Comparative proteomic analysis identifies proteins associated with the development and progression of colorectal carcinoma Liang Zhao 1,2, *, Hui Wang 3, *, Xuegang Sun 4 and Yanqing Ding 1 1 Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China 2 Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China 3 Department of Medical Oncology, Affiliated Tumor Hospital of Guangzhou Medical College, China 4 School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China Introduction Colorectal cancer (CRC) is the third most common cancer worldwide in both men and women, especially in ageing populations. It ranks third as the cause of death from carcinoma, surpassed only by lung and prostate neoplasms in men, and lung and breast can- cers in women [1,2]. As in most malignant diseases, early diagnosis and especially detection of metastases are of importance for patient prognosis. Presently, clinical parameters combined with histopathological staging and grading are the most important diagnostic and prognostic variables. The evaluation of carcino- embryonic antigen in serum has not fulfilled the prom- ise of a simple test that would offer early diagnosis of colon cancer. A number of other, less well-explored, potential markers exist, but are currently not used in routine clinical diagnosis [3–5]. Therefore, more exten- sive proteome tests are desirable for diagnosis, progno- sis evaluation and monitoring recurrent disease. Using the technologies of two-dimensional electro- phoresis ⁄ MS and immunohistochemistry in combina- tion, the aim of this study was to investigate the genesis- and metastasis-associated proteins, and to Keywords carcinogenesis; colorectal carcinoma; proteomics; tumour progression; two-dimensional electrophoresis Correspondence Y. Ding, Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China Fax ⁄ Tel: +86 20 61642148 E-mail: dyqsmu@sina.com *These authors contributed equally to this paper (Received 9 April 2010, revised 1 July 2010, accepted 5 August 2010) doi:10.1111/j.1742-4658.2010.07808.x To better understand the mechanism underlying colorectal carcinoma (CRC) genesis or metastasis, and to search for potential markers for CRC prognosis, a comparative proteomic analysis was performed on CRC tissue. Proteins were extracted from normal colorectal mucosa, non-metastatic CRC (nmCRC) and metastatic CRC (mCRC) tissue samples. Protein pro- filing of each sample was performed by two-dimensional electrophoresis coupled with MALDI-TOF MS, followed by confirmation by Western blotting. Thirty-one proteins were found to be differentially expressed between normal mucosa, nmCRC and mCRC tissue. In 126 paraffin- embedded CRC samples, three differentially expressed proteins, identified as LASP-1, S100A9 and RhoGDI by proteomic analysis, were detected by immunohistochemical staining to determine the clinicopathological charac- teristics of these proteins in CRC. Increased expression levels of these proteins were found in CRC, especially mCRC, compared with normal mucosa. The results provide the basis for searching for potential markers for CRC genesis and metastasis, and also provide clues for elucidating the mechanism of CRC progression. The pattern changes identified have the potential to be used for the design of marker panels for assistance in diag- nostic and therapeutic strategies in CRC. Abbreviations CRC, colorectal carcinoma; mCRC, metastatic colorectal carcinoma; nmCRC, non-metastatic colorectal carcinoma. FEBS Journal 277 (2010) 4195–4204 ª 2010 The Authors Journal compilation ª 2010 FEBS 4195 evaluate the correlation between clinicopathological characteristics of CRC and expression of these target proteins, in order to better understand the mechanisms underlying CRC progression. Results Differential protein expression among normal colorectal mucosa, nmCRC and mCRC tissue A total of 1107 ± 27, 1130 ± 23 and 1135 ± 28 pro- tein spots were visualized in two-dimensional gels using image analysis software. Compared with the nor- mal tissue control, the mCRC and nmCRC groups had average matching rates of 70.2% and 72.6%. To identify a CRC genesis-specific protein expression pat- tern, comparative two-dimensional analysis of normal tissue and primary CRC tissue samples was performed. pdquest software analysis identified 22 spots that were present in both CRC groups but not in the nor- mal tissue. With regard to determination of a CRC metastasis-specific protein expression pattern, compar- ative proteomic analysis identified 11 proteins exhibit- ing consistent up-regulated expression in mCRC compared with nmCRC. Three representative gel images for each group are shown in Fig. S1. All the protein spots of interest were successfully identified by MALDI-TOF MS (Fig. 1), and by subsequent com- parative sequence searches in the Mascot database (Table 1). The MSDB identification number, the theo- retical molecular mass, the theoretical pI, the sequence coverage and the MASCOT score are shown in Table 1. Among them, the three proteins, identified as Rho GDP dissociation inhibitor alpha (RhoGDI), S100A9 and LIM and SH3 protein 1 (LASP-1), were found to be significantly up-regulated in tumour tissue specimens, especially in metastatic CRC. Enlarged images of the three protein spots are shown in Fig. 2A. Validation of the identify of differentially expressed proteins by Western blotting To confirm and extend the two-dimensional electro- phoresis results, Western blotting was used to confirm that expression of RhoGDI, S100A9 and LASP-1 was significantly higher in mCRC tissue than in the nmCRC group, while the normal tissue had the lowest expression. Equal protein loading was confirmed by parallel GAPDH immunoblotting, and signal quantifi- cation was performed by densitometric scanning. A representative Western blotting result is shown in Fig. 2B. Immunohistochemical analysis Expression and subcellular localization of proteins was determined by immunohistochemistry in paraffin- embedded normal colorectal mucosa and CRC tissues. A representative immunohistochemistry staining is shown in Fig. 3. The rates of RhoGDI, S100A9 and LASP-1 over-expression in normal mucosa, nmCRC and mCRC tissue are shown in Table 2. Statistical analysis demonstrated that the mCRC samples had sig- nificantly higher positive over-expression rates of Rho- GDI, S100A9 and LASP-1 than the nmCRC samples (Table 2). However, there was no significant correla- tion between the three profiles (P > 0.05). Discussion In the present study, 31 proteins were identified as differentially expressed among normal colorectal mucosa, nmCRC and mCRC. To some extent, this result is consistent with data reported by other groups [2,6–9], who listed several proteins involved in protein synthesis and folding (heat shock proteins), cell communication and signal transduction (annexin), cellular reorganization and the cytoskeleton (tropo- myosin, tubulin and actin) and toxin catabolism and water deprivation (glutathione transferase) in proteo- mic profiles of CRC cell lines and tissue. However, Fig. 1. Two-dimensional gel pattern showing all the spots identified (1–31). Table 1 gives the identities of the protein. Proteins with the genesis and progression of CRC L. Zhao et al. 4196 FEBS Journal 277 (2010) 4195–4204 ª 2010 The Authors Journal compilation ª 2010 FEBS there are some differences between our data and that of other researchers, such as differential expression of RhoGDI and LASP-1. We consider that two-dimen- sional electrophoresis and MALDI-TOF MS-based peptide mass fingerprinting analysis of human tissues is more complex than for cell lines. It is difficult for a single laboratory to fully analyze extensive biological information that are generated by two-dimensional electrophoresis. Systemic collection and analysis of complementary data from various research groups will assist in producing global protein profiles of CRC. Moreover, differences between races and region distributions, as well as the various methods of tissue collection and processing, may contribute to the dif- ferences between laboratories. The methods used in this study, involving tissue washing and surface scraping of tissue, are important in order to collect pure tumour cell populations that are free of con- taminating serum proteins, red blood cells, connective tissue and necrotic tissue [10]. The 31 spots representing differentially expressed proteins among normal colorectal mucosa, nmCRC and mCRC were excised from the two-dimensional electrophoresis gels for subsequent analysis in this study. All these spots were successfully identified. The Western blotting results confirmed our proteomic identification of the proteins RhoGDI, S100A9 and LASP-1, showing elevated expression in the case of CRC, especially mCRC, compared with normal colo- rectal mucosa. Immunohistochemical analysis revealed that over-expression of the three proteins was signifi- cantly associated with the genesis and progression of CRC. The functional implications of the alterations in the levels of these proteins are discussed in detail. Table 1. The 31 proteins differentially expressed among normal colorectal mucosa, nmCRC and mCRC tissue. Protein index Theoretical M r (kDa) ⁄ pI Summary score Protein coverage (%) MSDB ID Protein description Protein level (tumour ⁄ normal) Protein level (mCRC ⁄ nmCRC) 1 52 200 ⁄ 5.35 101 30 Q5SP14 Heat shock 70 kDa protein 1B Down – 2 48 599 ⁄ 5.6 186 62 S37780 Keratin 20, type I-like, cytoskeletal Down – 3 58 339 ⁄ 7.95 117 39 KPYM Pyruvate kinase, isozymes M1 ⁄ M2 Down – 4 68 354 ⁄ 5.67 146 45 E973181 a-fetoprotein Down – 5 53 580 ⁄ 5.62 115 27 Q53HF2 Heat shock 70 kDa protein 8, isoform 2 variant Down – 6 41 973 ⁄ 6.69 101 44 1HJOA Heat-shock 70 kDa protein, 42 kDa fragment Down – 7 20 146 ⁄ 6.76 127 70 CYHUAB a-crystallin chain B Down – 8 68 354 ⁄ 5.67 109 27 E973181 a-fetoprotein Down – 9 12 312 ⁄ 6.95 73 84 Q59FA5 Transgelin variant Down Up 10 58 339 ⁄ 7.95 205 50 KPYM Pyruvate kinase, isozymes M1 ⁄ M2 Up – 11 29 678 ⁄ 5.5 139 65 Q6PJ43 ACTG1 protein Up – 12 56 577 ⁄ 8.54 71 32 FGHUB Fibrinogen b chain precursor Up – 13 42 568 ⁄ 5.72 76 40 A36898 Maspin Up – 14 30 185 ⁄ 6.11 118 42 S68234 LASP-1 protein Up – 15 28 769 ⁄ 6.75 137 60 PGAM1 Phosphoglycerate mutase 1 Up – 16 30 337 ⁄ 8.81 72 26 Q7KZ74 A+U-rich element RNA binding factor Up – 17 23 108 ⁄ 5.21 82 37 1YER Heat shock protein 90 Up – 18 36 393 ⁄ 5.63 137 49 ANXA3 Annexin A3 Up – 19 12 770 ⁄ 5.55 71 80 CAA00999 Calgranulin B Up – 20 28 512 ⁄ 5.19 107 46 PSA3 Proteasome subunit a, type 3 Up – 21 48 135 ⁄ 4.7 76 31 Q5JP53 Tubulin, b polypeptide Up – 22 20 571 ⁄ 6.73 96 53 1CC0E Rho GDP dissociation inhibitor a, chain E Up Up 23 40 270 ⁄ 4.89 79 28 Q6PK50 Heat shock 90kDa protein 1, Beta (HSPCB) – Up 24 33 027 ⁄ 4.63 105 60 A23562 Tropomyosin 1, fibroblast and epithelial cell – Up 25 34 980 ⁄ 4.81 117 57 T08796 Tropomyosin – Up 26 35 224 ⁄ 5.14 183 70 1HVG Annexin V – Up 27 7707 ⁄ 9.88 75 85 Q5KSY4 CC chemokine receptor 5 (fragment) – Up 28 23 444 ⁄ 5.42 111 56 A41177 Glutathione transferase – Up 29 19 697 ⁄ 4.84 84 41 S06590 IgE-dependent histamine-releasing factor – Up 30 22 826 ⁄ 5.98 127 68 HHHU27 Heat shock protein 27 – Up 31 20 155 ⁄ 5.25 85 39 1QINA Lactoylglutathione lyase – Up L. Zhao et al. Proteins with the genesis and progression of CRC FEBS Journal 277 (2010) 4195–4204 ª 2010 The Authors Journal compilation ª 2010 FEBS 4197 Rho GDIs (GDP dissociation inhibitors) have been identified as key regulators of Rho family GTPases, which are typified by their ability to prevent nucleotide exchange and membrane association. These function by extracting Rho family GTPases from membranes and solubilizing them in the cytosol. Moreover, they interact only with prenylated Rho proteins both in vitro and in vivo [11,12]. They also inhibit nucleotide exchange and GTP-hydrolyzing activities on Rho proteins by interacting with their switch regions and probably restricting accessibility to guanine exchange factors (GEFs) and GTPase-activating proteins (GAPs). We used comparative proteomic analysis to identify a mem- ber of the GDI family, namely RhoGDI, that is up-reg- ulated in metastatic CRC, in agreement with results obtained previously [13]. Despite the initial negative roles attributed to RhoGDI, recent evidence suggests that it may also act as a positive regulator that is neces- sary for correct targeting and regulation of Rho activi- ties by conferring cues for spatial restriction, guidance and availability to effectors [14,15]. For example, Rac1 regulation of NADPH oxidase activity in neutrophils may require formation of a protein complex with RhoGDI [16–18]. Similarly, Ras guanine nucleotide- releasing factor (RasGRF)-induced mitogen-activated protein kinase activation and Cdc42-mediated cellular transformation [2] may require formation of a complex between the respective GTPases and RhoGDI [19]. It also appears that RhoGDI can serve as an escort to shuttle Rho GTPases to membrane-associated signalling complexes, which is crucial for coupling the GTPases to their downstream effector proteins [20]. In a AB C D Fig. 2. Identification and further validation of differentially expressed protein spots. (A) Peptide mass fingerprinting of protein spots 14, 19 and 22, representing RhoGDI, S100A9 and LASP-1, respectively. (B) Enlarged images of RhoGDI, S100A9 and LASP-1 in two-dimensional gels of normal colorectal mucosa, nmCRC and mCRC. (C) Protein expression of RhoGDI, S100A9 and LASP-1 in normal tissue, nmCRC and mCRC determined by Western blotting. There are three representative samples in each group, and the results show that expression of Rho- GDI, S100A9 and LASP-1 significantly increases in the nmCRC group. GAPDH is used as an internal loading control. (D) Immunosignals were quantified by densitometric scanning. Protein expression in the individual tissue samples was calculated as protein expression relative to GAPDH expression. Data are means ± SD from three independent experiments. *P < 0.05 compared with protein expression in normal mucosa; **P < 0.05 compared with protein expression in nmCRC. Proteins with the genesis and progression of CRC L. Zhao et al. 4198 FEBS Journal 277 (2010) 4195–4204 ª 2010 The Authors Journal compilation ª 2010 FEBS comparative proteomic analysis of non-invasive versus invasive ovarian tumours, RhoGDI was found to be over-expressed in invasive human ovarian cancer com- pared to non-invasive cancer [21]. All these results indi- cate that RhoGDI may play an important role in the progression and metastasis of CRC. The S100A9 protein, formerly called calgranulin B, MRP14 or LI heavy chain, is a protein of about 13 kDa that can occur in three different isoforms depending on its level of phosphorylation [22]. This protein is found predominantly in the cytosol, but can also be expressed on the cell surface or even secreted into the extracellular environment. The best character- ized intracellular function proposed for S100A9 is that of inhibition of casein kinase II, contributing to regulation of normal cellular transcription and transla- tion. The possible extracellular functions assigned to S100A9 include chemotactic activity on the one hand and cytotoxic ⁄ cytostatic activities against bacteria, fungi and tumour cells on the other hand [23]. Previous studies have reported that S100A8 and S100A9 are frequently co-expressed, and their expres- sion appears to be coordinately regulated [24,25]. Dif- ferential expression of S100A8 and S100A9 has been shown to contribute to the development and progres- sion of various types of cancer. For example, S100A8 and S100A9 are over-expressed in pancreatic adenocar- cinoma [26], bladder cancers [27] and breast cancers [28]. S100A9 expression is linked to de-differentiation of thyroid carcinoma [29]. Several studies have attempted to correlate the level of expression of S100A8 and S100A9 with the degree of non-inva- sive ⁄ invasive behaviour. Non-invasive MCF-7 breast cancer cells do not express S100A9. S100A9 expression in MCF-7 is induced by the cytokine oncostatin m through the STAT3 signalling cascade [30]. However, both S100 proteins are highly expressed in non-inva- sive MDA-MB-468 cells [31]. The invasive breast can- cer cell line MDA-MB-231 shows only a low transcript level of S100A9 [32], but S100A9 is over-expressed in invasive ductal carcinoma of the breast [1,33]. S100A8 and S100A9 have been suggested to represent novel Fig. 3. Immunohistochemical staining of RhoGDI, S100A9 and LASP-1 in normal colorectal mucosa, nmCRC and mCRC. Immunoreactivity to RhoGDI, S100A9 and LASP-1 staining was localized to the cytoplasm region of benign and malignant epithelial cells. Table 2. Over-expression of RhoGDI, S100A9 and LASP-1 proteins in normal mucosa, nmCRC and mCRC. Group RhoGDI (%) S100A9 (%) LASP-1 (%) Low High Low High Low High Normal 52 (88.1) 7 (11.9) 48 (75.0) 16 (25.0) 58 (82.9) 12 (17.1) nmCRC 61 (76.3) 19 (23.7) 55 (68.8) 25 (31.2) 62 (77.5) 18 (22.5) mCRC 22 (47.8) 24 (52.2) 19 (41.3) 27 (58.7) 23 (50.0) 23 (50.0) a v value 22.062 14.462 16.603 a P value < 0.001 0.001 < 0.001 a The statistical analyses were performed among normal mucosa, nmCRC and mCRC groups. L. Zhao et al. Proteins with the genesis and progression of CRC FEBS Journal 277 (2010) 4195–4204 ª 2010 The Authors Journal compilation ª 2010 FEBS 4199 diagnostic markers when measured in the serum of patients with prostate cancer and benign prostate hyperplasia [34]. In line with these observations, we detected up-regulated expression of S100A9 proteins in CRC tissues, especially in mCRC, indicating its possi- ble role in the development and progression of CRC. LASP-1 was initially identify from a cDNA library of metastatic axillary lymph nodes of breast cancer patients, and the gene was mapped to human chromo- some 17q21 [35,36]. The exact functions of LASP-1 are still not well known; however, its expression is local- ized to multiple sites of dynamic actin assembly, such as focal contacts, focal adhesions, lamellipodia mem- brane ruffles and pseudopodia [30,35,37–39]. It has been reported that LASP-1 is over-expressed in meta- static breast cancer, participating in migration of these cancer cells. Furthermore, silencing of LASP-1 in met- astatic breast cancer cell lines resulted in strong inhibi- tion of cell proliferation as well as migration, and led to a reduction of zyxin at the focal contacts [30,40]. Interestingly, a recent study also demonstrated that LASP-1 is over-expressed in ovarian cancer tissues and metastatic ovarian cancer cell lines [41]. In vitro silenc- ing of the gene encoding LASP-1 reduced cell prolifer- ation and migration and severely affected zyxin localization [41]. These results indicate that LASP-1 may play an important role in the progression and metastasis of CRC. In summary, the techniques of proteomic analysis provide a dramatic means of screening for genesis- and metastasis-associated proteins in CRC. The results sug- gest that RhoGDI, S100A9 and LASP-1 may play an important role in the development and progression of CRC. Further functional and clinical analysis of the proteins is necessary to elucidate their precise role in the process of CRC and the formation of metastases. Experimental procedures Tumour samples All cases were selected from the Nanfang Hospital tumour tissue bank. In total, 150 patients were involved in the study. In each case, a diagnosis of primary CRC had been made, and the patients had undergone elective surgery for CRC, in Nanfang Hospital, between 2001 and 2004. The Nanfang Hospital tumour tissue bank is linked to a com- prehensive set of clinicopathological data. Clinical data for all the samples used for two-dimensional electrophoresis and immunohistochemical study are shown in Table 3. The tumour samples were submitted to the Department of Pathology, Nanfang Hospital, Southern Medical Univer- sity, for pathological diagnosis. The tumour specimens were fixed in formalin, representative blocks were embedded in wax, and sections were stained with haematoxylin and eosin. Permission for this study was obtained from the Eth- ics Committee of Southern Medical University. The informed consent with a uniform format was designed by the Ethics Committee and signed by the patients involved in the study before the trial. All the patients understood the trial’s purpose and procedures. Proteomics Proteomics analysis, including two-dimensional gel electro- phoresis, gel visualization and assessment, and mass spec- trometry, was performed as previously described [42]. Proteins were extracted from normal colorectal mucosa (n = 12), non-metastatic CRC (nmCRC) (n = 12) and metastatic CRC (mCRC) (n = 12) tissue samples. Tissue samples (50–100 mg) were crushed in liquid nitrogen, and lysed in 1 mL lysis buffer consisting of 7 m urea, 2 m thio- urea, 4% Chaps, 65 mm dithiothreitol and 2% pharmalyte (pH3-10; GE Healthcare, Piscataway, NJ, USA) by sonica- tion on ice. The lysates were cleared by centrifugation at 12 000 g for 1 h at 4 °C. The protein concentration of the supernatants was determined by the modified Bradford method [43], and aliquots of the protein samples were stored at )80 °C. Prior to two-dimensional electrophoresis, the protein samples were purified using a 2D Clean-Up kit (GE Healthcare) according to the manufacturer’s instruc- tions. Differentially expressed proteins were identified using two-dimensional gel electrophoresis and mass spectrome- try. Two-dimensional gel electrophoresis was performed using Immoboline strips (pI range, 3–10; GE Healthcare, Piscataway, NJ, USA), with proteins being separated according to charge, and subsequently molecular weight. The gels were then stained with silver in order to visualize Table 3. CRC tissue samples used in the study. Samples for two-dimensional electrophoresis Samples for immunohistochemisty Normal nmCRC mCRC Normal nmCRC mCRC Lymph node status – Negative Positive – Negative Positive Number 12 12 12 Uncertain 80 46 Gender (male ⁄ female) 5 ⁄ 75⁄ 710⁄ 2 Unknown 52 ⁄ 28 27 ⁄ 19 Age (years, mean ± SD) 54 ± 17.9 52 ± 15.9 56 ± 14.7 Uncertain 54 ± 13.6 56 ± 14.8 Proteins with the genesis and progression of CRC L. Zhao et al. 4200 FEBS Journal 277 (2010) 4195–4204 ª 2010 The Authors Journal compilation ª 2010 FEBS proteins, and scanned using a Power-Look 1100 imaging scanner (Umax, Dallas, TX, USA). The pdquest 7.1 soft- ware package (Bio-Rad, Hercules, CA, USA) was used for image analysis, including background abstraction, spot intensity calibration, spot detection and matching. The intensity of each spot was quantified by calculation of spot volume after normalization of the gel image. Each experi- ment was performed in triplicate, and the paired Student’s t test was used to evaluate the mean change in protein abundance corresponding to each target spot across the gels. The protein spots of interest were cut from the gels. Proteins were digested with trypsin, and peptide mass mapping was performed by MALDI-TOF MS using an ABI Voyager DE-STR mass spectrometer (Applied Biosys- tems, Foster City, CA, USA). Protein identification using peptide mass fingerprinting was performed using the MAS- COT search engine (http://www.matrixscience.com/, Matrix Science Ltd, London, UK) against the MSDB protein database (ht tp://www.proteomics.leeds.ac.uk/bioinf/msdb. html). The database search was restricted to human pro- teins, with no constraints on either the molecular weight or the isoelectric point of the protein. The errors in pep- tide mass were in the range of 25 ppm. One missed tryptic cleavage site per peptide was allowed during the search. Proteins matching more than four peptides and with a MASCOT score higher than 63 were considered significant (P < 0.05). Carboamidomethylation of cysteine was used as the static modification and oxidation of methionine as the differential modification. The protein identification results were filtered using peakerazor software (Light- house Data, Odense, Denmark). Western blot analysis Samples from the different population were selected for Western blot validation. Sample preparation for immuno- blotting was performed as previously described [44]. Briefly, proteins were obtained from tissue samples as described above. The protein concentration was determined using the modified Bradford method [43]. Equal amounts of proteins were separated electrophoretically on 12% SDS ⁄ polyacryl- amide gels, and transferred onto polyvinylidene difluoride membranes (PVDF) (Amersham Pharmacia Biotech, Piscat- away, NJ, USA). The membrane was probed using rabbit anti-RhoGDI IgG (1 : 1000; Cell Signalling Technology, Danvers, MA, USA), mouse anti-S100A9 IgG (1 : 1000; Abcam, Cambridge, UK) and mouse anti-LASP-1 IgG (1 : 2000; Chemicon, Temecula, CA, USA). Expression of proteins was determined using horseradish peroxidase- conjugated anti-rabbit IgG (1 : 20 000; Jingmei Biotech, Shanghai, China) and enhanced chemiluminescence (ECL) (Pierce, Rockford, IL, USA). The immunoreactive bands were visualized on a Kodak 2000M camera system (Eastman Kodak, Rochester, NY, USA) according to the manufac- turer’s instructions. An anti-GAPDH goat polyclonal IgG (1 : 500; Santa Cruz Biotechnology, Santa Cruz, CA, USA) was used to confirm equal loading. The experiments were repeated three times. Immunohistochemistry Immunohistochemistry was performed to study altered pro- tein expression in 126 human CRC tissue samples. The pro- cedures used were similar to previously described methods [44]. Briefly, 4 lm sections mounted on aminopropylethox- ysilane slides and pre-treated for immunohistochemistry were de-waxed using xylene, and rehydrated through a graded series of ethanol and deionized water. An antigen retrieval step was performed. Before staining for immuno- histochemistry, the sections were incubated in a 750 W microwave oven for 15 min in 10 mm buffered citrate, pH 6.0, to complete antigen unmasking. The classical avidin– biotin peroxidase complex procedure was used for immuno- histochemistry. In the avidin–biotin peroxidase complex system, endogenous peroxidase was quenched by incubation of the sections in 0.1% sodium azide with 0.3% hydrogen peroxide for 30 min at room temperature. Non-specific binding was blocked by incubation with non-immune serum (1% bovine serum albumin for 15 min at room temperature). The sections were incubated with primary anti-RhoGDI (1 : 50), mouse anti-S100A9 (1 : 100) and anti-LASP-1 (1 : 500) antibodies overnight at 4 °C. The following con- trols were performed: (a) omission of the primary antibody, and (b) substitution of the primary antiserum with non-immune serum diluted 1 : 500 in blocking buffer. No immunostaining was observed after any of the control procedures. Biotinylated secondary goat anti-rabbit anti- bodies (MaiXin, Fuzhou, China) and subsequently a horse- radish peroxidase–streptavidin complex (MaiXin) were applied for 15 min each. Peroxidase activity was developed by use of a filtered solution of 5 mg 3,3-diaminobenzideine tetrahydrochloride (dissolved in 10 mL 0.05 m Tris buffer, pH 7.6) and 0.03% H 2 O 2 . Mayer’s haematoxylin was used for nuclear counterstaining. The sections were mounted using a synthetic medium. Evaluation of immunohistochemical staining Two observers independently reviewed and assessed the cel- lular localization and intensity of immunostaining in each section. Staining for proteins in tumour cells was scored semi-quantitatively using a quality control system. The pro- portion of cells expressing the proteins varied from 0% to 100%, and the intensity of staining varied from weak to strong. Scores representing the percentage of tumour cells stained positive were as follows: 0% (absent), 1–5% (spo- radic), 6–25% (local), 26–50% (occasional), 51–75% (majority) and 76–100% (large majority). The intensity of tumour cell staining was scored as 0 (no staining), 1 (weak staining, light yellow), 2 (moderate staining, yellowish L. Zhao et al. Proteins with the genesis and progression of CRC FEBS Journal 277 (2010) 4195–4204 ª 2010 The Authors Journal compilation ª 2010 FEBS 4201 brown) and 3 (strong staining, brown). Using this method of assessment as mentioned above, we evaluated the expres- sion of proteins in benign colorectal mucosa and malignant lesions as described previously [45]. Cut-off values were chosen on the basis of a measure of heterogeneity. An optimal cut-off value was identified. An intensity score of ‡ 2 with at least 50% of malignant cells showing positive staining was used to classify tumours with high expression (or over-expression), and < 50% of malignant cells with staining or an intensity score < 2 identified tumours with low expression. The small number of discrepancies (< 5%) were resolved by re-evaluation. Statistical analysis All statistical analyses were performed using the spss 12.0 statistical software package (SPSS, Chicago, IL, USA). The pdquest 7.1 software package (Bio-Rad) was used for image analysis, and a paired Student’s t test was used to evaluate the mean change in protein abundance corre- sponding to each target spot across the gels. For Western blot analysis, expression of differential protein between two groups was compared using a paired Student’s t test. For immunohistochemistry analysis, the significance of correla- tion between the protein expression and clinicopathological factors was determined using Pearson’s chi-square test. A P value < 0.05 was considered statistically significant in all cases. 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This supplementary material can be found in the online version of this article. Please note: As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer-reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Proteins with the genesis and progression of CRC L. Zhao et al. 4204 FEBS Journal 277 (2010) 4195–4204 ª 2010 The Authors Journal compilation ª 2010 FEBS . Comparative proteomic analysis identifies proteins associated with the development and progression of colorectal carcinoma Liang Zhao 1,2, *,. in the development and progression of CRC. Further functional and clinical analysis of the proteins is necessary to elucidate their precise role in the