bims-prodis 2018-05-20 papers

bims-prodis

Biomed News

on Proteomics in disease

Issue of 2018–05–20
ten papers selected by
Nancy Gough, Bioserendipity

Effects of salazosulfapyridine on the profile of cell surface proteins, revealed by biotinylation of cell surface proteins and 2-dimentional electrophoresis.
Identification and efficacy of glycine, serine and threonine metabolism in potentiating kanamycin-mediated killing of Edwardsiella piscicida.
Peptidome Analysis Reveals Novel Serum Biomarkers for Children with Autism Spectrum Disorder in China.
Imaging Mass Spectrometry for Characterization of Atrial Fibrillation Subtypes.
A novel approach of virulome based reverse vaccinology for exploring and validating peptide-based vaccine candidates against the most troublesome nosocomial pathogen: Acinetobacter baumannii.
Protein aggregation in cell biology: An aggregomics perspective of health and disease.
Development and validation of a targeted affinity-enrichment and LC-MS/MS proteomics approach for the therapeutic monitoring of adalimumab.
2-Deoxy-d-glucose increases GFAT1 phosphorylation resulting in endoplasmic reticulum-related apoptosis via disruption of protein N-glycosylation in pancreatic cancer cells.
Comparison of subacute and chronic scar tissues after complete spinal cord transection.
Axonal Guidance Signaling Pathway Is Suppressed in Human Nasal Polyps.

Biochim Biophys Acta. 2018 May 09. pii: S1570-9639(18)30074-8. [Epub ahead of print]

Effects of salazosulfapyridine on the profile of cell surface proteins, revealed by biotinylation of cell surface proteins and 2-dimentional electrophoresis.

Kazuki Omoteyama, Toshiyuki Sato, Mitsumi Arito, Masaaki Sato, Naoya Suematsu, Manae S Kurokawa, Tomohiro Kato.

   OBJECTIVE: We investigated effects of salazosulfapyridine (SASP) on the protein profile of cell surface (CS)-proteins of SW982, a human synovial sarcoma cell line, using biotinylation of CS-proteins and 2-dimensional fluorescence difference gel electrophoresis (2D-DIGE).
METHODS: SW982 cells were treated with SASP and its metabolites, sulfapyridine (SP) and 5-aminosalicylic acid (5ASA). Then the cells were treated with a membrane-impermeable biotinylating reagent. Biotinylated CS-proteins were isolated using NeutrAvidin-bound beads. CS-proteins affected by the drugs were detected by 2D-DIGE and subjected to mass spectrometry.
RESULTS: By the 2D-DIGE analysis, in total 576 spots were detected, 29 out of which showed more than ±1.5-fold different intensity in the SASP-, SP-, and 5ASA-treated cells, compared to non-treated cells (p < 0.05). Interestingly, 7 out of the 29 spots changed their intensity only by SASP and 17 spots changed their intensity only by SP. We identified 9 protein from 15 out of the 29 spots, most of which were evidenced to exist on the cell surface by flow cytometry.
CONCLUSION: We found novel effects of SASP and its metabolites on SW982 cells by the combination of biotinylation of cell surface proteins and 2D-DIGE analysis. These data would help understanding of anti-rheumatic actions of SASP. Furthermore, the combination would be a useful method for the analysis of CS-proteins in various conditions.

Keywords:  Biotinylation; Cell surface protein; Rheumatoid arthritis; Salazosulfapyridine; Two-dimensional electrophoresis

DOI:  https://doi.org/10.1016/j.bbapap.2018.05.007
J Proteomics. 2018 May 09. pii: S1874-3919(18)30208-2. [Epub ahead of print]

Identification and efficacy of glycine, serine and threonine metabolism in potentiating kanamycin-mediated killing of Edwardsiella piscicida.

Jin-Zhou Ye, Xiang-Min Lin, Zhi-Xue Cheng, Yu-Bin Su, Wan-Xin Li, Far-Man Ali, Jun Zheng, Bo Peng.

  We previously showed that glucose potentiated kanamycin to kill multidrug-resistant Edwardsiella piscicida through activation of the TCA cycle. However, whether other regulatory mechanism is involved requires further investigation. By quantitative proteomics technology, iTRAQ, we systematically mapped the altered proteins in the presence of glucose and identified 94 differentially expressed proteins. The analysis of the altered proteins by pathways, amino acid biosynthesis and metabolism were enriched. And the most significantly altered eight amino acids tyrosine, phenylalanine, valine, leucine, isoleucine, glycine, serine and threonine were investigated for their potentiation of kanamycin to kill EIB202, where glycine, serine and threonine showed the strongest efficacy than the others. The combinations of glycine and serine or glucose with glycine, serine or threonine had the best effects. Moreover, pyruvate dehydrogenase, α-ketoglutarate dehydrogenase and succinate dehydrogenase activities were increased as well as the proton motive force (PMF) and intracellular kanamycin. Finally, inhibitors that disrupt PMF production abolished the potentiation. These results shed light on the mechanism of how glucose promoting the amino acids biosynthesis and metabolism to potentiate kanamycin to kill antibiotic-resistant bacteria. More importantly, our results suggested that adjusting amino acid biosynthesis and metabolism might be a strategy to become phenotypic resistance to antibiotics in bacteria.
SIGNIFICANCE: Tackling antibiotic resistance is an emerging issue in current years. Despite the efforts made toward developing new antibiotics, the progress is still lagged behind expectation. Novel strategies are required. The use of metabolite to revert antibiotic resistant is highly appreciated in recent years due to the less toxicity, more economic and high efficacy. As a continued study of our previous report on glucose potentiating kanamycin to kill antibiotic-resistant bacteria. The current study further expands the previous discovery on the mechanism of how glucose potentiate this effect. This result provides more basis on the action of glucose in reverting antibiotic resistance. And more importantly, we may derive more metabolites other than glucose to manage antibiotic resistance.

Keywords:  Amino acid; Antibiotic resistance; Glucose; Glycine, serine and threonine metabolism; Kanamycin; Metabolic modulation

DOI:  https://doi.org/10.1016/j.jprot.2018.05.006
Proteomics Clin Appl. 2018 May 13. e1700164

Peptidome Analysis Reveals Novel Serum Biomarkers for Children with Autism Spectrum Disorder in China.

Juan Yang, Yanni Chen, Xiaofan Xiong, Xiaobo Zhou, Lin Han, Ei Ni, Wenjing Wang, Xiaofei Wang, Lingyu Zhao, Dongdong Shao, Chen Huang.

   PURPOSE: Autism spectrum disorder (ASD) is a neurological and developmental disorder that begins early in childhood and lasts throughout one's life. Early diagnosis is essential for ASD since early treatment can enable children with ASD to make significant gains in language and social skills, but remains challenging since there are currently no specific biomarkers of ASD. The study aimed to identify serum biomarkers for ASD.
EXPERIMENTAL DESIGN: Serum of Han Chinese children with ASD (n = 68) and age-matched healthy controls (n = 80) was analyzed using magnetic bead-based separation combined with mass spectrum.
RESULTS: Eight potential ASD serum biomarker peaks (m/z: 3886.69, 7775.12, 2381.71, 6638.63, 3319.17, 894.34, 4968.59, and 5910.53) with higher expression in ASD group were further identified as peptide regions of Plasma Serine Protease Inhibitor Precursor (SERPINA5), Platelet Factor 4 (PF4), Fatty Acid Binding Protein 1(FABP1), Apolipoprotein C-I Precursor (APOC1), Alpha-fetoprotein Precursor (AFP), Carboxypeptidase B2 (CPB2), Trace Amine-associated Receptor 6 (TAAR6) and Isoform1 of Fibrinogen Alpha Chain Precursor (FGA). The expression of identified proteins was validated by enzyme-linked immunosorbent assay (ELISA).
CONCLUSIONS AND MEDICAL RELEVANCE: Our findings reveal the exceptional disease etiology of ASD from a serum proteomic perspective, and the identified proteins might be potential biomarkers for ASD diagnosis. This article is protected by copyright. All rights reserved.

Keywords:  ASD; early diagnosis; mass spectrum; serum biomarker

DOI:  https://doi.org/10.1002/prca.201700164
Proteomics Clin Appl. 2018 May 13. e1700155

Imaging Mass Spectrometry for Characterization of Atrial Fibrillation Subtypes.

Oliver Klein, Thorsten Hanke, Grit Nerbrich, Junfeng Yan, Benedikt Schubert, Patrick Giavalisco, Frank Noack, Herbert Thiele, Salah A Mohamed.

PURPOSE: Atrial fibrillation (AF) is a cardiac arrhythmia characterized by a rapid and irregular heart rhythm. AF types, paroxysmal (PX), persistent (PE) and long-lasting persistent (LSP), requires differences in clinical management. Unfortunately, a significant proportion of AF patients are clinical misclassified. Therefore, our study aim that MALDI-Imaging (IMS) is valuable as a diagnostic aid in AF subtypes assessment.
EXPERIMENTAL DESIGN: Patients were clinically classified according guidelines of the European Society of Cardiology. FFPE tissue specimens from PE, PX and LSP subtype were analysed by MALDI-IMS and evaluated by multi-statistical testing. Proteins were subsequent identified using LC-MS/MS and findings were confirmed by immunohistochemistry and through the determination of potential fibrosis via histopathology RESULT: : Determined characteristic peptide signatures and peptide values facilitate to distinguish between PE, PE and LSP arterial fibrillation subtypes. In particular, peptide values from alpha 1 type I collagen were identified that were significantly higher in LSP and PE tissue but not in PX myocardial AF tissue. These findings were confirmed by immunohistochemistry and through the determination of potential fibrosis via histopathology.
CONCLUSION AND RELEVANCE: Our results represent an improvement in AF risk stratification by using MALDI-IMS as a promising approach for AF tissue assessment. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/prca.201700155
J Mol Graph Model. 2018 May 05. pii: S1093-3263(18)30046-9. [Epub ahead of print]83 1-11

A novel approach of virulome based reverse vaccinology for exploring and validating peptide-based vaccine candidates against the most troublesome nosocomial pathogen: Acinetobacter baumannii.

Sajjad Ahmad, Syed Sikander Azam.

  Acinetobacter baumannii is one of the major cause of nosocomial infections around the globe. The emergence of hyper-virulent strains of the pathogen greatly narrows down therapeutic options for patients infected with this red alert superbug. Development of a peptide-based vaccine can offers an alternative, attractive, and cost-effective remedy for multidrug-resistant A. baumannii associated complications. Herein, we introduced a novel virulome based Reverse Vaccinology for screening peptide based vaccine candidates against A. baumannii and its validation using a negative control. The pipeline screened "FYLNDQPVS" of polysaccharide export outer membrane protein (EpsA) and "LQNNTRRMK" of chaperone-usher pathway protein B (CsuB) as broad-spectrum peptides for induction of targeted immune responses. The 9-mer epitope of both proteins was rendered virulent, antigenic, non-allergen, and highly conserved among thirty-four completely annotated strains. Interactome examination unravels peptides protein direct and indirect interactions with biological significant pathways, essential for A. baumannii pathogenesis and survival. Protein-peptide docking aids in addition by unveiling deep binding of the epitopes in the active site of the most prevalent binding allele in the human population-the DRB1*0101. Both the proteins till to date are not characterized for immunoprotective efficacy and desirable to be deciphered experimentally. The designed series of in silico filters rejected few recently reported peptide and non-peptide vaccine targets and has delivered outcomes, which we believe will enrich the existing knowledge of vaccinology against this life-threatening human pathogen.

Keywords:  A. baumannii; Conservation; Docking; Epitope; Vaccine

DOI:  https://doi.org/10.1016/j.jmgm.2018.04.020
Semin Cell Dev Biol. 2018 May 12. pii: S1084-9521(17)30393-2. [Epub ahead of print]

Protein aggregation in cell biology: An aggregomics perspective of health and disease.

Dezerae Cox, Candice Raeburn, Xiaojing Sui, Danny M Hatters.

  Maintaining protein homeostasis (proteostasis) is essential for cellular health and is governed by a network of quality control machinery comprising over 800 genes. When proteostasis becomes imbalanced, proteins can abnormally aggregate or become mislocalized. Inappropriate protein aggregation and proteostasis imbalance are two of the central pathological features of common neurodegenerative diseases including Alzheimer, Parkinson, Huntington, and motor neuron diseases. How aggregation contributes to the pathogenic mechanisms of disease remains incompletely understood. Here, we integrate some of the key and emerging ideas as to how protein aggregation relates to imbalanced proteostasis with an emphasis on Huntington disease as our area of main expertise. We propose the term "aggregomics" be coined in reference to how aggregation of particular proteins concomitantly influences the spatial organization and protein-protein interactions of the surrounding proteome. Meta-analysis of aggregated interactomes from various published datasets reveals chaperones and RNA-binding proteins are common components across various disease contexts. We conclude with an examination of therapeutic avenues targeting proteostasis mechanisms.

Keywords:  Chaperone; Interactome; Misfolding; Protein aggregation; Therapeutics

DOI:  https://doi.org/10.1016/j.semcdb.2018.05.003
Clin Chim Acta. 2018 May 09. pii: S0009-8981(18)30224-9. [Epub ahead of print]

Development and validation of a targeted affinity-enrichment and LC-MS/MS proteomics approach for the therapeutic monitoring of adalimumab.

Yifei Yang, Emily Wysocki, Kwasi Antwi, Eric Niederkofler, Edward K Y Leung, Eszter Lazar-Molnar, Kiang-Teck J Yeo.

   BACKGROUND: The anti-tumor necrosis factor alpha (TNFα) therapeutic monoclonal antibodies (mAbs), such as adalimumab, are widely used in the treatment of rheumatoid arthritis, inflammatory bowel diseases, and other auto-immune diseases. The administration of adalimumab can elicit the immune responses from the patients, resulting in the formation of anti-drug antibodies (ADAbs). The ADAbs can diminish the therapeutic effects of adalimumab by neutralizing the TNFα binding site or increase its clearance from circulation.
METHODS: To effectively monitor the therapeutic concentrations of adalimumab, we developed and validated a targeted quantitative proteomic assay to determine the circulating concentrations of adalimumab. Since drug effects can be attenuated by ADAbs, the method also adopted an affinity-enrichment step to selectively quantify the bioavailable forms of adalimumab in patient serum samples.
RESULTS: The performance of the LC-MS/MS based assay provides the analytical measuring range and precisions applicable for the therapeutic monitoring of adalimumab. It also provides comparable results to a cell-based activity assay when evaluating patient samples with different concentrations of adalimumab.
CONCLUSION: Our assay can quantify both sub-therapeutic and therapeutic concentrations of bioavailable adalimumab in patient serum samples. This assay design also provides an alternative to isotope-labeled peptides approach currently adopted in targeted proteomics.

Keywords:  Anti-drug antibodies; Bioavailable adalimumab; Quantitative and targeted proteomics

DOI:  https://doi.org/10.1016/j.cca.2018.05.015
Biochem Biophys Res Commun. 2018 May 15. pii: S0006-291X(18)31090-8. [Epub ahead of print]

2-Deoxy-d-glucose increases GFAT1 phosphorylation resulting in endoplasmic reticulum-related apoptosis via disruption of protein N-glycosylation in pancreatic cancer cells.

Kousuke Ishino, Mitsuhiro Kudo, Wei-Xia Peng, Shoko Kure, Kiyoko Kawahara, Kiyoshi Teduka, Yoko Kawamoto, Taeko Kitamura, Takenori Fujii, Tetsushi Yamamoto, Ryuichi Wada, Zenya Naito.

  The glycolytic inhibitor 2-deoxy-d-glucose (2DG) causes energy starvation, affecting cell viability in a wide range of cancer cell lines. To determine the action of 2DG in pancreatic cancer, we performed proteomic analysis of pancreatic cancer cell line after 2DG treatment. Eighty proteins showed differential expression and among these, proteins involved in phosphohexose metabolism were upregulated. Up-regulation of glutamine: fructose 6-phosphate aminotransferase 1 (GFAT1), which belongs to the hexosamine biosynthesis pathway (HBP) that produces uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) to maintain glycoprotein, was validated by evaluation of mRNA and protein levels. Therefore, we assessed the amounts of total N-glycoproteins. Unexpectedly, we found a reduction of total N-glycoproteins and phosphorylation of GFAT1 by AMP-activated protein kinase (AMPK). These data may shed light on HBP dysfunction. Furthermore, we found endoplasmic reticulum (ER) stress accompanied by increased expression of ER stress markers, such as glucose response protein 78 (GRP78) and C/EBP-homologous protein (CHOP), in 2DG-treated cells. Moreover, the additive activation of AMPK by metformin (Met) synergistically enhanced the reduction of protein N-glycosylation and cell growth inhibition in the presence of 2DG. These results suggest that 2DG reduces N-glycosylation of proteins following the increase of phosphorylation of GFAT1 and results in the inhibition of cell growth mediated by ER stress in pancreatic cancer cells.

Keywords:  2-Deoxy-d-glucose; AMPK; GFAT1; Metformin; Protein N-linked glycosylation; Proteomics

DOI:  https://doi.org/10.1016/j.bbrc.2018.05.041
Exp Neurol. 2018 May 10. pii: S0014-4886(18)30117-1. [Epub ahead of print]

Comparison of subacute and chronic scar tissues after complete spinal cord transection.

Xing Li, Bin Yang, Zhifeng Xiao, Yannan Zhao, Sufang Han, Yanyun Yin, Bing Chen, Jianwu Dai.

  Traditional views consider scar tissue formed in the lesion epicenter after severe spinal cord injury (SCI) as both a physical barrier and chemical impediment for axonal regeneration. Recently, a controversial opinion suggested that astrocyte scar formation aids rather than prevents axonal regeneration in the CNS. Here, following complete transection of the thoracic spinal cord (T8) in rats, we found that scar tissue showed greater growth factor expression at 2 weeks than 8 weeks post-SCI. Further, tandem mass tag (TMT)-based quantitative proteomic analysis revealed that the components of scar tissue formed in the subacute phase are quite different from that formed in the chronic phase. We also found significantly increased axonal regrowth of sensory axons into the lesion center after chronically formed scar tissue was removed. This indicates that scar tissue formed at the chronic phase actually inhibits axonal regeneration, and that chronic removal of scar tissue may have clinical significance and benefit for SCI repair. Taken together, our study suggests that the features and roles of subacute and chronic scar tissues formed post-SCI is different and scar tissue-targeted strategies for spinal cord regeneration cannot be generalized.

Keywords:  Axon regeneration; Complete spinal cord transection; Neuronal relay; Quantitative proteomics; Scar tissue

DOI:  https://doi.org/10.1016/j.expneurol.2018.05.008
Am J Rhinol Allergy. 2018 Jan 01. 1945892418773558

Axonal Guidance Signaling Pathway Is Suppressed in Human Nasal Polyps.

Dawei Wu, Sarina K Mueller, Angela L Nocera, Kristen Finn, Towia A Libermann, Benjamin S Bleier.

  Background Dysfunctional innervation might contribute to the pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP), but the state of the axonal outgrowth signaling in CRSwNP is unknown. The purpose of this study was to explore the axonal outgrowth pathway-related protein expression in CRSwNP. Methods Institutional review board approved study in which tissue proteomes were compared between control and CRSwNP patients (n = 10/group) using an aptamer-based proteomic array and confirmed by whole transcriptomic analysis. Results Compared with controls, proteins associated with axonal guidance signaling pathway such as beta-nerve growth factor, semaphorin 3A, Ras-related C3 botulinum toxin substrate 1, Bcl-2, protein kinase C delta type, and Fyn were significantly decreased in patients with CRSwNP (fold change [FC] = -1.17, P = .002; FC = -1.09, P < .001; FC = -1.33, P < .001; FC = -1.31, P < .001; FC = -1.31, P = .004; and FC = -1.20, P = 0.012, respectively). In contrast, reticulon-4 receptor, an inhibitory factor, was significantly increased in patients with CRSwNP (FC = 1.25, P < .001). Furthermore, neuronal growth-associated proteins such as ciliary neurotrophic factor receptor subunit alpha, neuronal growth regulator 1, neuronal cell adhesion molecule, neural cell adhesion molecule L1, platelet-derived growth factor subunit A, and netrin-4 were all significantly decreased in patients with CRSwNP (FC = -1.25, P < .001; FC = -1.27, P = .002; FC = -1.65, P = .013; FC = -4.20, P < .001; FC = -1.28, P < .001; and FC = -2.31, P < .001, respectively). In contrast, tissue eosinophil count ( P < .001) and allergic inflammation factors such as IgE, periostin, and galectin-10 were all significantly increased in patients with CRSwNP (FC = 12.28, P < .001; FC = 3.95, P < .001; and FC = 2.44, P < .001, respectively). Furthermore, the log FC of the studied proteins expression significantly and positively correlated with log FC of their mRNA expression ( P < .001, r = .88). Conclusions Axonal guidance signaling and neural growth factors pathways proteins are significantly suppressed in eosinophilic CRSwNP.

Keywords:  axonal outgrowth; chronic rhinosinusitis; innervation; nasal polyps; nerve; proteome

DOI:  https://doi.org/10.1177/1945892418773558