U.S. patent application number 16/138338 was filed with the patent office on 2020-09-10 for methods of detecting mirna.
The applicant listed for this patent is Gensignia Life Sciences, Inc.. Invention is credited to Hovsep MELKONYAN, Vladimir SCHEINKER, Samuil R. UMANSKY.
Application Number | 20200283851 16/138338 |
Document ID | / |
Family ID | 1000004845334 |
Filed Date | 2020-09-10 |
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United States Patent
Application |
20200283851 |
Kind Code |
A1 |
UMANSKY; Samuil R. ; et
al. |
September 10, 2020 |
METHODS OF DETECTING miRNA
Abstract
Described are non-invasive methods of detecting in vivo cell
death by measuring levels of ubiquitous and tissue specific miRNA.
The method can be applied for detection of pathologies caused or
accompanied by cell death, as well as for diagnosis of infectious
disease, cytotoxic effects induced by different chemical or
physical factors, and the presence of specific fetal
abnormalities.
Inventors: |
UMANSKY; Samuil R.;
(Princeton, NJ) ; MELKONYAN; Hovsep; (Princeton,
NJ) ; SCHEINKER; Vladimir; (Congers, NY) |
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Applicant: |
Name |
City |
State |
Country |
Type |
Gensignia Life Sciences, Inc. |
San Diego |
CA |
US |
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|
Family ID: |
1000004845334 |
Appl. No.: |
16/138338 |
Filed: |
September 21, 2018 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15400157 |
Jan 6, 2017 |
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16138338 |
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13942706 |
Jul 16, 2013 |
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15400157 |
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12229378 |
Aug 22, 2008 |
8486626 |
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13942706 |
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60965871 |
Aug 22, 2007 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 2600/178 20130101;
C12Q 2600/118 20130101; C12Q 2600/158 20130101; C12Q 1/705
20130101; C12Q 1/6883 20130101 |
International
Class: |
C12Q 1/6883 20060101
C12Q001/6883; C12Q 1/70 20060101 C12Q001/70 |
Claims
1. A method of detecting at least one cell-free miRNA released from
at least one cell in a subject, the method comprising: a)
separating a soluble fraction of a sample of urine or blood
obtained from a subject; and b) detecting and quantitating at least
one cell-free miRNA in the soluble fraction with at least one
oligonucleotide primer or probe that is substantially complementary
to a part of said at least one cell-free miRNA, wherein the at
least one cell-free miRNA is indicative of in vivo cell death
associated with a disease or disorder.
2. The method of claim 1, wherein said disorder is a brain
stroke.
3. The method of claim 1, wherein said disorder is Alzheimer's
disease.
4. The method of claim 1, wherein said disorder is Parkinson's
disease.
5. The method of claim 1, wherein said at least one cell-free miRNA
is associated with fetal pathology.
6. The method of claim 5, wherein said fetal pathology is Down
syndrome.
7. The method of claim 1, wherein said disorder is a pathogen
infection, such as a virus infection.
8. The method of claim 1, wherein said detecting and quantitating
diagnoses said disease or disorder.
9. The method of claim 1, wherein said detecting and quantitating
is repeated over time to monitor the progression or regression of
said disease or disorder.
10. A method of detecting at least one cell-free miRNA released
from at least one cell in a subject, the method comprising: a)
separating a soluble fraction of a sample of urine or blood
obtained from a subject; and b) detecting and quantitating at least
one cell-free miRNA in the soluble fraction with at least one
oligonucleotide primer or probe that is substantially complementary
to a part of said at least one cell-free miRNA, wherein the at
least one cell-free miRNA is indicative of in vivo cell death
associated with acute pathology, chronic pathology, or the
cytotoxic effect of physical or chemical agents.
11. The method of claim 10, wherein the acute pathology is selected
from acute myocardial infarction associated with death of
cardiomyocytes, hepatitis or liver cirrhosis associated with
hepatocyte death caused by a viral or other infection or by action
of toxic agents, acute pancreatitis associated with death of
different pancreatic cells, rejection of a transplanted organ
associated with excessive cell death in the transplanted organ,
traumatic damage of various organs, acute infections, or
tuberculosis associated with cell death in lungs and/or other
infected organs.
12. The method of claim 10, wherein the chronic pathology is
selected from frontotemporal dementia, chronic heart failure
associated with the death of cardiomyocytes, emphysema associated
with death of lung cells, diabetes type 1 associated with the death
of pancreatic beta cells, glomerulonephritis associated with the
death of kidney cells, precancerous conditions associated with the
apoptotic death of actively proliferating precancerous cells,
cancers associated with massive necrotic cell death due to
insufficient blood supply, and cell death in chronically infected
organs or tissues.
13. The method of claim 10, wherein the cytotoxic effect of
physical or chemical agents is selected from radiation associated
with doses that kill bone marrow cells, doses that lead to the
death of epithelial cells of gastrointestinal system, and doses
that kill brain neurons, and chemical cytotoxicity associated with
cell death in different organ and tissues induced by natural or
synthetic toxic compounds.
14. A method of determining the prognosis the outcome of a disease
or disorder, the method comprising: a) separating a soluble
fraction of a sample of urine or blood obtained from a subject; and
b) detecting and quantitating at least one cell-free miRNA in the
soluble fraction with at least one oligonucleotide primer or probe
that is substantially complementary to a part of said at least one
cell-free miRNA, wherein the at least one cell-free miRNA is
indicative of the outcome of a disease or disorder.
15. The method of claim 14, wherein a change in the level of the at
least one cell-free miRNA over time is indicative of the
progression or regression of a disease or disorder, or is
indicative of the success of therapeutic or surgical intervention,
or monitors progress of a treatment in the subject.
16. The method of claim 1, wherein said sample is urine.
17. The method of claim 1, wherein said soluble fraction is
serum.
18. The method of claim 1, wherein said soluble fraction is plasma.
Description
RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 15/400,157, filed on Jan. 6, 2017, which is a
continuation of U.S. patent application Ser. No. 13/942,706, filed
on Jul. 16, 2013 which is a continuation of U.S. patent application
Ser. No. 12/293,378, filed Aug. 22, 2008, now U.S. Pat. No.
8,486,626, which claims the benefit of, and priority to, U.S.
Provisional Application No. 60/965,871, filed on Aug. 22, 2007. The
contents of each of these applications is incorporated herein by
reference in their entireties as if fully set forth.
INCORPORATION BY REFERENCE OF SEQUENCE LISTING
[0002] The contents of the text file name "GENS-006_C03US_ST25.txt"
which was created on Sep. 21, 2018 and is 5 KB in size, are hereby
incorporated by reference in their entirety.
FIELD OF THE INVENTION
[0003] The invention provides non-invasive methods for isolation
and detection of cell-free small RNA, in particular microRNA
(miRNA) sequences in bodily fluid. More specifically, the present
invention encompasses methods of detecting in vivo cell death by
analyzing urine and other body fluids for miRNA levels for clinical
diagnosis and treatment monitoring.
BACKGROUND OF THE INVENTION
[0004] Cell death is a normal component of development and
functioning of multicellular organisms. Being a natural process,
cell death is involved in the pathology of numerous diseases caused
by internal factors. Cell death also accompanies diseases caused by
external physical, chemical, of biological agents.
[0005] There exist two major types of cell death, necrosis and
apoptosis, marked by different morphological and molecular
characteristics (Kerr et al., Br. J. Cancer. 26, 239-257 (1972);
Umansky, Theor. Biol. 97, 591-602 (1982); Umansky et al., Adv
Pharmacol. 41, 383-407 (1997); Ameisen Cell Death Differ. 11, 4-10
(2004); Lockshin et al. Int J Biochem Cell Biol. 36, 2405-19
(2004); G. Kroemer, et al., Cell Death and Differentiation 12,
1463-1467 203224542 vl (2005)). Necrosis is considered to be
catastrophic metabolic failure resulting directly from severe
molecular and/or structural damage and leads to inflammation and
secondary damage to surrounding cells. Apoptosis is a much more
prevalent biological phenomenon than necrosis and can be induced by
specific signals such as hormones, cytokines, by absence of
specific signal such as growth or adhesion factors, or by molecular
damage that does not cause catastrophic loss of integrity.
Apoptosis is a result of an active cellular response involving
initiation of an orderly and specific cascade of molecular events.
Apoptosis leads to the appearance of distinctive chromatin
condensation and margination, nuclear fragmentation, cell
shrinkage, membrane blebbing and enzymatic internucleosomal
fragmentation of nuclear DNA (Umansky et al., Biochim Biophys Acta.
655, 9-17 (1981); Arends et al., Am J Pathol. 136, 593-608(1990)).
Other more rare forms of cell death, characterized by specific
morphology, for example, so called autophagic cell death have also
been described (Bredesen et al., Stroke. 38(2 Suppl):652-660
(2007).
[0006] Independent of a specific mechanism and type of cell death,
methods to detect dying cell types are important for diagnosis of
various diseases, critical for disease and treatment monitoring,
and helpful for differential diagnosis. Besides, the methods
capable of detection of specific cell death in vivo are useful for
developing drugs aiming at prevention or induction of cell death as
well as for analysis of the cytotoxicity of the newly developed
drugs.
[0007] There are some clinical tests for diagnosis of
disease-related excessive cell death based on detection of tissue
specific markers, such as for example antigens, enzymes and other
proteins in blood or in other bodily fluids. Measurement of the
activity of liver-specific enzymes in blood, for example, is a
widely used method for evaluation of hepatocyte death (Amacher, et
al., Regul Toxicol Pharmacol. April; 27(2):119-130 (1988);
Salaspuro, et al., Enzyme. 37:87-107 (1987); Herlong, Hosp. Pract.
(Off Ed). 29(11):32-38 (1994)). Evaluation of the level of
cardiomyocyte specific antigens has also been used for diagnosis of
the myocardial infarction (Mair et al., Clin Chem Lab Med.
37:1077-1084 (1999); Nunes et al., Rev Port Cardiol. 20:785-788
(2001)). However, the number of such techniques is limited to
diseases in which a marker and a method of detection are known in
order for the analysis to provide meaningful, tissue-specific
results (Oh S et al., Curr Gastroenterol Rep. 3:12-18 (2001);
Rochling et al., Clin Cornerstone. 3(6):1-12 (2001)). Other methods
require invasive biopsy of specific tissues suspected of having a
diseased condition to get a specimen for analysis. However, biopsy
of some organs and tissues, for example brain is highly invasive
and often difficult to perform.
[0008] It is well known that apoptosis, or programmed cell death,
which is a major form of cell death in the mamalian organism, is
accompanied by internucleosomal fragmentation of nuclear DNA. Many
laboratories have demonstrated that a portion of this DNA appears
in blood (Lo Y. M. Ann N Y Acad Sci. 945:1-7 (2001); Lichtenstein
et al., Ann N Y Acad Sci. 945:239-249 (2001); Taback et al., Curr
Opin Mol Ther. 6:273-278 (2004); Bischoff et al., Hum Reprod
Update. 8:493-500, (2002)). It has also been shown that this
fragmented DNA, called transrenal DNA (Tr-DNA) crosses the kidney
barrier and can be detected in the urine (Botezatu et al., Clin
Chem. 46:1078-1084, (2000); Su et al., J Mol Diagn. 6:101-107
(2004); Su et al., Ann N Y Acad Sci. 1022:81-89(2004).
[0009] Although both cell-free plasma DNA and Tr-DNA may be used as
diagnostic tools, they provide a rather limited approach when
evaluating tissue specific events, such as cell death. Thus
analytical methods that are non-invasive, and provide a broader
range of indications of specific pathology, due to their ability to
detect levels of dying cells in particular tissues and organs,
would be useful for diagnosing and monitoring the state of various
diseases or pathological conditions in patients. In addition,
tissue specific analytical methods that provide the means for
monitoring the response of a patient to a disease therapy would be
useful to determine the therapy effectiveness, and in the case of
drug treatment, the optimum dosage required for drug
administration.
[0010] To address these problems, the instant invention is focused
on the use of micro RNA (miRNA) as a diagnostic tool to monitor in
vivo cell death in bodily fluids, such as for example serum and
urine. Unlike cell-free plasma DNA and Tr-DNA, many miRNAs exhibit
cell, tissue and organ specific expression profiles (Liang et al.,
Genomics, 8:166 (2007); Lukiw et al, Neuroreport. 18:297-300
(2007); Lagos-Quintana et al., Curr Biol. 12:735-739 (2002); Chen
et al., Nat Genet. 38:228-233 (2006); Beuvink et al., J. Nucleic
Acids Res. 35:e52 (2007)). Furthermore, correlation of miRNA cell
and tissue specific profiles with different pathologies and tumor
types have been demonstrated (Visone R., et al. Oncogene.
26:7590-7595 (2007); Nelson et al., Neuropathol Exp Neurol.
66:461-468 (2007); Negrini et al., J Cell Sci. 120:18331840 (2007);
Chang et al., Annu Rev Genomics Hum Genet. 8:215-239 (2007); Jay et
al., Cell Biol. 26:293-300 (2007)).
[0011] Thus, the instant invention provides methods for measuring
in vivo cell death by detection of tissue-specific miRNAs,
characteristic of a specific pathology, in body fluids, such as for
example serum and urine. The instant methods based on detection of
miRNAs in bodily fluids are used for further development of
diagnostic or monitoring tests.
SUMMARY OF THE INVENTION
[0012] The instant invention relates to a novel method for
detecting and measuring in vivo cell-death by analyzing levels of
specific miRNA sequences in cell-free nucleic acids obtained from
bodily fluids, said miRNA originating from cells dying throughout
the body, and using the obtained analytical result to determine
state of a disease or abnormal medical condition in a patient.
[0013] The methods of the instant invention are based on adsorption
of cell-free nucleic acids on and elution from anion-exchangers,
which makes it possible to concentrate and isolate nucleic acid
fragments larger then 10 nucleotides. Specifically, the instant
invention demonstrates: (i) the presence of miRNA in body fluids;
(ii) detection in urine of miRNA that originated from organs
located outside of urinary system, which means that they have
crossed the kidney barrier, such as for example, transrenal miRNA
(Tr-miRNA); iii) detection of miRNA in serum (iv) pathology
associated with cell death in a particular cell, tissue and/or
organ is accompanied by changes in levels of miRNA specific for the
said organ.
[0014] The present invention provides a method of detecting and
quantitating cell, tissue and/or organ-specific cell-free miRNAs in
body fluid for evaluation of in vivo cell death in various tissue
and organs, wherein in vivo cell death is associated with a
disorder of a particular tissue and/or organ comprising obtaining a
body fluid sample from a subject; and analyzing said body fluid
sample for one or more specific sequences of miRNA, wherein said
analyzing comprises the step of detecting said miRNA with a primer
and/or probe that is substantially complementary to a part of said
specific miRNA sequences. In some embodiments of the present
invention, excessive or insufficient in vivo cell death is
associated with a disorder of particular tissue.
[0015] In one embodiment of the present invention, the body fluid
is urine. In another embodiment, the present method of analysis of
a urine sample includes a technique selected from the group
consisting of hybridization, cycling probe reaction, polymerase
chain reaction, nested polymerase chain reaction, PCR to analyze
single strand conformation polymorphisms and ligase chain reaction.
In yet another embodiment, nucleic acid degradation in said urine
sample is reduced.
[0016] The method of the present invention includes reducing
nucleic acid degradation comprising inhibiting nuclease activity by
addition of RNAse inhibitor(s), heat inactivation, or by treating
said urine sample with a compound selected from the group
consisting of: guanidine-HCI, guanidine isothiocyanate,
N-lauroylsarcosine, and sodium dodecylsulphate. In one embodiment
of the present invention, urine sample has been held in the bladder
less than 12 hours.
[0017] In one embodiment of the present invention, the body fluid
is serum. The method of the present invention includes analysis of
a serum sample including a technique selected from the group
consisting of hybridization, cycling probe reaction, polymerase
chain reaction, nested polymerase chain reaction, PCR to analyze
single strand conformation polymorphisms and ligase chain
reaction.
[0018] In yet another embodiment, the method of the instant
invention involves detecting cell-free miRNAs, as a specific marker
for the specific disorder associated with excessive or insufficient
cell death in a tissue or organ. Optionally, said disorder is a
pathogen infection. Preferably, said pathogen is a virus. More
preferably, said virus is an Epstein-Barr virus. Optionally, said
disorder is a brain stroke, Alzheimer's disease, Parkinson's
disease, associated with pregnancy and/or fetus or Down
syndrome.
[0019] The present invention provides a method of detecting in
urine cell-free miRNAs, originating in different organs and
tissues, including areas other than urinary system, in a subject as
a result of disorder associated with excessive or insufficient cell
death in a tissue or organ, comprising obtaining a urine sample
from a subject; and analyzing said urine sample for one or more
specific sequences of miRNA wherein said analyzing comprises the
step of detecting said miRNA with a primer and/or probe that is
substantially complementary to a part of said specific miRNA
sequences.
[0020] The method of the present invention provides a method of
disease and/or treatment monitoring in a subject by quantitative
analysis of specific cell-free miRNAs in a body fluid, comprising
periodically obtaining a body fluid sample from a subject; and
analyzing said sample for one or more specific sequences of miRNA
that are specific/over-expressed in cells, tissue or organ of
interest, wherein said analyzing comprises the step of detecting
said miRNA with primers and/or probe that is substantially
complementary to a part of said specific miRNA sequences. In one
embodiment, the body fluid is urine. In another embodiment, the
body fluid is serum.
BRIEF DESCRIPTION OF THE DRAWINGS
[0021] The foregoing and other objects, features, and advantages of
the invention will be apparent from the more particular description
of embodiments of the invention, as illustrated in the accompanying
drawings. The drawings are not necessary to scale, emphasis instead
being placed upon illustrating the principles of the invention.
[0022] FIG. 1 is a photograph of a polyacrylamide gel
electrophoresis of nucleic acids extracted from filtered urine
using Q-Sepharose.TM..
[0023] FIG. 2 is a photograph of a polyacrylamide gel analysis of
EBV derived BART1 miRNA specific RT-PCR product.
[0024] FIG. 3A to 3G are dot plot representations of the normalized
concentrations of miRNA in urine samples of patients at 12 and 24
hour time points after brain stroke.
[0025] FIGS. 4A and 4B are diagrams representing correlation
between changes in miRNAs 129 and 219 concentrations and brain
stroke outcome. The patients labeled as .smallcircle. and
.quadrature. improved their clinical status a month after stroke,
and the clinical status of the patient labeled x has deteriorated a
month after a stroke.
[0026] FIG. 5A to 5E are dot plot representations of the normalized
concentrations of miRNA in unfiltered urine samples of patients
with Alzheimer's disease and age matched controls.
[0027] FIG. 6A to 6C are dot plot representations of the normalized
concentrations of miRNA in filtered urine samples of patients with
Alzheimer's disease and age matched controls.
[0028] FIG. 7A to 7C are dot plot representations of the normalized
concentrations of miRNA in serum samples of patients with
Alzheimer's disease and age matched controls.
[0029] FIG. 8A to 8D are dot plot representations of the normalized
concentrations of miRNA in urine samples of patients with
Parkinson's disease and age matched controls.
[0030] FIG. 9 is a dot plot representation of the normalized
concentration of miRNA-9 in urine samples of women pregnant with
Down syndrome and normal fetuses.
DETAILED DESCRIPTION OF THE INVENTION
[0031] The technology of this invention is based on the discovery
that small RNAs, in particular specific micro RNAs (miRNAs),
including transrenal miRNA (Tr-miRNA), are presented in bodily
fluids and their concentrations reflect cell death associated with
organ damage or other pathology. The presence of these nucleic acid
sequences at levels lower or higher than that of a control group is
therefore an indication that an abnormality or pathological
condition is likely present in the patient from whom the sample was
obtained.
[0032] The methods of the present invention offer improvements over
previous methods of diagnosis, detection and monitoring due to
their inherently non-invasive nature.
[0033] To facilitate the understanding of the invention, a number
of terms are defined below:
[0034] The term "primer" refers to an oligonucleotide which is
capable of acting as a point of initiation of synthesis when placed
under conditions in which primer extension is initiated. An
oligonucleotide "primer" can occur naturally, as in a purified
restriction digest or be produced synthetically.
[0035] A primer is selected to be "substantially" complementary to
a strand of specific sequence of the template. A primer must be
sufficiently complementary to hybridize with a template strand for
primer elongation to occur. A primer sequence need not reflect the
exact sequence of the template. For example, a non-complementary
nucleotide fragment may be attached to the 5' end of the primer,
with the remainder of the primer sequence being substantially
complementary to the strand. Non-complementary bases or longer
sequences can be interspersed into the primer, provided that the
primer sequence has sufficient complementarity with the sequence of
the template to hybridize and thereby form a template primer
complex for synthesis of the extension product of the primer.
[0036] A "target" nucleic acid is a miRNA sequence to be evaluated
by hybridization, amplification or any other means of analyzing a
nucleic acid sequence, including a combination of analysis
methods.
[0037] "Hybridization" methods involve the annealing of a
complementary sequence to the target nucleic acid (the sequence to
be analyzed). The ability of two polymers of nucleic acid
containing complementary sequences to find each other and anneal
through base pairing interaction is a well-recognized phenomenon.
The initial observations of the "hybridization" process by Marmur
and Lane, Proc. Natl. Acad. Sci. USA 46:453 (1960) and Doty et al.,
Proc. Natl. Acad. Sci. USA 46:461 (1960) have been followed by the
refinement of this process into an essential tool of modern
biology. Hybridization encompasses, but not be limited to, slot,
dot and blot hybridization techniques.
[0038] It is important for some diagnostic applications to
determine whether the hybridization represents complete or partial
complementarity. For example, where it is desired to detect simply
the presence or absence of pathogen miRNA, it is only important
that the hybridization method ensures hybridization when the
relevant sequence is present; conditions can be selected where both
partially complementary probes and completely complementary probes
will hybridize. Other diagnostic applications, however, may require
that the hybridization method distinguish between partial and
complete complementarity. It may be of interest to detect genetic
polymorphisms.
[0039] The term "probe" as used herein refers to an oligonucleotide
(i.e., a sequence of nucleotides), whether occurring naturally as
in a purified restriction digest or produced synthetically, which
forms a duplex structure or other complex with a sequence of
another nucleic acid, due to complementarity or other means of
reproducible attractive interaction, of at least one sequence in
the probe with a sequence in the other nucleic acid. Probes are
useful in the detection, identification and isolation of particular
gene sequences. It is contemplated that any probe used in the
present invention will be labeled with any "reporter molecule," so
that it is detectable in any detection system, including, but not
limited to, enzyme (e.g., ELISA, as well as enzyme-based
histochemical assays), fluorescent, radioactive, and luminescent
systems. It is further contemplated that the oligonucleotide of
interest (i.e., to be detected) will be labeled with a reporter
molecule. It is also contemplated that both the probe and
oligonucleotide of interest will be labeled. It is not intended
that the present invention be limited to any particular detection
system or label.
[0040] As used herein, the term "miRNA" is a subclass of small
non-coding single stranded RNA, approximately 18-23 nucleotides in
length which plays an important role in regulation of metabolic
processes, particularly due to their involvement in regulation of
stability and translation of mRNA encoding specific proteins. miRNA
also participate in other important processes, like heterochromatin
formation and genome rearrangement.
[0041] The terms "excessive" and "insufficient" in vivo cell death
describe the situation when the number of cells dying in a
particular organ or tissue is respectively higher or lower than in
age and gender matched controls.
[0042] As used herein, the terms "purified", "decontaminated" and
"sterilized" refer to the removal of contaminant(s) from a
sample.
[0043] As used herein, the terms "substantially purified" and
"substantially isolated" refer to nucleic acid sequences that are
removed from their natural environment, isolated or separated, and
are preferably 60% free, more preferably 75% free, and most
preferably 90% free from other components with which they are
naturally associated. An "isolated polynucleotide" is therefore a
substantially purified polynucleotide. It is contemplated that to
practice the methods of the present invention polynucleotides can
be, but need not be substantially purified. A variety of methods
for the detection of nucleic acid sequences in unpurified form are
known in the art.
[0044] As used herein, the terms "PCR product" and "amplification
product" refer to the resultant mixture of compounds after two or
more cycles of the PCR steps of denaturation, annealing and
extension are complete. These terms encompass the case where there
has been amplification of one or more segments of one or more
target sequences.
[0045] The term "urinary tract" as used herein refers to the organs
and ducts which participate in the secretion and elimination of
urine from the body.
[0046] "Patient" or "subject" as the terms are used herein, refer
to the recipient of the treatment. Mammalian and non-mammalian
patients are included. In a specific embodiment, the patient is a
mammal, such as a human, canine, murine, feline, bovine, ovine,
swine, or caprine. In a particular embodiment, the patient is a
human.
[0047] In one embodiment of the present invention, the detected
miRNAs originate from and are specifically expressed in a specific
cell type, tissue, or organ in the body, wherein alterations in the
level of said miRNAs are indicative of acute pathology of said
tissue, such as for example acute myocardial infarction associated
with death of cardiomyocytes; brain stroke associated with death of
neurons and glial cells; hepatitis or liver cirrhosis associated
with hepatocyte death caused by a viral or other infection or by
action of toxic agents; acute pancreatitis associated with death of
different pancreatic cells; rejection of a transplanted organ
associated with excessive cell death in the transplanted organ;
traumatic damage of various organs; numerous acute infections, for
example tuberculosis associated with cell death in lungs and/or
other infected organs.
[0048] In another embodiment of the present invention, the detected
miRNAs originate from and are specifically expressed in a specific
cell type, tissue, or organ in the body, wherein alterations in the
level of said miRNAs are indicative of chronic pathology of said
tissue, such as for example Alzheimer's disease, Parkinson disease,
frontotemporal dementia and other diseases of the central nervous
system that are caused or accompanied by neuronal death; chronic
heart failure associated with the death of cardiomyocytes,
emphysema associated with death of lung cells; diabetes type 1
associated with the death of pancreatic beta cells,
glomerulonephritis associated with the death of kidney cells,
precancerous conditions associated with the apoptotic death of
actively proliferating precancerous cells, cancers associated with
massive necrotic cell death due to insufficient blood supply, and
cell death in chronically infected organs or tissues.
[0049] In yet another embodiment of the present invention, the
detected miRNAs originate from and are specifically expressed in a
specific cell type, tissue, or organ in the body, and alterations
in the level of said miRNAs are indicative of cytotoxic effects of
physical and chemical agents, such as for example radiation
associated with relatively low doses that kill bone marrow cells
higher doses that lead to the death of epithelial cells of
gastrointestinal system, and even higher doses that kill brain
neurons; and chemical cytotoxicity, associated with cell death in
different organ and tissues induced by natural or synthetic toxic
compounds.
[0050] In yet another embodiment of the present invention, the
detected miRNAs originate from and are specifically expressed in a
specific cell type, tissue, or organ in the body and can be used
for prognosis of disease outcome. Changes in the levels of
respective miRNAs, that are indicative of disease
progression/regression, success of therapeutic or surgical
intervention, are used for disease and treatment monitoring.
[0051] In another embodiment of the invention, the detected miRNAs
originate from transplanted cells, tissues, or organs and their
levels are indicative of rejection episodes and corresponding
treatment.
[0052] In another embodiment of the invention, the detected miRNAs
originate from a pathogen and are used for infection diagnosis and
monitoring. In a specific embodiment of the instant invention, the
pathogen is a virus, for example Epstein-Barr virus.
[0053] In yet another embodiment of the invention, the detected
miRNAs originate from cells of an infected organ and can be used
for diagnosis support, evaluation of infected tissue damage, and
further disease and treatment monitoring.
[0054] In yet another embodiment of the invention, the detected
miRNAs originate from the fetus of a pregnant female, and are
characteristic of a condition or pathology of the fetus, such as
for example pre-eclampsia, which is characterized by excessive
death of trophoblasts in placenta. In yet another embodiment, the
detected miRNAs originate from a fetus of a pregnant female, and
are characteristic of a condition or pathology of the fetus, such
as for example Down syndrome and other trisomies accompanied by the
delay of organ development and excessive or inhibited cell
death.
[0055] In yet another embodiment of the invention, the information
about the levels of tissue or cell-specific miRNAs alone or in
combination with other markers are used for diagnosis or monitoring
of cancer and pre-cancerous conditions, such as for example liver
cancer, kidney cancer, prostate cancer, colorectal cancer,
pancreatic cancer and other known cancers.
[0056] In some embodiments, the levels of cell- and/or
tissue-specific miRNAs are normalized using the levels of
ubiquitous miRNA in serum, the levels of albumin or creatinine in
urine, or the levels of placenta-specific miRNAs for normalization
of other tissue-specific fetal miRNAs.
[0057] In one aspect of the invention, the step of analyzing said
urine sample to detect specific miRNAs includes a technique
selected from the group consisting of hybridization, cycling probe
reaction, polymerase chain reaction, nested polymerase chain
reaction, PCR to analyze single strand conformation polymorphisms
and ligase chain reaction.
[0058] In certain aspects of the invention, the nucleic acid
degradation in said urine sample is reduced. The method of reducing
nucleic acid degradation comprises inhibiting nuclease activity by
use of RNAse inhibitors, or by treating said urine sample with a
compound selected from the group consisting of: guanidine-HCl,
guanidine isothiocyanate, N-lauroylsarcosine, and sodium
dodecylsulphate. In another aspect of the invention, said urine
sample has been held in the bladder less than 12 hours.
[0059] In one embodiment of the present invention, the miRNA
sequences measured are specifically related to tissues in the body,
which may be selected from but are not limited to, lung, heart,
liver, nervous system, brain, blood, kidney, bone, eye or
pancreas.
[0060] The tissues selected for the analysis may be normal or
abnormal (e.g., malignant). Malignant tissues and tumors include
carcinomas, sarcomas, melanomas and leukemia generally and more
specifically selected from malignant tissues and tumors associated
with biliary tract cancer, bladder cell carcinoma, bone cancer,
brain and CNS cancer, breast cancer, cervical cancer,
choriocarcinoma, chronic myelogenous leukemia, colon cancer,
connective tissue cancer, cutaneous T-cell leukemia, endometrial
cancer, esophageal cancer, eye cancer, follicular lymphoma, gastric
cancer, hairy cell leukemia, Hodgkin's lymphoma, intraepithelial
neoplasms, larynx cancer, lymphomas, liver cancer, lung cancer
(e.g. small cell and non-small cell), melanoma, multiple myeloma,
neuroblastomas, oral cavity cancer, ovarian cancer, pancreatic
cancer, prostate cancer, rectal cancer, renal cell carcinoma,
sarcomas, skin cancer, squamous cell carcinoma, testicular cancer,
thyroid cancer, and renal cancer. The method may be used to
distinguish between benign and malignant tumors.
[0061] Subjects from whom such tissue samples may be harvested
include those at risk of developing a cancer. A subject at risk of
developing a cancer is one who has a high probability of developing
cancer (e.g., a probability that is greater than the probability
within the general public). These subjects include, for instance,
subjects having a genetic abnormality, the presence of which has
been demonstrated to have a correlative relation to a likelihood of
developing a cancer that is greater than the likelihood for the
general public, and subjects exposed to cancer causing agents
(i.e., carcinogens) such as tobacco, asbestos, or other chemical
toxins, or a subject who has previously been treated for cancer and
is in apparent remission.
[0062] The instant methods include isolation of miRNAs from the
bodily fluids of the patients. In one aspect of the invention, a
miRNA of interest may be detected in a body fluid such as blood,
amniotic fluid, cerebrospinal fluid, plasma, milk, semen, serum,
sputum, saliva and urine. In one aspect of the instant invention,
the miRNA is detected in urine. In another embodiment, the miRNA is
detected in serum.
[0063] The instant method of the miRNA isolation of the instant
invention can utilize commercially available anion exchange
materials. Either strong or weak anion exchangers may be employed.
By utilizing selected solutions for adsorption and elution, the
miRNA can be purified, concentrated, and substantially
isolated.
[0064] By employing a solution at known ionic strength for the
initial binding of the miRNA to the anion exchange column
materials, most of the water soluble components including other
electronegative molecules such as proteins (weakly-bound
contaminants) can be washed through the column. For elution, the
required ionic strength is reached by using known concentrations of
a salt such as NaCl, which may be mixed with a buffer to control
pH, ideally corresponding to the lowest ionic strength at which the
nucleic acids will completely elute. Contaminating substances bound
to the anion exchange resin with higher stringency than the nucleic
acids may thereby be left within the column, i.e., stronger bound
contaminants are separated away from the nucleic acids.
[0065] A preferred weak exchanger is one in which primary,
secondary, or tertiary amine groups (i.e., protonatable amines)
provide exchange sites. The strong base anion exchanger has
quaternary ammonium groups (i.e., not protonatable and always
positively charged) as exchange sites. Both exchangers are selected
in relation to their respective absorption and elution ionic
strengths and/or pH for the miRNA being separated. The solution
strengths are higher than the binding strengths.
[0066] In one aspect of the invention, a method is provided for
isolation tranrenal miRNA from urine, the method comprising
providing urine from a subject; optionally separating cells and
cell debris from the urine by filtration or centrifugation; adding
EDTA and Tris-HCl to the urine, adding silica free anion exchange
resin to urine, incubating the mixture, removing the anion exchange
medium from the urine, and eluting miRNA from the resin.
[0067] In one embodiment of the method of isolating miRNA from
urine, the concentration of EDTA and Tris-HCl after it is added to
the urine is in a range of 10-100 mM, and the pH of the solution is
between about 8.0 and about 8.5.
[0068] In a further embodiment, the body fluid is optionally
pre-filtered through a membrane prior to adsorption onto the
anion-exchange medium.
[0069] In a further embodiment, the anion exchange medium is a
sepharose-based resin functionalized with cationic quaternary
ammonium groups. Examples of sepharose-based resins, functionalized
with cationic ammonium groups include Q-Sepharose.TM. ANX-4
Sepharose.TM. Fast Flow, DEAE-Sepharos.TM., and Q-Sepharose-XL.TM.
DEAE Sepharose Fast Flow (GE Healthcare).
[0070] In a further embodiment, the anion exchange medium is
selected from sepharose-based quaternary ammonium anion exchange
medium such as Q-filters or Q-resin.
[0071] In a further embodiment of the invention, the anion-exchange
medium is immobilized on an individualized carrier wherein such a
carrier is a column, cartridge or portable filtering system which
can be used for transport or storage of the medium/nucleoprotein
bound complex.
[0072] In another embodiment of the present invention, periodic
analysis of miRNA sequences present, for example, in the urine
samples of the same person can give early information about a
pathological process in a particular organ or tissue. For example,
miRNA122 is synthesized in liver only and increases in its amount
may be a marker of hepatitis or another liver pathology.
Alzheimer's syndrome can be accompanied by increases in the
concentration of miRNA specifically expressed in neurons.
[0073] In another embodiment, more detailed monitoring of
tissue-specific miRNA in the bodily fluid sample of the patient
will be useful for estimation of a severity of the disease and for
evaluation of effectiveness of therapeutic efforts.
[0074] In yet another embodiment, in combination with analysis of
tumor-specific mutations the data on the tissue-specific miRNA can
help in determination of tumor localization.
[0075] Other aspects of the instant invention relate to diseases
caused by or accompanied by changes in a specific miRNA(s)
expression. The described technology will help in diagnosis of such
type pathologies.
[0076] In yet another embodiment, the application of the instant
method may be extended to monitoring pharmacokinetics of synthetic
siRNA in the patient's urine to enhance optimization of the siRNA
drug design.
[0077] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention pertains.
Although methods and materials similar or equivalent to those
described herein can be used in the practice of the present
invention, suitable methods and materials are described below. All
publications, patent applications, patents, and other references
mentioned herein are expressly incorporated by reference in their
entirety. In cases of conflict, the present specification,
including definitions, will control. In addition, the materials,
methods, and examples described herein are illustrative only and
are not intended to be limiting.
EXAMPLES
[0078] The examples are presented in order to more fully illustrate
the various embodiments of the invention. These examples should in
no way be construed as limiting the scope of the invention recited
in the appended claims.
Example 1
[0079] Extraction of miRNA from Urine:
[0080] Urine Collection:
[0081] For these experiments, urine specimens from patients or
volunteers were collected in a sterile 110 ml urine collection cup
and were immediately supplemented with EDTA up to final
concentration between 10 and 150 mM, preferably 50 mM. Specimens
were stored in 10-50 ml aliquots at -80.degree. C. Optional
filtration of urine was carried out on Stericup.TM. (Millipore,
Vacuum Driven Filtration System, 0.45.mu. Durapore.TM. filter)
immediately after specimen collection before the EDTA was
added.
[0082] Q Binding:
[0083] In a 50 ml tube 20 mL of urine was diluted with equal volume
of 50 mM EDTA (pH 8.0) and 50 mM Tris-HCl (pH 8.0) which was then
supplemented with 1-2 ml of Q-Sepharose.TM. (GE Healthcare;
17-0510-10) slurry and rigorously mixed 10-30 min at room
temperature. The resin, with bound nucleic acids, was collected by
centrifugation at 2000 g for 5 minutes at room temperature in a
table top clinical centrifuge using a swing bucket rotor. All but
.about.500 .mu.l of supernatant was removed by aspiration. The
resin pellet was resuspended in the remaining supernatant and
transferred to a Micro Bio-Spin Chromatography Column (Bio-Rad) or
equivalent, which was operated either by centrifugation of vacuum.
The resin in the column was washed three times with 500 .mu.l
2.times.SSC (300 mM NaCL/30 mM sodium citrate (pH 7.0)) or with
buffer with comparable ionic strength (e.g. 300 mM NaCl or LiCl).
Nucleic acids can be eluted from Q-Sepharose with high ionic
strength (e.g. 1M NaCl or LiCl) but the methods described below
preserves RNA better.
[0084] Elution from Q-Sepharose.TM. and TRIzol.TM. Phase
Separation:
[0085] Bound nucleic acids were further eluted with 500 .mu.l of
TRIzol.TM. reagent (Invitrogen). The extraction of nucleic acids
from TRIzol was carried out according manufacturer's
recommendations. Briefly, for phase separation TRIzol eluate was
supplemented with 100 .mu.l chloroform, mixed vigorously, incubated
at room temperature for 3-5 minutes and centrifuged at
12,000.times.g for 15 min at 4.degree. C. While avoiding touching
the interphase, 300 .mu.l of the upper phase was transferred into a
fresh centrifuge tube. Then the nucleic acids were precipitated or
additionally cleaned and desalted on a silica column.
[0086] Nucleic Acid Precipitation:
[0087] For nucleic acid precipitation, the above described
preparation was supplemented with 1 .mu.l of 20 mg/mL glycogen
(Roche) and 300 .mu.l of 100% isopropyl alcohol. Nucleic acids were
collected by centrifugation, the pellet was washed twice with 200
.mu.l of 70% ethanol, allowed to air dry for 5 min at room
temperature, and then the nucleic acids were dissolved in 30 .mu.l
of 0.1 mM EDTA/1.times.RNA Secure (Ambion). The samples were
incubated at 60.degree. C. for 10 min to inactivate any residual
RNase activity.
[0088] Silica Column Cleaning of Nucleic Acids:
[0089] For binding to a silica column (Qiagen PCR clean columns or
equivalent) 3 volumes of 96% ethanol were added to nucleic acid
preparation from the TRIzol upper phase, and, after 3 minutes
incubation at room temperature, the mixture was loaded onto the
column. The column was washed twice with 500 .mu.l 2 M LiCl/80%
ethanol and twice with 500 .mu.l 80% ethanol. Nucleic acids were
eluted with 50 .mu.l of 0.1 mM EDTA/lx RNA Secure (Ambion). The
samples were incubated at 60.degree. C. for 10 min to inactivate
any residual RNase.
[0090] DNase I and RNase A Digestion:
[0091] To verify the nucleic acid identity of the material
extracted from urine with the above described protocol, the instant
prep was digested with DNase I and/or RNase A. DNase I digestion
was carried out in the DNase I Reaction Buffer (NEB) containing 2
units of RNase free DNase I (NEB). RNase A digestion was performed
in TE buffer supplemented with 50 ng/mL boiled RNase A. Samples
were incubated at 37.degree. C. for 60 min and after addition of
loading dye samples were subjected to electrophoresis on 5%
polyacrylamide 1.times.TBE gels and stained with 1/10000 diluted
SYBR.RTM. Gold (Invitrogen). As shown in FIG. 1, the isolated
material represents low molecular weight nucleic acids, mainly RNA
and their fragments. In addition, (see FIG. 1), for comparison
nucleic acids from Q-resin were eluted by 3 M NaCl, lanes 2 and 3,
and Trizol.TM., lanes 4 and 5.
[0092] In the FIG. 1, lanes 1 and 5, represent nucleic acids
isolated with high salt and TriZol elution from Q-Sepharose,
respectively; lanes 2 and 6; 3 and 7; 4 and 8, represent nucleic
acids after treatment with DNAse, RNAse, or DNAse plus RNAse,
respectively.
[0093] Also, to demonstrate existence and molecular size of RNA,
RNA aliquots of purified nucleic acids were digested with DNaseI,
lanes 3 and 5.
Extraction of RNA from Serum
[0094] For these experiments, 1.2 ml of TRIzol LS were added to 0.4
ml of serum, and the mixture was centrifuged 10 at 14,000 rpm. The
supernatant was transferred into a 2 ml Eppendorf tube, 0.3 ml of
chloroform was added, and the mixture was shaken for 15 seconds.
After centrifugation at 14,000 rpm for 15 min, the supernatant was
transferred into a 5 ml tube and ethanol was added up to final
concentration of 70%. The mixture was loaded on a Qiagen Quick
column on a vacuum manifold, and the column was washed twice with
0.5 ml of 2M LiCl-80% EtOH, once with 0.5 ml of 80% ethanol-80 mM
sodium acetate (pH 5.0), and finally with 0.5 ml of 95% ethanol.
The column was centrifuged in 1.5 ml Eppendorf tube 3 min at 14,000
rpm, and RNA was eluted with 40 .mu.l H.sub.2O.
Example 2
[0095] This Example demonstrates that miRNA, from dying cells,
cross the kidney barrier and may be detected in the urine of a
patient.
Detection of Human miRNA Molecules in Urine
[0096] Micro RNA species that were analyzed in this example can be
grouped in three distinct types, namely ubiquitous miRNAs, which
are expressed in all or multiple tissues, tissue-specific miRNAs,
and miRNAs in which expression is significantly altered in a
particular tissue or cell type. As shown by Table 1, 20 different
miRNAs were obtained from urine of 16 healthy volunteers and
enrolled donors and later detected by real time RT-PCR using
commercially available miRNA expression analysis kit (ABI).
Corresponding synthetic miRNA oligonucleotides were used as
standards. Reactions were carried out strictly as recommended by
the supplier.
TABLE-US-00001 TABLE 1 Detected miRNA SEQ ID NO: ID Sequence
Expression 1 hsa-miR- UCGGAUCCGUCUGAGCU Brain 127 UGGCU
overexpressed 2 hsa-miR- UUGCAUAGUCACAAAAG Brain 153 UGA
overexpressed 3 hsa-miR- CUUUUUGCGGUCUGGGC Brain-specific 129 UUGC
4 hsa-miR- UAUUGCUUAAGAAUACG Brain 137 CGUAG overexpressed 5
hsa-miR- UUGUGCUUGAUCUAACC Ubiquitous, Brain 218 AUGU overexpressed
6 hsa-miR- UGAUUGUCCAAACGCAA Brain-specific 219 UUCU 7 hsa-miR-
UCACAGUGAACCGGUCU Brain-specific 128a CUUUU 8 hsa-miR-
UCUUUGGUUAUCUAGCU Brain 9 GUAUGA overexpressed 9 hsa-miR-
AGCUGGUGUUGUGAAUC Brain, Thyroid 138 10 hsa-miR- UGUGACUGGUUGACCAG
Brain and several 134 AGGG other tissues 11 hsa-miR-
UUAAGGCACGCGGUGAA Brain-specific 124a UGCCA 12 hsa-miR-
UGGAGUGUGACAAUGGU Liver-specific 122a GUUUGU 13 hsa-miR-
UUGGUCCCCUUCAACCA Heart and Muscle 133a GCUGU overexpressed 14
hsa-miR- UGGAAUGUAAAGAAGUA Heart and Muscle 1 UGUA overexpressed 15
hsa-miR- UCAAGAGCAAUAACGAA Ubiquitous 335 AAAUGU 16 hsa-miR-
UAGCAGCACGUAAAUAU Ubiquitous 16 UGGCG 17 hsa-miR- AUGACCUAUGAAUUGAC
Small intestine 215 AGAC and colon overexpressed 18 hsa-miR-
UAUGGCUUUUCAUUCCU Placenta- 135b AUGUG overexpressed 19 hsa-miR-
AUCGUGCAUCCUUUUAG Placenta- 517c AGUGU overexpressed 20 hsa-miR-
AAAGCGCUUCCCUUCAG Placenta- 518e AGUGU overexpressed
[0097] All three types of miRNA were detected in most preps of
urinary RNA. The highest copy numbers were characteristic of
ubiquitous miRNA. However, tissue-specific miRNA or miRNA
over-expressed in a particular tissue or cell type were also
detectable. It has been unequivocally demonstrated that a portion
of miRNA from dying cells is not degraded but appears in the
bloodstream and is finally excreted into urine.\
Example 3
[0098] The Example demonstrates that miRNA from human
nasopharyngeal carcinoma (NPC) cells can cross the patient's kidney
barrier and can be detected in patient's urine by real time
RT-PCR.
Virus-Derived miRNA in Urine
[0099] It is known that some viruses also encode and produce
miRNAs. Since Epstein-Barr virus (EBV) is involved in development
of nasopharyngeal carcinoma (NPC), the instant system was used to
find out if viral miRNA from NPC cells can reach a patient's urine
and be detected there. Urine samples from NPC patients were
collected and stored according to the procedures described in the
Example 1 of this application. EBV infection was confirmed by the
detection of virus-specific DNA sequences in urine. Urine collected
from healthy donor was negative for EBV specific DNA sequences. Two
EBV-specific miRNAs BART3-3p and BART1-3p were analyzed in this
study:
TABLE-US-00002 BART3-3P SEQ ID NO: 21 CGC ACC ACU AGU CAC CAG GUG U
BART1-3P SEQ ID NO: 22 UAG CAC CGC UAU CCA CUA UGU Cu
[0100] Reverse transcription was performed in 15 .mu.l, one tenth
of the RT reaction was subjected to PCR amplification using
JumpStart DNA polymerase from Sigma. The following primers were
used at 500 nM concentration:
TABLE-US-00003 SEQ ID ID Sequence NO: BART3- GTC GTA TCC AGT GCA
GGG TCC 23 3PRT GAG GTA TTC GCA CTG GAT ACG ACA CAC CT BART1- GTC
GTA TCC AGT GCA GGG TCC 24 3PRT GAG GTA TTC GCA CTG GAT ACG ACA GAC
AT BART3- CGC CGC ACC ACT AGT CAC 25 3PF BART1- CGC TAG CAC CGC TAT
CCA 26 3PF miRNACR GTG CAG GGT CCG AGG T 27
[0101] Products were analyzed in 15% polyacrylamide gel (PAAG).
[0102] As demonstrated by FIG. 2, both BART3 and BART 1 miRNA
species were detected in urine from NPC patients but not in the
urine sample from a healthy donor. These data again indicate that
miRNA from dying cells located outside of urinary system can be
detected in the urine. In the FIG. 2, lane 1, represents markers;
lanes 2 and 3, represent patients with nasopharyngeal carcinoma,
lanes 4 and 5, represent control patients, and lane 6, represents
positive control, which represents respective synthetic miRNAs.
Example 4
[0103] This example demonstrates that the neuronal death caused by
stroke can be registered in vivo by measurements of the
concentrations of neuron-specific miRNA in the patient's urine.
Brain Stroke Diagnosis
[0104] For these experiments, patients with brain stroke were
investigated for analysis of changes in concentrations of
brain-specific miRNA or miRNA which are over-expressed in brain,
after stroke. Since currently it is not known in what brain cell
types and in what brain areas these miRNA are expressed, 9
different brain specific miRNA were studied.
[0105] Patients:
[0106] Urine samples were collected from patients accepted at a
hospital through the emergency room. Diagnosis of brain stroke was
based on clinical symptoms. Urine samples were collected at 12 and
24 hours after the stroke. Control urine samples were donated by
age matched volunteers but without stroke symptoms. Samples were
collected and stored according to the procedures described in the
Example 1 of this application.
[0107] miRNA Species:
[0108] miRNA from urine was extracted according to the procedure
described in the Example 1. An amount of RNA equivalent to that
isolated from 675 .mu.l of urine underwent reverse transcription
PCR and 1/10 of the RT-PCR mixture underwent final real time PCR,
which was carried out using the protocol provided by the
manufacturer. Data obtained were normalized for individual kidney
filtration rates by re-calculation per creatinine concentration in
urine. For these experiments, urine samples collected from healthy
donors from same age group were used as baseline. Different miRNA
species are presented as follows:
[0109] A. hsa-mir-128a
[0110] B. hsa-mir-9
[0111] C. hsa-mir-127
[0112] D. hsa-mir-137
[0113] E. hsa-mir-129
[0114] F. hsa-mir-219
[0115] G. hsa-mir-218
[0116] Results summarized in FIG. 3A to 3G clearly demonstrate that
after brain stroke, there is a significant increase in the levels
of several brain specific miRNA (128a, 129, 218, 219)--reflecting
kinetics of the brain cell death.
Example 5
[0117] This example demonstrates that kinetics of the miRNA
concentrations in patient's urine after stroke provides information
about disease outcome.
Brain Stroke Monitoring
[0118] For the experiments, patients with brain stroke were
investigated for analysis of correlation between changes in
concentrations of brain-specific miRNA and disease development.
[0119] Patients:
[0120] Urine samples were collected from patients accepted at a
hospital through the emergency room. Diagnosis of brain stroke was
based on clinical symptoms and MRI analysis. Urine samples were
collected at 12, 24, 48 hours and a week after the stroke. Patient
clinical status was evaluated 30 days after stroke. Control urine
samples were donated by age matched volunteers but without stroke
symptoms. Samples were collected and stored according to the
procedures described in the Example 1 of this application.
[0121] miRNA Species:
[0122] miRNA from urine was extracted according to the procedure
described in Example 1 and analyzed with TaqMan miRNA assays
(Applied Biosystems). An amount of RNA equivalent to that isolated
from 400 .mu.l of urine underwent reverse transcription PCR and
1/10 of the RT-PCR mixture underwent final real time PCR, which was
carried out using the protocol provided by the manufacturer. Data
obtained were normalized for individual kidney filtration rates by
re-calculation per creatinine concentration in urine. For these
experiments, urine samples collected from healthy donors from same
age group were used as baseline.
[0123] Results summarized in FIGS. 4A and B clearly demonstrate
that the dynamics of changes in Tr-miRNA 129 and Tr-miRNA 219 after
brain stroke are different in different patients and correlates
with the disease development. The increase in neuronal death a week
after stroke in patient #3 corresponds to worsening in the patient
clinical status. At the same time two patients, whose transrenal
neuron-specific miRNA had tendency to normalization, demonstrated
significant improvement.
Example 6
Alzheimer's Disease Diagnosis
[0124] Alzheimer's disease is a progressive neurological disease
that is caused by the death of neurons, particularly in the cortex
and hippocampus. The diagnosis is based on neurological examination
and the exclusion of other causes of dementia whereas the
definitive diagnosis can be made only at autopsy. The instant
invention demonstrates that excessive neuronal death characterizing
Alzheimer's disease may be monitored by measuring levels of
specific brain miRNAs isolated from the patient's urine.
[0125] For these experiments, patients diagnosed with Alzheimer's
disease were investigated for analysis of changes in concentrations
of brain-specific or over-expressed miRNA as a result of neuronal
death.
[0126] Patients:
[0127] Urine and serum samples were collected from patients
diagnosed with various stages of the Alzheimer's disease. Control
urine and serum samples were donated by age matched volunteers but
without symptoms of Alzheimer's disease. Samples were collected and
stored according to the procedures described in the Example 1 of
this application. Some urine samples were filtered after collection
as described in Example 1 to delete cells and cell debris.
[0128] miRNA Species:
[0129] RNA from urine and serum was extracted according to the
procedures described in the Example 1.
[0130] In one set of experiments an amount of RNA equivalent to
that isolated from 750 .mu.l of urine underwent reverse
transcription PCR and 1/10 of the RT-PCR mixture underwent final
real time PCR, which was carried out using the protocol provided by
the manufacturer (Applied Biosystems). Data obtained were
normalized for individual kidney filtration rates by re-calculation
per creatinine concentration in urine. FIG. 5A to 5E clearly
demonstrates that concentrations of several brain specific miRNAs
is increased in the urine of Alzheimer's patients.
[0131] In another set of experiments, RNA isolated from filtered
urine or serum was analyzed. An amount of RNA equivalent to that
isolated from 0.6 ml of urine or 50 .mu.l of serum underwent
reverse transcription PCR and 1/10 of the RT-PCR mixture underwent
final real time PCR, which was carried out using the protocol
provided by the manufacturer (Applied Biosystems). Data obtained
for urinary miRNA were normalized for individual kidney filtration
rates by re-calculation per creatinine concentration in urine. Data
obtained for plasma miRNA were normalized per ubiquitous miRNA-16.
FIGS. 6A to 6C and 7A to 7C show that the levels of some
neuron-specific miRNAs are higher in both filtered urine and serum
of the Alzheimer's patients compared to age-matched controls.
Example 7
Parkinson's Disease
[0132] Parkinson's disease is a degenerative disorder of the
central nervous system that often impairs the sufferer's motor
skills and speech. The instant invention demonstrates that
excessive cellular death of dopaminergic neurons, characterizing
Parkinson's disease may be monitored by measuring levels of
specific brain miRNAs isolated from the patient's urine.
[0133] For these experiments, patients diagnosed with Parkinson's
were investigated for analysis of changes in concentrations of
brain-specific miRNA or over-expressed miRNA as a result of
neuronal death.
[0134] Patients:
[0135] Urine samples were collected from patients diagnosed with
various stages of the Parkinson's disease. Control urine samples
were donated by age matched volunteers without symptoms of
Parkinson's disease. Samples were collected and stored according to
the procedures described in the Example 1 of this application.
[0136] miRNA Species:
[0137] For these experiments, RNA from urine was extracted
according to the procedure described in the Example 1. Amount of
RNA equivalent to that isolated from 750 .mu.l of urine underwent
reverse transcription PCR and 1/10 of the RT-PCR mixture underwent
final real time PCR, which was carried out using the protocol
provided by the manufacturer (Applied Biosystems). Data obtained
were normalized for individual kidney filtration rates by
re-calculation per creatinine concentration in urine. FIG. 8A to 8D
demonstrates that concentrations of several brain specific miRNAs
is increased in the urine of the patients with Parkinson
disease.
Example 8
Prenatal Testing for Pregnancy-Related or Fetal Diseases
[0138] The principal finding of permeability of the kidney barrier
for miRNA molecules opens the way for the use of maternal urine to
perform completely noninvasive prenatal diagnosis of congenital
diseases. One can perform such a noninvasive screen as follows.
[0139] First, a sample of urine is gathered from a pregnant
patient. Where desired, miRNA in the urine sample is then be
isolated, purified and/or treated to prevent degradation using
methods described above. MiRNA profiling is then performed using
quantitative PCR or miRNA array and the data obtained are used to
determine different fetal pathologies, as described for other
pathologies above.
Example 9
Down Syndrome
[0140] For the experiments, differences in concentrations of
brain-specific miRNA in maternal urine between women pregnant with
normal and Down syndrome fetuses were investigated.
[0141] Patients:
[0142] Urine samples were collected from pregnant women diagnosed
with Down syndrome by amniocentesis. Control urine samples were
donated by age matched women with normal pregnancies. Samples were
collected and stored according to the procedures described in the
Example 1 of this application.
[0143] miRNA Species:
[0144] miRNA from urine was extracted according to the procedure
described in the Example 1. An amount of RNA equivalent to that
isolated from 750 .mu.l of urine underwent reverse transcription
PCR and 1/10 of the RT-PCR mixture underwent final real time PCR,
which was carried out using the protocol provided by the
manufacturer. Data obtained were normalized per placenta-specific
miRNA 518. FIG. 9 demonstrates lower concentration the
brain-specific miRNA 9 in urine of women pregnant with Down
syndrome fetuses compared to urine of women with normal
pregnancies, which indicates insufficient cell death compared to
respective controls.
Sequence CWU 1
1
27122RNAHomo sapiens 1ucggauccgu cugagcuugg cu 22220RNAHomo sapiens
2uugcauaguc acaaaaguga 20321RNAHomo sapiens 3cuuuuugcgg ucugggcuug
c 21422RNAHomo sapiens 4uauugcuuaa gaauacgcgu ag 22521RNAHomo
sapiens 5uugugcuuga ucuaaccaug u 21621RNAHomo sapiens 6ugauugucca
aacgcaauuc u 21722RNAHomo sapiens 7ucacagugaa ccggucucuu uu
22823RNAHomo sapiens 8ucuuugguua ucuagcugua uga 23917RNAHomo
sapiens 9agcugguguu gugaauc 171021RNAHomo sapiens 10ugugacuggu
ugaccagagg g 211122RNAHomo sapiens 11uuaaggcacg cggugaaugc ca
221223RNAHomo sapiens 12uggaguguga caaugguguu ugu 231322RNAHomo
sapiens 13uugguccccu ucaaccagcu gu 221421RNAHomo sapiens
14uggaauguaa agaaguaugu a 211523RNAHomo sapiens 15ucaagagcaa
uaacgaaaaa ugu 231622RNAHomo sapiens 16uagcagcacg uaaauauugg cg
221721RNAHomo sapiens 17augaccuaug aauugacaga c 211822RNAHomo
sapiens 18uauggcuuuu cauuccuaug ug 221922RNAHomo sapiens
19aucgugcauc cuuuuagagu gu 222022RNAHomo sapiens 20aaagcgcuuc
ccuucagagu gu 222122RNAHomo sapiens 21cgcaccacua gucaccaggu gu
222223RNAHomo sapiens 22uagcaccgcu auccacuaug ucu
232350DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 23gtcgtatcca gtgcagggtc cgaggtattc gcactggata
cgacacacct 502450DNAArtificial SequenceDescription of Artificial
Sequence Synthetic primer 24gtcgtatcca gtgcagggtc cgaggtattc
gcactggata cgacagacat 502518DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 25cgccgcacca ctagtcac
182618DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 26cgctagcacc gctatcca 182716DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
27gtgcagggtc cgaggt 16
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