Proteome profiling of vitreoretinal diseases by cluster analysis

Vitreous samples collected in retinopathic surgeries have diverse properties, making proteomics analysis difficult. We report a cluster analysis to evade this difficulty. Vitreous and subretinal fluid samples were collected from 60 patients during surgical operation of non‐proliferative diabetic retinopathy, proliferative diabetic retinopathy, proliferative vitreoretinopathy, and rhegmatogenous retinal detachment. For controls, we collected vitreous fluid from patients of idiopathic macular hole, epiretinal, and from a healthy postmortem donor. Proteins from these samples were subjected to quantitative proteomics using two‐dimensional gel electrophoresis. We selected 105 proteins robustly expressed among ca. 400 protein spots and subjected them to permutation test. By using permutation test analysis we observed unique variations in the expression of some of these proteins in vitreoretinal diseases when compared to the control and to each other: (i) the levels of inflammation‐associated proteins such as alpha1‐antitrypsin, apolipoprotein A4, albumin, and transferrin were significantly higher in all four types of vitreoretinal diseases, and (ii) each vitreoretinal disease elevated a unique set of proteins, which can be interpreted based on the pathology of retinopathy. Our protocol will be effective for the study of protein expression in other types of clinical samples of diverse properties.     

Proteomic Investigations of In Vitro and In Vivo Models of Periodontal Disease

Proteomics has currently been a developing field in periodontal diseases to obtain protein information of certain samples. Periodontal disease is an inflammatory disorder that attacks the teeth, connective tissues, and alveolar bone within the oral cavity. Proteomics information can provide proteins that are differentially expressed in diseased or healthy samples. This review provides insight into approaches researching single species, multi species, bacteria, non‐human, and human models of periodontal disease for proteomics information. The approaches that have been taken include gel electrophoresis and qualitative and quantitative mass spectrometry. This review is carried out by extracting information about in vitro and in vivo studies of proteomics in models of periodontal diseases that have been carried out in the past two decades. The research has concentrated on a relatively small but well‐known group of microorganisms. A wide range of models has been reviewed and conclusions across the breadth of these studies are presented in this review.     

Plasma proteome of buffaloes

The proteomic approach has aroused the interest of veterinary medicine researchers, especially regarding the production of biopharmaceuticals and diagnosis of diseases in farm animals. Water buffaloes have gained prominence in the world economy due to the quality of their milk, meat, and leather, in addition to being an important donor of blood components. This work aimed to identify and characterize the proteins present in the blood plasma of Murrah buffaloes (Bubalus bubalis) through 2D electrophoresis, in gel protein digestion followed by mass spectrometry technique and for albumin depletion, in solution protein digestion followed by shotgun analysis. Our results showed the identification of 112 protein spots and 35 individual proteins, respectively. The abundant proteins were represented by albumin, fibrinogen‐α, fibrinogen‐β, fibrinogen‐γ, immunoglobulins in general, α‐1‐antiproteinase, α‐1B‐glycoprotein, α‐2‐HS‐glycoprotein, α‐macroglobulin, apolipoprotein A1, antithrombin‐III, endopin 2B, fetuin‐B, retinol‐binding protein, serotransferrin, transthyretin and vitamin D‐binding protein. Most of these proteins are related to the signaling pathways of the complement system and coagulation cascade. The results allowed a better understanding of the protein composition of these blood components, thus promoting studies on animal health in the search for molecular markers of zoonotic diseases in buffaloes.     

Understanding TGEV–ETEC Coinfection through the Lens of Proteomics: A Tale of Porcine Diarrhea

Porcine diarrhea and gastroenteritis are major causes of piglet mortality that result in devastating economic losses to the industry. A plethora of pathogens can cause these diseases, with the transmissible gastroenteritis virus (TGEV) and enterotoxigenic Escherichia coli K88 (ETEC) being two of the most salient. In the December 2017 issue of Proteomics Clinical Aplications, Xia and colleagues used comparative proteomics to shed light on how these microbes interact to cause severe disease 1 . The authors discovered that TGEV induces an epithelial‐mesenchymal transition‐like phenotype that augments cell adhesion proteins mediating the attachment of ETEC to intestinal epithelial cells. Moreover, coinfection was found to modulate several host proteins that could bolster pathogen persistence. Importantly, the authors observed that ETEC suppresses the production of inflammatory cytokines induced by TGEV, which may in turn promote the long‐term survival of both microbes.     

Characterisation of tumoral markers correlated with ErbB2 (HER2/Neu) overexpression and metastasis in breast cancer

The receptor tyrosine kinase ErbB2 (HER2/neu) is overexpressed in ?30% of breast cancers and is associated with poor prognosis and an increased likelihood of metastasis. Clinical treatments such as trastuzumab are effective in less than 35% of women diagnosed as ErbB2‐positive, highlighting the necessity of searching for novel targets and alternative therapies. Herein, a proteomic screening strategy combining quantitative‐based gel electrophoresis and MS was used to compare the protein expression of 48 normal human breast and tumour tissues differing in ErbB2 expression and lymph node status. The aim was to identify proteins associated with the aggressive phenotype of ErbB2‐positive breast cancer which could be potential biomarkers of the disease as well as therapy targets. In total, 177 protein isoforms (107 gene products) differentially expressed between tissue groups were identified. Immunohistochemical staining of a tissue‐microarray was used for validation of selected protein candidates. We found that expression of HSP90α, laminin and GSTP1 significantly correlated with ErbB2 expression, while others such as AGR2, NM23H1 and Annexin 2 were overexpressed in greater than 40% of tumours. Finally, knocking‐down the expression by RNA interference of three candidates, AGR2, Transgelin2 and NM23H1 resulted in an enhanced invasive capacity of MDA‐MB435 cells. These data support the involvement of these targets in tumour progression and identify them as novel biomarkers of the disease.     

Identification of novel inhibitors against Mycobacterium tuberculosis l-alanine dehydrogenase (MTB-AlaDH) through structure-based virtual screening

Mycobacterium tuberculosis (MTB) the etiological agent of tuberculosis (TB) survives in the human host for decades evading the immune system in a latent or persistent state. The Rv2780 (ald) gene that codes for l-alanine dehydrogenase (l-AlaDH) enzyme catalyzes reversible oxidative deamination of l-alanine to pyruvate and is overexpressed under hypoxic and nutrient starvation conditions in MTB. At present, as there is no suitable drug available to treat dormant tuberculosis; it is essential to identify drug candidates that could potentially treat dormant TB. Availability of crystal structure of MTB l-AlaDH bound with co-factor NAD⁺ facilitated us to employ structure-based virtual screening approach to obtain new hits from a commercial library of Asinex database using energy-optimized pharmacophore modeling. The resulting pharmacophore consisted of three hydrogen bond donor sites (D) and two hydrogen bond acceptor sites (A). The database compounds with a fitness score more than 1.0 were further subjected to Glide high-throughput virtual screening and docking. Thus, we report the identification of best five hits based on structure-based design and their in vitro enzymatic inhibition studies revealed IC₅₀ values in the range of 35–80 μM.     

Design of novel camphane-based derivatives with antimycobacterial activity

Although tuberculosis (TB) continues to be one of the leading infectious disease killers globally, it is curable and preventable. Despite the existence of safe, well tolerated and effective drugs used in the TB treatment, the interest in new entities, combinations and regimens increases during the last 10 years. Recently, we reported for a new class of anti-TB agents – camphane-based derivatives with nanomolar activity against Mycobacterium tuberculosis strains. The quantitative structure–activity relationship (QSAR) study on 12 compounds revealed several structural requirements for antimycobacterial activity: two hydrogen bond donors, two or three rings and no large branched substituents. Here, we describe the design of a set of nine novel camphane-based derivatives following these requirements. The compounds were synthesized and tested against M. tuberculosis strain H37Rv. Four of them showed activities in the nanomolar range, significantly higher than the activities in the initial set. The QSAR study based on all 21 derivatives pointed to two main structural requirements for anti-TB activity: two hydrogen bond donors and a side chain with aromatic ring.     

Discovery of a Novel Connecting Link between Renin–Angiotensin System and Cancer in Barrett's Esophagus by Proteomic Screening

The renin–angiotensin system (RAS) plays a central role in the regulation of homeostasis and blood pressure. This involves an important enzyme called angiotensin‐converting enzyme that leads to the conversion of angiotensin I into angiotensin II. RAS has been reported to show association with inflammation, and in sporadic studies, with cancer. In particular, angiotensin II has been reported to be prevalent in the hypoxic microenvironment and associated with cancer signaling pathways. In a recent study, Bratlie et al. (Proteomics Clin. Appl. 2019 , 4, 1800102) is shown to exploit 2D gel electrophoresis, and mass spectrometry (MS) to identify differentially expressed proteins by comparing low‐grade dysplasia in Barrett's Esophagus (BE) following administration of agents that interfere with RAS, that is, enalapril and candesartan, and identified specific modulation of HSP60, PDIA3, and PPA1. Though 2D gel coupled with MS is a commonly‐used tool for studying proteomes, it still has limitations in terms of a comprehensive analysis due to lack of absolute quantitation in a high‐throughput manner. Despite technical limitations and the small size of the study, preliminary data emerging from the investigation show interference caused by clinically approved RAS inhibitors resulting in alteration of molecular markers associated with tumorigenicity. The authors propose potential factors that may influence the progression of the disease. However, these are conspicuous changes in high‐abundance proteins only. Therefore, there is a need to carry out detailed experimental studies either using an in vitro labeling technique (isobaric labeling for relative and absolute quantitation) for tissues or an in vivo labeling technique (stable isotope labeling in animal cell culture) coupled with LC‐MS/MS to identify differentially‐regulated proteins to delineate the role of RAS in BE.     

Multi‐view 3‐D display employing a flat‐panel display with slanted pixel arrangement

Abstract— A flat‐panel display with a slanted subpixel arrangement has been developed for a multi‐view three‐dimensional (3‐D) display. A set of 3M × N subpixels (M × N subpixels for each R, G, and B color) corresponds to one of the cylindrical lenses, which constitutes a lenticular lens, to construct each 3‐D pixel of a multi‐view display that offers M × N views. Subpixels of the same color in each 3‐D pixel have different horizontal positions, and the R, G, and B subpixels are repeated in the horizontal direction. In addition, the ray‐emitting areas of the subpixels within a 3‐D pixel are continuous in the horizontal direction for each color. One of the vertical edges of each subpixel has the same horizontal position as the opposite vertical edge of another subpixel of the same color. Cross‐talk among viewing zones is theoretically zero. This structure is suitable for providing a large number of views. A liquid‐crystal panel having this slanted subpixel arrangement was fabricated to construct a mobile 3‐D display with 16 views and a 3‐D resolution of 256 × 192. A 3‐D pixel is comprised of 12 × 4 subpixels (M = 4 and N = 4). The screen size was 2.57 in.     

The long path towards implementation of clinical proteomics: Exemplified based on CKD273

Clinical proteomics aims at the development and the implementation of novel biomarkers that demonstrate a clear clinical benefit in the management of diseases. However, though the attention in the field is increasing and multiple articles on biomarker research are published, clinical implementation of these biomarkers is scarce. In this paper, we aim towards identifying the hurdles on the path towards implementation, and present one successful approach, based on capillary electrophoresis coupled with mass spectrometry. A panel of biomarkers identified and assessed using this approach, termed CKD273, has recently received a Letter‐of‐Support from the US‐Food and Drug Administration (FDA), and is now implemented in the (early) management of chronic kidney disease. Based on this experience in the process towards implementation of CKD273, issues associated with implementation and suggestions how to meet these challenges are given.     

Proteomics in Drug Development: The Dawn of a New Era?

Mass spectrometry offers the potential of acquiring high resolution data depicting the functional status of a group of healthy or diseased individuals, according to different conditions. As most of the drugs are currently targeting proteins, proteomics has a dual value, both in the discovery of new molecules as therapeutic targets, but also as a methodology to perform high throughput drug profiling. As there is an evident need for drugs to be improved in terms of efficacy, a mechanistic insight for downstream effectors can be valuable in order to predict side effects and resistance mechanisms. Recently developed assays, like thermal proteome profiling enables comprehensive drug target profiling and is, therefore, of high value in drug discovery. In this review, a systematic literature search is conducted and the most prominent proteomics studies as implicated in assisting drug discovery and development is presented. Focus is placed on investigations that are closer to implementation, therefore particular emphasis is given in studies conducted in human diseased population and further verified in vitro or in vivo.     

Membrane Proteome of Invasive Retinoblastoma: Differential Proteins and Biomarkers

Purpose: Retinoblastoma (RB) is a pediatric ocular cancer which is caused due to the aberrations in the RB1 gene. The changes in the membrane proteomics would help in understanding the development of the retinoblastoma and could identify candidates for biomarkers and therapy. Experimental design: Quantitative proteomics is performed on the enriched membrane fractions from pooled normal retina (n = 5) and pooled retinoblastoma tissues (n = 5). The proteins are tryptic‐digested and tagged with iTRAQ labels. Orbitrap mass spectrometry is used to analyze and quantify the deregulated membrane proteins involved in the RB tumor progression. Immunohistochemistry (IHC) is used to further validate few of the differentially expressed proteins. Results: A total of 3122 proteins are identified of which, 663 proteins are found to be deregulated with ≥two fold change in the RB tumor compared to the retina. 282 proteins are upregulated and 381 are downregulated with ≥2 peptide identifications. Bioinformatic analysis revealed that, most of the proteins are involved in the transport, cellular communication, and growth. Overexpression of lamin B1 (LMNB1) and transferrin receptor (TFRC) are observed in RB tumors using IHC. Conclusion and clinical relevance: The present study, is the first comprehensive quantitative membrane proteomic atlas of the differentially regulated proteins in RB compared to the retina. LMNB1 and TFRC could be potential biomarkers for this childhood cancer.     

Volumetric three‐dimensional up‐conversion display medium

Abstract— Several rare‐earth‐doped fluoride crystals that are excited to emit visible light by sequential two‐photon absorption have been investigated as display‐medium candidates for static volumetric three‐dimensional displays. Dispersion of powders of these materials in a refractive‐index‐matched polymer is reported because such a medium may result in a scalable display. The scattering problem in such a medium is greatly reduced by index‐matching the polymer to the crystalline particles. An index‐matching condition that optimizes the performance is identified.     

Proteomics and Leishmaniasis: Potential Clinical Applications

Leishmaniases are diseases caused by protozoan parasites of the genus Leishmania. They are endemic in 98 countries, affect around 12 million people worldwide and may present several distinct clinical forms. Unfortunately, there are only a few drugs available for treatment of leishmaniasis, which are toxic and not always effective. Different parasite species and different clinical forms require optimization of the treatment or more specific therapies, which are not available. The emergence of resistance is also a matter of concern. Besides, diagnosis can sometimes be complicated due to atypical manifestations and associations with other pathologies. In this review, proteomic data are presented and discussed in terms of their application in important issues in leishmaniasis such as parasite resistance to chemotherapy, diagnosis of active disease in patients and dogs, markers for different clinical forms, identification of virulence factors, and their potential use in vaccination. It is shown that proteomics has contributed to the discovery of potential biomarkers for prognosis, diagnosis, therapeutics, monitoring of disease progression, treatment follow‐up and identification of vaccine candidates for specific diseases. However, the authors believe its capabilities have not yet been fully explored for routine clinical analysis for several reasons, which will be presented in this review.     

Assessment by Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectrometry of the Effects of Preanalytical Variables on Serum Peptidome Profiles Following Long‐Term Sample Storage

Purpose

Human serum and plasma are often used as clinical specimens in proteomics analyses, and peptidome profiling of human serum is a promising tool for identifying novel disease‐associated biomarkers. Matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) is widely used for peptidomic biomarker discovery. Careful sample collection and handling are required as either can have a profound impact on serum peptidome patterns, yet the effects of preanalytical variables on serum peptidome profiles have not been completely elucidated. The present study investigated the effects of preanalytical variables, including storage temperature, duration (up to 12 months), and thawing methods, on MALDI‐TOF MS‐based serum peptidome patterns.

Experimental design

Aliquots of serum samples were pretreated with weak cation exchanger magnetic beads using an automated ClinProtRobot system and then analyzed by MALDI‐TOF MS.

Results

A number of significant differences in peak intensities were observed depending on sample processing variables.

Conclusions and clinical relevance

These peaks can be used as sample quality markers to assess the effects of long‐term storage on serum peptidome profiles using MALDI‐TOF MS.

     

Euler angles: conversion of arbitrary rotation sequences to specific rotation sequence

Euler angles have been used to describe the orientation of objects in two‐dimensional and three‐dimensional spaces since its formulation by Leonhard Euler. Many applications intended to represent the rotation of a body have been developed on the basis of Euler angles. Two‐dimensional rotations are combined in sequence to represent three‐dimensional rotations. Because there are three axes in a three‐dimensional Euclidean space (X, Y and Z), 12 rotation sequences in three dimensions are possible: XYZ, XZY, YXZ, YZX, ZXY, ZYX, XYX, ZYZ, ZXZ, YXY, XZX and YZY. Each rotation sequence yields different results, and different applications implement a different rotation sequence. Thus, conversion between different rotation sequences becomes essential to make applications developed in different rotation sequences compatible with each other. In this paper, a new method is introduced to convert arbitrary rotation sequences to a specific rotation sequence of choice. A sample program is also developed in a MATLAB‐Simulink environment to demonstrate the use of the new method in converting an arbitrary Euler rotation sequence to the specific Euler rotation sequence of XYZ. A six‐degrees‐of‐freedom animation block is used in the program to aid users to graphically see the rotation of a body in three‐dimensional space. Copyright © 2013 John Wiley & Sons, Ltd.     

Formations on directed cycles with bearing‐only measurements

This paper studies a bearing‐only–based formation control problem for a group of single‐integrator agents with directed cycle sensing topology. In a 2‐dimensional space, a necessary and sufficient condition for the set of desired bearing vectors to be feasible is derived. Then, we propose a bearing‐only control law for every agent and prove that the formation asymptotically converges to a formation specified by a set of feasible desired bearing vectors. Analysis of the equilibrium formations in the plane for a 3‐agent system and subsequent extension to an n‐agent system is provided. We further extend the analysis on directed triangular formation into a 3‐dimensional space. Finally, simulations validate the theoretical results.