Restricted accessResearch articleFirst published online 2014-06
HFIP Extraction Followed by 2D CTAB/SDS-PAGE Separation: A New Methodology for Protein Identification from Tissue Sections after MALDI Mass Spectrometry Profiling for Personalized Medicine Research
Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and profiling technology have become the easiest methods for quickly accessing the protein composition of a tissue area. Unfortunately, the demand for the identification of these proteins remains unmet. To overcome this bottleneck, we combined several strategies to identify the proteins detected via MALDI profiling including on-tissue protein extraction using hexafluoroIsopropanol (1,1,1,3,3,3-hexafluoro-2-propanol, HFIP) coupled with two-dimensional cetyl trimethylammonium bromide/sodium dodecyl sulfate–polyacrylamide gel electrophoresis (2D CTAB/SDS-PAGE) for separation followed by trypsin digestion and MALDI-MS analyses for identification. This strategy was compared with an on-tissue bottom-up strategy that we previously developed. The data reflect the complementarity of the approaches. An increase in the number of specific proteins identified has been established. This approach demonstrates the potential of adapted extraction procedures and the combination of parallel identification approaches for personalized medicine applications. The anatomical context provides important insight into identifying biomarkers and may be considered a first step for tissue-based biomarker research, as well as the extemporaneous examination of biopsies during surgery.
Get full access to this article
View all access options for this article.
References
1.
BalluffB, RauserS, MedingS, et al. (2011). MALDI imaging identifies prognostic seven-protein signature of novel tissue markers in intestinal-type gastric cancer. Am J Pathol, 179, 2720–2729.
2.
BekkuS, MochizukiH, YamamotoT, UenoH, TakayamaE, and TadakumaT. (2000). Expression of carbonic anhydrase I or II and correlation to clinical aspects of colorectal cancer. Hepatogastroenterology, 47, 998–1001.
3.
BonnelD, LonguespeeR, FranckJ, et al. (2011). Multivariate analyses for biomarkers hunting and validation through on-tissue bottom-up or in-source decay in MALDI-MSI: Application to prostate cancer. Anal Bioanal Chem, 401, 149–165.
4.
BraunRJ, KinklN, BeerM, and UeffingM. (2007). Two-dimensional electrophoresis of membrane proteins. Anal Bioanal Chem, 389, 1033–1045.
5.
CalligarisD, LonguespeeR, DeboisD, et al., (2013). Selected protein monitoring in histological sections by targeted MALDI-FTICR in-source decay imaging. Anal Chem, 85, 2117–2126.
6.
ColingeJ, ChiappeD, LagacheS, MoniatteM, and BougueleretL. (2005). Differential proteomics via probabilistic peptide identification scores. Anal Chem, 77, 596–606.
7.
DeiningerSO, EbertMP, FuttererA, GerhardM, and RockenC. (2008). MALDI imaging combined with hierarchical clustering as a new tool for the interpretation of complex human cancers. J Proteome Res, 7, 5230–5236.
8.
Di MicheleM, MarconeS, CicchillittiL, et al. (2010). Glycoproteomics of paclitaxel resistance in human epithelial ovarian cancer cell lines: Towards the identification of putative biomarkers. J Proteomics, 73, 879–898.
9.
DongHP, HolthA, KleinbergL, et al. (2009). Evaluation of cell surface expression of phosphatidylserine in ovarian carcinoma effusions using the annexin-V/7-AAD assay: Clinical relevance and comparison with other apoptosis parameters. Am J Clin Pathol, 132, 756–762.
10.
El AyedM, BonnelD, LonguespeeR, et al. (2010). MALDI imaging mass spectrometry in ovarian cancer for tracking, identifying, and validating biomarkers. Med Sci Monit, 16, BR233–245.
11.
ElsnerM, RauserS, MaierS, et al. (2012). MALDI imaging mass spectrometry reveals COX7A2, TAGLN2 and S100-A10 as novel prognostic markers in Barrett's adenocarcinoma. J Proteomics, 75, 4693–4704.
12.
FranckJ, LonguespeeR, WisztorskiM, et al. (2010). MALDI mass spectrometry imaging of proteins exceeding 30,000 daltons. Med Sci Monit, 16, BR293–299.
13.
GagnonH, FranckJ, WisztorskiM, DayR, FournierI, and SalzetM. (2012). Targeted mass spectrometry imaging: Specific targeting mass spectrometry imaging technologies from history to perspective. Prog Histochem Cytochem, 47, 133–174.
14.
IwanickiMP, DavidowitzRA, NgMR, et al. (2012). Ovarian cancer spheroids use myosin-generated force to clear the mesothelium. Cancer Discov, 1, 144–157.
15.
LemaireR, DesmonsA, TabetJC, DayR, SalzetM, and FournierI. (2007). Direct analysis and MALDI imaging of formalin-fixed, paraffin-embedded tissue sections. J Proteome Res, 6, 1295–1305.
16.
LemaireR, WisztorskiM, DesmonsA, et al. (2006). MALDI-MS direct tissue analysis of proteins: Improving signal sensitivity using organic treatments. Anal Chem, 78, 7145–7153.
17.
LokmanNA, WeenMP, OehlerMK, and RicciardelliC. (2011). The role of annexin A2 in tumorigenesis and cancer progression. Cancer Microenviron, 4, 199–208.
18.
LonguespeeR, BoyonC, CastellierC, et al. (2012a). The C-terminal fragment of the immunoproteasome PA28S (Reg alpha) as an early diagnosis and tumor-relapse biomarker: Evidence from mass spectrometry profiling. Histochem Cell Biol, 138, 141–154.
19.
LonguespeeR, BoyonC, DesmonsA, et al. (2013a). Spectroimmunohistochemistry: A novel form of MALDI mass spectrometry imaging coupled to immunohistochemistry for tracking antibodies. Omics, 2, 132–141.
20.
LonguespeeR, BoyonC, DesmonsA, et al. (2012b). Ovarian cancer molecular pathology. Cancer Metastasis Rev, 31, 713–732.
21.
LonguespeeR, GagnonH, BoyonC, et al. (2013b). Proteomic analyses of serous and endometrioid epithelial ovarian cancers—Cases studies—Molecular insights of a possible histological etiology of serous ovarian cancer. Proteomics Clin Appl, 7, 337–354.
22.
LyubimovaT, CaglioS, GelfiC, RighettiPG, and RabilloudT. (1993). Photopolymerization of polyacrylamide gels with methylene blue. Electrophoresis, 14, 40–50.
23.
MaierSK, HahneH, Moghaddas GholamiA, et al. (2013). Comprehensive identification of proteins from MALDI imaging. Mol Cell Proteomics, 12, 2901–2910.
24.
MedingS, BalluffB, ElsnerM, et al. (2012). Tissue-based proteomics reveals FXYD3, S100A11 and GSTM3 as novel markers for regional lymph node metastasis in colon cancer. J Pathol doi: 10.1002/path.4021 [Epub ahead of print].
25.
NanduriB, LawrenceML, VanguriS, PechanT, and BurgessSC. (2005). Proteomic analysis using an unfinished bacterial genome: The effects of subminimum inhibitory concentrations of antibiotics on Mannheimia haemolytica virulence factor expression. Proteomics, 5, 4852–4863.
26.
PocsfalviG, VottaG, De VincenzoA, et al. (2011). Analysis of secretome changes uncovers an autocrine/paracrine component in the modulation of cell proliferation and motility by c-Myc. J Proteome Res, 10, 5326–5337.
27.
PolatiR, ZapparoliG, GiudiciP, and BossiA. (2009). A CTAB based method for the preparation of total protein extract of wine spoilage microrganisms for proteomic analysis. J Chromatog B, Anal Technol Biomed Life Sci, 877, 887–891.
28.
ProkocimerM, DavidovichM, Nissim-RafiniaM, et al. (2009). Nuclear lamins: Key regulators of nuclear structure and activities. J Cell Mol Med, 13, 1059–1085.
29.
QuanicoJ, FranckJ, DaulyC, et al. (2013). Development of liquid microjunction extraction strategy for improving protein identification from tissue sections. J Proteomics, 79, 200–218.
30.
RaoLV, TaitJF, and HoangAD. (1992). Binding of annexin V to a human ovarian carcinoma cell line (OC-2008). Contrasting effects on cell surface factor VIIa/tissue factor activity and prothrombinase activity. Thromb Res, 67, 517–531.
31.
StauberJ, AyedME, WisztorskiM, SalzetM, and FournierI. (2010). Specific MALDI-MSI: Tag-Mass. Methods Mol Biol, 656, 339–361.
32.
StauberJ, LemaireR, FranckJ, et al. (2008). MALDI imaging of formalin-fixed paraffin-embedded tissues: Application to model animals of Parkinson disease for biomarker hunting. J Proteome Res, 7, 969–978.
33.
SternbergerLA, HardyPHJr., CuculisJJ, and MeyerHG. (1970). The unlabeled antibody enzyme method of immunohistochemistry: Preparation and properties of soluble antigen-antibody complex (horseradish peroxidase-antihorseradish peroxidase) and its use in identification of spirochetes. J Histochem Cytochem, 18, 315–333.
34.
StevensSMJr., ChungAY, ChowMC, et al. (2005). Enhancement of phosphoprotein analysis using a fluorescent affinity tag and mass spectrometry. Rapid Commun Mass Spectrom, 19, 2157–2162.
35.
SugimuraM, DonatoR, KakkarVV, and ScullyMF. (1994). Annexin V as a probe of the contribution of anionic phospholipids to the procoagulant activity of tumour cell surfaces. Blood Coagul Fibrinolysis, 5, 365–373.
36.
Van RemoortereA, Van ZeijlRJ, Van Den OeverN, Fet al. (2010). MALDI imaging and profiling MS of higher mass proteins from tissue. J Am Soc Mass Spectrom, 21, 1922–1929.
37.
WisztorskiM, FatouB, FranckJ, et al. (2013). Microproteomics by liquid extraction surface analysis: Application to FFPE tissue to study the fimbria region of tubo-ovarian cancer. Proteomics Clin Appl, 7, 234–240.
38.
XueLY, TengLH, ZouSM, et al. (2007). [Expression of annexin I in different histological types of carcinomas]. Zhonghua Zhong Liu Za Zhi, 29, 444–448.
39.
YamaguchiY, MiyagiY, and BabaH. (2008a). Two-dimensional electrophoresis with cationic detergents, a powerful tool for the proteomic analysis of myelin proteins. Part 1: Technical aspects of electrophoresis. J Neurosci Res, 86, 755–765.
40.
YamaguchiY, MiyagiY, and BabaH. (2008b). Two-dimensional electrophoresis with cationic detergents, a powerful tool for the proteomic analysis of myelin proteins. Part 2: Analytical aspects. J Neurosci Res, 86, 766–775.
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
