U.S. patent application number 10/428912 was filed with the patent office on 2003-11-06 for gel microdroplets in genetic analysis.
This patent application is currently assigned to Cellay, LLC c/o One Cell Systems, Inc.. Invention is credited to McGrath, Patricia, Trnovsky, Jan.
Application Number | 20030207260 10/428912 |
Document ID | / |
Family ID | 22253300 |
Filed Date | 2003-11-06 |
United States Patent
Application |
20030207260 |
Kind Code |
A1 |
Trnovsky, Jan ; et
al. |
November 6, 2003 |
Gel microdroplets in genetic analysis
Abstract
The invention provides methods of nucleic acid analysis. Such
methods entail forming a population of gel microdrops encapsulating
a population of biological entities, each entity comprising a
nucleic acid, whereby at least some microdrops in the population
each encapsulate a single entity. The population of gel microdrops
is then contacted with a probe under conditions whereby the probe
specifically hybridizes to at least one complementary sequence in
the nucleic acid in at least one gel microdrop. At least one gel
microdrop is then analyzed or detected. The biological entities can
be cells, viruses, nuclei and chromosomes.
Inventors: |
Trnovsky, Jan; (Saugus,
MA) ; McGrath, Patricia; (Cambridge, MA) |
Correspondence
Address: |
TOWNSEND AND TOWNSEND AND CREW, LLP
TWO EMBARCADERO CENTER
EIGHTH FLOOR
SAN FRANCISCO
CA
94111-3834
US
|
Assignee: |
Cellay, LLC c/o One Cell Systems,
Inc.
100 Inman Street
Cambridge
MA
US
|
Family ID: |
22253300 |
Appl. No.: |
10/428912 |
Filed: |
May 2, 2003 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10428912 |
May 2, 2003 |
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09369640 |
Aug 6, 1999 |
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6586176 |
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60095721 |
Aug 7, 1998 |
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Current U.S.
Class: |
435/5 ; 435/6.11;
435/6.14; 435/91.2 |
Current CPC
Class: |
C12Q 1/6834 20130101;
C12Q 1/6816 20130101; C12Q 1/6827 20130101; C12Q 1/70 20130101;
C12Q 1/6813 20130101; C12Q 2600/158 20130101; C12Q 1/6816 20130101;
C12Q 1/6834 20130101; C12Q 1/6841 20130101; C12Q 1/68 20130101;
C12Q 2600/156 20130101; C12Q 1/6813 20130101; C12Q 1/689 20130101;
C12Q 2563/161 20130101; C12Q 2565/501 20130101; C12Q 2563/161
20130101; C12Q 2523/101 20130101; C12Q 2565/501 20130101; C12Q
2523/101 20130101; C12Q 1/6827 20130101 |
Class at
Publication: |
435/5 ; 435/6;
435/91.2 |
International
Class: |
C12Q 001/70; C12Q
001/68; C12P 019/34 |
Claims
What is claimed is:
1. A method of nucleic acid analysis, comprising forming a
population of gel microdrops encapsulating a population of
biological entities, each entity comprising a nucleic acid, whereby
at least some microdrops in the population each encapsulate a
single entity; contacting the population of gel microdrops with a
probe under conditions whereby the probe specifically hybridizes to
at least one complementary sequence in the nucleic acid in at least
one gel microdrop; isolating or detecting the at least one gel
microdrop.
2. The method of claim 1, wherein the biological entities are
selected from the group consisting of cells, viruses, nuclei and
chromosomes.
3. The method of claim 1, wherein the biological entities are not
fixed chemically before the contacting step.
4. The method of claim 1, further comprising amplifying the nucleic
acids before the contacting step.
5. The method of claim 1, wherein the biological entities are
chromosomes.
6. The method of claim 1, wherein the population of gel microdrops
is formed by forming a preparation of biological entities in a
liquid gel, and dispersing the preparation into a hydrophobic
solvent to form drops encapsulating the entities.
7. The method of claim 1, wherein the populations of gel microdrops
is formed by forming a preparation of biologicial entities in a
liquid gel and passing the preparation through a puslating
orifice.
8. The method of claim 7, wherein the pulsating orifice is a
component of an ink jet printer.
9. The method of claim 1, wherein most drops contain zero
chromosomes, and 1-30% of drops contain a single chromosome.
10. The method of claim 1, wherein the drops are 2-200 .mu.m in
diameter.
11. The method of claim 1, wherein the gel is selected from
agarose, alginate, carrageenan, or polyacrylamide.
12. The method of claim 1, further comprising digesting the gel at
least one isolated microdrop with agarase to isolate a nucleic acid
within the microdrop.
13. The method of claim 1, further comprising denaturing the
nucleic acid in the microdrops before the contacting step.
14. The method of claim 1, wherein the gel is agarose and the
method further comprising crosslinking hydroxyl groups in the
agarose with each other and with hydroxyl groups in the nucleic
acid between the denaturation and contacting steps.
15. The method of claim 14, wherein the hybridization is performed
at a temperature of over 68.degree. C. or in the presence of a
formamide concentration greater than 20%.
16. The method of claim 5, wherein the biological entities are are
obtained from a human, nonhuman mammal, plant, bacterium, fungus,
fish, or insect.
17. The method of claim 1, wherein the probe is labelled.
18. The method of claim 17, wherein the microdrops further comprise
a reagent that amplifies a signal from the labelled probe.
19. The method of claim 17, wherein the probe is labelled with an
enzyme, and the reagent is a substrate for the enzyme.
20. The method of claim 17, wherein the probe is fluorescently
labelled.
21. The method of claim 1, wherein the probe specifically
hybridizes to a subpopulation of the microdrops each containing a
nucleic acid bearing a complementary sequence to the probe.
22. The method of claim 1, wherein the at least one gel microdrop
is isolated by fluorescent activated cell sorting.
23. The method of claim 1, wherein the at least one gel microdrop
is detected by flow cytometry, microscopy, digital image analyzing,
scanning cytometry, photon counting or ccd.
24. The method of claim 1, wherein the probe is a nucleic acid.
25. The method of claim 24, wherein the probe is a locus-specific
probe.
26. The method of claim 5, wherein the probe comprises first and
second probes respectively complementary to different chromosomes
in a wildtype individual, whereby co-hybridization of the first and
second probes to the same chromosome indicates a chromosomal
translocation in an individual.
27. The method of claim 1, wherein the probe hybridizes to a
satellite DNA sequence, centromeric, a telomeric region or a
repetitive sequence.
28. The method of claim 1, wherein the probe is a chromosome
specific probe.
29. The method of claim 5, wherein the population of chromosomes
are obtained from a single cell or a homogeneous cell line from a
patient.
30. The method of claim 1, further comprising labelling microdrops
containing an entity with a second label without labelling empty
microdrops with the second label.
31. The method of claim 5, wherein the population of chromosomes is
obtained from a population of different cells in a patient.
32. The method of claim 31, further comprising determining the
ratio of a subpopulation of microdrops containing a chromosome
hybridized to the probe to a supopulation of microdrops containing
a chromosome not hybridized to the probe.
33. The method of claim 32, wherein the ratio is less than
1:10.
34. The method of claim 32, wherein the probe hybridizes to a
nucleic acid segment bearing a mutation and the ratio indicates the
proportion of cells in the population bearing the mutation.
35. The method of claim 32, wherein the mutation is a somatic
mutation.
36. The method of claim 32, wherein the mutation is a germline
mutation.
37. The method of claim 1, further comprising contacting an
isolated gel drop containing a nucleic acid with a restriction
enzyme, whereby the restriction enzyme cleaves the nucleic acid
within the drop.
38. The method of claim 5, further comprising preparing a single
chromosomal fragment library from a chromosome in an isolated gel
microdrop.
39. The method of claim 5, further comprising preparing probes from
a single chromosome in an isolated gel microdrop.
40. The method of claim 39, wherein the probes are chromosome
painting probes.
41. The method of claim 39, wherein the probes are reverse
chromosome painting probes.
42. The method of claim 1, further comprising storing a gel
microdrop encapsulating a biological entity for at least one
hour.
43. The method of claim 42, wherein the biological entity is stored
before the contacting step.
44. The method of claim 42, wherein the biological entity is stored
after the isolating or detecting step.
45. The method of claim 42, wherein the gel microdrop is stored for
at least six months.
46. The method of claim 5, further comprising viewing the isolated
gel microdrop under a microscope to determine which regions of the
chromosome have hybridized to the probe.
47. The method of claim 1, further comprising contacting the at
least one gel drop containing a nucleic acid hybridized to the
probe with a label that binds to the probe.
48. The method of claim 1, wherein the population of chromosomes
comprises at least 10,000 chromosomes.
49. The method of claim 1, wherein the biological entities are
cells and the probe hybridizes to an RNA molecule with the
cells.
50. A method of diagnosing a disease due to a mutation, comprising:
obtaining a sample of cells from a patient; encapsulating a
population of chromosomes from the sample in a population of
microdrops; contacting the microdrops with a first probe that is
complementary to a nucleic acid segment containing the somatic
mutation, and a second probe complementary to the chromosome in
which the somatic mutation occurs at a site distal to the somatic
mutation, whereby the first probe hybridizes to microdrops bearing
the chromosome with a somatic mutation and the second probe
hybridizes to microdrops bearing the chromosome irrespective
whether the somatic mutation is present; determining the ratio of
microdrops hybridizing to the first probe and hybridizing to the
second probe; diagnosing the existence or prognosis of the disease
from the ratio.
51. The method of claim 50, wherein the disease is cancer.
52. The method of claim 51, wherein the mutation occurs in a p53,
BRCA-1, BRCA-2, ras or retinoblastoma gene.
53. A method of chromosome analysis, comprising forming a
population of gel micropdrops encapsulating a population of
nucleic, whereby at least some microdrops in the population each
encapsulate a single nucleus; contacting the population of gel
microdrops with a probe under conditions whereby the probe
specifically hybridizes to at least one complementary sequence in
at least one chromosome in a nucleus of least one gel microdroplet;
isolating or detecting the at least one gel microdroplet.
54. A method of isolating chromosomes comprising: culturing a
population of cells in genistein and colcemid to synchronize
chromosomes in metaphase; isolating chromosomes from the cells.
55. A method of isolating chromosomes comprising: lysing a
population of cells to form a lysate; treating the lysate with an
antibody linked to a magnetic particles, wherein the antibody
specifically binds to one or more chromosomes in the cells;
isolating magnetic particles from the lysate.
56. A method of chromosome analysis, comprising forming a
population of gel micropdrops encapsulating a population of cells
or nuclei, whereby at least some microdrops in the population each
encapsulate a single nucleus; contacting the population of gel
microdrops with a probe under conditions whereby the probe
specifically hybridizes to at least one complementary sequence in
at least one nucleus in at least one gel microdrop; isolating or
detecting the at least one gel microdrop.
57. The method of claim 56, wherein the probe is labelled with an
enzyme and the gel microdrops contain a substrate for the
enzyme.
58. The method of claim 56, wherein gel microdrops are formed from
a biotinylated gel, and the. substrate is linked to biotin via an
avidin or streptavidin moiety.
59. The method of claim 58, wherein the substrate is
chemieluminescent.
60. The method of claim 59, wherein the enzyme is horseradish
peroxidase or alkaline phosphatase.
61. The method of claim 56, wherein the detecting comprising
analyzing the at least one gel microdrop with a fluorescence
microscope, a digital image analyser, a scanning cytometer, a
photon counting device or a ccd.
62. The method of claim 61, wherein the detecting indicates the
distribution of the probe within the nucleus of the at least one
microdrop.
63. The method of claim 56, wherein the detecting comprising
placing a plurality of gel microdrops on a microscope slip and
detecting a hybridization signal using a fluorescence microscope, a
digital image analyser, a scanning cytometer, a photon counting
device or a ccd.
64. The method of claim 56, wherein the probe hybridizes to a
single copy genomic sequence shorter than 50 kb.
65. The method of claim 56, wherein the probe hybridizes to a
single copy genomic sequence shorter than 10 kb.
66. The method of claim 56, wherein the isolating or detecting is
effected by flow cytometry, optionally with FACS, or MACS.
67. A kit comprising a high melting temperature agarose,
emulsification equipment, a label indicating how to use the kit for
probe hybridization analysis.
68. The kit of claim 67, further comprising at least one probe that
hybridizes to a nucleic acid.
Description
CROSS-REFERENCE TO RELATED APPLICATION
[0001] The present application derives priority from U.S. S No.
60/095,721, filed Aug. 7, 1998, which is incorporated by reference
in its entirety for all purposes.
TECHNICAL FIELD
[0002] The present invention resides in the field of genetic
analysis.
BACKGROUND
[0003] Cytogenetic testing is still in its infancy. Current
cytogenetic methods are limited to analysis of gene aberrations
easily detectable in cells, nuclei, or chromosomes, in part,
because slide based methods are highly manual. Analysis of
aberrations present in low frequency is not routinely performed in
the clinical setting because many slides of cells, nuclei or
chromosomes would have to be evaluated to establish statistical
frequency.
[0004] Banding is the classical approach used for analyzing
chromosomes in metaphase spreads. This method is based -on staining
which results in dark bands in the region of the chromosome where
the chromatin occurs at higher density. The banding pattern is
specific for each chromosome and allows identification for
karyotyping, which is the determination of each chromosome's copy
number. However, banding resolution is not sufficient to detect
small deletions or additions of chromosomal mass, which occur in a
variety of disease conditions, particularly in cancers.
[0005] Fluorescent in situ hybridization is another approach used
to localize genomic DNA fragments or to paint whole chromosomes and
to detect and characterize genetic abnormalities including
translocations (31, 40), aneusomy (41, 42), and gene amplification
(43). These genetic abnormalities can be detected in individual
cells, chromosomes, or nuclei to assess of tumor genotype, analyze
genetic heterogeneity, and detect malignant cells. To preserve
integrity in FISH applications, chromosomes are typically adsorbed
onto glass slides for analysis. Analysis therefore requires
microscopic evaluation of individual slides limiting automation and
rapid sample processing. Fluorescent in situ hybridizations
prepared on glass slides rely not only on the assay and reagents
but on the instrumentation and the expertise and ingenuity of the
scientists using it resulting in poor reproducibility. An inherent
limitation to this technology is that at least 100 kb of DNA
sequence in a single cell must be present for detection (68-70). In
addition, harsh conditions for fixing either tissue or intact cells
to a glass slide are less than optimal: up to 90% of the assay
sample can be lost from the glass support.
[0006] Some chromosomes can also be resolved by fluorescent
staining followed by flow cytometry (14,15). Successful chromosome
sorting is, however, dependent on the binding characteristics of
fluorescent dyes and the extent to which the chromosome of interest
can be distinguished from chromosomes of similar size, clumps of
chromosomes, and debris containing DNA (13). Although this approach
has resulted in the construction of yeast artificial chromosome
(YAC) libraries for mapping studies (16) in species which have
chromosomes of similar size, such as mouse, arabidopsis, and 20% of
the human chromosomes, unambiguous resolution has not been
possible. Flow sorting based on dye uptake is possible for well
resolved chromosomes, but this method works poorly for chromosomes
which are similar in size and base composition, mainly human
chromosomes 9-12 and the majority of mouse chromosomes.
Furthermore, flow cytometry cannot currently be used to analyze
hybridized chromosomes prepared by conventional methods because
unfixed chromosomes fall apart using high temperatures and/or
formamide.
SUMMARY OF THE CLAIMED INVENTION
[0007] The invention provides methods of nucleic acid analysis.
Such methods entail forming a population of gel microdrops
encapsulating a population of biological entities, each entity
comprising a nucleic acid, whereby at least some microdrops in the
population each encapsulate a single entity. Nucleic acids can be
DNA or RNA. The population of gel microdrops is then contacted with
a probe under conditions whereby the probe specifically hybridizes
to at least one complementary sequence in the nucleic acid in at
least one gel microdrop. At least one gel microdrop is then
analyzed or detected. The biological entities can be cells,
viruses, nuclei and chromosomes.
[0008] In some methods, at -least 10,000 biological entities are
encapsulated. In some methods, the biological entities are not
fixed chemically before the contacting step. In some methods,
nucleic acids are amplified before the contacting step. Suitable
materials for forming droplets include agarose, alginate,
carrageenan, or polyacrylamide.
[0009] In some methods, nucleic acids are recovered from microdrops
by digestion with agarase. Optionally, the recovered DNA can be
digested with a restriction enzyme with or without prior digestion
of agarase. In some methods, the gel matrix is crosslinked with
itself and/or nucleic acid being analyzed, typically, between the
denaturation and contacting steps. In some method, the
hybridization is performed at a temperature of over 68.degree. C.
or in the presence of a formamide concentration greater than 20%.
In some methods, the microdrops further comprise a reagent that
amplifies a signal from the labelled probe. For example, the probe
can be labelled with an enzyme, and the reagent can be a substrate
for the enzyme.
[0010] In some methods, microdrops are isolated by FACS.TM.. In
some methods, the biological entities are a population of
chromosomes obtained from a population of different cells in a
patient. In some methods, the ratio of a subpopulation of
microdrops containing a chromosome hybridized to the probe to a
subpopulation of microdrops containing a chromosome not hybridized
to the probe is determined. In some methods, the probe hybridizes
to a nucleic acid segment bearing a mutation and the ratio
indicates the proportion of cells in the population bearing the
mutation. Such methods are particularly useful for analyzing
somatic mutations.
[0011] In some methods, an isolated microdrop containing a single
chromosome is used to prepare a single chromosomal fragment
library. Such a library can in turn be used for preparing probes
for a single chromosome, such as painting or reverse painting
probes.
[0012] Gel microdrops encapsulated biological entities can be
stored before or after the hybridization step for a period of at
least six months.
[0013] The invention further provides methods of diagnosing a
disease due to a genetic mutation. Such methods entail obtaining a
sample of cells from a patient. A population of chromosomes from
the sample in then encapsulated in a population of microdrops. One
then contacts the microdrops with a first probe that is
complementary to a nucleic acid segment containing the somatic
mutation, and a second probe complementary to the chromosome in
which the somatic mutation occurs at a site distal to the somatic
mutation. The first probe hybridizes to microdrops bearing the
chromosome with a somatic mutation and the second probe hybridizes
to microdrops bearing the chromosome irrespective whether the
somatic mutation is present. One then determines the ratio of
microdrops hybridizing to the first probe and hybridizing to the
second probe. The ration can then be used to diagnose the existence
or prognosis of the disease from the ratio. Such methods are
particular useful for diagnosing existence or prognosis of
cancer.
[0014] The invention further provides methods of chromosome
analysis. Such methods entail forming a population of gel
microdrops encapsulating a population of nucleic, whereby at least
some microdrops in the population each encapsulate a single
nucleus. One then contacts the population of gel microdrops with a
probe under conditions whereby the probe specifically hybridizes to
at least one complementary sequence in at least one chromosome in a
nucleus of least one gel microdrop. One then isolates or detects
the at least one gel microdrop.
[0015] The invention further provides methods of isolating
chromosomes. Some such methods entail culturing a population of
cells in genistein and colcemid to synchronize chromosomes in
metaphase, and isolating chromosomes from the cells. Other methods,
which can be used in conjunction or independently of the previously
described methods, entail lysing a population of cells to form a
lysate. The lysate is then treated with an antibody linked to a
magnetic particles, wherein the antibody specifically binds to one
or more chromosomes in the cells. Magnetic particles are then
isolated from the lysate.
[0016] The invention further provides methods of chromosome
analysis. Such methods entail forming a population of gel
micropdrops encapsulating a population of cells or nuclei, whereby
at least some microdrops in the population each encapsulate a
single nucleus. One then contacts the population of gel microdrops
with a probe under conditions whereby the probe specifically
hybridizes to at least one complementary sequence in at least one
nucleus in at least one gel microdrop. One then isolates or detects
the at least one gel microdrop.
[0017] The invention further provides a kit comprising high melting
temperature agarose, emulsification equipment, and a label
indicating how to use the kit for probe hybridization analysis.
Optionally, the kit also includes at least one probe that
hybridizes to a nucleic acid.
BRIEF DESCRIPTION OF THE FIGURES
[0018] FIG. 1 shows encapsulated and unencapsulated human, mouse
and plant chromosomes.
[0019] FIG. 2 shows gel electrophoresis of chromosomal DNA.
Unencapsulated, freshly isolated chromosomes: b-mouse, e-human
K-562, g-human REH; Unencapsulated chromosomes one month after
isolation: c-mouse, f-human K-562, h-human REH; Encapsulated
chromosomes stored for 6 months: d-mouse, i-human K-562, j-human
REH;lambda DNA (0.1 .mu.g) used as a control: a,k.
[0020] FIG. 3A shows flow sorting of human chromosome 22 following
microdrops in situ hybridization using a bcr locus specific probe.
FIG. 3B shows sorted chromosomes visualized using fluorescent
microscopy.
[0021] FIG. 4 shows purity of chromosome 22 after sorting measure
by the polymerase chain reaction using primer sets specific from
chromosomes 10, 21 or 22
[0022] FIG. 5 Restriction digestion of encapsulated
chromosomes.
[0023] FIG. 6 detection of translocated chromosome 22 left
chromosome 9 middle, and translocation-free chromosome 22 right by
MISH are shown.
[0024] FIG. 7 shows flow cytometric detection of gag HIV RNA in
encapsulated HIV infected cells after hybridization with two
HRP-labeled oligo probes.
[0025] FIG. 8 shows detection of telomerase mRNA in HL-60 (model
cancer cell line) and human PBMCs using fluorescein-labeled
oligonucleotide probes
DEFINITIONS
[0026] An isolated species means an object species invention that
is the predominant species present (i.e., on a molar basis it is
more abundant than any other individual species in the
composition). Preferably, an isolated species comprises at least
about 50, 80 or 90 percent (on a molar basis) of all macromolecular
species present. Most preferably, the object species is purified to
essential homogeneity (contaminant species cannot be detected in
the composition by conventional detection methods).
[0027] Polymorphism refers to the occurrence of two or more
genetically determined alternative sequences or alleles in a
population. A polymorphic marker or site is the locus at which
divergence occurs.
DETAILED DESCRIPTION
[0028] I. General
[0029] The invention provides methods of analyzing populations of
nucleic-acid containing biological entities by probe hybridization.
For example, the methods can be used to analyze cells, viruses,
isolated nuclei or isolated chromosomes. The methods work by
encapsulating biological entities in gel microdrops, such that at
least some microdrops in a population contain a single entity. The
gel droplet provides a stabilization matrix for hybridization and
holds hybridized nucleic acids together for subsequent analysis.
Encapsulated entities are hybridized with one or more probes. GMDs
are easily recovered using low speed centrifugation. Probes can,
for example, be designed to hybridize to particular chromosomes or
to specific chromosomal loci which are the site of genetic
abnormality. After hybridization, the encapsulated entities are
detected and/or isolated based on hybridization signal.
[0030] The methods allow very large numbers of biological entities
to be analyzed simultaneously and can detect entities with rare
genotypes from within such populations. For example, the methods
can be used to identify rare cancerous cells in a population of
normal cells at an early stage in the development of the cancer.
Other applications included gene identification, isolating cells
expressing a particular gene, preparation of specific hybridization
probes, and isolation of pure starting material for DNA sequencing.
An additional benefit is that encapsulation in a permeable matrix
permits hybridization in free solution, improving the reaction
kinetics. A further benefit is that the encapsulation matrix can
serve as a repository for a substrate for a reaction catalyzed by
an enzyme bound to a probe. Use of chemiluminescent substrates in
this manner results in highly sensitive detection.
[0031] II. Formation of Droplets
[0032] Gel Microdrop (GMD) encapsulation evolved from an interest
in studying individual cells (1-11). GMD's provide a defined
microenvironment around a biologically entity. The gel does not
impede diffusion and allows analysis of large numbers of individual
GMDs using flow cytometry, as well as recovery of GMDs of interest
using FACS. The number of biological entities encapsulated within
each GMD is approximated by Poisson statistics, similar to limiting
dilution cloning or petri dish inoculation. To obtain a preparation
with a high probability that each GMD contains 0 or 1 initial
chromosomes, about 10% of the GMDs should be occupied. GMDs can be
prepared by dispersing entities in liquefied gel, such as agarose,
into an excess of a hydrophobic fluid to form an emulsion. The
emulsion is transiently cooled, causing gelling. Once formed, GMDs
are physically distinct and robust and can be removed from the oil
into an aqueous medium by low speed centrifugation. Alternatively,
GMD's can be formed by passing a mixture of liquefied gel and
entities through a pulsating nozzle, such as the printhead of an
inkjet printer.
[0033] Instrumentation for microdrop formation, the CellSys 100.TM.
Microdrop Maker, is a specially designed emulsifier coupled to a
high precision motor available from OneCell Systems, Inc. By
varying the rotation speed, type and amount of surfactant, and
emulsion viscosity, microdrops ranging from, for example, 2-200
.mu.m can be prepared. Although the Microdrop Maker currently
available from One Cell Systems is most efficient for making large
numbers of microdrops (e.g., 10.sup.7), which in turn requires one
million biological entities to meet the single occupancy
requirement of the microencapsulation procedure, it can be
miniaturized for encapsulation of smaller chromosomal preparations.
Such is useful for clinical applications, e.g., evaluation of bone
marrow samples in which only a small number of cells are
present.
[0034] Several types of gel can be used for making droplets
including agarose, alginate, carrageenan, or polyacrylamide. High
melting temperature agarose is preferred for encapsulating larger
human and plant chromosomes.
[0035] III. Biological Entities
[0036] The methods are generally applicable for screening nucleic
acids, and any biological entity containing them. Examples of
biological entities include cells, organelles, such as nuclei,
mitochondria and chloroplasts; chromosomes and fragments thereof,
and viruses. Such entities can be from any species including
mammals, fish, amphibians, avians, insects, bacteria, eubacteria
and plants. Preferred mammals include humans, primates, bovines,
and rodents, such as mice, rats and rabbits.
[0037] In some methods, biological entities are obtained from a
tissue from a human patient. The tissue sample often contains a
nonclonal population of cells. Samples can be obtained from any
tissue, but blood samples, and samples from tissues from the loci
of diseases to which the patient is suspected of being susceptible
are preferred. In some methods, cells from primary tissue samples
are propagated before analysis. In some methods, biological
entities are pooled from more than one individual before analysis.
In some methods, biological entities (e.g., chromosomes) are
obtained from a homogenous cell line. Cells can be encapsulated and
analyzed directly, or nuclei or chromosomes can be isolated from
cells for analysis.
[0038] IV. Pretreatment of GMD's before Hybridization
[0039] Preferably, polymers forming the gel are crosslinked to each
other and/or to the biological entity. Preferably, such
crosslinking is reversible without damage to the biological entity,
thereby allowing the biological entity to be recovered after
hybridization and subjected to further DNA manipulations. Such
crosslinking assists in preservation of structural integrity of
GMD's in the subsequent denaturation step and hybridization steps.
Harsh chemical fixation treatments, such as the formaldehyde
treatment, used in conventional FISH, are not required. Such
fixation treatments form an internal matrix by cross-linking
endogenous primary amino groups in a biological entity.
[0040] Crosslinked gel microdrops can withstand high temperatures
(at least 68.degree.) or concentrations of denaturing solvents such
as formamide (e.g., 10, 20, 30, 40 or up to 50% concentration of
formamide). Optionally, segments of DNA or RNA can be amplified
within the droplets using PCR. A PCR buffer including primers is
diffused into droplets, and the droplets are subject to temperature
cycling as in a conventional PCR reaction. Irrespective whether
amplification is performed, nucleic acids within the GMD's are
typically denatured (e.g., by treatment with alkali, heat,
formamide or other chemical denaturant) before performing the
hybridization step.
[0041] V. Probes
[0042] Probes are designed to hybridize with selected segment(s) in
the nucleic acids of biological entities being screened. Typical
probes are those used in conventional genetic and cytogenetic
analyses. In many methods, two or more probes with different
binding specifies are used. In some methods, a large population of
different probes is used. Typically, probes bear detectable labels.
If more than-one type of probe is used, the different types
sometimes bear different labels.
[0043] Some probes used in the methods are locus-specific probes,
including allele-specific probes and species-specific probes.
Allele-specific probes hybridize to one allele of a gene within a
species without hybridizing to other alleles. Similarly,
species-specific probes hybridize to a gene from one species
without hybridizing to the cognate gene in another species. Some
probes used in the method hybridize to a variant form of chromosome
associated with disease without hybridizing to a wildtype form of
the chromosome found in normal individuals. Some probes are
mixtures of probes designed to hybridize to one chromosome from an
individual or species without hybridizing to other chromosomes. For
example, a population of probes can be designed to hybridize to the
human X chromosome without hybridizing to other human chromosomes.
Some probes are mixtures designed to hybridize to several different
chromosomes. For example, a mixture of probes can be designed to
hybridize to each of the human chromosomes. Some probes hybridize
to satellite or repeat regions within chromosomes. Some probes
hybridize to centromeric regions of chromosomes.
[0044] Some probes are chromosome painting probes or reverse
chromosome painting probes. Chromosome painting probes are a
collection of probes designed to hybridize to a segment of a
chromosome. Microscopic analysis of a chromosome hybridized to such
probes shows a contiguous segment of label if the entire segment of
the chromosome is present. If the segment is interrupted by a
substitution, deletion or insertion, a gap appears in the pattern
of label, signifying the presence of a genetic abnormality. Reverse
chromosome painting probes are designed to hybridize to a
contiguous segment of a chromosome bearing a known mutation.
Microscopic analysis of a chromosome bearing such a mutation
hybridized to reverse painting probes shows a contiguous segment of
label.
[0045] Reverse chromosome painting has been useful for determining
the origin of de novo unbalanced chromosome duplications and the
extent of deletions or balanced translocations (20). However,
aberrant chromosomes are often difficult to distinguish in
conventional FISH methods because the derivative chromosome can
overlay normal chromosomes. Use of reverse chromosome painting
after separation of chromosomes by flow cytometry eliminates this
problem.
[0046] Some probes are designed to bind to mRNA within a cell. Such
probes can be designed incorporating a segment from the antisense
strand of a cDNA sequence.
[0047] Probes are typically nucleic acids, and can be RNA, DNA or
PNA. Probes can also be antibodies or other proteins with capacity
to bind to DNA in a sequence-specific manner.
[0048] VI. Labels
[0049] Probes are typically labelled. The labels used permit
separation based on flow cytometry and/or microscopic visualization
of label. In some methods, probes are labelled with fluorescent
label such as fluorescein. If multiple probes are used
simultaneously the probes can be labelled with different
fluorescent molecules emitting at different wavelengths to allow
differential detection.
[0050] In some method, the signal from a label attached to a probe
is amplified by binding molecules bearing secondary labels to the
label. For example, a hybridized probe labelled with fluorescein
can be incubated 15-30 min with rabbit anti-fluorescein IgG
conjugated with biotin (Accurate Chemical & Scientific). After
washing with PBS buffer, GMDs are incubated for 15-30 min with
avidin-FITC or avidin-phycoerythrin (Sigma, St. Louis, Mo.).
Because, on average, each anti-fluorescein is labeled with five
biotin molecules and each biotin molecule can bind 2-4 avidin
molecules, a 10-20 fold amplification in signal is obtained.
[0051] In some methods, probes are labelled with an enzyme that
catalyzes conversion of a substrate to a secondary label that
allows separation and/or visualization of GMD's.
[0052] In some methods, as well as being hybridized to
sequence-specific probes, GMD's are labelled with compounds that
binds to any DNA sequence. Such labelling serves to distinguish
GMD's containing a biological entity with empty GMD's.
[0053] VII. Separation and Analysis of Hybridized GMDs
[0054] After hybridization with labelled probes, GMDs can be
analyzed on a flow cytometer. In the simplest case, in which a
single probe type is used, the flow cytometer counts the number of
GMDs bearing a label and the number of GMD's lacking a label. If
two different probes bearing different labels are used, the flow
cytometer can count GMD's bearing first label only, GMD's bearing
second label only, GMD's bearing both labels, and GMD's bearing
neither label. In methods employing larger numbers of probes, still
further categories of GMD's can be distinguished.
[0055] If a probe is directed to a particular sequence (e.g., a
specific chromosomal defect), detection of GMD's hybridized to that
probe signals that the defect is present in at least some of the
biological entities being analyzed. If all GMD's bearing biological
entities are labelled with a second label, it is possible to
determine a ratio of the GMD's hybridized to the specific probe
with all GMD's encapsulating a biological entity. This ratio is the
proportion of biological entities in a sample preparation bearing a
defect. The methods are sufficiently sensitive to detect rare cells
in larger populations, e.g., one cell in 10, 100, 1000, 10,000,
100,000 or 1,000,000. This ratio can be significant in determining
the existence or prognosis of a disease. For example, if a sample
of a cell is from a tissue suspected of being susceptible to
cancer, the ratio of cells bearing a defect associated with cancer
to the total number of cells in a sample is a measure of how far
the cancer has progressed.
[0056] In some methods, GMD's encapsulating chromosomes are
hybridized with two different probes which are complementary to
segments normally found on different chromosomes but which are
translocated into the same chromosome in cancerous cells. In this
situation, the ratio of GMD's binding to both probes relative to
the GMD's binding to one probe or the other but not both, gives the
ratio of cancerous to normal cells in a population.
[0057] Optionally, flow cytometry can be followed by FACS sorting
to make different classes of GMD's available for further analysis,
such as microscopy, or chromosome preparation. Alternatively, gel
microdroplets can be labelled with magnetic particles and subjected
to magnetic separation (MACS). Magnetic particles can be directly
attached to hybridization probes or can be supplied in a form that
they specifically bind to hybridization probes.
[0058] VIII. Visualization of Hybridized Chromosomes
[0059] Encapsulated biological entities can be visualized with or
without prior flow cytometry and FACS separation to determine the
location(s) at which probe has bound. Analysis after flow cytometry
and FACS separation can be advantageous because at that stage one
has a relatively pure population of biological entities that has
hybridized to a given probe. Biological entities can be visualized
by microscopy, digital image analyzing, scanning cytometry, photon
counting or ccd. Visualization is useful for analyzing
hybridization of chromosome painting probes or reverse chromosome
painting probes. Visualization is also useful for determining
chromosomal copy number within a cell, and hence the existence of
chromosomal deletions or duplications. For biological entities
containing multiple chromosomes (e.g., cells and nucleic)
visualization can also be used to distinguish between two different
probes binding to separate chromosomes or to the same chromosome.
As noted, such analysis is useful in identifying some forms of
cancer.
[0060] Biological entities are preferably immobilized on microscope
slides or the like for visualization. For example, placing a small
quantity (10 .mu.l) of GMDs dispersed in substrate on the glass
slide with a cover slip sufficiently immobilizes GMDs permitting
reliable detection of emitted light.
[0061] Digital imaging has become an indispensable tool for
biological research due to several advantages when compared to the
human eye. The higher sensitivity imaging detector enables one to
visualize very low light objects which are not detectable by the
unaided human eye. The spectrum sensitivity of the human eye is
limited from 400 to 700 nm. In contrast, the spectrum sensitivity
range of imaging detectors is more broad, and signals from the
range of x-ray to infrared can be detected.
[0062] A charged-coupled device (CCD) camera providing exposures
ranging from seconds to minutes and has advantages for detecting
low light levels. These cameras are coupled to a microscope; then
digital images are collected with the help of appropriate
instrumentation. For low light applications, there are two types of
CCD cameras available. The first is the Intensified CCD (ICCD)
camera which uses an Image Intensifier and a CCD camera. The Image
Intensifier enhances low light image and the intensified image is
projected onto a CCD camera through relay optics, such as a relay
lens, enabling one to visualize low light image undetectable using
a CCD alone. The second is a Cooled CCD (CCCD) camera which uses a
similar CCD chip for high light imaging. The CCCD reduces camera
noise by cooling and slowly reading out the signal. The reduction
of noise enables one to visualize a low light image ordinarily
buried in the noise of a regular CCD camera.
[0063] IX. DNA Isolation
[0064] The gel environment preserves chromosomal DNA molecules in
intact form. DNA in encapsulated chromosomes containing GMD's can
be cleaved to fragments in situ with restriction enzymes. For large
fragments, partial digestion is preferred. DNA fragments can then
be released from drops by digesting the gel matrix. For example, if
the matrix is agarose, the gel matrix can be digested with the
enzyme agarose. Large fragments are then cloned into vectors such
as YACs, BACs or PACs. Libraries from purified human chromosomes
preparable by the above methods are useful for sequencing or
mapping the human genome and for positional cloning. Pure sorted
chromosomes are also useful as a source of chromosome painting and
reverse chromosome painting probes. Such probes can be prepared by
amplification of chromosomal DNA using degenerate primers.
[0065] X. Storage of Encapsulated Biological Entities
[0066] Encapsulated biological entities such as chromosomes can be
stored for an hour, a day, a week, a month, six months, a year, two
years or five years or more without visible degradation of nucleic
acids. Stored chromosomes can eventually be used for isolating
specific genes, for preparing PCR probes, and for generating high
quality starting material for DNA sequencing, or for clinical
analysis.
[0067] XI. Applications
[0068] The above methods can be applied to diagnosing the presence,
susceptibility, or prognosis of diseases associated with genetic
defects. The methods are particularly useful in diagnosing and
monitoring diseases due to genetic defects that are only present in
a subpopulation of cells, such as defects arising from somatic
mutation. Examples of such diseases associated with genetic defects
include autoimmune diseases, inflammation, cancer, diseases of the
nervous system, and hypertension. Some examples of autoimmune
diseases include rheumatoid arthritis, multiple sclerosis, diabetes
(insulin-dependent and non-independent), systemic lupus
erythematosus and Graves disease. Some examples of cancers include
cancers of the bladder, brain, breast, colon, esophagus, kidney,
leukemia, liver, lung, oral cavity, ovary, pancreas, prostate,
skin, stomach and uterus.
[0069] Many cancers arise due to mutations in rare subpopulations
of cells. Cancers develop and progress through the accumulation of
genetic abnormalities at critical loci (34, 35). These
abnormalities may involve alterations of one or a few bases of DNA,
deletions ranging from sub-microscopic to whole chromosomes,
duplications or higher-level amplifications of chromosomal regions,
or rearrangements producing abnormal juxtapositions of DNA
sequences (36). In some case, such as the abl-bcr fusion on the
original Philadelphia chromosome, specific translocations are
associated with activation or modification of human proto-oncogenes
(37, 38). Similarly, Ewing's sarcoma is associated with a
translocation involving the EWS gene on chromosome 22.
Determination of the proportion of cancerous cells in a tumor
allows grading of the tumor for improved diagnosis, prognosis and
treatment planning. The ratio can also be valuable in evaluating
both the adequacy of surgical margins and the presence of
microscopic metastases in bone marrow or other sites.
[0070] The methods are also useful for diagnosing the presence of
latent viruses. For example, some viruses, such as Herpes viruses
and retroviruses, integrate into genomic DNA of some cells within
the body and remain dormant until activated. Analysis of a tissue
sample from a patient having or suspected of being infected with
such a virus can identify the percentage of cells infected with the
virus and the copy number of the virus in different cells. Such
information is useful in diagnosing the presence of virus, the
severity of infection and the recommended course of treatment.
Presence of a virus can be detected using a probe designed to
hybridize either to viral genomic nucleic acid or to viral mRNA, or
both. The methods can similarly be used to determine copy number of
viral mRNA in cells from the patient. Such information can be
useful in monitoring the progress of disease, for example, in
response to treatment with a drug.
[0071] The methods are also useful for determining allelic
frequencies in a population, and correlating such frequencies with
a phenotype. For example, cells taken from a population of
individuals can be pooled, and screened to determine the
frequencies of different allelic forms of a gene. If the population
has a common phenotype (e.g., a disease), a correlation can be
performed to determine whether the presence of one of the allelic
forms is statistically associated with the phenotype.
[0072] The methods are also useful for identifying cell types
expressing a gene of interest. For example, if a new gene of
unknown function has been discovered, one can design a probe that
is complementary to an exonic segment and optionally, to segments
in successive exons. Hence, the probe can hybridize to mRNA
expressed from the gene. A population of cells is obtained from
different tissues of an individual, and the cells are screened for
hybridization to the probe. Cells hybridizing to the probe express
the gene. The nature of cells expressing a gene provides valuable
information concerning the function of the gene.
[0073] Similar methods can be used to clone a cDNA if only a
portion of the coding sequence is known. The portion of known
sequence is used to design a probe. A population of different cells
is then encapsulated and hybridized with the probe. Cells are then
separated according to extent of expression. Cells showing the
highest level of expression provide a suitable source material from
which to clone the cDNA.
[0074] The methods are also useful for comparing or monitoring the
expression of a given gene or gene(s) in different cell types. A
probe is designed to hybridize to a mRNA transcript of each gene of
interest. Optionally, different probes can bear different labels.
Probes are then hybridized with mRNA in a microdrop encapsulated
cell population, which typically includes cells of different types.
The extent of hybridization of each cell with each probe is then
determined. Optionally, cells hybridizing with a particular probe
at significantly above or below average levels are isolated and
cell type determined, allowing correlation between cell type and
expression level. Optionally, different cell types in a population
can themselves be labelled with reagents that specifically bind to
a particular cell type. For example, a particular cell type can be
labelled using an antibody that binds to a receptor specific to the
cell type. Microdrops are then analyzed for both cell type labels
and probe labels, thereby facilitating comparison of expression
levels of particular mRNA species between the cell types that have
been specifically labelled.
[0075] The methods are also useful for preparing isolated
chromosomes. As noted, isolated chromosomes are useful for e.g.,
positional cloning studies and for preparing probes.
[0076] XII. Kits
[0077] The invention also includes kits for the practice of the
methods of the invention. The kits comprise equipment and/or
reagent(s) for making gel microdrops and optionally, probe(s) for
performing hybridization to encapsulated nucleic acids. Examples of
equipment include a CellSys 100.TM. Microdrop Maker and components
thereof, an instrument providing a pulsating novel, such as an
inkjet printer, and a vortexer. Examples of reagents include
chemicals for making a gel, such as agarose or acrylamide,
cross-linking reagents, denaturing agents, and hybridization
buffer. The kits can also include label(s) and other chemicals to
amplify label signal. The kits usually include labelling or
instructions indicating the suitability of the kits for performing
hybridization in gel drops and/or flow cytometrix analysis. The
term "label" is used generically to encompass any written or
recorded material that is attached to, or otherwise accompanies the
kit at any time during its manufacture, transport, sale or use.
EXAMPLES
[0078] 1. Encapsulation, Hybridization and Screening of
Chromosomes, and Stability of Encapsulated Chromosomes
[0079] Materials and Methods
[0080] Cell Lines and Culture Conditions Human chronic myelogenous
leukemia, K-562, human acute lymphocytic leukemia, REH (American
Type Culture Collection, Rockville, Md.), and mouse fibroblast, Mus
Spretus C1-SA (Los Alamos National Laboratory, Los Alamos, N. Mex.)
cells were grown in RPMI 1640 medium supplemented with 10% fetal
bovine serum at 37.degree. C. in the presence of 5% CO.sub.2.
Normal human lymphoblast cells GM130 (NIGMS Human Genetic Mutant
Cell Repository, Coriell Institute for Medical Research, Camden,
N.J.) were grown under identical conditions, except that RPMI 1640
medium was supplemented with 15% heat inactivated fetal bovine
serum.
[0081] Source of Plant Chromosomes Plant chromosomes from the field
bean Vicia faba, (from J. Dolezel, Institute of Experimental
Botany, Olomouc, Czech Republic), were isolated from root meristems
after cell cycle synchronization with hydroxyurea and metaphase
accumulation with amiprophos methyl (21).
[0082] Mitotic Cell Preparation Mouse C1-5A cells (an adherent cell
line) undergoing logarithmic growth were treated with 0.2 .mu.g/ml
colcemid (Sigma, St. Louis, Mo.) for 12-15 hours. Mitotic cells,
which become less adherent, were shaken-off and resuspended in
hypotonic solution (55 mM KCl). Human K-562 cells undergoing
exponential growth were treated with 60 .mu.M genistein (Sigma) for
24 hours to synchronize growth (23). Cells were then pelleted and
washed once with Hank's balanced salt solution (Sigma). Fresh media
containing 0.1 .mu.g/ml of colcemid was added and cells were grown
for an additional 24 hours. After counting, cells were pelleted by
centrifugation (100 g for 10 min at 4.degree. C.) and resuspended
in hypotonic solution (75 mM KCl). Human REH cells were grown to
stationary phase, to synchronize growth, then were left for 2 days.
Cells were harvested by low speed centrifugation and grown in fresh
media containing 0.1 .mu.g/ml colcemid for 24 hours. After
pelleting, cells were resuspended in hypotonic solution (75 mM
KCl).
[0083] Chromosome Isolation Human and mouse chromosomes were
isolated using the polyamine method (31,32), with minor
modifications. Approximately 2.times.10.sup.7 cells were swelled in
10 ml of hypotonic solution either for 30 min (human REH) or for 1
hr (human K-562 and mouse C1-5A cells) at room temperature. After
swelling, cells were pelleted by 5 min centrifugation at 40 g, and
gently resuspended in 0.1 ml of fresh hypotonic solution. Two ml of
chromosome isolation buffer (CIB; 15 mM Tris-HCl, 80 mM KCl, 20 mM
NaCl, 2 mM EDTA, 0.5 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine,
pH 7.2) supplemented with 0.1% (v/v) 2-mercaptoethanol and 0.2%
(v/v) Triton X-100 was added and solutions were mixed by brief (10
sec) vortexing. Tubes were kept at 0.degree. C. for approximately
10 min. C1-5A cells were passed through a 25 gauge needle until
chromosomes were released, as monitored by fluorescence microscopy.
Nuclei and cellular fragments were removed by three successive 5
min centrifugations at 40 g. The top two thirds of the supernatant,
after the final centrifugation, was kept at 4.degree. C. for 16 hr.
The supernatant was then carefully decanted to avoid disturbing the
settled chromosomal pellet. Chromosomes were resuspended in 0.2 ml
of CIB and aggregates were pelleted by centrifugation for 5 min at
40 g. Chromosomes were either stored in CIB or immediately
encapsulated in agarose gel microdrops (GMDs).
[0084] Chromosome Encapsulation The chromosome/agarose mixture
(2.3% Type XII agarose; (Sigma) 0.1% Triton X-100 (Sigma)
containing 10.sup.6 chromosomes/0.55 ml) was prepared by melting
the agarose in CIB at 100.degree. C., cooling the agarose to
58.degree. C., and adding 100 .mu.l of chromosome suspension and 50
.mu.l of 11% (v/v) Triton X-100 (pre-warmed to 58.degree. C.) to
0.4 ml of melted agarose. The mixture was held at 58.degree. C. for
5 min and added dropwise to 15 ml of CelMiX.TM. 200 emulsion matrix
(One Cell Systems, Cambridge, Mass.) which was also pre-warmed to
58.degree. C. GMDs were generated with a CellSys100.TM. Microdrop
Maker (One Cell Systems, Cambridge, Mass.) equipped with a 1.6 cm
blade using successive rotor speeds of 1,500 rpm for 1 min at
20-25.degree. C., 1,500 rpm for 1 min at 0.degree. C., and 1,500
rpm for 5 min at 0.degree. C. GMDs were separated from the emulsion
matrix by centrifugation at 350 g for 10 min. The encapsulated
chromosome-containing pellet was washed twice with 13 ml of CIB,
re-pelleted by centrifuging 5 min at 250 g, and stored at 4.degree.
C. in 10 ml of the same buffer.
[0085] Chromosome Staining Encapsulated chromosomes were stained
with propidium iodide (0.4 .mu.g/ml) for microscopic examinations
and with 7-actinomycin (7AAD) at the same concentration, both from
Sigma, for flow cytometry.
[0086] Hybridization Probes LSI.TM. 22q (bcr-locus specific, Vysis,
Downers Grove, Ill.), which hybridizes to a 300 kb region of the
bcr gene on chromosome 22, was used. This probe was directly
labeled with Spectrum Green T (fluorescein). After labeling, the
probe size distribution ranged from 50-500 nt. The DNA probe was
denatured at 95.degree. C. for 5 min before hybridization.
[0087] Microdrop In Situ Hybridization (MISH) of Human
Chromosomes
[0088] Encapsulated chromosomal DNA was denatured in 0.1 N NaOH,
50% (v/v) ethanol for 1.5 min. GMDs were washed once in 0.5 M
sodium carbonate, pH 10.2. After denaturation, the hydroxyl groups
in the agarose microdrops were mildly crosslinked with 5 .mu.M
divinylsulfone by incubating 30 min at room temperature. Excess
reactive groups from divinylsulfone were blocked with 2% (v/v)
2-mercaptoethanol for 30 min in 40 mM Tris-HCl, pH 8.0. GMDs were
then washed with 2.times.SSC (0.15M NaCl, 0.015M sodium
citrate).
[0089] 100 .mu.l (approximately 2.times.10.sup.5) of human
chromosomes encapsulated in GMDs was hybridized with 2.0 .mu.l of
the denatured probes (probe concentration was proprietary for the
manufacturer) in a hybridization mixture (2.times.SSC, 10% (v/v)
dextran sulfate, 50 .mu.g/ml salmon sperm ssDNA for 16 hours at
68.degree. C. After hybridization, non-specifically bound probe was
removed by incubating GMDs with 1.0 ml 0.4.times.SSC at 72.degree.
C. for 5 min (LSI/22) and washing twice with 0.4.times.SSC at room
temperature. Cot DNA was added to prevent non-specific
hybridization to repetitive sequences.
[0090] Microscopy and Digital Image Analysis The integrity of
chromosomes after fluorescent staining or MISH was checked visually
using an Olympus BH-2 microscope (40.times.SPlan 0.4 objective or
phase contrast A40 PL 0.65 objective) equipped for epifluorescence
with appropriate filters for fluorescein and 7AAD.
[0091] Flow Cytometric Analysis After staining or MISH,
encapsulated chromosomes were analyzed using a FACS Vantage flow
cytometer (Becton Dickinson Immunocytometry Systems, San Jose,
Calif.) equipped with a standard 100 .mu.m nozzle. LYSYS II Ver.2.0
software was used for data analysis. To remove large particles, the
GMDs were sieved through a 53 .mu.m nylon mesh (Small Parts Inc.,
Miami Lakes, Fla.). For flow cytometry analysis, a concentration of
microdrops not exceeding 2.times.10.sup.5/ml was used. Forward and
side scatter signals were analyzed on a log scale and examined in
scatter plot format, permitting identification of and gating on
GMDs. 7ADD fluorescence was used to identify GMDs containing
encapsulated chromosomes. To identify 7ADD, an argon laser with a
356 nm spectral line was used. To identify chromosomes which
hybridized to the Spectrum Green.TM. labeled probe, fluorescein
(FITC) intensity was measured. For measuring FITC fluorescence, an
argon laser with a 488 nm spectral line was used.
[0092] Fluorescence Activated GMD Sorting Encapsulated chromosomes
were sorted using a FACS Vantage fluorescence activated cell sorter
(Becton Dickinson) adapted with a macrosort option. The sheath
pressure was set at 2 psi with a sample differential of 1 psi. A
large diameter sample line was used to avoid clogging. The GMD
samples were sieved through a 53 .mu.m mesh before sorting. Sorting
speed was in the range of 50 FITC-labeled chromosomes/sec. Sorted
GMD-encapsulated chromosomes were pelleted by low speed
centrifugation and taken up with 20 .mu.l of Antifade solution
(Oncor, Gaithersburg, Md.), diluted 1:1 with CIB and analyzed using
a fluorescence microscope.
[0093] Digestion of Denatured Encapsulated Chromosomal DNA with
HindIII Encapsulated chromosomes were denatured, as previously
described, washed with 40 mM Tris-HCl, pH 8.0 and subsequently
digested with Proteinase K (2 mg/ml) supplemented with lithium
dodecyl sulfate (1%) in CIB for 12 hours at 50.degree. C.
Chromosomes were then washed three times with a 200-fold excess of
CIB and two times with 20-fold excess of HindIII digestion buffer
(50 mM NaCl/10 mM Tris-HCl, pH 8.0/10 mM MgCl.sub.2). Digestion of
encapsulated chromosomes was done using 20 units of HindIII
(Gibco-BRL) in a reaction volume of 50 .mu.l for 90 min at
37.degree. C. Gel loading buffer was added and samples were
electrophoresed as described below.
[0094] Gel Electrophoresis of Chromosomal DNA Both free and
encapsulated chromosomes were treated with proteinase K and lithium
dodecyl sulfate as described above for three hours at 50.degree. C.
Gel-loading buffer (6.times., 0.25% bromphenol blue, 0.25% xylene
cyanol FF, 30% glycerol) was added and samples were electrophoresed
on 0.8% SeaKem Gold (FMC BioProducts, Rockland, Me.) agarose in TAE
buffer (0.04 M Tris-acetate, 1 mM EDTA) at 56 volts for 2-6 hours.
Propidium iodide was present in the gel (0.5 .mu.g/ml) and in the
electrophoresis buffer (0.05 .mu.g/ml) during electrophoresis. 0.25
.mu.g of lambda DNA or 1.0 .mu.g .phi.X174 DNA cut with HinFI
(Gibco-BRL) was used as a standard.
[0095] Chromosome Storage and Recovery Free and encapsulated
chromosomes were kept at 4.degree. C. for up to 6 months in CIB.
Agarose (from Pseudomonas atlantica, Sigma) was used to digest GMDs
to recover chromosomes of interest. Encapsulated chromosomes were
pelleted, resuspended in phosphate buffered saline solution, pH 7.0
(Sigma), and agarose (30 units per 1000 GMDs) was added. This
suspension was incubated at 40.degree. C. for two hours, treated
with proteinase K as described above, and chromosomal DNA was
analyzed by gel electrophoresis.
[0096] Results
[0097] FIG. 1 shows encapsulated and unencapsulated human, mouse,
and plant chromosomes. Encapsulated chromosomes appear visually
more compact than unencapsulated chromosomes, with narrow
centromeric regions and tightly bound chromatid extensions. The
centromeric region of encapsulated chromosomes appear physically
unseparated, which would be an indication of chromatid loss.
Interestingly, encapsulation of intact plant chromosomes, which are
approximately 3 times larger than human chromosomes, was also
successfully performed using this procedure.
[0098] Stability of Encapsulated Chromosomes To assess the long
term stability of encapsulated chromosomes, we examined DNA
fragmentation using gel electrophoresis. As depicted in FIG. 2, no
DNA fragmentation was found by electrophoretic analysis, even 6
months after encapsulation. In contrast, one month after isolation,
DNA from unencapsulated human and mouse chromosomes has a smeared
banding pattern, indicative of DNA fragmentation due to nuclease
cleavage. This result indicates that encapsulated chromosomal DNA
remains intact and can be used for preparing chromosome-specific
libraries. Intact-isolation and long term stability of high
quality, high molecular weight DNA will be a major convenience for
researchers and an innovation for sample storage for clinical
use.
[0099] In Situ Hybridization of Encapsulated Chromosomes An
important improvement was development of a matrix crosslinking
method which allowed use of up to 50% formamide and temperatures as
high as 95.degree. C., necessary for reproducible hybridizations.
The agarose hydroxyl groups were mildly crosslinked with divinyl
sulfone. Although this procedure also partially crosslinks
chromosomal DNA to the agarose matrix, because this process is
reversible at pH 10, DNA can be released from GMDs after MISH,
which is important for eventual construction of chromosome-specific
libraries.
[0100] Using a FACS Vantage both for flow cytometric analysis and
cell sorting, dual-parameter dotplots were produced by plotting
FITC-fluorescence, which was detecting probes hybridized to the
chromosomes versus 7AAD fluorescence, which as a general DNA stain
was used to detect all chromosomes. FIG. 3A shows flow sorting of
human chromosome 22 following microdrops in situ hybridization
using a bcr locus specific probe. Chromosomes were counter-stained
with 7-amino-actino-mycin (Vysis, Downer's Grove, Ill.).
Chromosomes were counter-stained with 7AAD. R1 includes high FITC,
low 7AAD fluorescence specific for gel microdrops containing
chromosome 22. The scattergram also display empty GMDs,
encapsulated chromosomes, and noise. FIG. 3B shows sorted
chromosomes visualized using fluorescent microscopy. The
hybridization signal is depicted in green (FITC) color.
Hybridization signals were amplified using the TSA method, which
provides a 10-100 increase in signal intensity.
[0101] FIG. 4 shows purity of chromosome 22 after sorting measure
by the polymerase chain reaction using primer sets specific from
chromosomes 10, 21 or 22. Amplification results for each primer set
were compared using unsorted and sorted chromosome populations.
Unsorted chromosomes generated specific amplicons for each primer
(lanes 3-5), Sorted chromosome 22 showed no contamination with
chromosome 10 (lane 8 vs. 60 and were less than 1% contaminated
with chromosome 21 (lane 8 vs. lane 7).
[0102] Recovery of Encapsulated Chromosomes We determined that
after recovering chromosomes from agarose microdrops, DNA was not
fragmented, even 6 months after encapsulation. We also tested the
integrity of DNA after digesting microdrops with agarase and found
that the electrophoretic pattern was the same as that of untreated
encapsulated chromosomes used as controls. These observations show
that after release from gel microdrops, encapsulated chromosomes
will be a convenient source of high quality DNA for molecular
genetics studies.
[0103] Digestion of Denatured Encapsulated Chromosomes A major
concern for eventual use of sorted chromosomes to construct
chromosome-specific libraries was that digestion of chromosomal DNA
with restriction enzymes, which is necessary for cloning large DNA
fragments (>100 kb) into BAC libraries, would be impossible
because denaturation would destroy the DNA secondary structure. To
address this concern, we tested the hypothesis that brief alkaline
use would only partially denature the DNA and that subsequent
digestion with proteinase K at 50.degree. C. in low salt buffer
overnight would restore double strandedness, thus making specific
enzyme digestion possible. Human chromosomes isolated from the GM
130 cell line were digested with proteinase K and cleaved with
HindIII. The electrophoretic result depicted in FIG. 5 shows that
the restriction endonuclease HindIII cleaved restored DNA and
generated typical sized fragments, demonstrating that MISH treated
chromosomes can be used for library construction.
Example 2
Construction of Chromosome-Specific BAC Libraries
[0104] A major unrealized goal of fluorescence in situ
hybridization assays has been the use of flow cytometry to isolate
specific chromosomes for library construction. Prior to development
of the MISH method, after hybridization, only a small fraction of
chromosomes remain intact and free in suspension. Without the
protection gained using the agarose microspheres, most chromosomes
are clumped or fragmented, making them largely unsuitable for flow
cytometric analysis (27). We have shown not only that we can
hybridize and flow sort encapsulated chromosomes, but also that
alkaline-denatured chromosomes can be digested with restriction
endonucleases. As a result of this finding, we propose construction
of chromosome-specific libraries. Human chromosome 21 was chosen
because it is often difficult to identify and sort using
conventional dual fluorescent staining since it is small and
indistinguishable in the presence of cellular debris (29). The
second BAC library will be constructed using human chromosomes 9,
which belongs to the group of chromosomes not resolvable by
conventional dual fluorescent staining because of its similarity in
size to several other chromosomes (13). Chromosome libraries are
constructed using the steps below.
Sort MISH-labeled chromosomes
.dwnarw.
Remove hybridized probes
.dwnarw.
Digest sorted chromosomes with proteinase K in low salt buffer
.dwnarw.
Digest chromosomal DNA with restriction enzymes
.dwnarw.
Ligate DNA fragments into BAC vector
.dwnarw.
Electroporate ligated product into E. coli host
Screen transformants for chromosome-specific inserts
Example 3
Use of MISH-Sorted Chromosomes for Reverse Chromosome Painting
[0105] The development of in situ hybridizations with flow sorted
chromosome libraries (25,26), combined with non-isotopic signal
detection (30), has become a powerful approach for rapidly
analyzing human chromosomal aberrations, such as aneuploidy and
translocations. These techniques, termed chromosome painting, are
becoming widely used in clinical cytogenetics. However, small
rearrangements, additions, or deletions are not detectable using
conventional chromosome painting, but these aberrations are
detectable by reverse chromosome painting, which is performed using
a probe prepared from aberrant chromosomes. A method of using
MISH-sorted chromosomes is depicted below.
Sort MISH-labeled aberrant chromosomes Deproteinize sorted
chromosomes
.dwnarw.
First round of chromosomal DNA PCR amplification
.dwnarw.
Biotin-label probe production by a second round of PCR
amplification
.dwnarw.
Use probe in FISH painting of normal chromosome metaphase
spreads
Example 4
Detection of the Philadelphia Chromosome
[0106] The Philadelphia chromosome is a shortened chromosome 22
that results from a balanced translocation between chromosomes 9
and 22 with the translocation breakpoints at 9q34 and 22q11. As a
result of this translocation, most of the abl oncogene, located on
chromosome 9, is juxtaposed to part of the bcr gene, located on
chromosome 22, creating a new bcr-abl gene fusion (40, 51, 52, 53,
54). This gene fusion encodes an abnormal protein with strong
tyrosine kinase activity compared with the weak tyrosine kinase
activity of the normal abl protein. The abnormal tyrosine kinase
produced from bcr-abl causes increased cell proliferation and
contributes to leukemogenesis by unknown cellular pathways.
[0107] Translocations such as bcr/abl are currently detected by
cytogenetic examination of metaphase chromosome preparations
prepared from bone marrow cultures. Although this method is
adequate to detect most chronic myelogenous leukemia cases (CML) in
which Ph.sup.1-positive chromosomal translocations are visible
after banding due to the size difference in metaphase spreads, in
acute lymphoblastic leukemia (ALL), cytogenetic examination is
successful in only 65-80% of the cases, depending on the experience
of each laboratory (55). The lower yield in ALL is the result of
the following factors. First, many ALL patients have inaspirable
bone marrows, so no cells are available. Second, lymphoblasts can
be difficult to culture, so there is little enrichment of leukemia
cells. And third, the percentage of Ph.sup.1 carrying cells in a
sample may be as low as 30%, in contrast with CML in which
virtually 100% of the cancerous cells in the sample carry Ph.sup.1.
In cases where chromosomal rearrangements are not visible in
classical metaphase spreads, which can occur in Ph.sup.1-positive
chromosomes, both in CML or ALL leukemias, fluorescence in situ
hybridization, Southern blot (DNA) analysis, or polymerase chain
reaction (PCR) analysis must be performed to detect rearrangements
(55).
[0108] In CML, Southern blot analysis has been useful in detecting
evidence of Ph.sup.1 chromosome in patients in whom the
cytogenetics are negative despite a clinical presentation of CML
(53). This approach is only of limited utility in ALL because only
25-50% of Ph.sup.1 chromosome positive ALL patients have M-bcr
(Major breakpoin't rearrangements). Nearly all M-bcr negative
patients have translocation breakpoints in m-bcr (minor breakpoint
rearrangements) anywhere in the first intron, which is 70-kb in
size, requiring performance of an impractical number of Southern
blots in order to adequately investigate this entire region.
[0109] The chromosomal breakpoints in CML and acute leukemias may
occur over large DNA sequences: 5.8 kb for the bcr region in CML
and over 90 kb for the first intron of the bcr 1 gene in acute
leukemias. Therefore, PCR amplification of the fusion bcr/abl gene
sequences cannot be performed on DNA from patient specimens. All
PCR based methods are designed to amplify and detect the abnormal
fusion of mRNA (RT PCR). The design of these methods takes
advantage of the fact that mRNA sequences are much shorter, lacking
intron sequences. Assuming primers can be designed to amplify short
stretches of mRNA specific for particular translocation (currently
available for Ph.sup.1 fused mRNA), amplified target can be
detected after hybridization with specific probes followed by gel
electrophoresis and Northern blotting. The size of bcr/abl fused
mRNA for different patients varies within certain ranges for CML
and acute leukemia breakpoints, but the same size fusion mRNA is
characteristic for each malignant clone and can be monitored for
each patient over the clinical course of the leukemia.
[0110] An advantage of using mRNA as a target for PCR amplification
is that mitotic cells are unnecessary. The practical limit of
sensitivity of detection is approximately 1 malignant per 10,000
non-malignant cells. While the exquisite sensitivity of PCR could
be advantageous in molecular diagnostic testing, its use is
troublesome in the clinical laboratory. Contamination with minute
amounts of amplified DNA and/or RNA from patient samples or cell
line controls, even in the range of 1 to 10 copies, may generate
false-positive results. Aerosols and carryover are the main sources
of contamination. A potential problem with monitoring the presence
of the Ph.sup.1 chromosome after chemotherapy or bone marrow
transplant by RT PCR is the presence of residual dead leukemia
cells with intact mRNA complicating therapeutic assessment.
[0111] The MISH technique combined with flow cytometric analysis
makes a significant contribution to analysis of translocations.
Because metaphase chromosomes are required, only live leukemia
cells contribute Ph.sup.1 chromosomes for detection. As long as
leukemia cells proliferate and reach mitosis, approximately 20
Ph.sup.1 positive chromosomes in the presence of 50,000
chromosomes, including those from Philadelphia-negative cells, can
be detected in about 5 min. This corresponds to detection of 20
cells with a single copy of Ph.sup.1 chromosome, or 10 cells with
two defective copies, in an environment of approximately 1,000
cells which are Ph.sup.1 chromosome negative (2% leukemia cells
present). To improve statistical significance, analysis of 100,000
events can be performed in approximately 10 minutes, provided that
metaphase chromosomes are available from both cell types. In
contrast, in current FISH procedure using metaphase spreads
obtained from bone marrow cultures which have a mitotic index of
10%, one would have to find one Ph-positive spread in the presence
of 1,000 Ph-negative spreads, a labor intensive and impractical
approach by conventional microscopy.
[0112] Materials and Methods
[0113] Chromosome encapsulation and hybridization conditions were
as described above. The LSI.TM. bcr/abl DNA probe was used for in
situ hybridization. The probe was directly-labeled with
SpectrumGreen.TM./SpectrumOrange.TM. which was designed to detect
translocations between chromosome 9 and 22 (Vysis, Downers Grove,
Ill.). This probe detects bcr/abl gene fusions, the molecular
equivalent of the Philadelphia chromosome (Ph.sup.1), in both
metaphase and interphase cells. It can be used to identify bcr/abl
gene fusion involving either of the two breakpoint regions (M-bcr
and m-bcr) in the bcr gene on chromosome 22. The bcr/abl
translocation probe is qualified for use on both cultured
lymphocytes and bone marrow cells. The LSI.TM. probe does not
contain repetitive sequences and is composed of an abl probe
directly labeled with SpectrumOrange fluorophore and a bcr probe
directly labeled with SpectrumGreen fluorophore. The abl probe
begins between c-abl exons 4 and 5 and continues for about 200 kb
toward the telomere of chromosome 9. The bcr probe begins either
between bcr exons 13 and 14 (m-bcr) or between bcr exons 2 and 3
(M-bcr) and extends toward the centromere approximately 300 kb
crossing well beyond the m-bcr region. The probe size distribution
is within a range of 50-500 nt (after labeling).
[0114] After hybridization, chromosomes containing M-bcr/abl gene
fusion in Chronic Myelogenous Leukemia (CML) and in Acute
Lymphoblastic Leukemia (ALL) can be expected to contain fused
orange and green signals in translocated chromosome 22, which are
sometimes perceived as yellow. Normal chromosomes 22 should display
green signal and normal chromosomes 9 should display orange signal.
Hybridized chromosomes that have the m-bcr/abl gene fusion in ALL
should contain fused green/orange signal in chromosome 22 and faint
green signal not fused with orange signal on chromosome 9 (from the
chromosome 22 region between m-bcr and M-bcr that is translocated
to chromosome 9).
[0115] Results
[0116] Chromosome Isolation To increase the yield of human mitotic
cells, K-562 cells were synchronized by a novel method using
genistein, an isoflavone which blocks the cell cycle at G.sub.2/M.
An important advantage of genistein for cell cycle synchronization
was that it did not appear to penetrate cells and was easily
eliminated by washing. After synchronization, growth of K-562 cells
was not significantly affected by the presence of colcemid for up
to 24 hours, and a high percentage (75%) of cells, therefore,
reached mitosis. Use of genistein yielded a ready supply of
millions of chromosomes facilitating extensive experimentation with
encapsulation and fluorescent in situ hybridization conditions. The
method can also be used to isolate chromosomes for other
purposes.
[0117] In FIG. 6, detection of translocated chromosome 22 left
chromosome 9 middle, and translocation-free chromosome 22 right by
MISH are shown. Translocated chromosome 22 is identifiable by the
presence of both green and red colors on a background of a blue
colored whole chromosome. Fused red and green signals may be
perceived as yellow (bottom left of FIG. 6). This yellow color also
represents fused bcr/abl gene (translocated chromosome 22).
Translocation-free chromosome 22 is detectable by the presence of
single green color and chromosome 9 by the presence of single red
color. Digital images created by a CELLscan digital image system
with Exhaustive Photon Reassignment (EPR), which was available
through collaboration, are presented here, but a fluorescence
microscope equipped with a triple bandpass filter for DAPI,
fluorescein and rhodamine was adequate to identify translocations
in Philadelphia.sup.1 chromosome.
Example 6
Analyzing Encapsulated Human Nuclei Using Microscopy and Flow
Cytometry
[0118] Analyzing MISH signals in nuclei provides improved contrast
relative to MISH detection in chromosomes. Moreover, MISH analysis
of nuclei can be performed in cases where cell proliferation is
difficult or impossible. The applications are numerous and include
detection of: translocations, deletions, monosomies or trisomies
for diagnostic and prognostic analysis of aberrations. This method
can also be used in research applications including gene
amplifications and gene mapping. In this example, we use human
nuclei with deleted chromosome 3 as a model system. This genetic
defect presents numerous clinical symptoms in affected people
including mental retardation and multiple congenital anomalies.
[0119] Isolation of Nuclei
[0120] Nuclei are isolated from human lymphoblastoid cell line
GM11428 (NIGMS Human Genetic Mutant Cell Repository, NIH, Bethesda,
Md.). HL-60 cells are a source of normal nuclei (control) with no
deletions in any chromosome. Cells in logarithmic phase of growth
are collected and swelled in hypotonic solution (75 mM KCl) for 1
hour. Cells are then pelleted by low speed centrifugation and
resuspended in 2-mercaptoethanol-free CIB buffer (1 million
cells/ml). Triton X-100 is then added to obtain final concentration
of 0.2%. Nuclei released from cells are kept in this solution for 1
hour at 4.degree. C., then pelleted by centrifugation at 100 x g
and resuspended in original cell volume of the same buffer and re
pelleted. Finally, nuclei are resuspended at a concentration of 10
million nuclei per ml of 2-mercaptoethanol-free CIB buffer.
[0121] Encapsulation of Nuclei
[0122] Encapsulation of nuclei is performed essentially as
described previously for chromosome encapsulation. However, GMD
size can be adjustment from 25-35 to 45-55 .mu.m to account for the
larger size of nuclei by modification of blade speed during the
emulsification process.
Example 7
Improved Method of Chromosome Isolation
[0123] Chromosomes can be synchronized in metaphase by culturing
cells from which chromosomes are to be isolated with the flavonoid
genistein together with colcemid, which is commonly used to block
the cell-cycle at metaphase. This procedure yields a mitotic index
of about 75%: (i.e., three out of four cells yielded metaphase
chromosomes).
[0124] Chromosomes are released from cells by hypotonic treatment.
Quantitative release of chromosomes requires at least some physical
shearing force, such as vortexing or passage through a gauge
needle, and generate some cell debris. After chromosome release,
nuclei are removed by low speed centrifugation to remove nuclei. To
remove proteins, chromosome lysates are then dialyzed in a
Slide-A-Lyzer.TM. (Pierce, Rockford, Ill.), which has a large pore
membrane (100,000 molecular weight cut off), against a 100 fold
volume of CIB (with two changes). Two alternatives for separating
chromosomes from cellular debris can be employed.
[0125] In the first approach, chromosomes are captured with
magnetic beads conjugated to antibodies specific for the double
stranded DNA of human chromosomes. These antibodies are present in
sera of patients suffering from scleroderma (Chemicon
International, Temecula, Calif.). The immunoglobulin fraction of
the sera is isolated using protein A-agarose (Pierce, Rockford,
Ill.). The IgG fraction is then biotinylated with biotin-NHS ester
(Molecular Probes, Eugene, Oreg.) using the manufacturer's
procedure. Streptavidin magnetic microbeads (Miltenyi Biotec,
Auburn, Calif.) are used to bind the biotinylated IgG fraction of
the human sera from scleroderma patients. The microbeads are then
used to capture chromosomes. Chromosomes covered with magnetic
beads are separated from non-chromosomal material by means of a
strong field MACS Separator (Miltenyi Biotec). This approach also
allows enrichment of occupied GMDs from the pool of mostly
unoccupied GMDs.
[0126] In the second approach, cellular debris is separated from
chromosomes using antibodies specific for cytoskeletal proteins
conjugated to a solid support. In the chromosome release step,
buffer containing detergent (Triton X-100) is used to solubilize
membranes. But cytoskeletal proteins, such as fibronectin
filaments, actin filaments, or intermediate microfilaments, are
mostly present in an insoluble form. Although most microtubule
proteins are solubilized by colcemid treatment, some remain.
Antibodies against cytoskeletal proteins (fibronectin, actin,
vimentin), are available from Accurate Chemical & Scientific
(Westbury, N.Y.), Biosource International (Camarillo, Calif.) and
Cytoskeleton (Denver, Colo.). These antibodies are conjugated
through reductive amination to AminoLink Plus Coupling agarose gel
(Pierce, Rockford, Ill.). 0.5 ml of antibody-derivatized gel (in a
Compact Reaction Column, United States Biochemical, Cleveland,
Ohio) is used to capture insoluble fragments of cellular debris by
passing dialyzed and concentrated chromosome solution through a
column.
Example 8
Detection with Chemiluminescent Substrates
[0127] Exothermic chemical reactions generally release energy in
the form of vibrational or rotational excitation or heat. In
chemiluminescent reactions, however, the electronically excited
state is reached by a chemical reaction and light rather than heat
is generated. The energy-rich source in most chemiluminescent
reactions is peroxide, hydroperoxide, 1,2 dioxetane, or dioxetane
bonds. During the transition of these excited intermediates to the
electronic ground state, light is emitted in a process known as
direct chemiluminescence. Novel acridane or dioxetane
chemiluminescent substrates, developed by Tropix, BioTecx, and
collaborators at Lumigen allow detection of 10.sup.-19 moles of
horseradish peroxidase or 10.sup.-21 moles of alkaline phosphatase
(74-76), a substantial improvement in sensitivity over fluorescence
based detection at 10.sup.-14 moles per liter.
[0128] Chemiluminescent substrates for alkaline phosphatase are
currently all phenyl phosphate dioxetanes (PPD). PPD
(4-methoxy-4-(3-phosphatepheny-
l)spiro[1,2dioxetane,-3,2'-adamantane] disodium salt) or CSPD.RTM.
(chlorine derivative of PPD) are now widely used in clinical
immunossays and protein and nucleic acid detection test kits. PPD
or CSPD.RTM. based substrates also contain fluorescent enhancers
which promote more efficient generation of chemiluminescent light
through extended glow kinetics.
[0129] Other substrates such as PS-1, a substrate for HRP which has
just become commercially available, exploits Lumigen's discovery
that esters of N-alkylacridancarboxylic acid are efficiently
oxidized by peroxidase enzymes in the presence of hydrogen peroxide
and a phenolic enhancer. The reaction, which requires only a
minimal catalytic quantity of a peroxidase, converts the acridan
compounds to the corresponding N-alkylacridinium ester. The PS-1
HRP substrate reaction produces an intense chemiluminescence,
reaching a peak in approximately 10 minutes, with an extended decay
over several hours. In a direct comparison with enhanced luminol
based chemiluminescent reagents, previously the most sensitive
system for detecting HRP, PS-1 was shown to be 100 times brighter
(74).
[0130] The current detection limit using fluorescence in situ
hybridization (FISH) and non-isotopically-labeled probes is
approximately 100 kb DNA target or 10-30 copies of mRNA (77-79).
Although slightly stronger signals can be obtained using probes
labeled with radioactive isotopes, unacceptably long exposure times
of days to weeks are required to detect approximately the same
length DNA targets. Furthermore, health and disposal concerns make
this technology unsuitable for most laboratories.
[0131] In situ hybridization techniques have dramatically improved
in recent years both in terms of safety and sensitivity, primarily
due to use of enzymes instead of isotopes as reporter molecules.
Due to high reaction turnover, horseradish peroxidase (HRP) or
alkaline phosphatase (AP) are the most frequently used reporter
enzymes. Using reporter enzymes, localization of hybridization
signals can be performed either with calorimetric
immunohistochemistry methods, which are less sensitive, or with
fluorescent methods, which increase sensitivity 10-100 fold, in
comparison to the non-enzymatic methods (80).
[0132] The highest detection limits for both reporter enzymes are
obtained, however, using chemiluminescent substrates which
facilitate the emmission of light triggered by an enzymatic
reaction. Approximate detection limits of several approaches are
shown below.
1 Detection Method Detection Limit.sup.a Base Pairs.sup.b Color
10.sup.-10-10.sup.-12 200-400 Fluorescence 10.sup.-13-10.sup.-15
100-200 Radioisotopes 10.sup.-20 10-100 PCR 10.sup.-22 0.4-10
Chemiluminescence 10.sup.-19-10.sup.-21 10-100 Microdrop CL-
10.sup.-21 10-100.sup.c moles, kilobases, per each GMD
[0133] Tyramide Signal Amplification
[0134] The recently available Tyramide Signal Amplification (TSA)
system (NEN Life Sciences Products, Boston, Mass.) designed for
fluorescence in situ hybridization was used in order to compare
amplified fluorescence signal with chemiluminescence. TSA
technology (80) uses horseradish peroxidase (HRP) to catalyze
deposition of fluorophore or biotin labeled tyramide near the site
of the hybridized probe, proximal to the enzyme. HRP can deposit
10.sup.2-10.sup.3 tyramide molecules in 10 min, resulting in
powerful signal amplification. In addition, since tyramide can be
labeled both with fluorophores (TSA-Direct) and biotin
(TSA-Indirect), both fluorescent or chemiluminescent signal can be
detected.
[0135] For fluorescent measurements after MISH, GMDs were incubated
in TNB blocking buffer (0.1M Tris-HCl, pH 7.5, 0.15M NaCl, 0.5%
Blocking Reagent, NEN) with diluted conjugates of HRP with
streptavidin for biotin labeled probes, or anti-fluorescein for
fluorescein labeled probes (both from NEN) for 30 min. After three
subsequent washes with TNT (0.1M Tris-HCl, pH 7.5, 0.15M NaCl,
0.05% TWEEN 20), GMDs were incubated with 300 .mu.l of diluted
fluorescein-tyramide for 10 min. Unreacted tyramide was removed by
washing GMDs twice with TNT. MISH signals were then visualized
using fluorescence microscopy.
[0136] Chemiluminescent Detection of Hybridized Probes
[0137] GMDs hybridized with biotin labeled probes were incubated
for 30 min in TNB blocking buffer containing conjugate of either
streptavidin-HRP (NEN) or HRP (Sigma) at dilutions of 1:100. GMDs
hybridized with fluorescein-labeled probes were incubated with the
conjugate of anti-fluorescein-HRP (NEN) diluted 1:100. In some
signal amplification experiments, prior to chemiluminescent
measurements, tyramide labeled with biotin was subsequently bound
to streptavidin conjugate of either HRP or AP. Unreacted conjugates
were removed by three successive washes with TNT. GMDs were than
pelleted by low speed centrifugation and resuspended in 0.05 ml
0.4.times.SSC. Aliquots diluted in a ratio of 1:5 with the
appropriate chemiluminescent substrate were than examined either
using a microscope equipped with a photon counting device or a
luminometer.
[0138] For horseradish peroxidase detection, three Luminol-based
and one acridinium-based substrates were used. Two luminol-based
substrates, LumiGLO.TM. and BM Chemiluminescence ELISA Substrate,
were obtained from Kirkegaard and Perry LaboraLories (KPL Inc.,
Gaithersburg, Md.) and Boehringer Mannheim Corp. (Indianapolis,
Ind.), respectively. A third luminol-based substrate, NF-1, which
does not require phenolic enhancers, was recently developed by
BioTecx, Inc. (Houston, Tex.) and available for experimentation.
The acridinium-based substrate, PS-1, was obtained from Lumigen,
Inc. (Southfield, Mich.).
[0139] For alkaline phosphatase detection, two adamantyl
1,2-dioxetane aryl phosphate (PPD)-based substrates were used.
Lumi-Phos 530, obtained from Lumigen, is a premixed formulation
containing phenyl phosphate dioxetane, MgCl.sub.21
cetyltrimethylammonium bromide, and an enhancer. CSPD, a derivative
of PPD mixed with the Emerald II enhancer, was obtained from
Tropix, Inc. (Bedford, Mass.).
[0140] GMDs were incubated in substrate solutions for 5-10 min at
room temperature for HRP or 10-15 min at 37.degree. C. for AP.
Light emitted from GMDs soaked in chemiluminescent substrates was
measured using an OPTOCOMP.RTM. I luminometer (MGM Instruments,
Hamden, Conn.).
[0141] Derivatization of GMDs with HRP and AP
[0142] GMDs were formed from biotinylated agarose (FMC Bioproducts,
Rockland, Me.) using standard emulsification procedures and sieved
sequentially through 62 and 45 pm nylon mesh (Small Parts, Miami
Lakes, Fla.) to obtain uniform size microdrops. GMDs were then
blocked with TNB blocking buffer for 15 min. Aliquots containing
5.times.10.sup.5 GMDs were reacted with appropriate dilutions of
streptavidin-HRP or streptavidin-AP (both from Sigma) for 30 min.
After binding, GMDs were washed 3 times with TNT washing
buffer.
[0143] Digital Image Microscopy
[0144] For imaging chemiluminescence, an Olympus BH-2 microscope,
equipped with phase contrast objectives for visualizing GMDs, was
connected to a photon counting device through a C-mount. A
Hamamatsu (Bridgewater, N.J.) C2400-32 ICCD (intensified CCD)
camera was used as a photon counting device. The camera consists of
an image intensifier and a CCD camera coupled with a relay lens and
a control unit (Hamamatsu II controller, model M4314). In this
configuration, the CCD camera effectively visualizes 756.times.485
pixels (pixel size 8.4.times.9.8 .mu.m). Images were created and
modified using the Hamamatsu ARGUS 20 Image Processor, which
permits real time image observation.
[0145] For fluorescence imaging, the microscope was connected to a
Hamamatsu C5985 cooled CCD camera and images, were created using a
Hamamatsu controller and an Argus 20 Image Processor. The CCD
camera was cooled to 20.degree. C. below the ambient temperature
with a built in Peltier effect device. Both chemiluminescent and
fluorescent images were analyzed and superimposed or pseudocolored
using Adobe.RTM. Photoshop.RTM. 4.0 software (Adobe Systems, San
Jose, Calif.) running on Windows.RTM. 95 operating system.
[0146] Results
[0147] This research has demonstrated the feasibility of detecting
at least 2-10 kb DNA sequences located on single copy genes using
probes hybridized to encapsulated nuclei and then imaged using
microscopy and a CCD camera. A 2.2 kb DNA sequence of a single copy
gene located on human chromosome Y can be detected using a
chemiluminescent substrate for HRP. This sequence was not
detectable using fluorescently labeled probes.
[0148] We evaluated a variety of substrates for both HRP and AP
reporter enzymes. Although the lowest detection limit for HRP,
measured in a luminometer, was obtained using acridinium-based
substrate, low light level required for microscopic visualization
destroyed the substrate. Two PPD (phenyl phosphate dioxetane) based
substrates for AP were also unaffected by red light required to
focus specimens for microscopy.
[0149] To detect low chemiluminescent light levels we used several
CCD cameras, including a Hamamatsu Peltier effect-cooled CCD and a
Photometrics CH250 cooled to -40.degree. C. Low light levels
generated from probe hybridizing to single copy gene sequences,
which had approximately 4.times.10.sup.2-10.sup.3 molecules of
reporter enzyme, were best detected using photon counting devices.
By comparison, about 10.sup.5 reporter molecules of enzyme bound to
agarose GMDs were needed for detection using a cooled CCD camera,
such as the Photometrics CH250 (see Table 1 below).
2TABLE 1 CCD camera detection limits for reporter enzyme molecules
conjugated to streptavidin. Reporter enzyme molecules CCD Camera
detected/GMD Hamamatsu C5985 CCCD >10.sup.5 Photometrics CH250
CCCD 10.sup.5 Hamamatsu C2400-32 ICCD 10.sup.3
Example 9
RNA detection in Encapsulated Cells
[0150] The ability rapidly to detect the presence of virus-specific
or cancer-specific RNAs in individual cells present in low
frequences has applications in disease diagnosis, monitoring and
treatment as well as blood screening. Microdrop in situ
hybridrization (MISII) is particularly suited for these
applications because it eliminates the need for cell fixation and
prevents cell clumping which makes the detection of rare cells
diffcult. This examples describes detecting both cancer cells
(positive for telomerase mRNA expression) and HIV-infected cells by
using a combination of MISH and flow cytometry.
[0151] Materials and Methods
[0152] 1. Cell Lines and Culture Conditions
[0153] Human promyelocytic leukemia HL-60 cells leukemia were
purchased from American Type Culture Collection (ATCC, Rockville,
Md.). A3.01 cells and HIV infected cells H9/HTLV-III NIH 1983 were
obtained from the NIH AIDS Research and Reference Reagent Program,
Rockville, Md. All cells were cultured in RPMI 1640 medium
supplemented with 10% fetal bovine serum (FBS) and were grown at
37.degree. C. in the presence of 5% CO.sub.2.
[0154] 2. Probes and Fluorescent Labeling
[0155] Oligonucleotide probes for detecting RNA labeled with
fluorescein at 5' end were purchased from Oligoes Etc.,
Wilsonville, Oreg. Oligos labeled with horseradish peroxidase were
purchased from Biosorce International, Camarillo, Calif.
Oligonucleotide probes for detection of HIV RNA are derived from
gag region of HIV genome. Sequences of oligonucleotide probes are
depicted below:
3 HIV RNA detection H1 5'-(HRP) CCA TTC TGC AGC TTC CTC ATT GAT GGT
CTC-3' H2 5'-(HRP) CTT GTC TTA TGT CCA GAA TGC TGG TAG GGC-3'
Telomerase mRNA detection BF-1 5'FITC-CCA ACA AGA AAT CAT CCA CCA
AAC GCA GGA GC 3' BF-3 5'FITC-GAG GCT GTT CAC CTG CAA ATC CAG AAA
CAG 3' BF-4 5'FITC-GAA GGT TTT CGC GTG GGT GAG GTG AGG TG 3'
[0156] 3. Cell Encapsulation
[0157] Human cells harvested from various stages of growth were
pelleted by low speed centrifugation, washed with Hanks Balanced
Salt Solution (HBSS) containing 0.1% diethylpyrocarbonate (DEPC),
and resuspended in the same buffer at concentrations
20.times.10.sup.6 cells per ml. For encapsulation of cells,
pluronic acid was used as a surfactant because it does not affect
cell membrane integrity during emulsification.
[0158] A cell-agarose mixture (2.3% Type XII agarose and 0.1%
pluronic acid in IIBSS containing 2.times.10.sup.6 cells per 0.52
ml) was prepared by melting 0.4 ml agarose in HBSS at 100.degree.
C., cooling the agarose to 57.degree. C., and adding 100 .mu.l of
cell suspension and 20 .mu.l of 10% pluronic acid. The mixture was
held at 65.degree. C. for 5 min and then quickly added dropwise to
15 ml of CelMix 200 emulsion matrix (One Cell Systems, Cambridge,
Mass.) pre-warmed to 6.degree. C. Gel microdrops were created using
a CellSys100 Microdrop Maker (One Cell Systems, Cambridge, Mass.)
equipped with a 1.6 cm blade using successive rotor speeds of 2,200
rpm for 1 min at 20-25.degree. C., 2,200 rpm for 1 min at 0.degree.
C., and 1,200 rpm for 7 min at 0.degree. C. The GMDs were then
separated from the emulsion matrix by centrifugation at 400 x g for
7 min. The pellet containing encapsulated cells was washed twice
with DEPC treated HBSS and stored at 4.degree. C. in the same
buffer and used within a week. However, encapsulated cells can be
stored long-term (at least for a month) in 70% ethanol at
-20.degree. C.
[0159] 4. Microdrop In Situ Hybridization (MISH) of Encapsulated
Human Cells
[0160] All solutions used for cellular RNA detection were prepared
in DEPC treated water. 1 .mu.l of DEPC (10% in 70% ethylalcohol)
was added to approximately 100,000 GMDs containing 10,000
cell-occupied GMDs in a volume of 50 pl. After a 15 min incubation
at room temperature, an equal volume of 2.times. hybridization
buffer was added and the mixture was incubated for a given time at
temperatures ranging from 50 to 58.degree. C. For hybridization
with the oligo probes, 2.times. hybridization solution contained,
1.2 M Tris-IIC1, pH 8.0, 0.1 mg/ml salmon sperm DNA, 0.1 mg/ml E.
coli tRNA, 100 units of placental RNAsc inhibitor/ml and 200 .mu.l
of Vanadyl Ribonucleoside Complex/ml (BRL, Bethesda, Md.). Before
mixing with encapsulated cells 10-20 picomoles/0.1 ml of
oligonucleotide probes were added to 2.times. hybridization buffer.
After performing hybridization at 55.degree. C., GMDs were washed
using wash buffer (WB, 0.05 M Tris-IIC1, pH 0.0, 0.15 M NaCl, 0.2
mM EDTA, 0.1% Tween 20) at temperatures ranging from 20 to
55.degree. C. Hybridization signals were amplified by a Tyramide
Signal Amplification (TSA, NEN.TM. Life Science Products, Boston,
Mass.) either directly (with HRP labeled probes) or after binding
with anti-fluoresecin-HRP (with fluorescein-labeled probes).
[0161] To detect HIV RNA with oligo probes directly labeled with
HRP, encapsulated cells were first washed three times with HRP
stabilizing buffer (Biotecx, Cambridge, Mass.) before adding
2.times. hybridization buffer.
[0162] 5. Tyramide Signal Amplification
[0163] The Tyramide Signal Amplification (TSA) system (NEN Life
Sciences Products, Boston, Mass.) is designed for non-isotopic in
situ hybridization. TSA technology (37) uses horseradish peroxidase
(HRP) to catalyze deposition of tyramide labeled with fluorophores
near the site of the hybridized probe, proximal to the enzyme. HRP
can deposit 10.sup.2-10.sup.3 tyramide molecules in 10 min,
resulting in powerful signal amplification. After MISH, GMDs were
incubated in TNB blocking buffer (0.1M Tris-HCl, pH 7.5, 0.15 M
NaCl, 0.5% Blocking Reagent, NEN) with 1:200 diluted conjugate of
anti-fluorescein HRP (NEN) for 30 min. After three subsequent
washes with TNT (0.1 M Tris-HCl, pH 7.5, 0.15 M NaCl, 0.05% Tween
20), GMDs were incubated with 1:100 diluted tyramide-fluorescein
for 10 min. Unreacted tyramide was removed by washing GMDs twice
with TNT.
[0164] 6. Microscopy and Digital Image Analysis
[0165] The integrity of encapsulated cellular nucleic acids (both
DNA and RNa after fluorescent staining with 0.2 .mu.g/ml acridine
orange) and MISH fluorescence signals were examined visually using
an Olympus BH-2 microscope (phase contrast 40 X SPlan 0.4
objective) equipped for epifluorescence with appropriate filters
for DAPI, fluorescein or phycoerythrin. Digital images were taken
with a cooled CCD camera (B/W Hamamatsu C5985-02 with control unit)
connected to the microscope. Digital images were processed with the
assistance of computer software (Adobe Photoshop version 4.0, Adobe
Systems, San Jose, Calif.).
[0166] 7. Flow Cytometric Analysis of Encapsulated Cells after
MISH
[0167] Flow cytometric analysis after MISH was performed using an
EPICS Elite.TM. (Coulter Corporation, Miami, Fla.). 15 mW of a 488
nm line of an air cooled argon laser was used to excite the
fluorescein in hybridized probes. The trigger parameter for
collecting events was forward scatter (detecting encapsulated
cells). 10,000 list mode events were collected at a rate of
approximately 600 occupied GMDs per second and analyzed using elite
4.01 software.
[0168] Results
[0169] FIG. 7 shows flow cytometric detection of gag HIV RNA in
encapsulated HIV infected cells after hybridization with two
HRP-labeled oligo probes. A2.01 cells with the same lineage as H9
cells were used as control cells. Both control and HIV infected
cells were vultured for 4 days. The peaks are color coded and
represent the following: Red peak, A3.01 cells, probes not present
(mean fluorescence 0.258); Blue peak, H9 HTLVIII cells, probes not
present (mean fluorescence=0.289); Yellow peak, A3.01 cells, probes
present (mean fluoresce ce=3.41); Green peak, H9HTI.VIII cells,
probes present (mean fluorescence-19.2). Mean fluorescence of HIV
infected and non-infected cells hybridized with oligo probes was
used for the calculation of S/N value, which was found to be 5. It
has previously been estimated that H9/HTLV-III cells express
approximately 250-500 copies of HIV-specific RNA. Detection of such
a low copy RNA number indicates the sensitivity of the assay for
detection of HIV-infected cells in human blood.
[0170] FIG. 8 shows detection of telomerase mRNA in HL-60 (model
cancer cell line) and human PBMCs using fluorescein-labeled
oligonucleotide probes followed by TSA signal amplification.
Hybridization conditions and TSA amplification are described in
Materials and Methods. The histograms are color coded as follows:
red=HL-60 cells; black=human PBMCs. Left peak represents
unoccupiewd GMDs and right peak represents GMDs occupied with
single cells. The relative mean fluoresence of the right peaks in
220 for HL-60 cells and 78 for human PBMCs (S/N-2.8). These results
show the power of this methodology for detecting differential
expression of mRNA in different cell types, and particularly
between normal and cancer cells.
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[0254] While the foregoing invention has been described in some
detail for purposes of clarity and understanding, it will be clear
to one skilled in the art from a reading of this disclosure that
various changes in form and detail can be made without departing
from the true scope of the invention. All publications and patent
documents cited in this application are incorporated by reference
in their entirety for all purposes to the same extent as if each
individual publication or patent document were so individually
denoted.
* * * * *