WO2004011664A2 - Protein or carbohydrate profiling - Google Patents

Protein or carbohydrate profiling Download PDF

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Publication number
WO2004011664A2
WO2004011664A2 PCT/SE2003/001244 SE0301244W WO2004011664A2 WO 2004011664 A2 WO2004011664 A2 WO 2004011664A2 SE 0301244 W SE0301244 W SE 0301244W WO 2004011664 A2 WO2004011664 A2 WO 2004011664A2
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WIPO (PCT)
Prior art keywords
bio
sample
tissue
molecules
protein
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PCT/SE2003/001244
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French (fr)
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WO2004011664A3 (en
Inventor
Thomas Fehniger
György MARKO-VARGA
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Astrazeneca Ab
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Priority to AU2003251261A priority Critical patent/AU2003251261A1/en
Publication of WO2004011664A2 publication Critical patent/WO2004011664A2/en
Publication of WO2004011664A3 publication Critical patent/WO2004011664A3/en

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00—Sampling; Preparing specimens for investigation
    • G01N1/28—Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/42—Low-temperature sample treatment, e.g. cryofixation
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00—Sampling; Preparing specimens for investigation
    • G01N1/28—Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/286—Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q involving mechanical work, e.g. chopping, disintegrating, compacting, homogenising
    • G01N2001/2873—Cutting or cleaving
    • G01N2001/2886—Laser cutting, e.g. tissue catapult

Definitions

  • This invention relates to a protein profiling process whereby high levels of protein identification can be achieved from mammalian tissues and cells especially from human and rodent sources throughout a detailed mapping process.
  • the process can in particular but not solely be applied to liver lung tissue, or other tissue.
  • the process allows identification of specific disease related patterns of protein expression.
  • differential display of protein expression can be verified by both qualitative and quantitative analysis, in example but not limited to pulmonary cells and tissues from humans and animals.
  • the present invention may be broadly be said to consist of a process for isolating and identifying and bio-molecules present in a bio sample using a tissue acquisition process comprising the following steps; (1) partitioning the bio sample (2) embedding the partitioned sample (3) freezing the embedded and partitioned bio sample 4) sectioning of individual component slices (5) optionally laser micro dissecting the prepared sample (6) cell lysis and protein solubilisation (6) protein separation of the prepared bio-sample (7) spot excising the sample (8) sample preparation and digestion (9) high throughput bio molecule sequencing (10) real-time or post sequence bio molecule identification
  • the tissue is mammalian.
  • the tissue is lung tissue.
  • the tissue is liver tissue.
  • the sample preparation is automated
  • the bio molecules identified are proteins.
  • the present invention comprises a database of bio molecules identified by means of the a process for isolating and identifying and bio-molecules present in a bio sample using a tissue acquisition process comprising the following steps; (1) partitioning the bio sample (2) embedding the partitioned sample (3) freezing the embedded and partitioned bio sample 4) sectioning of individual component slices (5) optionally laser micro dissecting the prepared sample (6) cell lysis and protein solubilisation (6) protein separation of the prepared bio-sample (7) spot excising the sample (8) sample preparation and digestion (9) high throughput bio molecule sequencing (10) real-time or post sequence bio molecule identification
  • the present invention may be broadly be said to consist of a diagnostic technique utilising a database of bio molecules identified by means of the a process for isolating and identifying bio-molecules present in a bio sample using a tissue acquisition process comprising the following step s (1) partitioning the bio sample (2) embedding the partitioned sample (3) freezing the embedded and partitioned bio sample 4) sectioning of individual component slices (5) optionally laser micro dissecting the prepared sample (6) cell lysis and protein solubilisation (6) protein separation of the prepared bio-sample (7) spot excising the sample (8) sample preparation and digestion (9) high throughput bio molecule sequencing (10) real-time or post sequence bio molecule identification
  • Yet another aspect of the present invention is a process for relating amongst sets of individual samples representing defined and undefined states of clinical disease a precise annotation pattern of expression. This collected data could be linked to a subset of disease biology and the precise cellular localization of said expression. Each sample thus represents a statistical object for comparison to other samples.
  • the collected dataset of each sample further can be addressed as a whole or partial representation of the disease biology influenced by the said biomolecules present in a biosample using a tissue acquisition process comprising the following steps; (1) partitioning the biosample (2) embedding the partitioned sample (3) freezing the embedded and partitioned bio sample 4) sectioning of individual component slices (5) optionally laser micro dissecting the prepared sample (6) cell lysis and protein solubilisation (6) protein separation of the prepared bio-sample (7) spot excising the sample (8) sample preparation and digestion (9) high throughput bio molecule sequencing (10) real-time or post sequence bio molecule identification.
  • the process provides interfaced technologies and methods for the isolation and selection of bio-molecules present in a tissue.
  • the same process can be applied to multiple organ tissue sets, multiple disease tissue sets, and cells derived from these tissues.
  • the output of the process will allow semi-automated process steps whereby identification of protein expressions can be made.
  • the tissue-based process includes an interface to high-sensitivity mass spectrometry that is utilised to generate large sets of protein sequence coverage.
  • Yet another aspect of the present invention is a process for creating libraries of antibodies to the biomloecules, including but not limited to proteins, present in the retrieved fractions of products from each step of the aforementioned process.
  • This may include but is not limited to the creation of phage display antibody libraries, conventional antibodies made in animals or synthetic antibodies.
  • This may include but is not limited to the creation of antibody libraries to the biomolecules recovered from laser capture microscopy.
  • the antibody library may preferably be phage display antibodies selected for binding to the biomolecules present in the laser capture microscopy-processed tissue.
  • the antibody library may also be a conventional antibody raised to the whole fractions or components of the products in the protein separation process. Background to the invention
  • the invention allows a universal process to be applied to proteins derived from any tissue process as described and presented in figure 1.
  • the present invention provides a process with interfaced building blocks that allows protein sequencing in a high throughput mode to be made semi-automated with real-time data base annotations.
  • This protein profiling tissue acquisition process also reduces the manual input for histology and pathology that can be made under a given time. Protein profiling will create a new (currently non existent) scheme for defining the absolute amounts of specific proteins regardless of the cell of origin. Description of the present invention.
  • One form of he present invention comprises a biological process whereby high throughput identification of protein and bio-molecules present in tissue sections can be made.
  • Protein separation may but not exclusively be performed by Chromatographic separation where we will utilise mechanisms including but not limited to;
  • Affinity binding i/ chiral affinity - chiral small molecules may lend itself to be used as selective ligands for proteins/peptides to interact with binding whereby separations will be obtained.
  • Biochemical bindings iii/ Antibody binding - Traditional biochemical bindings antibody-antigen immunoaffinity bindings with both weak-medium-strong affinities with binding constants ranging
  • This fully integrated process line comprises the steps of: obtaining protein sequences that were specifically isolated and present in diseased tissue.
  • the named process comprises technology process steps that improve the ease of detection of said protein and bio- molecule sequences.
  • the isolated tissue compartment areas that comprise a specific sub-set of cells and microenvironment can be stored afterwards under appropriate conditions.
  • tissue compartment library produced by the integrated process of; obtained from the isolated compartments of the tissue, isolated by laser capture micro dissection. Corresponding databases of protein sequences and the identified proteins will be linked to each specific pulmonary or tissue compartment.
  • Yet another component of the process is the creation of antibody libraries to the constituent bio molecules present in the recovered fractions at each step of the process.
  • the use of these antibodies as tools in diagnostic procedures subsequent to the aforementioned process is also an integral part of this application.
  • Snap frozen tissue contains biologically relevant proteins in disease-related stoichiometries.
  • Slices of frozen tissues contain resident and important non-resident inflammatory cells.
  • Frozen tissue contains the products of resident and non-resident cells.
  • Frozen tissue does contain cell products, which can be related to specific disease processes.
  • Frozen tissue can be histological examined to define disease foci and quantitatively determine relevant cell types.
  • Slices of frozen tissues can be efficiently solubilized with minimal protein degradation.
  • the frozen tissue solubilization methodology preserves protein activation states within their native environment within the sub-cellular organelle compartments.
  • LCM allows precise dissections of selected cell types.
  • LCM allows dissection of mucosal surfaces exposed to the environment.
  • LCM allows protein expression within dissected cell types to be compared to whole tissue protein expression. For example it has been found that 1000 to 5000 laser pulses can isolate pulmonary cells sufficiently and can be used and forms the basis to generate protein sequences whereby protein databases can be established.
  • the tissue library with isolated compartments may consist of a single or series of sets, which are stored under the appropriate conditions to ensure that they are not degraded over time.

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Immunology (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Hematology (AREA)
  • General Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Pathology (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Urology & Nephrology (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Microbiology (AREA)
  • Cell Biology (AREA)
  • Biotechnology (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

One form of the present invention comprises a biological process whereby high throughput identification of protein and bio-molecules present in tissue sections can be made. This fully integrated process line comprises the steps of: obtaining protein sequences that were specifically isolated and present in diseased tissue. The named process comprises of technology process steps that improves the ease of detection of said protein and bio-molecule sequences. The isolated pulmonary areas that comprise a specific sub-set of cells and microenvironment can be stored afterwards under appropriate conditions.

Description

PROFILING PROCESS
This invention relates to a protein profiling process whereby high levels of protein identification can be achieved from mammalian tissues and cells especially from human and rodent sources throughout a detailed mapping process.
It further relates to profiling of protein classes isolated and identified by protein sequencing by the said process and/or methods therein and the cataloguing of the sequences produced thereby so as to develop diagnostic methods and treatments. The process can in particular but not solely be applied to liver lung tissue, or other tissue. The process allows identification of specific disease related patterns of protein expression. In addition, differential display of protein expression can be verified by both qualitative and quantitative analysis, in example but not limited to pulmonary cells and tissues from humans and animals.
The present invention may be broadly be said to consist of a process for isolating and identifying and bio-molecules present in a bio sample using a tissue acquisition process comprising the following steps; (1) partitioning the bio sample (2) embedding the partitioned sample (3) freezing the embedded and partitioned bio sample 4) sectioning of individual component slices (5) optionally laser micro dissecting the prepared sample (6) cell lysis and protein solubilisation (6) protein separation of the prepared bio-sample (7) spot excising the sample (8) sample preparation and digestion (9) high throughput bio molecule sequencing (10) real-time or post sequence bio molecule identification
Preferably the tissue is mammalian. Preferably the tissue is lung tissue. Alternatively the tissue is liver tissue.
Preferably the sample preparation is automated Preferably the bio molecules identified are proteins. In another aspect the present invention comprises a database of bio molecules identified by means of the a process for isolating and identifying and bio-molecules present in a bio sample using a tissue acquisition process comprising the following steps; (1) partitioning the bio sample (2) embedding the partitioned sample (3) freezing the embedded and partitioned bio sample 4) sectioning of individual component slices (5) optionally laser micro dissecting the prepared sample (6) cell lysis and protein solubilisation (6) protein separation of the prepared bio-sample (7) spot excising the sample (8) sample preparation and digestion (9) high throughput bio molecule sequencing (10) real-time or post sequence bio molecule identification
In yet another aspect the present invention may be broadly be said to consist of a diagnostic technique utilising a database of bio molecules identified by means of the a process for isolating and identifying bio-molecules present in a bio sample using a tissue acquisition process comprising the following step s (1) partitioning the bio sample (2) embedding the partitioned sample (3) freezing the embedded and partitioned bio sample 4) sectioning of individual component slices (5) optionally laser micro dissecting the prepared sample (6) cell lysis and protein solubilisation (6) protein separation of the prepared bio-sample (7) spot excising the sample (8) sample preparation and digestion (9) high throughput bio molecule sequencing (10) real-time or post sequence bio molecule identification
Yet another aspect of the present invention is a process for relating amongst sets of individual samples representing defined and undefined states of clinical disease a precise annotation pattern of expression. This collected data could be linked to a subset of disease biology and the precise cellular localization of said expression. Each sample thus represents a statistical object for comparison to other samples. The collected dataset of each sample further can be addressed as a whole or partial representation of the disease biology influenced by the said biomolecules present in a biosample using a tissue acquisition process comprising the following steps; (1) partitioning the biosample (2) embedding the partitioned sample (3) freezing the embedded and partitioned bio sample 4) sectioning of individual component slices (5) optionally laser micro dissecting the prepared sample (6) cell lysis and protein solubilisation (6) protein separation of the prepared bio-sample (7) spot excising the sample (8) sample preparation and digestion (9) high throughput bio molecule sequencing (10) real-time or post sequence bio molecule identification.
The process provides interfaced technologies and methods for the isolation and selection of bio-molecules present in a tissue. The same process can be applied to multiple organ tissue sets, multiple disease tissue sets, and cells derived from these tissues.
The output of the process will allow semi-automated process steps whereby identification of protein expressions can be made. The tissue-based process includes an interface to high-sensitivity mass spectrometry that is utilised to generate large sets of protein sequence coverage.
Yet another aspect of the present invention is a process for creating libraries of antibodies to the biomloecules, including but not limited to proteins, present in the retrieved fractions of products from each step of the aforementioned process. This may include but is not limited to the creation of phage display antibody libraries, conventional antibodies made in animals or synthetic antibodies. This may include but is not limited to the creation of antibody libraries to the biomolecules recovered from laser capture microscopy. The antibody library may preferably be phage display antibodies selected for binding to the biomolecules present in the laser capture microscopy-processed tissue. The antibody library may also be a conventional antibody raised to the whole fractions or components of the products in the protein separation process. Background to the invention
The invention allows a universal process to be applied to proteins derived from any tissue process as described and presented in figure 1.
There are technologies available to select and identify proteins retrieved from healthy and diseased tissue. However, these technologies are used separately and have not been connected and interfaced optimally. Linked together these process blocks form a process line whereby sections of tissues can be made compatible with several other technologies currently used for the identification of proteins present in a cell derived from these tissue sections. Diseased tissue will express quantitatively different sets of proteins from non-diseased tissue. Diseased tissue reflects a definition, which includes changes in the steady state, changes in destructive processes present in resident and non-resident cells, changes in differential states and changes in repair processes. Differentiation states in this case are defined as stages of maturity in cell function and/or phenotype.
The present invention provides a process with interfaced building blocks that allows protein sequencing in a high throughput mode to be made semi-automated with real-time data base annotations. This protein profiling tissue acquisition process also reduces the manual input for histology and pathology that can be made under a given time. Protein profiling will create a new (currently non existent) scheme for defining the absolute amounts of specific proteins regardless of the cell of origin. Description of the present invention.
One form of he present invention comprises a biological process whereby high throughput identification of protein and bio-molecules present in tissue sections can be made.
Protein separation may but not exclusively be performed by Chromatographic separation where we will utilise mechanisms including but not limited to;
Chemical binding if size exclusion - in samples where fractionation is required based upon size. ii/ hydrophobic interactions-utilisation of reversed phase separation mechanisms whereby peptides and proteins will be separated by its hydrophobicity. iii/ polar interactions - silanol, and other types of polar functionalities readily interact with polar peptides/proteins and can be separated based upon polar chromatographic interactions.
Affinity binding i/ chiral affinity - chiral small molecules may lend itself to be used as selective ligands for proteins/peptides to interact with binding whereby separations will be obtained. ii/ Metal affinity - Chelation by metal ion interaction of amine, and or carboxy-hydroxy functional groups, as well as Nickel ion-Histidine peptide residues, iron-, Gallium-ions and phosphate functionalities on peptides which binds strongly.
Biochemical bindings: iii/ Antibody binding - Traditional biochemical bindings antibody-antigen immunoaffinity bindings with both weak-medium-strong affinities with binding constants ranging
105 - 1010 This fully integrated process line comprises the steps of: obtaining protein sequences that were specifically isolated and present in diseased tissue. The named process comprises technology process steps that improve the ease of detection of said protein and bio- molecule sequences. The isolated tissue compartment areas that comprise a specific sub-set of cells and microenvironment can be stored afterwards under appropriate conditions.
Another aspect of the present invention provides a tissue compartment library produced by the integrated process of; obtained from the isolated compartments of the tissue, isolated by laser capture micro dissection. Corresponding databases of protein sequences and the identified proteins will be linked to each specific pulmonary or tissue compartment.
Yet another component of the process is the creation of antibody libraries to the constituent bio molecules present in the recovered fractions at each step of the process. The use of these antibodies as tools in diagnostic procedures subsequent to the aforementioned process is also an integral part of this application.
Snap frozen tissue contains biologically relevant proteins in disease-related stoichiometries. Slices of frozen tissues contain resident and important non-resident inflammatory cells. Frozen tissue contains the products of resident and non-resident cells. Frozen tissue does contain cell products, which can be related to specific disease processes.
Frozen tissue can be histological examined to define disease foci and quantitatively determine relevant cell types.
Slices of frozen tissues can be efficiently solubilized with minimal protein degradation.
The frozen tissue solubilization methodology preserves protein activation states within their native environment within the sub-cellular organelle compartments.
Laser capture microscopy allows precise dissections of selected cell types. LCM allows dissection of mucosal surfaces exposed to the environment. LCM allows protein expression within dissected cell types to be compared to whole tissue protein expression. For example it has been found that 1000 to 5000 laser pulses can isolate pulmonary cells sufficiently and can be used and forms the basis to generate protein sequences whereby protein databases can be established.
The tissue library with isolated compartments may consist of a single or series of sets, which are stored under the appropriate conditions to ensure that they are not degraded over time.
Finally, it will be understood by a person skilled in the art that the present invention has been described in at least one preferred embodiment and can be modified in many different ways without departing from the scope of the invention as defined in the appended claims.

Claims

ClaimsWhat we claim is;
1. A process for isolating and identifying and bio-molecules present in a bio sample using a tissue acquisition process comprising the following steps; partitioning the bio sample (2) embedding the partitioned sample (3) freezing the embedded and partitioned bio sample 4) optionally laser micro dissecting the prepared sample (4) cell lysis and protein solubilisation (5) protein separation of the prepared bio- sample 6) spot excising the sample (7) sample preparation and digestion (8) high throughput bio molecule sequencing (9) real-time or post sequence bio molecule identification
2. A process for isolating and identifying bio-molecules as claimed in claim 1 wherein the tissue is mammalian.
3 A process for isolating and identifying bio-molecules as claimed in claim 1 or 2 wherein the tissue is lung tissue.
4 A process for isolating and identifying bio-molecules as claimed in claim 1 or 2 wherein the tissue is liver tissue.
5. A process for isolating and identifying bio-molecules as claimed in any one of claims 1 to 4 wherein the sample preparation is automated
6. A process for isolating and identifying bio-molecules as claimed in any one of claims 1 to 5 wherein the bio molecules identified are proteins.
7. A database of bio molecules identified by means of the processes as claimed in any one of claims 1 to 6.
8. A diagnostic technique utilising the database as claimed in claim 7. A process for isolating and identifying bio-molecules as claimed in any one of claims 1 to 5 wherein the bio-molecules identified are carbohydrates.
PCT/SE2003/001244 2002-07-30 2003-07-30 Protein or carbohydrate profiling WO2004011664A2 (en)

Priority Applications (1)

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AU2003251261A AU2003251261A1 (en) 2002-07-30 2003-07-30 Protein or carbohydrate profiling

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SE0202346-3 2002-07-30
SE0202346A SE0202346D0 (en) 2002-07-30 2002-07-30 Profiling process

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WO2004011664A3 WO2004011664A3 (en) 2004-06-24

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Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000049410A2 (en) * 1999-02-16 2000-08-24 The Government Of The United States Of America, As Represented By The Secretary Department Of Health & Human Services, The National Institutes Of Health Lcm (laser capture microdissection) for cellular protein analysis
WO2001007915A2 (en) * 1999-07-26 2001-02-01 The Government Of The United States Of America, As Represented By The Secretary, Department Of Health & Human Services, The National Institutes Of Health Layered device with capture regions for cellular analysis

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000049410A2 (en) * 1999-02-16 2000-08-24 The Government Of The United States Of America, As Represented By The Secretary Department Of Health & Human Services, The National Institutes Of Health Lcm (laser capture microdissection) for cellular protein analysis
WO2001007915A2 (en) * 1999-07-26 2001-02-01 The Government Of The United States Of America, As Represented By The Secretary, Department Of Health & Human Services, The National Institutes Of Health Layered device with capture regions for cellular analysis

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
BANKS R E, ET AL.: 'The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis - Preliminary findings' ELECTROPHORESIS vol. 20, 1999, pages 689 - 700 *
JAIN K K: '[14] Application of alser capture microdissection to proteomics' METHODS AND ENZYMOLOGY vol. 356, 2002, pages 157 - 167 *
ORNSTEIN D K, ET AL.: 'Proteomic analysis of laser capture microdissected human prostate cancer and in vitro prostate cell lines' ELECTROPHORESIS vol. 21, 2000, pages 2235 - 2242 *

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SE0202346D0 (en) 2002-07-30
AU2003251261A1 (en) 2004-02-16
AU2003251261A8 (en) 2004-02-16
WO2004011664A3 (en) 2004-06-24

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