共查询到20条相似文献，搜索用时 15 毫秒
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Valérie Broeckx Lise Peeters Evelyne Maes Lentel Pringels Eddy-Tim Verjans Bart Landuyt 《Proteomics. Clinical applications》2014,8(9-10):735-736
Tissue is the most relevant biological material to gather insight in disease mechanisms by means of omics technologies. However, fresh frozen tissue, which is generally regarded as the best imaginable source for such studies, is often not available. In case it is available, the different ways of storage (e.g. −20°C, −80°C, liquid nitrogen, etc.) hamper the conduction of reproducible multicenter studies because of different protein degradation rates. Formalin-fixed paraffin-embedded (FFPE) tissue on the contrary is considered as a valuable alternative for fresh frozen tissue, because only a few standard operation procedures are applied worldwide for the preparation of these tissues and because they are all stored in the same way. However, a study on the impact of the different preparation protocols for FFPE tissue was still lacking. Therefore, Bronsert et al. in this issue [Bronsert, P., Weißer, J., Biniossek, M. L., Kuehs, M. et al., Proteomics Clin. Appl. 2014, 8 786–804] conducted such a study that provides proof that there is no significant effect between these sample preparations procedures, and thereby they further open the gate for FFPE tissues to enter the field of clinical proteomics. 相似文献
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Aggeliki Kolialexi Danai Mavreli Georgia Tounta Ariadni Mavrou Nikolas Papantoniou 《Proteomics. Clinical applications》2015,9(5-6):501-506
Preeclampsia (PE) is a multisystem disorder of pregnancy that develops after 20 wk of gestation in previously normotensive women and complicates 5–8% of pregnancies. This rapidly progressive syndrome is usually diagnosed when the mother develops hypertension and proteinuria. The only effective treatment is delivery of the baby although early low-dose aspirin has been shown to significantly reduce the risk for PE. Recent advances in proteomic methods of protein separation, identification, and quantitation may allow for the identification of proteins and peptides that could facilitate early detection of disease, improve assessment of prognosis, and allow closer monitoring of women at risk for PE. This review summarizes all currently available markers for prediction and diagnosis of PE and presents urine proteomic studies performed for the identification of novel biomarkers. 相似文献
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Proteomics is a rapidly evolving ‘‘post-genomic’’ science utilizing advanced technologies in protein separation, identification, quantitation and heavily relying on bioinformatics. Proteomic research in pediatrics is important and most of the successes thus far are seen in research that utilize samples that require less invasive procedures and focus on prevailing childhood diseases such as acute lymphoblastic leukaemia and neuroblastoma. Recent advances in proteomics are helping to elucidate platelet processes that are relevant to bleeding and clotting disorders, as well as other important roles of platelets such as in angiogenesis and inflammation. Nevertheless, most of platelet proteome data obtained to date are derived from the adult population and the potential of platelet proteomic application in children has not yet been explored. As it happens in all research fields, there are additional challenges in studying children such as procuring sufficient biological samples and access to less common disease cohorts as compared to in adults. Furthermore, many of the prevalent platelet-mediated diseases in adults, such as coronary heart disease and atherosclerotic lesions, are believed to have origins during childhood. Hence, platelet proteomic research in children may reveal some important information on how platelet plays a role in the pathogenesis of disease. In this article, we refer to the current knowledge from platelet proteomic research strategies in adults and address the specific concerns in the study of pediatric samples. 相似文献
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Judy Gopal Manikandan Muthu Se-Chul Chun Hui-Fen Wu 《Proteomics. Clinical applications》2015,9(5-6):469-481
Urine proteomics has become a subject of interest, since it has led to a number of breakthroughs in disease diagnostics. Urine contains information not only from the kidney and the urinary tract but also from other organs, thus urinary proteome analysis allows for identification of biomarkers for both urogenital and systemic diseases. The following review gives a brief overview of the analytical techniques that have been in practice for urinary proteomics. MALDI-MS technique and its current application status in this area of clinical research have been discussed. The review comments on the challenges facing the conventional MALDI-MS technique and the upgradation of this technique with the introduction of nanotechnology. This review projects nano-based techniques such as nano-MALDI-MS, surface-assisted laser desorption/ionization, and nanostructure-initiator MS as the platforms that have the potential in trafficking MALDI-MS from the lab to the bedside. 相似文献
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Tara K. Sigdel Amit Kaushal Marina Gritsenko Angela D. Norbeck Wei‐Jun Qian Wenzhong Xiao David G. Camp II Richard D. Smith Minnie M. Sarwal 《Proteomics. Clinical applications》2010,4(1):32-47
Purpose: Acute rejection (AR) remains the primary risk factor for renal transplant outcome; development of non‐invasive diagnostic biomarkers for AR is an unmet need. Experimental design: We used shotgun proteomics applying LC‐MS/MS and ELISA to analyze a set of 92 urine samples, from patients with AR, stable grafts (STA), proteinuria (NS), and healthy controls. Results: A total of 1446 urinary proteins (UP) were identified along with a number of non‐specific proteinuria‐specific, renal transplantation specific and AR‐specific proteins. Relative abundance of identified UP was measured by protein‐level spectral counts adopting a weighted fold‐change statistic, assigning increased weight for more frequently observed proteins. We have identified alterations in a number of specific UP in AR, primarily relating to MHC antigens, the complement cascade and extra‐cellular matrix proteins. A subset of proteins (uromodulin, SERPINF1 and CD44), have been further cross‐validated by ELISA in an independent set of urine samples, for significant differences in the abundance of these UP in AR. Conclusions and clinical relevance: This label‐free, semi‐quantitative approach for sampling the urinary proteome in normal and disease states provides a robust and sensitive method for detection of UP for serial, non‐invasive clinical monitoring for graft rejection after kidney transplantation. 相似文献
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Daniel S. Spellman Kristin R. Wildsmith Lee A. Honigberg Marianne Tuefferd David Baker Nandini Raghavan Angus C. Nairn Pascal Croteau Michael Schirm Rene Allard Julie Lamontagne Daniel Chelsky Steven Hoffmann William Z. Potter Alzheimer's Disease Neuroimaging Initiative the Foundation for NIH Biomarkers Consortium CSF Proteomics Project Team 《Proteomics. Clinical applications》2015,9(7-8):715-731
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Globozoospermia is a form of teratozoospermia characterized by round‐headed spermatozoa and lack of acrosome. These spermatozoa cannot penetrate the zona pellucida of the oocyte, resulting in unsuccessful fertilization and infertility. When intracytoplasmic sperm injection is performed, the fertilization rate tends to be low. Until now, the causes of this disorder remain to be elucidated; however, mutations of some genes segregating on an autosomal recessive mode have been associated with this infertile condition. DPY19L2 (dpy‐19‐like 2 [Caenorhabditis elegans]) codes for a transmembrane protein expressed predominantly in spermatids, with specific localization limited to the internal nuclear membrane. Genetic defects in the DPY19L2 gene have been demonstrated the most frequent genetic cause of globozoospermia; however, intracellular molecular pathways related to its encoded protein are largely unknown. In this issue of Proteomics Clinical Applications, Guo and co‐workers investigate the proteome of gloobozoospermic spermatozoa. The authors identified 491 proteins that are differentially expressed in globozoospermia (370 are upregulated and 121 are downregulated in DPY19L2‐deficient globozoospermic sperm). Notably, the molecular defects identified by the authors are closely related to biological processes involved in acrosome formation, chromatin composition, sperm‐egg binding, and fertilization. 相似文献
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Dong-Sic Choi 《Proteomics. Clinical applications》2015,9(5-6):447-448
Extracellular vesicles (EVs) are bilayered lipid vesicles, 50–1000 nm in diameter and secreted by most types of cells. They contain many proteins, mRNAs, miRNAs, and lipids that reflect the pathophysiological state of the cells they originate from, and are therefore considered to be a rich source of potential biomarkers. In this issue (Pocsfalvi, G. et al., Proteomics Clin. Appl. 2015, 9, 552–567), Pocsfalvi et al. conducted pioneering investigations to determine whether changes in the protein content of EVs occur during progression of autosomal dominant polycystic kidney disease (ADPKD), a common genetic disorder that predominantly affects the kidneys. Most significantly, iTRAQ-based quantitative proteomics showed that cytoskeleton-regulating and Ca2+-binding proteins are differentially expressed in urinary EVs of ADPKD patients. Impressively, these proteins are involved in biological processes that are closely related to the pathogenic state of tubular epithelial cells in ADPKD, demonstrating the possibility to monitor the status of patients using urinary EVs. 相似文献
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Bao H Song P Liu Q Liu Y Yun D Saiyin H Du R Zhang Y Fan H Yang P Chen X 《Proteomics. Clinical applications》2009,3(6):705-719
To comprehensively measure global changes in protein expression associated with human hepatocellular carcinoma (HCC), comparative proteomic analysis of two cell lines derived from the healthy and carcinoma tissue of a same donor respectively was conducted using quantitative amino acid-coded mass tagging /stable isotope labeling with amino acids in cell culture-based LC-MS/MS approach. Among a total of 501 proteins precisely quantified, the expressions of 128 proteins were significantly altered including 70 proteins up-regulated and 58 down-regulated in HCC cells. According to their previously characterized functions, the differentially expressed proteins were found associated with nine functional categories including glycolysis, stress response, cell communication, cell cycle, apoptosis/death, etc. For example, multiple enzymes involving glycolysis pathway were found differentially regulated in HCC cells, illustrating the critical participation of glycolysis in the HCC transformation. The accuracy of certain differentially expressed proteins identified through the amino acid-coded mass tagging-based quantification was validated in the paired cell lines, and later their pathological correlations were examined in multiple clinical pairs of normal versus tumor tissues from HCC specimen by using a variety of biological approaches including Western blotting and in situ immunoassays. These consistencies suggested that multiple proteins such as HSP27, annexin V, glyceraldehyde-3-phosphate dehydrogenase, nucleolin and elongation factor Tu could be the biomarkers candidates for diagnosis of HCC. 相似文献
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Keith Ho Qing Xiao Estelle M. Fach Jeffrey D. Hulmes Deidra Bethea Gregory J. Opiteck Joseph Y. Lu Paul S. Kayne Stanley A. Hefta 《Journal of The Association for Laboratory Automation》2004,9(4):238-249
The discovery of new biomarkers will be an essential step to enhance our ability to better diagnose and treat human disease. The proteomics research community has recently increased its use of human blood (plasma/serum) as a sample source for these discoveries. However, while blood is fairly non-invasive and readily available as a specimen, it is not easily analyzed by liquid chromatography (LC)/mass spectrometry (MS), because of its complexity. Therefore, sample preparation is a crucial step prior to the analysis of blood. This sample preparation must also be standardized in order to gain the most information from these valuable samples and to ensure reproducibility. We have designed a semi-automated and highly parallel procedure for the preparation of human plasma samples. Our process takes the samples through eight successive steps before analysis by LC/MS: (1) receipt, (2) reformatting, (3) filtration, (4) depletion, (5) concentration determination and normalization, (6) digestion, (7) extraction, and (8) randomization, triplication, and lyophilization. These steps utilize a number of different liquid handlers and liquid chromatography (LC) systems. This process enhances our ability to discover new biomarkers from human plasma. 相似文献
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Kelly L. Wormwood Roshanak Aslebagh Devika Channaveerappa Emmalyn J Dupree Megan M. Borland Jeanne P. Ryan Costel C. Darie Alisa G. Woods 《Proteomics. Clinical applications》2015,9(9-10):899-906
Biomarkers are greatly needed in the fields of neurology and psychiatry, to provide objective and earlier diagnoses of CNS conditions. Proteomics and other omics MS-based technologies are tools currently being utilized in much recent CNS research. Saliva is an interesting alternative biomaterial for the proteomic study of CNS disorders, with several advantages. Collection is noninvasive and saliva has many proteins. It is easier to collect than blood and can be collected by professionals without formal medical training. For psychiatric and neurological patients, supplying a saliva sample is less anxiety-provoking than providing a blood sample, and is less embarrassing than producing a urine specimen. The use of saliva as a biomaterial has been researched for the diagnosis of and greater understanding of several CNS conditions, including neurodegenerative diseases, autism, and depression. Salivary biomarkers could be used to rule out nonpsychiatric conditions that are often mistaken for psychiatric/neurological conditions, such as fibromyalgia, and potentially to assess cognitive ability in individuals with compromised brain function. As MS and omics technology advances, the sensitivity and utility of assessing CNS conditions using distal human biomaterials such as saliva is becoming increasingly possible. 相似文献
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A principal task in dissecting the genetics of complex traits is to identify causal genes for disease phenotypes. Millions of genes have been sequenced in data-driven genomics era, but their causal relationships with disease phenotypes remain limited, due to the difficulty of elucidating underlying causal genes by laboratory-based strategies. Here, we proposed an innovative deep learning computational modeling alternative (DPPCG framework) for identifying causal (coding) genes for a specific disease phenotype. In terms of male infertility, we introduced proteins as intermediate cell variables, leveraging integrated deep knowledge representations (Word2vec, ProtVec, Node2vec, and Space2vec) quantitatively represented as ‘protein deep profiles’. We adopted deep convolutional neural network (CNN) classifier to model protein deep profiles relationships with male infertility, creatively training deep CNN models of single-label binary classification and multi-label eight classification. We demonstrate the capabilities of DPPCG framework by integrating and fully harnessing the utility of heterogeneous biomedical big data, including literature, protein sequences, protein–protein interactions, gene expressions, and gene–phenotype relationships, and effective indirect prediction of 794 causal genes of male infertility and associated pathological processes. We present this research in an interactive ‘Smart Protein’ intelligent (demo) system (http://www.smartprotein.cloud/public/home). Researchers can benefit from our intelligent system by (i) accessing a shallow gene/protein-radar service involving research status and a knowledge graph-based vertical search; (ii) querying and downloading protein deep profile matrices; (iii) accessing intelligent recommendations for causal genes of male infertility and associated pathological processes, and references for model architectures, parameter settings, and training outputs; and (iv) carrying out personalized analysis such as online K-Means clustering. 相似文献
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The application of proteomics in drug development could be a major source of novel biomarkers to improve the efficacy and safety of new drugs. Training of US Food and Drug Administration (FDA) reviewers on current applications of proteomics is important for the future review of proteomic data. A Grand Rounds in Proteomics was held on April 3, 2007 at the FDA in White Oak, Silver Spring, MD, USA. The goal of this activity was to contribute to reviewer training as well as to generate discussions regarding the readiness of proteomic platforms in drug development, similar in scope to applications in genomics and metabolomics. Several speakers from industry and academia presented data on proteomic applications in drug development (meeting agenda available in the Supporting Information). An additional goal of this meeting was to encourage proteomic data submissions within the Voluntary eXploratory Data Submissions (VXDS) at the FDA. VXDS meetings represent key venues for exchange between the FDA and sponsors of scientific and clinical data on exploratory biomarkers. The FDA has received a limited number of VXDS submissions containing proteomic data. This meeting was an opportunity to identify possible areas in proteomics where future VXDS submissions may be received. Voluntary submissions have been transformed into regulatory submissions in genomics, and a similar path may also be followed by proteomic data in the future. Proteomic biomarkers may also be suitable for submission to the Pilot Process for Biomarker Qualification at the FDA. 相似文献
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Samir Hanash 《Proteomics. Clinical applications》2012,6(9-10):443-446
Serum and plasma from which serum is derived represent a substantial challenge for proteomics due to their complexity. A landmark plasma proteome study was initiated a decade ago by the Human Proteome Organization (HUPO) that had as an objective to examine the capabilities of existing technologies. Given the advances in proteomics and the continued interest in the plasma proteome, it would timely reassess the depth and breadth of analysis of plasma that can be achieved with current methodology and instrumentation. A collaborative project to define the plasma proteome and its variation, with a plan to build a plasma proteome database would be timely. 相似文献