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Expert Review of Proteomics

Binbin Yu, Wei Cao, Chenping Zhang, Ronghui Xia, Jinlin Liu, Ming Yan, Wantao Chen
OBJECTIVE: Lymph node metastasis leads to high mortality rates of oral squamous cell carcinoma (OSCC). However, it is still controversial to define clinically negative neck (cN0) and positive neck (cN1-3). METHODS: We retrieved candidate biomarkers identified by proteomic analysis in OSCC from published literatures. In training stage, immunohistochemistry (IHC) analysis was used to determine expression of proteins and logistic regression models with stepwise variable selection were used to identify potential factors that might affect lymph node metastasis and life status...
February 19, 2019: Expert Review of Proteomics
Chandra Sekhar Amara, Venkatrao Vantaku, Yair Lotan, Nagireddy Putluri
Metabolomics is a chemical process, involving the characterization of metabolites and cellular metabolism. Recent studies indicate that numerous metabolic pathways are altered in bladder cancer (BLCA), providing potential targets for improved detection and possible therapeutic intervention. We review recent advances in metabolomics related to BLCA and identify various metabolites that may serve as potential biomarkers for BLCA. Areas covered. In this review, we describe the latest advances in defining the BLCA metabolome and discuss the possible clinical utility of metabolic alterations in BLCA tissues, serum, and urine...
February 16, 2019: Expert Review of Proteomics
Aayushi Vasani, Maushmi S Kumar
Amniotic fluid (AF) is a dynamic and complex mixture that reflects the physiological condition of developing fetus. In the last decade, proteomic analysis of AF for 16-18 weeks normal pregnancy has been done for the composition and functions of this fluid. Other body fluids such as urine, sweat, tears, etc. are being used for diagnosis of disease, but an insight into protein biomarkers of amniotic fluid can save the fetus and mother from future complications. Areas covered: We have covered the proteomics of amniotic fluid done since 2000, in order to strengthen the establishment of this techniques as a recognized diagnostic tool in the field...
February 5, 2019: Expert Review of Proteomics
Alain Beck, Valentina D'Atri, Anthony Ehkirch, Szabolcs Fekete, Oscar Hernandez-Alba, Rabah Gahoual, Emmanuel Leize-Wagner, Yannis François, Davy Guillarme, Sarah Cianférani
The development and optimization of antibody drug conjugates (ADCs) rely on improving their analytical and bioanalytical characterization, by assessing critical quality attributes (CQAs). Among the CQAs, the glycoprofile, drug load distribution (DLD), the amount of unconjugated antibody (D0), the average drug-to-antibody ratio (DAR), the drug conjugation sites and the residual drug-linker and related product proportions (SMDs) in addition to high and low molecular weight species (H/LMWS), and charge variants are the most important ones...
February 1, 2019: Expert Review of Proteomics
Amanda Lorentzian, Anuli Uzozie, Philipp F Lange
Cancer changes the proteome in complex ways that reach well beyond simple changes in protein abundance. Genomic and transcriptional variations and post translational protein modification create functional variants of a protein, known as proteoforms. Childhood cancers have fewer genomic alterations but show equally dramatic phenotypic changes as malignant cells in adults. Therefore, unraveling the complexities of the proteome is even more important in pediatric malignancies. Areas covered: In this review, the biological origins of proteoforms and technological advancements in the study of proteoforms are discussed...
January 31, 2019: Expert Review of Proteomics
Sandra Murphy, Paul Dowling, Margit Zweyer, Dieter Swandulla, Kay Ohlendieck
Distinct subtypes of contractile fibres are highly diverse in their proteomic profile and greatly adaptable to physiological or pathological challenges. A striking biochemical feature of heterogeneous skeletal muscle tissues is the presence of a considerable number of extremely large protein species, which often present a bioanalytical challenge for the systematic separation and identification of muscle proteomes during large-scale screening surveys. Areas covered: This review outlines the proteomic characterization of skeletal muscles with a special focus on giant proteins of the sarcomere, the cytoskeleton and the sarcoplasmic reticulum...
January 25, 2019: Expert Review of Proteomics
Jordy Evan Sulaiman, Henry Lam
Persisters, a small subpopulation of bacterial cells that can survive antibiotic treatment due to transient growth inhibition, pose a serious threat in clinics. Given the nature of persistence as an emergent property of a biological network, proteomics is well-suited to study this phenomenon. Areas covered: In this review, we introduce the phenomenon of bacterial persistence, review previous proteomics studies on persisters, discuss challenges in studying persisters by proteomics, and provide future perspectives in applying proteomics to study persisters...
January 25, 2019: Expert Review of Proteomics
Xinqiang Yin, Yuanyuan Jing, Hanmei Xu
Small open reading frames (sORFs) with potential protein-coding capacity have been disclosed in various transcripts, including long noncoding RNAs (LncRNAs), mRNAs (5'-upstream, coding domain, and 3'-downstream), circular RNAs, pri-miRNAs, and ribosomal RNAs (rRNAs). Recent characterization of several sORF-encoded peptides (SEPs or micropeptides) revealed their important roles in many fundamental biological processes in a broad range of species from yeast to human. The success in mining of micropeptides attributes to the advanced bioinformatics and high-throughput sequencing techniques...
January 22, 2019: Expert Review of Proteomics
Angelo D'Alessandro
Blood transfusion is the single most frequent in-hospital medical procedure, a life-saving intervention for millions of recipients worldwide every year. Storage in the blood bank is an enabling strategy for this critical procedure, as it logistically solves the issue of making ~110 million units available for transfusion every year. Unfortunately, storage in the blood bank promotes a series of biochemical and morphological changes to the red blood cell that compromise the integrity and functionality of the erythrocyte in vitro and in animal models, and could negatively impact transfusion outcomes in the recipient...
January 18, 2019: Expert Review of Proteomics
José González-Gomariz, Elizabeth Guruceaga, Macarena López-Sánchez, Victor Segura
The technological and scientific progress performed in the Human Proteome Project (HPP) has provided to the scientific community a new set of experimental and bioinformatic methods in the challenging field of shotgun and SRM/MRM-based Proteomics. The requirements for a protein to be considered experimentally validated are now well established and the information about the human proteome is available in the neXtProt database, while targeted proteomic assays are stored in SRMAtlas. However, the study of the missing proteins continues being an outstanding issue...
January 18, 2019: Expert Review of Proteomics
Varvara Trachana, Evanthia Mourmoura, Ioanna Papathanasiou, Aspasia Tsezou
Proteomic analyses have been acknowledged to carry a significant prospective in elucidating the pathogenesis of several diseases, including osteoarthritis (OA). But it hasn't been an easy road: major technical issues, mainly derived from the complex and rigid nature of the cartilage tissue, had to be faced; an obstacle that led to the development of different approaches. Areas covered: In this review, we categorized the proteomic studies undertaken (proteomic analyses of the cartilage, cartilage explants, cultured chondrocytes and chondrocytes' secretome) as are part of the different strategies developed in order to overcome tissue and disease specific challenges...
January 17, 2019: Expert Review of Proteomics
Issa Diallo, Michel Seve, Valérie Cunin, Frédéric Minassian, Jean-François Poisson, Sylvie Michelland, Sandrine Bourgoin-Voillard
Acetylation is a widely occurring post-translational modification (PTM) of proteins that plays a crucial role in many cellular physiological and pathological processes. Over the last decade, acetylation analyses required the development of multiple methods to target individual acetylated proteins, as well as to cover a broader description of acetylated proteins that comprise the acetylome. Areas covered: This review discusses the different types of acetylation (N-ter/K-/O-acetylation) and then describes some major strategies that have been reported in the literature to detect, enrich, identify and quantify protein acetylation...
December 24, 2018: Expert Review of Proteomics
Samantha Louise Edwards, Lucas Mergan, Bhavesh Parmar, Bram Cockx, Wouter De Haes, Liesbet Temmerman, Liliane Schoofs
Neuropeptides are neuro-endocrine signaling molecules capable of signaling as neurotransmitters, neuromodulators or neurohormones. Studying how neuropeptide signaling is integrated in endocrine pathways and how neuropeptides regulate endogenous processes is crucial to understanding how multicellular organisms respond to environmental and internal cues. Areas covered: This review will cover proteomics and peptidomics approaches used in researching peptide signaling systems and breakthroughs that were achieved in this field...
December 21, 2018: Expert Review of Proteomics
Abhishek Chanda, Bhargab Kalita, Aparup Patra, Wanigasingha D Sandani T Senevirathne, Ashis K Mukherjee
BACKGROUND: Snakebite is a severe problem in the tropical countries including Indian subcontinent. Premier cases of cobra bites are being reported from western India (WI). RESEARCH DESIGN AND METHODS: The proteome of WI N. naja venom (NnV) was deciphered by high resolution mass spectrometry analysis of venom, further fractionated by gel filtration (GF) or RP-HPLC followed by SDS-PAGE and then tandem mass spectrometric analysis of protein bands. The efficacy of commercial polyantivenom (PAV) towards WINnV was assessed by ELISA, immuno-blot, neutralization, and venom-PAV immunoaffinity chromatography studies...
December 17, 2018: Expert Review of Proteomics
Nasibeh Khayer, Mehdi Mirzaie, Sayed-Amir Marashi, Mostafa Rezaie-Tavirani, Fatemeh Goshadrou
Identification of functionally-related genes is an important step in understanding biological systems. The most popular strategy to infer functional dependence is to study pairwise correlations between gene expression levels. However, certain functionally-related genes may have a low expression correlationdue to their nonlinear interactions. The use of a three-way interaction (3WI) model with switching mechanism (SM) is a relatively new strategy to trace functionally-related genes. The 3WI model traces the dynamic and nonlinear nature of the co-expression relationship of two genes by introducing their link to the expression level of a third gene...
December 17, 2018: Expert Review of Proteomics
Ventzislava A Hristova, Daniel W Chan
Cancer is often diagnosed at late stages when the chance of cure is relatively low and although research initiatives in oncology discover many potential cancer biomarkers, few transition to clinical applications. This review addresses the current landscape of cancer biomarker discovery and translation with a focus on proteomics and beyond. Areas covered: The review examines proteomic and genomic techniques for cancer biomarker detection and outlines advantages and challenges of integrating multiple omics approaches to achieve optimal sensitivity and address tumor heterogeneity...
December 17, 2018: Expert Review of Proteomics
Ramiro Alonso-Bastida, Sergio Encarnación-Guevara
No abstract text is available yet for this article.
December 7, 2018: Expert Review of Proteomics
Kokouvi Kassegne, Eniola Michael Abe, Yan-Bin Cui, Shen-Bo Chen, Bin Xu, Wang-Ping Deng, Hai-Mo Shen, Yue Wang, Jun-Hu Chen, Xiao-Nong Zhou
Plasmodium vivax and P. knowlesi account together for a considerable share of the global burden of malaria, along with P. falciparum. However, inaccurate diagnosis and undetectable asymptomatic/submicroscopic malaria infections remain very challenging. Blood-stage antigens involved in either invasion of red blood cells or sequestration/cytoadherence of parasitized erythrocytes have been immunomics-characterized, and are vital for the detection of malaria incidence. Areas covered: We review the recent advances in Plasmodium immunomics to discuss serological markers with potential for specific and sensitive diagnosis of malaria...
December 4, 2018: Expert Review of Proteomics
Dylan M Marchione, Benjamin A Garcia, John Wojcik
Epigenetic dysregulation drives or supports numerous human cancers. The chromatin landscape in cancer cells is often marked by abnormal histone post-translational modification (PTM) patterns and by aberrant assembly and recruitment of protein complexes to specific genomic loci. Mass spectrometry-based proteomic analyses can support the discovery and characterization of both phenomena. Areas covered: We broadly divide this literature into two parts: 'modification-centric' analyses that link histone PTMs to cancer biology; and 'complex-centric' analyses that examine protein-protein interactions that occur de novo as a result of oncogenic mutations...
November 27, 2018: Expert Review of Proteomics
Thomas A Guerrero-Garcia, Sara Gandolfi, Jacob P Laubach, Teru Hideshima, Dharminder Chauhan, Constantine Mitsiades, Kenneth C Anderson, Paul G Richardson
Proteasome inhibitors (PIs) are therapeutic backbones of multiple myeloma treatment, with PI-based therapies being standards of care throughout the treatment algorithm. Proteasome inhibition affects multiple critical signaling pathways in myeloma cells and interacts synergistically with mechanisms of action of other conventional and novel agents, resulting in substantial anti-myeloma activity and at least additive effects. Areas covered: This review summarizes the biologic effects of proteasome inhibition in myeloma and provides an overview of the importance of proteasome inhibition to the current treatment algorithm...
December 2018: Expert Review of Proteomics
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