bims-prodis 2018-06-17 papers

bims-prodis

Biomed News

on Proteomics in disease

Issue of 2018–06–17
eight papers selected by
Nancy Gough, Bioserendipity

Acellular vascular matrix grafts from human placenta chorion: Impact of ECM preservation on graft characteristics, protein composition and in vivo performance.
Impact of diet-induced obesity on the mouse brain phosphoproteome.
Unveiling Brain Aβ Heterogeneity Through Targeted Proteomic Analysis.
Analysis of Covalent Modifications of Amyloidogenic Proteins Using Two-Dimensional Electrophoresis: Prion Protein and Its Sialylation.
Genome-wide linear B-cell epitopes of enterovirus 71 in a hand, foot and mouth disease (HFMD) population.
Cooperative multi-targeting of signaling networks by angiomiR-204 inhibits vasculogenic mimicry in breast cancer cells.
Translating molecular advances in Down syndrome and Fragile X syndrome into therapies.
Remodeling of the HDL proteome with treatment response to abatacept or adalimumab in the AMPLE trial of patients with rheumatoid arthritis.

Biomaterials. 2018 May 29. pii: S0142-9612(18)30395-8. [Epub ahead of print]177 14-26

Acellular vascular matrix grafts from human placenta chorion: Impact of ECM preservation on graft characteristics, protein composition and in vivo performance.

Karl H Schneider, Marjan Enayati, Christian Grasl, Ingrid Walter, Lubos Budinsky, Gabriel Zebic, Christoph Kaun, Anja Wagner, Klaus Kratochwill, Heinz Redl, Andreas H Teuschl, Bruno K Podesser, Helga Bergmeister.

  Small diameter vascular grafts from human placenta, decellularized with either Triton X-100 (Triton) or SDS and crosslinked with heparin were constructed and characterized. Graft biochemical properties, residual DNA, and protein composition were evaluated to compare the effect of the two detergents on graft matrix composition and structural alterations. Biocompatibility was tested in vitro by culturing the grafts with primary human macrophages and in vivo by subcutaneous implantation of graft conduits (n = 7 per group) into the flanks of nude rats. Subsequently, graft performance was evaluated using an aortic implantation model in Sprague Dawley rats (one month, n = 14). In situ graft imaging was performed using MRI angiography. Retrieved specimens were analyzed by electromyography, scanning electron microscopy, histology and immunohistochemistry to evaluate cell migration and the degree of functional tissue remodeling. Both decellularization methods resulted in grafts of excellent biocompatibility in vitro and in vivo, with low immunogenic potential. Proteomic data revealed removal of cytoplasmic proteins with relative enrichment of ECM proteins in decelluarized specimens of both groups. Noteworthy, LC-Mass Spectrometry analysis revealed that 16 proteins were exclusively preserved in Triton decellularized specimens in comparison to SDS-treated specimens. Aortic grafts showed high patency rates, no signs of thrombus formation, aneurysms or rupture. Conduits of both groups revealed tissue-specific cell migration indicative of functional remodeling. This study strongly suggests that decellularized allogenic grafts from the human placenta have the potential to be used as vascular replacement materials. Both detergents produced grafts with low residual immunogenicity and appropriate mechanical properties. Observed differences in graft characteristics due to preservation method had no impact on successful in vivo performance in the rodent model.

Keywords:  Biocompatibility; Cell migration; Decellularized matrix; Human placenta; Small diameter vascular grafts

DOI:  https://doi.org/10.1016/j.biomaterials.2018.05.045
J Nutr Biochem. 2018 May 01. pii: S0955-2863(17)30800-8. [Epub ahead of print]58 102-109

Impact of diet-induced obesity on the mouse brain phosphoproteome.

Valentina Siino, Antonella Amato, Francesca Di Salvo, Gaetano Felice Caldara, Marcello Filogamo, Peter James, Sonya Vasto.

  Obesity is closely associated to several diseases such as type 2 diabetes, cardiovascular disease, hepatic steatosis, airway disease, neurodegeneration, biliary diseases and certain cancers. It is, therefore, of importance to assess the role of nutrition in disease prevention as well as its effect in the course of such pathologies. In the present study, we addressed the impact of the exposure to different obesogenic diets in the mice brains phosphoproteome. To analyze if the obesity could be able to modify the protein pattern expression of brain neurons, obesity was induced in two different groups of mice. One group of mice was fed with hyperglycemic diet (HGD) and the other one was fed with high-fat diet (HFD), both for 12 weeks. A control group of lean mice was fed with a standard diet (SD). Metabolic parameters were measured before sacrifice, and brains were harvested for label-free phosphoproteomic analysis. Mice brains were analyzed to find differences, if any, in protein phosphorylation. Interestingly, the changes were independent of the obesogenic diet as no changes were detected between the two obese groups. Dephosphorylation of proteins involved in neuronal development (among others SYNGAP1 and PPP1R9B), in vesicle trafficking (for example SNAP91 and AMPH) and in cytoskeletal functions (for example, CLASP2 and GSK3B) was identified, while increased phosphorylation was detected for microtubule proteins (such as MAP2 and MAPT). Phospho site analysis of the mouse brain proteome reveals important changes that point to a connection between diet-induced obesity and impairment of neuronal functions and signaling.

Keywords:  High-fat diet; Hyperglycemic diet; Neuronal impairment; Nutrition; Obesity; Phosphoproteomics

DOI:  https://doi.org/10.1016/j.jnutbio.2018.04.015
Methods Mol Biol. 2018 ;1779 23-43

Unveiling Brain Aβ Heterogeneity Through Targeted Proteomic Analysis.

Agueda Rostagno, Thomas A Neubert, Jorge Ghiso.

  Amyloid β (Aβ) is the major constituent of the brain deposits found in parenchymal plaques and cerebral blood vessels of patients with Alzheimer's disease (AD). Besides classic full-length peptides, biochemical analyses of brain deposits have revealed high degree of Aβ heterogeneity likely resulting from the action of multiple proteolytic enzymes. This chapter describes a sequential extraction protocol allowing the differential fractionation of soluble and deposited Aβ species taking advantage of their differential solubility properties. Soluble Aβ is extracted by water-based buffers like phosphate-buffered saline-PBS-whereas pre-fibrillar and fibrillar deposits, usually poorly soluble in PBS, are extractable in detergent containing solutions or more stringent conditions as formic acid. The extraction procedure is followed by the biochemical identification of the extracted Aβ species using Western blot and a targeted proteomic analysis which combines immunoprecipitation with MALDI-ToF mass spectrometry. This approach revealed the presence of numerous C- and N-terminal truncated Aβ species in addition to Aβ1-40/42. Notably, the more soluble C-terminal cleaved fragments constitute a main part of PBS homogenates. On the contrary, N-terminal truncated species typically require more stringent conditions for the extraction in agreement with their lower solubility and enhanced aggregability. Detailed assessment of the molecular diversity of Aβ species composing interstitial fluid and amyloid deposits at different disease stages, as well as the evaluation of the truncation profile during various pharmacologic approaches will provide a comprehensive understanding of the still undefined contribution of Aβ truncations to AD pathogenesis and their potential as novel therapeutic targets.

Keywords:  Amyloid-β; C-terminal truncations; Immunoprecipitation; Mass spectrometry; N-terminal truncations; Posttranslational modifications; Proteolytic cleavage

DOI:  https://doi.org/10.1007/978-1-4939-7816-8_3
Methods Mol Biol. 2018 ;1779 241-255

Analysis of Covalent Modifications of Amyloidogenic Proteins Using Two-Dimensional Electrophoresis: Prion Protein and Its Sialylation.

Elizaveta Katorcha, Ilia V Baskakov.

  A number of proteins associated with neurodegenerative disease undergo several types of posttranslational modifications. They include N-linked glycosylation of the prion protein and amyloid precursor protein, phosphorylation of tau and α-synuclein. Posttranslational modifications alter physical properties of proteins including their net and surface charges, affecting their processing, life-time and propensity to acquire misfolded, disease-associated states. As such, analysis of posttranslational modifications is important for understanding the mechanisms of pathogenesis. Recent studies documented that sialylation of the disease-associated form of the prion protein or PrPSc controls the fate of prions in an organism and outcomes of prion infection. For assessing sialylation status of PrPSc, we developed a reliable protocol that involves two-dimensional electrophoresis followed by Western blot (2D). The current chapter describes the procedure for the analysis of sialylation status of PrPSc from various sources including central nervous system, secondary lymphoid organs, cultured cells, or PrPSc produced in Protein Misfolding Cyclic Amplification.

Keywords:  Amyloidogenic proteins; Glycosylation; Posttranslational modifications; Prion diseases; Prion proteins; Sialic acid; Sialylation; Two-dimensional electrophoresis

DOI:  https://doi.org/10.1007/978-1-4939-7816-8_15
J Clin Virol. 2018 Jun 03. pii: S1386-6532(18)30151-3. [Epub ahead of print]105 41-48

Genome-wide linear B-cell epitopes of enterovirus 71 in a hand, foot and mouth disease (HFMD) population.

Huiying Zhang, Zhigang Song, Huiju Yu, Xiaoling Zhang, Shanshan Xu, Zhong Li, Jingzhi Li, Hongke Xu, Zhenghong Yuan, Hongwei Ma, Zhigang Yi, Yunwen Hu.

   BACKGROUND: Enteroviruses cause hand, foot and mouth disease (HFMD). The host B-cells recognize the viral proteins and provoke humoral responses. Deciphering the B-cell responses to the viral epitopes helps diagnosis and vaccine development.
OBJECTIVES: The objective of the present study was to investigate for the first time the landscape of genome-wide linear B-cell epitopes of enterovirus 71 in HFMD population.
STUDY DESIGN: The peptides encompassing the entire coding region of EV71 were chemically synthesized and displayed on a microarray. The peptide microarray was used to screen serum samples from an HFMD population, including EV71-, CAV10-, CAV16- and CAV6-infected patients. We identified the dominant epitope-containing-peptides (DECPs) that react with the sera of more than 20% of the HFMD population and the common DECPs that cross-react with the sera from other enteroviruses-infected population.
RESULTS: Ten DECPs reacting with IgM and 9 DECPs reacting with IgG antibodies were identified, of which, 6 IgM and 5 IgG common DECPs cross-reacted with the sera from other enteroviruses. Some DECPs preferentially reacted with IgG or IgM antibodies and some epitope-antibody interactions correlated with the severity of HFMD.
CONCLUSIONS: We uncovered the DECPs and the common DECPs among a group of enteroviruses in HFMD population and found that some epitope-antibody reactions were associated with the outcome of HFMD. These data may guide developing vaccines against the enteroviruses and help the diagnosis and prognosis of HFMD.

Keywords:  Cross-reactive antibody; Enterovirus71; Epitopes; HFMD; Peptide array

DOI:  https://doi.org/10.1016/j.jcv.2018.06.001
Cancer Lett. 2018 Jun 06. pii: S0304-3835(18)30399-9. [Epub ahead of print]432 17-27

Cooperative multi-targeting of signaling networks by angiomiR-204 inhibits vasculogenic mimicry in breast cancer cells.

Yarely M Salinas-Vera, Laurence A Marchat, Raúl García-Vázquez, Claudia Haydée González de la Rosa, Eduardo Castañeda-Saucedo, Napoleón Navarro Tito, Carlos Palma Flores, Carlos Pérez-Plasencia, José L Cruz-Colin, Ángeles Carlos-Reyes, José Sullivan López-González, María Elizbeth Álvarez-Sánchez, César López-Camarillo.

  RNA-based multi-target therapies focused in the blocking of signaling pathways represent an attractive approach in cancer. Here, we uncovered a miR-204 cooperative targeting of multiple signaling transducers involved in vasculogenic mimicry (VM). Our data showed that invasive triple negative MDA-MB-231 and Hs-578T breast cancer cells, but not poorly invasive MCF-7 cells, efficiently undergoes matrix-associated VM under hypoxia. Ectopic restoration of miR-204 in MDA-MB-231 cells leads to a potent inhibition of VM and reduction of number of branch points and patterned 3D channels. Further analysis of activation state of multiple signaling pathways using Phosphorylation Antibody Arrays revealed that miR-204 reduced the expression and phosphorylation levels of 13 proteins involved in PI3K/AKT, RAF1/MAPK, VEGF, and FAK/SRC signaling. In agreement with phospho-proteomic profiling, VM was impaired following pharmacological administration of PI3K and SRC inhibitors. Mechanistic studies confirmed that miR-204 exerts a negative post-transcriptional regulation of PI3K-α and c-SRC proto-oncogenes. Moreover, overall survival analysis of a large cohort of breast cancer patients indicates that low miR-204 and high FAK/SRC levels were associated with worst outcomes. In conclusion, our study provides novel lines of evidence indicating that miR-204 may exerts a fine-tuning regulation of the synergistic transduction of PI3K/AKT/FAK mediators critical in VM formation.

Keywords:  Breast cancer; Phospho-proteomics; Signaling pathways; Vasculogenic mimicry; miR-204

DOI:  https://doi.org/10.1016/j.canlet.2018.06.003
Eur Neuropsychopharmacol. 2018 Jun 07. pii: S0924-977X(18)30069-5. [Epub ahead of print]

Translating molecular advances in Down syndrome and Fragile X syndrome into therapies.

Down Syndrome and Other Genetic Developmental Disorders ECNP Network

  Ongoing treatments for genetic developmental disorders of the central nervous system are mostly symptomatic and do not correct the genetic cause. Recent identification of common mechanisms between diseases has suggested that new therapeutic targets could be applied across intellectual disabilities with potential disease-modifying properties. The European Down syndrome and other genetic developmental disorders (DSG2D) network joined basic and clinical scientists to foster this research and carry out clinical trials. Here we discuss common mechanisms between several intellectual disabilities from genetic origin including Down's and Fragile X syndromes: i) how to model these complex diseases using neuronal cells and brain organoids derived from induced pluripotent stem cells; ii) how to integrate genomic, proteomic and interactome data to help defining common mechanisms and boundaries between diseases; iii) how to target common pathways for designing clinical trials and assessing their efficacy; iv) how to bring new neuro-therapies, such as noninvasive brain stimulations and cognitive training to clinical research. The basic and translational research efforts of the last years have utterly transformed our understanding of the molecular pathology of these diseases but much is left to be done to bring them to newborn babies and children to improve their quality of life.

Keywords:  Brain stimulation; Down syndrome; Fragile X syndrome; Intellectual disabilities; Neuroplasticity; iPS cells

DOI:  https://doi.org/10.1016/j.euroneuro.2018.03.006
Atherosclerosis. 2018 Apr 17. pii: S0021-9150(18)30177-1. [Epub ahead of print]275 107-114

Remodeling of the HDL proteome with treatment response to abatacept or adalimumab in the AMPLE trial of patients with rheumatoid arthritis.

C Charles-Schoeman, G B Gugiu, H Ge, A Shahbazian, Y Y Lee, X Wang, D E Furst, V K Ranganath, M Maldonado, Terry Lee, S T Reddy.

   BACKGROUND AND AIMS: To evaluate changes in the high-density lipoprotein (HDL) proteome and HDL function in active rheumatoid arthritis (RA) patients initiating therapy with abatacept or adalimumab in the Abatacept Versus Adalimumab Comparison in Biologic-Naïve RA Subjects with Background Methotrexate (AMPLE) study.
METHODS: Ultra high-pressure liquid chromatography (UHPLC) coupled with ion mobility mass spectrometry (LC-IM-MS) was used to analyze proteins associated with immunoaffinity-captured HDL from plasma of 30 patients with RA randomized to either abatacept (n = 15) or adalimumab (n = 15) therapy. Paraoxonase 1 (PON1) activity, HDL anti-oxidant capacity, cholesterol profiles, and homocysteine levels were also measured at baseline and following treatment. Repeated-measures analyses were performed using mixed-effect linear models to model the within-subject covariance over time.
RESULTS: In models controlling for age, sex and treatment group, improvement in inflammation measured by decreases in CRP was associated with improvement in HDL function and changes in several HDL-associated proteins including significant decreases in lipopolysaccharide-binding protein, serum amyloid A-I (SAA-I) and inter-alpha-trypsin inhibitor heavy chain H4 (p values < 0.05). Improvement in disease activity was also associated with changes in multiple HDL-associated proteins. Adalimumab was associated with higher PON1 activity, HDL-associated serotransferrin, and HDL-associated immunoglobulin J chain, and lower HDL-associated SAA-I over time compared with abatacept.
CONCLUSIONS: Improvement in inflammation associated with treatment of RA, using either abatacept or adalimumab in the AMPLE study, was associated with improvement in HDL function and significant alterations in the HDL proteome, including proteins involved in the immune response, proteinase inhibition, and lipid metabolism.

Keywords:  Abatacept; Adalimumab; High density lipoproteins; Rheumatoid arthritis

DOI:  https://doi.org/10.1016/j.atherosclerosis.2018.04.003