Proteomes

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Open AccessFeature PaperArticle

Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb

by Antonio Palomba, Alessandro Tanca, Cristina Fraumene, Marcello Abbondio, Francesco Fancello, Alberto Stanislao Atzori and Sergio Uzzau

Proteomes 2017, 5(4), 36; https://doi.org/10.3390/proteomes5040036 - 18 Dec 2017

Cited by 13 | Viewed by 4809

Abstract

The digestive functions of the pre-weaned lamb gastrointestinal tracts (GITs) have been the subject of much research in recent years, but the microbial and host functions underlying these complex processes remain largely unknown. Here, we undertook a proof-of-principle metaproteogenomic investigation on luminal and [...] Read more.

The digestive functions of the pre-weaned lamb gastrointestinal tracts (GITs) have been the subject of much research in recent years, but the microbial and host functions underlying these complex processes remain largely unknown. Here, we undertook a proof-of-principle metaproteogenomic investigation on luminal and mucosal samples collected from 10 GITs of a 30-day-old pre-weaned lamb. We demonstrate that the analysis of the diverse ecological niches along the GITs can reveal microbiota composition and metabolic functions, although low amounts of microbial proteins could be identified in the small intestinal and mucosal samples. Our data suggest that a 30-day lamb has already developed mature microbial functions in the forestomachs, while the effect of the milky diet appears to be more evident in the remaining GITs. We also report the distribution and the relative abundance of the host functions, active at the GIT level, with a special focus on those involved in digestive processes. In conclusion, this pilot study supports the suitability of a metaproteogenomic approach to the characterization of microbial and host functions of the lamb GITs, opening the way to further studies aimed at investigating the impact of early dietary interventions on the GIT microbiota of small ruminants. Full article

(This article belongs to the Special Issue Metaproteomics)

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Open AccessReview

Proteomic Contributions to Medicinal Plant Research: From Plant Metabolism to Pharmacological Action

by Akiko Hashiguchi, Jingkui Tian and Setsuko Komatsu

Proteomes 2017, 5(4), 35; https://doi.org/10.3390/proteomes5040035 - 7 Dec 2017

Cited by 18 | Viewed by 5889

Abstract

Herbal medicine is a clinical practice of utilizing medicinal plant derivatives for therapeutic purposes. It has an enduring history worldwide and plays a significant role in the fight against various diseases. Herbal drug combinations often exhibit synergistic therapeutic action compared with single-constituent dosage, [...] Read more.

Herbal medicine is a clinical practice of utilizing medicinal plant derivatives for therapeutic purposes. It has an enduring history worldwide and plays a significant role in the fight against various diseases. Herbal drug combinations often exhibit synergistic therapeutic action compared with single-constituent dosage, and can also enhance the cytotoxicity induced by chemotherapeutic drugs. To explore the mechanism underlying the pharmacological action of herbs, proteomic approaches have been applied to the physiology of medicinal plants and its effects on animals. This review article focuses on the existing proteomics-based medicinal plant research and discusses the following topics: (i) plant metabolic pathways that synthesize an array of bioactive compounds; (ii) pharmacological action of plants tested using in vivo and in vitro studies; and (iii) the application of proteomic approaches to indigenous plants with scarce sequence information. The accumulation of proteomic information in a biological or medicinal context may help in formulating the effective use of medicinal plants. Full article

(This article belongs to the Special Issue Selected Papers from “International Proteomics Conference 2017—Proteomics in Biotechnology and Life Sciences”)

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Open AccessArticle

Isolation and Characterization of Serum Extracellular Vesicles (EVs) from Atlantic Salmon Infected with Piscirickettsia Salmonis

by Leidy Lagos, Julia Tandberg, Alexander Kashulin-Bekkelund, Duncan J. Colquhoun, Henning Sørum and Hanne C. Winther-Larsen

Proteomes 2017, 5(4), 34; https://doi.org/10.3390/proteomes5040034 - 1 Dec 2017

Cited by 22 | Viewed by 4522

Abstract

Secretion of extracellular vesicles (EVs) is a common feature of both eukaryotic and prokaryotic cells. Isolated EVs have been shown to contain different types of molecules, including proteins and nucleic acids, and are reported to be key players in intercellular communication. Little is [...] Read more.

Secretion of extracellular vesicles (EVs) is a common feature of both eukaryotic and prokaryotic cells. Isolated EVs have been shown to contain different types of molecules, including proteins and nucleic acids, and are reported to be key players in intercellular communication. Little is known, however, of EV secretion in fish, or the effect of infection on EV release and content. In the present study, EVs were isolated from the serum of healthy and Piscirickettsia salmonis infected Atlantic salmon in order to evaluate the effect of infection on EV secretion. P. salmonis is facultative intracellular bacterium that causes a systemic infection disease in farmed salmonids. EVs isolated from both infected and non-infected fish had an average diameter of 230–300 nm, as confirmed by transmission electron microscopy, nanoparticle tracking, and flow cytometry. Mass spectrometry identified 180 proteins in serum EVs from both groups of fish. Interestingly, 35 unique proteins were identified in serum EVs isolated from the fish infected with P. salmonis. These unique proteins included proteasomes subunits, granulins, and major histocompatibility class I and II. Our results suggest that EV release could be part of a mechanism in which host stimulatory molecules are released from infected cells to promote an immune response. Full article

(This article belongs to the Special Issue Proteomic Analysis of Host-Microbial Pathogen Interactions)

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Open AccessArticle

Variety and Dynamics of Proteoforms in the Human Proteome: Aspects of Markers for Hepatocellular Carcinoma

by Stanislav Naryzhny, Victor Zgoda, Artur Kopylov, Elena Petrenko, Olga Kleist and Аlexander Archakov

Proteomes 2017, 5(4), 33; https://doi.org/10.3390/proteomes5040033 - 23 Nov 2017

Cited by 11 | Viewed by 4160

Abstract

We have previously developed an approach, where two-dimensional gel electrophoresis (2DE) was used, followed by sectional analysis of the whole gel using high-resolution nano-liquid chromatography-mass spectrometry (ESI LC-MS/MS). In this study, we applied this approach on the panoramic analysis of proteins and their [...] Read more.

We have previously developed an approach, where two-dimensional gel electrophoresis (2DE) was used, followed by sectional analysis of the whole gel using high-resolution nano-liquid chromatography-mass spectrometry (ESI LC-MS/MS). In this study, we applied this approach on the panoramic analysis of proteins and their proteoforms from normal (liver) and cancer (HepG2) cells. This allowed us to detect, in a single proteome, about 20,000 proteoforms coded by more than 4000 genes. A set of 3D-graphs showing distribution of these proteoforms in 2DE maps (profiles) was generated. A comparative analysis of these profiles between normal and cancer cells showed high variability and dynamics of many proteins. Among these proteins, there are some well-known features like alpha-fetoprotein (FETA) or glypican-3 (GPC3) and potential hepatocellular carcinoma (HCC) markers. More detailed information about their proteoforms could be used for generation of panels of more specific biomarkers. Full article

(This article belongs to the Special Issue Selected Papers from “Clinical Proteomics. Postgenome Medicine 2017”)

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Open AccessArticle

A Proteomic Approach to Investigate the Drought Response in the Orphan Crop Eragrostis tef

by Rizqah Kamies, Jill M. Farrant, Zerihun Tadele, Gina Cannarozzi and Mohammed Suhail Rafudeen

Proteomes 2017, 5(4), 32; https://doi.org/10.3390/proteomes5040032 - 15 Nov 2017

Cited by 20 | Viewed by 6131

Abstract

The orphan crop, Eragrostis tef, was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50% [...] Read more.

The orphan crop, Eragrostis tef, was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50% relative water content (RWC) before adverse effects in leaf tissues were observed. Proteomic analysis using isobaric tag for relative and absolute quantification (iTRAQ) mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with the imposed stress conditions. Validation of the iTRAQ dataset was done with selected stress-related proteins, fructose-bisphosphate aldolase (FBA) and the protective antioxidant proteins, monodehydroascorbate reductase (MDHAR) and peroxidase (POX). Western blot analyses confirmed protein presence and showed increased protein abundance levels during water deficit while enzymatic activity for FBA, MDHAR and POX increased at selected RWC points. Gene ontology (GO)-term enrichment and analysis revealed terms involved in biotic and abiotic stress response, signaling, transport, cellular homeostasis and pentose metabolic processes, to be enriched in tef upregulated proteins, while terms linked to reactive oxygen species (ROS)-producing processes under water-deficit, such as photosynthesis and associated light harvesting reactions, manganese transport and homeostasis, the synthesis of sugars and cell wall catabolism and modification, to be enriched in tef downregulated proteins. Full article

(This article belongs to the Special Issue Plant Proteomics 2017)

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Open AccessArticle

Quantification of Cardiovascular Disease Biomarkers in Human Platelets by Targeted Mass Spectrometry

by Sebastian Malchow, Christina Loosse, Albert Sickmann and Christin Lorenz

Proteomes 2017, 5(4), 31; https://doi.org/10.3390/proteomes5040031 - 15 Nov 2017

Cited by 13 | Viewed by 6120

Abstract

Platelets are known to be key players in thrombosis and hemostasis, contributing to the genesis and progression of cardiovascular diseases. Due to their pivotal role in human physiology and pathology, platelet function is regulated tightly by numerous factors which have either stimulatory or [...] Read more.

Platelets are known to be key players in thrombosis and hemostasis, contributing to the genesis and progression of cardiovascular diseases. Due to their pivotal role in human physiology and pathology, platelet function is regulated tightly by numerous factors which have either stimulatory or inhibitory effects. A variety of factors, e.g., collagen, fibrinogen, ADP, vWF, thrombin, and thromboxane promote platelet adhesion and aggregation by utilizing multiple intracellular signal cascades. To quantify platelet proteins for this work, a targeted proteomics workflow was applied. In detail, platelets are isolated and lyzed, followed by a tryptic protein digest. Subsequently, a mix of stable isotope-labeled peptides of interesting biomarker proteins in concentrations ranging from 0.1 to 100 fmol is added to 3 μg digest. These peptides are used as an internal calibration curve to accurately quantify endogenous peptides and corresponding proteins in a pooled platelet reference sample by nanoLC-MS/MS with parallel reaction monitoring. In order to assure a valid quantification, limit of detection (LOD) and limit of quantification (LOQ), as well as linear range, were determined. This quantification of platelet activation and proteins by targeted mass spectrometry may enable novel diagnostic strategies in the detection and prevention of cardiovascular diseases. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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Open AccessReview

A Systematic Review and Meta-Analysis of Proteomics Literature on the Response of Human Skeletal Muscle to Obesity/Type 2 Diabetes Mellitus (T2DM) Versus Exercise Training

by Kanchana Srisawat, Sam O. Shepherd, Paulo J. Lisboa and Jatin G. Burniston

Proteomes 2017, 5(4), 30; https://doi.org/10.3390/proteomes5040030 - 11 Nov 2017

Cited by 26 | Viewed by 7123

Abstract

We performed a systematic review and meta-analysis of proteomics literature that reports human skeletal muscle responses in the context of either pathological decline associated with obesity/T2DM and physiological adaptations to exercise training. Literature was collected from PubMed and DOAJ databases following PRISMA guidelines [...] Read more.

We performed a systematic review and meta-analysis of proteomics literature that reports human skeletal muscle responses in the context of either pathological decline associated with obesity/T2DM and physiological adaptations to exercise training. Literature was collected from PubMed and DOAJ databases following PRISMA guidelines using the search terms ‘proteom*’, and ‘skeletal muscle’ combined with either ‘obesity, insulin resistance, diabetes, impaired glucose tolerance’ or ‘exercise, training’. Eleven studies were included in the systematic review, and meta-analysis was performed on a sub-set (four studies) of the reviewed literature that reported the necessary primary data. The majority of proteins (n = 73) more abundant in the muscle of obese/T2DM individuals were unique to this group and not reported to be responsive to exercise training. The main response of skeletal muscle to exercise training was a greater abundance of proteins of the mitochondrial electron transport chain, tricarboxylic acid cycle and mitochondrial respiratory chain complex I assembly. In total, five proteins were less abundant in muscle of obese/T2DM individuals and were also reported to be more abundant in the muscle of endurance-trained individuals, suggesting one of the major mechanisms of exercise-induced protection against the deleterious effects of obesity/T2DM occurs at complex I of the electron transport chain. Full article

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Open AccessArticle

Proteomic Investigations of Proteases Involved in Cotyledon Senescence: A Model to Explore the Genotypic Variability of Proteolysis Machinery Associated with Nitrogen Remobilization Efficiency during the Leaf Senescence of Oilseed Rape

by Marine Poret, Balakumaran Chandrasekar, Renier A. L. Van der Hoorn, Laurent Coquet, Thierry Jouenne and Jean-Christophe Avice

Proteomes 2017, 5(4), 29; https://doi.org/10.3390/proteomes5040029 - 2 Nov 2017

Cited by 11 | Viewed by 4281

Abstract

Oilseed rape is characterized by a low nitrogen remobilization efficiency during leaf senescence, mainly due to a lack of proteolysis. Because cotyledons are subjected to senescence, it was hypothesized that contrasting protease activities between genotypes may be distinguishable early in the senescence of [...] Read more.

Oilseed rape is characterized by a low nitrogen remobilization efficiency during leaf senescence, mainly due to a lack of proteolysis. Because cotyledons are subjected to senescence, it was hypothesized that contrasting protease activities between genotypes may be distinguishable early in the senescence of cotyledons. To verify this assumption, our goals were to (i) characterize protease activities in cotyledons between two genotypes with contrasting nitrogen remobilization efficiency (Ténor and Samouraï) under limiting or ample nitrate supply; and (ii) test the role of salicylic acid (SA) and abscisic acid (ABA) in proteolysis regulation. Protease activities were measured and identified by a proteomics approach combining activity-based protein profiling with LC-MS/MS. As in senescing leaves, chlorophyll and protein contents decrease in senescing cotyledons and are correlated with an increase in serine and cysteine protease activities. Two RD21-like and SAG-12 proteases previously associated with an efficient proteolysis in senescing leaves of Ténor are also detected in senescing cotyledons. The infiltration of ABA and SA provokes the induction of senescence and several cysteine and serine protease activities. The study of protease activities during the senescence of cotyledons seems to be a promising experimental model to investigate the regulation and genotypic variability of proteolysis associated with efficient N remobilization. Full article

(This article belongs to the Special Issue Plant Proteomics 2017)

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Open AccessReview

Comprehensive Analysis of Cancer-Proteogenome to Identify Biomarkers for the Early Diagnosis and Prognosis of Cancer

by Hem D. Shukla

Proteomes 2017, 5(4), 28; https://doi.org/10.3390/proteomes5040028 - 25 Oct 2017

Cited by 30 | Viewed by 5846

Abstract

During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it [...] Read more.

During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it has steered us into therapeutic target discovery, enabling us to mine the genome using cutting edge proteogenomics tools. A number of novel and promising cancer targets have emerged from the genome project for diagnostics, therapeutics, and prognostic markers, which are being used to monitor response to cancer treatment. The heterogeneous nature of cancer has hindered progress in understanding the underlying mechanisms that lead to abnormal cellular growth. Since, the start of The Cancer Genome Atlas (TCGA), and the International Genome consortium projects, there has been tremendous progress in genome sequencing and immense numbers of cancer genomes have been completed, and this approach has transformed our understanding of the diagnosis and treatment of different types of cancers. By employing Genomics and proteomics technologies, an immense amount of genomic data is being generated on clinical tumors, which has transformed the cancer landscape and has the potential to transform cancer diagnosis and prognosis. A complete molecular view of the cancer landscape is necessary for understanding the underlying mechanisms of cancer initiation to improve diagnosis and prognosis, which ultimately will lead to personalized treatment. Interestingly, cancer proteome analysis has also allowed us to identify biomarkers to monitor drug and radiation resistance in patients undergoing cancer treatment. Further, TCGA-funded studies have allowed for the genomic and transcriptomic characterization of targeted cancers, this analysis aiding the development of targeted therapies for highly lethal malignancy. High-throughput technologies, such as complete proteome, epigenome, protein–protein interaction, and pharmacogenomics data, are indispensable to glean into the cancer genome and proteome and these approaches have generated multidimensional universal studies of genes and proteins (OMICS) data which has the potential to facilitate precision medicine. However, due to slow progress in computational technologies, the translation of big omics data into their clinical aspects have been slow. In this review, attempts have been made to describe the role of high-throughput genomic and proteomic technologies in identifying a panel of biomarkers which could be used for the early diagnosis and prognosis of cancer. Full article

(This article belongs to the Special Issue Cancer Proteomics)

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Open AccessReview

Mass Spectrometric Studies of Apolipoprotein Proteoforms and Their Role in Lipid Metabolism and Type 2 Diabetes

by Dobrin Nedelkov

Proteomes 2017, 5(4), 27; https://doi.org/10.3390/proteomes5040027 - 15 Oct 2017

Cited by 15 | Viewed by 4398

Abstract

Apolipoproteins function as structural components of lipoprotein particles, cofactors for enzymes, and ligands for cell-surface receptors. Most of the apoliporoteins exhibit proteoforms, arising from single nucleotide polymorphisms (SNPs) and post-translational modifications such as glycosylation, oxidation, and sequence truncations. Reviewed here are recent studies [...] Read more.

Apolipoproteins function as structural components of lipoprotein particles, cofactors for enzymes, and ligands for cell-surface receptors. Most of the apoliporoteins exhibit proteoforms, arising from single nucleotide polymorphisms (SNPs) and post-translational modifications such as glycosylation, oxidation, and sequence truncations. Reviewed here are recent studies correlating apolipoproteins proteoforms with the specific clinical measures of lipid metabolism and cardiometabolic risk. Targeted mass spectrometric immunoassays toward apolipoproteins A-I, A-II, and C-III were applied on large cross-sectional and longitudinal clinical cohorts. Several correlations were observed, including greater apolipoprotein A-I and A-II oxidation in patients with diabetes and cardiovascular disease, and a divergent apoC-III proteoforms association with plasma triglycerides, indicating significant differences in the metabolism of the individual apoC-III proteoforms. These are the first studies of their kind, correlating specific proteoforms with clinical measures in order to determine their utility as potential clinical biomarkers for disease diagnosis, risk stratification, and therapy decisions. Such studies provide the impetus for the further development and clinical translation of MS-based protein tests. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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Open AccessFeature PaperReview

Proteogenomics in Aid of Host–Pathogen Interaction Studies: A Bacterial Perspective

by Ursula Fels, Kris Gevaert and Petra Van Damme

Proteomes 2017, 5(4), 26; https://doi.org/10.3390/proteomes5040026 - 11 Oct 2017

Cited by 14 | Viewed by 6523

Abstract

By providing useful tools to study host–pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, [...] Read more.

By providing useful tools to study host–pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, the depth of quantitative gene expression profiling has proven to be unsatisfactory when focusing on bacterial pathogens, thus preferentially requiring specific strategies or the development of novel methodologies based on complementary omics approaches. In this review, we focus on the difficulties encountered when making use of proteogenomics approaches to study bacterial pathogenesis. In addition, we review different omics strategies (i.e., transcriptomics, proteomics and secretomics) and their applications for studying interactions of pathogens with their host. Full article

(This article belongs to the Special Issue Proteomic Analysis of Host-Microbial Pathogen Interactions)

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Open AccessArticle

Differential Proteome Analysis of Extracellular Vesicles from Breast Cancer Cell Lines by Chaperone Affinity Enrichment

by Steven G. Griffiths, Michelle T. Cormier, Aled Clayton and Alan A. Doucette

Proteomes 2017, 5(4), 25; https://doi.org/10.3390/proteomes5040025 - 8 Oct 2017

Cited by 42 | Viewed by 7258

Abstract

The complexity of human tissue fluid precludes timely identification of cancer biomarkers by immunoassay or mass spectrometry. An increasingly attractive strategy is to primarily enrich extracellular vesicles (EVs) released from cancer cells in an accelerated manner compared to normal cells. The Vn96 peptide [...] Read more.

The complexity of human tissue fluid precludes timely identification of cancer biomarkers by immunoassay or mass spectrometry. An increasingly attractive strategy is to primarily enrich extracellular vesicles (EVs) released from cancer cells in an accelerated manner compared to normal cells. The Vn96 peptide was herein employed to recover a subset of EVs released into the media from cellular models of breast cancer. Vn96 has affinity for heat shock proteins (HSPs) decorating the surface of EVs. Reflecting their cells of origin, cancer EVs displayed discrete differences from those of normal phenotype. GELFrEE LC/MS identified an extensive proteome from all three sources of EVs, the vast majority having been previously reported in the ExoCarta database. Pathway analysis of the Vn96-affinity proteome unequivocally distinguished EVs from tumorigenic cell lines (SKBR3 and MCF-7) relative to a non-tumorigenic source (MCF-10a), particularly with regard to altered metabolic enzymes, signaling, and chaperone proteins. The protein data sets provide valuable information from material shed by cultured cells. It is probable that a vast amount of biomarker identities may be collected from established and primary cell cultures using the approaches described here. Full article

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Open AccessArticle

Performance of a Multiplex Serological Helicobacter pylori Assay on a Novel Microfluidic Assay Platform

by Angela Filomena, Anna Guenther, Hannes Planatscher, Francois Topin, Joseph She, Luca Formichella, Laurent Terradot, Markus Gerhard, Thomas O. Joos, Hannelore Meyer and Nicole Schneiderhan-Marra

Proteomes 2017, 5(4), 24; https://doi.org/10.3390/proteomes5040024 - 3 Oct 2017

Cited by 11 | Viewed by 5372

Abstract

Infection with Helicobacter pylori (H. pylori) occurs in 50% of the world population, and is associated with the development of ulcer and gastric cancer. Serological diagnostic tests indicate an H. pylori infection by detecting antibodies directed against H. pylori proteins. In [...] Read more.

Infection with Helicobacter pylori (H. pylori) occurs in 50% of the world population, and is associated with the development of ulcer and gastric cancer. Serological diagnostic tests indicate an H. pylori infection by detecting antibodies directed against H. pylori proteins. In addition to line blots, multiplex assay platforms provide smart solutions for the simultaneous analysis of antibody responses towards several H. pylori proteins. We used seven H. pylori proteins (FliD, gGT, GroEL, HpaA, CagA, VacA, and HP0231) and an H. pylori lysate for the development of a multiplex serological assay on a novel microfluidic platform. The reaction limited binding regime in the microfluidic channels allows for a short incubation time of 35 min. The developed assay showed very high sensitivity (99%) and specificity (100%). Besides sensitivity and specificity, the technical validation (intra-assay CV = 3.7 ± 1.2% and inter-assay CV = 5.5 ± 1.2%) demonstrates that our assay is also a robust tool for the analysis of the H. pylori-specific antibody response. The integration of the virulence factors CagA and VacA allow for the assessment of the risk for gastric cancer development. The short assay time and the performance of the platform shows the potential for implementation of such assays in a clinical setting. Full article

(This article belongs to the Special Issue Proteomic Biomarkers in Human Diseases)

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Proteomes, Volume 5, Issue 4 (December 2017) – 13 articles

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