PROTEOMICS - CLINICAL APPLICATIONS (Proteonomics Clin Appl)

Publications in this journal

• Article: Proteomics in Aortic Aneurysm - What Did we Learn so Far?

  Nada Abdulkareem, Philipp Skroblin, Marjan Jahangiri, Manuel Mayr
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  ABSTRACT: Aortic aneurysm is a deceptively indolent disease that can cause severe complications such as aortic rupture and dissection. In the normal aorta, vascular smooth muscle cells within the medial layer produce and sustain the extracellular matrix that provides structural support but also retains soluble growth factors and regulates their distribution. Although the extracellular matrix is an obvious target to identify molecular processes leading to structural failure within the vessel wall, an in-depth proteomics analysis of this important sub-proteome has not been performed. Most proteomics analyses of the vasculature to date used homogenized tissue devoid of spatial information. In such homogenates, quantitative proteomics comparisons are hampered by the heterogeneity of clinical samples (i.e. cellular composition) and the dynamic range limitations stemming from highly abundant cellular proteins. An unbiased proteomics discovery approach targeting the extracellular matrix instead of the cellular proteome may decipher the complex, multivalent signals that are presented to cells during aortic remodelling. A better understanding of the extracellular matrix in healthy and diseased vessels will provide important pathogenic insights and has potential to reveal novel biomarkers. This article is protected by copyright. All rights reserved.
  PROTEOMICS - CLINICAL APPLICATIONS 05/2013;
• Article: Development of a label-free LC-MS/MS strategy to approach the identification of candidate protein biomarkers of disease recurrence in prostate cancer patients in a clinical trial of combined hormone and radiation therapy.

  Brian Morrissey, Carmel O' Shea, John Armstrong, Cathy Rooney, Lisa Staunton, Martina Sheehan, Aoife Shannon, Stephen R Pennington
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  ABSTRACT: Prostate cancer is one of the leading causes of male mortality in the Western world. Currently, radiation combined with hormone treatment is one of the principle curative regimes for localised disease. Significantly, of the patients treated this way approximately 25% subsequently experience disease recurrence and may require further treatment. At present, prostate specific antigen (PSA) is used to monitor treatment and a rising serum PSA level can be indicative of treatment failure. However, PSA is relatively insensitive as both transient increases in PSA without disease recurrence and disease recurrence without a rise in PSA occur. Hence, more effective biomarkers to monitor treatment and predict disease recurrence are needed. In this proof of principle study we used samples accrued under strict clinical trial governance and have applied a mass spectrometry based proteomic pipeline consisting of label free LC-MS biomarker discovery and multiple reaction monitoring confirmation strategy to identify a potential serum protein signature of disease recurrence. Ultimately, when extended and combined with validation studies using samples from other clinical trials we anticipate that this proteomics strategy will facilitate the development of a protein signature of significant clinical utility. This article is protected by copyright. All rights reserved.
  PROTEOMICS - CLINICAL APPLICATIONS 05/2013;
• Article: Effects of gamma irradiation and 15 days of subsequent ex vivo storage on the cytosolic red blood cell proteome analyzed by 2D DIGE and Orbitrap MS.

  Katja Walpurgis, Maxie Kohler, Andreas Thomas, Folker Wenzel, Hans Geyer, Wilhelm Schänzer, Mario Thevis
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  ABSTRACT: PURPOSE: Gamma irradiation of red blood cell (RBC) concentrates is routinely used to prevent transfusion-associated graft-versus-host disease (TA-GvHD). So far, the effects of ionizing radiation on RBC structure and function and especially the proteome are not fully understood. EXPERIMENTAL DESIGN: RBC concentrates were irradiated with 30 Gy and stored for 1 or 15 days at 4 ± 2°C. Following cell lysis and hemoglobin depletion, 2D DIGE was used to examine the changes of the cytosolic RBC proteome. Significantly altered spots were analyzed using bottom-up proteomic approaches and selected marker proteins validated by western blotting. RESULTS: Gamma irradiation was found to enhance conventional RBC storage lesions. Following 15 days of post-irradiation storage, the abundances of a total of 27 spots were significantly altered and three out of 13 identified proteins were selected and validated as potential marker proteins for the assessment of irradiation-induced cytosolic RBC lesions. CONCLUSIONS AND CLINICAL RELEVANCE: Gamma irradiation and subsequent ex vivo storage according to the European CE guidelines were found to affect RBC protein structures. The validated marker proteins can serve as a basis for the development of a screening assay to monitor the quality of irradiated RBC concentrates during ex vivo storage. This article is protected by copyright. All rights reserved.
  PROTEOMICS - CLINICAL APPLICATIONS 05/2013;
• Article: Proteomics of plaques and novel sources of potential biomarkers for atherosclerosis.

  Onno B Bleijerveld, Ya-Nan Zhang, Serap Beldar, Imo E Hoefer, Siu K Sze, Gerard Pasterkamp, Dominique P V de Kleijn
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  ABSTRACT: Cardiovascular disease (CVD) is the leading cause of death and loss of productive life years in the world. The underlying syndrome of CVD, atherosclerosis, is a complex disease process which involves lipid metabolism, inflammation, innate and adaptive immunity, and many other pathophysiological aspects. Furthermore, CVD is influenced by genetic as well as environmental factors. Early detection of CVD and identification of patients at risk are crucial to reduce the burden of disease and to allow personalized treatment. As established risk factors fail to accurately predict which part of the population is likely to suffer from the disease, novel biomarkers are urgently needed. Proteomics can play a significant role in identifying these biomarkers. In this review, we describe the progress made in proteome profiling of the atherosclerotic plaque and several novel sources of potential biomarkers, including circulating cells and plasma extracellular vesicles (PEV). The importance of longitudinal biobanking in biomarker discovery is highlighted and exemplified by several plaque proteins identified in the biobank study Athero-Express. Finally, we discuss the post-translational modifications of proteins that are involved in atherosclerosis, which may become one of the foci in the ongoing quest for biomarkers through proteomics of plaque and other matrices relevant to the progression of atherosclerosis. This article is protected by copyright. All rights reserved.
  PROTEOMICS - CLINICAL APPLICATIONS 05/2013;
• Article: Enrichment strategies in glycomics based lung cancer biomarker development.

  L Renee Ruhaak, Uyen Thao Nguyen, Carol Stroble, Sandra L Taylor, Ayumu Taguchi, Samir M Hanash, Carlito B Lebrilla, Kyoungmi Kim, Suzanne Miyamoto
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  ABSTRACT: PURPOSE: There is a need to identify better glycan biomarkers for diagnosis, early detection and treatment monitoring in lung cancer using biofluids such as blood. Biofluids are complex mixtures of proteins dominated by a few high abundance proteins that may not have specificity for lung cancer. Therefore two methods for protein enrichment were evaluated; affinity capturing of IgG and enrichment of medium abundance proteins, thus allowing us to determine which method yields the best candidate glycan biomarkers for lung cancer. EXPERIMENTAL DESIGN: N-glycans isolated from plasma samples from 20 cases of lung adenocarcinoma and 20 matched controls were analyzed using nLC-PGC-chip-TOF-MS. N-glycan profiles were obtained for five different fractions: total plasma, isolated IgG, IgG depleted plasma, and the bound and flow-through fractions of protein enrichment. RESULTS: Four glycans differed significantly (FDR<0.05) between cases and controls in whole unfractionated plasma, while four other glycans differed significantly by cancer status in the IgG fraction. No significant glycan differences were observed in the other fractions. CONCLUSIONS AND CLINICAL RELEVANCE: These results confirm that the N-glycan profile in plasma of lung cancer patients is different from healthy controls and appears to be dominated by alterations in relatively abundant proteins. This article is protected by copyright. All rights reserved.
  PROTEOMICS - CLINICAL APPLICATIONS 05/2013;
• Article: Reconstruction of a robust glycodiagnostic agent supported by multiple lectin-assisted glycan profiling.

  Atsushi Kuno, Takashi Sato, Hiroko Shimazaki, Sachiko Unno, Kozue Saitou, Katsue Kiyohara, Maki Sogabe, Chikayuki Tsuruno, Youichi Takahama, Yuzuru Ikehara, Hisashi Narimatsu
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  ABSTRACT: Purpose: Wisteria floribunda agglutinin-positive human Mac-2 binding protein (WFA(+) -hM2BP) was recently validated as a liver fibrosis glycobiomarker with a fully automated lectin-antibody sandwich immunoassay. In this study, we supplied recombinant WFA(+) -hM2BP as the standard glycoprotein and the overlaid antibody to enhance the robustness of WFA(+) -hM2BP quantification. Experimental design: The optimum conditions for producing recombinant WFA(+) -hM2BP were selected by cell glycome analysis based on a lectin microarray. Interlot variability of recombinant WFA(+) -hM2BP was determined using an antibody-overlay lectin microarray. Screening of anti-M2BP monoclonal antibody was completed by incorporating a WFA-antibody sandwich ELISA and an antibody-overlay lectin microarray. Results: The lectin microarray analysis revealed that human embryonic kidney 293 (HEK293) cells efficiently and stably produced WFA(+) -hM2BP in DMEM containing 10% FCS without any lot variation in the M2BP glycosylation level. A spiking experiment with recombinant WFA(+) -hM2BP was mostly effective for antibody screening. The reconstituted sandwich immunoassay was useful for the continuous quantification and cutoff index (COI) expression of serum WFA(+) -hM2BP. Conclusions and clinical relevance: The multiple use of lectin-assisted glycan profiling enabled us to construct a reliable sandwich assay kit for monitoring liver fibrosis in patients with viral hepatitis. This will assist in the development pipeline for other glycodiagnostic agents. This article is protected by copyright. All rights reserved.
  PROTEOMICS - CLINICAL APPLICATIONS 05/2013;
• Article: Glycoproteomic strategies: from discovery to clinical application of cancer carbohydrate biomarkers.

  Koji Ueda
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  ABSTRACT: Carbohydrate antigens are the most frequently and traditionally used biomarkers for cancer, such as CA19-9, CA125, DUPAN-II, AFP-L3, and many others. The diagnostic potential of them was simply based on the cancer-specific alterations of glycan structures on particular glycoproteins in serum/plasma. In spite of the facts that glycosylation disorders are feasible for cancer biomarkers and glycomic analysis technologies to explore them have been rapidly developed, it remains difficult to sensitively screen glycan structure changes on cancer-associated glycoproteins from clinical specimens. Moreover a lot of additional issues should be appropriately addressed for the clinical application of newly identified glycosylation biomarkers, including analytical throughput, quantitative confirmation of structural changes, and biological explanation for the alterations. In the last decade, significant improvement of mass spectrometric techniques is being made in the aspects of both hardware spec and pre-analytical purification procedures for glycoprotein analysis. Here we review potential approaches to perform comprehensive analysis of glycoproteomic biomarker screening from serum/plasma and to realize high throughput validation of site-specific oligosaccharide variations. The power and problems of mass spectrometric applications on the clinical use of carbohydrate biomarkers are also discussed in this review. This article is protected by copyright. All rights reserved.
  PROTEOMICS - CLINICAL APPLICATIONS 05/2013;
• Article: O-GlcNAcomics - Revealing Roles of O-GlcNAcylation in Disease Mechanisms and Development of Potential Diagnostics.

  Ronald J Copeland, Guanghui Han, Gerald W Hart
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  ABSTRACT: O-linked-β-N-acetylglucosamine (O-GlcNAc) is a dynamic post-translational modification of the 3'-hydroxyl groups of serine or threonine residues of nuclear, cytoplasmic, and mitochondrial proteins. The cycling of this modification is regulated in response to nutrients, stress, and other extracellular stimuli by the catalytic activities of O-GlcNAc transferase and O-GlcNAcase. O-GlcNAc is functionally similar to phosphorylation and has been demonstrated to play critical roles in numerous biological processes, including cell signaling, transcription, and disease etiology. Since its discovery nearly thirty years ago, studies have demonstrated that the O-GlcNAc is highly abundant and widespread, like phosphorylation however, the development of methodologies to study O-GlcNAc at the site level has been challenging. Recently, a number of studies have overcome these challenges and describe new tagging, enrichment, and mass spectrometric-based approaches to study O-GlcNAc in terms of its site identification, stoichiometry, and dynamics on proteins. The development of these methods are key for elucidation of O-GlcNAc's functional crosstalk with phosphorylation and other PTMs, and will serve to provide the necessary information for the development of site-specific antibodies, which will aid in the determination of a particular protein's site specific function. In this review, we describe these methods and summarize results obtained from them demonstrating the roles of O-GlcNAc in diabetes, cancer, Alzheimer's, and in learning and memory, while also describing how these new strategies have implicated O-GlcNAc as a potential diagnostic for the screening of patients for prediabetes. This article is protected by copyright. All rights reserved.
  PROTEOMICS - CLINICAL APPLICATIONS 05/2013;
• Article: Viewpoints in clinical proteomics - bringing proteomics into the clinic: The need for the field to finally take itself seriously.

  Lennart Martens
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  ABSTRACT: Proteomics has fast become a standard tool in the life sciences, with increasingly sophisticated approaches and instruments delivering ever growing numbers of identified and quantified proteins. Yet despite the enormous technological progress, and the triumphant papers published on whole-cell proteomes being collected and analyzed, proteomics has so far failed to enter the clinic for routine applications. This is a peculiar contradiction, and one that warrants some closer study. I here argue that for proteomics to make a difference in the clinic, it needs to stop shirking responsibility, and to mature into an analytical, transparent and reproducible discipline that also invests in the consolidation of its technology rather than only focusing on the next big leap forward. A key enabling factor in this maturation process is quality control and quality assurance, with bioinformatics, in its least noticeable but most influential form, as a key underlying technology. This article is protected by copyright. All rights reserved.
  PROTEOMICS - CLINICAL APPLICATIONS 05/2013;
• Article: Comparative mitochondrial proteomic analysis of hepatocellular carcinoma from patients.

  Yunbin Ye, Aimin Huang, Chuanzhong Huang, Jingfeng Liu, Bin Wang, Kecan Lin, Qiang Chen, Yongyi Zeng, Huijing Chen, Xuan Tao, Guangya Wei, Yanbin Wu
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  ABSTRACT: PURPOSE: To define mitochondrial protein markers related to liver cancer. EXPERIMENTAL DESIGN: Mitochondrial sub-proteomes of 20 patient-derived liver carcinoma and tumor-free control tissues were performed by two-dimensional electrophoresis (2-DE) coupled with MALDI-TOF/TOF. The altered patterns of three identified proteins were validated by Western blot and immunohistochemistry. RESULTS: The results showed that compared with tumor-free control samples, nine proteins were down-regulated and six proteins were up-regulated in carcinoma samples. The increased expression of Arg1 mRNA and protein was validated by Western blot, Q-RT-PCR, paraffin tissue microarray and immunohistochemistry. Furthermore, a literature review shows that 10-kDa heat shock protein (Hsp10), single-stranded DNA-binding protein (SSBP1), and peptidyl-prolyl cis-trans isomerase A (PPIA), which were identified as being increased in the tumor samples in this study, may be closely related to protein folding and translation. CONCLUSIONS AND CLINICAL RELEVANCE: These results show that in addition to changes in the signaling pathways, such as the Ras-Raf-MEK-ERK pathway, altered mitochondrial DNA replication and protein folding in liver cancer are also worth studying further. Collectively, these results suggest that specific mitochondrial proteins are uniquely susceptible to alterations in expression and carry implications for the investigation of their potential as therapeutic and prognostic markers. Further studies focusing on these proteins will be used to predict treatment response and reverse the apoptosis resistance.
  PROTEOMICS - CLINICAL APPLICATIONS 04/2013;
• Article: Proteomic analyses of serous and endometrioid epithelial ovarian cancers: cases studies :molecular insights of a possible histological etiology of serous ovarian cancer.

  Rémi Longuespée, Hugo Gagnon, Charlotte Boyon, Kurstin Strupat, Claire Dauly, Olivier Kerdraon, Adesuwa Ighodaro, Annie Desmons, Jocelyn Dupuis, Maxence Wisztorski, Denis Vinatier, Isabelle Fournier, Robert Day, Michel Salzet
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  ABSTRACT: PURPOSE: Epithelial ovarian carcinogenesis may occur de novo on the surface of ovarian mesothelial epithelial cells or from cells originating in other organs. Foreign müllerian cell intrusion into the ovarian environment has been hypothesized to explain the latter scenario. In this study, MALDI mass spectrometry (MS) profiling technology was used to provide molecular insights regarding these potentially different mechanisms EXPERIMENTAL DESIGN: Using MALDI MS profiling, the molecular disease signatures were established in their molecular context. MALDI MS profiling was used on serous and endometrioid cancer biopsies to investigate cases of epithelial ovarian cancer. We then applied bioinformatic methods and identification strategies on the LC-MS/MS analyses of extracts from digested FFPE tissues. Extracts from selected regions (i.e., serous ovarian adenocarcinoma, fallopian tube serous adenocarcinoma, endometrioid ovarian cancer, benign endometrium and benign ovarian tissues) were performed, and peptide digests were subjected to LC-MS/MS analysis. RESULTS: Comparison of the proteins identified from benign endometrium or three ovarian cancer types (i.e., serous ovarian adenocarcinoma, endometrioid ovarian adenocarcinoma and serous fallopian tube adenocarcinoma) provided new evidence of a possible correlation between the fallopian tubes and serous ovarian adenocarcinoma. Here, we propose a workflow consisting of the comparison of multiple tissues in their anatomical context in an individual patient. CONCLUSION AND CLINICAL RELEVANCE: The present study provides new insights into the molecular similarities between these two tissues and an assessment of highly specific markers for an individualized patient diagnosis and care.
  PROTEOMICS - CLINICAL APPLICATIONS 04/2013;
• Article: Using proteomics to uncover extracellular matrix interactions during cardiac remodeling.

  Nicolle L Patterson, Rugmani Padmanabhan Iyer, Lisandra De Castro Bras, Yaojun Li, Thomas G Andrews, Gregory J Aune, Richard A Lange, Merry L Lindsey
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  ABSTRACT: The left ventricle (LV) responds to a myocardial infarction (MI) with an orchestrated sequence of events that results in fundamental changes to both the structure and function of the myocardium. This collection of responses is termed LV remodeling. Myocardial ischemia resulting in necrosis is the initiating event that culminates in the formation of an extracellular matrix (ECM)-rich infarct scar that replaces necrotic myocytes. While the cardiomyocyte is the major cell type that responds to ischemia, infiltrating leukocytes and cardiac fibroblasts coordinate the subsequent wound healing response. The matrix metalloproteinase (MMP) family of enzymes regulates the inflammatory and ECM responses that modulate scar formation. Matridomics is the proteomic evaluation focused on ECM, while degradomics is the proteomic evaluation of proteases as well as their inhibitors and substrates. This review will summarize the use of proteomics to better understand MMP roles in post-MI LV remodeling.
  PROTEOMICS - CLINICAL APPLICATIONS 03/2013;
• Article: Network views for personalized medicine.

  Antonia Vlahou
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  ABSTRACT: Clinical Proteomics has traveled long way pinpointing potential biomarkers for a variety of diseases. However, the absence of clinical implementation of proteomics findings has led to a frank evaluation and re-consideration of applied practices in biomarker discovery, recruitment of technological tools for biomarker verification and generation of new guidelines for data reporting. Nevertheless, considering the need for vast clinical resources for biomarker validation, the frequent lack of clear definitions of contexts of use, in combination to the biomarker "high offer", progress towards biomarker implementation will even more require the adoption of an extensive open-minded approach: disease-focused networks are needed to ensure rapid exchange of information, initiation of appropriate studies, parallel validation of multiple biomarkers and sharing of valuable clinical resources. This viewpoint article targets to reflect on these issues and advocates the added value of multi-disciplinary networks in biomarker development using bladder cancer as a paradigm.
  PROTEOMICS - CLINICAL APPLICATIONS 03/2013;
• Article: Shotgun proteomics of archival triple-negative breast cancer samples.

  Angelo Gámez-Pozo, Nuria Ibarz Ferrer, Eva Ciruelos, Rocío López-Vacas, Fernando García Martínez, Enrique Espinosa, Juan Ángel Fresno Vara
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  ABSTRACT: PURPOSE: Triple-negative breast cancer (TNBC) accounts for 15-20% of all breast cancers, and has a worse prognosis compared with hormone receptor-positive disease. Its unfavorable outcome and the lack of hormonal receptors determine the use of adjuvant chemotherapy as part of the standard treatment for these tumors, although several studies have documented that the current standard combination chemotherapy is suboptimal. Therefore, a new functional taxonomy of breast cancer and new targets for therapeutic development are urgently needed. EXPERIMENTAL DESIGN: In this study, we have analyzed the proteome of TNBC applying a high-throughput proteomics approach to routinely archived formalin-fixed, paraffin-embedded tumor tissues. RESULTS: We have been able to identify and quantify more than 1000 protein groups. Some of these proteins are of outstanding interest in the biology and clinical management of this disease, such as CD44 and PARP1. Moreover, we have characterized some signaling pathways that could be related to TNBC genesis and development. CONCLUSION AND CLINICAL RELEVANCE: Our results open up new avenues for the use of proteomics technologies in clinically relevant studies using archival samples. Shotgun LC-MS/MS studies could serve to discover new biomarkers and may provide clues to the genesis of TNBC and underlying molecular alterations.
  PROTEOMICS - CLINICAL APPLICATIONS 02/2013;
• Article: Application of chromosomal DNA and protein targeting for the identification of Yersinia pestis.

  Marilynn A Larson, Shi-Jian Ding, Shawn R Slater, Anna Hanway, Amanda M Bartling, Paul D Fey, Oksana Lockridge, Stephen C Francesconi, Steven H Hinrichs
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  ABSTRACT: PURPOSE: A comprehensive strategy was developed and validated for the identification of pathogens from closely-related near neighbors using both chromosomal and protein biomarkers, with emphasis on distinguishing Yersinia pestis from the ancestral bacterium Yersinia pseudotuberculosis. EXPERIMENTAL DESIGN: Computational analysis was used to discover chromosomal targets unique to Y. pestis. Locus identifier YPO1670 was selected for further validation and PCR was used to confirm that this biomarker was exclusively present in Y. pestis strains, while absent in other Yersinia species. RT-PCR and western blot analyses were utilized to evaluate YPO1670 expression and multiple-reaction monitoring mass spectrometry (MRM MS) was performed to identify the YPO1670 protein within cell lysates. RESULTS: The described study validated that YPO1670 was exclusive to Y. pestis. PCR confirmed the locus to be unique to Y. pestis. The associated transcript and protein were produced throughout growth with the highest abundance occurring in stationary phase and MRM MS conclusively identified the YPO1670 protein in cell extracts. CONCLUSIONS AND CLINICAL RELEVANCE: These findings validated YPO1670 as a reliable candidate biomarker for Y. pestis and that a dual DNA and protein targeting approach is feasible for the development of next generation assays to accurately differentiate pathogens from near neighbors.
  PROTEOMICS - CLINICAL APPLICATIONS 02/2013;
• Article: Proteomic analysis of the aqueous humor in patients with wet age-related macular degeneration.

  Jiaqi Yao, Xiaoyi Liu, Qin Yang, Min Zhuang, Feng Wang, Xi Chen, Hui Hang, Weiwei Zhang, Qinghuai Liu
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  ABSTRACT: PURPOSE: A number of studies have shown that the levels of some proteins in the aqueous humor (AH) are altered and correlate with the mechanisms or prognosis of many eye diseases. To identify the possible mechanisms that lead to the development of wet age-related macular degeneration (AMD), a proteomic analysis of the AH composition from wet AMD patients was performed and compared with that from non-AMD cataract patients. EXPERIMENTAL DESIGN: Six wet AMD and 6 non-AMD cataract patients were enrolled. A proteomic approach which included two-dimensional electrophoresis (2-DE) coupled with mass spectrometry and bioinformatics methods were used to identify AH proteins with altered expression in wet AMD compared with non-AMD patients. An enzyme-linked immunosorbent assay was used to validate the proteomic results. RESULTS: We separated 78 protein spots and identified 68 that were differently expressed in the wet AMD group and controls. Numerous proteins identified in this study are implicated in inflammation, apoptosis, angiogenesis and oxidative stress. CONCLUSIONS AND CLINICAL RELEVANCE: The AH protein composition was significantly different between wet AMD and non-AMD patients. The proteins identified in this study may be potential biomarkers of wet AMD development and might play a role in the mechanisms of wet AMD.
  PROTEOMICS - CLINICAL APPLICATIONS 02/2013;
• Article: Proteomic profiling of the autoimmune response to breast cancer antigens uncovers a suppressive effect of hormone therapy.

  Timothy Chao, Jon J Ladd, Ji Qiu, Melissa M Johnson, Rebecca Israel, Alice Chin, Hong Wang, Ross L Prentice, Ziding Feng, Mary L Disis, Samir Hanash
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  ABSTRACT: PURPOSE: Proteomics technologies are well suited for harnessing the immune response to tumor antigens for diagnostic applications as in the case of breast cancer. We previously reported a substantial impact of hormone therapy (HT) on the proteome. Here we investigated the effect of HT on the immune response toward breast tumor antigens. EXPERIMENTAL DESIGN: Plasmas collected 0-10 months prior to diagnosis of ER+ breast cancer from 190 post-menopausal women and 190 controls that participated in the Women's Health Initiative (WHI) Observational Study were analyzed for the effect of HT on IgG reactivity against arrayed proteins from MCF-7 or SKBR3 breast cancer cell line lysates following extensive fractionation. RESULTS: HT user cases exhibited significantly reduced autoantibody reactivity against arrayed proteins compared to cases who were not current users. An associated reduced level of IL-6 and other immune-related cytokines was observed among HT users relative to non-users. CONCLUSION AND CLINICAL RELEVANCE: Our findings suggest occurrence of a global altered immune response to breast cancer derived proteins associated with HT. Thus a full understanding of factors that modulate the immune response is necessary to translate autoantibody panels into clinical applications.
  PROTEOMICS - CLINICAL APPLICATIONS 02/2013;
• Article: Serum fibrinogen alpha C-chain 5.9 kDa fragment (FIC 5.9) as a biomarker for early detection of hepatic fibrosis related to hepatitis C virus.

  Kazuyuki Sogawa, Kenta Noda, Hiroshi Umemura, Masanori Seimiya, Takahisa Kuga, Takeshi Tomonaga, Motoi Nishimura, Fumihiko Kanai, Fumio Imazeki, Hirotaka Takizawa, Masato Yoneda, Atsushi Nakajima, Mikihiro Tsutsumi, Osamu Yokosuka, Fumio Nomura
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  ABSTRACT: PURPOSE: Clinical application of biomarker candidates discovered by proteomic analysis is challenging. The purpose of this study was to standardize preanalytical conditions for measurement of serum levels of fibrinogen alpha C-chain 5.9 kDa fragment (FIC 5.9) and to test the diagnostic value of this peptide for detection of early hepatic fibrosis in patients with hepatitis C virus (HCV)-related chronic hepatitis. EXPERIMENTAL DESIGN: Serum FIC5.9 levels were measured by a sandwich ELISA. Effects on the serum FIC5.9 level of temperature, the time between venipuncture and serum separation, and the types of collection tubes used were examined. The diagnostic value of serum FIC 5.9 as an early indicator of hepatic fibrosis due to HCV was then assessed. RESULTS: FIC 5.9 was produced in a time- and temperature-dependent manner after venipuncture. Abnormal FIC 5.9 values were found in 89.5% of FI stage patients. ROC analyses confirmed the superiority of FIC 5.9 over other conventional markers for early detection of fibrosis. CONCLUSIONS AND CLINICAL RELEVANCE: The serum FIC 5.9 level may be an early indicator of hepatic fibrosis in HCV-related chronic liver diseases. This study provides an example of a pipeline from biomarker discovery by proteome analysis to assay optimization and preliminary clinical validation.
  PROTEOMICS - CLINICAL APPLICATIONS 02/2013;
• Article: Proteomic Patterns of Colonic Mucosal and Submucosal Tissues Delineates Crohn's Colitis and Ulcerative Colitis.

  Michael W Schäffer, Erin H Seeley, Joan C Smith, Roberta L Muldoon, Roger K Moreira, Purva P Gopal, William V Chopp, Mary K Washington, Duane T Smoot, Harold L Moses, Billy R Ballard, Alan J Herline, Richard M Caprioli, Samuel E Adunyah, Amosy E M'koma
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  ABSTRACT: PURPOSE: Although Crohn's colitis (CC) and ulcerative colitis (UC) share several clinical features, they have different causes, mechanisms of tissue damage, and treatment options. Therefore, the accurate diagnosis is of paramount importance in terms of medical care. The distinction between UC/CC is made on the basis of clinical, radiologic, endoscopic, and pathologic interpretations but cannot be differentiated in up to 15% of IBD patients. Correct management of this "indeterminate colitis" (IC) depends on the accuracy of future, and yet not known, destination diagnosis (CC or UC). EXPERIMENTAL DESIGN: We have developed a proteomic methodology that has the potential to discriminate between UC/CC. The histologic layers of 99-confirmed UC/CC tissues were analyzed using MALDI-MS for proteomic profiling. RESULTS: Eight-protein-signatures differentiated UC/CC. These signals are independent of the tissue of origin and represent potential disease specific markers. Some of these signatures are primarily found in the colonic mucosa (mz 8413, 3666 and 3595) and would be amenable to proteomic interrogation from endoscopic biopsies. Others are primarily submucosal (mz 4122 and 8774) and have the potential to become amenable to proteomic studies in the serum. Some protein-signatures (mz 5045, 6139 and 9245) were found in both two layers. CONCLUSION/CLINICAL RELEVANCE: This information may provide new-avenues for the development of novel evidenced personalized therapeutic targets.
  PROTEOMICS - CLINICAL APPLICATIONS 02/2013;