EP3899026A1 - Procédé in vitro pour mettre en évidence au moins un acide nucléique présent chez un être vivant dans le sang total en dehors des cellules sanguines et dispositif et kit correspondants - Google Patents

Procédé in vitro pour mettre en évidence au moins un acide nucléique présent chez un être vivant dans le sang total en dehors des cellules sanguines et dispositif et kit correspondants

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Publication number
EP3899026A1
EP3899026A1 EP19831685.3A EP19831685A EP3899026A1 EP 3899026 A1 EP3899026 A1 EP 3899026A1 EP 19831685 A EP19831685 A EP 19831685A EP 3899026 A1 EP3899026 A1 EP 3899026A1
Authority
EP
European Patent Office
Prior art keywords
dna
detection
whole blood
living
reaction mixture
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP19831685.3A
Other languages
German (de)
English (en)
Inventor
Ralf Himmelreich
Perikles Simon
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Fraunhofer Gesellschaft zur Forderung der Angewandten Forschung eV
Johannes Gutenberg Universitaet Mainz
Original Assignee
Fraunhofer Gesellschaft zur Forderung der Angewandten Forschung eV
Johannes Gutenberg Universitaet Mainz
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Fraunhofer Gesellschaft zur Forderung der Angewandten Forschung eV, Johannes Gutenberg Universitaet Mainz filed Critical Fraunhofer Gesellschaft zur Forderung der Angewandten Forschung eV
Publication of EP3899026A1 publication Critical patent/EP3899026A1/fr
Pending legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6804—Nucleic acid analysis using immunogens
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
    • G01N33/54366—Apparatus specially adapted for solid-phase testing
    • G01N33/54386—Analytical elements
    • G01N33/54387—Immunochromatographic test strips
    • G01N33/54388—Immunochromatographic test strips based on lateral flow

Definitions

  • nucleic acid In whole blood of living beings there can be a nucleic acid (eg DNA and / or RNA) which is outside the blood cells or not enclosed in a biological double membrane in the whole blood and thus circulates "free" in the blood of living beings, so to speak.
  • cell-free Nucleic acid which can be, for example, cell-free DNA (“cfDNA” for short)
  • cfDNA cell-free DNA
  • cfDNA is double-stranded and predominantly has a size in the range of approx. 60 to 300 base pairs (abbreviation for "Base pairs” in the following: "bp"). Often cfDNA has a length of 140 bp, because this corresponds approximately to the DNA portion of a nucleosome.
  • Free-circulating DNA is currently the focus of many oncological questions. Increased concentrations in the blood (blood plasma or blood serum) correlate with the clinical stages in the acute phase of cancer development.
  • the somatic cfDNA then also contains a portion of tumor-generated cfDNA, which is also referred to as “ctDNA”.
  • a simple and fast method for the quantification of cell-free nucleic acid, e.g. cfDNA, from a blood sample would be very interesting and helpful for various medical questions. In the event of an unclear finding, such a procedure could provide an indication of the direction in which further diagnostic test procedures make sense.
  • cell-free nucleic acid such as cell-free DNA
  • PCR polymerase chain reaction
  • Detection reaction of the cfDNA is started.
  • blood plasma is first obtained from whole blood in a time-consuming manner, i.e. the blood cells in the whole blood are separated from the cell-free whole blood. This is followed either by nucleic acid purification or a dilution step.
  • Nucleic acid purification is very time consuming.
  • the alternative of diluting the blood plasma is faster, but due to the dilution of the sample it is inevitably associated with a deterioration in the detection limit (ie a lower detection sensitivity to be expected).
  • Prior art methods also use PCR for the amplification of the cfDNA, which takes a very long time from start to finish (often a few hours) and requires a relatively large amount of knowledge and patience in sample preparation.
  • the known detection methods are therefore all time-consuming and a large number of devices are required for the detection (for example a centrifuge and a PCR device). Some of the devices (eg the PCR device) can only be operated by trained persons.
  • the object of the present invention to provide a device and a device and a kit for carrying out the method which does not have the above-mentioned disadvantages from the prior art.
  • the method, the device and the kit should be the detection of at least one nucleic acid (e.g. DNA and / or RNA), which is located in a living being in whole blood outside of the blood cells, with less work, less equipment, a higher detection accuracy (detection accuracy ) and enable the highest possible detection sensitivity.
  • nucleic acid e.g. DNA and / or RNA
  • a // i-wiro method is provided for the detection of at least one nucleic acid (preferably DNA and / or RNA, particularly preferably DNA) which is found outside the blood cells of a living being in whole blood.
  • the process includes the steps
  • reaction mixture which is suitable together with at least one pair of primers for carrying out an isothermal amplification reaction, the reaction mixture containing at least one pair of primers which is particularly preferred for the amplification of at least one nucleic acid present in whole blood (preferably DNA and / or RNA) DNA) is suitable or at least one such pair of primers is added to the reaction mixture;
  • step c) detection of DNA using at least one detection reagent, the detection being carried out during step c) or after step c);
  • reaction mixture is suitable for preventing lysis of blood cells contained in the animal in whole blood.
  • nucleic acid is preferably understood to mean DNA and / or RNA, particularly preferably DNA. Consequently, the nucleic acid to be detected or the nucleic acid to be amplified can be, for example, DNA and / or RNA.
  • RNA-DNA hybrids are also preferably included. Such RNA-DNA hybrids are, for example, single, short DNA and RNA strands (in particular strands 20-22 nucleotides in length) which have attached to one another.
  • the reaction mixture preferably contains an enzyme or an enzyme is added to it, which can copy RNA into DNA (eg the enzyme reverse transcriptase).
  • the reaction mixture can contain proteins from the group of nucleic acid ligases (for example a T7 RNA polymerase) or proteins from the group of nucleic acid ligases can be added to it.
  • RNAse H reverse transcriptase
  • SD polymerase reverse transcriptase
  • T7 RNA polymerase T7 RNA polymerase
  • an isothermal amplification of free RNA or an RNA located in an RNA-DNA hybrid can be achieved via a modification of the NASBA method, which is referred to as "linker ligation" - NASBA method
  • RNA is amplified by the interaction of the enzymes poly (A) polymerase, RNAse H and T7 RNA polymerase in the reaction mixture even at constant temperature (eg room temperature, 25 ° C.) (using at least one primer which contains a T7 promoter sequence)
  • constant temperature eg room temperature, 25 ° C.
  • the reaction mixture contains these enzymes and at least one primer with a T7 promoter sequence, or that these enzymes and this primer are added to it.
  • NASBA procedure can also be carried out in combination with an RPA procedure.
  • DNA present in whole blood is first converted into RNA (NASBA amplicon) by the RPA method, the RNA then being amplified using the NASBA method.
  • the method according to the invention can be used to detect at least one nucleic acid (for example DNA and / or RNA) which is found in whole blood outside the blood cells in the case of a living being (so-called “cell-free DNA” in the case of DNA as nucleic acid or "cfDNA” for short), even if a purified blood sample is not used, as is customary in the prior art.
  • whole blood is used directly, ie without pretreatment. The prerequisite for this is that the reaction mixture is suitable for preventing lysis of blood cells which are contained in the whole being in the living being.
  • nucleic acids eg DNA and / or RNA
  • cell nuclei eg leukocytes
  • the reaction mixture is generally suitable for preventing lysis of nucleic acid-containing, lipid double membrane-enclosed compartments which are contained in whole blood in the living being.
  • nucleic acid-containing, lipid double membrane-enclosed compartments is widely understood according to the invention, ie it includes all conceivable nucleic acid-containing compartments which are surrounded by a biological lipid double membrane. These include, for example, mitochondria, extracellular vesicles (Exosomes and microparticles), peroxisomes, viruses, unicellular organisms and bacteria.
  • the advantage of the method according to the invention compared to known methods is that sample preparation, i.e. there is no need to purify the whole blood.
  • the method according to the invention therefore requires fewer method steps and can be carried out more quickly.
  • the method according to the invention is thus outstandingly suitable for being carried out outside a laboratory.
  • a patient can determine on an outpatient basis (e.g. at home with a suitable device or a suitable kit for performing the method) whether there is at least one cell-free nucleic acid (e.g. cfDNA) in his blood (Use of non-specific primers) or whether there is at least one certain cell-free nucleic acid (eg a certain cfDNA) in his blood (use of specific primers).
  • a patient can determine on an outpatient basis (e.g. at home with a suitable device or a suitable kit for performing the method) whether there is at least one cell-free nucleic acid (e.g. cfDNA) in his blood (Use of non-specific primers) or whether there is at least one certain cell-free nucleic acid (eg a certain cfDNA) in his blood (use of specific primers).
  • cell-free nucleic acid e.g. cfDNA
  • At the person tested can be an athlete and / or a patient such as an accident or emergency patient, who can be examined directly on the spot immediately after exercising or immediately after an accident or medical emergency, whether there is at least one (certain) nucleic acid (e.g. cfDNA), or an increased amount of at least one (certain) nucleic acid (e.g. cfDNA) in his bloodstream.
  • the information received can be a decisive advantage for promptly arranging adequate treatment for a patient.
  • the nucleic acid to be detected for example DNA
  • the nucleic acid to be detected is lost (for example DNA and / or RNA can adsorb onto certain surfaces). and therefore can no longer be detected in the actual detection method.
  • the consequence is a low detection sensitivity or false negative results.
  • the risk of losing nucleic acids to be detected (e.g. DNA and / or RNA) on the way to detection is reduced with the method according to the invention, since whole blood is used directly. As a result, the detection sensitivity and detection accuracy are higher than in the known methods.
  • the method according to the invention is suitable for detecting genes in the whole blood with a low copy number genes or even with a copy number of only one (single copy number genes).
  • the process according to the invention can be characterized in that the reaction mixture forms a liquid mixture with the whole blood, which is essentially isotonic with blood cells.
  • the reaction mixture with the whole blood can form a liquid mixture which has an osmolarity which essentially corresponds to the osmolarity of blood cells, preferably an osmolarity in the range from 230 to 350 mosmol / kg, preferably 260 to 320 mosmol / kg, particularly preferably 270 up to 310 mosmol / kg, in particular 280 to 300 mosmol / kg.
  • the reaction mixture contains no surfactants in concentrations which are suitable for causing a lysis of blood cells, preferably no substances or mixtures of substances which are suitable for causing a lysis of blood cells.
  • concentrations which are suitable for causing a lysis of blood cells preferably no substances or mixtures of substances which are suitable for causing a lysis of blood cells.
  • This is understood in particular to mean that the reaction mixture contains no surfactants, or no substances or substance mixtures, in a concentration which is suitable for causing a lysis of blood cells.
  • This feature optionally relates not only to blood cells but also to nucleic acid-containing, lipid double-membrane-enclosed compartments which are contained in whole blood in the living being.
  • nucleic acid-containing, lipid double membrane-enclosed compartments is widely understood here, ie it encompasses all conceivable nucleic acids which are surrounded by a biological double membrane. These include, for example, mitochondria, exosomes, single-celled organisms and bacteria .
  • the reaction mixture used in the process can contain at least one of the following substances or at least one of the following substances can be added to the reaction mixture:
  • nucleotide triphosphates preferably dATP, dCTP, dGTP, dTTP, ATP, GTP; and or
  • a magnesium salt preferably magnesium acetate
  • reaction mixture can contain at least one of the following proteins or at least one of the following proteins can be added to the reaction mixture:
  • a strand-displacing polymerase preferably selected from the group consisting of Sau DNA polymerase, Bsu DNA polymerase, Klenow fragment, phi29 and combinations thereof; and or
  • a recombinase preferably RecA recombinase and / or T 4 UvsX; and or
  • a single strand binding protein preferably SSB and / or T 4 gp32; and or
  • exonuclease preferably exonuclease III and / or exonuclease IV.
  • the detection reagent used in the method is not suitable for passing through the cell membrane of blood cells that are contained in whole blood.
  • this feature can apply not only to blood cells, but generally to compartments containing lipid double membranes containing nucleic acid.
  • amplified nucleic acid eg DNA
  • the advantage of this embodiment is that the detection of amplified nucleic acid (eg DNA) can also be carried out without prior separation of cells containing DNA or the above-mentioned compartments, since there is no risk of binding the detection reagent to DNA within the cells or the above-mentioned compartments to obtain false positive results.
  • the method can therefore be carried out more easily and quickly (e.g. no step is required to allow the reaction mixture to flow from a reaction space via a partition to a separate detection space).
  • the detection reagent can be suitable for the detection of single-stranded and / or double-stranded DNA and can be used for this.
  • the detection reagent can be selected from the group consisting of probe with fluorophore, DNA-binding dye molecule, reagent for the detection of pyrophosphate and combinations thereof.
  • the fluorophore probe can contain or consist of an oligonucleotide which contains or consists of a quencher, a fluorophore and a DNA sequence located between the quencher and the fluorophore, the DNA sequence (by an internal modification) is suitable for being cleaved by an endonuclease or exonuclease and is preferably a DHF or AP DNA sequence.
  • the DNA-binding dye molecule can be selected from the group consisting of EVAGreen, SYBR-Green, Syto-Dyes, TOPO-Dyes and combinations thereof. Dye molecules which have an absorption and an emission spectrum which differ (preferably clearly) from the corresponding spectra of a whole blood sample are preferred for the particularly sensitive detection.
  • an absorption spectrum of less than 525 nm, one of between 545 nm and 570 nm or one of more than 590 nm is particularly advantageous since there are relative local absorption minima of the whole blood.
  • the dye should not (strongly) absorb at a wavelength of 525 nm to 545 and / or a wavelength of 570 to 590 nm.
  • the reagent for the detection of pyrophosphate can be a magnesium salt.
  • the detection of DNA takes place via a detection unit, the detection unit preferably being selected from the group consisting of an absorption measuring device, fluorescence measuring device, turbidimeter, camera, mobile phone (for example internal camera of the mobile phone, possibly in conjunction with evaluation software on the mobile phone), and combinations thereof.
  • the detection unit preferably being selected from the group consisting of an absorption measuring device, fluorescence measuring device, turbidimeter, camera, mobile phone (for example internal camera of the mobile phone, possibly in conjunction with evaluation software on the mobile phone), and combinations thereof.
  • the amount of amplified DNA can be quantified in the method via an evaluation unit, the evaluation unit preferably being communicatively connected to a detection unit (preferably a detection unit mentioned above).
  • At least one primer can have a length of 20 to 45 bp, particularly preferably 25 to 40 bp, in particular 30 to 35 bp.
  • At least one primer of the primer pair can be suitable for linking to a repetitive DNA sequence in the To bind DNA of the living being, preferably to a repetitive sequence selected from the group consisting of LINE sequence, SINE sequence and ALU sequence.
  • primers or pairs of primers that bind to repetitive sequences are suitable for non-specific amplification of all conceivable unknown DNAs that contain occurrences and repetitive DNA sequences in the whole blood of living beings. Since practically every DNA or DNA fragment of a certain length has repetitive DNA sequences, it is possible to use such primers or pairs of primers to amplify any conceivable DNA that is in whole blood. In other words, the sequence of the DNA to be amplified need not be known before the amplification reaction. In principle, the method can provide evidence of whether there is any free DNA in the blood of the living being.
  • the method actually detects free DNA in whole blood, this can of course be sequenced using standard methods. If the specific sequence of the free DNA (or the free DNAs) in the blood of a certain living being (eg a certain patient) is known, the method according to the invention can of course also be carried out with primer pairs which are specifically for the detection of the known DNA (see ) are suitable. The method according to the invention can thus also be used to monitor specific free DNAs in a patient's whole blood over a certain period of time (e.g. minutes, hours, days and / or months).
  • a primer of the primer pair may be suitable for attaching to a DNA sequence in the DNA of the living being, which is at the beginning, during or after an illness and / or at the beginning, during, or after excessive muscle strain in the living being in the bloodstream of the living being.
  • the living being can be a human or an animal.
  • the isothermal DNA amplification reaction used in the method can be carried out at a temperature in the range from 20 ° C. to 44 ° C., preferably 25 ° C. to 42 ° C., particularly preferably 30 ° C. to 41 ° C., in particular 35 ° C. to 40 ° C, be performed.
  • the temperature required for this can be generated or set via a temperature control unit.
  • the reaction can either take place at room temperature or the required reaction temperature can be generated via body heat (from a human or an animal).
  • body heat from a human or an animal. The latter is possible, for example, by bringing the reaction mixture of the device so close to a human or animal body that heat transfer from the body to the reaction mixture is possible.
  • the isothermal DNA amplification reaction can be a semi-quantitative isothermal DNA amplification reaction or a quantitative isothermal DNA amplification reaction.
  • the isothermal DNA amplification reaction can be an amplification reaction which is selected from the group consisting of recombinase polymerase amplification reaction, Siba HDA, NASBA and SDA amplification reaction, optionally it is selected from the group consisting of recombinase polymerase amplification reaction, Siba and SDA amplification reaction. It is preferably a recombinase polymerase amplification reaction.
  • the reaction mixture optionally contains a helicase for the amplification reaction.
  • a preferred temperature for the amplification is 37 ° C, i.e. the reaction mixture is preferably heated to a temperature of 37 ° C.
  • step d) of the method according to the invention in the case of (detected) amplified DNA, the presence of a disease and / or excessive muscle strain can be concluded.
  • the disease is particularly selected from the group consisting of inflammation, cancer, autoimmune disease, heart attack, stroke, sepsis, chromosomal aberration, gene copy number change, gene mutation, and combinations thereof.
  • the reaction mixture used can contain several pairs of primers, optionally at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 pairs of primers, each for Amplification of at least one nucleic acid in the whole blood (eg DNA) are suitable.
  • several such primer pairs can be added to the reaction mixture, the respective primer pairs preferably being suitable for amplifying a different nucleic acid (for example DNA), preferably a nucleic acid (for example DNA) which is associated with excessive muscle strain and / or an illness selected from the group consisting of inflammation, cancer, autoimmune disease, heart attack, stroke, sepsis, chromosomal aberration, change in the number of copies of genes, gene mutation, and combinations thereof, is present in the whole blood of a living being.
  • reaction mixture and the detection reagent are contained in a lateral flow strip.
  • a device and / or kit which is suitable for the // iv / fro detection of at least one nucleic acid (preferably DNA and / or RNA, particularly preferably DNA) which is outside of a whole being in whole blood the blood cells.
  • the device and / or the kit contains
  • a reaction mixture which, together with at least one pair of primers, is suitable for carrying out an isothermal amplification reaction at a temperature in the range of ⁇ 45 ° C.
  • At least one pair of primers which is suitable for the amplification of at least one nucleic acid present in whole blood (preferably DNA and / or RNA, particularly preferably DNA), the at least one pair of primers optionally being present in the reaction mixture;
  • reaction mixture is suitable for preventing the lysis of blood cells which are contained in a living being in whole blood.
  • the advantages mentioned above in connection with the method according to the invention apply to the device according to the invention and the invention. appropriate kit accordingly.
  • the device according to the invention can have the features mentioned above in connection with the method according to the invention or can be configured to carry them out.
  • the reaction mixture preferably contains an enzyme that can copy RNA into DNA (e.g. the enzyme reverse transcriptase).
  • the reaction mixture can contain proteins from the group of nucleic acid ligases (e.g. a T7 RNA polymerase).
  • nucleic acid ligases e.g. a T7 RNA polymerase
  • the reaction mixture preferably contains RNAse H, reverse transcriptase, SD polymerase, T7 RNA polymerase and at least one primer with a T7 promoter sequence.
  • the reaction mixture can also preferably contain the enzymes poly (A) polymerase, RNAse H, T7 RNA polymerase and at least one primer with a T7 promoter sequence.
  • the reaction mixture contained in the device and / or the kit may be suitable for forming a liquid mixture with whole blood which is essentially isotonic with blood cells.
  • the reaction mixture can be suitable for forming a liquid mixture with whole blood which has an osmolarity which essentially corresponds to the osmolarity of blood cells, preferably an osmolarity in the range from 230 to 350 mosmol / kg, preferably 260 to 320 mosmol / kg, be particularly preferably 270 to 310 mosmol / kg, in particular 280 to 300 mosmol / kg.
  • the device and / or the kit does not contain any surfactants which are suitable for causing a lysis of blood cells, preferably does not contain any substances or mixtures which are suitable for lysing To cause blood cells.
  • the reaction mixture has no surfactants, or no substances or substance mixtures, in one concentration contains, which is suitable for lysing blood cells.
  • This feature optionally relates not only to blood cells, but also to compartments which contain nucleic acid and contain lipid double membranes and which are contained in whole blood in the living being.
  • nucleic acid-containing, lipid double membrane-enclosed compartments is widely understood here, ie it encompasses all conceivable nucleic acids which are surrounded by a biological double membrane. These include, for example, mitochondria, exosomes, unicellular organisms and bacteria.
  • the reaction mixture can contain at least one of the following substances:
  • nucleotide triphosphates preferably dATP, dCTP, dGTP, dTTP, ATP, GTP; and or
  • a magnesium salt preferably magnesium acetate
  • the reaction mixture can also contain at least one of the following proteins:
  • a strand-displacing polymerase preferably selected from the group consisting of Sou DNA polymerase, ⁇ su DNA polymerase, Klenow fragment, phi29 and combinations thereof; and or
  • a recombinase preferably RecA recombinase and / or T 4 UvsX; and or
  • a single strand binding protein preferably SSB and / or T 4 gp32; and or
  • exonuclease preferably exonuclease III and / or exonuclease IV.
  • the detection reagent contained in the device and / or the kit is not suitable for passing through the cell membrane of blood cells which are contained in whole blood.
  • this feature can apply not only to blood cells, but generally to the lipid double membrane containing nucleic acid, lipid double membrane around closed compartments.
  • the advantage of this embodiment is that the detection of amplified DNA can also be carried out without prior separation of DNA-containing cells or the above-mentioned compartments can be carried out since there is no risk of obtaining false-positive results by binding the detection reagent to DNA within the cells or the above-mentioned compartments.
  • the device and / or the kit can therefore be kept simpler and in a smaller size (for example, no reaction space and separate detection space with a partition in between is necessary).
  • the detection reagent can be suitable for the detection of single-stranded and / or double-stranded DNA.
  • the detection reagent of the device and / or the kit can be selected from the group consisting of a probe with fluorophore, DNA-binding dye molecule, reagent for the detection of pyrophosphate and combinations thereof.
  • the fluorophore probe may contain or consist of an oligonucleotide which contains or consists of a quencher, a fluorophore and a DNA sequence located between the quencher and the fluorophore, the DNA sequence being suitable for being cleaved by an endonuclease or exonuclease and is preferably a DHF or AP DNA sequence.
  • the DNA-binding dye molecule can be selected from the group consisting of EVAGreen, SYBR-Green, Syto-Dyes, TOPO-Dyes and combinations here of.
  • Dye molecules which have an absorption and an emission spectrum which differ (preferably clearly) from the corresponding spectra of a whole blood sample are preferably used for the particularly sensitive detection.
  • an absorption spectrum of less than 525 nm, one between 545 nm and 570 nm or one above 590 nm is particularly advantageous, since there are relative local absorption minima of the whole blood in these areas.
  • the dye should not (strongly) absorb at a wavelength of 525 nm to 545 and / or a wavelength of 570 to 590 nm.
  • An emission spectrum between 580 nm and 610 nm, in particular 590 nm to 610 nm, is particularly advantageous for the emission.
  • the reagent for the detection of pyrophosphate can be a magnesium salt.
  • the device and / or the kit contains a detection unit for the detection of DNA, the detection unit preferably being selected from the group consisting of an absorption measuring device, fluorescence measuring device, turbidimeter, camera, mobile phone (for example internal camera of the mobile phone, possibly in connection with evaluation software on the mobile phone), and combinations thereof.
  • a detection unit for the detection of DNA the detection unit preferably being selected from the group consisting of an absorption measuring device, fluorescence measuring device, turbidimeter, camera, mobile phone (for example internal camera of the mobile phone, possibly in connection with evaluation software on the mobile phone), and combinations thereof.
  • the device and / or the kit can contain an evaluation unit for quantifying a quantity of amplified DNA, the evaluation unit preferably being communicatively connected to a detection unit.
  • At least one primer of the primer pair can have a length of 20 to 45 bp, particularly preferably 25 to 40 bp, in particular 30 to 35 bp.
  • a primer of the primer pair can be suitable for binding to a repetitive DNA sequence in the DNA of the living being, preferably to a repetitive sequence selected from the group consisting of LINE sequence, SINE sequence and ALU sequence.
  • At least one primer of the primer pair may be suitable for attaching to a DNA sequence in the DNA of the living being that is present at the beginning, during or after an illness and / or at the beginning, during or after an excessive Muscle stress of the living being is present in the bloodstream of the living being to bind.
  • the living being can be a human or an animal.
  • the device and / or the kit can contain a temperature control unit that is configured to temperature control the reaction mixture to a temperature in the range of ⁇ 45 ° C., preferably to a temperature in the range from 20 ° C. to 44 ° C., particularly preferably 25 ° C to 42 ° C, very particularly preferably 30 ° C to 41 ° C, in particular 35 ° C to 40 ° C.
  • the temperature control unit is preferably supplied with energy from a voltage source which has a voltage in the range from 1 to 12 V.
  • the device and / or the kit do not contain a temperature control unit.
  • the reaction can then either take place at room temperature or be generated by body heat (from a human or a animal). The latter is possible, for example, by bringing the reaction mixture of the device so close to a body of a human or animal that heat transfer from the body to the reaction mixture is possible.
  • the isothermal DNA amplification reaction can be a semi-quantitative isothermal DNA amplification reaction or a quantitative isothermal DNA amplification reaction.
  • the isothermal DNA amplification reaction can be an amplification reaction which is selected from the group consisting of recombinase polymerase amplification reaction, Siba, HDA, NASBA and SDA amplification reaction, optionally it is selected from the group consisting of recombinase polymerase amplification reaction , Siba and SDA amplification reaction. It is preferably a recombinase polymerase amplification reaction.
  • the reaction mixture optionally contains a helicase for the amplification reaction.
  • a preferred temperature for the amplification is 37 ° C, i.e. the reaction mixture is preferably heated to a temperature of 37 ° C.
  • the device and / or kit can be configured to indicate the presence of a disease and / or excessive muscle strain in the event of a detection of DNA by the detection reagent, optionally via a limitation of the device that is transparent to visible light.
  • the disease is selected from the group consisting of inflammation, cancer, autoimmune disease, heart attack, stroke, sepsis, chromosomal aberration, change in the number of copies of genes, gene mutation, and combinations thereof.
  • the device and / or the kit contains several pairs of primers, optionally at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 pairs of primers, each pair of primers for the amplification of at least one nucleic acid in the whole blood (eg DNA) is suitable and the respective primer pairs are preferably suitable for amplifying a different nucleic acid (eg DNA), preferably a nucleic acid (eg DNA) which is selected from in the event of excessive muscle strain and / or an illness the group consisting of inflammation, cancer, autoimmune disease, heart attack, stroke, sepsis, chromosomal aberration, change in the number of copies of genes, gene mutation, and combinations thereof, is present in the whole blood of a living being.
  • a nucleic acid eg DNA
  • the device is preferably a lateral flow strip.
  • the kit is preferably characterized in that it has a lateral flow strip which contains the reaction mixture; or contains the reaction mixture and the detection reagent.
  • the device according to the invention and / or the kit according to the invention for the direct, semi-quantitative or quantitative detection of at least one nucleic acid (eg DNA and / or RNA) in whole blood, preferably for the detection of at least one nucleic acid (eg DNA and / or RNA), which is present in a living being's disease in the whole blood of the living being outside of the blood cells in the event of a disease of a living being and / or an excessive muscle strain on the living being.
  • at least one nucleic acid eg DNA and / or RNA
  • FIG. 1 shows the result of a quantitative isothermal amplification reaction of a certain cfDNA via a probe using direct whole blood (see example 2).
  • the amplification plot shows that the detection with the probe also works when direct (not purified) whole blood is used. It also becomes clear that an increase in cfDNA can be demonstrated in the subject from whom the whole blood originates from training.
  • FIG. 2 shows the result of a quantitative isothermal amplification reaction of a specific cfDNA via a DNA-intercalating fluorescent dye using whole blood directly (see Example 4).
  • the amplification plot shows that the detection with the fluorescent dye also works when direct (non-purified) whole blood is used. It also becomes clear that an increase in cfDNA can be demonstrated in the subject from whom the whole blood originates from training.
  • FIG. 3 shows the result of a quantitative isothermal amplification reaction of a specific cfDNA via a probe using human gDNA which was contaminated with different amounts of hemolysate (see Example 3).
  • the amplification plot shows that hemolysate has a significant inhibitory influence on the amplification reaction, which disappears only after a strong dilution of 1: 10000 (v: v) with water.
  • Example 1 Detection of a cell-free DNA by probe using direct whole blood
  • An isothermal amplification reaction was carried out at a temperature of 40 ° C. to amplify at least one specific cell-free DNA using a sample of whole blood that contains cell-free DNA (so-called cfDNA).
  • the amplified DNA was detected using a probe.
  • FIG. 1 The result is shown in FIG. 1. It can be clearly seen that the detection method according to the invention works with a probe as a detection reagent and a direct use of (not purified) whole blood.
  • concentration of cfDNA in the whole blood of the test subject before training is lower than after training (see signal at 1).
  • the control plasma sample from a mouse shows no amplification of the target cfDNA (see signal at 3), which demonstrates the specificity of the amplification reaction presented here for human cfDNA.
  • An isothermal amplification reaction was carried out at a temperature of 40 ° C. to amplify at least one specific cell-free DNA using a sample of whole blood that contains cell-free DNA (so-called cfDNA).
  • the amp lifi graced DNA was detected via a fluorescent dye ( "EvaGreen ® Dye” Biotium Inc., Fremont, USA). The following protocol was used:
  • the detection method according to the invention works with an intercalating fluorescent dye as a detection reagent and a direct use of (not purified) whole blood.
  • concentration of cfDNA in whole blood the test subject before training is less than after training (see signal at 1).
  • the control plasma sample from a mouse shows no amplification of the target cfDNA (see signal at 3), which demonstrates a specificity of the amplification reaction shown here for human cfDNA.
  • a hemolysate is first prepared by treating mouse blood through several defrosting and freezing cycles, which leads to the lysis of the blood cells.
  • Primer Forward primer ("301" primer) and reverse primer ("302" -
  • the result is shown in FIG. 3 and shown in Table 1.
  • the sample with 1 ml of human gDNA (50 ng / ml) and 1 ml of water can be seen at 1.
  • the samples with 1 ml of human gDNA (50 ng / ml) and a different amount of hemolysate can be seen at 2, 3, 4, 5 and 6.

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Abstract

La présente invention concerne un procédé in vitro, un dispositif et un kit pour détecter au moins un acide nucléique (de préférence l'ADN et/ou l'ARN, de manière particulièrement préférée l'ADN) présent chez un être vivant dans le sang total en dehors des cellules sanguines. Le procédé de l'invention est avantageux en ce que sa mise en œuvre est moins longue et nécessite moins de dépenses d'équipement que le procédé de l'état de la technique connu et en ce que le risque de contamination et de perte de l'acide nucléique acellulaire à amplifier (par exemple, de l'ADN acellulaire) est minimisé. Le procédé est donc économique et présente une meilleure précision de détection que le procédé de détection connu des acides nucléiques acellulaires (par exemple, l'ADN acellulaire). La sensibilité de détection est en outre améliorée surtout par rapport aux procédés de détection de l'état de la technique qui sont basés sur une dilution du sang total. L'invention concerne en outre une utilisation du dispositif et du kit fournis.
EP19831685.3A 2018-12-19 2019-12-18 Procédé in vitro pour mettre en évidence au moins un acide nucléique présent chez un être vivant dans le sang total en dehors des cellules sanguines et dispositif et kit correspondants Pending EP3899026A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
DE102018222357.2A DE102018222357A1 (de) 2018-12-19 2018-12-19 In-vitro-Verfahren zum Nachweis von mindestens einer Nukleinsäure, die sich bei einem Lebewesen im Vollblut außerhalb der Blutzellen befindet und Vorrichtung und Kit hierzu
PCT/EP2019/086122 WO2020127604A1 (fr) 2018-12-19 2019-12-18 Procédé in vitro pour mettre en évidence au moins un acide nucléique présent chez un être vivant dans le sang total en dehors des cellules sanguines et dispositif et kit correspondants

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EP3899026A1 true EP3899026A1 (fr) 2021-10-27

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US (1) US20220081709A1 (fr)
EP (1) EP3899026A1 (fr)
CN (1) CN113728111A (fr)
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WO (1) WO2020127604A1 (fr)

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Publication number Priority date Publication date Assignee Title
EP2336361B1 (fr) * 2004-06-01 2019-01-23 Alere San Diego, Inc. Kit approprié pour amplification par recombinase et polymérase
US20090005268A1 (en) * 2005-07-18 2009-01-01 Epigenomics Ag Compositions and Methods for Cancer Diagnostics Comprising Pan-Cancer Markers
WO2010141940A1 (fr) * 2009-06-05 2010-12-09 Alere San Diego, Inc. Réactifs et kits d'amplification par recombinase polymérase
EP3058100A4 (fr) * 2013-10-18 2017-04-19 California Institute of Technology Identification et détection d'acide nucléique améliorées
US20150353989A1 (en) * 2014-06-09 2015-12-10 Illumina Cambridge Limited Sample preparation for nucleic acid amplification
WO2016168844A1 (fr) * 2015-04-17 2016-10-20 The Translational Genomics Research Institute Évaluation de qualité d'adn acellulaire en circulation au moyen d'une pcr numérique à gouttelettes multiplexée
US11118206B2 (en) * 2016-01-13 2021-09-14 The Trustees Of The University Of Pennsylvania Multiple stage isothermal enzymatic amplification
RU2630648C2 (ru) * 2016-02-05 2017-09-11 Общество С Ограниченной Ответственностью "Биомаркер-Ру" Способ диагностики заболевания, сопровождающегося повышенной гибелью клеток, и набор для его осуществления
US20210254186A1 (en) * 2016-08-08 2021-08-19 The Secretary Of State For Health Flavivirus diagnostic array
CN110016435B (zh) * 2019-05-16 2020-11-03 西安交通大学 一种用于游离核酸提取的离心微流控芯片及其在提取游离核酸的方法

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US20220081709A1 (en) 2022-03-17
DE102018222357A1 (de) 2020-06-25
WO2020127604A1 (fr) 2020-06-25

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