U.S. patent application number 13/343503 was filed with the patent office on 2012-07-12 for method for isolating nucleic acids and protein from a single sample.
This patent application is currently assigned to INVITROGEN DYNAL AS. Invention is credited to Marie BOSNES.
Application Number | 20120178090 13/343503 |
Document ID | / |
Family ID | 27614783 |
Filed Date | 2012-07-12 |
United States Patent
Application |
20120178090 |
Kind Code |
A1 |
BOSNES; Marie |
July 12, 2012 |
METHOD FOR ISOLATING NUCLEIC ACIDS AND PROTEIN FROM A SINGLE
SAMPLE
Abstract
The present invention comprises a method of isolating nucleic
acid and protein from the same sample with solid supports, wherein
nucleic acid and protein components contained in the sample become
bound to distinct solid supports. The invention also allows for
kits for isolating nucleic acid and protein from the same sample
and for use of the method of isolating nucleic acid and protein for
the analysis and/or comparison of mRNA and/or protein expression
and/or their correlation to genomic information.
Inventors: |
BOSNES; Marie; (Oslo,
NO) |
Assignee: |
INVITROGEN DYNAL AS
Oslo
NO
|
Family ID: |
27614783 |
Appl. No.: |
13/343503 |
Filed: |
January 4, 2012 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10501162 |
Apr 26, 2005 |
8110351 |
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PCT/GB03/00156 |
Jan 16, 2003 |
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13343503 |
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Current U.S.
Class: |
435/6.12 ;
435/6.1; 435/7.23 |
Current CPC
Class: |
G01N 33/54306 20130101;
G01N 33/68 20130101; G01N 33/6842 20130101 |
Class at
Publication: |
435/6.12 ;
435/6.1; 435/7.23 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68; G01N 33/566 20060101 G01N033/566 |
Foreign Application Data
Date |
Code |
Application Number |
Jan 16, 2002 |
GB |
0200927.2 |
Nov 21, 2002 |
GB |
0227239.1 |
Claims
1. A method of isolating nucleic acid and protein from the same
sample, said method comprising contacting said sample with solid
supports, wherein nucleic acid and protein components contained in
said sample become bound to distinct solid supports.
2. The method of claim 1, wherein both DNA and RNA are bound to the
same solid support.
3. The method of claim 1, wherein DNA and RNA are bound to distinct
solid supports.
4. The method of claim 3, wherein DNA and RNA are bound to
different solid supports in separate steps.
5. The method of any one of claims 1 to 4, wherein RNA and protein,
or DNA and protein, or DNA, RNA and protein are isolated from the
same sample.
6. The method of claim 5, wherein said RNA is mRNA.
7. The method of claim 5 or 6, wherein said DNA is genomic.
8. The method of any one of claims 1 to 7 wherein the total RNA
and/or the total DNA is isolated.
9. The method of any one of claims 1 to 7 wherein the total nucleic
acid component is isolated.
10. The method of any one of claims 1 to 9 wherein the total
protein component is isolated.
11. The method of any one of claims 1 to 10, wherein said sample is
a food or allied product, or is a clinical, environmental or
biological sample.
12. The method of any one of claims 1 to 11, wherein prior to
contacting said sample with said solid supports, the sample is
subjected to a preliminary treatment step to free the nucleic acid
and/or protein components from structures or'entities in which they
may be contained.
13. The method of any one of claims 1 to 12, wherein prior to
contacting said sample with said solid supports, the sample is
subjected to a cell isolation procedure.
14. The method of claim 13, wherein one or more particular cell
populations are specifically isolated.
15. The method of any one of claims 1 to 14, wherein the sample, or
a cell population isolated therefrom, is subjected to a cell lysis
step prior to contacting said sample with said solid supports.
16. The method of claim 15, wherein cell surface proteins of cells
within or isolated from said sample are subjected to an in vitro
modification procedure prior to the cell lysis step.
17. The method of any one of claims 1 to 16, wherein the sample is
not divided at any stage of the method.
18. The method of any one of claims 12 to 16, wherein the sample is
divided after cell isolation and/or lysis or after said preliminary
treatment step.
19. The method of any one of claims 1 to 18, wherein said sample is
contacted with said solid supports sequentially or simultaneously
or in parallel.
20. The method of claim 19, wherein in a first step DNA is isolated
from said sample, in a second step RNA is isolated from said sample
and in a third step, protein is isolated from said sample, and
wherein said steps may be performed in any order.
21. The method of any one of claims 1 to 20, wherein DNA is
isolated on a support carrying surface carboxyl groups.
22. The method of any one of claims 1 to 21, wherein DNA is
isolated by binding to a solid support, in the presence of a
detergent.
23. The method of any one of claims 13 to 21, wherein cell lysis
and nucleic acid or DNA binding to a solid support occur
simultaneously or concomitantly.
24. The method of any one of claims 1 to 23, wherein RNA is
isolated using an RNA-specific capture-probe carried by or attached
to, or capable of binding to said solid support.
25. The method of claim 24, wherein said capture probe is or
comprises a dT oligonucleotide or dU oligonucleotide.
26. The method of any one of claims 1 to 25, wherein protein is
isolated using an appropriate binding partner/ligand carried by or
attached to or capable of binding to said solid support.
27. The method of any one of claims 1 to 25 wherein protein is
isolated using a solid support having a surface capable of
effecting a chromatographic interaction.
28. The method of any one of claims 1 to 27, wherein said solid
supports comprise particles.
29. The method of claim 28, wherein said particles are magnetic
particles.
30. A kit for isolating nucleic acid and protein from the same
sample comprising: (a) a solid support suitable for binding nucleic
acid components; (b) a solid support suitable for binding proteins,
wherein said supports of a) and b) are distinct solid supports.
31. The kit of claim 30, wherein the solid support of (a) comprises
a support which is selective for binding DNA or RNA or both types
of nucleic acid.
32. The kit of claim 30 or 31 wherein the kit also comprises (c) a
solid support suitable for isolation of a specific cell population
and/or (d) means for lysing said cells, and/or (e) a means for
detecting the nucleic acid and/or protein.
33. Use of the method of any one of claims 1 to 32 for the analysis
and/or comparison of mRNA and/or protein expression and/or the
correlation thereof to genomic information.
Description
[0001] The present invention relates to a method of analysing a
single sample for DNA, mRNA and protein expression. This is
advantageous in correlating information relating to both mRNA and
protein expression to genomic information.
[0002] The human genome is now more or less mapped and the gene
number has been found to be much lower than first estimated. This
shows that human complexity does not lie in the number of genes,
but in how the genes are utilized and gene products combined and
modified. Thus, the focus on studying the gene products and their
interaction has become more significant.
[0003] It is known that only a fraction of the genes are
transcribed in a single cell or cell type, and that one gene can
give rise to many different proteins. This is partly due to
alternative reading frames, alternative translational start/stop
codons and alternative splicing of mRNA. It is also known that the
relative quantitative levels of mRNA and protein do not always- or
seldom correspond. One mRNA species can also give rise to different
proteins because of post-translational modifications.
[0004] Thus an individual's genome (the collection of all genes),
can be regarded as representing the genetic "possibilities" of an
individual, while the transcriptome (the collection of mRNAs
transcribed from the genome) represents what might possibly happen.
The proteome, however (i.e. the total collection of all proteins
translated from the transcriptome and modified
post-translationally) represents reality, i.e. what really
happened.
[0005] Accordingly, all three levels, DNA, RNA and protein, give
information which is valuable for different reasons. The DNA or
genotype gives important information about genetic pre-dispositions
and acquired mutations/local rearrangements. Both mRNA and protein
profiles generate "molecular portraits" of a biological state/stage
or disease, and may also be used for staging and monitoring of the
disease development and treatment. As opposed to the DNA, both mRNA
and protein profiles represent "snap shots" of the cell's biology,
since they are continuously changing in response to the surrounding
environment. Due to regulatory mechanisms acting both at the
transcriptional, translational and post-translational levels, mRNA
and protein levels do not always correlate. It is therefore crucial
to study both mRNA and protein from the same sample.
[0006] Thus, as mentioned above, there is however not necessarily a
1:1 correlation between mRNA and protein levels. If protein levels
and corresponding mRNA levels are compared, then for every protein
for which the ratio of mRNA and protein is not 1:1 then this
protein is subject to some form of interesting post transcriptional
and/or post translational regulation. mRNA/protein ratios for
specific genes are often shifted during disease conditions. To be
able to study regulatory mechanisms and to unravel the reasons
behind such a shift in mRNA/protein ratios, it is crucial to
isolate mRNA and protein from the same sample. A novel and
advantageous method for carrying out such isolation is presented
herein.
[0007] Variation in protein or mRNA levels between individuals, for
example in an individual with a disease state compared with a
"normal" patient, are often due to single nucleotide polymorphisms
(SNPs) or other forms of mutation or genetic predisposition in
their genes (i.e. their DNA) or their regulatory regions. For this
reason it is advantageous to be able to isolate DNA and protein,
preferably DNA, RNA and protein, and especially DNA, mRNA and
protein from the same sample to enable direct comparison. Such
methods are also provided by the present invention.
[0008] In particular, it has now been found that nucleic acid and
protein, and in particular DNA, RNA and protein can be isolated
from a single sample in a form suitable for downstream manipulation
and analysis, by a simple and easy to perform procedure. This
isolation method involves binding nucleic acid and protein or
preferably DNA, RNA and protein from the same sample on to distinct
solid supports or areas of solid supports so that the isolated
components can be analysed separately. Advantageously these methods
can be combined with a further initial step involving the specific
isolation of one or more particular cell types or populations (e.g.
B-cells, T-cells, monocytes) from the sample before the isolation
of nucleic acid and protein is carried out. In particular, it has
been shown that DNA (e.g. genomic DNA), RNA (e.g. mRNA) and
proteins may be isolated from a single sample with a high,
documented purity. Different cell populations can also be isolated
sequentially from the same sample and then each of these can be
subjected to DNA, RNA and protein isolation.
[0009] In one aspect, the present invention thus provides a method
of isolating nucleic acid and protein from the same sample, said
method comprising contacting said sample with solid supports,
whereby the nucleic acid and protein components in said sample
become bound to distinct solid supports.
[0010] The nucleic acid to be isolated may be DNA, RNA or any
naturally occurring modification thereof, and combinations thereof.
Thus, the entire nucleic acid based component of a sample can be
isolated in the method of the invention. In a preferred embodiment
of the invention however DNA and/or RNA are separately isolated
from the same sample onto distinct solid supports.
[0011] Thus, in preferred embodiments the present invention
provides a method of isolating RNA and protein or DNA and protein
from the same sample. In especially preferred embodiments the
invention provides a method of isolating DNA, RNA and protein from
the same sample.
[0012] In embodiments and steps of the methods of the invention,
where the nucleic acid to be isolated from the sample is DNA,
preferably the DNA is genomic DNA (gDNA) and may be in a single or
double stranded or in any other form. In certain embodiments a
specific DNA molecule, e.g comprising a gene encoding a specific
protein may be isolated.
[0013] In embodiments and steps of the methods of the invention,
where the nucleic acid to be isolated from the sample is RNA, total
RNA may be isolated or a particular form or subset of RNA may be
isolated. In preferred embodiments of the invention mRNA is
isolated from the sample. In certain embodiments a specific RNA
molecule, e.g. a specific mRNA encoding a specific protein may be
isolated.
[0014] In the methods of the present invention described herein the
steps of isolating nucleic acid and protein onto distinct solid
phases involving contacting the sample with said solid phases can
be carried out sequentially or simultaneously. Similarly, in
embodiments where it is desired to isolate protein, DNA and RNA as
separate components then these isolations can be carried out in the
same step or in separate sequential steps. As will be described
further below, in certain situations it may be desirable to carry
out protein and nucleic acid (e.g. DNA and/or RNA) isolations on
separate aliquots (or fractions) of the same sample (i.e. on a
divided or split sample). In such cases the isolations may be
carried out in parallel steps, e.g. simultaneously in parallel.
[0015] Preferably the required isolations are carried out in
separate sequential steps which can, in turn, be carried out in any
order. Thus, although in the preferred embodiments of the invention
DNA is isolated in a first step, followed by RNA in a second step
and protein in a third step the different components can be
isolated in any order.
[0016] The term "distinct solid phases" as used herein includes the
use of different solid supports (i.e. supports with different
binding and surface properties) in different steps of the method of
the invention (for example in embodiments where sequential steps
are used to bind the desired nucleic acid components and proteins),
different supports added in same step (for example in embodiments
where the isolation of the desired nucleic acid components and
protein are carried out in the same step) and the use of supports
with the same surface properties added in different steps, where
binding of a particular nucleic acid or protein component is
enabled by virtue of different incubation conditions. Furthermore,
in some situations a particular solid support may bind different
components (e.g. protein and nucleic acid, or cells and protein or
nucleic acid etc.) when placed under different conditions e.g.
different incubation conditions, reagents, environment etc. Such
differences may also be exploited to bind different components to
the same solid support, but in distinct or different steps, e.g. at
different stages of the procedure, such that the desired components
may be separately isolated. This term also includes different areas
of a single solid support, which may for example be designed to
have different surface properties such that particular nucleic acid
and protein components bind to different areas or different ligands
of the same support.
[0017] As mentioned above, it is an important aspect of the
invention that nucleic acid and protein are analysed from the same
sample.
[0018] "Same sample" as used herein refers to the isolation of the
appropriate nucleic acid and protein components from a single, i.e.
undivided sample. In this way the method of the invention is
distinguished from prior art methods which may involve obtaining
multiple samples or equivalent procedures, for example obtaining
one initial sample, and straightaway at the outset dividing it into
aliquots e.g. obtaining a sample and dividing it into aliquots on
which a separate analysis of DNA, RNA and protein (one for each
aliquot) is carried out and the results compared. Thus, an
"undivided sample" may be viewed as a sample which is not divided
straightaway e.g. immediately or initially after sampling, or at
the outset before any isolation procedures are carried out. Thus,
subsequent later division of the sample is not precluded, but it is
not divided initially, or as a first step in the sample treatment
process. Conveniently, as will be described further below, prior to
carrying out nucleic acid and/or protein isolation procedures, it
may be advantageous, or desirable first to isolate a particular
desired population or sub-population of cells, or indeed to isolate
all (or substantially all) the cells or any desired fraction
thereof from the sample, and/or to lyse the cells in the sample or
in any isolated population or fraction thereof. In such situations
it may be desired or convenient to divide the single (i.e. same)
sample after the cell isolation or cell lysis steps have been
carried out.
[0019] Thus, division of the sample after an initial, or first,
isolation step, or after two or more isolation steps is
contemplated. This may be desirable if, for example, if it is
desired to change conditions (e.g. ionic strength, salt
concentration etc), e.g. to isolate different components. Thus, for
example, protein and nucleic acid components (i.e. DNA and/or RNA)
may be isolated from different aliquots of the sample after such a
sample splitting or division-step. However, in one advantageous
embodiment of the invention, the method is carried out using a
single sample which is not divided at any stage or at any time. The
fact that the multiple analysis of DNA, RNA and protein can be
carried out on a single, undivided sample using the methods of the
present invention is clearly advantageous and will allow for a more
direct and accurate comparison between the various nucleic acid and
protein components of the sample.
[0020] The samples suitable for use in the methods of the present
invention may be any material containing nucleic acid and protein,
including for example foods and allied products, clinical and
environmental samples. However, the sample will generally be a
biological sample, which may contain any viral or cellular
material, including all prokaryotic or eukaryotic cells, viruses,
bacteriophages, mycoplasmas, protoplasts and organelles. Such
biological material may thus comprise all types of mammalian and
non-mammalian animal cells, plant cells, algae including blue-green
algae, fungi, bacteria, protozoa etc. Representative samples thus
include whole blood and blood-derived products such as plasma,
serum and buffy coat, bone marrow and samples obtained from other
haematopoetic tissues, urine, faeces, cerebrospinal fluid or any
other body fluids, tissues (for example solid tissues), cell
cultures, cell suspensions etc. Preferably the sample is a live
(e.g. a non-fixed sample), i.e. comprises viable cells, or at least
cells which have not been treated in any way.
[0021] The sample may be freshly obtained, or stored or treated in
any desired or convenient way, for example by dilution, or adding
buffer, or other solutions or solvents, enzyme-containing solutions
etc.), as long as the integrity of the nucleic acids and proteins,
or the cells or other entities containing such nucleic acids and
proteins within the original sample are maintained, i.e. are not
substantially degraded. Nucleic acids and protein may be denatured
but not degraded.
[0022] It is further advantageous that a crude sample can be taken
directly from its source, e.g. directly from a patient or from the
environment (e.g. a direct clinical or environmental sample) and
its protein and nucleic acid analysed using the methods of the
invention.
[0023] The nucleic acid- and protein-containing sample may,
generally speaking, simply be contacted with the appropriate solid
supports under conditions whereby the nucleic acids or proteins as
appropriate will become bound to the solid support. If necessary,
e.g. if the nucleic acid and protein to be isolated is not
available for binding within the initial sample e.g. is contained
within a biological particle as described above e.g. a viral coat
or a cell membrane or wall, the initial binding step may be
preceded by one or more separate steps to free the nucleic acid and
protein components, e.g. by disrupting structural components such
as cell walls or to achieve lysis. Procedures for achieving this
are well known in the art. Thus, for example, although some cells
e.g. blood cells, may be lysed by reagents such as detergent alone,
other cells, e.g. plant or fungal cells or solid animal tissues may
require more vigorous treatment such as, for example, grinding in
liquid nitrogen, heating in the presence of detergent, alkaline
lysis in the presence of detergent. The main requirement is that
procedures for freeing the nucleic acid and protein are chosen such
that the particular nucleic acid and protein species which are to
be isolated in the methods of the invention remain sufficiently
intact, e.g. are not substantially degraded.
[0024] Preferably samples are 10 .mu.l to 100 ml in size,
preferably from 200 .mu.l to 10 ml. The method of the invention may
be used for small samples, e.g. less than 1 ml or for larger
samples e.g. at least 2 ml, e.g. more than 5 ml or 10 ml or 50 ml.
A major advantage of the present invention is that small sample
volumes may be used, and in particular that protein may be isolated
from such small sample volumes following, or concurrently with, DNA
and/or RNA isolation. This feature makes the method of the
invention particularly suitable for automation. Advantageously the
sample volume as subjected to the nucleic acid/protein isolation
procedures is 1 ml or less, e.g. 10 to 800 .mu.l, e.g. 20 to 500
.mu.l, or 50 to 200 .mu.l. For example, the method may be performed
on a sample containing 1.times.10.sup.4 to 1.times.10.sup.6 cells,
preferably 1-10.times.10.sup.5 cells. The method described is
highly scalable and can be used to detect DNA/RNA/protein in 1, 5,
10, 20, 200 or 2000 or more cells.
[0025] As mentioned above an optional and preferred initial step
once the sample has been obtained is to enrich the sample for
particular populations, e.g. particular populations of cells or
organelles for which the nucleic acid and protein is to be
analysed.
[0026] Methods of enrichment are well known and documented in the
art. Preferred methods involve the use of a solid phase, i.e. the
binding of the population(s) in question to a solid phase and
exemplary methods will be discussed in more detail below. In such
methods, one or more steps of positive and/or negative solid phase
selection can be used, as appropriate, depending on the desired
purity of sub-population required. Such techniques are well known
and described in the art. Briefly, in a negative selection step,
the cells/populations which bind to the solid phases are removed
from the sample to be analysed, whereas in a positive selection
step the cells/populations which bind to the solid phases are
retained in the sample to be analysed.
[0027] Exemplary and preferred antibodies for use in the isolation
of specific cell populations are CD15 and CD45 antibodies (specific
for leukocytes), CD14 antibodies (specific for monocytes), CD2,
CD3, CD4 and CD8 antibodies (specific for T-cells), CD19 antibodies
(specific for B-cells) and Anti Ber EP4 antibodies (specific for
epithelial cells and in particular circulating carcinoma cells).
Other antigens may also be used as the basis for detection by
binding to specific antibodies (or antibody fragments, derivatives
etc.), as indeed may any other cell surface molecule which may bind
specifically to a binding partner or ligand.
[0028] If desired, prior to cell lysis, cell surface proteins may
be subjected to an in vitro modification procedure for example
chemical modification, e.g. biotinylation or radiolabelling, for
example to introduce a label or reporter or marker group etc.,
prior to nucleic acid and protein isolation steps. Such modified
surface proteins may then be isolated by a specific or adapted
isolation procedure. Thus, for example, a biotinylated surface
(e.g. membrane) protein may be isolated by binding to a solid
support carrying streptavidin or avidin.
[0029] Other methods of isolating a desired cell population may
also be used, as desired, for example Laser Capture
Microdissection.
[0030] Where the method of the invention involves such a
preliminary cell/organelle etc. isolation step, it will be
appreciated that larger sample volumes may be used, e.g. 1-50 ml,
e.g. 2 to 20 ml or 5-10 ml, for example of a blood or other
clinical sample.
[0031] Sample preparation is one of the bottlenecks in proteomics
in that due to the variation in abundancy and lack of specific
amplification technology for proteins, it is advantageous to reduce
sample complexity in order to increase resolution. Thus the
optional step of the present invention by which a particular sample
can be treated to specifically enrich for a particular specific
population or populations of cells, organelles, etc., and thereby
proteins is extremely advantageous. Thus, it can be seen that the
methods of the invention allow the enrichment of a particular
population of cells and the analysis of DNA, RNA and protein
therefrom using the same single sample. The fact that this sample
can be taken directly from a patient is a further advantage.
[0032] The feature of specifically or selectively isolating a
desired population may be applied advantageously to comparing
multiple (e.g. 2 or more, e.g. 2 to 10 or 2 to 6) populations from
the same sample. Thus, for example, by the use of different
appropriate binding partners specific for particular desired
populations and coupled to different solid supports, different
populations may be isolated, or separated from the same sample.
[0033] Thus, a preferred embodiment of the invention provides a
method of isolating DNA, RNA, and protein from the same sample,
said method comprising the following steps:
[0034] a) isolating from said sample the populations from which the
nucleic acid and protein is to be isolated and preferably isolating
one or more specific populations;
[0035] b) lysis of the populations, e.g. cell populations, to
obtain a sample containing nucleic acid and protein in a free form
available for binding to a solid support;
[0036] c) contacting sample with an appropriate solid phase under
conditions whereby DNA, preferably genomic DNA, becomes bound to
the solid support;
[0037] d) separation of this solid phase from the remainder of the
sample;
[0038] e) contacting said remainder of the sample with an
appropriate solid phase under conditions whereby RNA, preferably
mRNA, becomes bound to the solid support;
[0039] f) separation of this solid phase from the remainder of the
sample;
[0040] g) contacting said remainder of the sample with an
appropriate solid phase under conditions whereby a specific protein
or population of proteins becomes bound to the solid support;
[0041] h) separation of this solid phase from the remainder of the
sample.
[0042] The method outlined above is a preferred embodiment of the
invention and clearly these specific steps can be altered depending
on the overall analysis it is wished to achieve to form further
embodiments of the invention. In particular, some of the above
discussed steps are optional and need not be included. For example,
steps a) and b) are optional and whether or not they are carried
out depends on the nature of the sample which is initially
obtained. If this sample does not contain the nucleic acid and
protein which it is desired to analyse in a free and released form,
for example if the nucleic acid and protein is contained within
cells or tissues or other biological packages, then generally steps
a) and b) will be carried out.
[0043] In addition, the above described methods describes the
sequential isolation of DNA, RNA and protein in separate steps. The
isolation of the whole nucleic acid component as one fraction and
protein, and the isolation of DNA and protein, and RNA and protein,
are also within the scope of the invention and the steps of the
method can be adapted as appropriate to fulfil this purpose. For
example, if it is desired to isolate the total nucleic acid and
protein, step c) can be replaced by a step which involves
contacting the sample with an appropriate solid phase under
conditions whereby the total nucleic acid component, e.g. DNA and
RNA, becomes bound to the solid support. Step e) would then be
omitted. If it is desired to isolate DNA and protein then the RNA
steps e) and f) can be omitted. Vice versa, if it is desired to
isolate RNA and protein then the DNA steps c) and d) can be
omitted.
[0044] In addition, the nucleic acid and protein isolation steps of
the above described methods can be carried out in any order. Thus,
although in a preferred embodiment the order is DNA followed by RNA
followed by protein (if all three components are to be analysed),
the steps may be carried in any order, e.g. the RNA or the protein
may be isolated first. In methods where nucleic acid and protein
are to be isolated, or DNA and protein, or RNA and protein are to
be isolated, although in preferred embodiments the nucleic acid
component is isolated first, the protein component may be isolated
first.
[0045] In addition, in a further embodiment of the invention the
desired nucleic acid and protein components can be isolated
simultaneously from the same sample in the same step. This may be
achieved in any appropriate manner but will generally be carried
out by contacting the sample simultaneously with distinct solid
supports which have different surface properties and are able to
bind specifically to DNA (e.g. genomic DNA), RNA (e.g. mRNA), all
nucleic acid species, or protein, as appropriate. Appropriate solid
supports which have specificity for the various nucleic acid and
protein components which it is desired to isolate from a particular
sample are described herein and any of these may be used. These
distinct solid supports with different surface properties may be
provided on different areas of the same solid support, or may be
provided as separate solid supports which are brought into contact
with the sample in the same step. These separate solid supports may
conveniently be provided for example as separate dipsticks with
different appropriate surface properties. Once the desired nucleic
acid and protein components have been isolated in such a single
step then they can be used and analysed in the same way as if
isolated in separate steps.
[0046] Once the desired nucleic acid and protein components have
been separated onto solid phases these can be subjected to further
analysis, e.g. by conventional methods. Again appropriate-methods
of further analysis will be discussed in more detail below.
[0047] The binding of nucleic acid to a solid support is generally
independent of its sequence and the specificity of binding is
controlled by varying the properties of the solid support and the
conditions under which binding of the nucleic acid is induced. As
described above the whole nucleic acid component of a sample can be
induced to bind to a solid phase or the appropriate choice of
binding conditions and/or nature of the solid support can be
effected so that DNA or RNA can be selectively bound to a solid
phase, thereby enabling a selective DNA or RNA isolation procedure,
which may be carried out simultaneously or preferably sequentially.
Appropriate methods and conditions whereby all nucleic acid may be
bound or DNA and RNA are selectively bound to a solid phase are
well known and documented in the art and any of these methods can
be used in the methods of the present invention. Some appropriate
and preferred methods are discussed briefly here and in more detail
below where alternative methods are also discussed.
[0048] Conveniently, where DNA and RNA are isolated in two separate
steps the sequential separation may take place using two different
solid phases, for example solid supports which can differentiate
between DNA and RNA. Thus, such embodiments may comprise carrying
out a first separation step to isolate DNA. A further solid support
can then be added to the sample to capture the RNA remaining in the
sample, either by using a solid support that can bind the RNA, e.g.
a silica based support (described in more detail below), or a solid
support that can capture specific RNA molecules (e.g. by carrying a
complementary nucleic acid probe), or a solid support which can
capture a subset of RNA molecules e.g. polyadenylated RNA, using
for example a poly-dT or poly-dU based oligonucleotide capture
probe. In this way it is possible rapidly to isolate and separate
DNA and RNA or subsets of both from the same sample.
[0049] In a representative procedure, the sample is lysed in the
presence of detergent and the DNA is allowed to bind to a solid
support, whereupon the DNA may readily be separated from the sample
by removal of the support. Such procedures are described in more
detail in WO96/18731 (and in particular Example 12) the disclosure
of which is incorporated herein by reference. The procedure of
specific DNA capture described in WO96/18731 is also known as the
DNA DIRECT method and can be made selective for genomic DNA.
Appropriate conditions and methods for carrying out such
separations are also described in the Dynabeads DNA DIRECT kit
(which is commercially available from Dynal Biotech AS, Oslo,
Norway). In methods of the invention where it is desired to isolate
DNA and in particular genomic DNA, the DNA DIRECT method of
separation is one preferred embodiment. Alternatively, other solid
supports having surface chemistries or surface properties
supporting DNA binding may be used, for example a support
(preferably magnetic beads) carrying surface carboxyl groups.
[0050] The RNA may then be isolated from the remaining sample. This
can be by a solid phase based system as described above wherein a
different solid phase is added to the sample to which RNA becomes
specifically bound. Alternatively the same solid phase may be used
and the RNA made to bind thereto by inducing an appropriate change
in the sample conditions.
[0051] Preferably in embodiments where the RNA is isolated by
binding to a solid phase, and in the representative procedure as
described here, the RNA is mRNA and the surface of the solid phase
used has been engineered to carry a capture probe specific for
mRNA, e.g. the support has attached to its surface dT
oligonucleotides or dU oligonucleotides, e.g. Dynabeads oligo (dT),
Dynabeads cDNA release (available from Dynal Biotech ASA) or
Dynabeads T.sub.7-oligo(dT) (a modified construct) in which a T7
promoter is included following the principles set out in Eberwine
et. al., Biotechniques (1996), 20(4): 584-91 and U.S. Pat. No.
5,514,575). The oligonucleotide attached to the "T7 beads" is a
combined oligo dT and T7 promoter sequence of the structure
5'AAAAAA-T7sequence(39 nt)-dT(20-25).dbd.. VN is added to the 3'
end of the oligonucleotide for Dynabeads T.sub.7-oligo(dT).
[0052] Appropriate conditions and methods for carrying out such RNA
separations are also described in the product inserts provided with
the Dynabeads commercial product. In particular Dynabeads oligo
(dT)(which are commercially available from Dynal Biotech AS, Oslo,
Norway) are sold with an mRNA DIRECT kit protocol which describes
how mRNA separation may be carried out. In methods of the invention
where it is desired to isolate RNA and in particular mRNA, the mRNA
DIRECT method of separation is preferred.
[0053] The choice of oligo dT or dU beads to be used depends on the
downstream applications of the isolated mRNA (see further
discussion below).
[0054] Support bound oligo dU may be used for isolation of mRNA as
discussed in WO 00/58329 of Dynal Biotech ASA. This is analogous to
the use of oligo dT, but with the added advantage that the "U's"
provide a site for cleavage by a glycosylase enzyme.
[0055] In preferred embodiments, the oligo dT/dU (including the T7
modification) constructs additionally include a further nucleotide
sequence (designated "VN", wherein "V" may be any nucleotide other
than T (e.g. A, G or C) and "N" may be any nucleotide, including T.
This additional "VN" sequence serves the advantageous purpose of
assisting in the targeting or positioning of binding of the oligo
dU/dT probe sequence to the nucleic acid; the positioning of probe
binding is advantageously at the border between the poly A tail and
the coding sequence of the mRNA.
[0056] In the step of the method where protein is isolated, this is
conveniently carried out by any appropriate method using a solid
phase with appropriate surface properties. Appropriate methods will
depend on the type of proteins it is desired to analyse. In one
embodiment specific proteins may be isolated using a solid support,
which has an appropriate binding partner/ligand attached to its
surface, e.g. an antibody to the particular protein which it is
desired to isolate. A particularly preferred antibody to be used in
this regard is anti-CK19 (a support, e.g. beads can be coated with
anti-CK19 and can be used to isolate specific problems. Anti-CK19
antibodies are commercially available). This thus applies well
known principles of affinity separation of proteins, as widely
described in the prior art. Any such standard and well known
methods may be used or adapted for the present invention.
[0057] Alternatively a solid phase with more general surface
binding properties can be selected, e.g. a solid phase which has
surface chemistry which effects classical chromatography
interactions such as ion exchange (including both anion exchange
and cation exchange), reverse phase interactions or hydrophobic
interactions. Such surfaces are conveniently provided on magnetic
beads. The use of these more general surfaces conveniently allows
the fractionation of proteins in the sample into subsets depending
on the structure and properties (charge, hydrophobicity) etc. of
the proteins present.
[0058] Such general solid phase surfaces can be prepared using
conventional techniques which are standard and well documented in
the art of column chromatography. Furthermore, supports (e.g.
particles or beads) have been widely described in the art for
fluidised bed separation technology, and have properties e.g. ion
exchange, designed for protein separation (e.g. U.S. Pat. No.
5,084,169, U.S. Pat. No. 5,079,155 and U.S. Pat. No. 473,231).
Magnetic particulate solid supports having such surface chemistry
are not known in the art and thus form a further embodiment of the
invention. A solid support suitable for protein isolation comprises
on its surface positively charged amine groups, which are believed
to bind negatively charged proteins. The bound proteins may be
eluted under conditions of high salt and low pH. Amine beads are
available from Dynal Biotech AS as Dynabeads M-270 amine.
[0059] In embodiments of the invention where the protein isolation
step is carried out after the various nucleic acid isolation steps,
the remaining sample may be subjected to any convenient treatment
before the protein is isolated using the appropriate solid support.
For example, if it is desired to fractionate the proteins present
in the sample, for example using the solid supports with more
general surface binding properties as described above, this step
can be preceded by a step whereby the protein sample is subdivided
into different fractions, e.g. subdivided into one or more of
membrane fraction, cytosolic fraction and nuclear fraction. Methods
for carrying out such subdivision are standard and well documented
in the art of protein analysis.
[0060] In all the embodiments of the invention described herein,
whilst any solid support formats may be used, as well known in the
art and widely described in the literature, preferred solid
supports are particles and more preferably magnetic particles.
Magnetic particles (beads) are well known in the art and widely
commercially available. Different sizes of beads are available, or
may be prepared, and different applications (e.g. different DNA,
mRNA, protein etc. separations) may be optimised on beads of
different sizes, e.g. 4.5 .mu.m, 2.8 .mu.m, 2.7 .mu.m, 1.0 .mu.m in
diameter.
[0061] The methods of the invention are advantageously amenable to
automation, particularly if particles, and especially, magnetic
particles are used as the support. In a particularly favoured
embodiment of the invention, the nucleic acid and protein isolation
method is performed using an automated system for handling of the
solid support during the cell lysis, nucleic acid binding, protein
binding and, optionally, washing steps. Thus the isolated
support-bound cells may be transferred to such an apparatus, washed
if desired, and lysed; the nucleic acid (i.e. whole nucleic acid
component, DNA or RNA) or protein, as appropriate depending on the
particular step of the method and the particular support and
conditions used may bind to the support, and the bound nucleic acid
or protein may readily be washed, using such an apparatus.
Furthermore, such an apparatus may also be used to handle the
support during the cell/population isolation stage. Thus, it can be
seen that the option is there to automate all of the steps of the
method if desired.
[0062] Particular mention may be made in this regard of the Bead
Retriever.TM., available from Dynal Biotech ASA, Norway. The
apparatus has a system for ready and efficient transfer of the
support (carrying cells or nucleic acid or protein) from one well
to another. Other automated robotic workstations which may be used
include the BioMek 2000 with the Dynal MPC-auto96 magnet station
and the TECAN GENESIS RSP with its own built in magnet station.
Both the BioMek and the TECAN GENESIS RSP are liquid handling
robots.
[0063] The present invention provides the first description of a
technology which can isolate specific cell populations, DNA, mRNA
and proteins from the same sample in an automated way, e.g. by
carrying out all the steps using a solid phase and in particular a
magnetic solid phase. Other methods such as laser microdissection
are much slower than the methods described herein, are not
automatable and require fixed, sectioned material.
[0064] The various reactants and components required to perform the
methods of the invention may conveniently be supplied in kit form.
Such kits represent a further aspect of the invention.
[0065] At its simplest, this aspect of the invention provides a kit
for isolating nucleic acid and protein from the same sample
comprising:
[0066] (a) a solid support suitable for binding nucleic acid
components; and
[0067] (b) a solid support suitable for binding proteins.
[0068] In preferred embodiments the supports of (a) comprise
supports which are selective for binding to DNA, or supports which
are selective for binding to RNA, or both types of support.
[0069] Further optional components of the kit include (c) solid
supports suitable for isolation of specific cell populations, (d)
means for lysing said cells.
[0070] The various components (a), (b), (c) and (d) may be as
described and discussed above in relation to the methods of the
invention.
[0071] A further optional component is (e), means for detecting the
nucleic acid and/or protein. As discussed above, for detecting
nucleic acids such means may include appropriate probe or primer
oligonucleotide sequences for use in hybridisation and/or
amplification-based detection techniques. For detecting proteins
such means include appropriate antibodies.
[0072] Optionally further included in such a kit may be buffers,
salts, polymers, enzymes etc.
[0073] Once one or more nucleic acid and protein components have
been isolated onto a solid phase, these can then be analysed or
used in any appropriate way. For example, the methods of the
invention can be used in any application which involves analysis or
comparison of the genome (DNA), transcriptome (RNA) and proteome
(expressed protein), or in any analysis where it is desired to
compare a particular DNA and/or RNA and the expressed protein, or
more preferably a particular DNA, RNA and protein. Such methods are
very useful for gene expression studies as they allow analysis and
comparison of mRNA levels with protein levels. In addition, the
ability to analyse and compare mRNA and protein levels and profiles
of samples (e.g. from different cells and tissues) gives a snapshot
of the cell's biology. Furthermore, being able to study the
mRNA/protein ratio gives an indication of which genes are subject
to post-transcriptional regulation. Such ratios are often shifted
during disease states, thereby allowing an indication as to which
genes may be involved in disease and allowing a study of the
possible regulatory mechanisms behind such a shift in mRNA/protein
ratio.
[0074] The methods of the invention are also useful for example in
determining the molecular changes and mechanisms involved in
disease states, e.g. determining which genes are mutated, or which
proteins are over or under expressed or incorrectly processed.
Studying the DNA composition of a sample can provide information on
genetic predispositions and acquired mutations, whereas the mRNA
and protein profiles generate "molecular portraits" of a cell's
biological state or the stage of disease and may also be used for
the staging and monitoring of the disease development and
treatment. As mentioned above, the methods described are
particularly advantageous for such analysis, as they allow the
comparison of DNA, RNA and protein from the same sample which is
important to allow a more accurate and direct comparison.
[0075] The method of the invention also has use as a method for
isolating nucleic acid and protein fractions from a single
sample.
[0076] More specifically, in the case of the DNA, once isolated
this can be used in nucleic acid based detection procedures, e.g.
in genotyping, SNP analysis, sequencing reactions etc.
[0077] Advantageously the bound nucleic acid need not be eluted or
removed from the support prior to carrying out the detection step,
although this may be performed if desired. Whether or not the
nucleic acid is eluted may also depend on the particular method
which was used in the nucleic acid binding step. Thus certain
nucleic acid-binding procedures will bind the nucleic acid more
tightly than others. In the case of DNA-binding using detergents
(e.g. by DNA Direct) for example, the nucleic acid will elute from
the solid support when an elution buffer or other appropriate
medium is introduced. Nucleic acid bound by means of a precipitant
such as alcohol or a chaotrope will remain more tightly bound and
may not elute when placed in a buffer medium, and may require
heating to be eluted. A preferred use of the DNA is in solid phase
SNP analysis, which may optionally be fully automated. Such SNP
analysis can be carried out using any appropriate technique. For
example, PCR can be carried out using one biotinylated primer,
followed by single stranded DNA template generation on streptavidin
beads, followed by probe annealing, ddN incorporation and a
labelling reaction.
[0078] Thus, the support-bound nucleic acid may be used directly in
a nucleic acid based detection procedure, especially if the support
is particulate, simply by resuspending the support in, or adding to
the support, a medium appropriate for the detection step. Either
the nucleic acid may elute into the medium, or as mentioned above,
it is not necessary for it to elute.
[0079] A number of different techniques for detecting nucleic acids
are known and described in the literature and any of these may be
used. Conveniently, nucleic acid may be detected by optical
methods, for example by measuring or determining optical density
(OD). Alternatively, the nucleic acid may be detected by
hybridisation to a probe (which may be a labelled probe for
detection) and very many such hybridisation protocols have been
described (see e.g. Sambrook et al., 1989, Molecular Cloning: A
Laboratory Manual, 2nd Ed. Cold Spring Harbor Press, Cold Spring
Harbor, N.Y.). Most commonly, the detection will involve an in situ
hybridisation step, and/or an in vitro amplification step using any
of the methods described in the literature for this, for example
probe annealing/hybridization followed by ddN incorporation (which
may be labelled for detection). Thus, techniques such as LAR, 3SR
and the Q-beta-replicase system may be used. However, PCR and its
various modifications e.g. the use of nested primers, or the use of
one or more biotinylated primers will generally be the method of
choice (see e.g. Abramson and Myers, 1993, Current Opinion in
Biotechnology, 4: 41-47 for a review of nucleic acid amplification
technologies).
[0080] Other detection methods may be based on a sequencing
approach, for example, the minisequencing approach as described by
Syvanen and Soderlund, 1990, Genomics, 8: 684-692.
[0081] In amplification techniques such as PCR, the heating
required in the first step to melt the DNA duplex may release the
bound DNA from the support. Thus, in the case of a subsequent
detection step, such as PCR, the support bound nucleic acid may be
added directly to the reaction mix, and the nucleic acid will elute
in the first step of the detection process. The entire isolated
support bound nucleic acid sample obtained according to the
invention may be used in the detection step, or an aliquot.
[0082] The results of the PCR or other detection step may be
detected or visualised by many means, which are described in the
art. For example the PCR or other amplification products may be run
on an electrophoresis gel e.g. an ethidium bromide stained agarose
gel using known techniques.
[0083] The amplified nucleic acid may also be detected, or the
result confirmed, by sequencing, using any of the many different
sequencing technologies which are now available, e.g. standard
sequencing, solid phase sequencing, cyclic sequencing, automatic
sequencing and minisequencing.
[0084] If mRNA is isolated, for example using oligo(dT) beads, or
oligo(dU) beads (e.g. using Dynabeads oligo(dT), Dynabeads cDNA
release or Dynabeads T7 oligo(dT) as described herein) this mRNA
can be used or analysed in any appropriate way. The mRNA can for
example be analysed using appropriate conventional techniques, e.g.
by Northern blotting, or can be used to generate cDNA which may
then be subjected to any appropriate DNA based analysis such as
those described above.
[0085] It can be seen that mRNA and cDNA libraries from specific
samples, e.g. specific populations or sub-populations of cells,
viruses, etc can be produced using the methods of the invention.
This application can either be carried out while the mRNA is still
on the solid phase, i.e. resulting in solid phase cDNA libraries,
or can be carried out after the mRNA has been eluted. The mRNA may
also be used as a substrate for RT-PCR. Solid phase cDNA libraries
can be used in any appropriate application and can be re-used, for
example as template in different PCRs (or other amplifications),
thereby enabling PCR (or other) analysis of multiple transcripts,
e.g. from single isolated cells. For example, it can be seen from
FIG. 2 that a solid phase c-DNA library has been re-used in
multiple PCR experiments to detect different transcripts in
cultured carcinoma cells.
[0086] If Dynabeads cDNA release beads (or commercial or generic
equivalents) are used to isolate the mRNA, as described above,
these beads have oligo(dU)VN coupled to their surface. These
oligo(dU)VN molecules bind to the mRNA and can be used to prime one
strand of solid phase cDNA synthesis. The solid phase cDNA can then
be released enzymatically by UNG treatment and used, e.g. for probe
generation for gene expression profiling.
[0087] If Dynabeads T7 oligo(dT) beads (or commercial or generic
equivalents) are used to isolate the mRNA, as described above,
these beads have coupled to their surface a T7 promoter 5-prime to
the oligo(dT)VN. After double stranded solid phase cDNA synthesis
(first strand synthesis carried out using the oligo (dT) as a
primer and second strand synthesis initiated with random hexamers),
the T7 promoter (which is a 39 nucleotide sequence specific for the
enzyme T7 polymerase, which recognises this sequence in double
stranded DNA) can be used to in vitro transcribe antisense RNA and
thereby amplify mRNA from small samples for further analysis, or
e.g. for probe generation for gene expression profiling, e.g. for
microarray analysis. Such probes are conveniently generated by
carrying out reverse transcription of the antisense RNA (with
random hexamers) to give cDNA which can be labelled and used to
probe microarrays. These cDNAs can also be used in a second round
of amplification using T7 beads.
[0088] Although microarrays are a powerful high throughput tool,
they are not very sensitive--at least 1-2 .mu.g of mRNA is required
per array. This is often impossible to achieve, e.g. by single cell
analysis. Thus, in vitro transcription methods are required to
amplify the RNA. For this reason the ability to use the Dynabeads
T7 oligo(dT) beads to amplify RNA is advantageous in microarray
applications and any other applications where amplification of mRNA
is advantageous.
[0089] Once isolated by binding to a solid phase using the methods
of the invention, subsets of proteins (e.g. those isolated using
the supports with more generalised chromatography type surfaces) or
individual proteins (e.g. those isolated using supports carrying
specific ligands) can be subjected to direct analysis whilst still
on the bead (e.g. Bead ELISA) or can be subjected to elution from
the solid support followed by analysis by any appropriate
conventional technique such as SDS-PAGE/Western blotting,
immunoprecipitation, etc.
[0090] As discussed extensively above, one of the main advantages
of the method of the invention is that one or more of DNA, RNA and
protein can be isolated from the same sample ready for analysis.
Thus, results obtained by analysing the DNA, RNA and protein from
the same sample using any of the individual techniques described
above can be compared as appropriate depending on the aim of the
analysis.
[0091] If the initial sample contains cells or other biological
particles which contain the nucleic acid and protein which is to be
analysed, then generally the cells/particles to be analysed will
need to be separated from the remainder of the sample. Such
separation can be carried out by any of the methods which are
standard and conventional in the art, such as sedimentation or
centrifugation or cell sorting procedures. Alternatively affinity
based separation systems may be used and these are described in
more detail below. Such affinity based systems are especially
preferred if it is desired to analyse the nucleic acid and protein
from a sub-population of the cells or particles contained within
the initial sample. Where such affinity-based systems are used, the
separation is generally carried out by binding the cells or
particles to a solid support carrying an appropriate binding
partner.
[0092] Affinity-based separation or isolation systems for desired
target cells are well known in the art, and rely on the specificity
of a binding partner, specific or selective for the target cell, to
achieve selective isolation of the cell. Such a system is employed
as an optional step according to the present invention in order to
achieve selective isolation of one or more particular populations
of cells or other biological "particles" from the sample before it
is treated in order to free the nucleic acid and protein and
provide the nucleic acid and protein containing sample. Thus, a
suitable binding partner for use in this regard may be one or more
moieties having a binding affinity for the desired cell or other
population(s).
[0093] The binding partner may be any molecule or moiety capable of
binding to the required populations of cells or other particles,
but conveniently will be a protein, polypeptide or peptide. Other
moieties or molecules of a different chemical nature, for example
carbohydrates or small organic molecules may however also be used.
Nucleic acid binding partners e.g. aptamers may also be used.
[0094] The binding partner may bind to molecules or structures
present on the surface of the cells or other particles, for example
to cell surface antigens which are expressed (e.g. specifically) on
the surface (e.g. cell specific Dynabeads such as Dynabeads
Epithelial Enrich, anti CD14, anti CD3, anti CD4, anti CD8, anti
CD19). Alternatively, the binding partner may be any moiety binding
to a cell surface expressed protein e.g. a cell surface
receptor.
[0095] The binding partner may, for example, conveniently be an
antibody specific for a particular surface antigen. Antibody
fragments and derivatives may also be used, according to techniques
well known in the art. Methods for preparing such fragments or
derivatives are well known in the art and widely described in the
literature.
[0096] Thus, using knowledge of the molecules or other entities
present on the surface of the desired population(s), a binding
partner, or combination or mixture of binding partners, may be
selected to achieve a desired separation or isolation of cell or
other populations from the sample. Advantageously, all or
substantially all (i.e. close to all) of the desired cells or other
particles present in the sample may be separated. The separation
achievable may be dependent not only on the binding partner(s)
selected, but also on the nature of the sample, binding conditions
etc. Also, biological systems are by their nature variable, and
100% separation may not always be achieved, and, indeed, is not
necessary according to the present invention; as in any biological
system, some tolerance must be allowed for. However, in preferred
embodiments of the invention at least 60%, 65%, 70%, 75%, 80%, 85%,
90% or 95% of the desired populations present in the sample may be
separated.
[0097] Where more than one different type of binding partner is
used they may be attached to the same or different solid supports.
Such a system using different solid supports, is applicable
particularly in the case of a particulate support such as beads.
Thus, different binding partners may be attached to different
beads.
[0098] In embodiments where more than one different type of binding
partner is used, appropriate amounts or ratios at which the
different types of binding partner may be used will be readily
determined by a person skilled in the art.
[0099] As mentioned above, cell separation techniques based on
solid phase affinity binding (e.g. immunomagnetic separation (IMS))
are well known in the art and conditions to achieve this may
readily be determined by the skilled worker in this field. IMS is a
preferred and advantageous cell separation procedure to use, since
it enables the isolation of specific cell populations with high
purity, for example more than 99% purity from whole blood, as
analysed by flow cytometry and molecular techniques. Thus, in the
embodiments where a separate affinity isolation step is used, for
example a solid support carrying appropriate binding partner(s) may
be brought into contact with the sample. A particulate solid
support may, for example, be added to the sample contained (e.g.
suspended) in an appropriate medium (e.g. a buffer). The support
may then be left in contact with the sample (e.g. incubated) for a
length of time to enable binding to the cells or other particles to
occur. Time/temperature conditions during the step are not
critical, and the sample-support mixture may be incubated at e.g. 4
to 20.degree. C. for 10 minutes to 2 hours e.g. 20-45 minutes. As
regards other conditions, these may be determined appropriately
having regard to the cells under investigation and the isolation
methods used, according to principles and procedures known in the
art. The cell isolation procedure however focuses on minimizing the
probability of affecting the physiological state of the cells and
thus enabling downstream molecular characterisation and profiling.
Laser capture microdissection can also be used to isolate cell
populations for the downstream applications described.
[0100] Following cell binding, or any other steps carried out to
separate a desired population of cells from which nucleic acid and
protein are to be analysed, the isolated or support-bound cells are
lysed to release their nucleic acid and protein. Methods of cell
lysis are well known in the art and widely described in the
literature and any of the known methods may be used. Any of the
following methods could, for example, be used: detergent lysis
using e.g. SDS, LiDS, Triton-X-100, urea or sarkosyl in appropriate
buffers; the use of chaotropes such as Guanidium hydrochloride
(GHCl), Guanidium thiocyanate (GTC), sodium iodide (NaI),
perchlorate etc; mechanical disruption, such as by a French press,
sonication, grinding with glass beads, alumina or in liquid
nitrogen; enzymatic lysis, for example using lysozyme, pronases or
cellulases or any of the other lysis enzymes commercially
available; lysis of cells by bacteriophage or virus infection;
freeze drying; osmotic shock; microwave treatment; temperature
treatment; e.g. by heating or boiling, or freezing, e.g. in dry ice
or liquid nitrogen, and thawing; alkaline lysis. As mentioned
above, all such methods are standard lysis techniques and are well
known in the art, and any such method or combination of methods may
be used. The only requirement is that an appropriate method is
chosen such that the species of nucleic acid and protein to be
analysed in the subsequent procedure remain substantially intact,
i.e. substantially non-degraded.
[0101] The use of agents such as solvents, alcohols and chaotropes
in isolation methods is sometimes disadvantageous. The present
invention affords the advantage that the use of such agents may be
avoided. Thus, whilst lysis methods such as those mentioned above
using such agents may be employed, in advantageous embodiments of
the invention the use of such agents is avoided.
[0102] Conveniently, lysis may be achieved according to the present
invention by using detergents. An exemplary suitable lysis agent
thus includes a detergent such as SDS or another alkali metal
alkylsulphate salt, e.g. LIDS, or Sarkosyl or combinations thereof.
The lysis agents may be supplied in simple aqueous solution, or
they may be included in a buffer solution, to form a so-called
"lysis buffer". Any suitable buffer may be used, including for
example Tris, Bicine, Tricine and phosphate buffers. Alternatively
the lysis agents may be added separately. Salts, for example LiCl
and NaCl, may also be included in or added to the lysis buffers. In
particular, LiCl is preferred when LiDS is used and NaCl is
preferred when SDS is used.
[0103] Suitable concentrations and amounts of lysis agents will
vary according to the precise system etc. and may be appropriately
determined, but concentrations of e.g. 2M to 7M chaotropes such as
GTC GHCl, NaI or perchlorate may be used, 0.1M to 1M alkaline
agents such as NaOH, and 0.1 to 500 (w/v) e.g. 0.5 to 15%
detergent.
[0104] To carry out the method of the invention, the support-bound
or otherwise isolated cells, may conveniently be removed or
separated from the remainder of the sample, thereby concentrating
or enriching the cells. To facilitate subsequent steps, it may be
desirable, prior to the lysis step, to dilute the isolated cells,
e.g. in an appropriate buffer or other medium. If desired the cells
may further be treated, e.g. by heating or mixing (e.g. vortexing).
A dilution step may be advantageous to prevent
agglomeration/aggregation of a particulate support such as beads.
Lysis then may conveniently be achieved by adding an appropriate
lysis buffer containing the desired lysis agents or by subjecting
the isolated cells to the desired lysis conditions. For example, in
the case of simply adding a lysis buffer containing appropriate
lysis agents, the isolated cells may simply be incubated in the
presence of the lysis buffer for a suitable interval to allow lysis
to take place. Different incubation conditions may be appropriate
for different lysis systems, and are known in the art. For example
for a detergent containing lysis buffer, incubation may take place
at room temperature or at higher temperatures e.g. 37.degree. C.,
50.degree. C. or 65.degree. C. Likewise, time of incubation may be
varied from a few minutes e.g. 5 or 10 minutes to hours, e.g. 20 to
40 minutes or 1 to 2 hours. For enzymatic lysis, longer treatment
times may be required, e.g. overnight.
[0105] Following the obtaining of a sample containing free or
released nucleic acid and protein (e.g. following lysis, if
required), the steps to be taken will depend on the particular type
of analysis it is desired to carry out. For example, in the methods
of the invention, solid phases can be used to isolate nucleic acid
and protein, DNA and protein, RNA and protein or most preferably
DNA, RNA and protein from the same sample. Which entity is isolated
depends on the nature of the solid support added and/or the
conditions to which the sample and nucleic acid is exposed.
[0106] Appropriate conditions and solid supports whereby nucleic
acids become bound to the solid support are well known and
documented in the art and any of these methods may be used in the
embodiments and steps of the invention wherein it is desired that
all the released nucleic acids (i.e. DNA and RNA) in a sample are
bound to a solid support. Conveniently, the nucleic acid is bound
non-specifically to the support i.e. independently of sequence.
Thus, for example the released nucleic acid may be precipitated
onto the support using any of the known precipitants for nucleic
acid, e.g. alcohols, alcohol/salt combinations, polyethylene
glycols (PEGS) etc. Precipitation of nucleic acids onto beads in
this manner is described for example in WO 91/12079. Thus, salt may
be added to the support and released nucleic acid in solution,
followed by addition of alcohol which will cause the nucleic acid
to precipitate. Alternatively, the salt and alcohol may be added
together, or the salt may be omitted. As described above in
relation to the cell binding step, any suitable alcohol or salt may
be used, and appropriate amounts or concentrations may readily be
determined. However, as mentioned above, it is preferred to avoid
the use of solvents, alcohols and similar agents. Thus alternative
techniques, avoiding the use of such agents are preferred.
[0107] In preferred methods of the invention the DNA and RNA are
bound to different solid supports in different steps. Again
appropriate conditions and solid supports which allow the selective
binding of DNA or RNA are well known in the art and any of these
techniques can be used. For example, such preferred techniques
whereby DNA and RNA can be separated sequentially from the same
sample is described in WO96/18731, the teaching of which is
incorporated herein by reference.
[0108] For example in this regard, by selecting appropriate
"nucleic acid binding" conditions (e.g. appropriate buffer or
lysis/binding medium compositions), it may be selected whether to
bind DNA released from the cells, or RNA released from the cells to
the solid support. Thus, "binding medium" compositions may be
selected favouring DNA binding (or more particularly genomic DNA
binding) to the solid support. Such binding medium compositions
include those mentioned above, those described in the Examples
below, and the compositions of WO96/18731. For example, a
representative DNA binding medium may include GuHCl and optionally
EDTA.
[0109] Briefly, DNA is bound to appropriate non-specific solid
supports in the presence of various detergents as described in WO
96/18731 of Dynal AS (the so-called "DNA Direct" procedure).
Various detergent-based systems for binding nucleic acids to a
solid support are described in this publication and may be used
according to the present invention. The solid support is then
separated from the rest of the sample, e.g. by the use of a
magnetic field.
[0110] To bind RNA, appropriate medium compositions or conditions
are known in the art, or may readily be determined from RNA
isolation procedures known in the art, and may include, for
example, the buffers and procedures described in EP-A-0389063 and
U.S. Pat. No. 5,234,809 of Akzo Nobel NV.
[0111] Representative RNA-binding compositions may thus include
guanidine thiocyanate (GTC) with EDTA.
[0112] For RNA binding, the nature of the solid support may be of
importance and in particular a "silica" (i.e. comprising silica
itself or being based on silica or a silica derivative) solid
surface should be used (see further below)
[0113] Advantageously, when the method of the invention is used to
isolate DNA, it may be combined with a further step separately to
isolate the RNA from the sample. Thus, following the procedure
discussed above, and selecting DNA-binding conditions in the
nucleic acid binding step (e.g. a lysis/binding or binding medium
favouring DNA binding), DNA released from the support-bound cells
may be bound to the support, and removed from the sample. RNA, most
notably mRNA, released from the leucocytes, remains in the sample
(more precisely in the supernatant). This RNA may readily be
isolated from the sample using standard procedures, for example by
binding to a capture probe, conveniently immobilised (e.g. by
binding to a solid support), consisting of oligo dT.
[0114] A further solid support can then be added to the sample
under conditions such that the RNA in the sample becomes captured.
This can be done by for example suing a solid support that can bind
the RNA or a solid support that can capture specific RNA molecules
(e.g. by carrying a complementary nucleic acid probe), or a subset
if RNA molecules, e.g. by carrying a capture probe for
polyadenylated RNA, i.e. specific for mRNA.
[0115] Conveniently, the nucleic acid or DNA binding step may take
place simultaneously or concomitantly with the cell lysis step.
This may conveniently be achieved using the detergent-based methods
of WO96/18731. Thus, for example, an agent or agents for lysis and
nucleic acid binding may conveniently be contained in an
appropriate medium (e.g. a buffer or other aqueous solution) and
added to the support-bound cells. The cells may then be maintained
in contact with the medium e.g. incubated (e.g. as described above)
to allow lysis and nucleic acid binding to take place. Such a
medium may be referred to as a "lysis/binding" medium. A detergent
may function as both lysis agent and to assist in the binding of
the nucleic acid to the support.
[0116] The detergent may be any detergent, and a vast range are
known and described in the literature. Thus, the detergent may be
ionic, including anionic and cationic, non-ionic or zwitterionic.
The term "ionic detergent" as used herein includes any detergent
which is partly or wholly in ionic form when dissolved in water.
Anionic detergents have been shown to work particularly well and
are preferred. Suitable anionic detergents include for example
sodium dodecyl sulphate (SDS) or other alkali metal alkylsulphate
salts or similar detergents, sarkosyl, or combinations thereof.
[0117] Conveniently, the detergent may be used in a concentration
of 0.2 to 30% (w/v), e.g. 0.5 to 30%, preferably 0.5 to 15%, more
preferably 1 to 10%. For anionic detergents concentrations of 1.0
to 5% e.g. 0.5 to 5% have been shown to work well.
[0118] The detergent may be supplied in simple aqueous solution,
which may be alkaline or acidic, or more preferably in a buffer.
Any suitable buffer may be used, including for example Tris,
Bicine, Tricine, and phosphate buffers. Conveniently, a source of
monovalent cations, e.g. a salt, may be included to enhance nucleic
acid capture, although this is not necessary. Suitable salts
include chloride salts, e.g. sodium chloride, lithium chloride etc.
at concentrations of 0.1 to 1M, e.g. 250 to 500 mM. As mentioned
above, other components such as enzymes, may also be included.
[0119] Other optional components in the detergent composition
include chelating agents e.g. EDTA, EGTA and other polyamino
carboxylic acids conveniently at concentrations of 1 to 50 mM etc.,
reducing agents such as dithiotreitol (DTT) or
.beta.-mercaptoethanol, at concentrations of for example 1 to 10
mM.
[0120] Preferred detergent compositions may for example
comprise:
[0121] 100 mM Tris-HCl pH 7.5
[0122] 10 mM EDTA
[0123] 2% SDS [0124] or:
[0125] 100 mM TrisCl pH 7.5
[0126] 10 mM EDTA
[0127] 5% SDS
[0128] 10 mM NaCl [0129] or:
[0130] 100 mM TrisCl pH 7.5
[0131] 500 mM LiCl
[0132] 10 mM EDTA
[0133] 1% LiDS
[0134] Reference is made to WO96/18731 for further details,
exemplary reaction Conditions etc.
[0135] Alternative nucleic acid binding techniques may also be used
in order to achieve the step of binding released nucleic acid to
the solid support. For example, one such method may take advantage
of the well known principle of nucleic acid binding to a silica
surface.
[0136] Thus, in such an embodiment, the solid support may comprise
or consist of a silica or silica-based or derived material. Many
such materials are known and described in the art, and the
literature is replete with references describing the isolation of
nucleic acids by binding to silica surfaces (see e.g. EP-A-0389063
of AKZO N.V., U.S. Pat. No. 5,342,931, U.S. Pat. No. 5,503,816 and
U.S. Pat. No. 5,625,054 of Becton Dickinson, U.S. Pat. No.
5,155,018 of Hahnemann University, U.S. Pat. No. 6,027,945 of
Promega Corp. and U.S. Pat. No. 5,945,525 of Toyo Boseki KK).
[0137] Ionic binding of the nucleic acid to the support may be
achieved by using a solid support having a charged surface, for
example a support coated with polyamines.
[0138] The support which is used in the method of the invention may
also carry functional groups which assist in the specific or
non-specific binding of nucleic acids, for example DNA binding
proteins e.g. leucine zippers or histones or intercalating dyes
(e.g. ethidium bromide or Hoechst 42945) which may be coated onto
the support.
[0139] Likewise, the support may be provided with binding partners
to assist in the selective capture of nucleic acids. For example,
complementary DNA or RNA sequences, or DNA binding proteins may be
used. The attachment of such proteins to the solid support may be
achieved using techniques well known in the art. Conveniently, such
nucleic acid-binding partners may be intermixed on the solid
support with the anti-leucocyte binding partners.
[0140] The solid supports used for any of the steps of the methods
described herein may be any of the well-known supports or matrices
which are currently widely used or proposed for immobilisation,
separation etc. These may take the form of particles, sheets, gels,
filters, membranes (e.g. nylon membranes), fibres, capillaries,
needles or microtitre strips, tubes, plates or wells, etc, combs,
pipette tips, micro arrays, chips, or indeed any solid surface
material.
[0141] Conveniently the support may be made of glass, silica,
latex, plastic or any polymeric material. Generally speaking, for
isolation of nucleic acids, the nature of the support is not
critical and a variety of surface materials may be used. The
surface of the solid support may be hydrophobic or hydrophilic.
Preferred are materials presenting a high surface area for binding
of the cells, and subsequently, of the nucleic acid. Such supports
will generally have an irregular surface and may be for example be
porous or particulate e.g. particles, fibres, webs, sinters or
sieves. Particulate materials e.g. beads are generally preferred
due to their greater binding capacity, particularly polymeric
beads/particles.
[0142] Conveniently, a particulate solid support used according to
the invention will comprise spherical beads. The size of the beads
is not critical, but they may for example be of the order of
diameter of at least 1 and preferably at least 2 .mu.m, and have a
maximum diameter of preferably not more than 10 and more preferably
not more than 6 .mu.m. For example, beads of diameter 2.8 .mu.m,
2.7 .mu.m and 4.5 .mu.m have been shown to work well.
[0143] Monodisperse particles, that is those which are
substantially uniform in size (e.g. size having a diameter standard
deviation of less than 5%) have the advantage that they provide
very uniform reproducibility of reaction. Monodisperse polymer
particles produced by the technique described in U.S. Pat. No.
4,336,173 are especially suitable.
[0144] Non-magnetic polymer beads suitable for use in the method of
the invention are available from Dynal Biotech AS as well as from
Qiagen, Amersham Pharmacia Biotech, Serotec, Seradyne, Merck,
Nippon Paint, Chemagen, Promega, Prolabo, Polysciences, Agowa,
Bangs Laboratories and Dyno Particles or Dyno Specialty
Polymers.
[0145] However, to aid manipulation and separation, magnetic beads
are preferred. The term "magnetic" as used herein means that the
support is capable of having a magnetic moment imparted to it when
placed in a magnetic field, and thus is displaceable under the
action of that field. In other words, a support comprising magnetic
particles may readily be removed by magnetic aggregation, which
provides a quick, simple and efficient way of separating the
particles following any cell, nucleic acid and protein binding
steps, and is a far less rigorous method than traditional
techniques such as centrifugation which generate shear forces which
may disrupt cells or degrade proteins or nucleic acids.
[0146] Thus, using the method of the invention, the magnetic
particles with cells, nucleic acids, or proteins attached may be
removed onto a suitable surface by application of a magnetic field
e.g. using a permanent magnet. It is usually sufficient to apply a
magnet to the side of the vessel containing the sample mixture to
aggregate the particles to the wall of the vessel and to remove the
remainder of the sample for further steps.
[0147] Especially preferred are superparamagnetic particles for
example those described by Sintef in EP-A-106873, as magnetic
aggregation and clumping of the particles during reaction can be
avoided, thus ensuring uniform cell, nucleic acid and protein
extraction. The well-known magnetic particles sold by Dynal Biotech
ASA (Oslo, Norway, previously Dynal AS) as DYNABEADS, are
particularly suited to use in the present invention. Beads are also
automation friendly and allow binding at varying salt
concentrations and/or pH. Beads also allow the possibility to
manipulate binding and elution conditions of single samples.
[0148] Functionalised coated particles for use in the present
invention may be prepared by modification of the beads according to
U.S. Pat. Nos. 4,336,173, 4,459,378 and 4,654,267. Thus, beads, or
other supports, may be prepared having different types of
functionalised surface, for example positively or negatively
charged, hydrophilic or hydrophobic.
[0149] In embodiments where an affinity-based separation of cells
or other particles is used, the binding partner(s) may be attached
to the solid support in any convenient way, before or after binding
to the cells/particles, according to techniques well known in the
art and described in the literature. Thus the binding partner may
be attached directly or indirectly to the solid support.
[0150] In a convenient embodiment, the binding partner may be
attached to the support, prior to contact with the sample. Such
attachment may readily be achieved by methods (e.g. coupling
chemistries) well known in the art, and conveniently the binding
partner is bound directly to the solid support, for example by
coating. However it may also be attached via spacer or linker
moieties. The binding partner may be covalently or reversibly
attached according to choice.
[0151] Alternatively, as mentioned above, the binding partner may
first be brought into contact with the sample, to bind to the
cells/particles before being attached to the solid support. In this
case, the solid support may conveniently carry or be provided with
a binding moiety capable of binding to the particular specific
binding partner used. Again, such binding systems are well known in
the art. For example, the solid surface may carry a (secondary)
antibody capable of binding to the particular binding partner (e.g.
a polyclonal anti-species antibody).
[0152] In an advantageous embodiment of the invention the lysis
step of the method (and indeed the other steps of the method
involving the use of a solid support) may include a further step
involving the addition of a further or extra amount of solid
support (also referred to herein as a "second" solid support) to
the reaction mixture.
[0153] The use of a second solid support has been found to offer
advantages in sample collection for example by improving pellet
formation and hence isolation of the first solid support. The
improved pellet formation may also reduce non-specific binding of
substances or entities in the pellet, or in other words reduces
contamination of the pellet. Whilst not wishing to be bound by
theory it is believed that when only a first solid support is used
the isolated nucleic acid binds to the first solid support as a
loose, non-compact mesh, thereby resulting in a relatively loose
non-compact pellet. However, where a second support is used and
particularly when this second solid support comprises particles
which are smaller or larger than the first solid support, the
second solid support fills in the gaps (or vice versa) in the loose
mesh, thereby making the pellet tighter and more compact thus
reducing the tendency to trap contaminating material.
[0154] Further details of the nature and characteristics of
appropriate second solid supports for use in the methods of the
present invention are described in WO 01/94572, the disclosure of
which is incorporated herein by reference.
[0155] Briefly, the second solid support may be of comparable size
and density to the first solid support. Preferably however, the
second solid support is of a smaller size than the first solid
support. For example, where the supports are particulate the second
solid support comprises particles of a smaller diameter (e.g.
approximately half the diameter), than those comprising the first
solid support. In especially preferred embodiments the first solid
support comprises particles of 4.5 .mu.m diameter (e.g. the M450
beads described herein) whereas the second solid support comprises
particles of 2.8 .mu.m diameter (e.g. the M280 and M270 beads
described herein). Alternatively, the first support may be smaller
than the second support and the dimensions described above may be
reversed.
[0156] Especially preferably the second solid support may take a
more active role in the isolation of the nucleic acid and in such
cases the second solid phase is capable of binding to nucleic acid,
i.e. has nucleic acid binding properties. Preferably therefore the
second solid support may be made of glass, silica, latex, plastic
or any polymeric material (i.e. an uncoated surface) capable of
binding nucleic acid and such a solid support may optionally be
functionalised, for example to aid or improve nucleic acid binding.
Particularly preferred in this regard are functionalised solid
supports which have a surface charge, preferably a negative surface
charge. Most preferred are solid supports coated with carboxylic
acid functional groups. Such solid supports are commercially
available, for example the M-270 carboxylic acid beads or M-280
Hydroxyl beads manufactured by Dynal Biotech ASA. Preferably the
second solid supports are particulate, e.g. beads, and especially
preferably are magnetic.
[0157] The provision of a further or extra amount of solid support
after the cell isolation step results in an improved yield of
nucleic acid and also makes the elution of nucleic acid from the
solid support easier, particularly where solid supports with a
negatively charged surface are used. Whilst not wishing to be bound
by theory, as described above it is believed that the addition of
an extra amount of a "second" solid support improves the
compactness of the bead and nucleic acid pellet and particularly
where DNA is able to bind to the second solid support, more
effective and complete binding of nucleic acid molecules, rather
than the nucleic acid molecules being attached to the beads only at
one end or being attached to the beads loosely is achieved.
[0158] The terms "additional" or "extra" or "further" amount when
used herein in connection with the addition of a second solid
phase, is used to indicate the addition of any amount (by weight)
of second solid phase such that the isolation of nucleic acid is
improved, for example the yield of isolated nucleic acid is
improved. For example the amount of second solid phase added might
be the same amount as the amount of first solid phase used or may
be up to approximately 3 to 5 times the amount of first solid phase
used. Alternatively, the amount of second solid phase added may be
less than the amount of first solid phase providing that the
isolation of nucleic acid is improved. Preferably the amount of
second solid phase used is 0.5 to 3 times the amount of first solid
phase.
[0159] As the "amount" of solid phase refers to the weight of the
solid phase, in the preferred embodiments of the invention where
the first and second solid phases are particulate and the particles
making up the second solid phase are smaller (or larger) than the
particles making up the first solid phase, the number of particles
used for the first and second solid phases will generally be
different.
[0160] The invention will now be described in more detail in the
following non-limiting Example, with reference to the drawings in
which:
[0161] FIG. 1a represents a schematic diagram showing a summary of
a model system according to the present invention; leukocytes are
isolated by positive selection, binding to beads carrying
anti-CD45. DNA is isolated from the captured leukocytes and bound
onto DNA-binding beads, from which it may be eluted in purified
form, e.g. for subsequent analysis. As an alternative, the isolated
leukocyte population may be further fractionated by selection for
circulating carcinoma cells (SW480 cells; Ber EP4.sup.+ cells)
using beads (Dynabeads.RTM. Epthelial Enrich) carrying a specific
binding partner for such cells. This fractionated population may
also be subjected to genomic DNA isolation as previously, allowing
the general (e.g. leukocyte) and sub-fractionated (e.g. SW.sub.480)
cell populations to be compared. The isolated cell populations may
be subjected to mRNA and protein (specific or general fraction)
isolation;
[0162] FIG. 1b represents a schematic diagram showing a summary of
a model system according to the present invention; carcinoma cells
(SW480) that have been spiked into blood sample, are isolated by
positive selection, binding to beads carrying anti-Ber EP4
(Dynabeads Epithelial enrich). DNA is isolated from the captured
carcinoma cells by lysing the cells and adding DNA binding
Dynabeads, from which it may be eluted in purified form, e.g. for
subsequent analysis. Different blood cell population (e.g. B-cells,
T-cells, monocytes) may be isolated from the remaining blood sample
subsequently, and subjected to DNA isolation as described. The
isolated cell populations may be subjected to mRNA and protein
isolation.
[0163] FIG. 2 is a photograph of a gel showing the results of
sequential PCR experiments carried out as described in Example 1 on
solid phase cDNA obtained from isolated mRNA (isolated from
cultured carcinoma cells spiked into blood samples), in order to
detect different transcripts: Lane 1--ESX (1st round of PCR); lane
2-Mucin 1; Lane 3--CK19 (third round of PCR); Lane 4-CK19 (first
(nested) round of PCR); Lane 4--ESX (second (nested) round of
PCR);
[0164] FIG. 3 is a photograph of a gel showing the results of PCR
and RT-PCR experiments carried out as described in Example 1,
showing isolation of genomic DNA (gDNA) and mRNA encoding CK19
sequentially from the same sample: Lane 1-100 bp DNA ladder 1
.mu.g; Lane 2--cDNA CK19 (mRNA isolation)a; Lane 3--gDNA CK19
(g-DNA isolation)a; Lane 4--cDNA CK19 (mRNA isolation)b; Lane
5--gDNA CK19 (gDNA isolation)b; Lane 6--Positive control; Lane
7--Negative control;
[0165] FIG. 4 shows the results of protein fractionation of a
cultured carcinoma cell sample as described in Example 1; FIG. 4A
shows the results of Bead-DELFIA following specific protein
isolation using anti-CK19; FIG. 4B shows the results of SDS-PAGE
comparing the cell lysate against a fractionated cell lysate
(fractionated by binding to Dynabeads.RTM. M270-amine).
[0166] FIG. 5a shows the results of an IMS separation of B cells by
CD19-IMS and T cells by CD3-IMS, CD8-IMS and CD4-IMS, where mRNA
from each cell population isolated after gDNA removal is subjected
to an RT-PCR for CD19 as described in Example 2. The gels compare
the amount of CD19 (and hence B cells) present in each sample to
investigate unspecific binding in IMS;
[0167] FIG. 5b shows the results of an IMS separation of monocytes
by Dynabeads CD14, as described in Example 2. This figure shows
that RT PCR for CD14 gives a positive result, but RT PCR for CD19
or CD4 result in only low levels being detected and hence
demonstrates the low levels of unspecific binding for IMS;
[0168] FIG. 6 shows the results of an IMS separation of carcinoma
cells from whole blood (into which they had been spiked), where RT
PCR for CK19 gives a positive result indicating the isolation of
the carcinoma cells. RT PCRs for CD4 and CD14 are not detected and
CD19 barely detected in the negative controls (unspiked blood
samples, lanes 3 and 4) and this again demonstrates that only low
levels of unspecific binding occur for IMS;
[0169] FIG. 7 is a schematic representation of the DNA isolation
protocol in Example 3;
[0170] FIG. 8 shows that DNA obtained from IMS isolated cells is
not degraded;
[0171] FIG. 9a shows the results for protein isolated using ion
exchanger beads from a cell lysate comparing Dynabeads ion
exchanger prototypes with AP-Biotechs 15 Q/S ion exchange
resins;
[0172] FIG. 9b shows the results for protein isolated from
different numbers of carcinoma cells using the cation exchanger
prototype beads;
[0173] FIG. 10a shows PCR results for CK19, CD14, CD4 and CD19 for
IMS isolated carcinoma cells, where 2000, 200 or 20 cells were
spiked into whole blood. CK19 was detected in samples which only
represented mRNA from 20, 2 or 0.2 cells;
[0174] FIG. 10b shows PCR results for CK19 for IMS isolated
carcinoma cells where 1, 5 or 10 cells were spiked into whole
blood. CK19 was detected in one of two parallels for one cell;
[0175] FIG. 11 shows the re-use of the solid phase cDNA library
generated from down to one cell in PCR, detecting a second
transcript from the same sample, demonstrating the flexibility and
scalability of the methods.
EXAMPLE 1
[0176] Combined Isolation of Nucleic Acid and Proteins from Single
Samples
Experimental Procedures:
[0177] Cell pellets containing 2.times.10.sup.5 cultured carcinoma
cells (SW480) were lysed in 200 .mu.l lysis-binding buffer (100 mM
Tris-HCl pH 7.5, 500 mM LiCl, 10 mM EDTA pH 8.0, 5 mM DTT, 1% LiDS)
containing Dynabeads Epithelial. Enrich (200 .mu.g) which were
present to improve pellet formation and Dynabeads M270 carboxylic
Acid (300 .mu.g), which bind the DNA. DNA is isolated by incubating
the mix on a roller at room temperature for 5 minutes. The bead-DNA
complex is separated from the remaining lysate, and washed
3.times.500 .mu.l in 1.times. Washing buffer (10 mM Tris-HCl pH
7.5, 150 mM LiCl, 1.0 mM EDTA), followed by elution in 100 .mu.l
elution buffer (10 mM Tris-HCl pH 8.0, 0.01% Tween 20) at
80.degree. C. for 5-10 minutes. The DNA is ready for e.g. PCR (1
.mu.l is more than enough). Reference is made to FIG. 3 which shows
gel analysis of PCR products obtained from inter alia, isolated
genomic DNA.
[0178] To the remaining lysate, 20 .mu.l oligo(dT) beads
(Dynabeads.RTM. Oligo (dT) 25 can be used) were added and mRNA
annealed for 5 minutes at room temperature on roller. Bead-mRNA
complex is separated from the remaining lysate, washed (as standard
Dynal procedure ie. as indicated by the manufacturer) and
resuspended in 100 .mu.l ice cold 10 mM Tris-HCl, and ready for
RT-PCR. The results are shown in FIGS. 2 and 3.
[0179] The remaining lysate is diluted (200 .mu.l lysate+800 .mu.l
10 mM Tris-HCl pH 8.0) and added to 1.5 mg Dynabeads M270-amine,
which have been pre-washed in 10 mM Tris-HCl pH 8.0. The suspension
is incubated on a roller for 1 hour at room temperature. The
bead-protein complex is then washed 3.times.100 .mu.l in 10 mM
Tris-HCl pH 8.0, and eluted by boiling all the beads for 2-5
minutes in 10 .mu.l SDS-PAGE sample buffer (20 mM Tris-HCl pH 8.0,
1 mM EDTA, 2.5% SDS, 5% b-mercapto-ethanol, 0.01% BPB) and 1 .mu.l
is applied on 10-15% SDS-PAGE Phast gel. The results are shown in
FIG. 4 (specifically in FIG. 4B).
[0180] For specific protein isolation, the lysate was diluted: 5
.mu.l, 10 .mu.l and 20 .mu.l lysate in 100 .mu.l PBS with 0.1% BSA,
prior to bead-DELFIA (ie separation of specific CK19 protein using
anti-CK19 beads). The results are shown in FIG. 4A.
[0181] Isolated LMW in FIG. 4B refers to experiments where we
dissolved Low Molecular Weight standard (MW protein from Amersham
Pharmacia) in lysis/Binding buffer to a conc. of 1 .mu.g/.mu.l and
mixed 20 .mu.l of this with 80 .mu.l 10 mM Tris-HCl, added 1.5 mg
amine beads and incubated and washed, eluted and analysed as
described for lysate. This shows that the beads bind proteins.
EXAMPLE 2
Isolation of Cell Populations by IMS (Immunomagnetic
Separation)
[0182] The presence/co-isolation of B cells in different
populations of T cells isolated by IMS were investigated. Cells
positive for CD19, CD3, CD8 and CD4 were selected by IMS, gDNA was
removed and mRNA was then extracted from the isolated cell
populations and cDNA was synthesised. PCR was then carried out
using CD19 primers on a dilution series for each sample,
representing from 40 000 to 75 cells. The results for this
experiment can be seen in FIG. 5a, where the sensitivity of the
CD19 RT-PCR is indicated in the first gel panel. The remaining gels
demonstrate the low level of unspecific binding in IMS, since CD19
PCR for the T cell populations demonstrated weak bands and hence
only a very low level of unspecific B cell binding had
occurred.
[0183] A similar experiment was carried out, demonstrating a low
level of unspecific B cell binding or T.sub.H cell (T helper cells)
binding (<0.2% unspecific) when IMS was used with CD14 to
isolate monocytes (FIG. 5b).
EXAMPLE 3
[0184] Spiking of Carcinoma Cells into a Blood Sample and the
Isolation of the Carcinoma Cells by IMS
[0185] Cultured colon carcinoma cells (SW480) were resuspended in
culture medium, diluted and counted in a Coulter counter. Different
numbers of carcinoma cells (from 1.times.10.sup.6 to 1 cell) were
spiked into diluted blood samples (1 ml whole blood+1 ml DPBS) or
used directly as positive controls. Un-spiked blood samples were
treated identically and served as negative controls. Samples were
kept at 4.degree. C.
[0186] Pre-washed Dynabeads Epithelial Enrich (4.times.10.sup.7
beads) were added to each spiked and un-spiked blood sample, and
the samples were incubated at 4.degree. C. for 15 minutes on a
roller.
[0187] The cell-bead complex was captured by applying a magnet,
washed once in cold DPBS/0.1% BSA and transferred to a new tube.
The cell-bead complex was washed 3 times in 1 ml cold DPBS. In the
last wash, the sample was split by transferring 500 .mu.l
resuspended bead-cell complex to a new tube (sample a/b).
Sample a (5.times.10.sup.5 Cells):
DNA Isolation
[0188] Washing buffer was removed, and the rosetted cells were
lysed by adding lysis-binding buffer, containing DNA binding
Dynabeads. The cell lysate was incubated at room temperature, on a
roller for 5 minutes.
[0189] The DNA-bead complex was captured by applying a magnet. The
supernatant, containing mRNA and proteins was transferred to a new
tube. The DNA-bead complex was washed 3.times. in 1.times. Washing
buffer (10 mM Tris-HCl pH 7.5, 150 mM LiCl, 1.0 mM EDTA) by turning
the tube upside down 3-5 times. After the third wash, the DNA-bead
complex was resuspended in Elution buffer (10 mM Tris-HCl pH 8.0,
0.01% Tween 20) and the tube incubated at 80.degree. C. for 10
minutes. The eluted DNA was transferred to a new tube and was ready
for e.g. PCR (1 .mu.l is more than enough). As can be seen from
FIG. 8, there was no degradation of the DNA.
Subsequent mRNA Isolation
[0190] The remaining lysate was subjected to mRNA isolation by
adding pre-washed Dynabeads oligo(dT)25 and incubated at room
temperature on a roller for 5 minutes.
[0191] The mRNA-bead complex was captured by applying a magnet and
washed 2.times. in washing buffer with LiDS, 2.times. in washing
buffer without LIDS and 1.times. in 10 mM Tris HCl pH 7.5 (as
standard Dynal Procedure . . . ) and was then ready for cDNA
synthesis or RT-PCR. cDNA synthesis was performed as follows:
[0192] Solid-phase cDNA was synthesised by using the
oligo(dT)-sequences on the beads as primer in 1st strand cDNA
synthesis. cDNA was synthesised using Thermoscript, following the
manufacturers protocol except for the incubation step. Samples were
incubated for 30 minutes at 50.degree. C. followed by 30 minutes at
65.degree. C. with constant mixing. The solid-phase cDNA was used
as template in PCR.
[0193] PCR was then carried out using CK19 primers, which amplify a
transcript not present in blood. The isolation of carcinoma cells
could be seen from the results of the CK19 PCR. CD14, CD4 and CD19
PCRs were then carried out to show the specificity of the IMS
process for isolating carcinoma cells in this experiment rather
than blood cells (FIG. 6a).
EXAMPLE 4
[0194] Protein Isolation with Anion and Cation Exchanger Beads
[0195] Protein fractionation from carcinoma cells was carried out
using 50 .mu.l (1.5 mg) ion exchanger beads for each sample. The
cation exchanger beads were pre-treated in 100 .mu.l 1 M NaCl, 20
mM Citric Acid, pH 3.5 for 15 minutes. The beads were then washed
2.times. in 100 .mu.l washing buffer (50 mM NaCl, 20 mM Citric
Acid, 0.5% Tween 20, pH 3.5). The anion exchanger beads were
pre-treated in 100 .mu.l 1M NaCl, 20 mM Tris-HCl pH 10.0 for 15
minutes. The beads were then washed 2.times. in 100 .mu.l washing
buffer (50 mM NaCl, 20 mM Tris-HCl, 0.5% Tween 20, pH 3.5).
Cell Lysis and Ion Exchange
[0196] Anion/Cation Exchange (FIG. 9a):
[0197] Cell pellets were lysed in 500 .mu.l lysis buffer (20 mM
Tris, 1% Triton-x-100, 150 mM NaCl, 5 mM EDTA, pH 8) and incubated
on a roller for 10 min at 4.degree. C. The lysate was transferred
to tubes containing pre-treated ion exchanger beads and incubated
on a roller for 15 minutes at 4.degree. C. The bead-protein complex
was washed 3.times. in 20 mM Tris-HCl, 50 mM NaCl, pH 8.0. The
proteins were eluted from the anion exchanger beads by adding 1M
NaCl, 20 mM Citrate, pH 3.5, and incubating on a roller for 15
minutes. The proteins were eluted from the cation exchanger beads
by adding 1 M NaCl, 20 mM Tris HCl pH 10.0 and incubating on a
roller for 15 minutes. Analysed by SDS-PAGE.
[0198] Sample b (from Example 3, i.e. 5.times.10.sup.5 Cells):
[0199] Removed washing buffer from cells. The rosetted cells were
lysed in 300 .mu.l lysis buffer (20 mM Citric Acid, 50 mM NaCl, 20
mM Tris, 1% Triton-x-100, 5 mM EDTA, pH 3.5). Incubated on a roller
at 4.degree. C. for 15 minutes. Transferred the lysate to a new
tube, containing pre-treated cation exchanger beads. Incubated on a
roller at 4.degree. C. for 15 minutes. Washed the beads 3.times. in
300 .mu.l washing buffer (20 mM Citric Acid, 50 mM NaCl, 0.5% Tween
20, pH 3.5).
[0200] Resuspended beads in 100 .mu.l elution buffer (20 mM Tris
HCl, 1 M NaCl, pH 10.0) and incubated on a roller for 15 minutes.
Eluted proteins were transferred to a new tube and analysed by
SDS-PAGE.
[0201] The ion exchanger Dynabeads gave similar results for protein
isolation as Amersham Pharmacia Biotech, ion exchangers (FIG. 9a).
Protein fractionation was also carried out using cation exchanger
beads from spiked carcinoma cells and compared to the cell lysate
directly. FIG. 9b shows the results from this, where the negative
control shows the unspecific background from unspiked blood.
EXAMPLE 5
Scaling Down the Techniques to Isolate Reduced Numbers of Cells
[0202] 2000, 200 and 20 carcinoma cells were spiked into 1 ml of
whole blood. The cell isolation was carried out as described in
Example 3 and mRNA was obtained (using 500 .mu.g oligo (dT) beads).
cDNA was synthesised on the oligo (dT) beads using the same amount
of beads as in previous experiments. PCR was carried out for these
samples using CK19, CD14, CD4 and CD19 primers. Analysis was
carried out on samples representing mRNA from 20, 2 and 0.2 cells.
(FIG. 10a). It can be seen that all samples gave positive results
for CK19, indicating the presence of carcinoma cells. The results
for CD14 and CD4 were negative and low levels of CD19 were detected
indicating again the very low levels of unspecific binding for IMS.
Therefore 20 cells could easily be isolated and detected by this
method.
[0203] The experiment was then repeated by spiking whole blood with
1, 5 and 10 carcinoma cells, where single cells had been picked
with a micromanipulator. The cells were isolated as previously
described, mRNA was isolated using less oligo (dT) beads (100
.mu.g) and a solid phase cDNA library was generated as before. PCR
was then carried out using the whole library from each isolation in
one reaction with CK19 primers.
[0204] FIG. 10b shows the results of these experiments, where the
first 7 lanes show the MW-marker and then the results for unspiked
cells (positive controls). The remaining lanes show the results for
the spiked cells which were isolated. It can be seen that in one of
two parallels, a single cell could be recovered from a spiked blood
sample and detected using CK19 PCR.
[0205] This shows that the method described here is highly
scalable. FIG. 11 shows the re-use of the cDNA libraries from FIG.
10b in a second PCR, detecting another transcript. The technology
is also flexible and allows multiple mRNA analysis of single small
samples.
* * * * *