Liquid-phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis-An update covering the period 2014-2016

Quantitative proteomics reveals common and unique molecular mechanisms underlying beneficial effects of caffeine and trigonelline on human hepatocytes

Caffeine and trigonelline are the major bioactive compounds in coffee. Caffeine alone or combined with other coffee compounds shows hepatoprotective effects. However, molecular mechanisms underlying such hepatoprotective effects remain unclear. We therefore addressed molecular effects of caffeine and trigonelline on human hepatocytes using quantitative proteomics followed by bioinformatic analyses to obtain topological and functional significance. HepG2 cells were treated with 100 μM caffeine or trigonelline for 24-h and evaluated by quantitative proteomics using nanoLC-ESI-LTQ-Orbitrap MS/MS. A total of 26 and 25 significantly altered proteins were identified in caffeine-treated and trigonelline-treated cells, respectively, compared with control cells. Topological analyses revealed that ribosomal and translation regulatory proteins predominantly served as the hub proteins associated with protein clusters. Functional analyses also revealed that these two bioactive compounds shared some molecular mechanisms via induction of translational processes. There were also other unique molecular functions and biological processes triggered or suppressed by either caffeine or trigonelline. These data highlight common and unique molecular mechanisms underlying the hepatoprotective effects of caffeine and trigonelline that may be useful for future clinical applications.

Biomarkers in Neurodegenerative Diseases: Proteomics Spotlight on ALS and Parkinson’s Disease

Neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD) are both characterized by pathogenic protein aggregates that correlate with the progressive degeneration of neurons and the loss of behavioral functions. Both diseases lack biomarkers for diagnosis and treatment efficacy. Proteomics is an unbiased quantitative tool capable of the high throughput quantitation of thousands of proteins from minimal sample volumes. We review recent proteomic studies in human tissues, plasma, cerebrospinal fluid (CSF), and exosomes in ALS and PD that identify proteins with potential utility as biomarkers. Further, we review disease-related post-translational modifications in key proteins TDP43 in ALS and α-synuclein in PD studies, which may serve as biomarkers. We compare relative and absolute quantitative proteomic approaches in key biomarker studies in ALS and PD and discuss recent technological advancements which may identify suitable biomarkers for the early-diagnosis treatment efficacy of these diseases.

Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases

Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.

Evaluation of the Molecular Mechanisms of Sepsis Using Proteomics

Sepsis is a complex syndrome promoted by pathogenic and host factors; it is characterized by dysregulated host responses and multiple organ dysfunction, which can lead to death. However, its underlying molecular mechanisms remain unknown. Proteomics, as a biotechnology research area in the post-genomic era, paves the way for large-scale protein characterization. With the rapid development of proteomics technology, various approaches can be used to monitor proteome changes and identify differentially expressed proteins in sepsis, which may help to understand the pathophysiological process of sepsis. Although previous reports have summarized proteomics-related data on the diagnosis of sepsis and sepsis-related biomarkers, the present review aims to comprehensively summarize the available literature concerning “sepsis”, “proteomics”, “cecal ligation and puncture”, “lipopolysaccharide”, and “post-translational modifications” in relation to proteomics research to provide novel insights into the molecular mechanisms of sepsis.

Microfluidic devices for glycobiomarker detection in cancer

During oncogenesis, several alterations occur within cells, one of them being the abnormal glycosylation of proteins, resulting in the formation of glycoproteins with aberrant glycan structures, which can be secreted into the blood stream. Their specific association to tumour cells makes them useful indicators (biomarkers) of the oncogenic process and their detection in blood can be employed in different stages of tumour development for early detection, prognosis and therapeutic drug monitoring. Due to the importance of detecting cancer-associated glycoproteins with aberrant glycosylation in blood or serum, analytical methodologies with improved performance are required to ameliorate the laboratorial tests currently used for the detection of these analytes. Microfluidics was created to facilitate the implementation of simple and point-of-care analysis, away from a centralized laboratory. The massive use of microfluidic systems in clinical settings can be seen in pregnancy tests and diabetes control, for example. But what about other clinical domains, such as the detection of glycoproteins with aberrant glycans secreted by tumour cells? Are microfluidic systems helpful in this case? This review analyses the requirements of a microfluidic assay for the detection of low-abundant blood/serum cancer-associated glycoproteins with abnormal glycans and the progresses that have been made in the last years to develop integrated microfluidic devices for this particular application. The diverse microfluidic systems found in literature present, in general, the same analytical performance as the conventional assays but have additional advantages, namely a reduction in assay times, a decrease of sample and reagent consumption and lower costs. The review will also focus on the improvements that are still needed for better biosensing of this type of cancer biomarkers using microfluidic devices.

Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery

Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.

Suitable simple and fast methods for selective isolation of phospholipids as a tool for their analysis

Lipids are gaining relevance over the last 20 years, as our knowledge about their role has changed from merely energy/structural molecules to compounds also involved in several biological processes. This led to the creation in 2003 of a new emerging research field: lipidomics. In particular the phospholipids have pharmacological/food applications, participate in cell signalling/homeostatic pathways while their analysis faces some challenges. Their fractionation/purification is, in fact, especially difficult, as they are amphiphilic compounds. Moreover, it usually involves SPE or TLC procedures requiring specific materials hampering their suitableness for routine analysis. Finally, they can interfere with the ionization of other molecules during mass spectrometry analysis. Thus, simple high-throughput reliable methods to selectively isolate these compounds based on the difference between chemical characteristics of lipids would represent valuable tools for their study besides that of other compounds. The current review work aims to describe the state-of-the-art related to the extraction of phospholipids using liquid-liquid methods for their targeted isolation. The technological and biological importance of these compounds and ion suppression phenomena are also reviewed. Methods by precipitation with acetone or isolation using methanol seem to be suitable for selective isolation of phospholipids in both biological and food samples.

Recent developments in capillary and microchip electroseparations of peptides (2015-mid 2017)

The review brings a comprehensive overview of recent developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) to analysis, microscale isolation, purification, and physicochemical and biochemical characterization of peptides in the years 2015, 2016, and ca. up to the middle of 2017. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis (sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, and detection) are described. New developments in particular CE and CEC methods are presented and several types of their applications to peptide analysis are reported: qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC methods to provide important physicochemical characteristics of peptides are demonstrated.

Protein biomarkers for early detection of diseases: The decisive contribution of combinatorial peptide ligand libraries

The present review deals with biomarker discovery, especially in regard to sample treatment via combinatorial peptide ligand libraries, perhaps the only technique at present allowing deep exploration of biological fluids and tissue extracts in search for low- to very-low-abundance proteins, which could possibly mark the onset of most pathologies. Early-stage biomarkers, in fact, might be the only way to detect the beginning of most diseases thus permitting proper intervention and care. The following cancers are reviewed, with lists of potential biomarkers suggested in various reports: hepatocellular carcinoma, ovarian cancer, breast cancer and pancreatic cancer, together with some other interesting applications. Although panels of proteins have been presented, with robust evidence, as potential early-stage biomarkers in these different pathologies, their approval by FDA as novel biomarkers in routine clinical chemistry settings would require plenty of additional work and efforts from the pharma industry. The science environment in universities could simply not afford such heavy monetary investments.

SIGNIFICANCE

After more than 16years of search for novel biomarkers, to be used in a clinical chemistry set-up, via proteomic analysis (mostly in biological fluids) it was felt a critical review was due. In the present report, though, only papers reporting biomarker discovery via combinatorial peptide ligand libraries are listed and assessed, since this methodology seems to be the most advanced one for digging in depth into low-to very-low-abundance proteins, which might represent important biomarkers for the onset of pathologies. In particular, a large survey has been made for the following diseases, since they appear to have a large incidence on human population and/or represent fatal diseases: ovarian cancer, breast cancer, pancreatic cancer and hepatocellular carcinoma.

Capillary electrophoresis tandem mass spectrometry determination of glutamic acid and homocysteine's metabolites: Potential biomarkers of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that affects both lower and upper motor neurons, leading to muscle atrophy, paralysis, and death caused by respiratory failure or infectious complications. Altered levels of homocysteine, cysteine, methionine, and glutamic acid have been observed in plasma of ALS patients. In this context, a method for determination of these potential biomarkers in plasma by capillary electrophoresis tandem mass spectrometry (CE-MS/MS) is proposed herein. Sample preparation was carefully investigated, since sulfur-containing amino acids may interact with plasma proteins. Owing to the non-thiol sulfur atom in methionine, it was necessary to split sample preparation into two methods: i) determination of homocysteine and cysteine as S-acetyl amino acids; ii) determination of glutamic acid and methionine. All amino acids were separated within 25min by CE-MS/MS using 5molL^-1 acetic acid as background electrolyte and 5mmolL^-1 acetic acid in 50% methanol/H₂O (v/v) as sheath liquid. The proposed CE-MS/MS method was validated, presenting RSD values below 6% and 11% for intra- and inter-day precision, respectively, for the middle concentration level within the linear range. The limits of detection ranged from 35 (homocysteine) to 268nmolL^-1 (glutamic acid). The validated method was applied to the analysis of plasma samples from a group of healthy individuals and patients with ALS, showing the potential of glutamic acid and homocysteine metabolites as biomarkers of ALS.

The potential impact of recent insights into proteomic changes associated with glaucoma

INTRODUCTION

Glaucoma, a major ocular neuropathy, is still far from being understood on a molecular scale. Proteomic workflows revealed glaucoma associated alterations in different eye components. By using state-of-the-art mass spectrometric (MS) based discovery approaches large proteome datasets providing important information about glaucoma related proteins and pathways could be generated. Corresponding proteomic information could be retrieved from various ocular sample species derived from glaucoma experimental models or from original human material (e.g. optic nerve head or aqueous humor). However, particular eye tissues with the potential for understanding the disease's molecular pathomechanism remains underrepresented. Areas covered: The present review provides an overview of the analysis depth achieved for the glaucomatous eye proteome. With respect to different eye regions and biofluids, proteomics related literature was found using PubMed, Scholar and UniProtKB. Thereby, the review explores the potential of clinical proteomics for glaucoma research. Expert commentary: Proteomics will provide important contributions to understanding the molecular processes associated with glaucoma. Sensitive discovery and targeted MS approaches will assist understanding of the molecular interplay of different eye components and biofluids in glaucoma. Proteomic results will drive the comprehension of glaucoma, allowing a more stringent disease hypothesis within the coming years.