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  • Automatic identification and quantification of extra-well fluorescence in microarray images
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-22
    Robert Rivera, Jie Wang, xiaobo yu, Gokhan Demirkan, Marika Hopper, Xiaofang Bian, Tasnia Tahsin, D. Mitchell Magee, Ji Qiu, Joshua LaBaer, Garrick Wallstrom

    In recent studies involving NAPPA microarrays, extra-well fluorescence is used as a key measure for identifying disease biomarkers since there is evidence to support that it is better correlated with strong antibody responses than statistical analysis involving intra-spot intensity. Since this feature is not well quantified by traditional image analysis software, identification and quantification of extra-well fluorescence is performed manually, which is both time consuming and highly susceptible to variation between raters. A system that could automate this task efficiently and effectively would greatly improve the process of data acquisition in microarray studies, thereby accelerating the discovery of disease biomarkers. In this study, we experimented with different machine learning methods, as well as novel heuristics, for identifying spots exhibiting extra-well fluorescence (rings) in microarray images, and assigning each ring a grade of 1-5 based on its intensity and morphology. The sensitivity of our final system for identifying rings was found to be 72% at 99% specificity and 98% at 92% specificity. Our system performs this task significantly faster than a human, while maintaining high performance, and therefore, represents a valuable tool for microarray image analysis.

    更新日期:2017-09-23
  • The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-22
    Jochen M Schwenk, Gilbert S Omenn, Zhi Sun, David S Campbell, Mark S. Baker, Christopher M Overall, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch

    Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome Organization’s Human Plasma Proteome Project (HPPP) has been promoting advances in the study and understanding of the full protein complement of human plasma and on determining the abundance and modifications of its components. In 2017, we review the history of the HPPP and the advances of human plasma proteomics in general, including several recent achievements. We then present the latest 2017-04 build of Human Plasma PeptideAtlas, which yields ~43 million peptide-spectrum matches and 122,730 distinct peptide sequences from 178 individual experiments at a 1% protein-level FDR globally across all experiments. Applying the latest Human Proteome Project Data Interpretation Guidelines, we catalog 3509 proteins that have at least two non-nested uniquely-mapping peptides of 9 amino acids or more and >1300 additional proteins with ambiguous evidence. We apply the same two-peptide guideline to historical PeptideAtlas builds going back to 2006 and examine the progress made in the past ten years in plasma proteome coverage. We also compare the distribution of proteins in historical PeptideAtlas builds in various RNA-abundance and cellular localization categories. We then discuss advances in plasma proteomics based on targeted mass spectrometry as well as affinity assays, which during early 2017 target ~2000 proteins. Finally we describe considerations about sample handling and study design, concluding with an outlook for future advances in deciphering the human plasma proteome.

    更新日期:2017-09-23
  • Urinary metabolic phenotyping of women with lower urinary tract symptoms
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-22
    Rhiannon Bray, Stefano Cacciatore, Beatriz Jimenez, Rufus Cartwright, Alex Digesu, Ruwan Fernando, Elaine Holmes, Jeremy Kirk Nicholson, Phillip R. Bennett, David A. MacIntyre, Vik Khullar

    Lower urinary tract symptoms (LUTS), including urinary incontinence, urgency and nocturia, affect approximately half of women worldwide. Current diagnostic methods for LUTS are invasive and costly, while available treatments are limited by side effects leading to poor patient compliance. In this study, we aimed to identify urine metabolic signatures associated with LUTS using proton nuclear magnetic resonance (1H-NMR) spectroscopy. A total of 214 urine samples were collected from women attending tertiary urogynaecology clinics (cases; n=176) and healthy control women attending general gynecology clinics (n=36). Despite high variation in the urine metabolome across the cohort, associations between urine metabolic profiles and BMI, parity, overactive bladder syndrome, frequency, straining and bladder storage were identified using KODAMA (knowledge discovery by accuracy maximization). Four distinct urinary metabotypes were identified, one of which was associated with increased urinary frequency and low BMI. Urine from these patients was characterized by increased levels of isoleucine and decreased levels of hippurate. Our study suggests that metabolic profiling of urine samples from LUTS patients offers the potential to identify differences in underlying aetiology, which may permit stratification of patient populations and the design of more personalized treatment strategies.

    更新日期:2017-09-23
  • Identification of Siglec Ligands Using a Proximity Labeling Method
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-22
    Lanyi Chang, Yi-Ju Chen, Chan-Yo Fan, Chin-Ju Tang, Yi-Hsiu Chen, Penk-Yeir Low, Albert Ventura, Chun-Cheng Lin, Yu-Ju Chen, Takashi Angata
    更新日期:2017-09-22
  • Human Prestin: A Candidate PE1 Protein Lacking Stringent Mass Spectrometric Evidence?
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-21
    Abidali Mohamedali, Seong Beom Ahn, Varun K. A. Sreenivasan, Shoba Ranganathan, Mark S. Baker
    更新日期:2017-09-21
  • We are not alone: The iMOP initiative and its roles in a Biology and Disease driven Human Proteome Project.
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-21
    Andreas Tholey, Nicolas L Taylor, Joshua L. Heazlewood, Emøke Bendixen

    The Human Proteome is nearly fully mapped and will provide a knowledge base to accelerate our understanding of how proteins and protein networks can affect human health and disease. However, providing solutions to human health challenges will likely fail if insights are exclusively based on studies of human samples and human proteomes. In recent years, it has become evident that human health depends on an integrated understanding of the many species that make human life possible. These include the commensal microorganisms which are essential to human life, pathogens and food species as well as the classic model organisms that enable studies of biological mechanisms. The Human Proteome Organization (HUPO) initiative on multi-organism proteomes (iMOP) works to support proteome research undertaken on non-human species which remain widely under-studied compared to the progress in human proteome research. This perspective argues the need for further research on multiple species that impact human life. We also present an update on recent progress in model organisms, microbiota, and food species, address the emerging problem of antibiotics resistance, and outline how iMOP activities could lead to a more inclusive approach for the human proteome project (HPP) to better support proteome research aimed at improving human health and furthering knowledge on human biology.

    更新日期:2017-09-21
  • Quantitative Proteomics Reveals the Regulatory Networks of Circular RNA CDR1as in Hepatocellular Carcinoma Cells
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-20
    Xue Yang, Qian Xiong, Ying Wu, Siting Li, Feng Ge
    更新日期:2017-09-20
  • Decoding the Effect of Isobaric Substitutions on Identifying Missing Proteins and Variant Peptides in Human Proteome
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-20
    Wai-Kok Choong, Tung-Shing Mamie Lih, Yu-Ju Chen, Ting-Yi Sung

    To confirm the existence of missing proteins, we need to identify at least two unique peptides with length of 9-40 amino acids of a missing protein in bottom-up mass spectrometry-based proteomic experiments. However, an identified unique peptide of the missing protein, even identified with high level of confidence, could possibly coincide with a peptide of a commonly observed protein due to isobaric substitutions, mass modifications, alternative splice isoforms, or single amino acid variants (SAAVs). Besides unique peptides of missing proteins, identified variant peptides (SAAV-containing peptides) could also alternatively map to peptides of other proteins due to the aforementioned issues. Therefore, we conducted a thorough comparative analysis on data sets in PeptideAtlas Tiered Human Integrated Search Proteome (THISP, 2017-03 release), including neXtProt (2017-01 release), to systematically investigate the possibility of unique peptides in missing proteins (PE2-4), unique peptides in dubious proteins, and variant peptides affected by isobaric substitutions, causing doubtful identification results. In this study, we considered eleven isobaric substitutions. From our analysis, we found <5% of the unique peptides of missing proteins and >6% of variant peptides became shared with peptides of PE1 proteins after isobaric substitutions.

    更新日期:2017-09-20
  • Protein corona analysis of silver nanoparticles links to their cellular effects
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-20
    Sabine Juling, Alicia Niedzwiecka, Linda Böhmert, Dajana Lichtenstein, Soeren Selve, Albert Braeuning, Andreas F. Thünemann, Eberhard Krause, Alfonso Lampen

    The breadth of applications of nanoparticles and the access to food-associated consumer products containing nano-sized materials lead to oral human exposure to such particles. In biological fluids nanoparticles dynamically interact with biomolecules and form a protein corona. Knowledge about the protein corona is of great interest for understanding the molecular effects of particles as well as their fate inside the human body. We used a mass spectrometry-based toxicoproteomics approach to elucidate mechanisms of toxicity of silver nanoparticles and to comprehensively characterize the protein corona formed around silver nanoparticles in Caco-2 human intestinal epithelial cells. Results were compared with respect to the cellular function of proteins either affected by exposure to nanoparticles or present in the protein corona. A transcriptomic dataset was included in the analyses in order to obtain a combined multi-omics view of nanoparticle-affected cellular processes. A relationship between corona proteins and the proteomic or transcriptomic responses was revealed showing that differentially regulated proteins or transcripts were engaged in the same cellular signaling pathways. Protein corona analyses of nanoparticles in cells might therefore help obtaining information about the molecular consequences of nanoparticles treatment.

    更新日期:2017-09-20
  • Discovery of Tamoxifen and N-Desmethyl Tamoxifen Protein Targets in MCF-7 Cells Using Large-Scale Protein Folding and Stability Measurements
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-19
    Ryenne N. Ogburn, Lorrain Jin, He Meng, Michael C Fitzgerald

    The proteins in an MCF-7 cell line were probed for tamoxifen (TAM) and n-desmethyl tamoxifen (NDT) induced stability changes using the Stability of Proteins from Rates of Oxidation (SPROX) technique in combination with two different quantitative proteomics strategies, including one based on SILAC and one based on isobaric mass tags. Over 1000 proteins were assayed for TAM- and NDT- induced protein stability changes, and a total of 163 and 200 protein hits were identified in the TAM and NDT studies, respectively. A subset of 27 high confidence protein hits were reproducibly identified with both proteomics strategies and/or with multiple peptide probes. One-third of the high confidence hits have previously established experimental links to the estrogen receptor, and nearly all of the high confidence hits have established links to breast cancer. One high confidence protein hit that has known estrogen receptor binding properties, Y-box binding protein 1 (YBX1), was further validated as a direct binding target of TAM using both the SPROX and pulse proteolysis techniques. Proteins with TAM- and/or NDT-induced expression level changes were also identified in the SILAC-SPROX experiments. These proteins with expression level changes included only a small fraction of those with TAM- and/or NDT-induced stability changes.

    更新日期:2017-09-20
  • Proteomic Analysis of Peripheral Blood Mononuclear Cells (PBMC) after a High-Fat, High-Carbohydrate Meal With Orange Juice
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-19
    Daniela F. Seixas Chaves, Paulo C. Carvalho, Elisa Brasili, Marcelo Macedo Rogero, Neuza Mariko Aymoto Hassimotto, Jolene K Diedrich, James J Moresco, John R. Yates, Franco Maria Lajolo

    Oxidative stress and inflammation play a role in the physiopathology of insulin resistance, diabetes and cardiovascular disease. A single high-fat, high-carbohydrate (HFHC) meal induces an increase in inflammatory and oxidative stress markers in peripheral blood mononuclear cells (PBMC). Previous studies have shown that orange juice is able to prevent this response by inhibiting toll like receptors (TLR) expression and endotoxemia. Our goal was to study the proteome response in PBMC after the consumption of a HFHC meal consumed with water, orange juice or an isocaloric beverage (water with glucose). Twelve healthy individuals completed the protocol in a cross-over design and blood samples were obtained before and 1, 3, and 5 h after consumption. Proteomic profile, glucose, insulin, lipid and cytokines levels were investigated. The glycemic and insulinemic response was higher when the meal was consumed with glucose while there was no difference in the response between water and orange juice. Proteome analysis in PBMC was carried out using TMT ten-plex. A total of 3,813 proteins, originating from 15,662 peptides were identified. Three proteins showed significantly altered expression in the three treatments: apolipoprotein A-II, ceruloplasmin and hemopexin. When the HFHC meal was consumed with water there was an increase in some inflammatory pathways such as the Fc-gamma receptor dependent phagocytosis and the complement cascade, but the immune system as a whole was not significantly altered. However, when the meal was consumed with glucose, the immune system was up regulated. Among the pathways induced after 3 h were those of the adaptive immune system and cytokine signaling. Five hours after the meal, pathways of the complement cascade and classical antibody mediated complement activation were up regulated. When the meal was consumed with orange juice there was an up regulation of proteins involved in signal transduction, DNA replication and cell cycle. The promyelocytic leukemia protein (PML) showed a 28.2-fold increase. This protein was down regulated when the meal was consumed with water. Regarding the immune system, several of the pathways induced by glucose were down regulated when the meal was consumed with orange juice: proteins involved with the adaptive immune system and cytokine signaling. Therefore, we have shown that orange juice can not only suppress diet induced inflammation, but also regulate the expression of proteins such as PML, that may play a key role in the regulation of metabolism.

    更新日期:2017-09-20
  • Ultradeep Lysine Crotonylome Reveals the Crotonylation Enhancement on Both Histones and Nonhistone Proteins by SAHA Treatment
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-19
    Quan Wu, Wenting Li, Chi Wang, Pingsheng Fan, Lejie Cao, Zhiwei Wu, Fengsong Wang
    更新日期:2017-09-19
  • Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-19
    Nadia G. D’Lima, Alexandra Khitun, Aaron D. Rosenbloom, Peijia Yuan, Brandon M. Gassaway, Karl W. Barber, Jesse Rinehart, Sarah A. Slavoff
    更新日期:2017-09-19
  • Absolute quantification of human milk caseins and the whey/casein ratio during the first year of lactation
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-19
    Yalin Liao, Darren Weber, Wei Xu, Blythe P. Durbin-Johnson, Brett S Phinney, Bo Lönnerdal

    Abstract Whey proteins and caseins in breast milk provide bioactivities and also have different amino acid composition. Accurate determination of these two major protein classes will therefore provide a better understanding of human milk composition and function, further aid in developing improved infant formulas based on bovine whey proteins and caseins. In this study, we implemented a LC-MS/MS quantitative analysis based on iBAQ label-free quantitation, to estimate absolute concentrations of alpha-casein, beta-casein and kappa-casein in human milk samples (n=88) collected between day 1 and day 360 post partum. Total protein concentration ranged from 2.03 to 17.52 with a mean of 9.37±3.65 g/L. Casein subunits ranged from 0.04 to 1.68 g/L (alpha-), 0.04 to 4.42 g/L (beta-), and 0.10 to 1.72 g/L (kappa-), with beta-casein having the highest average concentration among the three subunits. Calculated whey/casein ratio ranged from 45:55 to 97:3. Linear regression analyses show significant decreases in total protein, beta-casein, kappa-casein, total casein, and significant increase of whey/casein ratio during the course of lactation. Our study presents a novel and accurate quantitative analysis of human milk casein content, demonstrating a lower casein content than earlier believed, which has implications for improved infants formulas.

    更新日期:2017-09-19
  • Metabolomic Fingerprinting in Various Body Fluids of a Diet-Controlled Clinical Smoking Cessation Study Using a Validated GC-TOF-MS Metabolomics Platform
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-18
    Michael Goettel, Reinhard Niessner, Daniel Mueller, Max Scherer, Gerhard Scherer, Nikola Pluym
    更新日期:2017-09-19
  • Quantitative Proteomics for the Comprehensive Analysis of Stress Responses of Lactobacillus paracasei subsp. paracasei F19
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-18
    Ann-Sophie Schott, Jürgen Behr, Andreas J. Geißler, Bernhard Kuster, Hannes Hahne, Rudi F. Vogel
    更新日期:2017-09-19
  • PTML Model for Proteome Mining of B-cell Epitopes and Theoretic-Experimental Study of Bm86 Protein Sequences from Colima Mexico
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-18
    Saúl Gabriel Martínez, Esvieta Tenorio-Borroto, Alberto Barbabosa Pliego, Hector Diaz-Albiter, Juan C. Vazquez-Chagoyan, Humbert Gonzalez-Diaz

    In this work, we developed a general Perturbation Theory and Machine Learning (PTML) method for data mining of proteomes, in order to discover new B-cell epitopes useful for vaccine design. The method predicts the epitope activity εq(cqj) of one query peptide (q-peptide) in a set of experimental query conditions (cqj). The method uses as input the sequence of the q-peptide. The method also uses as input information about the sequence and epitope activity εr(crj) of a peptide of reference (r-peptide) assayed on similar experimental conditions (crj). The model proposed here is able to classify 1,048,190 pairs of query and reference peptide sequences from the proteome of many organisms reported on IEDB database. These pairs have variations (perturbations) in sequence or assay conditions. The model has accuracy, sensitivity, and specificity between71% and 80% for training and external validation series. The retrieved information contains structural changes in 83683 peptides sequences (Seq) determined in experimental assays with boundary conditions involving 1448 Epitope Organisms (Org), 323 Host Organisms (Host), 15 types of In vivo Process (Proc), 28 Experimental Techniques(Tech), and 505 Adjuvant additives(Adj). Afterwards, we reported the experimental sampling, isolation, and sequencing of 15 complete sequences of Bm86 gene from state of Colima, Mexico. Last, we used the model to predict the epitope immunogenic scores in different experimental conditions for the 26112 peptides obtained from these sequences. The model may become a useful tool for epitope selection towards vaccine design. The theoretic-experimental results on Bm86 protein may help on the future design of a new vaccine based on this protein.

    更新日期:2017-09-19
  • Serum Proteomic Variability Associated with Clinical Phenotype in Familial Transthyretin Amyloidosis (ATTRm)
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-18
    Gloria G. Chan, Clarissa M. Koch, Lawreen H. Connors

    Transthyretin (TTR), normally a plasma circulating protein, can become misfolded and aggregated, ultimately leading to extracellular deposition of amyloid fibrils usually targeted to heart or nerve tissues. Referred to as TTR-associated amyloidoses (ATTR), this group of diseases is frequently life threatening and fatal if untreated. ATTR, caused by amyloid-forming variant TTR proteins (ATTRm) which arise from point mutations in the TTR gene, were classically referred to as familial amyloid cardiomyopathy (FAC) or familial amyloid polyneuropathy (FAP) reflecting the clinical phenotype. FAC and FAP are pathologies that can be challenging to diagnose as there are no definitive biomarkers of disease; moreover, disease-specific measures of progression are lacking and treatment options are limited. Thus, the discovery of sensitive and specific indicators of disease has the potential to improve recognition, enable accurate measurement of amyloid progression and response to treatment, and reveal key information regarding FAC and FAP pathobiological mechanisms. In this study, the goal was to investigate serum proteomic features unique to FAC and FAP types of ATTRm. Multiple-reaction monitoring mass spectrometry (MRM-MS), a powerful technique in profiling proteomes, was used to measure the serum concentrations of 160 proteins in samples from FAC and FAP patients. Results were compared to data from healthy control sera obtained from individuals matched to age (≥ 60 years), gender (male), and race (Caucasian). Proteomic analyses of ATTRm (FAC and FAP) and control samples showed significant concentration differences in 107 of 192 (56%) of the serum proteins that were studied. In comparing FAC to FAP, differences in concentrations, and interactions and functions of several proteins were identified as unique to each disease; significantly lower levels of TTR were specific to FAC, but not to FAP. Annotated functional clustering identified extracellular region, signal and signal peptide as terms common to FAC and FAP. Conversely, disulfide bond was unique to FAC; secreted, glycosylation site:N-linked, glycosylation, glycoprotein, polymorphism, and sequence variant were associated solely with FAP. Predicted protein-protein associations in FAC were seen for reaction, binding, and activation processes; no associations were found in FAP. This study demonstrates significant proteomic differences between ATTRm patient and control sera, as well as ATTRm phenotype-associated variations in the circulating levels of several proteins including TTR. The identification of serum proteins unique to FAC and FAP may have diagnostic and prognostic utility, and could possibly provide important clues about disease mechanisms.

    更新日期:2017-09-19
  • Unrestricted mass spectrometric data analysis for identification, localization and quantification of oxidative protein modifications
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-18
    Martin Rykær, Birte Svensson, Michael J. Davies, Per Hägglund

    Oxidation generates multiple diverse post-translational modifications resulting in changes in protein structure and function, associated with a wide range of diseases. Of these modifications, carbonylations have often been used as hallmarks of oxidative damage. However, accumulating evidence supports the hypothesis that other oxidation products may be quantitatively more important under physiological conditions. To address this issue we have developed a holistic mass spectrometry-based approach for simultaneous identification, localization and quantification of a broad range of oxidative modifications based on so-called ‘dependent peptides’. The strategy involves unrestricted database searches with rigorous filtering focusing on oxidative modifications. The approach was applied to bovine serum albumin and human serum proteins subjected to metal ion-catalyzed oxidation resulting in identification of more than sixty different types of oxidative modifications. The most common modification in the oxidized samples is hydroxylation, but carbonylation, decarboxylation and dihydroxylation, are also abundant. Carbonylation however showed the largest increase in abundance relative to non-oxidized control samples. Site specific localization of modified residues reveals several ‘oxidation hotspots’ showing high levels of modification occupancy, including specific histidine, tryptophan, methionine, glutamate and aspartate residues, even though the majority of the modifications occur at low occupancy levels on a diversity of side-chains.

    更新日期:2017-09-18
  • Nε- and O-Acetylation in Mycobacterium tuberculosis Lineage 7 and Lineage 4 strains: Proteins Involved in Bioenergetics, Virulence and Antimicrobial Resistance are Acetylated
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-18
    Alemayehu Godana Birhanu, Solomon Abebe Yimer, Carol Holm-Hansen, Gunnstein Norheim, Abraham Aseffa, Markos Abebe, Tone Tønjum

    Increasing evidence demonstrates that lysine acetylation is involved in Mycobacterium tuberculosis (Mtb) virulence and pathogenesis. However, previous investigations in Mtb have only monitored acetylation at lysine residues using selected reference strains. We analyzed the global Nε- and O-acetylation of 3 Mtb isolates; 2 lineage 7 clinical isolates and the lineage 4 H37Rv reference strain. Quantitative acetylome analysis resulted in identification of 2490 class-I acetylation sites, among them 2349 O-acetylation and 141 Nε-acetylation sites, derived from 953 unique proteins. Mtb O-acetylation was thereby significantly more abundant than Nε-acetylation. The acetylated proteins were found to be involved in central metabolism, translation, stress responses and antimicrobial drug resistance. Notably, 261 acetylation sites on 165 proteins were differentially regulated between lineage 7 and lineage 4 strains. A total of 257 acetylation sites on 161 proteins were hypoacetylated in lineage 7 strains. These proteins are involved in Mtb growth, virulence, bioenergetics, host-pathogen interaction and stress responses. This study provides the first global analysis of O-acetylated proteins in Mtb. This quantitative acetylome data expand the current understanding regarding the nature and diversity of acetylated proteins in Mtb, and opens a new avenue of research for exploring the role of protein acetylation in Mtb physiology. Keywords: Mycobacterium tuberculosis; lineage 7; post-translational modifications; acetylome; Nε-acetylation; O-acetylation.

    更新日期:2017-09-18
  • New insight of common regulatory pathways in human trabecular meshwork cells in response to dexamethasone and prednisolone using an integrated quantitative proteomics: SWATH and MRM-HR mass spectrometry
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-18
    Sze Wan Shan, Chi Wai Do, Thomas Chuen Lam, Ricky Pak Wing Kong, King Kit Li, Ka Man Chun, William Daniel Stamer, Chi Ho To

    The molecular pathophysiology of corticosteroid-induced ocular hypertension (CIH) is not well understood. To determine the biological mechanisms of CIH, this study investigated protein expression profiles of human trabecular meshwork (hTM) cells in response to dexamethasone and prednisolone treatment. Both discovery-based Sequential Windowed data independent Acquisition of the Total High-resolution mass spectra (SWATHTM-MS) and targeted based high resolution multiple reaction monitoring (MRM-HR) confirmation were applied using a hybrid quadrupole-time-of-flight mass spectrometer. A comprehensive list of 1,759 proteins (1% FDR) was generated from the hTM. Quantitative proteomics revealed twenty differentially expressed proteins (p-value of ≤0.05 and a fold-change of ≥1.5 or ≤ 0.67) commonly induced by prednisolone and dexamethasone, both at 300nM. These included connective tissue growth factor (CTGF) and thrombospondin-1 (THBS1), two proteins previously implicated in ocular hypertension, glaucoma, and the transforming growth factor-β pathway. Their gene expressions in response to corticosteroids were further confirmed using Reverse-transcription-PCR. Together with other novel proteins identified in the datasets, additional pathways implicated by these regulated proteins were the phosphatidylinositol 3-kinase (PI3K)-protein kinase B (Akt) signaling pathway, integrin cell surface interaction, extracellular matrix (ECM) proteoglycans, and ECM-receptor interaction. Our results indicated that an integrated platform of SWATHTM-MS and MRM-HR allows high throughput identification and confirmation of novel and known corticosteroid-regulated proteins in trabecular meshwork cells, demonstrating the power of this technique in extending the current understanding of the pathogenesis of CIH.

    更新日期:2017-09-18
  • Mass spectrometric analysis of SOX11-binding proteins in head and neck cancer cells demonstrates the interaction of SOX11 and HSP90α
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-15
    Naseim Elzakra, Li Cui, Tong Liu, Hong Li, Junwei Huang, Shen Hu

    Deregulated expression of SOX11 has been shown to involve in the progression of various types of cancer. However, the role of SOX11 in head and neck cancer remains largely unknown. In this study, co-immunoprecipitation (Co-IP) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were performed to identify the proteins that binds to SOX11 at significant higher levels in head and neck cancer cells compared to the normal human oral keratinocytes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that many potential SOX11-binding partners were associated with protein synthesis, cell metabolism and cell-cell adhesion. One of the identified proteins, heat shock protein 90 alpha (HSP90α), was selected for further investigation. The binding of HSP90α with SOX11 in head and neck cancer cells was validated by Co-IP with Western blotting. In addition, HSP90α was found to be remarkably overexpressed in head and neck cancer cell lines when compared to the normal human oral keratinocytes, and knockdown of HSP90α inhibited the proliferation and invasion capacity of the cancer cells. Based on The Cancer Genome Atlas (TCGA) data analysis, HSP90AA1 gene was overexpressed in head and neck cancer tissues compared to normal controls and increased HSP90AA1 gene expression was positively associated with extracapsular spread and clinical stage. Head and neck cancer patients with higher HSP90AA1 expression had significantly poorer long term overall and disease free survival rates than those with lower HSP90AA1 expression. Collectively, our studies indicate that SOX11 binds to HSP90α, a highly over-expressed protein that may promote invasion and progression of head and neck cancer cells.

    更新日期:2017-09-15
  • Chromosome-Centric Human Proteome Project Allies with Developmental Biology: a Case Study of the Role of Y chromosome Genes in Organ Development
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-15
    Anna Meyfour, Paria Pooyan, Sara Pahlavan, Mostafa Rezaei-Tavirani, Hamid Gourabi, Hossein Baharvand, Ghasem Hosseini Salekdeh

    One of the main goals of Chromosome-Centric Human Proteome Project is to identify protein evidence for missing proteins (MPs). Here, we present a case study of the role of Y chromosome genes in organ development and how to overcome the challenges facing MPs identification by employing human pluripotent stem cell differentiation into cells of different organs yielding unprecedented biological insight into adult silenced proteins. Y chromosome is a male-specific sex chromosome which escapes meiotic recombination. From an evolutionary perspective, Y chromosome has preserved 3% of ancestral genes compared to 98% preservation of the X chromosome based on Ohno’s law. Male specific region of Y chromosome (MSY) contains genes that contribute to central dogma and govern the expression of various targets throughout the genome. One of the most well-known functions of MSY genes are to decide the male-specific characteristics including sex, testis formation and spermatogenesis which are majorly formed by ampliconic gene families. Beyond its role in sex-specific gonad development, MSY genes in co-expression with their X counterparts, as single copy and broadly expressed genes, inhibit haplolethality and play a key role in embryogenesis. The role of X-Y related gene mutations in the development of hereditary syndromes suggests an essential contribution of sex chromosome genes to development. MSY genes, solely and independent of their X counterparts and/or in association with sex hormones, have a considerable impact on fetus development. In this review, we present major recent findings on the contribution of MSY genes to gonad formation, spermatogenesis, and the brain, heart and kidney development and discuss how Y chromosome proteome project may exploit developmental biology to find missing proteins.

    更新日期:2017-09-15
  • Proteomics Standards Initiative: Fifteen Years of Progress and Future Work
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-15
    Eric W. Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert, Yasset Perez-Riverol, Reza M. Salek, David L. Tabb, Stefan Tenzer, Juan Antonio Vizcaíno, Mathias Walzer, Andrew R. Jones
    更新日期:2017-09-15
  • Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-15
    Bin Han, Yu Fang, Mao Feng, Han Hu, Yue Hao, Chuan Ma, Xinmei Huo, Lifeng Meng, Xufeng Zhang, Fan Wu, Jianke Li
    更新日期:2017-09-15
  • Proteome-Wide Analysis of N-Glycosylation Stoichiometry Using SWATH Technology
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-15
    Xiangyun Yang, Zhiyuan Wang, Lin Guo, Zhengjiang Zhu, Yaoyang Zhang
    更新日期:2017-09-15
  • Antibiotic Treatment Preventing Necrotising Enterocolitis Alters Urinary and Plasma Metabolomes in Preterm Pigs
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-14
    Pingping Jiang, Alessia Trimigno, Jan Stanstrup, Bekzod Khakimov, Nanna Viereck, Søren Balling Engelsen, Per Torp Sangild, Lars Ove Dragsted
    更新日期:2017-09-15
  • Targeted Proteomic Analyses of Histone H4 Acetylation Changes Associated with Homologous-Recombination-Deficient High-Grade Serous Ovarian Carcinomas
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-14
    Stefani N. Thomas, Lijun Chen, Yang Liu, Naseruddin Höti, Hui Zhang
    更新日期:2017-09-15
  • Radiation-Induced Endothelial Inflammation Is Transferred via the Secretome to Recipient Cells in a STAT-Mediated Process
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-14
    Jos Philipp, Omid Azimzadeh, Vikram Subramanian, Juliane Merl-Pham, Donna Lowe, Daniela Hladik, Nadine Erbeldinger, Svetlana Ktitareva, Claudia Fournier, Michael J. Atkinson, Ken Raj, Soile Tapio
    更新日期:2017-09-15
  • Lessons from the Hamster: Cricetulus griseus Tissue and CHO Cell Line Proteome Comparison
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-14
    Kelley M. Heffner, Deniz Baycin Hizal, George S. Yerganian, Amit Kumar, Özge Can, Robert O’Meally, Robert Cole, Raghothama Chaerkady, Herren Wu, Michael A. Bowen, Michael J. Betenbaugh
    更新日期:2017-09-14
  • Membrane Proteomics of Impaired Energetics and Cytoskeletal Disorganization in Elderly Diet-Induced Diabetic Mice
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-13
    Chung-Lieh Hung, Szu-Hua Pan, Chia-Li Han, Ching-Wei Chang, Yuan-Ling Hsu, Cheng-Huang Su, Shou-Chuan Shih, Yu-Jun Lai, Jen-Shiu Chiang Chiau, Hung-I Yeh, Chia-Yuan Liu, Hung-Chang Lee, Carolyn S.P. Lam
    更新日期:2017-09-14
  • Low Focal Adhesion Signaling Promotes Ground State Pluripotency of Mouse Embryonic Stem Cells
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-13
    Sara Taleahmad, Mehdi Mirzaei, Azam Samadian, Seyedeh-Nafiseh Hassani, Paul A. Haynes, Ghasem Hosseini Salekdeh, Hossein Baharvand
    更新日期:2017-09-14
  • Primary Metabolism and Medium-Chain Fatty Acid Alterations Precede Long-Chain Fatty Acid Changes Impacting Neutral Lipid Metabolism in Response to an Anticancer Lysophosphatidylcholine Analogue in Yeast
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-13
    Nicolas P. Tambellini, Vanina Zaremberg, Saikumari Krishnaiah, Raymond J. Turner, Aalim M. Weljie
    更新日期:2017-09-14
  • MS/MS-free protein identification in complex mixtures using multiple enzymes with complementary specificity
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-14
    Mark V. Ivanov, Irina A Tarasova, Lev I. Levitsky, Elizaveta M. Solovyeva, Marina L Pridatchenko, Anna A. Lobas, Julia A. Bubis, Mikhail V Gorshkov

    In this work, we present the results of evaluation of a workflow employing a multi-enzyme digestion strategy for MS1-based protein identification in “shotgun” proteomic applications. In the proposed strategy, several cleavage reagents of different specificity were used for parallel digestion of the protein sample followed by MS1 and retention time (RT) based search. Proof of principle for the proposed strategy was performed using experimental data obtained for the annotated 48-protein standard. Using the developed approach, up to 90% of proteins from the standard were unambiguously identified. The approach was further applied to HeLa proteome data. For the sample of this complexity, the proposed MS1-only strategy determined correctly up to 34% of all proteins identified using standard MS/MS-based database search. It was also found that the results of MS1-only search are independent of the chromatographic gradient time in a wide range of gradients from 15 to 120 min. Potentially, rapid MS1-only proteome characterization can be an alternative and/or complementary to the MS/MS-based “shotgun” analyses in the studies, in which the experimental time is more important than the depth of the proteome coverage.

    更新日期:2017-09-14
  • Identification of novel protein expression changes following cisplatin treatment and application to combination therapy
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-13
    Amy L. Stark, Ashraf G Madian, Sawyer W. Williams, Vincent Chen, Claudia Wing, Ronald J. Hause Jr, Lida Anita To, Amy L. Gill, Jamie L. Myers, Lidija K. Gorsic, Mark F. Ciaccio, Kevin P. White, Richard B. Jones, M. Eileen Dolan

    Determining the effect of chemotherapeutic treatment on changes in protein expression can provide important targets for overcoming resistance. Due to challenges in simultaneously measuring large numbers of proteins, a paucity of data exists on global changes. To overcome these challenges, we utilized microwestern arrays that allowed us to measure the abundance and modification state of hundreds of cell signaling and transcription factor proteins in cells following drug exposure. HapMap lymphoblastoid cell lines (LCLs) were exposed to cisplatin, a chemotherapeutic agent commonly used to treat testicular, head and neck, non-small cell lung, and gynecological cancers. We evaluated the expression of 259 proteins following 2, 6, and 12 hours of cisplatin treatment in two LCLs with discordant sensitivity to cisplatin. Of these 259 proteins, 66 displayed significantly different protein expression changes (p<0.05). Fifteen of these proteins were evaluated in a second pair of LCLs with discordant sensitivities to cisplatin; six demonstrated significant differences in expression. We then evaluated a subset of 63 proteins in a second set of LCLs with discordant sensitivity and 40% of those that were significant in the first pair were also significant in the second part with concordant directionality (p<0.05). We functionally validated one of the top proteins identified, PDK1, and demonstrated a synergistic relationship between cisplatin and a PDK1 inhibitor in multiple lung cancer lines. This study highlights the potential for identifying novel targets through an understanding of cellular changes in protein expression and modification following drug treatments.

    更新日期:2017-09-14
  • Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-13
    Tiziana Alberio, Luisa Pieroni, Maurizio Ronci, Cristina Banfi, Italia Bongarzone, Patrizia Bottoni, Maura Brioschi, Marianna Caterino, Clizia Chinello, Antonella Cormio, Flora Cozzolino, Vincenzo Cunsolo, Simona Fontana, Barbara Garavaglia, Laura Giusti, Viviana Greco, Antonio Lucacchini, Elisa Maffioli, Fulvio Magni, Francesca Monteleone, Maria Monti, Valentina Monti, Clara Musicco, Giuseppe Petrosillo, Vito Porcelli, Rosaria Saletti, Roberto Scatena, Alessio Soggiu, Gabriella Tedeschi, Mara Zilocchi, Paola Roncada, Andrea Urbani, Mauro Fasano
    更新日期:2017-09-13
  • Y Chromosome Missing Protein, TBL1Y, May Play an Important Role in Cardiac Differentiation
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-13
    Anna Meyfour, Hassan Ansari, Sara Pahlavan, Shahab Mirshahvaladi, Mostafa Rezaei-Tavirani, Hamid Gourabi, Hossein Baharvand, Ghasem Hosseini Salekdeh
    更新日期:2017-09-13
  • Scanning Quadrupole Data Independent Acquisition – Part A. Qualitative and Quantitative Characterization
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-13
    M. Arthur Moseley, Christopher J. Hughes, Praveen R. Juvvadi, Erik J. Soderblom, Sarah Lennon, Simon R. Perkins, J. Will Thompson, William J. Steinbach, Scott J Geromanos, Jason Wildgoose, James I. Langridge, Keith Richardson, Johannes P.C. Vissers

    A novel data independent acquisition (DIA) method incorporating a scanning quadrupole in front of a collision cell and orthogonal acceleration time-of-flight mass analyzer is described. The method has been characterized for the qualitative and quantitative label-free proteomic analysis of typical complex biological samples. The principle of the scanning quadrupole DIA method is discussed and analytical instrument characteristics, such as the quadrupole transmission width, scan/integration time, and chromatographic separation, have been optimized in relation to sample complexity for a number of different model proteomes of varying complexity and dynamic range including human plasma, cell lines, and bacteria. In addition, the technological merits over existing DIA approaches are described and contrasted. The qualitative and semi-quantitative performance of the method is illustrated for the analysis of relatively simple protein digest mixtures and a well-characterised human cell line sample using untargeted and targeted search strategies. Finally, the results from a human cell line were compared against publically available data that used similar chromatographic conditions, but were acquired with DDA technology and alternative mass analyzer systems. Qualitative comparison showed excellent concordance of results with over 90% overlap of the detected proteins.

    更新日期:2017-09-13
  • Identification of Siglec ligands using a proximity labeling method
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-13
    Lanyi Chang, Yi-Ju Chen, Chan-Yo Fan, Chin-Ju Tang, Yi-Hsiu Chen, Penk-Yeir Low, Albert Ventura, Chun-Cheng Lin, Yu-Ju Chen, Takashi Angata

    Siglecs are a family of receptor-type glycan recognition proteins (lectins) involved in self-nonself discrimination by the immune system. Identification of Siglec ligands is necessary to understand how Siglec-ligand interaction translates into biological outcomes. However, this is challenging because the interaction is weak. To facilitate identification of Siglec ligands, we adopted a proximity labeling method based on the tyramide radicalization principle. Cells that express Siglec ligands were labeled with Siglec-peroxidase complexes and incubated with biotin tyramide and hydrogen peroxide, to generate short-lived tyramide radicals that covalently label the proteins near the Siglec-peroxidase complex. A proof-of-principle experiment using CD22 (Siglec-2) probe identified its known ligands on B cells, including CD22 itself, CD45, and IgM among others, demonstrating the validity of this method. The specificity of labeling was confirmed by sialidase treatment of target cells and using glycan recognition-deficient mutant CD22 probes. Moreover, possible interactions between biotin-labeled proteins were revealed by literature-based protein-protein interaction network analysis, implying the presence of a molecular cluster comprising CD22 ligands. Further application of this method identified CD44 as a hitherto unknown Siglec-15 ligand on RAW264.7-derived osteoclasts. These results demonstrated the utility of proximity labeling for the identification of Siglec ligands, which may extend to other lectins.

    更新日期:2017-09-13
  • Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-12
    Xuehui Peng, Feng Xu, Shu Liu, Suzhen Li, Qingbo Huang, Lei Chang, Lei Wang, Xin Ma, Fuchu He, Ping Xu
    更新日期:2017-09-12
  • Human Prestin: A Candidate PE1 Protein Lacking Stringent Mass Spectrometric Evidence?
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-12
    Abidali Mohamedali, Seong Beom Ahn, Varun K. A. Sreenivasan, Shoba Ranganathan, Mark S. Baker

    The evidence that any protein exists in the Human Proteome Project (HPP; protein evidence 1 or PE1) has revolved primarily (though not exclusively) around mass spectrometry (MS) (93% of PE1 proteins have MS evidence in the latest neXtProt release), with robust and stringent, well-curated metrics that have served the community well. This has led to a significant number of proteins still considered ‘missing’ (i.e., PE2-4). Many PE2-4 proteins have either MS evidence of unacceptable quality (small or not enough unitypic peptides and unacceptably high protein/peptide FDRs), transcriptomic and/or antibody evidence. Here we use a Chromosome 7 PE2 example called Prestin, to demonstrate that clear and robust criteria/metrics need to be developed for proteins that may not/cannot produce clear-cut MS evidence, whilst possessing significant non-MS evidence, including disease-association data. Many of the PE2-4 proteins are either inaccessible, spatio-temporally expressed in a limited way or expressed at such a very low copy number as to be unable to be detected by current MS methodologies. We propose that the HPP community consider and lead a communal initiative to accelerate the discovery and characterization of these types of ‘missing’ proteins.

    更新日期:2017-09-12
  • SERUM METABOLIC FINGERPRINTING IDENTIFIED PUTATIVELY ANNOTATED SPHINGANINE ISOMER AS A BIOMARKER OF WOLFRAM SYNDROME
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-12
    Agnieszka Zmyslowska, Michal Ciborowski, Maciej Borowiec, Wojciech Fendler, Karolina Pietrowska, Ewa Parfieniuk, Karolina Antosik, Aleksandra Pyziak, Arleta Waszczykowska, Adam Kretowski, Wojciech Mlynarski

    Wolfram syndrome (WFS) is an example of a rare neurodegenerative disease with coexisting endocrine symptoms including diabetes mellitus as the first clinical symptom. Treatment of WFS is still only symptomatic and associated with poor prognosis. Potential markers of disease progression which could be useful for possible intervention trials are not available. Metabolomics has potential to identify such markers. In the present study serum fingerprinting by LC-QTOF-MS was performed in patients with WFS (n=13) and in patients with T1D (n=27). Based on obtained results aminoheptadecanediol (17:0 sphinganine isomer) (+50%, p=0.02), as the most discriminatory metabolite, was selected for validation. The 17:0 sphinganine isomer level was determined using the LC-QQQ method in the samples from WFS patients at two time points and compared with samples obtained from patients with T1D (n=24) and healthy controls (n=24). Validation analysis showed higher 17:0 sphinganine isomer level in patients with WFS compared to patients with T1D (p=0.0097) and control group (p<0.0001) with progressive reduction of its level after two-year follow-up period. Patients with WFS show a unique serum metabolic fingerprint, differentiating them from patients with T1D. Sphinganine derivate seems to be a marker of the ongoing process of neurodegeneration in WFS patients.

    更新日期:2017-09-12
  • Quantitative Proteomics Reveals the Regulatory Networks of Circular RNA CDR1as in Hepatocellular Carcinoma Cells
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-11
    Yang Xue, Qian Xiong, Ying Wu, Siting Li, Feng Ge

    Circular RNAs (circRNAs), a class of widespread endogenous RNAs, play crucial roles in diverse biological processes and are potential biomarkers in diverse human diseases and cancers. Cerebellar degeneration-related protein 1 antisense RNA (CDR1as), an oncogenic circRNA, is involved in human tumorigenesis and is dysregulated in hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying CDR1as functions in HCC remain unclear. Here, we explored the functions of CDR1as and searched for CDR1as-regulated proteins in HCC cells. A quantitative proteomics strategy was employed to globally identify CDR1as-regulated proteins in HCC cells. In total, we identified 330 differentially expressed proteins (DEPs) upon enhanced CDR1as expression in HepG2 cells, indicating that they could be proteins regulated by CDR1as. Bioinformatic analysis revealed that many DEPs were involved in cell proliferation and the cell cycle. Further functional studies of epidermal growth factor receptor (EGFR) found that CDR1as exerts its effects on cell proliferation at least in part through the regulation of EGFR expression. We further confirmed that CDR1as could inhibit the expression of microRNA-7 (miR-7). EGFR is a validated target of miR-7; therefore, CDR1as may exert its function by regulating EGFR expression via targeting miR-7 in HCC cells. Taken together, we revealed novel functions and underlying mechanisms of CDR1as in HCC cells. This study serves as the first proteome-wide analysis of a circRNA-regulated protein in cells and provides a reliable and highly efficient method for globally identifying circRNA-regulated proteins.

    更新日期:2017-09-12
  • Antigen-Specific Gut Inflammation and Systemic Immune Responses Induced by Prolonging Wheat Gluten Sensitization in BALB/c Murine Model
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-11
    M. Vijaykrishnaraj, B. V. Mohan Kumar, S. P. Muthukumar, Nawneet K. Kurrey, P. Prabhasankar
    更新日期:2017-09-11
  • Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-11
    Tiaan Heunis, Anzaan Dippenaar, Robin M. Warren, Paul D. van Helden, Ruben G. van der Merwe, Nicolaas C. Gey van Pittius, Arnab Pain, Samantha L. Sampson, David L. Tabb
    更新日期:2017-09-11
  • Validating missing proteins in human sperm cells by targeted mass spectrometry- and antibody-based methods
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-11
    Christine Carapito, Paula Duek, Charlotte Macron, Marine Seffals, Karine Rondel, Francois Delalande, Cecilia Lindskog, Thomas Freour, Yves Vandenbrouck, Lydie Lane, Charles Pineau

    The present study is a contribution to the “neXt50 challenge”, a coordinated effort across C-HPP teams to identify the 50 most tractable missing proteins (MPs) on each chromosome. We report the targeted search of 38 theoretically detectable MPs from chromosomes 2 and 14 in Triton X-100 soluble and insoluble sperm fractions from a total of 15 healthy donors. A targeted mass spectrometry-based strategy consisting in the development of LC-PRM assays (with heavy labeled synthetic peptides) targeting 92 proteotypic peptides of the 38 selected MPs was used. Out of the 38 selected MPs, 12 were identified with 2 or more peptides and 3 with 1 peptide after extensive SDS-PAGE fractionation of the two samples and with overall low intensity signals. The PRM data are available via ProteomeXchange in PASSEL (PASS01013). Further validation by immunohistochemistry on human testes sections and cytochemistry on sperm smears was performed for eight MPs with antibodies available from the Human Protein Atlas. Deep analysis of human sperm still allows the validation of MPs and therefore contributes to the C-HPP worldwide effort. We anticipate that our results will be of interest to the reproductive biology community as an in-depth analysis of these MPs may identify potential new candidates in the context of human idiopathic infertilities.

    更新日期:2017-09-11
  • Proteomic Analysis of Human Angiogenin Interactions Reveals Cytoplasmic PCNA as a Putative Binding Partner
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-08
    Demetra S. M. Chatzileontiadou, Martina Samiotaki, Annika N. Alexopoulou, Marina Cotsiki, George Panayotou, Melina Stamatiadi, Nikolaos A. A. Balatsos, Demetres D. Leonidas, Maria Kontou
    更新日期:2017-09-08
  • Improving Visualization and Interpretation of Metabolome-Wide Association Studies: An Application in a Population-Based Cohort Using Untargeted 1H NMR Metabolic Profiling
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-08
    Raphaële Castagné, Claire Laurence Boulangé, Ibrahim Karaman, Gianluca Campanella, Diana L. Santos Ferreira, Manuja R. Kaluarachchi, Benjamin Lehne, Alireza Moayyeri, Matthew R. Lewis, Konstantina Spagou, Anthony C. Dona, Vangelis Evangelos, Russell Tracy, Philip Greenland, John C. Lindon, David Herrington, Timothy M. D. Ebbels, Paul Elliott, Ioanna Tzoulaki, Marc Chadeau-Hyam
    更新日期:2017-09-08
  • Ultra-deep Lysine Crotonylome Reveals the Crotonylation Enhancement on both Histones and Non-histone Proteins by SAHA Treatment
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-08
    Quan Wu, Wenting Li, Chi Wang, Pingsheng Fan, Lejie Cao, Zhiwei Wu, Fengsong Wang

    Lysine crotonylation is a newly discovered protein post-translational modification and was reported to share transferases and de-acylases with lysine acetylation. The acetyltransferase p300 was reported also contain crotonyltransferase activity and class I histone deacetylases were demonstrated to be the major histone decrotonylases. However, the decortonylases for non-histone proteins are unclear. Moreover, due to the lack of high-quality pan-antibodies, large-scale analysis of crotonylome still remains challenge. In this work, we comprehensively studied lysine crotonylome on both histones and non-histone proteins upon SAHA treatment and dramatically identified 10,163 lysine crotonylation sites in A549 cells. This is the first identification of 10,000s of lysine crotonylation sites and also the largest lysine crotonylome dataset up to now. Moreover, a parallel reaction monitoring-based experiment was performed for validation, which presented highly consistent results with the SILAC experiments. By intensive bioinformatic analysis, it was found that lysine crotonylation participate in a wide range of biological functions and processes. More importantly, it was revealed that both the crotonylation and acetylation level of most core histones sites and a number of non-histone proteins as well as some known substrates of class IIa and IIb HDACs were up-regulated after SAHA treatment. These results suggest that SAHA may have decrotonylation inhibitory activities on both histones and non-histone proteins by inhibiting HDACs.

    更新日期:2017-09-08
  • Comparative Proteomic and Transcriptomic Analysis of Follistatin-Induced Skeletal Muscle Hypertrophy
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-07
    Caroline Barbé, Fabrice Bray, Marine Gueugneau, Stéphanie Devassine, Pascale Lause, Caroline Tokarski, Christian Rolando, Jean-Paul Thissen
    更新日期:2017-09-07
  • Luxurious Nitrogen Fertilization of Two Sugar Cane Genotypes Contrasting for Lignin Composition Causes Changes in the Stem Proteome Related to Carbon, Nitrogen, and Oxidant Metabolism but Does Not Alter Lignin Content
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-07
    Fernanda Salvato, Rashaun Wilson, Juan Pablo Portilla Llerena, Eduardo Kiyota, Karina Lima Reis, Luis Felipe Boaretto, Tiago S. Balbuena, Ricardo A. Azevedo, Jay J. Thelen, Paulo Mazzafera
    更新日期:2017-09-07
  • Therapeutic Mechanism Studies of ShuFengJieDu Capsule on an Acute Lung Injury Animal Model Using Quantitative Proteomics Technology
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-07
    Zhengang Tao, Xia Meng, Yan-qi Han, Ming-ming Xue, Shifei Wu, Ping Wu, Ying Yuan, Zhu Qiang, Tie-Jun Zhang, Catherine CL Wong

    ShuFengJieDu Capsule (SFJDC), a traditional Chinese Medicine (TCM) that comprises eight medicinal herbs, has been extensively utilized in the treatment of acute lung injury (ALI) and respiratory infections for more than 30 years in China. SFJDC has also been listed in the official guidelines of the CFDA (China Food and Drug Administration) because of its stabilized clinical manifestations. However, the underlying mechanism of SFJDC in repairing ALI remains unclear. In the present study, we explored the protective and therapeutic mechanism of SFJDC in a rat model using qualitative and quantitative proteomics. After establishing lipopolysaccharide (LPS)-induced ALI rat models, we profiled both isolated macrophage cells from freshly resected rat lung tissues from ALI models and section ALI rat lung tissues using a HPLC-MS/MS shotgun proteomics approach to identify changes in the levels of expression of proteins of interest. Based on the results of proteomics results and dysregulated protein analyses of ALI rat lung tissues and rat lung macrophages, AKT1 was selected as a putative key factor that might play an important role in the SFJDC treatment of ALI progression. Follow-up validation studies revealed that AKT1 expression effectively regulates various ALI-related molecules, and Gene Ontology analysis indicated that SFJDC-treated ALI rat macrophages were influenced by AKT1-based networks. Gain- and loss-of-function analyses via lentivirus-AKT1 or lentivirus-si-AKT1 infections into macrophages also indicated that AKT1 was essential for the development of ALI by regulating oxidative stress, apoptosis, or inflammatory responses. In summary, SFJDC effectively manipulated the biological activity in anti-inflammatory and immunomodulation activity in ALI, which might be involved in AKT1 regulation in ALI progression. New insights into SFJDC mechanisms may facilitate the development of novel pharmaceutical strategies in controlling the expression of inflammatory factors.

    更新日期:2017-09-07
  • Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-07
    Bin Han, Yu Fang, Mao Feng, Han Hu, Yue Hao, Chuan Ma, Xinmei Huo, Lifeng Meng, Xufeng Zhang, Fan Wu, Jianke Li

    The brain is a vital organ in regulating complex social behaviors of honeybees including learning and memory. Knowledge of how brain membrane proteins and their phosphorylation underlie the age-related behavioral polyethism is still lacking. A hitherto age-resolved brain membrane proteome and phosphoproteome were reported in adult worker bees from two strains of honeybee (Apis mellifera ligustica): Italian bee (ITB) and Royal Jelly bee (RJB), a line selected from ITB for increased RJ outputs over 4 decades. There were 1079 membrane protein groups identified, and 417 unique phosphosites were located in 179 membrane protein groups mainly phosphorylated by kinase families of MAPKs, CDKs, and CK2. Age-resolved dynamics of brain membrane proteome and phosphoproteome are indicative of their correlation with the neurobiological requirements during the adult life of honeybee workers. To stimulate immature brain cell development in newly emerged bees (NEBs), the enriched functional classes associated with metabolism of carbohydrates, nucleosides, and lipids by the up-regulated proteins suggest their enhanced role in driving cell maturity of the brain. In nurse bees (NBs) and forager bees (FBs), a higher number of membrane proteins and phosphoproteins were expressed as compared to in the young stages, and the enriched signal transduction related pathways by the up-regulated proteins suggest their significances in sustaining the intensive information processing during nursing and foraging activities. Notably, RJB has shaped unique membrane proteome and phosphoproteome settings to consolidate nursing and foraging behaviors in response to decades of selection underpinning the elevated RJ yields. In RJB NBs, the enriched pathways of phosphatidylinositol signaling and arachidonic acid metabolism indicate a stronger olfaction sensation in response to larval pheromone stimulation. In RJB FBs, the enriched pathways related to signal processing such as SNARE interactions in vesicular transport, wnt signaling, TGF-beta signaling, and taurine and hypotaurine metabolism suggest an enhanced nerve sensitivity to prime the stronger tendency to pollen collection. Our data gain a novel insight into membrane proteome and phosphoproteome driven cerebral regulation of honeybee behaviors, which is potentially useful for further neurobiological investigation in both honeybees and other social insects.

    更新日期:2017-09-07
  • Scale-Invariant Biomarker Discovery in Urine and Plasma Metabolite Fingerprints
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-07
    Helena U. Zacharias, Thorsten Rehberg, Sebastian Mehrl, Daniel Richtmann, Tilo Wettig, Peter J. Oefner, Rainer Spang, Wolfram Gronwald, Michael Altenbuchinger
    更新日期:2017-09-07
  • 更新日期:2017-09-07
  • Lessons from the hamster: Cricetulus griseus tissue and CHO cell line proteome comparison
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-06
    Kelley M. Heffner, Deniz Baycin Hizal, George S. Yerganian, Amit Kumar, Özge Can, Robert N. O'Meally, Robert Cole, Raghothama Chaerkady, Herren Wu, Michael A. Bowen, Michael J. Betenbaugh

    Chinese hamster ovary cells represent the dominant host for therapeutic recombinant protein production. However, few large-scale datasets have been generated to characterize this host organism and derived CHO cell lines at the proteomics level. Consequently, an extensive label-free quantitative proteomics analysis of two cell lines (CHO-S and CHO DG44) and two Chinese hamster tissues (liver and ovary) was used to identify a total of 11801 unique proteins containing at least two unique peptides. 9359 unique proteins were identified specifically in the cell lines, representing a 56% increase over previous work. Additionally, 6663 unique proteins were identified across liver and ovary tissues providing the first Chinese hamster tissue proteome. Protein expression was more conserved within cell lines during both growth phases than across cell lines, suggesting large genetic differences across cell lines. Overall, both gene ontology and KEGG pathway analysis revealed enrichment of cell cycle activity in cells. In contrast, upregulated molecular functions in tissue include glycosylation and lipid transporter activity. Furthermore, cellular components including Golgi apparatus are upregulated in both tissues. In conclusion, this large-scale proteomics analysis enables us to delineate specific changes between tissues and cells derived from these tissues, which can help explain specific tissue function and the adaptations cells incur for applications in biopharmaceutical productions.

    更新日期:2017-09-07
  • Antibiotic Treatment Preventing Necrotising Enterocolitis Alters Urinary and Plasma Metabolomes in Preterm Pigs
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-05
    PINGPING JIANG, Alessia Trimigno, Jan Stanstrup, Bekzod Khakimov, Nanna Viereck, Soeren Balling Engelsen, Per Torp Sangild, Lars Ove Dragsted

    Necrotising enterocolitis (NEC) is a serious gut inflammatory condition in premature neonates, onset and development of which depends on the gut microbiome. Attenuation of the gut microbiome by antibiotics can reduce NEC incidence and severity. However, how the antibiotics-suppressed gut microbiome affects the whole-body metabolism in NEC-sensitive premature neonates is unknown. In formula-fed preterm pigs, used as a model for preterm infants, plasma and urinary metabolomes were investigated by LC-MS and 1H-NMR, with and without antibiotic treatment immediately after birth. While reducing the gut microbiome density and NEC lesions as previously reported, the antibiotic treatment employed in the current study affected the abundance of 44 metabolites in different metabolic pathways. In antibiotics-treated pigs, tryptophan metabolism favoured the kynurenine pathway, relative to the serotonin pathway, as shown by specific metabolites. Metabolites associated with the gut microbiome, including 3-phenyllactic acid, 4-hydroxyphenylacetic acid and phenylacetylglycine, all from phenylalanine, and three bile acids showed lower levels in the antibiotics-treated pigs where the gut microbiome was extensively attenuated. Findings in the current study warrant further investigation of metabolic and developmental consequences of antibiotic treatment in preterm neonates.

    更新日期:2017-09-05
  • NMR spectroscopy-based metabolomics of Drosophila model of Huntington’s disease suggests altered cell energetics
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-05
    Virender Singh, Raj Kumar Sharma, Thamarailingam Athilingam, Pradip Sinha, Neeraj Sinha, Ashwani Kumar Thakur

    Huntington’s disease (HD) is a neurodegenerative disorder induced by aggregation of the pathological form of Huntingtin protein that has expanded polyglutamine (polyQ) repeats. In the Drosophila model, for instance, expression of transgenes with polyQ repeats induce HD-like pathologies progressively correlating with the increasing lengths of these repeats. Previous studies on both animal models and clinical samples have revealed metabolite imbalances during HD progression. To further explore the physiological processes linked to metabolite imbalances during HD, we have investigated 1D 1H NMR spectroscopy-based metabolomics profile of Drosophila HD model. Using multivariate analysis (PCA and PLS-DA) of metabolites obtained from methanolic extracts of fly heads displaying retinal deformations due to polyQ overexpression, we show that the metabolite imbalance during HD are likely to affect cell energetics. Six out of the 35 metabolites analyzed, namely, nicotinamide adenine dinucleotide (NAD), lactate, pyruvate, succinate, sarcosine, and acetoin displayed segregation with progressive severity of HD. Specifically, HD progression was seen associated with reduction in NAD and increase in lactate-to-pyruvate ratio. Further, comparative analysis of fly HD metabolome with those of mouse HD model, and HD human patients, revealed comparable metabolite imbalances suggesting altered cellular energy homeostasis. These findings thus raise the possibility of therapeutic interventions for HD via modulation of cellular energetics.

    更新日期:2017-09-05
  • Pharmacometabolomics in Endogenous Drugs: A New Approach for Predicting the Individualized Pharmacokinetics of Cholic Acid
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-01
    Zhixin Zhang, Hao Gu, Huizhen Zhao, Yuehong Liu, Shuang Fu, Meiling Wang, Wenjuan Zhou, Ziye Xie, Honghong Yu, Zhenghai Huang, Xiaoyan Gao
    更新日期:2017-09-04
  • Determination of Rate-Limiting Factor for Formation of Beta-Catenin Destruction Complexes Using Absolute Protein Quantification
    J. Proteome Res. (IF 4.268) Pub Date : 2017-09-01
    Masashi Kitazawa, Tomohisa Hatta, Koji Ogawa, Eriko Fukuda, Naoki Goshima, Tohru Natsume
    更新日期:2017-09-04
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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