bims-prodis Biomed News
on Proteomics in disease
Issue of 2018–12–30
37 papers selected by
Nancy Gough, Bioserendipity
  1. Current Status of Proteomic Technologies for Discovering and Identifying Gingival Crevicular Fluid Biomarkers for Periodontal Disease.
  2. Quantitative iTRAQ-based proteomic analysis of piperine protected cerebral ischemia/reperfusion injury in rat brain.
  3. Human Periprostatic Adipose Tissue: Secretome from Patients With Prostate Cancer or Benign Prostate Hyperplasia.
  4. Proteomic Identification of Plasma Biomarkers in Children and Adolescents with Recurrent Hodgkin Lymphoma.
  5. A Comprehensive Proteome Analysis of Peripheral Blood Mononuclear Cells (PBMCs) to Identify Candidate Biomarkers of Pancreatic Cancer.
  6. Proteomics of acquired pellicle in gastroesophageal reflux disease patients with or without erosive tooth wear.
  7. Differential protein expression of blood platelet components associated with 1 adverse transfusion reactions.
  8. New Insights on the Mechanisms Affecting Fertility in Men with Non-Seminoma Testicular Cancer before Cancer Therapy.
  9. Comparative Proteomic Profiling of Mycobacterium tuberculosis and the Thai Vaccine Strain Mycobacterium bovis Bacille Calmette-Guerin Tokyo172: Diverse Biomarker Candidates for Species Differentiation.
  10. Identification of Levels of Serum Amyloid A and Apolipoprotein A1 in Serum Proteomic Analysis of Neuropsychiatric Systemic Lupus Erythematosus Patients.
  11. Exosomes Derived from Human Primary and Metastatic Colorectal Cancer Cells Contribute to Functional Heterogeneity of Activated Fibroblasts by Reprogramming Their Proteome.
  12. Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery.
  13. Brain proteome changes in female Brd1+/- mice unmask dendritic spine pathology and show enrichment for schizophrenia risk.
  14. Integrative Clustering in Mass Spectrometry Imaging for Enhanced Patient Stratification.
  15. p62/SQSTM1 Fuels Melanoma Progression by Opposing mRNA Decay of a Selective Set of Pro-metastatic Factors.
  16. Transcriptomic and proteomic host response to Aspergillus fumigatus conidia in an air-liquid interface model of human bronchial epithelium.
  17. Predictive value of targeted proteomics for coronary plaque morphology in patients with suspected coronary artery disease.
  18. Proteomic signature of neuroblastoma cells UKF-NB-4 reveals key role of lysosomal sequestration and the proteasome complex in acquiring chemoresistance to cisplatin.
  19. Multiomics of azacitidine-treated AML cells reveals variable and convergent targets that remodel the cell-surface proteome.
  20. Proteomic characterization of epithelial-like extracellular vesicles in advanced endometrial cancer.
  21. LXR/RXR pathway signaling associated with triple-negative breast cancer in African American women.
  22. Ryanodine Receptor Glycation Favors Mitochondrial Damage in the Senescent Heart.
  23. A Clinical, Proteomics, and Artificial Intelligence-Driven Model to Predict Acute Kidney Injury in Patients Undergoing Coronary Angiography.
  24. Protein changes in gastric epithelial cells RGM-1 in response to Helicobacter pylori infection.
  25. Protein array profiling of circulating angiogenesis-related factors during bevacizumab containing treatment in metastatic colorectal cancer.
  26. Proteomic Landscape of Aldosterone-Producing Adenoma.
  27. Proteins Altered by Surgical Weight Loss Highlight Biomarkers of Insulin Resistance in the Community.
  28. Comparison of blood serum protein analysis by MALDI-MS from either conventional frozen samples or storage disc-deposited samples: A study with human serum from pregnant donors and from patients with intrauterine growth restriction.
  29. Intravitreal bevacizumab upregulates transthyretin in experimental branch retinal vein occlusion.
  30. CLIC4/Arf6 Pathway - A New Lead in BMPRII Inhibition in Pulmonary Hypertension.
  31. Proteomic analysis of a urinary stone with two layers composed of calcium oxalate monohydrate and uric acid.
  32. Dietary salt promotes ischemic brain injury and is associated with parenchymal migrasome formation.
  33. Mouse serum protects against total body irradiation-induced hematopoietic system injury by improving the systemic environment after radiation.
  34. HMQ-T-B10 induces human liver cell apoptosis by competitively targeting EphrinB2 and regulating its pathway.
  35. Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination.
  36. Identification of Novel Protein Targets of Dimethyl Fumarate Modification in Neurons and Astrocytes Reveals Actions Independent of Nrf2 Stabilization.
  37. Comparative proteomics analyses of Acinetobacter baumannii strains ATCC 17978 and AB5075 reveal the differential role of type II secretion system secretomes in lung colonization and ciprofloxacin resistance.
  1. Int J Mol Sci. 2018 Dec 26. pii: E86. [Epub ahead of print]20(1):
    Current Status of Proteomic Technologies for Discovering and Identifying Gingival Crevicular Fluid Biomarkers for Periodontal Disease.
    Sachio Tsuchida, Mamoru Satoh, Masaki Takiwaki, Fumio Nomura.
      Periodontal disease is caused by bacteria in dental biofilms. To eliminate the bacteria, immune system cells release substances that inflame and damage the gums, periodontal ligament, or alveolar bone, leading to swollen bleeding gums, which is a sign of gingivitis. Damage from periodontal disease can cause teeth to loosen also. Studies have demonstrated the proteomic approach to be a promising tool for the discovery and identification of biochemical markers of periodontal diseases. Recently, many studies have applied expression proteomics to identify proteins whose expression levels are altered by disease. As a fluid lying in close proximity to the periodontal tissue, the gingival crevicular fluid (GCF) is the principal target in the search for periodontal disease biomarkers because its protein composition may reflect the disease pathophysiology. Biochemical marker analysis of GCF is effective for objective diagnosis in the early and advanced stages of periodontal disease. Periodontal diseases are also promising targets for proteomics, and several groups, including ours, have applied proteomics in the search for GCF biomarkers of periodontal diseases. This search is of continuing interest in the field of experimental and clinical periodontal disease research. In this article, we summarize the current situation of proteomic technologies to discover and identify GCF biomarkers for periodontal diseases.
    Keywords:  LC-MS; MALDI-TOF MS; MS; biomarker; gingival crevicular fluid; periodontal disease; proteomics
    DOI:  https://doi.org/10.3390/ijms20010086
  2. Neurochem Int. 2018 Dec 20. pii: S0197-0186(18)30534-5. [Epub ahead of print]
    Quantitative iTRAQ-based proteomic analysis of piperine protected cerebral ischemia/reperfusion injury in rat brain.
    Yichun Zou, Pian Gong, Wenyuan Zhao, Jianjian Zhang, Xiaolin Wu, Can Xin, Zhongwei Xiong, Zhengwei Li, Xiaohui Wu, Qi Wan, Xiang Li, Jincao Chen.
      Piperine is the key bioactive factor in black pepper, and has been reported to alleviate cerebral ischemic injury. However, the mechanisms underlying its neuroprotective effects following cerebral ischemia remain unclear. In this study, rats were administered vehicle (dimethyl sulfoxide) or piperine, 20 mg/kg, daily for 14 days before focal cerebral artery occlusion. After occlusion for 2 h followed by reperfusion for 24 h. Histological examinations were used to assess whether piperine has a neuroprotective effect in the rat model of cerebral ischemia/reperfusion injury. The levels of proteins in the ischemic penumbra were evaluated by isobaric tags for relative and absolute quantitation-based proteomics. A total of 3687 proteins were identified, including 23 proteins that were highly significantly differentially expressed between the control and piperine groups. The proteomic findings were verified by immunofluorescence and western blot analysis. Interestingly, piperine administration downregulated a number of critical factors in the complement and coagulation cascades, including complement component 3, fibrinogen gamma chain, alpha-2-macroglobulin, and serpin family A member 1. Collectively, our findings suggest that the neuroprotective effects of piperine following cerebral ischemia/reperfusion injury are related to the regulation of the complement and coagulation cascades.
    Keywords:  Complement and coagulation cascade; Ischemia penumbra; Piperine; Proteome; iTRAQ
    DOI:  https://doi.org/10.1016/j.neuint.2018.12.010
  3. Cancer Genomics Proteomics. 2019 Jan-Feb;16(1):16(1): 29-58
    Human Periprostatic Adipose Tissue: Secretome from Patients With Prostate Cancer or Benign Prostate Hyperplasia.
    Paula Alejandra Sacca, Osvaldo Néstor Mazza, Carlos Scorticati, Gonzalo Vitagliano, Gabriel Casas, Juan Carlos Calvo.
       BACKGROUND/AIM: Periprostatic adipose tissue (PPAT) directs tumour behaviour. Microenvironment secretome provides information related to its biology. This study was performed to identify secreted proteins by PPAT, from both prostate cancer and benign prostate hyperplasia (BPH) patients.
    PATIENTS AND METHODS: Liquid chromatography-mass spectrometry-based proteomic analysis was performed in PPAT-conditioned media (CM) from patients with prostate cancer (CMs-T) (stage T3: CM-T3, stage T2: CM-T2) or benign disease (CM-BPH).
    RESULTS: The highest number and diversity of proteins was identified in CM-T3. Locomotion was the biological process mainly associated to CMs-T and reproduction to CM-T3. Immune responses were enriched in CMs-T. Extracellular matrix and structural proteins were associated to CMs-T. CM-T3 was enriched in proteins with catalytic activity and CM-T2 in proteins with defense/immunity activity. Metabolism and energy pathways were enriched in CM-T3 and those with immune system functions in CMs-T. Transport proteins were enriched in CM-T2 and CM-BPH.
    CONCLUSION: Proteins and pathways reported in this study could be useful to distinguish stages of disease and may become targets for novel therapies.
    Keywords:  Periprostatic adipose tissue; benign prostate hyperplasia; fat tissue; microenvironment; prostate cancer; proteomic; secretome
    DOI:  https://doi.org/10.21873/cgp.20110
  4. J Cancer. 2018 ;9(24): 4650-4658
    Proteomic Identification of Plasma Biomarkers in Children and Adolescents with Recurrent Hodgkin Lymphoma.
    Ombretta Repetto, Lara Mussolin, Caterina Elia, Lia Martina, Maurizio Bianchi, Salvatore Buffardi, Alessandra Sala, Roberta Burnelli, Maurizio Mascarin, Valli De Re.
      The treatment of paediatric Hodgkin lymphoma (HL) has steadily improved over the years, so that 10- years survival exceed 80%. The purpose of this study was to identify prognostic markers for relapsed HL that might contribute to optimize therapeutic approaches. To this aim we retrospectively analysed differential protein expression profiles obtained from plasma of children/adolescents with HL (age ranging from 10 to 18 years) collected at diagnosis. We examined the protein profiles of 15 HL relapsed (R) patients compared with 14 HL not relapsed (NR) patients treated with the same LH-2004 protocol. Two dimensional difference in gel electrophoresis (2D-DIGE) revealed significant differences (fold change > 1.5; Student's T-test p<0.01) between R and NR patients in 10 proteins: α-1-antitrypsin chain a, apolipoprotein A-IV precursor; inter-α-trypsin inhibitor heavy chain; antithrombin-III; vitronectin; fibrinogen α, β and γ chains, complement C3, and ceruloplasmin. An up-regulation of fibrinogen α (spots 78, 196, 230, 234, 239) and β (spots 98, 291, 296, 300) chains together with a lower level of α-1-antitrypsin (spots 255, 264, 266, 272, 273) were found in R patients, and this difference was validated by immunoblotting. The functional role(s) of these proteins in the coagulation and inflammation associated with paediatric/adolescent HL progression and relapse deserves further investigations.
    Keywords:  DIGE; biomarkers; paediatric Hodgkin lymphoma; plasma proteins; relapse
    DOI:  https://doi.org/10.7150/jca.27560
  5. Cancer Genomics Proteomics. 2019 Jan-Feb;16(1):16(1): 81-89
    A Comprehensive Proteome Analysis of Peripheral Blood Mononuclear Cells (PBMCs) to Identify Candidate Biomarkers of Pancreatic Cancer.
    Hengchao Li, Yishen Mao, Yueting Xiong, Huan Huan Zhao, Fenglin Shen, Xing Gao, Pengyuan Yang, Xiaohui Liu, Deliang Fu.
       BACKGROUND/AIM: Pancreatic cancer (PC) is currently the fourth leading cause of cancer-related mortality worldwide. Peripheral blood mononuclear cells (PBMCs) is a subpopulation of accessible and functional immune cells. Comparative analysis of the proteome of PBMCs can help us elucidate the mechanism of disease and find potential biomarkers for diagnosis.
    MATERIALS AND METHODS: PBMCs were collected from healthy individuals, patients with benign diseases, and pancreatic cancer. iTRAQ-2DLC-MS/MS and SWATH methodologies were applied to make a comparative proteomics analysis of PBMCs.
    RESULTS: A total of 3,357 proteins with a false discovery rate (FDR) <1% were identified, of which 114 proteins were found dysregulated in the PC group. An extensive SWATH library was constructed which showed a potential application for large scale clinical sample analysis.
    CONCLUSION: A PBMCs proteome with extensive protein representation was achieved, which will potentially allow the identification of novel biomarkers for PC.
    Keywords:  PBMC; SWATH; blood; iTRAQ; pancreatic cancer
    DOI:  https://doi.org/10.21873/cgp.20114
  6. J Dent. 2018 Dec 20. pii: S0300-5712(18)30304-X. [Epub ahead of print]
    Proteomics of acquired pellicle in gastroesophageal reflux disease patients with or without erosive tooth wear.
    Tatiana Martini, Daniela Rios, Luiza Paula Silva Cassiano, Cíntia Maria de Souza Silva, Even Akemi Taira, Talita Mendes Silva Ventura, Heloísa Aparecida Barbosa Silva Pereira, Ana Carolina Magalhães, Thiago Saads Carvalho, Tommy Baumann, Adrian Lussi, Ricardo Brandt Oliveira, Regina Guenka Palma-Dibb, Marília Afonso Rabelo Buzalaf.
       OBJECTIVES: This in vivo study compared the protein profile of the acquired enamel pellicle (AEP) in volunteers 1) with gastroesophageal reflux disease (GERD) and erosive tooth wear (ETW) (BEWE ≥ 9; GE group); 2) with GERD without ETW (BEWE = 0; GNE group) and 3) control (without GERD and BEWE = 0; C group).
    MATERIALS AND METHODS: Twenty-four subjects (8/group) participated. AEP was formed during 120 min and collected. After protein extraction, the samples were submitted to reverse phase liquid chromatography coupled to mass spectrometry. Label-free proteomic quantification was performed using Protein Lynx Global Service software.
    RESULTS: In total, 458 proteins were identified. Seventy-six proteins were common to all the groups. The proteomic profile of the AEP was quite different among the distinct groups. The numbers of proteins exclusively found in the C, GE and GNE groups were 113, 110 and 81, respectively. Most of the proteins exclusively identified in the C and GNE groups bind metals, while those in the GE group are mainly membrane proteins. Many proteins were found exclusively in the reflux groups. In the quantitative analyses, when the GNE group was compared with the GE group, the proteins with the highest decreases were Lysozyme C, Antileukoproteinase, Cathepsin G, Neutrophil defensins and Basic salivary proline-rich proteins, while those with the highest increases were subunits of Hemoglobin, Albumin and isoforms of Cystatin.
    CONCLUSION: Profound alterations in the proteomic profile of the AEP were seen in GNE compared with GE volunteers, which might play a role in the resistance to ETW seen in the first.
    CLINICAL SIGNIFICANCE: This pioneer study compared the proteomic profile of the AEP of patients with GERD with or without ETW. Increased proteins in those without ETW might be protective and are good candidates to be added to dental products to protect against erosion caused by intrinsic acids.
    Keywords:  Acquired enamel pellicle; Erosive Tooth Wear; Gastroesophageal reflux; Proteomics
    DOI:  https://doi.org/10.1016/j.jdent.2018.12.007
  7. J Proteomics. 2018 Dec 24. pii: S1874-3919(18)30448-2. [Epub ahead of print]
    Differential protein expression of blood platelet components associated with 1 adverse transfusion reactions.
    Chaker Aloui, Céline Barlier, Stéphane Claverol, Jocelyne Fagan, Danielle Awounou, Emmanuelle Tavernier, Denis Guyotat, Hind Hamzeh-Cognasse, Fabrice Cognasse, Olivier Garraud, Sandrine Laradi.
      Platelets found within platelet components (PCs) intended for transfusion release inflammatory molecules. Despite the implementation of leukoreduction, some of these PCs are occasionally associated with adverse transfusion reactions (ATRs). The aim of this study was to decipher the platelet proteome in two types of PCs, buffy-coat-derived pooled PCs (PPCs) and single-donor apheresis PCs (SDA-PCs), associated with ATRs. A label-free LC-MS/MS method was used for the proteomic analysis of washed platelet pellets from 3 PPCs and 3 SDA-PCs associated with ATRs, compared to matched controls. Bioinformatics tools allowed us to characterise the differentially expressed (DE) proteins between cases (ATR-PCs) and controls (no.ATR-PCs). From the PPCs and SDA-PCs, 473 and 146 proteins were DE, respectively. The functional interpretation of these proteins revealed enrichment in platelet activation and degranulation as the most important biological process. The most dysregulated pathways were integrin signaling for PPCs and acute phase response signaling for SDA-PCs. Interestingly, inflammatory disorders were found to be enriched in both PC types. Profound proteome changes were found in the platelets of PCs that led to clinical ATRs in patients. This study presents the first exploration of the platelet proteomic signature associated with ATRs and could provide clues to improving transfusion medicine. BIOLOGICAL SIGNIFICANCE: Adverse transfusion reactions (ATRs) can still occur after transfusion of platelet components (PC). This is the first report on the proteomic analysis of PCs associated with ATR. In this study, the contents of PC bags implicated in ATRs were examined. The aims of this study were to characterise molecules that could be central to the inflammation of ATRs and to highlight dysregulated mechanisms to explain the onset of ATRs. Two types of PCs were used: 3 PPCs (each from 5 donors) and 3 SDA-PCs (each from one donor). We have shown that the two types of PCs, from bags undergoing different processing (i.e., sampling, preparation), involve two types of dysregulated - pathophysiological mechanisms associated with the onset of ATRs. The most dysregulated signaling pathways were cytoskeleton and integrin regulation for PPCs, acute phase response signaling and remodelling of adherens junctions for SDA-PCs. Inflammation, platelet activation and degranulation processes were present in both PC types but were more important for PPCs. This proteomics analysis provides a better understanding of the pathophysiological mechanisms involved in ATRs and may lead to novel steps to ensure safe PC transfusion.
    Keywords:  Adverse transfusion reaction; Bioinformatic analysis; Dysregulated mechanisms; Inflammatory disorders; Platelet proteome; Untargeted label-free method
    DOI:  https://doi.org/10.1016/j.jprot.2018.12.019
  8. World J Mens Health. 2018 Dec 21.
    New Insights on the Mechanisms Affecting Fertility in Men with Non-Seminoma Testicular Cancer before Cancer Therapy.
    Tania R Dias, Ashok Agarwal, Peter N Pushparaj, Gulfam Ahmad, Rakesh Sharma.
       PURPOSE: Patients with non-seminoma testicular cancer (NSTC) cancer can be subfertile or infertile, and present reduced sperm quality, but the underlying mechanisms are unknown. The aim of this study was to compare the sperm proteome of patients with NSTC, who cryopreserved their sperm before starting cancer treatment, with that from healthy fertile men.
    MATERIALS AND METHODS: Semen volume, sperm motility and sperm concentration were evaluated before the cryopreservation of samples from patients with NSTC (n=15) and the control group (n=15). Sperm proteomic analysis was performed by liquid chromatography-tandem mass spectrometry and the differentially expressed proteins (DEPs) between the two groups were identified using bioinformatic tools.
    RESULTS: A total of 189 DEPs was identified in the dataset, from which five DEPs related to sperm function and fertilization were selected for validation by Western blot. We were able to validate the underexpression of the mitochondrial complex subunits NADH:Ubiquinone Oxidoreductase Core Subunit S1 (NDUFS1) and ubiquinol-cytochrome C reductase core protein 2 (UQCRC2), as well as the underexpression of the testis-specific sodium/potassium-transporting ATPase subunit alpha-4 (ATP1A4) in the NSTC group.
    CONCLUSIONS: Our results indicate that sperm mitochondrial dysfunction may explain the observed decrease in sperm concentration, total sperm count and total motile count in NSTC patients. The identified DEPs may serve as potential biomarkers for the pathophysiology of subfertility/infertility in patients with NSTC. Our study also associates the reduced fertilizing ability of NSTC patients with the dysregulation of important sperm molecular mechanisms.
    Keywords:  Cancer therapy; Male fertility; Non-seminoma; Sperm quality; Testicular cancer
    DOI:  https://doi.org/10.5534/wjmh.180099
  9. J Glob Infect Dis. 2018 Oct-Dec;10(4):10(4): 196-200
    Comparative Proteomic Profiling of Mycobacterium tuberculosis and the Thai Vaccine Strain Mycobacterium bovis Bacille Calmette-Guerin Tokyo172: Diverse Biomarker Candidates for Species Differentiation.
    Songsri Kasempimolporn, Pornpimol Premchaiporn, Wichit Thaveekarn, Supatsorn Boonchang, Visith Sitprija.
       Background: Bacille Calmette-Guerin (BCG)-related complications can occur in vaccinated children. Comparison of the composition of cellular proteins of virulent Mycobacterium tuberculosis (MTB) H37Rv with of attenuated Mycobacterium bovis BCG Tokyo172 vaccine strain used in Thailand and identify protein candidates of value for differentiation between the two mycobacterial species may facilitate the diagnosis of etiologic agent of mycobacterial disease in vaccinated children, as most cases have been believed to have originated from BCG vaccine.
    Materials and Methods: The two-dimensional electrophoresis (2DE) proteomic profiles of cellular proteins from the Thai vaccine strain M. bovis BCG Tokyo172 and MTB were compared and the matched spots in 2DE gels were submitted to mass spectrometry analysis.
    Results: There were a number of similar protein contents with different intensity or position between MTB and M. bovis BCG Tokyo172. A higher expression of some immunogenic proteins was shown in BGG Tokyo172 when compared to MTB, while some were shown the opposite pattern.
    Conclusions: Proteomic approach reveals key proteins participating in different species of Mycobacteria, and may be useful for discrimination between MTB and the BCG Tokyo172 infection.
    Keywords:  Bacille Calmette–Guerin-related complications; Mycobacterium bovis BCG Tokyo172; Mycobacterium tuberculosis; proteomics
    DOI:  https://doi.org/10.4103/jgid.jgid_149_17
  10. Autoimmune Dis. 2018 ;2018 6728541
    Identification of Levels of Serum Amyloid A and Apolipoprotein A1 in Serum Proteomic Analysis of Neuropsychiatric Systemic Lupus Erythematosus Patients.
    Nancy P Duarte-Delgado, Tania P Lujan, Álvaro Arbeláez-Cortés, Jenny García-Valencia, Adriana Zapata, Mauricio Rojas, Mauricio Restrepo-Escobar, Gloria Vásquez, Blanca L Ortiz-Reyes.
      Neuropsychiatric Systemic Lupus Erythematosus (NPSLE) has multiple pathogenic mechanisms that cause diverse manifestations and whose diagnosis is challenging because of the absence of appropriate diagnostic tests. In the present study the application of proteomics using two-dimensional electrophoresis (2D) and mass spectrometry (MS) allowed the comparison of the protein profile of the serum low and high abundance protein fractions of NPSLE patients (NPSLE group) and SLE without neuropsychiatric syndromes (SLE group), Neuropsychiatric syndromes not associated with SLE (NPnoSLE groups), and healthy controls (CTRL group). The gels obtained were digitalized and analyzed with the PDQuest software. The statistical analysis of the spots was performed using the nonparametric Kruskal Wallis and Dunn's multiple comparison tests. Two spots showed significant differences and were identified by MS. Spot 4009 was significantly lower in NPSLE with regard to NPnoSLE (p= 0,004) and was identified as apolipoprotein A1 (APOA1) (score 809-1132). Spot 8001 was significantly higher in NPSLE regarding CTRL and NPnoSLE (p= 0,01 y 0,03, respectively) and was identified as serum amyloid A (SAA) (score 725-2488). The proinflammatory high density lipoproteins (HDL) have been described in SLE. In this HDL the decrease of APOA1 is followed by an increase in SAA. This altered level of both proteins may be related to the inflammatory state that is characteristic of an autoimmune disease like SLE, but this is not specific for NPSLE.
    DOI:  https://doi.org/10.1155/2018/6728541
  11. Proteomics. 2018 Dec 23. e1800148
    Exosomes Derived from Human Primary and Metastatic Colorectal Cancer Cells Contribute to Functional Heterogeneity of Activated Fibroblasts by Reprogramming Their Proteome.
    Alin Rai, David W Greening, Maoshan Chen, Rong Xu, Hong Ji, Richard J Simpson.
      Cancer-associated fibroblasts (CAFs) are a heterogeneous population of activated fibroblasts that constitute a dominant cellular component of the tumour microenvironment (TME) performing distinct functions. Here, we investigated the role of tumour-derived exosomes in activating quiescent fibroblasts into distinct functional subtypes. Proteomic profiling and functional dissection revealed that early (SW480) and late-stage (SW620) colorectal cancer (CRC) cell-derived exosomes both activated normal quiescent fibroblasts (α-SMA- , CAV+ , FAP+ , VIM+ ) into CAF-like fibroblasts (α-SMA+ , CAV- FAP+ , VIM+ ). Fibroblasts activated by early stage cancer-exosomes (SW480-Exos) were highly pro-proliferative and pro-angiogenic and displayed elevated expression of pro-angiogenic (IL8, RAB10, NDRG1) and pro-proliferative (SA1008, FFPS) proteins. In contrast, fibroblasts activated by late stage cancer-exosomes (SW620-Exos) displayed a striking ability to invade through extracellular matrix through upregulation of pro-invasive regulators of membrane protrusion (PDLIM1, MYO1B) and elevated secretion of matrix-remodelling proteins (MMP11, EMMPRIN, ADAM10). Conserved features of exosome-mediated fibroblast activation include enhanced ECM secretion (type I collagen, Tenascin C/X), oncogenic transformation and metabolic reprogramming (e.g., downregulation of metabolic switch CAV-1, upregulation of glycogen metabolism (GAA), amino acid biosynthesis (SHMT2, IDH2) and membrane transporters of glucose (GLUT-1), lactate (MCT4) and amino acids (SLC1A5/3A5)). This study highlights the role of primary and metastatic CRC tumour-derived exosomes in generating phenotypically and functionally distinct subsets of CAFs that may facilitate tumour progression. This article is protected by copyright. All rights reserved.
    Keywords:  Cancer; Cancer-associated fibroblasts; Exosomes; Fibroblast heterogeneity; Tumour microenvironment
    DOI:  https://doi.org/10.1002/pmic.201800148
  12. Proteomics. 2018 Dec 25. e1800135
    Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery.
    Shawn J Rice, Xin Liu, Jianhong Zhang, Chandra P Belani.
      The current state of proteomics requires a choice between targeted and global discovery methods. We have established and optimized a method that combines targeted and data-independent acquisition for absolute quantification of all identified plasma proteins in a single Sequential Window Acquisition of all THeoretical fragment ions (SWATH) acquisition run using a panel of Spike-In Standards (SIS). We compared the Absolute Quantification (AQ) of SWATH and Multiple-Reaction Monitoring-High Resolution (MRM-HR) acquisition methods using the 100 protein PlasmaDive SIS panel spiked into non-depleted human plasma. SWATH provided equivalent quantification and differentially abundant protein profiles as MRM-HR. Absolute quantities of the SIS peptides from the SWATH data were used to estimate the absolute quantities (eAQ) for all the proteins in the run. The eAQ values provided similar quantification and differentially abundant protein profiles as AQ and protein area (PA) values. As a proof-of-concept, we applied the eAQ method to 12 plasma samples from 6 non-small cell lung cancer (NSCLC) patients and evaluated the performance of eAQ values versus peak area quantification. There was a strong correlation between AQ and peak area ratios producing significant overlap of differentially abundant proteins. Our eAQ method can provide quantitative data equivalent to AQ or peak area values. This article is protected by copyright. All rights reserved.
    Keywords:  SWATH ; absolute quantification; data-independent acquisition; lung cancer; plasma biomarkers
    DOI:  https://doi.org/10.1002/pmic.201800135
  13. Neurobiol Dis. 2018 Dec 24. pii: S0969-9961(18)30767-8. [Epub ahead of print]
    Brain proteome changes in female Brd1+/- mice unmask dendritic spine pathology and show enrichment for schizophrenia risk.
    Veerle Paternoster, Maria Svanborg, Anders Valdemar Edhager, Anto P Rajkumar, Esben Ahlburg Eickhardt, Jonatan Pallesen, Jakob Grove, Per Qvist, Tue Fryland, Gregers Wegener, Jens Randel Nyengaard, Ole Mors, Johan Palmfeldt, Anders Dupont Børglum, Jane Hvarregaard Christensen.
      Genetic and molecular studies have implicated the Bromodomain containing 1 (BRD1) gene in the pathogenesis of schizophrenia and bipolar disorder. Accordingly, mice heterozygous for a targeted deletion of Brd1 (Brd1+/- mice) show behavioral phenotypes with broad translational relevance to psychiatric disorders. BRD1 encodes a scaffold protein that affects the expression of many genes through modulation of histone acetylation. BRD1 target genes have been identified in cell lines; however the impact of reduced Brd1 levels on the brain proteome is largely unknown. In this study, we applied label-based quantitative mass spectrometry to profile the frontal cortex, hippocampus and striatum proteome and synaptosomal proteome of female Brd1+/- mice. We successfully quantified between 1537 and 2196 proteins and show widespread changes in protein abundancies and compartmentalization. By integrative analysis of human genetic data, we find that the differentially abundant proteins in frontal cortex and hippocampus are enriched for schizophrenia risk further linking the actions of BRD1 to psychiatric disorders. Affected proteins were further enriched for proteins involved in processes known to influence neuronal and dendritic spine morphology e.g. regulation of cytoskeleton dynamics and mitochondrial function. Directly prompted in these findings, we investigated dendritic spine morphology of pyramidal neurons in anterior cingulate cortex and found them significantly altered, including reduced size of small dendritic spines and decreased number of the mature mushroom type. Collectively, our study describes known as well as new mechanisms related to BRD1 dysfunction and its role in psychiatric disorders, and provides evidence for the molecular and cellular dysfunctions underlying altered neurosignalling and cognition in Brd1+/- mice.
    Keywords:  Animal model; Bromodomain containing 1; Cytoskeleton; Dendritic spine; Mitochondria; Proteomics; Schizophrenia; TMT10plex
    DOI:  https://doi.org/10.1016/j.nbd.2018.12.011
  14. Proteomics Clin Appl. 2018 Dec 23. e1800137
    Integrative Clustering in Mass Spectrometry Imaging for Enhanced Patient Stratification.
    Benjamin Balluff, Achim Buck, Marta Martin-Lorenzo, Frédéric Dewez, Rupert Langer, Liam A McDonnell, Axel Walch, Ron M A Heeren.
      In biomedical research, mass spectrometry imaging (MSI) can generate molecular information in a spatially resolved manner from tissue sections. Especially matrix-assisted laser desorption/ionization (MALDI) MSI offers, depending on the type of matrix, the detection of a broad variety of molecules ranging from metabolites to proteins, thereby facilitating the collection of multi-level molecular data. Lately, integrative clustering techniques have been developed that make use of the complementary information of multi-level molecular data in order to better stratify patient cohorts, but which have not yet been applied in the field of MSI. In this study, the potential of integrative clustering is investigated for multi-level molecular MSI data to subdivide cancer patients into different prognostic groups. Metabolomic and peptidomic data were obtained by MALDI-MSI from tissue material of 46 esophageal cancer patients located on a tissue microarray. The integrative clustering methods Similarity Network Fusion, iCluster, and moCluster were applied and compared to non-integrated clustering. The results show that the combination of multi-level molecular data increases the capability of integrative algorithms to detect patient subgroups with different clinical outcome, compared to the single molecular level or the concatenated data. This underlines the potential of multi-level molecular data from the same subject using MSI with subsequent integrative clustering. This article is protected by copyright. All rights reserved.
    Keywords:  cancer; integrative clustering; mass spectrometry imaging; prognosis
    DOI:  https://doi.org/10.1002/prca.201800137
  15. Cancer Cell. 2018 Dec 01. pii: S1535-6108(18)30529-4. [Epub ahead of print]
    p62/SQSTM1 Fuels Melanoma Progression by Opposing mRNA Decay of a Selective Set of Pro-metastatic Factors.
    Panagiotis Karras, Erica Riveiro-Falkenbach, Estela Cañón, Cristina Tejedo, Tonantzin G Calvo, Raúl Martínez-Herranz, Direna Alonso-Curbelo, Metehan Cifdaloz, Eva Perez-Guijarro, Gonzalo Gómez-López, Pilar Ximenez-Embun, Javier Muñoz, Diego Megias, David Olmeda, Jorge Moscat, Pablo L Ortiz-Romero, Jose L Rodríguez-Peralto, María S Soengas.
      Modulators of mRNA stability are not well understood in melanoma, an aggressive tumor with complex changes in the transcriptome. Here we report the ability of p62/SQSTM1 to extend mRNA half-life of a spectrum of pro-metastatic factors. These include FERMT2 and other transcripts with no previous links to melanoma. Transcriptomic, proteomic, and interactomic analyses, combined with validation in clinical biopsies and mouse models, identified a selected set of RNA-binding proteins (RBPs) recruited by p62, with IGF2BP1 as a key partner. This p62-RBP interaction distinguishes melanoma from other tumors where p62 controls autophagy or oxidative stress. The relevance of these data is emphasized by follow-up analyses of patient prognosis revealing p62 and FERMT2 as adverse determinants of disease-free survival.
    Keywords:  FERMT2; IGF2BP1; RNA-binding proteins; gene networks; genetically engineered mouse models; interactomics; melanoma; metastasis; p62/SQSTM1; prognostic indicators; proteomics; transcriptomics
    DOI:  https://doi.org/10.1016/j.ccell.2018.11.008
  16. PLoS One. 2018 ;13(12): e0209652
    Transcriptomic and proteomic host response to Aspergillus fumigatus conidia in an air-liquid interface model of human bronchial epithelium.
    Amreen Toor, Luka Culibrk, Gurpreet K Singhera, Kyung-Mee Moon, Anna Prudova, Leonard J Foster, Margo M Moore, Delbert R Dorscheid, Scott J Tebbutt.
      Aspergillus fumigatus (A. fumigatus) is a wide-spread fungus that is a potent allergen in hypersensitive individuals but also an opportunistic pathogen in immunocompromised patients. It reproduces asexually by releasing airborne conidiospores (conidia). Upon inhalation, fungal conidia are capable of reaching the airway epithelial cells (AECs) in bronchial and alveolar tissues. Previous studies have predominantly used submerged monolayer cultures for studying this host-pathogen interaction; however, these cultures do not recapitulate the mucocililary differentiation phenotype of the in vivo epithelium in the respiratory tract. Thus, the aim of this study was to use well-differentiated primary human bronchial epithelial cells (HBECs) grown at the air-liquid interface (ALI) to determine their transcriptomic and proteomic responses following interaction with A. fumigatus conidia. We visualized conidial interaction with HBECs using confocal laser scanning microscopy (CLSM), and applied NanoString nCounter and shotgun proteomics to assess gene expression changes in the human cells upon interaction with A. fumigatus conidia. Western blot analysis was used to assess the expression of top three differentially expressed proteins, CALR, SET and NUCB2. CLSM showed that, unlike submerged monolayer cultures, well-differentiated ALI cultures of primary HBECs were estimated to internalize less than 1% of bound conidia. Nevertheless, transcriptomic and proteomic analyses revealed numerous differentially expressed host genes; these were enriched for pathways including apoptosis/autophagy, translation, unfolded protein response and cell cycle (up-regulated); complement and coagulation pathways, iron homeostasis, nonsense mediated decay and rRNA binding (down-regulated). CALR and SET were confirmed to be up-regulated in ALI cultures of primary HBECs upon exposure to A. fumigatus via western blot analysis. Therefore, using transcriptomics and proteomics approaches, ALI models recapitulating the bronchial epithelial barrier in the conductive zone of the respiratory tract can provide novel insights to the molecular response of bronchial epithelial cells upon exposure to A. fumigatus conidia.
    DOI:  https://doi.org/10.1371/journal.pone.0209652
  17. EBioMedicine. 2018 Dec 23. pii: S2352-3964(18)30610-8. [Epub ahead of print]
    Predictive value of targeted proteomics for coronary plaque morphology in patients with suspected coronary artery disease.
    Michiel J Bom, Evgeni Levin, Roel S Driessen, Ibrahim Danad, Cornelis C Van Kuijk, Albert C van Rossum, Jagat Narula, James K Min, Jonathon A Leipsic, João P Belo Pereira, Charles A Taylor, Max Nieuwdorp, Pieter G Raijmakers, Wolfgang Koenig, Albert K Groen, Erik S G Stroes, Paul Knaapen.
       BACKGROUND: Risk stratification is crucial to improve tailored therapy in patients with suspected coronary artery disease (CAD). This study investigated the ability of targeted proteomics to predict presence of high-risk plaque or absence of coronary atherosclerosis in patients with suspected CAD, defined by coronary computed tomography angiography (CCTA).
    METHODS: Patients with suspected CAD (n = 203) underwent CCTA. Plasma levels of 358 proteins were used to generate machine learning models for the presence of CCTA-defined high-risk plaques or complete absence of coronary atherosclerosis. Performance was tested against a clinical model containing generally available clinical characteristics and conventional biomarkers.
    FINDINGS: A total of 196 patients with analyzable protein levels (n = 332) was included for analysis. A subset of 35 proteins was identified predicting the presence of high-risk plaques. The developed machine learning model had fair diagnostic performance with an area under the curve (AUC) of 0·79 ± 0·01, outperforming prediction with generally available clinical characteristics (AUC = 0·65 ± 0·04, p < 0·05). Conversely, a different subset of 34 proteins was predictive for the absence of CAD (AUC = 0·85 ± 0·05), again outperforming prediction with generally available characteristics (AUC = 0·70 ± 0·04, p < 0·05).
    INTERPRETATION: Using machine learning models, trained on targeted proteomics, we defined two complementary protein signatures: one for identification of patients with high-risk plaques and one for identification of patients with absence of CAD. Both biomarker subsets were superior to generally available clinical characteristics and conventional biomarkers in predicting presence of high-risk plaque or absence of coronary atherosclerosis. These promising findings warrant external validation of the value of targeted proteomics to identify cardiovascular risk in outcome studies. FUND: This study was supported by an unrestricted research grant from HeartFlow Inc. and partly supported by a European Research Area Network on Cardiovascular Diseases (ERA-CVD) grant (ERA CVD JTC2017, OPERATION). Funders had no influence on trial design, data evaluation, and interpretation.
    Keywords:  Biomarkers; Coronary artery disease; Coronary computed tomography angiography; Proteomics; Risk assessment
    DOI:  https://doi.org/10.1016/j.ebiom.2018.12.033
  18. J Proteome Res. 2018 Dec 28.
    Proteomic signature of neuroblastoma cells UKF-NB-4 reveals key role of lysosomal sequestration and the proteasome complex in acquiring chemoresistance to cisplatin.
    Miguel Angel Merlos Rodrigo, Hana Buchtelova, Vivian de Los Rios, Jose Ignacio Casal, Tomas Eckschlager, Jan Hrabeta, Marie Belhajova, Zbynek Heger, Vojtech Adam.
      Cisplatin (CDDP) is a widely used agent in the treatment of neuroblastoma. Unfortunately, the development of acquired chemoresistance limits its clinical use. To gain a detailed understanding of the mechanisms underlying the development of such chemoresistance, we comparatively analysed established cisplatin-resistant neuroblastoma cell line (UKF-NB-4CDDP) and its sensitive counterpart (UKF-NB-4). First, using viability screenings, we confirmed the decreased sensitivity of tested cells to cisplatin and identified a cross-resistance to carboplatin and oxaliplatin. Then, the proteomic signatures were analysed using nanoLC MS/MS. Among the proteins responsible for UKF-NB-4CDDP chemoresistance, ion channels transport family proteins, ABC superfamily proteins, SLC-mediated trans-membrane transporters, proteasome complex subunits and V-ATPases were identified. Moreover, we detected markedly higher proteasome activity in UKF-NB-4CDDP cells and a remarkable lysosomal enrichment that can be inhibited by bafilomycin A to sensitize UKF-NB-4CDDP to CDDP. Our results indicate that lysosomal sequestration and proteasome activity may be one of key mechanisms responsible for intrinsic chemoresistance of neuroblastoma to CDDP.
    DOI:  https://doi.org/10.1021/acs.jproteome.8b00867
  19. Proc Natl Acad Sci U S A. 2018 Dec 24. pii: 201813666. [Epub ahead of print]
    Multiomics of azacitidine-treated AML cells reveals variable and convergent targets that remodel the cell-surface proteome.
    Kevin K Leung, Aaron Nguyen, Tao Shi, Lin Tang, Xiaochun Ni, Laure Escoubet, Kyle J MacBeth, Jorge DiMartino, James A Wells.
      Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are diseases of abnormal hematopoietic differentiation with aberrant epigenetic alterations. Azacitidine (AZA) is a DNA methyltransferase inhibitor widely used to treat MDS and AML, yet the impact of AZA on the cell-surface proteome has not been defined. To identify potential therapeutic targets for use in combination with AZA in AML patients, we investigated the effects of AZA treatment on four AML cell lines representing different stages of differentiation. The effect of AZA treatment on these cell lines was characterized at three levels: the DNA methylome, the transcriptome, and the cell-surface proteome. Untreated AML cell lines showed substantial overlap at all three omics levels; however, while AZA treatment globally reduced DNA methylation in all cell lines, changes in the transcriptome and surface proteome were subtle and differed among the cell lines. Transcriptome analysis identified five commonly up-regulated coding genes upon AZA treatment in all four cell lines, TRPM4 being the only gene encoding a surface protein, and surface proteome analysis found no commonly regulated proteins. Gene set enrichment analysis of differentially regulated RNA and surface proteins showed a decrease in metabolic pathways and an increase in immune defense response pathways. As such, AZA treatment led to diverse effects at the individual gene and protein levels but converged to common responses at the pathway level. Given the heterogeneous responses in the four cell lines, we discuss potential therapeutic strategies for AML in combination with AZA.
    Keywords:  AML; azacitidine; multiomics; surface proteomics; target discovery
    DOI:  https://doi.org/10.1073/pnas.1813666116
  20. J Proteome Res. 2018 Dec 26.
    Proteomic characterization of epithelial-like extracellular vesicles in advanced endometrial cancer.
    Javier Mariscal, Patricia Fernández-Puente, Valentina Calamia, Alicia Abalo, Maria Santacana, Xavier Matias-Guiu, Rafael Lopez-Lopez, Antonio Gil-Moreno, Lorena Alonso-Alconada, Miguel Abal.
      Endometrial cancer (EC) is the most frequent gynecological cancer. Tumor dissemination affecting around 20% of EC patients is characterized at the primary carcinoma by epithelial-to-mesenchymal transition (EMT) associated with myometrial infiltration. At distant sites, the interaction of circulating tumor cells (CTCs) with the microenvironment results crucial for metastatic colonization, with a participation of the extracellular vesicles (EVs). We comprehensively approached these primary and secondary sites to study the impact of tumor EVs on the metastatic efficiency of CTCs in EC. Tumor EVs in circulation reproduce the epithelial phenotype predominant in the primary carcinoma, while CTCs are characterized by an EMT phenotype. We modelled this EMT-related clinical scenario in the Hec1A endometrial cell line and characterized the epithelial-like EVs in circulation by SILAC proteome analysis. Identification of proteins involved in cell-cell and cell-matrix interaction and binding, together with in vitro evidences of an improved adhesion of CTC to a functionalized endothelium suggest a contribution of the epithelial-like EVs in the homing of CTCs at metastatic sites. Accordingly, adhesion protein LGALS3BP was found significantly enriched in circulating EVs from a cohort of EC patients with high risk of recurrence by targeted proteomics (MRM), highlighting their potential as liquid biopsy in EC.
    DOI:  https://doi.org/10.1021/acs.jproteome.8b00750
  21. Breast Cancer (Dove Med Press). 2019 ;11 1-12
    LXR/RXR pathway signaling associated with triple-negative breast cancer in African American women.
    Odalys Torres-Luquis, Krystal Madden, N'sanh Mr N'dri, Richard Berg, Olufunmilayo F Olopade, Wilfred Ngwa, Dafalla Abuidris, Suresh Mittal, Beverly Lyn-Cook, Sulma I Mohammed.
       Background: Triple-negative breast cancer (TNBC) is more prevalent in African and African American (AA) women compared to European American (EA) women. African and AA women diagnosed with TNBC experience high frequencies of metastases and less favorable outcomes. Emerging evidence indicates that this disparity may in fact be the result of the uniquely aggressive biology of African and AA disease.
    Purpose: To understand the reasons for TNBC in AA aggressive biology, we designed the present study to examine the proteomic profiles of TNBC and luminal A (LA) breast cancer within and across patients' racial demographic groups in order to identify proteins or molecular pathways altered in TNBC that offer some explanation for its aggressiveness and potential targets for treatment.
    Materials and methods: Proteomic profiles of TNBC, LA tumors, and their adjacent normal tissues from AA and EA women were obtained using 2-dimensional gel electrophoresis and bioinformatics, and differentially expressed proteins were validated by Western blot and immunohistochemistry. Our data showed that a number of proteins have significantly altered in expression in LA tumors compared to TNBC, both within and across patients' racial demographic groups. The differentially overexpressed proteins in TNBC (compared to LA) of AA samples were distinct from those in TNBC (compared to LA) of EA women samples. Among the signaling pathways altered in AA TNBC compared to EA TNBC are innate immune signaling, calpain protease, and pyrimidine de novo synthesis pathways. Furthermore, liver LXR/RXR signaling pathway was altered between LA and TNBC in AA women and may be due to the deficiency of the CYP7B1 enzyme responsible for cholesterol degradation.
    Conclusion: These findings suggest that TNBC in AA women enriched in signaling pathways that are different from TNBC in EA women. Our study draws a link between LXR/RXR expression, cholesterol, obesity, and the TNBC in AA women.
    Keywords:  African American; European American; breast; luminal; luminal breast cancer; triple-negative breast cancer
    DOI:  https://doi.org/10.2147/BCTT.S185960
  22. Circulation. 2018 Oct 25.
    Ryanodine Receptor Glycation Favors Mitochondrial Damage in the Senescent Heart.
    Marisol Ruiz-Meana, Marta Minguet, Diana Bou-Teen, Elisabet Miro-Casas, Celia Castans, José Castellano, Elena Bonzon-Kulichenko, Alberto Igual, Rafael Rodriguez-Lecoq, Jesús Vazquez, David García-Dorado.
       BACKGROUND: Senescent cardiomyocytes exhibit a mismatch between energy demand and supply that facilitates their transition towards failing cells. Altered calcium transfer from sarcoplasmic reticulum (SR) to mitochondria has been causally linked to the pathophysiology of aging and heart failure.
    METHODS: Because advanced glycation-end products (AGEs) accumulate throughout life, we investigated whether intracellular glycation occurs in aged cardiomyocytes and its impact on SR and mitochondria.
    RESULTS: Quantitative proteomics, W.blot and immunofluorescence demonstrated a significant increase in AGE-modified proteins in the myocardium of old mice (≥20months) compared to young ones (4-6months). Glyoxalase-1 activity (responsible for detoxification of dicarbonyl intermediates) and its cofactor glutathione were decreased in aged hearts. Immunolabeling and proximity ligation assay identified the ryanodine receptor (RyR2) in the sarcoplasmic reticulum (SR) as prominent target of glycation in aged mice, and the sites of glycation were characterized by quantitative mass spectrometry. RyR2 glycation was associated with more pronounced calcium leak, determined by confocal microscopy in cardiomyocytes and SR vesicles. Interfibrillar mitochondria -directly exposed to SR calcium release- from aged mice had increased calcium content compared to those from young ones. Higher levels of AGEs and reduced glyoxalase-1 activity and glutathione were also present in atrial appendages from surgical patients ≥75 years as compared to the younger ones. Elderly patients also exhibited RyR2 hyperglycation and increased mitochondrial calcium content that was associated with reduced myocardial aerobic capacity (mitochondrial O2 consumption/g) due to less respiring mitochondria. In contracting HL-1 cardiomyocytes, pharmacological glyoxalase-1 inhibition recapitulated RyR2 glycation and defective SR-mitochondria calcium exchange of aging.
    CONCLUSIONS: mitochondria from aging hearts develop calcium overload secondary to SR calcium leak. Glycative damage of RyR2, favored by deficient dicarbonyl detoxification capacity, contributes to calcium leak and mitochondrial damage in the senescent myocardium.
    Keywords:  Advanced glycation end-products
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.118.035869
  23. Clin Cardiol. 2018 Dec 23.
    A Clinical, Proteomics, and Artificial Intelligence-Driven Model to Predict Acute Kidney Injury in Patients Undergoing Coronary Angiography.
    Nasrien E Ibrahim, Cian P McCarthy, Shreya Shrestha, Hanna K Gaggin, Renata Mukai, Craig A Magaret, Rhonda F Rhyne, James L Januzzi.
       BACKGROUND: Standard measures of kidney function are only modestly useful for accurate prediction of risk for acute kidney injury (AKI).
    HYPOTHESIS: Clinical and biomarker data can predict AKI more accurately.
    METHODS: Using Luminex xMAP technology, we measured 109 biomarkers in blood from 889 patients prior to undergoing coronary angiography. Procedural AKI was defined as an absolute increase in serum creatinine of ≥0.3 mg/dL, a percentage increase in serum creatinine of ≥50%, or a reduction in urine output (documented oliguria of <0.5 mL/kg per hour for >6 hours) within 7 days after contrast exposure. Clinical and biomarker predictors of AKI were identified using machine learning and a final prognostic model was developed with least absolute shrinkage and selection operator (LASSO).
    RESULTS: Forty-three (4.8%) patients developed procedural AKI. Six predictors were present in the final model: four (history of diabetes, blood urea nitrogen to creatinine ratio, C-reactive protein, and osteopontin) had a positive association with AKI risk, while two (CD5 antigen-like and Factor VII) had a negative association with AKI risk. The final model had a cross-validated area under the receiver operating characteristic curve (AUC) of 0.79 for predicting procedural AKI, and an in-sample AUC of 0.82 (P<0.001). The optimal score cut-off had 77% sensitivity, 75% specificity, and a negative predictive value of 98% for procedural AKI. An elevated score was predictive of procedural AKI in all subjects (odds ratio=9.87; P<0.001).
    CONCLUSIONS: We describe a clinical and proteomics-supported biomarker model with high accuracy for predicting procedural AKI in patients undergoing coronary angiography. This article is protected by copyright. All rights reserved.
    Keywords:  coronary angiography; kidney injury; risk prediction; risk score
    DOI:  https://doi.org/10.1002/clc.23143
  24. J Cell Biochem. 2018 Dec 23.
    Protein changes in gastric epithelial cells RGM-1 in response to Helicobacter pylori infection.
    Zengfa Lv, Lizhi Zhao, Weimin Jin.
      Helicobacter pylori-induced inflammation significantly increases the risk of gastric cancer. To investigate the role of H. pylori infection in gastric epithelial cell carcinogenesis, flow cytometry was used to analyze the apoptosis of gastric epithelial cells infected by H. pylori. Next, LTQ MS mass spectrometry (MS) was applied to identify protein changes in gastric epithelial cells infected with H. pylori, and then bioinformatics was adopted to analyze the cellular localization and biological function of differential proteins. LTQ MS/MS successfully identified identified 22 differential proteins successfully, including 20 host-cell proteins and two H. pylori bacterial proteins. Also, human proteins were located in all areas of cells and involved in various cell biological functions. The oncogene proteins p53, p16, and C-erbB-2 proteins in H. pylori-infected RGM-1 cells were remarkably increased from the analysis by Western blot analysis. H. pylori infection of gastric epithelial cells leads to changes in various protein components in the cell, and enhances the expression of oncogene proteins, thereby increasing the possibility of possibility of carcinogenesis of H. pylori infection.
    Keywords:  Helicobacter pylori; gastric cancer; gastric epithelial cells; inflammatory response
    DOI:  https://doi.org/10.1002/jcb.27585
  25. PLoS One. 2018 ;13(12): e0209838
    Protein array profiling of circulating angiogenesis-related factors during bevacizumab containing treatment in metastatic colorectal cancer.
    Helga Hagman, Pär-Ola Bendahl, Jon Lidfeldt, Mattias Belting, Anders Johnsson.
       BACKGROUND: Prolonged angiogenesis inhibition may improve treatment outcome in metastatic colorectal cancer (mCRC) patients. However, due to the complexity of the angiogenic pathways there is a lack of valid predictive biomarkers for anti-angiogenic agents. Here, we describe and optimize a procedure for simultaneous dynamic profiling of multiple angiogenesis related proteins in patient serum to explore associations with the response and acquired resistance to anti-angiogenic therapy.
    MATERIALS AND METHODS: Patients (n=22) were selected from a clinical trial investigating maintenance treatment with bevacizumab alone after response to induction chemotherapy + bevacizumab in mCRC. Serum samples were analysed for 55 unique angiogenesis related proteins using a commercial proteome profiler array and a publicly available image analysis program for quantification. Samples were collected at baseline before induction treatment start, at start of maintenance treatment, and at end of treatment after tumour progression.
    MAIN RESULTS AND CONCLUSION: For eight proteins, the antibody array signals were below detection range in all patient samples. None of the proteins showed levels at baseline or at start of maintenance with strong evidence for correlation to time to progression (lowest nominal p-value 0.03). The dynamic ranges of protein levels measured during the induction treatment period and during the maintenance period were analysed separately for time trends. Evidence for changing trends (up/down) in the levels of MMP-8, TIMP-4 and EGF was observed both during response to induction treatment and at progressive disease, respectively. For three of the proteins (IL-8, Activin A and IGFBP-2), weak evidence for correlation between increasing protein levels during induction with chemotherapy and bevacizumab and time to progression was observed. In conclusion, semi-quantitative profiling of angiogenesis related proteins in patient serum may be a versatile tool to screen for protein patterns aiming at identifying resistance mechanisms of anti-angiogenic treatment in patients with mCRC.
    DOI:  https://doi.org/10.1371/journal.pone.0209838
  26. Hypertension. 2018 Dec 03. HYPERTENSIONAHA11811733
    Proteomic Landscape of Aldosterone-Producing Adenoma.
    Marta M Swierczynska, Matthias J Betz, Marco Colombi, Eva Dazert, Paul Jenö, Suzette Moes, Cécile Pfaff, Katharina Glatz, Martin Reincke, Felix Beuschlein, Marc Y Donath, Michael N Hall.
      Primary aldosteronism is a disease of excessive production of adrenal steroid hormones and the most common cause of endocrine hypertension. Primary aldosteronism results mainly from bilateral adrenal hyperplasia or unilateral aldosterone-producing adenoma (APA). Primary aldosteronism cause at the molecular level is incompletely understood and a targeted treatment preventing excessive adrenal steroid production is not available. Here, we perform deep quantitative proteomic and phosphoproteomic profiling of 6 pairs of APA and adjacent nontumoral adrenal cortex. We show that increased steroidogenesis in APA is accompanied by upregulation of steroidogenic enzymes (HSD3B2, CYP21A2, CYP11B2) and of proteins involved in cholesterol uptake (LSR). We demonstrate that HSD3B2 is phosphorylated at Ser95 or 96 and identify a novel phosphorylation site, Ser489, in CYP21A2, suggesting that steroidogenic enzymes are regulated by phosphorylation. Our analysis also reveals altered ECM (extracellular matrix) composition in APA that affects ECM-cell surface interactions and actin cytoskeleton rearrangements. We show that RHOC, a GTPase controlling actin organization in response to extracellular stimuli, is upregulated in APA and promotes expression of the aldosterone synthase gene CYP11B2. Our data also indicate deregulation of protein N-glycosylation and GABAergic signaling in APAs. Finally, we find that mTORC1 (mammalian target of rapamycin complex 1) signaling is the major pathway deregulated in APA. Our study provides a rich resource for future research on the molecular mechanisms of primary aldosteronism.
    Keywords:  adenoma; human; hyperaldosteronism; hypertension; mass spectrometry
    DOI:  https://doi.org/10.1161/HYPERTENSIONAHA.118.11733
  27. Arterioscler Thromb Vasc Biol. 2019 Jan;39(1): 107-115
    Proteins Altered by Surgical Weight Loss Highlight Biomarkers of Insulin Resistance in the Community.
    Ravi V Shah, Shih-Jen Hwang, Ashish Yeri, Kahraman Tanriverdi, Alexander R Pico, Chen Yao, Venkatesh Murthy, Jennifer Ho, Olga Vitseva, Danielle Demarco, Sajani Shah, Mark D Iafrati, Daniel Levy, Jane E Freedman.
      Objective- Mechanisms of early and late improvements in cardiovascular risk after bariatric surgery and applicability to larger, at-risk populations remain unclear. We aimed to identify proteins altered after bariatric surgery and their relations to metabolic syndrome and diabetes mellitus. Approach and Results- We identified 19 proteins altered in 32 nonfasting plasma samples from a study of patients undergoing bariatric surgery who were evaluated preoperatively (visit 1) versus both early (visit 2; ≈3 months) and late (visit 3; ≈12 months) postoperative follow-up using predefined protein panels (Olink). Using in silico methods and publicly available gene expression repositories, we found that genes encoding 8 out of 19 proteins had highest expression in liver relative to other assayed tissues, with the top biological and disease processes, including major obesity-related vascular diseases. Of 19 candidate proteins in the surgical cohort, 6 were previously measured in >3000 FHS (Framingham Heart Study) participants (IGFBP [insulin-like growth factor binding protein]-1, IGFBP-2, P-selectin, CD163, LDL (low-density lipoprotein)-receptor, and PAI [plasminogen activator inhibitor]-1). A higher concentration of IGFBP-2 at baseline was associated with a lower risk of incident metabolic syndrome (odds ratio per log-normal unit, 0.45; 95% CI, 0.32-0.64; P=7.7×10-6) and diabetes mellitus (odds ratio, 0.63; 95% CI, 0.49-0.79; P=0.0001) after multivariable adjustment. Conclusions- Using a directed protein quantification platform (Olink), we identified known and novel proteins altered after surgical weight loss, including IGFBP-2. Future efforts in well-defined obesity intervention settings may further define and validate novel targets for the prevention of vascular disease in obesity.
    Keywords:  biomarker; metabolic syndrome; obesity; risk; weight loss
    DOI:  https://doi.org/10.1161/ATVBAHA.118.311928
  28. Eur J Mass Spectrom (Chichester). 2018 Dec 26. 1469066718820991
    Comparison of blood serum protein analysis by MALDI-MS from either conventional frozen samples or storage disc-deposited samples: A study with human serum from pregnant donors and from patients with intrauterine growth restriction.
    Manja Wölter, Manuela Russ, Charles A Okai, Werner Rath, Ulrich Pecks, Michael O Glocker.
      Mass spectrometric profiling of intact serum proteins, i.e. determination of relative protein abundance differences, was performed using two different serum sample preparation methods: one with frozen and thawed serum, the other with at room temperature deposited and dried serum. Since in a typical clinical setting freezing of serum is difficult to achieve, sampling at room temperature is preferred and can be met when using the Noviplex™ card system. Once deposited and dried, serum proteins can be stored and shipped at room temperature. After resolubilization of serum proteins from "dried serum spots", mass spectra of high quality have been recorded comparable to those that were obtained using fresh-frozen and subsequently thawed serum samples. Differentiation between patients with intrauterine growth restriction and control individuals was achievable, independent from the sample work-up procedure. Having at hand a reliable and robust method for serum storage and shipment which works at room temperature bridges the gap between the clinics and the protein analysis laboratory. Our novel serum handling protocol reduces costs for both, storage and shipping, and ultimately enables clinical risk assessment based on mass spectrometric determination of intact protein abundance profiles.
    Keywords:  Dried serum spots; MALDI-ToF-MS; apolipoproteins; pregnancy complications; proteome profiling
    DOI:  https://doi.org/10.1177/1469066718820991
  29. Mol Vis. 2018 ;24 759-766
    Intravitreal bevacizumab upregulates transthyretin in experimental branch retinal vein occlusion.
    Lasse Jørgensen Cehofski, Anders Kruse, Alexander Nørgård Alsing, Jonas Ellegaard Nielsen, Shona Pedersen, Svend Kirkeby, Bent Honoré, Henrik Vorum.
       Purpose: To identify retinal protein changes that mediate beneficial effects of intravitreal bevacizumab in experimental branch retinal vein occlusion (BRVO).
    Methods: In six Danish Landrace pigs, BRVO was induced with argon laser in both eyes. After BRVO was induced, the right eye of each animal was given an intravitreal injection of bevacizumab while the left eye was treated with saline water. The retinas were collected 15 days after BRVO, and differentially expressed proteins were analyzed with tandem mass tags-based mass spectrometry. Validation of statistically significantly changed proteins was performed with immunohistochemistry and western blotting.
    Results: Fluorescein angiography showed no recanalization of the occluded vessels. A total of 4,013 proteins were successfully identified and quantified. Nine proteins were statistically significantly changed following bevacizumab intervention. In experimental BRVO, bevacizumab treatment resulted in upregulation of transthyretin (TTR) and pantothenate kinase 3. Bevacizumab downregulated protocadherin 7, protein FAM192A, and ATP synthase protein 8. Immunohistochemistry revealed that TTR was highly abundant in the choroid following bevacizumab intervention.
    Conclusions: Bevacizumab intervention in experimental BRVO resulted in an increased level of TTR. This is the second study in which we showed an increased retinal level of TTR following anti-vascular endothelial growth factor (VEGF) intervention in experimental BRVO. We hypothesize that there is an interaction between TTR and VEGF and that bevacizumab may exert a beneficial effect on the retina by upregulating TTR.
  30. Circ Res. 2018 Oct 15.
    CLIC4/Arf6 Pathway - A New Lead in BMPRII Inhibition in Pulmonary Hypertension.
    Vahitha B Abdul-Salam, Giusy Russomanno, Chen Chien-Nien, Abdul S Mahomed, Luke A Yates, Martin R Wilkins, Lan Zhao, Magdalena Maria Gierula, Olivier Dubois, Ute Schaeper, Jens Endruschat, Beata Wojciak-Stothard.
       RATIONALE: Increased expression of chloride intracellular channel 4 (CLIC4) is a feature of endothelial dysfunction in pulmonary arterial hypertension but its role in disease pathology is not fully understood.
    OBJECTIVE: To identify CLIC4 effectors and evaluate strategies targeting CLIC4 signalling in pulmonary hypertension.
    METHODS AND RESULTS: Proteomic analysis of CLIC4-interacting proteins in human pulmonary artery endothelial cells (HPAECs) identified regulators of endosomal trafficking, including ADP Ribosylation Factor 6 (Arf6) GTPase activating proteins and clathrin, while CLIC4 overexpression affected protein regulators of vesicular trafficking, lysosomal function and inflammation. CLIC4 reduced BMPRII expression and signalling as a result of Arf6-mediated reduction in gyrating clathrin and increased lysosomal targeting of the receptor. BMPRII expression was restored by Arf6 siRNA, Arf inhibitor SecinH3 and inhibitors of clathrin-mediated endocytosis but was unaffected by chloride channel inhibitor indanyloxyacetic acid 94 or Arf1 siRNA. The effects of CLIC4 on NFkB, HIF and angiogenic response were prevented by Arf6 siRNA and SecinH3. Sugen/hypoxia mice and monocrotaline rats showed elevated expression of CLIC4, activation of Arf6 and NFκB and reduced expression of BMPRII in the lung. These changes were established early during disease development. Lung endothelium-targeted delivery of CLIC4siRNA or treatment with SecinH3 attenuated the disease, reduced CLIC4/Arf activation and restored BMPRII expression in the lung. Endothelial colony forming cells from idiopathic pulmonary hypertensive patients showed upregulation of CLIC4 expression and Arf6 activity, suggesting potential importane of this pathway in the human condition.
    CONCLUSIONS: Arf6 is a novel effector of CLIC4 and a new therapeutic target in pulmonary hypertension.
    Keywords:  Arf; BMPRII; chloride channel
    DOI:  https://doi.org/10.1161/CIRCRESAHA.118.313705
  31. Nucleosides Nucleotides Nucleic Acids. 2018 Dec 27. 1-7
    Proteomic analysis of a urinary stone with two layers composed of calcium oxalate monohydrate and uric acid.
    Kiyoko Kaneko, Mizuho Kabeya, Hirokazu Kondo, Tomoko Fukuuchi, Noriko Yamaoka, Makoto Yasuda, Satoshi Yamaguchi.
      We examined the mechanism of urinary stone formation by analyzing the matrix proteins in a urinary stone with two layers composed of different crystals. Micro-area X-ray spectrometry and infrared spectroscopy revealed calcium oxalate monohydrate in the outside and uric acid in the inside. We also examined the interface. After the outside, inside, and interface parts were separated, proteomic analysis identified 48, 7, and 4 matrix proteins, respectively. Urinary stones with two layers are considered to have grown under different conditions. The matrix proteins in each part differed among the crystal components and may reveal the stone-generating process. The proteins in the interface likely function to enlarge the stone via the addition of different crystals.
    Keywords:  Two-layered urinary stone; matrix protein; proteomic analysis
    DOI:  https://doi.org/10.1080/15257770.2018.1478095
  32. PLoS One. 2018 ;13(12): e0209871
    Dietary salt promotes ischemic brain injury and is associated with parenchymal migrasome formation.
    Antje Schmidt-Pogoda, Jan-Kolja Strecker, Marie Liebmann, Christina Massoth, Carolin Beuker, Uwe Hansen, Simone König, Sarah Albrecht, Stefanie Bock, Johanna Breuer, Clemens Sommer, Nicholas Schwab, Heinz Wiendl, Luisa Klotz, Jens Minnerup.
      Sodium chloride promotes vascular fibrosis, arterial hypertension, pro-inflammatory immune cell polarization and endothelial dysfunction, all of which might influence outcomes following stroke. But despite enormous translational relevance, the functional importance of sodium chloride in the pathophysiology of acute ischemic stroke is still unclear. In the current study, we show that high-salt diet leads to significantly worse functional outcomes, increased infarct volumes, and a loss of astrocytes and cortical neurons in acute ischemic stroke. While analyzing the underlying pathologic processes, we identified the migrasome as a novel, sodium chloride-driven pathomechanism in acute ischemic stroke. The migrasome was previously described in vitro as a migrating organelle, which incorporates and dispatches cytosol of surrounding cells and plays a role in intercellular signaling, whereas a pathophysiological meaning has not been elaborated. We here confirm previously reported characteristics of the migrasome in vivo. Immunohistochemistry, electron microscopy and proteomic analyses further demonstrate that the migrasome incorporates and dispatches cytosol of surrounding neurons following stroke. The clinical relevance of these findings is emphasized by neuropathological examinations, which detected migrasome formation in infarcted brain parenchyma of human stroke patients. In summary, we demonstrate that high-salt diet aggravates stroke outcomes, and we characterize the migrasome as a novel mechanism in acute stroke pathophysiology.
    DOI:  https://doi.org/10.1371/journal.pone.0209871
  33. Free Radic Biol Med. 2018 Dec 19. pii: S0891-5849(18)31657-5. [Epub ahead of print]
    Mouse serum protects against total body irradiation-induced hematopoietic system injury by improving the systemic environment after radiation.
    Junling Zhang, Xiaodan Han, Yu Zhao, Xiaolei Xue, Saijun Fan.
      Reactive oxygen species (ROS) play a critical role in total body irradiation (TBI)-induced hematopoietic system injury. However, the mechanisms involved in ROS production in hematopoietic stem cells (HSCs) post TBI need to be further explored. In this study, we demonstrated that hematopoietic system injury in mice radiated with TBI was effectively alleviated when the blood circulation environment was changed via the injection of serum from non-radiated mice. Serum injection increased the survival of radiated mice and ameliorated TBI-induced hematopoietic system injury through attenuating myeloid skew, increasing HSC frequency, and promoting the reconstitution of radiated HSCs. Serum injection also decreased ROS levels in HSCs and regulated oxidative stress-related proteins. A serum proteome sequence array showed that proteins related to tissue injury and oxidative stress were regulated, and a serum-derived exosome microRNA sequence assay showed that the PI3K-Akt and Hippo signaling pathways were affected in radiated mice injected with serum from non-radiated mice. Furthermore, a significant increase in cell viability and a decrease in ROS were observed in radiated lineage-c-kit+ cells treated with serum-derived exosomes. Similarly, an improvement in the impaired differentiation of HSCs was observed in radiated mice injected with serum-derived exosomes. Taken together, our observations suggest that serum from non-radiated mice alleviates HSC injury in radiated mice by improving the systemic environment after radiation, and exosomes contribute to this radioprotective effect as important serum active component.
    Keywords:  Hematopoietic stem cells; Mouse serum; Peripheral blood systemic environment; Reactive oxygen species; Serum-derived exosomes; Total body irradiation
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2018.12.021
  34. J Cell Mol Med. 2018 Nov;22(11): 5231-5243
    HMQ-T-B10 induces human liver cell apoptosis by competitively targeting EphrinB2 and regulating its pathway.
    Bingling Dai, Xianpeng Shi, Nan Ma, Weina Ma, Yanmin Zhang, Tianfeng Yang, Jie Zhang, Langchong He.
      Hepatocellular carcinoma (HCC) is a highly prevalent cancer worldwide and it is necessary to discover and develop novel preventive strategies and therapeutic approaches for HCC. Herein, we report that EphrinB2 expression is correlated with liver cancer progression. Moreover, by using phosphorylated proteomics array, we reveal a pro-apoptosis protein whose phosphorylation and activation levels are up-regulated upon EphrinB2 knockdown. These results suggest that EphrinB2 may act as an anti-apoptotic protein in liver cancer cells. We also explored the therapeutic potential of HMQ-T-B10 (B10), which was designed and synthesized in our laboratory, for HCC and its underlying mechanisms in vitro and in vivo. Our data demonstrate that B10 could bind EphrinB2 and show inhibitory activity on human liver cancer cells. Moreover, induction of human liver cancer cell apoptosis by B10 could be augmented upon EphrinB2 knockdown. B10 inhibited HCC cell growth and induced HCC cell apoptosis by repressing the EphrinB2 and VEGFR2 signalling pathway. Growth of xenograft tumours derived from Hep3B in nude mice was also significantly inhibited by B10. Collectively, these findings highlight the potential molecular mechanisms of B10 and its potential as an effective antitumour agent for HCC.
    Keywords:  EphrinB2; HMQ‐T‐B10; apoptosis; liver cancer cell
    DOI:  https://doi.org/10.1111/jcmm.13729
  35. Elife. 2018 Dec 28. pii: e37015. [Epub ahead of print]7
    Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination.
    Joseph J Campo, Timothy Q Le, Jozelyn V Pablo, Christopher Hung, Andy A Teng, Hervé Tettelin, Andrea Tate, William P Hanage, Mark R Alderson, Xiaowu Liang, Richard Malley, Marc Lipsitch, Nicholas J Croucher.
      Pneumococcal whole cell vaccines (WCVs) could cost-effectively protect against a greater strain diversity than current capsule-based vaccines. Immunoglobulin G (IgG) responses to a WCV were characterised by applying longitudinally-sampled sera, available from 35 adult placebo-controlled phase I trial participants, to a panproteome microarray. Despite individuals maintaining distinctive antibody 'fingerprints', responses were consistent across vaccinated cohorts. Seventy-two functionally distinct proteins were associated with WCV-induced increases in IgG binding. These shared characteristics with naturally immunogenic proteins, being enriched for transporters and cell wall metabolism enzymes, likely unusually exposed on the unencapsulated WCV's surface. Vaccine-induced responses were specific to variants of the diverse PclA, PspC and ZmpB proteins, whereas PspA- and ZmpA-induced antibodies recognised a broader set of alleles. Temporal variation in IgG levels suggested a mixture of anamnestic and novel responses. These reproducible increases in IgG binding a limited, but functionally diverse, set of conserved proteins indicate WCV could provide species-wide immunity.
    Keywords:  human; immunology; infectious disease; inflammation; microbiology
    DOI:  https://doi.org/10.7554/eLife.37015
  36. Mol Cell Proteomics. 2018 Dec 26. pii: mcp.RA118.000922. [Epub ahead of print]
    Identification of Novel Protein Targets of Dimethyl Fumarate Modification in Neurons and Astrocytes Reveals Actions Independent of Nrf2 Stabilization.
    Gerardo G Piroli, Allison M Manuel, Tulsi Patel, Michael D Walla, Liang Shi, Scott A Lanci, Jingtian Wang, Ashley Galloway, Pavel I Ortinski, Deanna S Smith, Norma Frizzell.
      The fumarate ester dimethyl fumarate (DMF) has been introduced recently as a treatment for relapsing remitting multiple sclerosis (RRMS), a chronic inflammatory condition that results in neuronal demyelination and axonal loss. DMF is known to act by depleting intracellular glutathione and modifying thiols on Keap1 protein, resulting in the stabilization of the transcription factor Nrf2, which in turn induces the expression of antioxidant response element genes. We have previously shown that DMF reacts with a wide range of protein thiols, suggesting that the complete mechanisms of action of DMF are unknown. Here, we investigated other intracellular thiol residues that may also be irreversibly modified by DMF in neurons and astrocytes. Using mass spectrometry, we identified 24 novel proteins that were modified by DMF in neurons and astrocytes, including cofilin-1, tubulin and collapsin response mediator protein 2 (CRMP2). Using an in vitro functional assay, we demonstrated that DMF-modified cofilin-1 loses its activity and generates less monomeric actin, potentially inhibiting its cytoskeletal remodeling activity, which could be beneficial in the modulation of myelination during RRMS. DMF modification of tubulin did not significantly impact axonal lysosomal trafficking. We found that the oxygen consumption rate of N1E-115 neurons and the levels of proteins related to mitochondrial energy production were only slightly affected by the highest doses of DMF, confirming that DMF treatment does not impair cellular respiratory function. In summary, our work provides new insights into the mechanisms supporting the neuroprotective and re-myelination benefits associated with DMF treatment in addition to the antioxidant response by Nrf2.
    Keywords:  Chemical biology; Dimethyl fumarate; Drug targets*; Mechanism of action; Post-translational modifications*; Protein adducts; Succination
    DOI:  https://doi.org/10.1074/mcp.RA118.000922
  37. Microb Pathog. 2018 Dec 20. pii: S0882-4010(18)31632-2. [Epub ahead of print]128 20-27
    Comparative proteomics analyses of Acinetobacter baumannii strains ATCC 17978 and AB5075 reveal the differential role of type II secretion system secretomes in lung colonization and ciprofloxacin resistance.
    Noha M Elhosseiny, Nada B Elhezawy, Ahmed S Attia.
      Acinetobacter baumannii is an emerging nosocomial pathogen with alarming antibiotic resistance profiles. A better understanding of the virulence and resistance mechanisms of this pathogen is necessary for identifying new methods to combat its infections in a more efficient way. In this regard, the type II secretion system (T2SS) of A. baumannii is an attractive target majorly secreting lipid-metabolizing enzymes and contributes significantly to its virulence. No attempts have been made to study the differential role, and the nature of T2SS secreted proteins among different strains of A. baumannii. In this study, we compare T2SS substrates and functions between A. baumannii strains ATCC 17978, and the MDR highly virulent strain AB5075. The functional categories of the T2-secreted proteins were analyzed, and the virulence potential of the tested strains was compared in vivo using a murine pneumonia model. Biofilm formation was compared using crystal violet assay in micro-titer plates. The contribution to antibiotic resistance was measured by determining the minimum inhibitory concentration (MIC) of different classes of antibiotic. Results indicate that the T2SS secretome gives a colonization advantage to AB5075 over ATCC 1797 but is more important for biofilm formation by the latter. Transposon insertional inactivation of the general secretory pathway protein D (gspD), which is a key component in the structure of the T2SS, significantly increased the MIC of AB5075 to ciprofloxacin. Our report is the first to describe the strain-dependent evolution of the T2SS secretome in relation to the virulence and antibiotic resistance attributes of Gram-negative species.
    Keywords:  AB5075; ATCC 17978; Acinetobacter baumannii; Lung colonization; Secretome; T2SS
    DOI:  https://doi.org/10.1016/j.micpath.2018.12.039
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