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Expert Review of Proteomics

Maura Brioschi, Cristina Banfi
Since the completion of genome sequencing, gene silencing technologies have emerged as powerful tools to study gene functions in various biological processes, both in vivo and in vitro. Moreover, they have also been proposed as therapeutic agents to inhibit selected genes in a variety of pathological conditions, such as cancer, neurodegenerative and cardiovascular diseases. Area covered: This review summarizes the mechanisms of action and applications of genome editing tools, from RNA interference to clustered regularly interspaced short palindromic repeats (CRISPR)-based systems, in research and in clinics...
September 11, 2018: Expert Review of Proteomics
José M Mato, Félix Elortza, Shelly C Lu, Virginie Brun, Alberto Paradela, Fernando J Corrales
Hepatocellular carcinoma (HCC) is recognized as the fifth most common neoplasm and currently represents the second leading form of cancer-related death worldwide. Despite great progress has been done in the understanding of its pathogenesis, HCC represents a heavy societal and economic burden as most patients are still diagnosed at advanced stages and the 5-year survival rate remain below 20%. Early detection and revolutionary therapies that rely on the discovery of new molecular biomarkers and therapeutic targets are therefore urgently needed to develop precision medicine strategies for a more efficient management of patients...
September 11, 2018: Expert Review of Proteomics
Marialaura Dilillo, Bram Heijs, Liam A McDonnell
Mass spectrometry imaging (MSI) is a label free, multiplex imaging technology able to simultaneously record the distributions of 100's to 1000's of species, and which may be configured to study metabolites, lipids, glycans, peptides and proteins simply by changing the tissue preparation protocol. Areas covered: The capability of MSI to complement established histopathological practice through the identification of biomarkers for differential diagnosis, patient prognosis, and response to therapy; the capability of MSI to annotate tissues on the basis of each pixel's mass spectral signature; the development of reproducible MSI through multicenter studies...
September 11, 2018: Expert Review of Proteomics
Charlotte Gaviard, Thierry Jouenne, Julie Hardouin
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen widely involved in human infections. The high occurrence of this bacterial species in the clinical field is due to its high ability to adapt to detrimental environments, in particular its strong inherent antibiotic resistance, its ability to form biofilms and to produce virulence factors. The application of proteomics to clinical microbiology is probably one of the most innovative strategies of the last decades to understand complex microbial systems, by providing individual proteome charts of pathogens...
September 10, 2018: Expert Review of Proteomics
Valerie Quarmby, Qui T Phung, Jennie R Lill
Introduction Anti-drug antibody (ADA) responses are becoming an increasing concern as more highly engineered and sophisticated biotherapeutics enter the clinic. An arsenal of tools has been developed to identify potential T cell epitopes that may drive unwanted immunological responses to protein therapeutics; one such tool is termed "Major Histocompatibility Complex-Associated Peptide Proteomics" (MAPPs). This review highlights the evolution of this MHC II profiling technology, its technological advantages and limitations, and its utility in helping to de-risk the immunogenicity of biotherapeutics...
September 8, 2018: Expert Review of Proteomics
Robert Popp, Huiyan Li, Christoph H Borchers
Biomarkers are commonly used to stratify cancer patients and guide targeted therapies, but most biomarkers are of a genomic nature. Discrepancies between the genome and proteome, and the high rates of drug resistance indicate that proteomic analyses may provide additional critically important information. Here we present immuno-matrix assisted laser desorption/ionization (iMALDI), the combination of immuno-affinity enrichment of peptides followed by MALDI-MS analysis. iMALDI is a highly sensitive, targeted protein-quantitation technique with the potential to measure clinically relevant signalling-pathway proteins using minimal sample amounts, thus improving upon existing methodologies...
August 31, 2018: Expert Review of Proteomics
Per Hägglund, Michele Mariotti, Michael J Davies
Protein cross-links are common in biological systems and are generated both deliberately as a part of normal metabolism and also accidently as a result of exposure to external factors such as oxidation and glycation stresses. These cross-links can be both positive and negative for biological function, with high levels of inappropriate cross-links being associated with multiple human pathologies, as well as loss of protein structure and function in the food, agricultural, and pharmaceutical fields. Areas covered: This review covers recent advances in the detection and identification of protein cross-links arising from oxidation reactions, mediated by both radicals and two-electron oxidants...
August 2018: Expert Review of Proteomics
Sri H Ramarathinam, Nathan P Croft, Patricia T Illing, Pouya Faridi, Anthony W Purcell
Our immune system discriminates self from non-self by examining the peptide cargo of human leukocyte antigen (HLA) molecules displayed on the cell surface. Successful recognition of HLA-bound non-self peptides can induce T cell responses leading to, for example, the destruction of infected cells. Today, largely due to advances in technology, we have an unprecedented capability to identify the nature of these presented peptides and unravel the true complexity of antigen presentation. Areas covered: In addition to conventional linear peptides, HLA molecules also present post-translationally modified sequences comprising a wealth of chemical and structural modifications, including a novel class of noncontiguous spliced peptides...
August 2018: Expert Review of Proteomics
Tobias Kroniger, Andreas Otto, Dörte Becher
No abstract text is available yet for this article.
August 2018: Expert Review of Proteomics
Sara Artigas-Jerónimo, José De La Fuente, Margarita Villar
Ticks are obligate hematophagous arthropod ectoparasites that transmit pathogens responsible for a growing number of tick-borne diseases (TBDs) throughout the world. Vaccines have been shown to be the most efficient, cost-effective, and environmentally friendly approach for the control of ticks and the prevention of TBDs. Although at its infancy, interactomics has shown the possibilities that the knowledge of the interactome offers in understanding tick biology and the molecular mechanisms involved in pathogen infection and transmission...
August 2018: Expert Review of Proteomics
Viviana Greco, Cristian Piras, Luisa Pieroni, Maurizio Ronci, Lorenza Putignani, Paola Roncada, Andrea Urbani
The development of precision medicine requires advanced technologies to address the multifactorial disease stratification and to support personalized treatments. Among omics techniques, proteomics based on Mass Spectrometry (MS) is becoming increasingly relevant in clinical practice allowing a phenotypic characterization of the dynamic functional status of the organism. From this perspective, Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) MS is a suitable platform for providing a high-throughput support to clinics...
August 2018: Expert Review of Proteomics
Angelica Dessì, Laura Corona, Roberta Pintus, Vassilios Fanos
The exposure to tobacco smoke during pregnancy is one of the leading causes of perinatal adverse outcomes such as stillbirth, intrauterine growth restriction (IUGR), and low birth weight, but the underlying biological mechanisms are still unclear. The incidence of this phenomenon maybe largely underestimated since the evaluation is made mainly by self-assessment questionnaires rather than measuring nicotine metabolites (such as cotinine) in biological fluids. In this context metabolomics may be useful to assess the actual number of pregnant women and to highlight the pathophysiological mechanisms that lead to the abovementioned adverse outcomes...
August 2018: Expert Review of Proteomics
Elisa Danese, Martina Montagnana, Giuseppe Lippi
Frailty is consequent to age-dependent deregulation of several biological pathways and systems, encompassing namely sarcopenia, age-associated hormonal derangements, inflammation, and nutritional or metabolic deficiencies. Although the prevalence of frailty is usually between 10% and 20% in the general elderly population, its overall burden will increase exponentially along with the predictable prolongation of life expectancy. Risk prediction and early diagnosis will hence become pivotal for mitigating the clinical, social, and economic impact of this condition...
August 2018: Expert Review of Proteomics
Juan J Calvete
Venoms are integrated phenotypes used by a wide range of organisms for predatory and defensive purposes. The study of venoms is of great interest in diverse fields, such as evolutionary ecology and biotechnology. Omics technologies have contributed to understanding the evolutionary mechanisms that molded snake venoms to their present-day structural and functional variability landscape. Areas covered: This review article reflects on two recent implementations in venomics: absolute quantification of intact proteins by elemental mass spectrometry, and top-down molecular mass spectrometry...
July 2018: Expert Review of Proteomics
Yuanhui Ma, John R Yates
Measuring the immediate changes in cells that arise from changing environmental conditions is crucial to understanding the underlying mechanisms involved. These changes can be measured with metabolic stable isotope fully labeled proteomes, but requires looking for changes in the midst of a large background. In addition, labeling efficiency can be an issue in primary and fully differentiated cells. Area covered: Azidohomoalanine (AHA), an analog of methionine, can be accepted by cellular translational machinery and incorporated into newly synthesized proteins (NSPs)...
July 2018: Expert Review of Proteomics
Arada Vinaiphat, Visith Thongboonkerd
Knowledge of the function of molecular chaperones is required for a better understanding of cellular proteostasis. Nevertheless, such information is currently dispersed as most of previous studies investigated chaperones on a single-angle basis. Recently, a new subdiscipline of chaperonology, namely 'chaperonomics' (defined as 'systematic analysis of chaperone genes, transcripts, proteins, or their interaction networks using omics technologies'), has been emerging to better understand biological, physiological, and pathological roles of chaperones...
July 2018: Expert Review of Proteomics
Christian Delles, Emma Carrick, Delyth Graham, Stuart A Nicklin
Hypertension is a complex and multifactorial cardiovascular disorder. With different mechanisms contributing to a different extent to an individual's blood pressure, the discovery of novel pathogenetic principles of hypertension is challenging. However, there is an urgent and unmet clinical need to improve prevention, detection, and therapy of hypertension in order to reduce the global burden associated with hypertension-related cardiovascular diseases. Areas covered: Proteomic techniques have been applied in reductionist experimental models including angiotensin II infusion models in rodents and the spontaneously hypertensive rat in order to unravel mechanisms involved in blood pressure control and end organ damage...
July 2018: Expert Review of Proteomics
Anna Psaroulaki, Dimosthenis Chochlakis
No abstract text is available yet for this article.
July 2018: Expert Review of Proteomics
Anna Mantsiou, Antonia Vlahou, Jerome Zoidakis
Prostate cancer (PCa) is one of the leading causes of death in the male population worldwide. Various clinical samples such as urine, blood serum, and prostatic fluid have been commonly used for the identification of PCa-associated molecular changes. Tissue, the site of oncogenesis, is increasingly gaining more attention as a study material for studies aimed at the discovery of biomarkers for predicting the disease outcome and therapeutic targets. Areas covered: This review is the output of a systematic literature search on PubMed to retrieve articles relevant to the proteomic analysis of tissues for the study of PCa...
July 2018: Expert Review of Proteomics
Shichen Shen, Xue Wang, Benjamin C Orsburn, Jun Qu
No abstract text is available yet for this article.
July 2018: Expert Review of Proteomics
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