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Expert Review of Proteomics

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https://www.readbyqxmd.com/read/28737967/integral-membrane-proteins-bottom-up-top-down-and-structural-proteomics
#1
Upendra Karr, Margaret Simonian, Julian P Whitelegge
Integral membrane proteins and lipids constitute the bilayer membranes that surround cells and sub-cellular compartments, and modulate movements of molecules and information between them. Since membrane protein drug targets represent a disproportionately large segment of the proteome, technical developments need timely review. Areas covered and literature search strategy: Publically available resources such as Pubmed were surveyed. Bottom-up proteomics analyses now allow efficient extraction and digestion such that membrane protein coverage is essentially complete, making up around one third of the proteome...
July 24, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28715921/the-role-of-secreted-heat-shock-protein-90-hsp90-in-wound-healing-how-could-it-shape-future-therapeutics
#2
Jiacong Guo, Cheng Chang, Wei Li
Defects in tissue repair or wound healing pose a clinical, economic and social problem worldwide. Despite decades of studies, there have been few effective therapeutic treatments. Areas covered: We discuss the possible reasons for why growth factor therapy did not succeed. We point out the lack of human disorder-relevant animal models as another blockade for therapeutic development. We summarize the recent discovery of secreted heat shock protein-90 (Hsp90) as a novel wound healing agent. Expert commentary: Wound healing is a highly complex and multistep process that requires participations of many cell types, extracellular matrices and soluble molecules to work together in a spatial and temporal fashion within the wound microenvironment...
July 18, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28695748/proteomic-profiling-of-the-cancer-cell-secretome-informing-clinical-research
#3
Yung-Chin Hsiao, Lichieh Julie Chu, Jen-Ting Chen, Ta-Sen Yeh, Jau-Song Yu
Cancer represents one of the major causes of human deaths. Identification of proteins as biomarkers for early detection of cancer and therapeutic targets for cancer treatment are important issues in precision medicine. Secretome of cancer cells represents the collection of proteins secreted or shed from cancer cells. Proteomic profiling of the cancer cell secretome has been proven to be a convenient and efficient way to discover cancer biomarker and/or therapeutic targets. Areas covered: There have been numerous reviews describing the history and application of secretome analysis in cancer biomarker/therapeutic target research...
July 11, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28693350/proteogenomics-approaches-for-studying-cancer-biology-and-their-potential-in-the-identification-of-acute-myeloid-leukemia-biomarkers
#4
Maria Hernandez-Valladares, Marc Vaudel, Frode Selheim, Frode Berven, Øystein Bruserud
Mass spectrometry (MS)-based proteomics has become an indispensable tool for the characterization of the proteome and its post-translational modifications (PTM). In addition to standard protein sequence databases, proteogenomics strategies search the spectral data against the theoretical spectra obtained from customized protein sequence databases. Up to date, there are no published proteogenomics studies on acute myeloid leukemia (AML) samples. Areas covered: Proteogenomics involves the understanding of genomic and proteomic data...
July 27, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28689450/recent-advances-and-clinical-insights-into-the-use-of-proteomics-in-the-study-of-atherosclerosis
#5
Laura Mourino-Alvarez, Montserrat Baldan-Martin, Raul Rincon, Tatiana Martin-Rojas, Nerea Corbacho-Alonso, Tamara Sastre-Oliva, Maria G Barderas
The application of new proteomics methods may help to identify new diagnostic/predictive molecular markers in an attempt to improve the clinical management of atherosclerosis. Areas covered: Technological advances in proteomics have enhanced its sensitivity and multiplexing capacity, as well as the possibility of studying protein interactions and tissue structure. These advances will help us better understand the molecular mechanisms at play in atherosclerosis as a biological system. Moreover, this should help identify new predictive/diagnostic biomarkers and therapeutic targets that may facilitate effective risk stratification and early diagnosis, with the ensuing rapid implementation of treatment...
July 10, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28689445/abundance-matters-role-of-albumin-in-diabetes-a-proteomics-perspective
#6
Shweta Bhat, Mashanipalya G Jagadeeshaprasad, Vinashya Venkatasubramani, Mahesh J Kulkarni
Human serum albumin (HSA) is a multifaceted protein with vital physiological functions. It is the most abundant plasma protein with inherent capability to bind to diverse ligands, and thus susceptible to various post-translational modifications (PTMs) which alter its structure and functions. One such PTM is glycation, a non-enzymatic reaction between reducing sugar and protein leading to formation of heterogeneous advanced glycation end products (AGEs). Glycated albumin (GA) concentration increases significantly in diabetes and is implicated in development of secondary complications...
July 10, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28635376/advances-in-understanding-the-role-of-disease-associated-proteins-in-spinal-muscular-atrophy
#7
Seyyedmohsen Hosseinibarkooie, Svenja Schneider, Brunhilde Wirth
Spinal muscular atrophy (SMA) is a neurodegenerative disorder characterized by alpha motor neuron loss in the spinal cord due to reduced survival motor neuron (SMN) protein level. While the genetic basis of SMA is well described, the specific molecular pathway underlying SMA is still not fully understood. Areas covered: This review discusses the recent advancements in understanding the molecular pathways in SMA using different omics approaches and genetic modifiers identified in both vertebrate and invertebrate systems...
June 30, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28625086/hepatitis-c-virus-apolipoprotein-interactions-molecular-mechanisms-and-clinical-impact
#8
Emilie Crouchet, Thomas F Baumert, Catherine Schuster
Chronic hepatitis C virus (HCV) infection is a leading cause of cirrhosis, hepatocellular carcinoma and liver failure. Moreover, chronic HCV infection is associated with liver steatosis and metabolic disorders. With 130-150 million people chronically infected in the world, HCV infection represents a major public health problem. One hallmark on the virus is its close link with hepatic lipid and lipoprotein metabolism. Areas covered: HCV is associated with lipoprotein components such as apolipoproteins. These interactions play a key role in the viral life cycle, viral persistence and pathogenesis of liver disease...
June 30, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28649883/middle-down-proteomics-a-still-unexploited-resource-for-chromatin-biology
#9
Simone Sidoli, Benjamin A Garcia
Analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has become a fundamental tool for the characterization of chromatin composition and dynamics. Histone PTMs benchmark several biological states of chromatin, including regions of active enhancers, active/repressed gene promoters and damaged DNA. These complex regulatory mechanisms are often defined by combinatorial histone PTMs; for instance, active enhancers are commonly occupied by both marks H3K4me1 and H3K27ac. The traditional bottom-up MS strategy identifies and quantifies short (aa 4-20) tryptic peptides, and it is thus not suitable for the characterization of combinatorial PTMs...
June 28, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28649880/understanding-type-1-diabetes-through-proteomics
#10
Inne Crèvecoeur, Saurabh Vig, Chantal Mathieu, Lut Overbergh
Auto-immunity against pancreatic beta-cells leads to an absolute shortage of the hormone insulin, resulting in hyperglycemia and the onset of type 1 diabetes (T1D). Proteomic approaches have been used to elucidate the mechanisms of beta-cell dysfunction and death. Areas covered: In the present review, we discuss discoveries in the beta-cell proteome that have contributed to better insights in the role of the beta-cell in T1D. Techniques, such as 2D-DIGE and MALDI imaging, together with new approaches for sample preparation, including laser capture microdissection and immunopeptidomics, have resulted in novel mechanistic insights in the pathogenesis of T1D...
June 28, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28644690/advances-in-the-development-of-human-protein-microarrays
#11
Jessica Duarte, Jonathan M Blackburn
High-content protein microarrays in principle enable the functional interrogation of the human proteome in a broad range of applications, including biomarker discovery, profiling of immune responses, identification of enzyme substrates, and quantifying protein-small molecule, protein-protein and protein-DNA/RNA interactions. As with other microarrays, the underlying proteomic platforms are under active technological development and a range of different protein microarrays are now commercially available. However, deciphering the differences between these platforms to identify the most suitable protein microarray for the specific research question is not always straightforward...
June 23, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28621158/signaling-pathway-profiling-using-reverse-phase-protein-array-and-its-clinical-applications
#12
Mari Masuda, Tesshi Yamada
Increased accessibility to next-generation sequencing within the last decade has led to a paradigm shift in cancer treatment from one-size-fits-all medicine to precision medicine providing therapeutic strategies tailored to the requirements of individual patients. However, the effect of even the most successful agent yet tested is only transient, and durable efficacy has yet to be achieved. Genome- and transcriptome-based approaches cannot fully predict the diversity of protein expression patterns or post-translational modifications that directly contribute to cancer pathogenesis and physiology...
June 22, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28586280/a-decade-of-proteomics-accomplished-central-and-eastern-european-proteomic-conference-ceepc-celebrates-its-10th-anniversary-in-budapest-hungary
#13
Suresh Jivan Gadher, László Drahos, Károly Vékey, Hana Kovarova
The Central and Eastern European Proteomic Conference (CEEPC) proudly celebrated its 10th Anniversary with an exciting scientific program inclusive of proteome, proteomics and systems biology in Budapest, Hungary. Since 2007, CEEPC has represented 'state-of the-art' proteomics in and around Central and Eastern Europe and these series of conferences have become a well-recognized event in the proteomic calendar. Fresher challenges and global healthcare issues such as ageing and chronic diseases are driving clinical and scientific research towards regenerative, reparative and personalized medicine...
June 16, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28539064/recent-advances-in-applying-mass-spectrometry-and-systems-biology-to-determine-brain-dynamics
#14
Enzo Scifo, Giulio Calza, Martin Fuhrmann, Rabah Soliymani, Marc Baumann, Maciej Lalowski
Neurological disorders encompass various pathologies which disrupt normal brain physiology and function. Poor understanding of their underlying molecular mechanisms and their societal burden argues for the necessity of novel prevention strategies, early diagnostic techniques and alternative treatment options to reduce the scale of their expected increase. Areas covered: This review scrutinizes mass spectrometry based approaches used to investigate brain dynamics in various conditions, including neurodegenerative and neuropsychiatric disorders...
June 1, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28562112/major-depressive-disorder-insight-into-candidate-cerebrospinal-fluid-protein-biomarkers-from-proteomics-studies
#15
Mhd Rami Al Shweiki, Patrick Oeckl, Petra Steinacker, Bastian Hengerer, Carlos Schönfeldt-Lecuona, Markus Otto
Major Depressive Disorder (MDD) is the leading cause of global disability, and an increasing body of literature suggests different cerebrospinal fluid (CSF) proteins as biomarkers of MDD. The aim of this review is to summarize the suggested CSF biomarkers and to analyze the MDD proteomics studies of CSF and brain tissues for promising biomarker candidates. Areas covered: The review includes the human studies found by a PubMed search using the following terms: "depression cerebrospinal fluid biomarker", "major depression biomarker CSF", "depression CSF biomarker", "proteomics depression", "proteomics biomarkers in depression", "proteomics CSF biomarker in depression", and "major depressive disorder CSF"...
May 31, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28535694/what-insights-can-proteomics-give-us-into-iga-nephropathy-berger-s-disease
#16
Matthew B Renfrow, Jan Novak
No abstract text is available yet for this article.
May 29, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28532233/updates-on-sj%C3%A3-gren-s-syndrome-from-proteomics-to-protein-biomarkers
#17
Chiara Baldini, Antonella Cecchettini, Alessia Gallo, Stefano Bombardieri
Primary Sjögren's syndrome (pSS) is a complex heterogeneous autoimmune disorder, typically affecting exocrine glands. Recently, a great interest has arisen in searching for novel biomarkers able to improve the diagnostic work-up of the disease as well as the general assessment and the prognostic stratification of pSS patients. From this perspective, salivary proteomics has appeared as a promising tool considering that salivary proteins may closely reflect the underlying disease processes in the salivary glands...
May 26, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28532181/exploring-ribosome-composition-and-newly-synthesized-proteins-through-proteomics-and-potential-biomedical-applications
#18
Miroslava Stastna, Roberta A Gottlieb, Jennifer E Van Eyk
Protein synthesis is the outcome of tightly regulated gene expression which is responsive to a variety of conditions. Efforts are ongoing to monitor individual stages of protein synthesis to ensure maximum efficiency and accuracy. Due to post-transcriptional regulation mechanisms, the correlation between translatome and proteome is higher than between transcriptome and proteome. However, the most accurate approach to assess the key modulators and final protein expression is directly by using proteomics. Areas covered: This review covers various proteomic strategies that were used to better understand post-transcriptional regulation, specifically during and early after translation...
May 26, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28521569/exploring-the-biochemistry-of-the-prenylome-and-its-role-in-disease-through-proteomics-progress-and-potential
#19
Maura Brioschi, Alma Martinez Fernandez, Cristina Banfi
Protein prenylation is a ubiquitous covalent post-translational modification characterized by the addition of farnesyl or geranylgeranyl isoprenoid groups to a cysteine residue located near the carboxyl terminal of a protein. It is essential for the proper localization and cellular activity of numerous proteins, including Ras family GTPases and G-proteins. In addition to its roles in cellular physiology, the prenylation process has important implications in human diseases and in the recent years, it has become attractive target of inhibitors with therapeutic potential...
May 26, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28513226/application-of-proteomics-to-the-study-of-helicobacter-pylori-and-implications-for-the-clinic
#20
Giulia Bernardini, Natale Figura, Antonio Ponzetto, Barbara Marzocchi, Annalisa Santucci
Helicobacter pylori (H. pylori) is a gram-negative bacterium that colonizes the gastric epithelium and mucous layer of more than half the world's population. H. pylori is a primary human pathogen, responsible for the development of chronic gastritis, peptic ulceration and gastric cancer. Proteomics is impacting several aspects of medical research: understanding the molecular basis of infection and disease manifestation, identification of therapeutic targets and discovery of clinically relevant biomarkers. Areas covered: The main aim of the present review is to provide a comprehensive overview of the contribution of proteomics to the study of H...
May 26, 2017: Expert Review of Proteomics
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