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Practical molecular biology: PROTEINS
Prof. Dr. Julia Kzhyshkowska
PD Dr. Alexei Gratchev
Prof. Dr. W. Kaminski
Protein analysis in tissues
Principles of protein detection Immunohistochemistry (IHC) Immunofluorescence (IF)
Protein Problem Molecular Weight (MW); how many forms; charge and shape;
Posttranslational modifications;
Biosynthetic pathways, half-life, degradation pathways;
Intracellular localisation; trafficking pathways
Integration in protein-protein networks; interaction with DNA, RNA, lipids;
Expression profile in cells and tissues;
Biological function: one or many, regulated or constitutive, intracellular or extracellular, ubiquitous or cell-type specific;
Proteins in pathology: biomarkers and their role in the molecular mechanism of a disease;
Therapeutic protein targeting
Protein identification
Direct sequencing (for purified protein);
MW: motility in the gel (usually for denatured proteins) or gel-filtration chromatography (usually for native proteins). These methods can be used for purified protein or protein complex with limited amount of components;
Proteomics-based approaches for complex protein mixtures, for example serum samples or cell lysates
Immunological detection (for purified proteins, protein complexes and crude material like cell lysates or tissue extracts)
Enzymatic activity
Protein quantification
Photometric detection: total protein amount in the sample
ELISA: measurement of particular protein concentration
Enzymatic reaction: quantification of activity, not the protein
FACS: relative quantification of protein amount in the cell
Western blotting, IHC, IF - semi-quantitative or qualitative
Immunological detection of the protein
Methods: Immunohistochemistry (IHC), Immunofluorescence (IF), Enzyime-Linked Immunosorbent Assay (ELISA) Western Blotting (WB), Immunoprecipitation (IP), Fluorescence Activated Cell Sorting (FACS)
Principle of recognition
primary antibody binds to specific epitope (one or several) in the protein
Principle of detection
primary antibody or secondary antibody that recognise primary antibody is labelled (examples: HRP for IHC and Western blotting, fluorescent dye for IF and FACS)
Material for IHC and IFFresh or frozen Tissue sections; Cells grown on cover slips; Cells sedimented on object glass
using cytospin centrifuge
Paraffin embedded Tissue sections
Advantages Disadvantages
Limited time of storage
Retrospective analysis is not possible
Advantages Disadvantages
Antigen-retrieval has to be designed individually for most of antigens
Only limited number of labeled primary antibodies recognize retrieved antigen
Antigens are in a good shape, and most of primary antibodies can be used
Intracellular localization studies are possible even in tissue sections
Extremely long storage time,
Retrospective analysis can be done on archive material
Methanol-Acetone FixationFix in cooled methanol, 10 minutes at –20 °C. Remove excess methanol. Permeabilize with cooled acetone for 1 minute at –20 °C. OrParaformaldehyde-Triton FixationFix in 3-4% paraformaldehyde for 10-20 minutes. Rinse briefly with PBS. Permeabilize with 0.5% Triton X-100 for 2-10 minutes. OrParaformaldehyde-Methanol FixationFix in 3-4% paraformaldehyde for 10-20 minutes. Rinse briefly with PBS. Permeabilize with cooled methanol for 5-10 minutes at –20 °C. OrPEM-Ethanol FixationFix in PEM buffer for 10 minutes. Rinse twice, briefly, with PBS. Permeabilize with cooled ethanol for 5-10 minutes at –20 °C
Fixation of fresh and frozen materialMethod of fixation has to be selected according to
1) the experimental task.
Examples: For simple identification of the protein in the cell: acetone fixation is sufficientFor precise identification of protein localization in the intracellular compartment PFA/triton is optimal
2) ability of the antibody to recognize fixed antigen.
Most of antibodies recognize antigens only in specific conditions. Example from our lab: MS-1 antibody recognizes stabilin-1 in acetone-fixed cells, but not in PFA fixed cells
IHC and IF: overlapping termsDirect Indirect
Cheap
Fast
Advantages Disadvantages
Only limited number of labeled primary antibodies are available commercially
Advantages Disadvantages
Takes more time, sometimes is more expensive
Additional control for the background staining is absolutely necessary
Wide range of labeled secondary antibodies are available commercially
It is always possible to design combination for double and triple staining
or enzyme
or enzyme
Controls
IHC
Background signal coming from substrate
IF
Auto fluorescence
2. Antibody-dependent non-specific signals/cross-reactions for IHC and IF:
2.1 Non-specific signal coming from antibody alone
Solution: optimization of concentration of secondary antibody (not signal has to be observed when primary antibody is not applied)
2.2 Non-specific signal coming from primary antibody. Following controls for primary antibody have to be used and concentrations have to be optimized:Isotype control for monoclonal antibodyPreimmune serum for polyclonal antibody-containing serumMatching Ig for purified polyclonal antibody
Important note: by optimization working concentrations has to be calculated NOT dilution
1. Antibody-independent of non-specific signals
Experimental design for IHC
1 2 3 4
Substrate (DAB) for IHC + + + +
1st antibody _ _+ Preimmune serum for
polyclonal ab or isotype control ab for monoclonal ab
+
Antigen- specific ab
2nd antibody
_ + + +
IHC and IF on frozen tissues: human lymph node samples
Martens, Kzhyshkowska et al, J Pathology, 2006
Identification of double positive cells by IF
Martens, Kzhyshkowska et al, J Pathology, 2006
IHC on frozen tissues: mouse tumour sections
Amount of stabilin-1+ TAM is significantly decreased in TS/A-SI-CLP tumors compared to TS/A-vector tumors
Schuiping Yin, TMR Student 2011/2012Master Thesis
IF on frozen tissues of mouse tumorAnalysis of co-expression of CD206 and stabilin-1 in TS/A-vector and TS/A-SI-CLP tumor
Stabilin-1-CD206+ and stabilin-1+CD206+ TAM appear in TS/A-vector and TS/A-SI-CLP tumors. The main phenotype of TAM in TS/A-vector tumor is stabilin-1+CD206+, while the main TAM phenotype in TS/A-SI-CLP tumor is stabilin-1-CD206+
stabilin-1+CD206+
stabilin-1-CD206+stabilin-1+CD206+
stabilin-1-CD206+
stabilin-1+CD206+
Schuiping Yin, TMR Student 2011/2012Master Thesis
Additional treatments are needed for staining of paraffin-embedded tissues
1. Deparaffinisation
2. Antigen retrieval
DeparaffinizationBefore proceeding with the staining protocol, the slides must be deparaffinized and rehydrated. Incomplete removal of paraffin can cause poor staining of the section.
Protocol
Place the slides in a rack, and perform the following washes:Xylene: 2 x 3 minXylene 1:1 with 100% ethanol: 3 min100% ethanol: 2 x 3 min95% ethanol: 3 min70 % ethanol: 3 min50 % ethanol: 3 minRunning cold tap water to rinse
Keep the slides in the tap water until ready to perform antigen retrieval. At no time from this point onwards should the slides be allowed to dry. Drying out will cause non-specific antibody binding and therefore high background staining
Antigen retrieval
The demonstration of many antigens can be significantly improved by the pre-treatment with the antigen retrieval reagents that break the protein cross-links formed by formalin fixation and thereby uncover hidden antigenic sites.
The techniques involved the application of heat for varying lengths of time to formalin-fixed, paraffin-embedded tissue sections in an aqueous solution (retrieval solution). This is called "Heat Induced Epitope Retrieval (HIER)". Another method uses enzyme digestion and is called "Proteolytic Induced Epitope Retrieval (PIER)".
HIER PIER
Citrate buffer pH 6.0Tris-EDTA buffer pH 9.0EDTA buffer pH 8.0
Proteinase KTrypsinChymotrypsinPepsinPronase
IHC staining of paraffin-embedded human breast cancer
Expression of CD68 and stabilin-1 in breast cancer by the stages: stage I CD68 (A1 and A2); stage II CD68 (B1 an B2); stage III CD68 (C1 and C2); stage IV CD68 (D1 and D2); stage I stabilin-1 (E1 and E2), stage II stabilin-1(F1 and F2); stage III stabilin-1(G1 and G2); stage IV stabilin-1 (H1 and H2). Scale bars 100 μm (A1 to H1), 50 μm (A2 to H2).
Aida Avdic, TMR Student 2011/2012Master Thesis
Immunofluorescence/confocal microscopy on of paraffin-embedded human breast cancerAnalysis of CD68+/stabilin-1+ macrophages
Aida Avdic, TMR Student 2011/2012Master Thesis
Multiple IF
PL-FITC
Stabilin-1 staining
TGN-46 Merge
Most frequently double and triple IF are usedColor codeRed + green = yellowRed + blue = pinkGreen + blue = cyanGreen + red + blue = white
Kzhyshkowska et al, JI, 2008
Human macrophage
Human placenta
Stabilin-1
Ab CLEVER Ab F4 Merge
Multuple IHC
Multiple staining can also be done with enzyme conjugated antibodies developed with different chromogen substrates to produce the end products of different colors
IHC: principle of EnVision detection system from DAKO
Enzyme: Alkaline Phosphatase (AP) or Horseradish Peroxidase (HRP)
Polymer permits binding of up to 100 HRP molecules and up to 20 antibody per backbone
Horseradish peroxidaseThe enzyme horseradish peroxidase (HRP), found in horseradish, is used extensively in molecular biology applications primarily for its ability to amplify a weak signal and increase detectability of a target molecule
In the presence of H202 (hydrogen peroxide) DAB (3,3'-Diaminobenzidine) is converted to an insoluble brown reaction product and water by the enzyme HRP
DAB + H202 ----------HRP----------> DAB ppt + H20
DAB ppt – insoluble, brown
IHC: New markers for sinusoidal cells in human lymph nodes
Martens, Kzhyshkowska et al, J Pathology, 2006
Literature
Current protocols in molecular biology www.methods.info www.dako.com
Questions?