dead neurons (indicative of traumatic brain injury, amyotrophic lateral sclerosis (ALS), stroke, Alzheimer's disease, Parkinson's disease or brain tumors, with or without treatment); dead pancreatic acinar cells (indicative of pancreatic cancer or pancreatitis); dead lung cells (indicative of lung pathologies including lung cancer); dead adipocytes (indicative of altered fat turnover), dead hepatocytes (indicative of liver failure, liver toxicity or liver cancer) dead cardiomyocytes (indicative of cardiac disease, or graft failure in the case of cardiac transplantation), dead skeletal muscle cells (indicative of muscle injury and myopathies), dead oligodendrocytes (indicative of relapsing multiple sclerosis, white matter damage in amyotrophic lateral sclerosis, or glioblastoma), dead colon cells is indicative of colorectal cancer.
  • As used herein, the term “diagnosing” refers to determining the presence of a disease, classifying a disease, determining a severity of the disease (grade or stage), monitoring disease progression and response to therapy, forecasting an outcome of the disease and/or prospects of recovery.
  • The method comprises quantifying the amount of cell-free DNA which is comprised in a fluid sample (e.g. a blood sample or serum sample) of the subject which is derived from a cell type or tissue. When the amount of cell free DNA derived from the cell type or tissue is above a predetermined level, it is indicative that there is a predetermined level of cell death. When the level of cell death is above a predetermined level, it is indicative that the subject has the disease or pathological state. Determining the predetermined level may be carried out by analyzing the amount of cell-free DNA present in a sample derived from a subject known not to have the disease/pathological state. If the level of the cell-free DNA derived from a cell type or tissue associated with the disease in the test sample is statistically significantly higher (e.g. at least two fold, at least three fold, or at least 4 fold) than the level of cell-free DNA derived from the same cell type or tissue in the sample obtained from the healthy (non-diseased subject), it is indicative that the subject has the disease. Alternatively, or additionally, determining the predetermined level may be carried out by analyzing the amount of cell-free DNA present in a sample derived from a subject known to have the disease. If the level of the cell-free DNA derived from a cell type or tissue associated with the disease in the test sample is statistically significantly similar to the level of the cell-free DNA derived from a cell type of tissue associated with the disease in the sample obtained from the diseased subject, it is indicative that the subject has the disease.
  • The severity of disease may be determined by quantifying the amount of DNA molecules having the specific methylation pattern of a cell population associated with the disease. Quantifying the amount of DNA molecules having the specific methylation pattern of a target tissue may be achieved using a calibration curve produced by using known and varying numbers of cells from the target tissue.
  • According to one embodiment, the method comprises determining the ratio of the amount of cell free DNA derived from a cell of interest in the sample: amount of overall cell free DNA.
  • According to still another embodiment, the method comprises determining the ratio of the amount of cell free DNA derived from a cell of interest in the sample: amount of cell free DNA derived from a second cell of interest.
  • The methods described herein may also be used to determine the efficacy of a therapeutic agent or treatment, wherein when the amount of DNA associated with a cell population associated with the disease is decreased following administration of the therapeutic agent, it is indicative that the agent or treatment is therapeutic.
  • According to some embodiments of the invention, screening of the subject for a specific disease is followed by substantiation of the screen results using gold standard methods.
  • The method can also be used to predict prognosis of the subject with the disease.
  • According to some embodiments of the invention, the method further comprising informing the subject of the predicted disease and/or the predicted prognosis of the subject.
  • As used herein the phrase “informing the subject” refers to advising the subject that based on the cfDNA levels, the subject should seek a suitable treatment regimen.
  • Once the cfDNA level is determined, the results can be recorded in the subject's medical file, which may assist in selecting a treatment regimen and/or determining prognosis of the subject.
  • According to some embodiments of the invention, the method further comprising recording the cfDNA levels of the subject in the subject's medical file.
  • As mentioned, the prediction can be used to select the treatment regimen of a subject and thereby treat the subject in need thereof.
  • As used herein the term “about” refers to ±10%
  • The terms “comprises”, “comprising”, “includes”, “including”, “having” and their conjugates mean “including but not limited to”.
  • The term “consisting of” means “including and limited to”.
  • The term “consisting essentially of” means that the composition, method or structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure.
  • As used herein, the singular form “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a compound” or “at least one compound” may include a plurality of compounds, including mixtures thereof.
  • Throughout this application, various embodiments of this invention may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.
  • Whenever a numerical range is indicated herein, it is meant to include any cited numeral (fractional or integral) within the indicated range. The phrases “ranging/ranges between” a first indicate number and a second indicate number and “ranging/ranges from” a first indicate number “to” a second indicate number are used herein interchangeably and are meant to include the first and second indicated numbers and all the fractional and integral numerals therebetween.
  • As used herein the term “method” refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts.
  • As used herein, the term “treating” includes abrogating, substantially inhibiting, slowing or reversing the progression of a condition, substantially ameliorating clinical or aesthetical symptoms of a condition or substantially preventing the appearance of clinical or aesthetical symptoms of a condition.
  • It is understood that any Sequence Identification Number (SEQ ID NO) disclosed in the instant application can refer to either a DNA sequence or a RNA sequence, depending on the context where that SEQ ID NO is mentioned, even if that SEQ ID NO is expressed only in a DNA sequence format or a RNA sequence format. For example, SEQ ID NO: XXX is expressed in a DNA sequence format (e.g., reciting T for thymine), but it can refer to either a DNA sequence that corresponds to an XXX nucleic acid sequence, or the RNA sequence of an RNA molecule nucleic acid sequence. Similarly, though some sequences are expressed in a RNA sequence format (e.g., reciting U for uracil), depending on the actual type of molecule being described, it can refer to either the sequence of a RNA molecule comprising a dsRNA, or the sequence of a DNA molecule that corresponds to the RNA sequence shown. In any event, both DNA and RNA molecules having the sequences disclosed with any substitutes are envisioned.
  • It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination or as suitable in any other described embodiment of the invention. Certain features described in the context of various embodiments are not to be considered essential features of those embodiments, unless the embodiment is inoperative without those elements.
  • Various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below find experimental support in the following examples.
    • EXAMPLES
  • Reference is now made to the following examples, which together with the above descriptions illustrate some embodiments of the invention in a non limiting fashion.
  • Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley & Sons, New York (1988); Watson et al., “Recombinant DNA”, Scientific American Books, New York; Birren et al. (eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Culture of Animal Cells—A Manual of Basic Technique” by Freshney, Wiley-Liss, N.Y. (1994), Third Edition; “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994); Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; “Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J., eds. (1985); “Transcription and Translation” Hames, B. D., and Higgins S. J., eds. (1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “Immobilized Cells and Enzymes” IRL Press, (1986); “A Practical Guide to Molecular Cloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317, Academic Press; “PCR Protocols: A Guide To Methods And Applications”, Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategies for Protein Purification and Characterization—A Laboratory Course Manual” CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated herein by reference.
    • Example 1 MATERIALS AND METHODS
  • Clinical specimens: Cardiac biomarkers used were troponin T and CPK.
  • Identification of cardiac methylation markers: Tissue-specific DNA methylation markers were selected after a comparison of publically available DNA methylation datasets generated by whole-genome bisulfite sequencing (Roadmap Epigenomics). The fragment of FAM101A used as a cariomyocyte-specific marker is located in chromosome 12, coordinates 124692462-124692551.
  • cfDNA analysis: Blood specimens were collected in EDTA tubes, and centrifuged within 2 hours to separate plasma from peripheral blood cells: first at 1500 g for 10 min, and then at 3000 g for 10 min to remove any remaining cells. Plasma was then stored at −80° C.
  • cfDNA was extracted using the QIAsymphony SP instrument and its dedicated QIAsymphony Circulating DNA Kit (Qiagen) according to the manufacturer's instructions.
  • DNA concentration was measured using the Qubit™ dsDNA HS Assay Kit. cfDNA was treated with bisulfite using a kit (Zymo Research), and PCR amplified with primers specific for bisulfite-treated DNA but independent of methylation status at the monitored CpG sites. Primers were bar-coded, allowing the mixing of specimens from different individuals when sequencing PCR products using MiSeq or NextSeq (Illumina). Sequenced reads were separated by barcode, aligned to the target sequence, and analyzed using custom scripts written and implemented in R. Reads were quality filtered based on Illumina quality scores, and identified by having at least 80% similarity to target sequences and containing all the expected CpGs in the sequence. CpGs were considered methylated if “CG” was read and were considered unmethylated if “TG” was read.
  • Digital Droplet PCR: A procedure was established for digital droplet PCR, in which bisulfite-treated cfDNA is amplified using a methylation-sensitive Taqman™ probe.
  • The limited length of probes (up to 30 bp) dictated that they could cover only 2 or 3 informative CpG sites in the FAM101A locus, predicting a relatively high frequency of “noise” (positive droplets) in DNA from non-cardiac tissue. In the sequencing-based assay, this problem was addressed by documenting the methylation status of multiple adjacent cytosines (FIGS. 1A-E), which greatly increased specificity.
  • To implement this concept in the ddPCR platform, two Taqman™ probes were designed, each recognizing lack of methylation in a different cluster of cytosines (one containing 2 CpG sites and one containing 3 CpG sites) within the same amplified 100 bp fragment from the FAM101A locus (FIG. 5A). Each probe was labeled with a different fluorophore, such that droplets could be identified in which both probes found a target. Such droplets would be interpreted as containing a FAM101A cfDNA fragment in which all 5 targeted cytosines were demethylated. This would provide ddPCR with the improved specificity afforded by interrogating multiple cytosines on the same DNA molecule.
  • For the analysis of 5 cytosines, located adjacent to the FAM101A locus, the following primers were used: 5′-TATGGTTTGGTAATTTATTTAGAG-3′ (SEQ ID NO: 1; forward) and 5′-AAATACAAATCCCACAAATAAA-3′ (SEQ ID NO: 120; reverse) in combination with probes that detected lack of methylation on 3 and 2 cytosines respectively: 5′-AATGTATGGTGAAATGTAGTGTTGGG-3′ (SEQ ID NO: 118; FAM-forward probe) and 5′-AAAAATACTCAACTTCCATCTACAATT-3′ (SEQ ID NO: 119, HEX-reverse probe).
  • Assay design is shown in FIG. 5A. Each 20-μL volume reaction mix consisted of ddPCR™ Supermix for Probes (No dUTP) (Bio-Rad), 900 nM primer, 250 nM probe, and 2 μL of specimen. The mixture and droplet generation oil were loaded onto a droplet generator (Bio-Rad). Droplets were transferred to a 96-well PCR plate and sealed. The PCR was run on a thermal cycler as follows: 10 minutes of activation at 95° C., 47 cycles of a 2 step amplification protocol (30 s at 94° C. denaturation and 60 s at 53.7° C.), and a 10-minute inactivation step at 98° C. The PCR plate was transferred to a QX100Droplet Reader (Bio-Rad), and products were analyzed with QuantaSoft (Bio-Rad) analysis software. Discrimination between droplets that contained the target (positives) and those which did not (negatives) was achieved by applying a fluorescence amplitude threshold based on the amplitude of reads from the negative template control.
    • Results
  • Identification of Cardiomyocyte Methylation Markers
  • To define genomic loci that are methylated in a cardiac-specific manner, the methylomes of human heart chambers (right atrium, left and right ventricle) were compared with the methylomes of 23 other human tissues, all publicly available12. Several differentially methylated loci were identified and a cluster of cytosines adjacent to the FAM101A locus was selected for further analysis (FIGS. 1A-B). PCR was used to amplify a 90 bp fragment around this cluster after bisulfite conversion of unmethylated cytosines, and the PCR product was sequenced to determine the methylation status of all 6 cytosines in the cluster. In purified cardiomyocyte DNA, 89% of the molecules were fully unmethylated, while in non-cardiac tissue <0.2% of molecules were unmethylated; specifically in leukocytes (the main contributor to cfDNA), <0.006% of molecules were unmethylated (FIG. 1C and FIGS. 6A-C). Thus, interrogating all CpGs simultaneously, the ratio of demethylated molecules in heart:blood DNA was 89:0.006 giving a signal to noise ratio of 15,000.
  • To determine the linearity and sensitivity of the assay, leukocyte DNA was spiked with increasing amounts of cardiac DNA. The fraction of cardiac DNA in the mixture was assessed using PCR amplification and massively parallel sequencing. The assay was able to correctly determine the fraction of cardiac DNA, even when it was only 0.5% of the DNA in the mixture (FIG. 1D).
  • Following bisulfite treatment, DNA becomes single stranded. Therefore, each strand can be considered an independent biomarker. To test this idea, the present inventors designed primers against the antisense strand of FAM101A post-bisulfite conversion. As expected, the sense and antisense templates showed a similar sensitivity and specificity (FIGS. 1B-E and 6A-C). It was reasoned that by testing both strands in a given specimen, both sensitivity and specificity of the assay will increase. For this reason further analysis of clinical specimens was performed using both sense and antisense specific primer sets.
  • Plasma levels of cardiomyocyte DNA in healthy individuals
  • The sense and antisense FAM101A markers were used to assess the concentration of cardiac cfDNA in the plasma of donors. cfDNA was extracted from plasma and treated with bisulfite. PCR and sequencing were performed, typically using material from 0.5 ml of plasma. The fraction of PCR products carrying the cardiac-specific methylation pattern was multiplied by the total concentration of cfDNA, to obtain an estimation of cardiac cfDNA content in plasma.
  • Healthy adult plasma from 83 healthy donors was tested and zero copies of cardiac cfDNA were detected in 73 of them (FIG. 2A). In ten individuals, 1-20 copies/ml cardiac cfDNA was found. This low level of a signal likely reflects the low rate of cardiomyocyte death in healthy adults13. The mean plus 2 standard deviations of the control group was 10 copies/ml, and this was thus defined as the cutoff level for a positive signal.
  • Plasma levels of cardiomyocyte DNA after myocardial infarction
  • As a positive control where high levels of cardiac cfDNA are expected, plasma from donors with myocardial infarction (MI) were used. Specimens from individuals that presented with chest pain, before and after they underwent angioplasty were used. The levels of cardiac cfDNA as well as troponin and CPK were assessed. MI patients showed dramatically higher levels of cardiac cfDNA than healthy controls (FIG. 2A and FIGS. 7A-F and 8A-B). To assess assay performance in discriminating healthy from MI plasma a Receiver Operator Characteristic (ROC) curve was plotted. The area under the curve (AUC) was 0.9345, indicating high sensitivity and specificity (FIG. 2B). The present inventors also compared cardiac cfDNA to standard cardiac damage markers CPK and troponin. Compared with healthy controls, cardiac cfDNA was significantly higher in MI patients that had CPK just above normal (<200), and was even higher in patients with high CPK (>200) (FIG. 2C). Similarly, cardiac cfDNA was higher than normal in plasma specimens that had either low or high levels of troponin (FIG. 2D and FIGS. 7A-F). Among the 6 specimens that had troponin levels above baseline but <0.03, there was no more cfDNA than in healthy controls (FIG. 2D).
  • A comparison of troponin levels to cardiac cfDNA in 57 specimens from MI patients yielded Spearman correlation value of 0.7975 and p<0.0001 (FIG. 2E). When plotting cardiac cfDNA vs troponin and marking on each axis the threshold of a positive signal, it was found that 79% of the MI specimens were positive for both troponin and cardiac cfDNA, and 7% were negative for both. 11% were positive only for troponin, and 4% were positive only for cardiac cfDNA (FIG. 2F). Importantly, total levels of cfDNA in MI did not correlate with troponin or CPK, nor with the percentage of cardiac cfDNA (FIGS. 7A-F). This reflects that fact that total cfDNA integrates all recent cell death events, including contributions from tissues that mask the cardiac signal. Thus, it is essential to calculate the specific contribution of the heart to cfDNA in order to assess cardiac damage. The sense and antisense markers correlated well in the MI plasma specimens (FIGS. 7A-F).
  • Finally, the present inventors examined the dynamics of cardiac cfDNA before and after angioplasty (Percutaneous Coronary Intervention, PCI). PCI causes the release of trapped cardiac material into blood, hence increased levels of troponin post PCI are typical of successful reperfusion. Cardiac cfDNA levels increased dramatically in most patients after PCI (FIG. 3A and supplemental FIGS. 8A-B), further supporting authenticity of the signal. A more detailed time course on a smaller group of patients revealed that cardiac cfDNA levels rose quickly after PCI and returned to baseline after 1-2 days, showing similar kinetics to troponin and CPK (FIG. 3B and supplemental FIGS. 8A-B). Importantly, the cardiac cfDNA signal was sufficient to distinguish people with MI prior to intervention (0-2 hours after onset of chest pain) from healthy individuals (AUC=0.7616, p=0.0044, FIG. 3C).
  • It can be concluded that measurements of cardiac cfDNA captures cardiomyocyte cell death associated with myocardial infarction, and that the cardiac cfDNA assay can in principle identify MI before intervention.
  • Cardiomyocyte cfDNA in patients with sepsis
  • Some septic patients have elevated levels of troponin and CPK14, although they do not show clinical evidence of cardiac damage15, 16. The biological significance of this observation is disputed, since high troponin could represent either cardiomyocyte death, or alternatively transient stress absent of cell death. Since renal dysfunction is common in sepsis, the elevation in circulating troponin may also result from slower clearance, rather than faster release of troponin17. Since cfDNA is a stronger marker of cell death and is cleared by the liver18, it was reasoned that measurements of cardiac cfDNA can be informative in this setting.
  • The present inventors determined the levels of cardiac cfDNA in a cohort of 100 patients with sepsis, for which 201 plasma specimens were available. Cardiac cfDNA was assessed blindly, and values were correlated to other biomarkers and to clinical parameters.
  • Septic patients had high levels of total cfDNA, reflective of broad tissue damage (FIGS. 9A-C), as reported19. Strikingly, many patients had high levels of cardiac cfDNA, similar in magnitude to the acute setting of MI (FIG. 4A). These findings argue strongly that in many septic patients, massive cardiomyocyte death occurs. The sense and antisense markers of FAM101A correlated well, supporting specificity of the signal (FIGS. 9A-C). Cardiac cfDNA and troponin levels did not correlate in the sepsis, unlike the situation in MI (FIG. 4B). This is not surprising, given the chronic nature of tissue damage in sepsis, which is expected to involve a major contribution of clearance rates on the actual measurements of biomarkers. A dramatic elevation of cardiac cfDNA was seen also in septic patients with normal renal function (data not shown), supporting the idea that cardiac cfDNA reflects cell death and not altered clearance rate.
  • The present inventors attempted to correlate the levels of cardiac cfDNA with clinical parameters recorded for the sepsis patients. The presence of cardiac cfDNA was strongly correlated with short-term mortality (FIG. 4C). When excluding cases with sepsis in the background of advanced cancer, patients with cardiac cfDNA were 4 times more likely to die within 90 days of hospitalization than patients with no cardiac cfDNA. The correlation was stronger than the correlation between troponin and mortality or between total cfDNA and mortality, but weaker than the correlation between age and mortality. These findings indicate that cardiac function is a central determinant of patient survival under sepsis, and that cardiac cfDNA can be used as a prognostic biomarker in sepsis.
  • A modified digital droplet PCR procedure for measurement of cardiac cfDNA
  • In order to translate analysis of cfDNA to a simpler and faster PCR format, the present inventors established a procedure using digital droplet PCR (ddPCR) to accurately count the number of molecules carrying the cardiac methylation signature at the FAM101A locus. They designed the assay to simultaneously interrogate 5 CpGs in the locus using two fluorescent probes, each capturing 2 or 3 unmethylated cytosines (FIG. 5A), leveraging the increased specificity attributed to regional methylation status9.
  • ddPCR analysis of cardiomyocyte and leukocyte DNA revealed that each probe alone was able to discriminate between DNA from the two sources, with a signal to noise ratio of 50 to 58. However, when only droplets positive for both probes were scored, the cardiomyocyte:leukocyte signal ratio increased to 258, affording a 5 fold increase in specificity (FIG. 5B). ddPCR on cardiac DNA spiked with leukocyte DNA gave a signal that increased linearly with the amount of cardiac DNA; scoring only dual-labeled probes gave a lower baseline signal than scoring individual probes, better reflecting cardiomyocyte contribution to the mixture (FIG. 5C).
  • Finally, the ddPCR assay was tested on plasma specimens. ddPCR revealed a clear signal in the plasma of MI patients and was able to distinguish well between controls and patients. A lower baseline signal was observed in healthy individuals when scoring only dual-labeled probes, indicating increased specificity (FIG. 5D). It can be concluded that the ddPCR assay for cardiac cfDNA provides a rapid and simple alternative to sequencing-based assays.
    • Example 2 Monitoring Liver Damage Using Hepatocyte-Specific Methylation Markers in Cell-Free Circulating DNA
  • Materials and Methods
  • Digital droplet PCR. Bisulfite-treated cfDNA was interrogated using methylation-sensitive TaqMan™ probes. The limited length of probes (up to 30 bp) dictated that they could cover only 2 to 4 informative CpG sites. In the IGF2R locus 4 CpGs were covered. However, in the VTN=locus, only 2 CpGs were covered by a probe predicting a relatively high frequency of “noise” (positive droplets) in DNA from non-liver tissue. Two TaqMan™ probes were designed, each recognizing lack of methylation in a different cluster of cytosines (each containing 2 CpG sites) within the same amplified 100 bp fragment from the VTN locus. Each probe was labeled with a different fluorophore, such that it was possible to identify droplets in which both probes found a target. Such droplets would be interpreted as containing a VTN cfDNA fragment in which all 4 targeted cytosines were unmethylated. This resulted in a ddPCR assay with the improved specificity afforded by interrogating multiple cytosines on the same DNA molecule.
  • Each 20 μL volume reaction mix consisted of ddPCR™ Supermix for Probes (No dUTP) (Bio-Rad), 900 nM primer, 250 nM probe, and 2 μL of sample. The mixture and droplet generation oil were loaded onto a droplet generator (Bio-Rad). Droplets were transferred to a 96-well PCR plate and sealed. The PCR was run on a thermal cycler as follows: 10 minutes of activation at 95° C., 47 cycles of a 2 step amplification protocol (30 s at 94° C. denaturation and 60 s at 56° C.), and a 10-minute inactivation step at 98° C. The PCR plate was transferred to a QX100 Droplet Reader (Bio-Rad), and products were analyzed with QuantaSoft (Bio-Rad) analysis software. Discrimination between droplets that contained the target (positives) and those that did not (negatives) was achieved by applying a fluorescence amplitude threshold based on the amplitude of reads from the negative template control.
  • Probe and Primer Sequences:
  • VTN: Probe 1—SEQ ID NO: 128
      • Probe 2—SEQ ID NO: 129
      • Primer 1—forward—SEQ ID NO: 131
      • Primer 2—reverse—SEQ ID NO: 132.
  • IGF2R: Probe 1—SEQ ID NO: 130
      • Primer 1—forward—SEQ ID NO: 133
      • Primer 2—reverse—SEQ ID NO: 134
  • Results
  • Primers were designed for digital droplet PCR (ddPCR) after bisulfite conversion of cfDNA, and probes were designed that recognize blocks of unmethylated CpGs in the amplified marker regions. In this example, the present inventors focused on the VTN and IGF2R markers, which had multiple CpGs in close proximity.
  • ddPCR using both amplicons showed no signal in leukocyte DNA and a strong signal in hepatocyte DNA (FIG. 14A). Next, the present inventors examined 6 sets of plasma samples from 6 patients before and after liver transplantation. The ddPCR assay revealed a strong and transient elevation of hepatocyte cfDNA in plasma shortly after transplantation, which declined thereafter, strongly suggesting validity of the assay (FIG. 14B).
    • Example 3 List of Additional Identified Targets
  • A list of identified targets is provided in Table 1 and 2 herein below. The methylation signature of the targets can be used to identify a cell type of the listed organ. It will be appreciated that the sequences provided are 500 base pairs. Preferably the target sequence (which is amplified which is less than all the 500 base pairs) comprises the nucleotides CG which are at position 250 and 251 of each of these sequences and additional nucleotides up and/or down-stream of this site.
  • TABLE 1
    Organ Name SEQ ID NO:
    Acinar CPA1 2
    Acinar LMF2 3
    Acinar NCLN 4
    Acinar BRF1 5
    Acinar FRY 6
    Astrocytes HDAC4 7
    Astrocytes AGAP1 8
    Astrocytes AST1 9
    Astrocytes PRDM 10
    Astrocytes FOXP4 11
    Astrocytes KIAA 12
    Astrocytes PRDM2 13
    Astrocytes WWOX 14
    B cells LRP5 15
    B cells SORL1 16
    B cells TRPV1 17
    BETA INSh 18
    BETA MTG1 19
    BETA ZC3H3 20
    BETA Leng8 21
    BETA Fbxw8 22
    BETA Fbxl19 23
    Blood Loc1/AGAP2 24
    Blood PTPRCAP 25
    BRAIN MAD1L1 26
    BRAIN PTPRN2 27
    BRAIN WM1 28
    BRAIN MBP 29
    BRAIN NUMBLE 30
    BRAIN LRRN3 31
    BRAIN cg0978 32
    BRAIN ZNF238 33
    Brain WB1 34
    Brain UBE4B 35
    Breast KRT19 36
    Breast LMX1B 37
    Breast ZNF296 38
    CD8 cells CD8A 39
    CD8 cells CD8A anti 40
    CD8 cells CD8B 41
    CD8 cells CD8B anti 42
    Colon FGFRL1 43
    Colon FAT1 44
    Colon col1 45
    Colon MG1 46
    Colon colnp 47
    Colon col2np 48
    Colon ECH1 49
    Colon ECH1 50
    Colon CNL (my name) 51
    Colon MAP7D1 52
    Colon col3np (my name) 53
    Eosinophils PCYT1A 54
    Eosinophils PCYT1A anti 55
    Heart FAM101A 56
    Heart FAM101A AS 57
    kidney cg00256155 58
    kidney PAX2 59
    kidney cg15767955 60
    kidney MCF2L 61
    kidney HOXC4 62
    kidney PAX2 63
    Liver ITIH4 64
    Liver SEBOX; VTN 65
    Liver IGF2R 66
    LUNG SFTP/A1 67
    LUNG SFTP/A2 68
    LUNG CLDN18 69
    LUNG RAB4 70
    LUNG CHST 71
    LUNG SFTPC 72
    Melanocytes GALNT3-B 73
    Melanocytes Melano1 74
    Melanocytes Melano1 anti 75
    Melanocytes RNF207-A 76
    Melanocytes RNF207-A anti 77
    Melanocytes RNF207-B 78
    Melanocytes RNF207-B anti 79
    Monocytes TCF7L2 80
    Monocytes MONO1 81
    Muscle MAD1L1 82
    Muscle TPO 83
    Muscle TNNI2 84
    Muscle TRIM72; PYDC1 85
    Neuron ZNF509 86
    Neuron ITFG3 87
    Neuron CTBP2 88
    Neuron SLC38A10 89
    neutrophils DENND3 90
    neutrophils NEUT1 91
    NK RFC2 92
    Oligodendrocytes PLEK 93
    Oligodendrocytes EVI5L 94
    Oligodendrocytes ZFP57 95
    Oligodendrocytes DNAH 96
    Oral cavity hH&N1 97
    Oral cavity CALML3 98
    Oral cavity hH&N4 99
    Pancreas CUX2 100
    Pancreas PAN4 101
    Pancreas REG1A 102
    Pancreas FRY 103
    Pancreas BRF1 104
    Pancreas PRDM16 105
    (not the same as above)
    Pancreatic duct PRDM16 106
    Small intestine ST5 107
    Small intestine BANP 108
    Small intestine SS18L1 109
    T cells PRKCH 110
    T cells SPATA13 111
    Thyroid ZNF500 112
    Thyroid ATP11A 113
    Treg FOXP3 114
    Treg FOXP3 ANTI 115
    Treg FOXP3 TSDR 116
    Treg FOXP3 TSDR anti 117
  • TABLE 2
    Organ Name SEQ ID NO:
    B cells NAT10 135
    BETA GALNTL4 136
    BETA cg06081580 137
    BETA RGS9 138
    BETA DLG5 139
    BETA GNAS 140
    BETA TTC15 141
    BETA MAD1L1 142
    BETA cg22406334 143
    BETA ZDHHC14 144
    BETA ZC3H3_a 145
    BETA SDK1 146
    BETA SFRS16 147
    BETA PUS3 148
    BETA ZC3H3-c 149
    BETA ACSF3 150
    BETA cg19441717me 151
    White Blood Cells SNX11 152
    Cardiomyocytes Cardio C 153
    Cardiomyocytes Cardio D 154
    Cardiomyocytes Cardio E 155
    Cardiomyocytes Cardio I 156
    Cardiomyocytes Cardio J 157
    Colon CNL2 158
    Colon CNL 159
    Colon col3np 160
    Eosinophils HTT 161
    Eosinophils ACOT7 162
    Kidney ATP11A 163
    Kidney PAX2-6032 164
    Kidney cg00256155 165
    Kidney PAX2-818 166
    Kidney MCF2L 167
    LUNG LUAD1 168
    LUNG LUAD5 169
    LUNG LUSC2 170
    LUNG LUSC3 171
    LUNG S3-unMe 172
    LUNG S4-unMe 173
    LUNG S5-unMe 174
    LUNG S5-Meth 175
    LUNG S10-unMe 176
    LUNG S11-unMe 177
    LUNG S13-unMe 178
    LUNG S12-Meth 179
    Melanocytes RNF207-A 180
    Melanocytes RNF207-B 181
    Melanocytes melano1 182
    Neutrophils HIPK3 183
    Oligodendrocyte NMRAL1 184
    Oligodendrocyte TAF8 185
    Tongue PIGG 186
    Tongue MAD1L1 187
    Tongue TP73 188
    Tongue BAIAP2 189
    Tongue HN1L 190
    T regs FOXP3 191
    TSDR
  • Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.
  • All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. To the extent that section headings are used, they should not be construed as necessarily limiting.
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    • 3. Roca, E. et al. The Dynamics of Cardiovascular Biomarkers in non-Elite Marathon Runners. J Cardiovasc Transl Res (2017).
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Claims (20)

What is claimed is:
1. A method of analyzing the methylation status of methylation sites of a double-stranded DNA molecule which comprises at least two methylation sites per single strand of said double-stranded DNA molecule, the double-stranded DNA molecule being comprised in a specimen, the method comprising:
(a) contacting the double-stranded DNA with bisulfite to generate single-stranded DNA molecules of which demethylated cytosines of said single-stranded DNA molecules are converted to uracils;
(b) fractionating the specimen into a plurality of specimen fractions wherein more than 50% of the fractions contain no more than one single-stranded DNA molecule per specimen fraction; and
(c) determining the methylation status of said at least two methylation sites of said single-stranded DNA molecule in at least one of said specimen fractions, wherein a methylation status of each of said at least two methylation sites on said single-stranded DNA molecule is indicative of the methylation status of methylation sites of a double-stranded DNA molecule.
2. The method of claim 1, wherein said determining comprises contacting said amplified DNA with:
(i) a first probe that hybridizes to said amplified DNA at a site which comprises the first of said at least two methylation sites; and
(ii) a second probe that hybridizes to said amplified DNA at a site which comprises a second of said at least two methylation sites.
3. The method of claim 2, wherein said first probe and said second probe are labeled with non-identical detectable moieties.
4. The method of claim 1, wherein
a. said double-stranded DNA molecule is no longer than 150 bp;
b. said at least two methylation sites are not more than 150 bp apart;
c. wherein each strand of said double-stranded DNA comprises at least four methylation sites; or
d. wherein each strand of said double-stranded DNA comprises at least four methylation sites which are not more than 150 bp apart.
5. The method of claim 1, wherein said determining is affected using at least two non-identical labels or using a single label.
6. The method of claim 5, wherein said first probe and said second probe comprise a quenching moiety;
wherein said contacting is affected under conditions that separate said quenching moiety from said first probe and said second probe to generate a non-quenched first probe and a non-quenched second probe; and
wherein the method further comprises analyzing the amount of said non-quenched first probe and said non-quenched second probe in at least one specimen fraction of said plurality of specimen fractions; or
wherein said first probe hybridizes to the forward strand of said amplified DNA and said second probe hybridizes to the reverse strand of said amplified DNA.
7. The method of claim 1, wherein said method further comprises contacting said single-stranded DNA with amplification primers under conditions that generate amplified DNA from said single-stranded DNA following step (b) and prior to step (c) and wherein said determining comprises contacting said amplified DNA with:
(i) a first probe that hybridizes to said amplified DNA at a site which comprises the first of said at least two methylation sites; and
(ii) a second probe that hybridizes to said amplified DNA at a site which comprises a second of said at least two methylation sites, wherein said first probe and said second probe are labeled with non-identical detectable moieties.
8. The method of claim 1, wherein said double-stranded DNA molecule is differentially methylated in a cell or tissue of interest.
9. The method of claim 8, wherein said cell of interest is selected from the group consisting of a pancreatic beta cell, a pancreatic exocrine cell, a hepatocyte, a brain cell, a lung cell, a uterus cell, a kidney cell, a breast cell, an adipocyte, a colon cell, a rectum cell, a cardiomyocyte, a skeletal muscle cell, a prostate cell and a thyroid cell or wherein said tissue is selected from the group consisting of pancreatic tissue, liver tissue, lung tissue, brain tissue, uterus tissue, renal tissue, breast tissue, fat, colon tissue, rectum tissue, cardiac tissue, skeletal muscle tissue, prostate tissue and thyroid tissue.
10. The method of claim 9, wherein said tissue is cardiac tissue and wherein said double-stranded DNA molecule is non-methylated in cells of cardiac tissue and methylated in leukocytes.
11. The method of claim 10, wherein said double-stranded DNA molecule comprises at least a part of the sequence of human chromosome 12, between coordinates 124692462-124692551 or comprises a sequence which is comprised in SEQ ID NOs: 56 or 57.
12. The method of claim 9, wherein said tissue is liver tissue and wherein said double-stranded DNA molecule comprises a sequence which is comprised in SEQ ID NOs: 65 or 66.
13. The method of claim 6, wherein said first probe comprises a sequence as set forth in SEQ ID NO: 118 and said second probe comprises a sequence as set forth in SEQ ID NO: 119, said first probe comprises a sequence as set forth in SEQ ID NO: 128 and said second probe comprises a sequence as set forth in SEQ ID NO: 129 or said first probe comprises a sequence as set forth in SEQ ID NO: 125 and said second probe comprises a sequence as set forth in SEQ ID NO: 126.
14. The method of claim 5, wherein said single label is comprised on a probe and wherein said probe comprises a sequence as set forth in SEQ ID NO: 130.
15. The method of claim 6, wherein the sequence of said first probe is selected such that said first probe binds to said amplified DNA when said methylation site of said double-stranded DNA molecule is non-methylated or wherein the sequence of said second probe is selected such that said second probe binds to said amplified DNA when said methylation site of said double-stranded DNA molecule is non-methylated.
16. The method of claim 6, wherein said detectable moiety is FAM or HEX.
17. The method of claim 1, wherein
a. said double-stranded DNA is cell-free DNA;
b. said double-stranded DNA is cellular DNA and wherein said method further comprises lysing the cells of said cellular DNA prior to said determining;
c. said specimen is a fluid specimen;
d. said specimen is a body fluid specimen;
e. said specimen is a body fluid specimen selected from the group consisting of blood, plasma, sperm, milk, urine, saliva and cerebral spinal fluid;
f. said specimen comprises DNA from a plurality of cell-types;
said specimen is blood; or
g. said method further comprises quantitating the amount of DNA of said cell or tissue origin.
18. A kit for analyzing methylation sites of a double-stranded DNA molecule, the kit comprising:
(i) a first oligonucleotide probe, wherein the 3′ end of said first probe comprises a quenching moiety and the 5′ end is labeled with a first detectable moiety;
(ii) a second oligonucleotide probe, wherein the 3′ end of said second probe comprises a quenching moiety and the 5′ end is labeled with a second detectable moiety;
wherein the sequence of said first probe is selected so as to determine a methylation status at a first methylation site of the double-stranded DNA molecule and the sequence of said second probe is selected so as determine a methylation status at a second methylation site of the same double-stranded DNA molecule, wherein said first methylation site and said second methylation site are no more than 300 base pairs apart; and
(iii) a Taqman™ polymerase.
19. The kit of claim 16, further comprising a droplet forming oil.
20. A kit for analyzing methylation sites of a double-stranded DNA molecule, the kit comprising:
(i) at least two oligonucleotides, wherein the sequence of said first oligonucleotide of said at least two oligonucleotides is selected so as to determine a methylation status at a first methylation site of the double-stranded DNA molecule and the sequence of said second oligonucleotide of said at least two oligonucleotides is selected so as determine a methylation status at a second methylation site of the same double-stranded DNA molecule, wherein said first methylation site and said second methylation site are no more than 300 base pairs apart; and
(ii) a droplet forming oil.
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