U.S. patent application number 11/747962 was filed with the patent office on 2008-04-24 for biopolymer marker indicative of disease state having a molecular weight of 1348 daltons.
Invention is credited to George Jackowski, John Marshall, Brad Thatcher, Tammy Vrees, Jason Yantha.
Application Number | 20080096286 11/747962 |
Document ID | / |
Family ID | 25295924 |
Filed Date | 2008-04-24 |
United States Patent
Application |
20080096286 |
Kind Code |
A1 |
Jackowski; George ; et
al. |
April 24, 2008 |
Biopolymer marker indicative of disease state having a molecular
weight of 1348 daltons
Abstract
The instant invention involves the use of a combination of
preparatory steps in conjunction with mass spectroscopy and
time-of-flight detection procedures to maximize the diversity of
biopolymers which are verifiable within a particular sample. The
cohort of biopolymers verified within such a sample is then viewed
with reference to their ability to evidence at least one particular
disease state; thereby enabling a diagnostician to gain the ability
to characterize either the presence or absence of said at least one
disease state relative to recognition of the presence and/or the
absence of the biopolymer.
Inventors: |
Jackowski; George;
(Kettleby, CA) ; Thatcher; Brad; (Toronto, CA)
; Marshall; John; (Toronto, CA) ; Yantha;
Jason; (Toronto, CA) ; Vrees; Tammy;
(Oakville, CA) |
Correspondence
Address: |
MCHALE & SLAVIN, P.A.
2855 PGA BLVD
PALM BEACH GARDENS
FL
33410
US
|
Family ID: |
25295924 |
Appl. No.: |
11/747962 |
Filed: |
May 14, 2007 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
09845715 |
Apr 30, 2001 |
7294688 |
|
|
11747962 |
May 14, 2007 |
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Current U.S.
Class: |
436/501 |
Current CPC
Class: |
G01N 33/6893
20130101 |
Class at
Publication: |
436/501 |
International
Class: |
G01N 33/566 20060101
G01N033/566 |
Claims
1. A method for determining presence of an isolated biopolymer
marker indicative of myocardial infarction (MI), intracerebral
hemorrhage (ICH) or congestive heart failure (CHF) consisting of
amino acid residues 2-12 of SEQ ID NO:1 from a mass spectrometric
analysis of a sample obtained from a patient comprising: (a)
preparing said sample for a mass spectrometric analysis by
subjecting peptides contained in said sample to chromatography; (b)
conducting mass spectrometric analysis on said sample as prepared
in step (a) to obtain mass spectral profiles of peptides contained
therein; (c) comparing a reference mass spectral profile
characteristic of said isolated biopolymer marker consisting of
amino acid residues 2-12 of SEQ ID NO:1 having an ion peak at about
1348 daltons to mass spectral profiles of peptides obtained from
said sample; and (d) matching said reference mass spectral profile
to a mass spectral profile of a peptide obtained from said sample
by identifying said ion peak at about 1348 daltons; wherein a match
confirms presence of a biopolymer marker indicative of myocardial
infarction, intracerebral hemorrhage or congestive heart failure
consisting of amino acid residues 2-12 of SEQ ID NO:1.
2. The method of claim 1 wherein said sample is selected from the
group consisting of blood, blood products, urine, saliva,
cerebrospinal fluid, and lymph.
3. The method of claim 1 wherein said mass spectrometric analysis
is Surface Enhanced Laser Desorption Ionization (SELDI) mass
spectrometry (MS), tandem mass spectrometry or a combination
thereof.
4. The method of claim 1 wherein said patient is a human.
5. A kit for determining presence of an isolated biopolymer marker
indicative of myocardial infarction, intracerebral hemorrhage or
congestive heart failure consisting of amino acid residues 2-12 of
SEQ ID NO:1 comprising: (a) a peptide consisting of amino acid
residues 2-12 of SEQ ID NO:1 and (b) an antibody that binds to said
peptide in a sample obtained from a patient.
6. The kit of claim 5 wherein said antibody is immobilized on a
solid support.
7. The kit of claim 5 wherein said antibody is labeled.
Description
CROSS REFERENCE TO RELATED APPLICATION
[0001] This application is a continuation of U.S. patent
application Ser. No. 09/845,715, filed on Apr. 30, 2001, the
contents of which is herein incorporated by reference.
FIELD OF THE INVENTION
[0002] This invention relates to the field of characterizing the
existence of a disease state; particularly to the utilization of
mass spectroscopy to elucidate particular biopolymer markers
indicative of disease state, and most particularly to specific
biopolymer sequences having a unique relationship to at least one
particular disease state.
BACKGROUND OF THE INVENTION
[0003] Methods utilizing mass spectrometry for the analysis of a
target polypeptide have been taught wherein the polypeptide is
first solubilized in an appropriate solution or reagent system. The
type of solution or reagent system, e.g., comprising an organic or
inorganic solvent, will depend on the properties of the polypeptide
and the type of mass spectrometry performed and are well known in
the art (see, e.g., Vorm et al. (1994) Anal. Chem. 66:3281 (for
MALDI) and Valaskovic et al. (1995) Anal. Chem. 67:3802 (for ESI)).
Mass spectrometry of peptides is further disclosed, e.g., in WO
93/24834 by Chait et al. In one prior art embodiment, the solvent
is chosen so that the risk that the molecules may be decomposed by
the energy introduced for the vaporization process is considerably
reduced, or even fully excluded. This can be achieved by embedding
the sample in a matrix, which can be an organic compound, e.g.,
sugar, in particular pentose or hexose, but also polysaccharides
such as cellulose. These compounds are decomposed thermolytically
into CO.sub.2 and H.sub.2O so that no residues are formed which
might lead to chemical reactions. The matrix can also be an
inorganic compound, e.g., nitrate of ammonium which is decomposed
practically without leaving any residues. Use of these and other
solvents are further disclosed in U.S. Pat. No. 5,062,935 by Schlag
et al.
[0004] Prior art mass spectrometer formats for use in analyzing the
translation products include ionization (I) techniques, including
but not limited to matrix assisted laser desorption (MALDI),
continuous or pulsed electrospray (ESI) and related methods (e.g.,
IONSPRAY or THERMOSPRAY), or massive cluster impact (MCI); these
ion sources can be matched with detection formats including linear
or non-linear reflection time-of-flight (TOF), single or multiple
quadropole, single or multiple magnetic sector, Fourier Transform
ion cyclotron resonance (FTICR), ion trap, and combinations thereof
(e.g., ion-trap/time-of-flight). For ionization, numerous
matrix/wavelength combinations (MALDI) or solvent combinations
(ESI) can be employed. Subattomole levels of protein have been
detected, for example, using ESI (Valaskovic, G. A. et al., (1996)
Science 273:1199-1202) or MALDI (Li, L. et al., (1996) J. Am. Chem.
Soc. 118:1662-1663) mass spectrometry.
[0005] ES mass spectrometry has been introduced by Fenn et al. (J.
Phys. Chem. 88, 4451-59 (1984); PCT Application No. WO 90/14148)
and current applications are summarized in recent review articles
(R. D. Smith et al., Anal. Chem. 62, 882-89 (1990) and B. Ardrey,
Electrospray Mass Spectrometry, Spectroscopy Europe, 4, 10-18
(1992)). MALDI-TOF mass spectrometry has been introduced by
Hillenkamp et al. ("Matrix Assisted UV-Laser Desorption/Ionization:
A New Approach to Mass Spectrometry of Large Biomolecules,"
Biological Mass Spectrometry (Burlingame and McCloskey, editors),
Elsevier Science Publishers, Amsterdam, pp. 49-60, 1990). With ESI,
the determination of molecular weights in femtomole amounts of
sample is very accurate due to the presence of multiple ion peaks
which all could be used for the mass calculation.
[0006] The mass of the target polypeptide determined by mass
spectrometry is then compared to the mass of a reference
polypeptide of known identity. In one embodiment, the target
polypeptide is a polypeptide containing a number of repeated amino
acids directly correlated to the number of trinucleotide repeats
transcribed/translated from DNA; from its mass alone the number of
repeated trinucleotide repeats in the original DNA which coded it,
may be deduced.
[0007] U.S. Pat. No. 6,020,208 utilizes a general category of probe
elements (i.e., sample presenting means) with Surfaces Enhanced for
Laser Desorption/Ionization (SELDI), within which there are three
(3) separate subcategories. The SELDI process is directed toward a
sample presenting means (i.e., probe element surface) with
surface-associated (or surface-bound) molecules to promote the
attachment (tethering or anchoring) and subsequent detachment of
tethered analyte molecules in a light-dependent manner, wherein the
said surface molecule(s) are selected from the group consisting of
photoactive (photolabile) molecules that participate in the binding
(docking, tethering, or crosslinking) of the analyte molecules to
the sample presenting means (by covalent attachment mechanisms or
otherwise).
[0008] PCT/EP97/04396 (WO98/07036) teaches a process for
determining the status of an organism by peptide measurement. The
reference teaches the measurement of peptides in a sample of the
organism which contains both high and low molecular weight peptides
and acts as an indicator of the organism's status. The reference
concentrates on the measurement of low molecular weight peptides,
i.e. below 30,000 Daltons, whose distribution serves as a
representative cross-section of defined controls. Contrary to the
methodology of the instant invention, the '396 patent strives to
determine the status of a healthy organism, i.e. a "normal" and
then use this as a reference to differentiate disease states. The
present inventors do not attempt to develop a reference "normal",
but rather strive to specify particular markers which are
evidentiary of at least one specific disease state, whereby the
presence of said marker serves as a positive indicator of disease.
This leads to a simple method of analysis which can easily be
performed by an untrained individual, since there is a positive
correlation of data. On the contrary, the '396 patent requires a
complicated analysis by a highly trained individual to determine
disease state versus the perception of non-disease or normal
physiology.
[0009] Richter et al, Journal of Chromatography B, 726 (1999)
25-35, refer to a database established from human hemofiltrate
comprised of a mass database and a sequence database. The goal of
Richter et al was to analyze the composition of the peptide
fraction in human blood. Using MALDI-TOF, over 20,000 molecular
masses were detected representing an estimated 5,000 different
peptides. The conclusion of the study was that the hemofiltrate
(HF) represented the peptide composition of plasma. No correlation
of peptides with relation to normal and/or disease states is
made.
[0010] As used herein, "analyte" refers to any atom and/or
molecule; including their complexes and fragment ions. In the case
of biological molecules/macromolecules or "biopolymers", such
analytes include but are not limited to: proteins, peptides, DNA,
RNA, carbohydrates, steroids, and lipids. Note that most important
biomolecules under investigation for their involvement in the
structure or regulation of life processes are quite large
(typically several thousand times larger than H.sub.2O. As used
herein, the term "molecular ions" refers to molecules in the
charged or ionized state, typically by the addition or loss of one
or more protons (H.sup.+).
[0011] As used herein, the term "molecular fragmentation" or
"fragment ions" refers to breakdown products of analyte molecules
caused, for example, during laser-induced desorption (especially in
the absence of added matrix).
[0012] As used herein, the term "solid phase" refers to the
condition of being in the solid state, for example, on the probe
element surface.
[0013] As used herein, "gas" or "vapor phase" refers to molecules
in the gaseous state (i.e., in vacuo for mass spectrometry).
[0014] As used herein, the term "analyte desorption/ionization"
refers to the transition of analytes from the solid phase to the
gas phase as ions. Note that the successful desorption/ionization
of large, intact molecular ions by laser desorption is relatively
recent (circa 1988)--the big breakthrough was the chance discovery
of an appropriate matrix (nicotinic acid).
[0015] As used herein, the term "gas phase molecular ions" refers
to those ions that enter into the gas phase. Note that large
molecular mass ions such as proteins (typical mass=60,000 to 70,000
times the mass of a single proton) are typically not volatile
(i.e., they do not normally enter into the gas or vapor phase).
However, in the procedure of the present invention, large molecular
mass ions such as proteins do enter the gas or vapor phase.
[0016] As used herein in the case of MALDI, the term "matrix"
refers to any one of several small, acidic, light absorbing
chemicals (e.g., nicotinic or sinapinic acid) that is mixed in
solution with the analyte in such a manner so that, upon drying on
the probe element, the crystalline matrix-embedded analyte
molecules are successfully desorbed (by laser irradiation) and
ionized from the solid phase (crystals) into the gaseous or vapor
phase and accelerated as intact molecular ions. For the MALDI
process to be successful, analyte is mixed with a freshly prepared
solution of the chemical matrix (e.g., 10,000:1 matrix:analyte) and
placed on the inert probe element surface to air dry just before
the mass spectrometric analysis. The large fold molar excess of
matrix, present at concentrations near saturation, facilitates
crystal formation and entrapment of analyte.
[0017] As used herein, "energy absorbing molecules (EAM)" refers to
any one of several small, light absorbing chemicals that, when
presented on the surface of a probe, facilitate the neat desorption
of molecules from the solid phase (i.e., surface) into the gaseous
or vapor phase for subsequent acceleration as intact molecular
ions. The term EAM is preferred, especially in reference to SELDI.
Note that analyte desorption by the SELDI process is defined as a
surface-dependent process (i.e., neat analyte is placed on a
surface composed of bound EAM). In contrast, MALDI is presently
thought to facilitate analyte desorption by a volcanic
eruption-type process that "throws" the entire surface into the gas
phase. Furthermore, note that some EAM when used as free chemicals
to embed analyte molecules as described for the MALDI process will
not work (i.e., they do not promote molecular desorption, thus they
are not suitable matrix molecules).
[0018] As used herein, "probe element" or "sample presenting
device" refers to an element having the following properties: it is
inert (for example, typically stainless steel) and active (probe
elements with surfaces enhanced to contain EAM and/or molecular
capture devices).
[0019] As used herein, "MALDI" refers to Matrix-Assisted Laser
Desorption/Ionization.
[0020] As used herein, "TOF" stands for Time-of-Flight. As used
herein, "MS" refers to Mass Spectrometry.
[0021] As used herein "MALDI-TOF MS" refers to Matrix-assisted
laser desorption/ionization time-of-flight mass spectrometry.
[0022] As used herein, "ESI" is an abbreviation for Electrospray
ionization.
[0023] As used herein, "chemical bonds" is used simply as an
attempt to distinguish a rational, deliberate, and knowledgeable
manipulation of known classes of chemical interactions from the
poorly defined kind of general adherence observed when one chemical
substance (e.g., matrix) is placed on another substance (e.g., an
inert probe element surface). Types of defined chemical bonds
include electrostatic or ionic (+/-) bonds (e.g., between a
positively and negatively charged groups on a protein surface),
covalent bonds (very strong or "permanent" bonds resulting from
true electron sharing), coordinate covalent bonds (e.g., between
electron donor groups in proteins and transition metal ions such as
copper or iron), and hydrophobic interactions (such as between two
noncharged groups).
[0024] As used herein, "electron donor groups" refers to the case
of biochemistry, where atoms in biomolecules (e.g, N, S, O)
"donate" or share electrons with electron poor groups (e.g., Cu
ions and other transition metal ions).
[0025] With the advent of mass spectroscopic methods such as MALDI
and SELDI, researchers have begun to utilize a tool that holds the
promise of uncovering countless biopolymers which result from
translation, transcription and post-translational transcription of
proteins from the entire genome.
[0026] Operating upon the principles of retentate chromatography,
SELDI MS involves the adsorption of proteins, based upon their
physico-chemical properties at a given pH and salt concentration,
followed by selectively desorbing proteins from the surface by
varying pH, salt, or organic solvent concentration. After selective
desorption, the proteins retained on the SELDI surface, the "chip",
can be analyzed using the CIPHERGEN protein detection system, or an
equivalent thereof. Retentate chromatography is limited, however,
by the fact that if unfractionated body fluids, e.g. blood, blood
products, urine, saliva, and the like, along with tissue samples,
are applied to the adsorbent surfaces, the biopolymers present in
the greatest abundance will compete for all the available binding
sites and thereby prevent or preclude less abundant biopolymers
from interacting with them, thereby reducing or eliminating the
diversity of biopolymers which are readily ascertainable.
[0027] If a process could be devised for maximizing the diversity
of biopolymers discernable from a sample, the ability of
researchers to accurately determine the relevance of such
biopolymers with relation to one or more disease states would be
immeasurably enhanced.
SUMMARY OF THE INVENTION
[0028] The instant invention is characterized by the use of a
combination of preparatory steps in conjunction with SELDI mass
spectroscopy and time-of-flight detection procedures to maximize
the diversity of biopolymers which are verifiable within a
particular sample. The cohort of biopolymers verified within a
sample is then viewed with reference to their ability to evidence
at least one particular disease state; thereby enabling a
diagnostician to gain the ability to characterize either the
presence or absence of said at least one disease state relative to
recognition of the presence and/or the absence of said
biopolymer.
[0029] Although all manner of biomarkers related to all disease
conditions are deemed to be within the purview of the instant
invention and methodology, particular significance was given to
those markers and diseases associated with the complement system
and Syndrome X and diseases related thereto.
[0030] The complement system is an important part of non-clonal or
innate immunity that collaborates with acquired immunity to destroy
invading pathogens and to facilitate the clearance of immune
complexes from the system. This system is the major effector of the
humoral branch of the immune system, consisting of nearly 30 serum
and membrane proteins. The proteins and glycoproteins composing the
complement system are synthesized largely by liver hepatocytes.
Activation of the complement system involves a sequential enzyme
cascade in which the proenzyme product of one step becomes the
enzyme catalyst of the next step. Complement activation can occur
via two pathways: the classical and the alternative. The classical
pathway is commonly initiated by the formation of soluble
antigen-antibody complexes or by the binding of antibody to antigen
on a suitable target, such as a bacterial cell. The alternative
pathway is generally initiated by various cell-surface constituents
that are foreign to the host. Each complement component is
designated by numerals (C1-C9), by letter symbols, or by trivial
names. After a component is activated, the peptide fragments are
denoted by small letters. The complement fragments interact with
one another to form functional complexes. Ultimately, foreign cells
are destroyed through the process of a membrane-attack complex
mediated lysis.
[0031] The C4 component of the complement system is involved in the
classical activation pathway. It is a glycoprotein containing three
polypeptide chains (.alpha., .beta., and .gamma.). C4 is a
substrate of component C1s and is activated when C1s hydrolyzes a
small fragment (C4a) from the amino terminus of the a chain,
exposing a binding site on the larger fragment (C4b).
[0032] The native C3 component consists of two polypeptide chains,
.alpha. and .beta.. As a serum protein, C3 is involved in the
alternative pathway. Serum C3, which contains an unstable thioester
bond, is subject to slow spontaneous hydrolysis into C3a and C3b.
The C3f component is involved in the regulation required of the
complement system which confines the reaction to designated
targets. During the regulation process, C3b is cleaved into two
parts: C3bi and C3f. C3bi is a membrane-bound intermediate wherein
C3f is a free diffusible (soluble) component.
[0033] Complement components have been implicated in the
pathogenesis of several disease conditions. C3 deficiencies have
the most severe clinical manifestations, such as recurrent
bacterial infections and immune-complex diseases, reflecting the
central role of C3. The rapid profusion of C3f moieties and
resultant "accidental" lysis of normal cells mediated thereby gives
rise to a host of auto-immune reactions. The ability to understand
and control these mechanisms, along with their attendant
consequences, will enable practitioners to develop both diagnostic
and therapeutic avenues by which to thwart these maladies.
[0034] In the course of defining a plurality of disease specific
marker sequences, special significance was given to markers which
were evidentiary of a particular disease state or with conditions
associated with Syndrome-X. Syndrome-X is a multifaceted syndrome,
which occurs frequently in the general population. A large segment
of the adult population of industrialized countries develops this
metabolic syndrome, produced by genetic, hormonal and lifestyle
factors such as obesity, physical inactivity and certain nutrient
excesses. This disease is characterized by the clustering of
insulin resistance and hyperinsulinemia, and is often associated
with dyslipidemia (atherogenic plasma lipid profile), essential
hypertension, abdominal (visceral) obesity, glucose intolerance or
noninsulin-dependent diabetes mellitus and an increased risk of
cardiovascular events. Abnormalities of blood coagulation (higher
plasminogen activator inhibitor type I and fibrinogen levels),
hyperuricemia and microalbuminuria have also been found in
metabolic syndrome-X.
[0035] The instant inventors view the Syndrome X continuum in its
cardiovascular light, while acknowledging its important metabolic
component. The first stage of Syndrome X consists of insulin
resistance, abnormal blood lipids (cholesterol and triglycerides),
obesity, and high blood pressure (hypertension). Any one of these
four first stage conditions signals the start of Syndrome X.
[0036] Each first stage Syndrome X condition risks leading to
another. For example, increased insulin production is associated
with high blood fat levels, high blood pressure, and obesity.
Furthermore, the effects of the first stage conditions are
additive; an increase in the number of conditions causes an
increase in the risk of developing more serious diseases on the
Syndrome X continuum.
[0037] A patient who begins the Syndrome X continuum risks
spiraling into a maze of increasingly deadly diseases. The next
stages of the Syndrome X continuum lead to overt diabetes, kidney
failure, and heart failure, with the possibility of stroke and
heart attack at any time. Syndrome X is a dangerous continuum, and
preventative medicine is the best defense. Diseases are currently
most easily diagnosed in their later stages, but controlling them
at a late stage is extremely difficult. Disease prevention is much
more effective at an earlier stage.
[0038] Subsequent to the isolation of particular disease state
marker sequences as taught by the instant invention, the
promulgation of various forms of risk-assessment tests are
contemplated which will allow physicians to identify asymptomatic
patients before they suffer an irreversible event such as diabetes,
kidney failure, and heart failure, and enable effective disease
management and preventative medicine. Additionally, the specific
diagnostic tests which evolve from this methodology provide a tool
for rapidly and accurately diagnosing acute Syndrome X events such
as heart attack and stroke, and facilitate treatment.
[0039] Accordingly, it is an objective of the instant invention to
define a disease specific marker sequence which is useful in
evidencing and categorizing at least one particular disease
state.
[0040] It is another objective of the instant invention to evaluate
samples containing a plurality of biopolymers for the presence of
disease specific marker sequences which evidence a link to at least
one specific disease state.
[0041] It is a further objective of the instant invention to
elucidate essentially all biopolymeric moieties contained therein,
whereby particularly significant moieties may be identified.
[0042] It is a further objective of the instant invention provide
at least one purified antibody which is specific to said disease
specific marker sequence.
[0043] It is yet another objective of the instant invention to
teach a monoclonal antibody which is specific to said disease
specific marker sequence.
[0044] It is a still further objective of the invention to teach
polyclonal antibodies raised against said disease specific
marker.
[0045] It is yet an additional objective of the instant invention
to teach a diagnostic kit for determining the presence of said
disease specific marker.
[0046] It is a still further objective of the instant invention to
teach methods for characterizing disease state based upon the
identification of said disease specific marker.
[0047] Other objectives and advantages of this invention will
become apparent from the following description taken in conjunction
with the accompanying drawings wherein are set forth, by way of
illustration and example, certain embodiments of this invention.
The drawings constitute a part of this specification and include
exemplary embodiments of the present invention and illustrate
various objects and features thereof.
BRIEF DESCRIPTION OF THE FIGURES
[0048] FIG. 1 is a representation of derived data which
characterizes a disease specific marker having a particular
sequence (SEQ ID NO:1) useful in evidencing and categorizing at
least one particular disease state. Each patient listed in the
table shown in FIG. 1 has a history of myocardial infarction (MI),
stroke (ICH, intracerebral hemorrhage) or congestive heart failure
(CHF) and each of these patients shows the presence of SEQ ID NO:1
in their serum.
[0049] FIGS. 2A and 2B show alternative representations of the
characteristic profile derived via SELDI/TOF MS of the disease
specific marker of FIG. 1 (SEQ ID NO:1).
DETAILED DESCRIPTION OF THE INVENTION
[0050] Serum samples from individuals were analyzed using Surface
Enhanced Laser Desorption Ionization (SELDI) using the Ciphergen
PROTEINCHIP system. The chip surfaces included, but were not
limited to IMAC-3-Ni, SAX2 surface chemistries, gold chips, and the
like.
[0051] Preparatory to the conduction of the SELDI MS procedure,
various preparatory steps were carried out in order to maximize the
diversity of discernible moieties from the sample. Utilizing a type
of micro-chromatographic column called a C18-ZIPTIP available from
the Millipore company, the following preparatory steps were
conducted.
[0052] 1. Dilute sera in sample buffer;
[0053] 2. Aspirate and dispense ZIP TIP in 50% Acetonitrile;
[0054] 3. Aspirate and dispense ZIP TIP in Equilibration;
solution;
[0055] 4. Aspirate and Dispense in serum sample;
[0056] 5. Aspirate and Dispense ZIP TIP in Wash solution;
[0057] 6. Aspirate and Dispense ZIP TIP in Elution Solution.
[0058] Illustrative of the various buffering compositions useful in
the present invention are:
[0059] Sample Buffers (various low pH's): Hydrochloric acid (HCl),
Formic acid, Trifluoroacetic acid (TFA),
[0060] Equilibration Buffers (various low pH's): HCl, Formic acid,
TFA;
[0061] Wash Buffers (various low pH's): HCl, Formic acid, TFA;
[0062] Elution Solutions (various low pH's and % Solvents) HCl,
Formic acid, TFA;
[0063] Solvents: Ethanol, Methanol, Acetonitrile.
[0064] Spotting was then performed, for example upon a Gold Chip in
the following manner:
[0065] 1. spot 2 .mu.l of sample onto each spot
[0066] 2. let sample partially dry
[0067] 3. spot 1 up of matrix, and let air dry.
[0068] HiQ Anion Exchange Mini Column Protocol
[0069] 1. Dilute sera in sample/running buffer;
[0070] 2. Add HiQ resin to column and remove any air bubbles;
[0071] 3. Add Uf water to aid in column packing;
[0072] 4. Add sample/running buffer to equilibrate column;
[0073] 5. Add diluted sera;
[0074] 6. Collect all the flow through fraction in EPPENDORF tubes
until level is at resin;
[0075] 7. Add sample/running buffer to wash column;
[0076] 8. Add elution buffer and collect elution in EPPENDORF
tubes.
[0077] Illustrative of the various buffering compositions useful in
this technique are:
[0078] Sample/Running buffers: including but not limited to Bicine
buffers of various molarities, pH's, NaCl content, BIS-TRIS buffers
of various molarities, pH's, NaCl content, Diethanolamine of
various molarities, pH's, NaCl content, Diethylamine of various
molarities, pH's, NaCl content, Imidazole of various molarities,
pH's, NaCl content, Tricine of various molarities, pH's, NaCl
content, Triethanolamine of various molarities, pH's, NaCl content,
TRIS of various molarities, pH's, NaCl content.
[0079] Elution Buffer: Acetic acid of various molarities, pH's,
NaCl content, Citric acid of various molarities, pH's, NaCl
content, HEPES of various molarities, pH's, NaCl content, MES of
various molarities, pH's, NaCl content, MOPS of various molarities,
pH's, NaCl content, PIPES of various molarities, pH's, NaCl
content, Lactic acid of various molarities, pH's, NaCl content,
Phosphate of various molarities, pH's, NaCl content, Tricine of
various molarities, pH's, NaCl content.
[0080] Chelating SEPHAROSE Mini Column
[0081] 1. Dilute Sera in Sample/Running buffer;
[0082] 2. Add Chelating SEPHAROSE slurry to column and allow column
to pack;
[0083] 3. Add UF water to the column to aid in packing;
[0084] 4. Add Charging Buffer once water is at the level of the
resin surface;
[0085] 5. Add UF water to wash through non bound metal ions once
charge buffer washes through;
[0086] 6. Add running buffer to equilibrate column for sample
loading;
[0087] 7. Add diluted serum sample;
[0088] 8. Add running buffer to wash unbound protein;
[0089] 9. Add elution buffer and collect elution fractions for
analysis;
[0090] 10. Acidify each elution fraction.
[0091] Illustrative of the various buffering compositions useful in
this technique are: Sample/Running buffers including but not
limited to Sodium Phosphate buffers at various molarities and
pH's;
[0092] Charging buffers including but not limited to Nickel
Chloride, Nickel Sulphate, Copper II Chloride, Zinc Chloride or any
suitable metal ion solution;
[0093] Elution Buffers including but not limited to Sodium
phosphate buffers at various molarities and pH's containing various
molarities of EDTA and/or Imidazole.
[0094] HiS Cation Exchange Mini Column Protocol
[0095] 1. Dilute sera in sample/running buffer;
[0096] 2. Add HiS resin to column and remove any air bubbles;
[0097] 3. Add UF water to aid in column packing;
[0098] 4. Add sample/running buffer to equilibrate column for
sample loading;
[0099] 5. Add diluted sera to column;
[0100] 6. Collect all flow through fractions in EPPENDORF tubes
until level is at resin.
[0101] 7. Add sample/running buffer to wash column.
[0102] 8. Add elution buffer and collect elution in EPPENDORF
tubes.
[0103] Illustrative of the various buffering compositions useful in
this technique are:
[0104] Sample/Running buffers: including but not limited to Bicine
buffers of various molarities, pH's, NaCl content, BIS-TRIS buffers
of various molarities, pH's, NaCl content, Diethanolamine of
various molarities, pH's, NaCl content, Diethylamine of various
molarities, pH's, NaCl content, Imidazole of various molarities,
pH's, NaCl content, Tricine of various molarities, pH's, NaCl
content, Triethanolamine of various molarities, pH's, NaCl content,
TRIS of various molarities, pH's, NaCl content.
[0105] Elution Buffer: Acetic acid of various molarities, pH's,
NaCl content, Citric acid of various molarities, pH's, NaCl
content, HEPES of various molarities, pH's, NaCl content, MES of
various molarities, pH's, NaCl content, MOPS of various molarities,
pH's, NaCl content, PIPES of various molarities, pH's, NaCl
content, Lactic acid of various molarities, pH's, NaCl content,
Phosphate of various molarities, pH's, NaCl content, Tricine of
various molarities, pH's, NaCl content.
[0106] The procedure for profiling serum samples is described
below:
[0107] Following the preparatory steps illustrated above, various
methods for use of the PROTEINCHIP arrays, available for purchase
from Ciphergen Biosystems (Palo Alto, Calif.), may be practiced.
Illustrative of one such method is as follows.
[0108] The first step involved treatment of each spot with 20 Cl of
a solution of 0.5 M EDTA for 5 minutes at room temperature in order
to remove any contaminating divalent metal ions from the surface.
This was followed by rinsing under a stream of ultra-filtered,
deionized water to remove the EDTA. The rinsed surfaces were
treated with 20 Cl of 100 mM Nickel sulfate solution for 5 minutes
at room temperature after which the surface was rinsed under a
stream of ultra-filtered, deionized water and allowed to air
dry.
[0109] Serum samples (2 Cl) were applied to each spot (now
"charged" with the metal-Nickel) and the PROTEINCHIP was returned
to the plastic container in which it was supplied. A piece of moist
KIMWIPE was placed at the bottom of the container to generate a
humid atmosphere. The cap on the plastic tube was replaced and the
chip allowed to incubate at room temperature for one hour. At the
end of the incubation period, the chip was removed from the humid
container and washed under a stream of ultra-filtered, deionized
water and allowed to air dry. The chip surfaces (spots) were now
treated with an energy-absorbing molecule that helps in the
ionization of the proteins adhering to the spots for analysis by
Mass Spectrometry. The energy-absorbing molecule in this case was
sinapinic acid and a saturated solution prepared in 50%
acetonitrile and 0.05% TFA was applied (1 Cl) to each spot. The
solution was allowed to air dry and the chip analyzed immediately
using MS (SELDI).
[0110] Serum samples from patients suffering from a variety of
disease states were analyzed using one or more protein chip
surfaces, e.g. a gold chip or an IMAC nickel chip surface as
described above and the profiles were analyzed to discern notable
sequences which were deemed in some way evidentiary of at least one
disease state.
[0111] In order to purify the disease specific marker and further
characterize the sequence thereof, additional processing was
performed.
[0112] For example, Serum (20 Cl) was (diluted 5-fold with
phosphate buffered saline) concentrated by centrifugation through a
YM3 MICROCON spin filter (Amicon) for 20 min at 10,000 RPM at 4CC
in a Beckman MICROCENTRIFuge R model bench top centrifuge. The
filtrate was discarded and the retained solution, which contained
the two peptides of interest, was analyzed further by tandem mass
spectrometry to deduce their amino acid sequences. Tandem mass
spectrometry was performed at the University of Manitoba's
(Winnipeg, Manitoba, Canada) mass spectrometry laboratory using the
procedures that are well known to practitioners of the art.
[0113] As a result of these procedures, the disease specific marker
identified as amino acid residues 2-12 of SEQ ID NO:1 was found.
This marker is characterized as a C3f fragment from the complement
system having a molecular weight of about 1348 daltons. The
characteristic profile of the marker is set forth in the
representations in FIGS. 2A and 2B. As easily deduced from the data
set forth in FIG. 1, this marker is indicative of an individual
suffering from myocardial infarction, intracerebral hemorrhage, or
congestive heart failure.
[0114] In accordance with various stated objectives of the
invention, the skilled artisan, in possession of the specific
disease specific marker as instantly disclosed, would readily carry
out known techniques in order to raise purified biochemical
materials, e.g. monoclonal and/or polyclonal antibodies, which are
useful in the production of methods and devices useful as
point-of-care rapid assay diagnostic or risk assessment devices as
are known in the art.
[0115] The specific disease markers which are analyzed according to
the method of the invention are released into the circulation and
may be present in the blood or in any blood product, for example
plasma, serum, cytolyzed blood, e.g. by treatment with hypotonic
buffer or detergents and dilutions and preparations thereof, and
other body fluids, e.g. cerebrospinal fluid (CSF), saliva, urine,
lymph, and the like. The presence of each marker is determined
using antibodies specific for each of the markers and detecting
specific binding of each antibody to its respective marker. Any
suitable direct or indirect assay method may be used to determine
the level of each of the specific markers measured according to the
invention. The assays may be competitive assays, sandwich assays,
and the label may be selected from the group of well-known labels
such as radioimmunoassay, fluorescent or chemiluminescence
immunoassay, or immunoPCR technology. Extensive discussion of the
known immunoassay techniques is not required here since these are
known to those of skill in the art. See Takahashi et al. (Clin Chem
1999; 45(8):1307) for S100B assay.
[0116] A monoclonal antibody specific against the disease marker
sequence isolated by the present invention may be produced, for
example, by the polyethylene glycol (PEG) mediated cell fusion
method, in a manner well-known in the art.
[0117] Traditionally, monoclonal antibodies have been made
according to fundamental principles laid down by Kohler and
Milstein. Mice are immunized with antigens, with or without,
adjuvants. The splenocytes are harvested from the spleen for fusion
with immortalized hybridoma partners. These are seeded into
microtitre plates where they can secrete antibodies into the
supernatant that is used for cell culture. To select from the
hybridomas that have been plated for the ones that produce
antibodies of interest the hybridoma supernatants are usually
tested for antibody binding to antigens in an ELISA (enzyme linked
immunosorbent assay) assay. The idea is that the wells that contain
the hybridoma of interest will contain antibodies that will bind
most avidly to the test antigen, usually the immunizing antigen.
These wells are then subcloned in limiting dilution fashion to
produce monoclonal hybridomas. The selection for the clones of
interest is repeated using an ELISA assay to test for antibody
binding. Therefore, the principle that has been propagated is that
in the production of monoclonal antibodies the hybridomas that
produce the most avidly binding antibodies are the ones that are
selected from among all the hybridomas that were initially
produced. That is to say, the preferred antibody is the one with
highest affinity for the antigen of interest.
[0118] There have been many modifications of this procedure such as
using whole cells for immunization. In this method, instead of
using purified antigens, entire cells are used for immunization.
Another modification is the use of cellular ELISA for screening. In
this method instead of using purified antigens as the target in the
ELISA, fixed cells are used. In addition to ELISA tests, complement
mediated cytotoxicity assays have also been used in the screening
process. However, antibody-binding assays were used in conjunction
with cytotoxicity tests. Thus, despite many modifications, the
process of producing monoclonal antibodies relies on antibody
binding to the test antigen as an endpoint.
[0119] The purified monoclonal antibody is utilized for
immunochemical studies.
[0120] Polyclonal antibody production and purification utilizing
one or more animal hosts in a manner well-known in the art can be
performed by a skilled artisan.
[0121] Another objective of the present invention is to provide
reagents for use in diagnostic assays for the detection of the
particularly isolated disease specific marker sequences of the
present invention.
[0122] In one mode of this embodiment, the marker sequences of the
present invention may be used as antigens in immunoassays for the
detection of those individuals suffering from the disease known to
be evidenced by said marker sequence. Such assays may include but
are not limited to: radioimmunoassay, enzyme-linked immunosorbent
assay (ELISA), "sandwich" assays, precipitin reactions, gel
diffusion immunodiffusion assay, agglutination assay, fluorescent
immunoassays, protein A or G immunoassays and immunoelectrophoresis
assays.
[0123] According to the present invention, monoclonal or polyclonal
antibodies produced against the disease specific marker sequence of
the instant invention are useful in an immunoassay on samples of
blood or blood products such as serum, plasma or the like, spinal
fluid or other body fluid, e.g. saliva, urine, lymph, and the like,
to diagnose patients with the characteristic disease state linked
to said marker sequence. The antibodies can be used in any type of
immunoassay. This includes both the two-site sandwich assay and the
single site immunoassay of the non-competitive type, as well as in
traditional competitive binding assays.
[0124] Particularly preferred, for ease and simplicity of
detection, and its quantitative nature, is the sandwich or double
antibody assay of which a number of variations exist, all of which
are contemplated by the present invention. For example, in a
typical sandwich assay, unlabeled antibody is immobilized on a
solid phase, e.g. microtiter plate, and the sample to be tested is
added. After a certain period of incubation to allow formation of
an antibody-antigen complex, a second antibody, labeled with a
reporter molecule capable of inducing a detectable signal, is added
and incubation is continued to allow sufficient time for binding
with the antigen at a different site, resulting with a formation of
a complex of antibody-antigen-labeled antibody. The presence of the
antigen is determined by observation of a signal which may be
quantitated by comparison with control samples containing known
amounts of antigen.
[0125] All patents and publications mentioned in this specification
are indicative of the levels of those skilled in the art to which
the invention pertains. All patents and publications are herein
incorporated by reference to the same extent as if each individual
publication was specifically and individually indicated to be
incorporated by reference.
[0126] It is to be understood that while a certain form of the
invention is illustrated, it is not to be limited to the specific
form or arrangement herein described and shown. It will be apparent
to those skilled in the art that various changes may be made
without departing from the scope of the invention and the invention
is not to be considered limited to what is shown and described in
the specification and drawings/figures.
[0127] One skilled in the art will readily appreciate that the
present invention is well adapted to carry out the objectives and
obtain the ends and advantages mentioned, as well as those inherent
therein. The oligonucleotides, peptides, polypeptides, biologically
related compounds, methods, procedures and techniques described
herein are presently representative of the preferred embodiments,
are intended to be exemplary and are not intended as limitations on
the scope. Changes therein and other uses will occur to those
skilled in the art which are encompassed within the spirit of the
invention and are defined by the scope of the appended claims.
Although the invention has been described in connection with
specific preferred embodiments, it should be understood that the
invention as claimed should not be unduly limited to such specific
embodiments. Indeed, various modifications of the described modes
for carrying out the invention which are obvious to those skilled
in the art are intended to be within the scope of the following
claims.
Sequence CWU 1
1
1 1 13 PRT Homo sapiens 1 Thr His Arg Ile His Trp Glu Ser Ala Ser
Leu Leu Arg 1 5 10
* * * * *