Protein profiling of bladder cancer using the 2D-PAGE and SELDI-TOF-MS technique

Impact of Effective Intravesical Therapies on Quality of Life in Patients with Non-Muscle Invasive Bladder Cancer: A Systematic Review

BACKGROUND

Conventional and newly emerged intravesical modalities have demonstrated prophylactic effectiveness that may improve quality of life (QoL) in non-muscle invasive bladder cancer. The purpose of this study is to analyze existing QoL evidence in patients receiving any form of intravesical therapy.

METHODS

A PubMed search without time restriction was conducted to identify all relevant studies in accordance with the PICOT question. Additionally, a search was also performed in the Cochrane library database, Internet, and citation. The CONSORT 2010 checklist and STROBE statement checklist were used to evaluate the risk of bias of the included studies.

RESULTS

A total of 24 eligible articles were included, which consisted of 11 interventional and 13 observational studies. Intravesical therapy with Bacillus Calmette-Guérin (BCG) or certain chemotherapeutic agents worsens symptom burdens and functional performance during the initial induction phase while continuous improved is observed throughout the maintenance treatment and beyond. Hyperthermia has shown a positive trend in enhancing QoL of patients receiving intravesical chemotherapy, which requires more investigations. However, QoL data were unavailable for other forms of immunotherapy, immune checkpoint inhibitors, electromotive drug administration, and photodynamic therapy.

CONCLUSIONS

Limited studies suggested the long-term positive impact of intravesical BCG immunotherapy and chemotherapy. However, existing evidence was lacking to clarify the impact of many emerging intravesical therapies that have suggested to be effective and safe, which demands treatment-specific QoL studies.

Quantitative Proteomics of Urinary Bladder Cancer Cell Lines Identify UAP1 as a Potential Therapeutic Target

Bladder carcinoma (BC) incidence and mortality rates are increasing worldwide. The development of novel therapeutic strategies is required to improve clinical management of this cancer. Aberrant protein expression may lead to cancer initiation and progression. Therefore, the identification of these potential protein targets and limiting their expression levels would provide alternative treatment options. In this study, we utilized a liquid-chromatography tandem mass spectrometry-based global proteomics approach to identify differentially expressed proteins in bladder cancer cell lines. A total of 3913 proteins were identified in this study, of which 479 proteins were overexpressed and 141 proteins were downregulated in 4 out of 6 BC cell lines when compared with normal human urothelial cell line (TERT-NHUC). We evaluated the role of UDP-N-acetylhexosamine pyrophosphorylase (UAP1) in bladder cancer pathogenesis. The silencing of UAP1 led to reduction in proliferation, invasion, colony formation and migration capability of bladder cancer cell lines. Thus, our study reveals UAP1 as a promising therapeutic target for bladder cancer.

Functional Association between Regulatory RNAs and the Annexins

Cells respond to pathophysiological states by activation of stress-induced signalling. Regulatory non-coding microRNAs (miRNAs) often form stable feed-forward loops which ensure prolongation of the signal, contributing to sustained activation. Members of the annexin protein family act as sensors for Ca²⁺, pH, and lipid second messengers, and regulate various signalling pathways. Recently, annexins were reported to participate in feedback loops, suppressing miRNA synthesis and attenuating stress-induced dysregulation of gene expression. They can directly or indirectly associate with RNAs, and are transferred between the cells in exosomes and shed microvesicles. The ability of annexins to recruit other proteins and miRNAs into exosomes implicates them in control of cell–cell interactions, affecting the adaptive responses and remodelling processes during disease. The studies summarized in this Review point to an emerging role of annexins in influencing the synthesis, localisation, and transfer of regulatory RNAs.

Plasma Protein Profiles Differ between Women Diagnosed with Cervical Intraepithelial Neoplasia (CIN) 1 and 3

Early detection of precancerous cells in the cervix and their clinical management is the main purpose of cervical cancer prevention and treatment programs. Cytological findings or testing for high risk (HR)-human papillomavirus (HPV) are inadequately sensitive for use in triage of women at high risk for cervical cancer. The current study is an exploratory study to identify candidate surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) mass spectrometry (MS) protein profiles in plasma that may distinguish cervical intraepithelial neoplasia (CIN 3) from CIN 1 among women infected with HR-HPV. We evaluated the SELDI-TOF-MS plasma protein profiles of HR-HPV positive 32 women with CIN 3 (cases) and 28 women with CIN1 (controls). Case-control status was kept blinded and triplicates of each sample and quality control plasma samples were randomized and after robotic sample preparations were run on WCX2 chips. After alignment of mass/charge (m-z values), an iterative method was used to develop a classifier on a training data set that had 28 cases and 22 controls. The classifier developed was used to classify the subjects in a test data set that has six cases and six controls. The classifier separated the cases from controls in the test set with 100% sensitivity and 100% specificity suggesting the possibility of using plasma SELDI protein profiles to identify women who are likely to have CIN 3 lesions.

Predicting early intrahepatic recurrence of hepatocellular carcinoma after microwave ablation using SELDI-TOF proteomic signature

BACKGROUND/AIMS

Despite great progress in the treatment of hepatocellular carcinoma (HCC) over the last-decade, intrahepatic recurrence is still the most frequent serious adverse event after all the treatments including microwave ablation. This study aimed to predict early recurrence of HCC after microwave ablation using serum proteomic signature.

METHODS

After curative microwave ablation of HCC, 86 patients were followed-up for 1 year. Serum samples were collected before microwave ablation. The mass spectra of proteins were generated using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). Serum samples from 50 patients were randomly selected as a training set and for biomarkers discovery and model development. The remaining serum samples were categorized for validation of the algorithm.

RESULTS

According to preablation serum protein profiling obtained from the 50 HCC samples in the training set, nine significant differentially-expressed proteins were detected in the serum samples between recurrent and non-recurrent patients. Decision classification tree combined with three candidate proteins with m/z values of 7787, 6858 and 6646 was produced using Biomarker Patterns Software with sensitivity of 85.7% and specificity of 88.9% in the training set. When the SELDI marker pattern was tested with the blinded testing set, it yielded a sensitivity of 80.0%, a specificity of 88.5% and a positive predictive value of 86.1%.

CONCLUSIONS

Differentially-expressed protein peaks in preablation serum screened by SELDI are associated with prognosis of HCC. The decision classification tree is a potential tool in predicting early intrahepatic recurrence in HCC patients after microwave ablation.

Down-regulation of annexin A1 in the urothelium decreases cell survival after bacterial toxin exposure

PURPOSE

We examined the role of annexins in bladder urothelium. We characterized expression and distribution in normal bladders, biopsies from patients with bladder pain syndrome, cultured human urothelium and urothelial TEU-2 cells.

MATERIALS AND METHODS

Annexin expression in bladder layers was analyzed by quantitative reverse transcriptase-polymerase chain reaction and immunofluorescence. We assessed cell survival after exposure to the pore forming bacterial toxin streptolysin O by microscopy and alamarBlue® assay. Bladder dome biopsies were obtained from 8 asymptomatic controls and 28 patients with symptoms of bladder pain syndrome.

RESULTS

Annexin A1, A2, A5 and A6 were differentially distributed in bladder layers. Annexin A6 was abundant in detrusor smooth muscle and low in urothelium, while annexin A1 was the highest in urothelium. Annexin A2 was localized to the lateral membrane of umbrella cells but excluded from tight junctions. TEU-2 cell differentiation caused up-regulation of annexin A1 and A2 and down-regulation of annexin A6 mRNA. Mature urothelium dedifferentiation during culture caused the opposite effect, decreasing annexin A1 and increasing annexin A6. Annexin A2 influenced TEU-2 cell epithelial permeability. siRNA mediated knockdown of annexin A1 in TEU-2 cells caused significantly decreased cell survival after streptolysin O exposure. Annexin A1 was significantly reduced in biopsies from patients with bladder pain syndrome.

CONCLUSIONS

Several annexins are expressed in human bladder and TEU-2 cells, in which levels are regulated during urothelial differentiation. Annexin A1 down-regulation in patients with bladder pain syndrome might decrease cell survival and contribute to compromised urothelial function.

Tissue and serum proteomic profiling for diagnostic and prognostic bladder cancer biomarkers

A panel of biomarkers for the early detection of bladder cancer has not yet been identified. Many different molecules, including DNA, RNA or proteins have been reported but none have provided adequate sensitivity for a single-tier screening test or a test to replace cystoscopy. Therefore, multimarker panels are discussed at present to give a more-precise answer to the biomarker quest. Mass spectrometry or 2D gel-electrophoresis have evolved greatly within recent years and are capable of analyzing multiple proteins or peptides in parallel with high sensitivity and specificity. However, transmission of screening results from one laboratory to another is still the main pitfall of those methods; a fact that emphasizes the need for consistent and standardized procedures as suggested by the Human Proteome Organization (HUPO). In this article, recent results in screening approaches and other proteomic techniques used for biomarker evaluation in bladder cancer are discussed with a focus on serum and tissue biomarkers.

MALDI-TOF MS combined with magnetic beads for detecting serum protein biomarkers and establishment of boosting decision tree model for diagnosis of colorectal cancer

The aim of present study is to study the serum protein fingerprint of patients with colorectal cancer (CRC) and to screen protein molecules that are closely related to colorectal cancer during the onset and progression of the disease with Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Serum samples from 144 patients with CRC and 120 healthy volunteers were adopted in present study. Weak cation exchange (WCX) magnetic beads and PBSII-C protein chips reader (Ciphergen Biosystems Ins.) were used. The protein fingerprint expression of all the Serum samples and the resulted profiles between cancer and normal groups were analyzed with Biomarker Wizard system. Several proteomic peaks were detected and four potential biomarkers with different expression profiles were identified with their relative molecular weights of 2870.7 Da, 3084 Da, 9180.5 Da, and 13748.8 Da, respectively. Among the four proteins, two proteins with m/z 2870.7 and 3084 were down-regulated, and the other two with m/z 9180.5 and 13748.8 were up-regulated in serum samples from CRC patients. The present diagnostic model could distinguish CRC from healthy controls with the sensitivity of 92.85% and the specificity of 91.25%. Blind test data indicated a sensitivity of 86.95% and a specificity of 85%. The result suggested that MALDI technology could be used to screen critical proteins with differential expression in the serum of CRC patients. These differentially regulated proteins were considered as potential biomarkers for the patients with CRC in the serum and of the potential value for further investigation.

New serum biomarkers for detection of esophageal carcinoma using Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

PURPOSE

To screen for the potential protein biomarkers in serum for the diagnosis of esophageal carcinoma (EC) using proteomic fingerprint technology.

METHODS

Proteomic fingerprint technology combining magnetic beads with MALDI-TOF-MS was used to profile and compare the serum proteins from 78 patients with EC and 95 healthy blood donors. Proteomic patterns associated with EC were identified by Biomarker Patterns Software. Model of biomarkers was constructed and evaluated using the Biomarker Patterns Software.

RESULTS

A total of 60 discriminating m/z peaks were identified that were related to EC (P < 0.01). The model of biomarkers constructed by the Biomarker Patterns Software based on the four biomarkers (2049.6, 3936.5, 5339.9, and 13748.8 Da) generated excellent separation between the EC and control groups. The sensitivity was 92.5% and the specificity was 88%. Blind test data indicated a sensitivity of 89.5% and a specificity of 84.4%.

CONCLUSIONS

Biomarkers for EC can be discovered in serum by MALDI-TOF-MS combining the use of magnetic beads. The pattern of combined markers provides a powerful and reliable diagnostic method for EC with a high sensitivity and specificity.

Galectin-3 expression is associated with bladder cancer progression and clinical outcome

Galectin-3 belongs to a family of carbohydrate-binding proteins whose function is not fully characterized. However, it is believed to play a role in adhesion, proliferation and apoptosis in solid tumors. We aimed at investigating galectin-3 expression in bladder cancer. Galectin-3 expression was assessed by transcript profiling (U133A arrays) in a series or frozen bladder tumors (n = 105). Immunohistochemistry was performed on tissue arrays containing bladder tumors (n = 389) to evaluate associations of protein expression patterns of galectin-3 with proliferation (Ki67), apoptosis (apopdetek), bcl-2, and clinicopathologic variables. Galectin-3 protein levels were then quantified in 160 urinary specimens of bladder cancer patients and controls by enzymeimmunoanalysis. Galectin-3 gene expression levels increased in invasive tumours as compared with non-muscle invasive lesions (p = 0.001) and were associated with poor survival in patients with advanced disease (p = 0.03). Protein expression patterns also correlated galectin-3 with tumor stage (p < 0.001), grade (p = 0.03), Ki67 and apopdetek (p < 0.001), and overall survival in patients with T1G3 tumors (p < 0.001). Furthermore, galectin-3 urinary levels segregated bladder cancer patients from controls with high diagnostic accuracy (AUC = 0.7). Independent series of bladder tumors showed that transcript and protein levels of galectin-3 were differentially expressed along bladder cancer progression. Urinary protein levels served to identify bladder cancer patients. These observations suggest a role for galectin-3 as a biomarker for bladder cancer diagnostics, staging, and outcome prognosis.

Proteomics and opportunities for clinical translation in urological disease

PURPOSE

Proteomics is a rapidly growing new discipline that has the potential to increase and improve the understanding of protein function and interaction in the context of systems biology. As a translational science it has the potential to identify many new therapeutic targets as well as diagnostic and prognostic biomarkers of disease. Proteomics approaches consist of a combination of powerful technologies such as protein/peptide separation, identification and bioinformatic detection, and quantitation based on powerful computational data processing tools. We present an overview of current proteomics technologies, a review of proteomics applications in urology and a perspective on the future of proteomics in clinical medicine.

MATERIALS AND METHODS

A literature search was performed on the basic concepts of proteomics and technologies commonly used in this field. Advantages, challenges and limitations of current proteomics approaches are discussed, and proteomics applications in the field of urology are presented.

RESULTS

The proteomics approaches to answer clinical questions have only recently been introduced. Many different technologies have been used in this field, which is moving from simple description to quantitative clinical applications.

CONCLUSIONS

Proteomics offers new approaches to the study of genitourinary tract diseases, and the potential to identify clinically relevant biomarkers and new therapeutic targets.

Identification of disease biomarkers by profiling of serum proteins using SELDI-TOF mass spectrometry

Proteins are the main actors in all physiological and pathological processes. Since the final structure of the protein does not depend on the DNA sequence or even the mRNA sequence alone, the search for direct approaches on the proteome has gained great interest. The most complex and probably the largest proteome is serum, making it clinically the most important. ProteinChip technology, in combination with modern mass spectrometry, allows the complex search for biomarkers, molecular interactions, signaling pathways, and the identification of novel therapeutic compounds. Here we describe the surface-enhanced laser desorption-ionization (SELDI) in combination with the time-of-flight (TOF) mass spectrometry for analyzing serum samples (SELDI was a patented technique from Ciphergen, Fremont, CA). Aluminum-based arrays contain chemical or biological surfaces allowing the capture of proteins, which interact with the surface. The bound proteins are laser desorbed and ionized for mass spectroscopy analysis. The differential mass spectral patterns reflect the protein expression bound on the chip surface and allow the comparison between various samples. Proteins of interest can be identified using peptide mass fingerprinting (PME).

Gene-expression signature of adhesion/growth-regulatory tissue lectins (galectins) in transitional cell cancer and its prognostic relevance

AIMS

Lectins, and especially galectins, appear to be important in malignancy-associated processes. The aim was to analyse comprehensively the presence of galectins in urothelial tumours.

METHODS AND RESULTS

Non-cross-reactive antibodies against seven family members from the three subgroups (prototype: galectin-1, -2 and -7; chimera type: galectin-3; tandem-repeat type: galectin-4, -8 and -9) were used. Gene expression was monitored in specimens of normal urothelium, fresh tumour tissue and cell lines by real-time polymerase chain reaction (PCR). The presence and evidence of tumour-associated up-regulation were shown for galectin-1 and -3. This was less clear-cut for galectin-4 and -8. Galectin-7 was expressed in all cell lines; galectin-2 and -9 were detected at comparatively low levels. Galectin-2, -3 and -8 up-regulation was observed in superficial tumours, but not in muscle-invasive tumours (P < 0.05). Immunoreactivity correlated with tumour grading for galectin-1, -2 and -8, and disease-dependent mortality correlated with galectin-2 and -8 expression. Binding sites were visualized using labelled galectins.

CONCLUSIONS

The results demonstrate a complex expression pattern of the galectin network in urothelial carcinomas. Galectin-1, -2, -3 and -8 are both potential disease markers and also possible targets for bladder cancer therapy.

High-resolution proteome/peptidome analysis of peptides and low-molecular-weight proteins in urine

All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance diagnosis and therapy of specific diseases. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its unique features, the technical challenges differ somewhat from those in "common" proteomics. In this manuscript, we focus on the low-molecular-weight urinary proteome. We review the methodological aspects of sample collection, preparation, analysis, and subsequent data evaluation. In the second part of this review, we summarize the recent progress in the definition and identification of clinically relevant polypeptide markers.

Downregulation of gelsolin family proteins counteracts cancer cell invasion in vitro

Gelsolin and CapG are both actin binding proteins that modulate a variety of physiological processes by interacting differently with the actin cytoskeleton. Several studies suggest that overexpression of these proteins promotes invasion in vitro. In this study we explored the contribution of these proteins in human cancer cell invasion and motility. We show that down regulation of CapG or gelsolin in several types of cancer cells, including MDA-MB 231 and PC-3 cells, significantly reduces the invasive and motile properties of cells, as well as cell aggregation. These results point to a role for CapG and gelsolin as tumor activator.

Fluorescence in situ hybridization: a multitarget approach in diagnosis and management of urothelial cancer

Noninvasive tests for detecting genetic or molecular alterations in urine indicative of urothelial cancer are increasingly becoming the focus of urological cancer research. Since its approval by the US FDA in 2001, the fluorescence in situ hybridization test (Vysis UroVysion) has been widely evaluated. In general, published data demonstrate better sensitivity and equal or better specificity compared with routine cytology, which is still considered the 'gold standard' in diagnosing and monitoring bladder tumors. However, the fluorescence in situ hybridization test seems to provide not only a useful tool in bladder cancer detection, but also in the diagnosis of upper urinary tract tumors, surveillance and determining therapy effectiveness. This multitarget assay that detects four different chromosomal aberrations in tumor cells is a kind of objective molecular cytology and has proven advantages over routinely used cytology.

Identification of novel proteins induced by estradiol, 4-hydroxytamoxifen and acolbifene in T47D breast cancer cells

Tamoxifen is currently used as adjuvant therapy for estrogen receptor (ER) positive breast cancer patients and as a chemopreventative agent. Although ER is a predictive marker for tamoxifen response, ER status fails to predict tamoxifen response in a significant number of patients highlighting the need to identify new pathways for tamoxifen sensitivity/resistance. To identify novel proteins induced by tamoxifen in breast cancer cells sensitive to tamoxifen growth inhibition, two-dimensional (2D) gel electrophoresis was used to profile proteins in T47D breast cancer cells. Six proteins were identified that were differentially regulated by 17beta-estradiol, 4-hydroxytamoxifen and the pure antagonist acolbifene (EM-652); calreticulin, synapse associated protein 1 (SYAP1), CD2 antigen binding protein 2 (CD2BP2), nucleosome assembly protein 1 like 1 (NAP1L1), d-3-phosphoglycerate dehydrogenase (3-PHGDH) and pyridoxine 5' phosphate oxidase (PNPO). At the mRNA level, these ligands differentially regulated expression of mRNAs encoding the identified proteins in T47D and MCF7 cells but had no effect on mRNA in ERalpha-negative MDA-MB-231 breast cancer cells. These novel SERM-regulated proteins may participate in new or existing pathways for sensitivity or resistance to SERMs.

Contributions of advanced proteomics technologies to cancer diagnosis

The ability of Medicine to effectively treat and cure cancer is directly dependent on their capability to detect cancers at their earliest stages. The advent of proteomics has brought with it the hope of discovering novel biomarkers in the early phases of tumorigenesis that can be used to diagnose diseases, predict susceptibility, and monitor progression. This discipline incorporates technologies that can be applied to complex biosystems such as serum and tissue in order to characterize the content of, and changes in, the proteome induced by physiological changes, benign or pathologic. These tools include 2-DE, 2D-DIGE, ICAT, protein arrays, MudPIT and mass spectrometries including SELDI-TOF. The application of these tools has assisted to uncover molecular mechanisms associated with cancer at the global level and may lead to new diagnostic tests and improvements in therapeutics. In this review these approaches are evaluated in the context of their contribution to cancer biomarker discovery. Particular attention is paid to the promising contribution of the ProteinChip/SELDI-TOF platform as a revolutionary approach in proteomic patterns analysis that can be applied at the bedside for discovering protein profiles that distinguish disease and disease-free states with high sensitivity and specificity. Understanding the basic concepts and tools used will illustrate how best to apply these technologies for patient benefit for the early cancer detection and improved patient care.