[Methods in Molecular Biology] Difference Gel Electrophoresis (DIGE) Volume 854 || 2D DIGE Analysis of Protein Extracts from Muscle Tissue

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Rainer Cramer and Reiner Westermeier (eds.), Difference Gel Electrophoresis (DIGE): Methods and Protocols, Methods in Molecular Biology, vol. 854, DOI 10.1007/978-1-61779-573-2_11, © Springer Science+Business Media, LLC 2012

Chapter 11

2D DIGE Analysis of Protein Extracts from Muscle Tissue

Cecilia Gelfi and Sara De Palma

Abstract

2D DIGE, two-dimensional difference gel electrophoresis, is a technology used to study the protein expression on two-dimensional gels. Protein samples are labeled with different color fl uorescent dyes designed not to affect the relative migration of proteins during electrophoresis. Here, we describe the practical procedures necessary to perform a 2D DIGE experiment for a muscle tissue protein extract fol-lowed by CyDye DIGE fl uors minimal labeling and the analysis of 2D DIGE gels for the assessment of quantitative differences.

Key words: 2D DIGE , 2D electrophoresis , CyDye DIGE fl uors , Differential analysis , Muscle proteome

The DIGE technique was fi rst described in 1997 ( 1 ) ; it is a modifi ed form of 2DE, two-dimensional electrophoresis ( 2– 4 ) , developed to overcome the problem of the irreproducibility of gels and to increase the sensitivity of 2DE methodology by labeling samples with a different fl uorescent dye prior to running them on the same gel (see Fig. 1 ).

Protein samples are labeled with up to three spectrally distinct, charge- and mass-matched fl uorescent dyes (CyDye DIGE fl uors) ( 1, 5, 6 ) : Cy2, Cy3, and Cy5. This means that the same protein labeled with any of the CyDye DIGE fl uors migrates to the same position on a 2D gel ( 7 ) eliminating intragel variation. Moreover, the dyes afford great sensitivity with a detection capability of 125 pg of a single protein and a linear response over at least fi ve orders of magnitude. CyDyes DIGE fl uors have an N -hydroxysuccinimide ester reactive group and are designed to covalently attach to the epsilon amino group of lysine via an amine linkage (see Fig. 2 ). The quantity of dye added to the sample limits the reaction; hence, this

1. Introduction

156 C. Gelfi and S. De Palma

Internal standard

Control

Cy5 Cy2 Cy3

Mix samples

2D-electrophoresis

Image Acquisition and Analysis

Protein ID

Treated

Fig. 1. Scheme of a DIGE experiment, using three fl uors and a single gel.

Fig. 2. Scheme of the DIGE labeling reaction.

method is referred to as “minimal labeling.” This ensures that the stoichiometry of protein to fl uor, results in only 1–2% of the total number of lysine residues being labeled.

After labeling, protein samples are mixed and separated on the same 2D gel. Different protein extracts labeled with different

15711 2D DIGE Analysis of Protein Extracts from Muscle Tissue

CyDye fl uors are then visualized separately using an imager containing appropriate laser wavelengths. Digital images of each sample will be analyzed by dedicated software. One of the most important advantages of 2D DIGE is the introduction of the inter-nal standard ( 8, 9 ) created by pooling an aliquot of all biological samples and labeled with one of the CyDye DIGE fl uors (usually Cy2 in a three-color experiment or Cy3 in a two-color experi-ment). This means that every protein from all samples will be rep-resented in the internal standard. Linking every sample in-gel to a common internal standard gives some advantages compared to conventional 2DE; in particular, it allows an accurate quantifi ca-tion and the separation of experimental from biological variation, and statistical analysis of spots between gels can be applied ( 10 ) .

All solutions have to be prepared using ultrapure water (18 M W cm at 20°C) and analytical grade reagents. Filtering all solution is strongly recommended.

1. Homogenizer for sample disruption (see Note 1). 2. Lysis buffer: 30 mM Tris, 7 M urea, 2 M thiourea, 4% (w/v)

CHAPS, pH 8.5. For a fi nal volume of 100 mL, dissolve 364 mg of Tris, 42 g of urea, 15.2 g of thiourea, and 4 g of CHAPS in about 50 mL of water. Adjust the pH with dilute HCl and make up to 100 mL with water. Prepare aliquots of 1 mL and store at −20°C. Prior to use, add 1 m L of PMSF 10 mM (see Note 2).

3. Sonicator (see Note 3). 4. Precipitation method to purify protein sample to remove non-

protein impurities (see Note 4). 5. pH indicator strips (pH 4.5–10.0) to check the pH of the pro-

tein extract and sodium hydroxide (50 mM) to adjust the pH. 6. Quantitation method to determine sample concentration

(see Note 5).

1. CyDye™ DIGE fl uor Cy2, Cy3, and Cy5 minimal dye (GE Healthcare) (see Note 6).

2. 99.8% DMF (anhydrous dimethylformamide) for the reconsti-tution of CyDye, less than 3 months old from the day of opening (see Note 7).

3. 10 mM lysine solution to stop the labeling reaction. The solu-tion can be stored at 4°C for several months.

2. Materials

2.1. Sample Preparation and Quantitation (Compatible with CyDye DIGE Minimal Labeling)

2.2. Protein Labeling


1. 2× sample buffer: 8 M urea, 130 mM DTT, 4% (w/v) CHAPS, and 2% (v/v) Pharmalyte™ 3–10 for isoelectric focusing (IEF). For a fi nal volume of 100 mL, dissolve 48.05 g of urea, 2 g of DTT, and 4 g of CHAPS in 50 mL of water and add 1 mL of Pharmalyte™ 3–10. Add water to a volume of 100 mL. Aliquots can be stored at −20°C.

2. Immobiline™ DryStrip immobilized pH gradient (IPG) gel strips (GE Healthcare). Precast Immobiline DryStrips are avail-able with different lengths (7, 11, 13, 18, and 24 cm) and dif-ferent pH gradients (3.5–4.5, 4.5–5.5, 4–7 linear, 6–11 linear, 3–10 nonlinear and linear, 3–11 nonlinear and linear, etc.).

3. Rehydration stock solution to rehydrate IPG strips prior to IEF: 7 M urea, 2 M thiourea, and 2% (w/v) CHAPS. For a fi nal volume of 100 mL, weigh out 42.04 g of urea, 15.22 g of thiourea, and 2 g of CHAPS and prepare a solution as in previ-ous steps. Store at −20°C. Prior to use, add 65 mM DTT and 0.5% (v/v) IPG buffer (GE Healthcare).

4. Bromophenol blue as tracking dye. 5. IPG cover fl uid (GE Healthcare) to minimize evaporation and

urea crystallization. 6. IPGphor IEF units (GE Healthcare) or similar for fi rst-dimen-

sion IEF of proteins. 7. IPGphor strip holder (GE Healthcare) having the same length

of the IPG strips or, alternatively, the IPGphor Manifold (GE Healthcare) that allows protein separation on 7–24-cm-long Immobiline DryStrips.

1. Equilibration buffer: 6 M urea, 2% (w/v) SDS, 20% (v/v) glycerol, 375 mM Tris–HCl, pH 8.8. For a fi nal volume of 100 mL, dissolve 36.036 g of urea and 2 g of SDS, add 20 mL of glycerol and 20 mL of Tris–HCl, pH 8.8, and prepare a solution as in previous steps. Store at −20°C. Prior to use, separate the equilibration buffer into two aliquots and add 65 mM DTT (100 mg/10 mL equilibration buffer) and 135 mM iodoacetamide (250 mg/10 mL equilibration buffer) respectively.

1. Resolving gel buffer 5×: 1.875 M Tris–HCl, pH 8.8. Add about 200 mL of water to a graduated 1-L cylinder or a glass beaker. Weigh out 227.1 g of Tris and add water to a volume of 900 mL. Mix and adjust the pH with concentrated HCl. Make up to 1 L with water and store at 4°C in a glass bottle.

2. 40% acrylamide/bis solution (39:1 acrylamide/bis): To pre-pare 1 L of stock solution, weigh out 390 g of acrylamide monomer and 10 g of bis (cross-linker) and dissolve in a grad-uated cylinder with about 400 mL of water. Mix and make up to 1 L with water. Store at 4°C in a glass bottle (see Note 8).

2.3. Gel Electrophoresis

2.3.1. Isoelectric Focusing (IEF)

2.3.2. IPG Strip Equilibration

2.3.3. SDS-PAGE


3. 10% ammonium persulfate: Prepare aliquots of 1 mL and store at −20°C.

4. N , N , N , N ¢ -tetramethylethylenediamine (TEMED). Store at 4°C. 5. SDS-PAGE running buffer (10×): 250 mM Tris, 1.92 M glycine,

and 1% SDS. For a fi nal volume of 1 L, weigh out 30.2 g of Tris and 144.2 g of glycine and dissolve in about 600 mL of water. Mix, fi lter the solution, add 10 g of SDS, and make up to 1 L with water. Store at 4°C in a glass bottle.

6. 30% (v/v) isopropanol. Store at room temperature in a dark glass bottle.

7. 0.5% agarose sealing solution: For a fi nal volume of 100 mL, weigh out 0.5 g of agarose, add 100 mL of 1× SDS-PAGE running buffer, and melt in a heating block or boiling water (see Note 9).

8. Low-fl uorescence glass plates (GE Healthcare). 9. Gel casting cassettes. 10. Electrophoretic unit.

1. Typhoon variable mode imager (GE Healthcare) or similar. 2. DeCyder software (GE Healthcare) or similar.

1. At least 15–20 mg of muscle tissue is necessary to perform a 2D DIGE experiment.

2. Grind muscle tissue in a frozen mortar. 3. After sample disruption, add lysis buffer and sonicate the sam-

ple on ice (20-s bursts with 60-s rest between bursts) until no particulate matter remains, or until no more of the particulate matter is dissolved.

4. Centrifuge the sample at 12,000 × g for 5 min at 4°C to remove any insoluble material.

5. Precipitate proteins in order to separate them from nonprotein impurities (salts, nucleic acids, lipids, etc.).

6. Resuspend pellets with lysis buffer for DIGE. 7. Check the pH of the sample on ice. The sample pH must be

pH 8.0–9.0. Adjust the pH using dilute NaOH, if required. 8. Accurately quantify protein samples.

1. Remove the CyDye from the −20°C-freezer and leave to warm for 5 min at room temperature.

2. After 5 min, add the specifi ed volume of DMF to each vial of CyDye to prepare a CyDye stock solution (i.e., 5 m L of DMF

2.4. Image Acquisition and Analysis

3. Methods

3.1. Protein Extraction from Muscle Tissue

3.2. Protein Labeling


for the 5 nmol pack size). The stock solution is stable for 3 months at −20°C.

3. Vortex vigorously for 30 s. 4. Centrifuge the vial for 30 s at 12,000 × g in a microcentrifuge. 5. Prepare the CyDye working solution adding 1 volume of CyDye

stock solution to 1.5 volumes of high-grade DMF to make 400 m M CyDye solution. For example, take 2 m L CyDye stock solution and add 3 m L DMF to give 400 pmol of CyDye in 1 m L. The CyDye fl uor working solution is stable for 1 week at −20°C.

6. Label 50 m g of each sample with 400 pmol of dye adding 1 m L of working solution.

7. Carry out the labeling reaction by incubating the sample on ice for 30 min in the dark.

8. Add 1 m L (for 50 m g of sample labeled) of 10 mM lysine solu-tion to stop the reaction. Mix by pipetting and spin briefl y in a microcentrifuge.

9. Leave for 10 min on ice in the dark. 10. After labeling, samples can be stored at −70°C for at least

3 months.

1. Add to the CyDye-labeled samples an equal volume of 2× sam-ple buffer and leave on ice for 10 min.

2. Combine the differentially labeled samples (two or three) into a single microfuge tube and mix. One of these samples should be the internal standard (see Note 10).

3. Add to the samples the appropriate volume of rehydration solution (see Note 11).

4. Pipette the appropriate volume of rehydration solution into each holder removing any larger bubbles (see Note 12).

5. Remove the protective cover from the IPG strip and position the strip with the gel side down. Be careful not to trap bubbles under the IPG strip.

6. Apply the appropriate volume of IPG cover fl uid on the strip (see Note 13).

7. Allow the IPG strip to rehydrate for a minimum of 10 h (see Note 14).

1. Run the appropriate IEF protocol (see Note 15). Figure 3 shows examples of 2D gels obtained separating labeled samples on dif-ferent pH gradient. The IEF protocols used are also described.

2. If the IPG strips are not run immediately on the second dimen-sion, they can be stored at −80°C in a sealed container. Do not equilibrate strips prior to storage.

3.3. Loading Samples onto IPG Strips

3.4. First Dimension (IEF)


Fig. 3. IEF protocols and 2D DIGE images of human skeletal muscle protein lysates using different IPG strip pH gradients.


1. Separate the equilibration buffer into two aliquots and just prior to use add 65 mM DTT (100 mg/10 mL equilibration buffer) and 135 mM iodoacetamide (250 mg/10 mL equili-bration buffer), respectively.

2. Equilibrate strips for 15 min in the fi rst solution (DTT) followed by equilibration in the second solution (iodoacet-amide) for 8 min.

3. After equilibration, place the strips on fi lter paper moistened with deionized water.

A commonly used second dimension gel for 2DE is a homoge-neous gel containing 12% total acrylamide (see Note 16):

1. Assemble the gel cassette. 2. Prepare a suffi cient volume of gel solution without adding 10%

(w/v) ammonium persulfate (APS) and TEMED. 3. Degas the gel solution for 10–15 min. 4. Add 10% APS solution and TEMED to the gel solution in order

to make a 0.5% (v/v) APS/0.03% TEMED gel solution. 5. Pour the gel solution into the gel cassette and pipette 1–1.5 mL

of 30% (v/v) isopropanol solution on top. 6. Allow gels to polymerize for at least 1–2 h. 7. Disassemble the gel cassette. 8. Prepare the appropriate volume of the 1× running buffer by

diluting the 10× SDS-PAGE running buffer. 9. Melt the agarose sealing solution and, for each Immobiline

DryStrip, slowly pipette the solution up to the top of the glass plate (see Note 17).

10. Carefully place the Immobiline DryStrip between the two glass plates holding one end of the strip with forceps. Using a thin plastic spacer, push the strip until it comes in contact with the surface of the gel avoiding the trapping of air bubbles (see Note 18).

11. Insert the glass plates into the electrophoresis apparatus and start the run (see Note 19).

12. At the end of the run, the gels are ready to be scanned.

After electrophoresis, take the images of the gel at the appropriate wavelength using a laser-based scanner such as a Typhoon variable scanner imager (GE Healthcare) ( 11 ) (see Note 20) or alterna-tively images can be taken using a CCD camera:

1. Rinse the gel sandwich with distilled water and wipe it dry with lint-free towels.

2. Place the gel sandwich on the scanner platen and take the images according to the manufacturer’s instructions.

3.5. IPG Strip Equilibration

3.6. Second Dimension (SDS-PAGE)

3.7. Image Acquisition


Various fully automated DIGE image analysis software packages (DeCyder from GE Healthcare, Progenesis SameSpots from Nonlinear Dynamics, Melanie from Bio-Rad) developed for spot detection, matching, and differential protein expression analysis are commercially available.

The most important steps involved in image analysis are:

Spot detection. – Background subtraction. – In-gel normalization. – Artifact removal. – Gel matching. – Statistical analysis. –

Here, we describe the principal steps of image analysis per-formed using the DeCyder software ( 5, 8, 11– 13 ) .

The software consists of three main modules:

DIA (differential in-gel analysis): to perform protein spot detec-tion and quantifi cation on a pair of images, from the same gel. A set of images is merged together, thereby incorporating all spot features in a single image. Spot detection and spot boundary defi -nition is performed using pixel data from all the individual raw images and the merged image. An estimation of the number of spots present on the images must be entered—it is recommended that this value is overestimated to compensate for the detection of nonproteinaceous spots on the image. One can later use the Exclude fi lter in order to eliminate nonproteinaceous spots (based on their physical characteristics). Numerical data for individual spots are calculated (volume, area, peak height, and slope). Spot volumes are always expressed with the background subtracted. Background is subtracted by excluding the lowest tenth percentile pixel value on the spot boundary from all other pixel values within the spot boundary. The spot volume is the summation of these corrected values.

BVA (biological variation analysis): to match multiple images from different gels to provide statistical data on differential protein expression levels between multiple groups.

EDA module (extended data analysis): to elaborate a set of data. There are different calculations that can be performed in EDA:

– Differential Expression Analysis . This kind of calculation per-mits to investigate differential expression between two or more experimental groups. There are different subanalyses related to the experimental setup. Student’s t test is used to evaluate the hypothesis of a difference between two groups. If more than two groups are included into the experimental design, ANOVA must be used. The simplest form of ANOVA is known as

3.8. Image Analysis


one-way ANOVA, and it is used to test for differences in standardized abundance among experimental groups; the test is accompanied by Tukey ’ s test (post hoc test) to get an indica-tion of which group is different. The two-way ANOVA is used to analyze two conditions in an experimental design in which two independent factors are taken into consideration. It calcu-lates the signifi cance of the difference between groups with the same condition 2 and different condition 1 (indicated as two-way ANOVA condition 1) and the other way around (two-way ANOVA condition 2). The two-way ANOVA analysis also calculates a signifi cance value of the mutual effect of the two factors (two-way ANOVA interaction). Signifi cantly changed proteins having a p value <0.01 are typically considered. – Principal Component Analysis ( PCA ). This analysis is essen-tially a method for reducing the dimension of the variables in a multidimensional space getting a simpler view of the proteins and the spot maps in the data set. It is thus possible to detect outliers in the data set and to identify spot maps that have simi-lar expression profi les. – Pattern Analysis . This process consists of algorithms that can help to fi nd the subsets of the data that show similar expression patterns. There are different types of pattern algorithms: one of the most important is Hierarchical Clustering , a method that combines or splits data pairwise and generates a tree-like structure called dendrogram. Protein and spot maps with simi-lar expression profi les are grouped together.

1. The cells or tissue should be disrupted in such a way as to mini-mize proteolysis and at low temperature with a minimum of heat generation. There are different disruption methods, both mechanical and chemical ( 14, 15 ) . Gentle lysis methods (osmotic lysis ( 16 ) , freeze-thaw lysis ( 14, 17, 18 ) , enzymatic lysis ( 19, 20 ) ) are generally employed when the sample of interest consists of easily lysed cells. More vigorous lysis meth-ods (sonication ( 21, 22 ) , grinding ( 23– 25 ) , mechanical homogenization ( 17, 26 ) , glass bead homogenization ( 27 ) ) are employed when cells are less easily disrupted (cells in solid tissue or cells with tough cell walls).

2. Appropriate sample preparation is absolutely essential for good 2D DIGE results. The optimal procedure must be determined empirically for each sample type. Ideally, the process will result in the complete solubilization, disaggregation, denaturation, and reduction of the proteins. It is important to remember

4. Notes


that CyDye DIGE fl uors are minimal dyes labeling primary amines. Exogenous sources of amines, such as DTT or ampho-lytes, must not be included in the buffer prior to labeling.

3. Sonicate samples in short bursts to avoid heating. Cool on ice between bursts.

Sonication is complete when the solution appears signifi -cantly less cloudy than the starting solution.

4. Protein precipitation is employed to selectively separate pro-teins in the sample from contaminating substances. Current methods of protein precipitation (TCA precipitation, acetone precipitation, TCA combined with acetone precipitation, etc.) suffer from several disadvantages: incomplete precipitation, diffi cult protein resuspension, and introduction of ions that could interfere with IEF. Kits specifi cally designed for protein precipitation for 2DE are commercially available (e.g., 2-D Clean-Up Kit from GE Healthcare).

5. Electrophoretic analysis of protein samples requires accurate quantifi cation of the sample to be analyzed. Use a standard protein quantitation method or, alternatively, use a kit designed specifi cally for the accurate determination of protein concen-tration in samples to be analyzed by 2DE (e.g., PlusOne™ 2-D Quant Kit from GE Healthcare). The recommended concen-tration of the protein lysate required for minimal labeling is between 5 and 10 mg/mL.

6. Store CyDyes in the dark at −20°C. 7. The quality of the DMF used in all experiment is critical to

ensure a successful protein labeling. The DMF must be anhy-drous, and it is necessary to avoid contamination with water. After opening, over a period of time, DMF will degrade pro-ducing amine compounds. Amines will react with CyDyes reducing fl uors concentration available for protein labeling.

8. Acrylamide is a neurotoxin; it is important to wear gloves and use appropriate handling precautions.

9. Prepare the agarose sealing solution during equilibration. 10. Two kinds of experimental design can be performed: the two-

or three-color experiment. In the two-color experiment, all samples are labeled with the same fl uor (usually Cy5) and the internal standard with Cy3 (the internal standard is created by pooling an aliquot of all samples and labeled with one of the CyDye fl uors). In the second case, all samples are labeled with two fl uors (Cy3 and Cy5), enabling dye swapping to control any dye-specifi c effects that might result from preferential labeling or different fl uorescence characteristics of the gel at the different excitation wavelengths. Here, the internal standard is labeled with Cy2. The major difference between the two


experimental designs is represented by the number of gels which is higher in a two-color experiment.

11. Just prior to use, add to the rehydration stock solution the appropriate amount of IPG buffer (0.5% v/v), 65 mM DTT, a trace of bromophenol blue, and the samples. The volume of the rehydration solution depends on the IPG strips’ length (i.e., for 24-cm IPG strips, the rehydration solution volume required per strip is 450 m L). Make sure the IPG buffer matches the pH gradient of the strip used for IEF.

12. Select the strip holders corresponding to the IPG strip length. Wash each holder with detergent to remove residual protein and rinse with distilled water. Before use, the holders must be completely dry.

13. The IPG cover fl uid volume to apply on the strip depends on the length of the holder used. Add the oil until the entire IPG strip is covered.

14. It is possible to rehydrate strips in the absence of protein sam-ples. In this case, protein samples are loaded after rehydration, using a cup loading technique.

15. A typical IEF protocol generally proceeds through a series of voltage steps that begins at a relatively low value. Voltage is gradually increased to the fi nal desired focusing voltage, which is held for up to several hours. A low initial voltage minimizes sample aggregation. It is important to remember that focusing parameters for different pH gradients and different protein loading need to be optimized.

16. Single percentage gels offer better resolution for a particular MW window. When a gradient gel is used, the separation inter-val is wider and spots are sharper because the decreasing pore size functions to minimize diffusion. Remember that stacking gels are not necessary for 2D gels.

17. Take care not to introduce bubbles and do not allow the aga-rose to cool or solidify before placing the strip.

18. By convention, the acidic end of the strip is placed on the left. 19. Recommended running condition:

16 h overnight run, 15°C (2 W per gel). – 8 h duration, 15°C (4 W per gel). – 4 h duration, 15°C (8 W per gel). – The run is fi nished when the bromophenol blue dye front –reaches the bottom of the gel.

20. The excitation and emission wavelength used for all three CyDyes are listed in Table 1 .


Acknowledgements

This work was supported by the Telethon foundation (grant N. GGP08107D to C.G.), EU community (grant BIO-NMD N. 241665 to C.G.), and Italian Ministry of University and Scientifi c Research (grant FIRB RBRN07BMCT to C.G.).

References

Table 1 Excitation and emission characteristics for the three common DIGE fl uors

Fluorescent dye Laser excitation source (nm) Emission fi lter (nm)

DIGE fl uor Cy3 minimal dye Green (532) 580 BP 30

DIGE fl uor Cy5 minimal dye Red (633) 670 BP 30

DIGE fl uor Cy2 minimal dye Blue (488) 520 BP 40

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[Methods in Molecular Biology] Difference Gel Electrophoresis (DIGE) Volume 854 || 2D DIGE Analysis of Protein Extracts from Muscle Tissue