Serum metabolomics of treatment response in myasthenia gravis

OBJECTIVE

High-dose prednisone use, lasting several months or longer, is the primary initial therapy for myasthenia gravis (MG). Upwards of a third of patients do not respond to treatment. Currently no biomarkers can predict clinical responsiveness to corticosteroid treatment. We conducted a discovery-based study to identify treatment responsive biomarkers in MG using sera obtained at study entry to the thymectomy clinical trial (MGTX), an NIH-sponsored randomized, controlled study of thymectomy plus prednisone versus prednisone alone.

METHODS

We applied ultra-performance liquid chromatography coupled with electro-spray quadrupole time of flight mass spectrometry to obtain comparative serum metabolomic and lipidomic profiles at study entry to correlate with treatment response at 6 months. Treatment response was assessed using validated outcome measures of minimal manifestation status (MMS), MG-Activities of Daily Living (MG-ADL), Quantitative MG (QMG) score, or a strictly defined composite measure of response.

RESULTS

Increased serum levels of phospholipids were associated with treatment response as assessed by QMG, MMS, and the Responders classification, but all measures showed limited overlap in metabolomic profiles, in particular the MG-ADL. A panel including histidine, free fatty acid (13:0), γ-cholestenol and guanosine was highly predictive of the strictly defined treatment response measure. The AUC in Responders' prediction for these markers was 0.90 irrespective of gender, age, thymectomy or baseline prednisone use. Pathway analysis suggests that xenobiotic metabolism could play a major role in treatment resistance. There was no association with outcome and gender, age, thymectomy or baseline prednisone use.

INTERPRETATION

We have defined a metabolomic and lipidomic profile that can now undergo validation as a treatment predictive marker for MG patients undergoing corticosteroid therapy. Metabolomic profiles of outcome measures had limited overlap consistent with their assessing distinct aspects of treatment response and supporting unique biological underpinning for each outcome measure. Interindividual variation in prednisone metabolism may be a determinate of how well patients respond to treatment.

Urethral Catheter Biofilms Reveal Plasticity in Bacterial Composition and Metabolism and Withstand Host Immune Defenses in Hypoxic Environment

Biofilms composed of multiple microorganisms colonize the surfaces of indwelling urethral catheters that are used serially by neurogenic bladder patients and cause chronic infections. Well-adapted pathogens in this niche are Escherichia coli, Proteus, and Enterococcus spp., species that cycle through adhesion and multilayered cell growth, trigger host immune responses, are starved off nutrients, and then disperse. Viable microbial foci retained in the urinary tract recolonize catheter surfaces. The molecular adaptations of bacteria in catheter biofilms (CBs) are not well-understood, promising new insights into this pathology based on host and microbial meta-omics analyses from clinical specimens. We examined catheters from nine neurogenic bladder patients longitudinally over up to 6 months. Taxonomic analyses from 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics revealed that 95% of all catheter and corresponding urinary pellet (UP) samples contained bacteria. CB biomasses were dominated by Enterobacteriaceae spp. and often accompanied by lactic acid and anaerobic bacteria. Systemic antibiotic drug treatments of patients resulted in either transient or lasting microbial community perturbations. Neutrophil effector proteins were abundant not only in UP but also CB samples, indicating their penetration of biofilm surfaces. In the context of one patient who advanced to a kidney infection, Proteus mirabilis proteomic data suggested a combination of factors associated with this disease complication: CB biomasses were high; the bacteria produced urease alkalinizing the pH and triggering urinary salt deposition on luminal catheter surfaces; P. mirabilis utilized energy-producing respiratory systems more than in CBs from other patients. The NADH:quinone oxidoreductase II (Nqr), a Na+ translocating enzyme not operating as a proton pump, and the nitrate reductase A (Nar) equipped the pathogen with electron transport chains promoting growth under hypoxic conditions. Both P. mirabilis and E. coli featured repertoires of transition metal ion acquisition systems in response to human host-mediated iron and zinc sequestration. We discovered a new drug target, the Nqr respiratory system, whose deactivation may compromise P. mirabilis growth in a basic pH milieu. Animal models would not allow such molecular-level insights into polymicrobial biofilm metabolism and interactions because the complexity cannot be replicated.

Monoclonal Antibody-Based Therapies for Myasthenia Gravis

Myasthenia gravis (MG) is an autoimmune, neuromuscular disorder that produces disabling weakness through a compromise of neuromuscular transmission. The disease fulfills strict criteria of an antibody-mediated disease. Close to 90% of patients have antibodies directed towards the nicotinic acetylcholine receptor (AChR) on the post-synaptic surface of skeletal muscle and another 5% to the muscle-specific kinase, which is involved in concentrating the AChR to the muscle surface of the neuromuscular junction. Conventional treatments of intravenous immunoglobulin and plasma exchange reduce autoantibody levels to produce their therapeutic effect, while prednisone and immunosuppressives do so by moderating autoantibody production. None of these treatments were specifically developed for MG and have a range of adverse effects. The extensive advances in monoclonal antibody technology allowing specific modulation of biological pathways has led to a tremendous increase in the potential treatment options. For MG, monoclonal antibody therapeutics target the effector mechanism of complement inhibition and the reduction of antibody levels by FcRn inhibition. Antibodies directed against CD20 and signaling pathways, which support lymphocyte activity, have been used to reduce autoantibody production. Thus far, only eculizumab, an antibody against C5, has reached the clinic. We review the present status of monoclonal antibody-based treatments for MG that have entered human testing and offer the promise to transform treatment of MG.

Urban wastelands: On the frontline between air pollution sources and residential areas

In urban areas, particulate matter (PM) represents an increasing threat to human health. The ability of plants in parks and along roads in cities to accumulate PM has already been demonstrated, but nothing is known about the effect of wasteland vegetation on air quality, despite a significant proportion of greenery in polluted areas being on wastelands. The aim of this study was to document the accumulation of PM and trace elements (TE) by wasteland species (Robinia pseudoacacia L., Populus × canescens (Aiton) Sm., Acer negundo L., Solidago gigantea (Aiton) and Poaceae) growing on Central European urban wastelands with differing levels of air pollution. On average, the largest amounts of PM accumulated on the foliage of R. pseudoacacia and S. gigantea, and the smallest amounts accumulated on P. × canescens leaves. However, accumulation of PM depended more on the distance from the emission source than on species selection, and was higher on the polluted wasteland where the plants' gas exchange was the lowest. The results also suggest that in order to effectively accumulate PM from the air, it is critical to have the correct configuration of plants, with the wasteland vegetation having a layered structure and layers differing in PM retention, as shown in this study using the examples of R. pseudoacacia (a tall tree with low PM retention) and S. gigantea (below-tree vegetation with high PM retention). P. × canescens accumulated the highest concentrations of Cd and Zn, S. gigantea accumulated the highest concentration of Cu, and Poaceae accumulated the highest concentrations of Cr and Ni. These findings have implications for urban vegetation management in areas where there is no organised greenery, and offer proof that vegetation in wasteland areas should be maintained since it is an excellent tool for reducing concentrations of PM at its place of origin.

Thus far but no further: predatory mites do not migrate effectively into strawberry plantations

Enhancing the performance of predatory mites is often regarded as the best biological control approach towards the spider mite Tetranychus urticae, the main pest of strawberry plantations. Optimizing the colonization of plantations by predators from adjacent areas such as field margins is seen as an important component of conservation biocontrol. We have investigated the factors contributing to enhancing the numbers of predatory mites (Acari: Phytoseidae), such as management of the field margins, vegetation composition and the effect of the presence of woody species. We also tested the penetration of the phytoseiids from the field margins into the crop. In a study carried out in 14 open-field extensively managed strawberry plantations in Poland we found phytoseiids to be abundant in field margins; 14 taxa were discovered. However, only two species Amblyseius andersoni and Euseius finlandicus dispersed a modest distance into the crop. We found that the diversity and densities of the predatory mites were enhanced somewhat by the management type of the field margins; especially the spontaneous vegetation favoured the presence of phytoseiids. However, despite the predatory mites being rather retained in the field margins also significant reduction in numbers of their prey T. urticae was recorded over the course of the year. The low penetration of predatory mites into the main part of the field, indicates that conservation biological control measures in the field margin might not be sufficient on their own to enhance the impact of predatory mites within the main part of the fields.

Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections

Neutrophils have an important role in the antimicrobial defense and resolution of urinary tract infections (UTIs). Our research suggests that a mechanism known as neutrophil extracellular trap (NET) formation is a defense strategy to combat pathogens that have invaded the urinary tract. A set of human urine specimens with very high neutrophil counts had microscopic evidence of cellular aggregation and lysis. Deoxyribonuclease I (DNase) treatment resulted in disaggregation of such structures, release of DNA fragments and a proteome enriched in histones and azurophilic granule effectors whose quantitative composition was similar to that of previously described in vitro-formed NETs. The effector proteins were further enriched in DNA-protein complexes isolated in native PAGE gels. Immunofluorescence microscopy revealed a flattened morphology of neutrophils associated with decondensed chromatin, remnants of granules in the cell periphery, and myeloperoxidase co-localized with extracellular DNA, features consistent with early-phase NETs. Nuclear staining revealed that a considerable fraction of bacterial cells in these structures were dead. The proteomes of two pathogens, Staphylococcus aureus and Escherichia coli, were indicative of adaptive responses to early-phase NETs, specifically the release of virulence factors and arrest of ribosomal protein synthesis. Finally, we discovered patterns of proteolysis consistent with widespread cleavage of proteins by neutrophil elastase, proteinase 3 and cathepsin G and evidence of citrullination in many nuclear proteins.

Urinary tract infections (UTIs) are one of the world’s most widespread infectious diseases, with an estimated number of 150 million cases per year. Neutrophils play an important role in the defense of human patients against microbes causing UTIs. Molecules produced by neutrophils that migrate into the urinary tract can kill the invading microbes and resolve an infection, often without a need to treat patients with an antibiotic. Our work shows strong support for a mechanism called the formation of neutrophil extracellular traps (NETs), previously described for other infections and autoimmune conditions, which are involved in killing pathogens that have invaded the urinary tract. We show evidence of extracellular chromatin-containing structures using immunofluorescence microscopy and identified proteins that bind to the chromatin DNA and have functions to damage and kill bacterial cells or stop their growth.

Comprehensive Metaproteomic Analyses of Urine in the Presence and Absence of Neutrophil-Associated Inflammation in the Urinary Tract

Inflammation in the urinary tract results in a urinary proteome characterized by a high dynamic range of protein concentrations and high variability in protein content. This proteome encompasses plasma proteins not resorbed by renal tubular uptake, renal secretion products, proteins of immune cells and erythrocytes derived from trans-urothelial migration and vascular leakage, respectively, and exfoliating urothelial and squamous epithelial cells. We examined how such proteins partition into soluble urine (SU) and urinary pellet (UP) fractions by analyzing 33 urine specimens 12 of which were associated with a urinary tract infection (UTI). Using mass spectrometry-based metaproteomic approaches, we identified 5,327 non-redundant human proteins, 2,638 and 4,379 of which were associated with SU and UP fractions, respectively, and 1,206 non-redundant protein orthology groups derived from pathogenic and commensal organisms of the urogenital tract. Differences between the SU and UP proteomes were influenced by local inflammation, supported by respective comparisons with 12 healthy control urine proteomes. Clustering analyses showed that SU and UP fractions had proteomic signatures discerning UTIs, vascular injury, and epithelial cell exfoliation from the control group to varying degrees. Cases of UTI revealed clusters of proteins produced by activated neutrophils. Network analysis supported the central role of neutrophil effector proteins in the defense against invading pathogens associated with subsequent coagulation and wound repair processes. Our study expands the existing knowledge of the urinary proteome under perturbed conditions, and should be useful as reference dataset in the search of biomarkers.

Urine sample preparation in 96-well filter plates for quantitative clinical proteomics

Urine is an important, noninvasively collected body fluid source for the diagnosis and prognosis of human diseases. Liquid chromatography mass spectrometry (LC-MS) based shotgun proteomics has evolved as a sensitive and informative technique to discover candidate disease biomarkers from urine specimens. Filter-aided sample preparation (FASP) generates peptide samples from protein mixtures of cell lysate or body fluid origin. Here, we describe a FASP method adapted to 96-well filter plates, named 96FASP. Soluble urine concentrates containing ~10 μg of total protein were processed by 96FASP and LC-MS resulting in 700-900 protein identifications at a 1% false discovery rate (FDR). The experimental repeatability, as assessed by label-free quantification and Pearson correlation analysis for shared proteins among replicates, was high (R ≥ 0.97). Application to urinary pellet lysates which is of particular interest in the context of urinary tract infection analysis was also demonstrated. On average, 1700 proteins (±398) were identified in five experiments. In a pilot study using 96FASP for analysis of eight soluble urine samples, we demonstrated that protein profiles of technical replicates invariably clustered; the protein profiles for distinct urine donors were very different from each other. Robust, highly parallel methods to generate peptide mixtures from urine and other body fluids are critical to increase cost-effectiveness in clinical proteomics projects. This 96FASP method has potential to become a gold standard for high-throughput quantitative clinical proteomics.

A second-generation protein-protein interaction network of Helicobacter pylori

Helicobacter pylori infections cause gastric ulcers and play a major role in the development of gastric cancer. In 2001, the first protein interactome was published for this species, revealing over 1500 binary protein interactions resulting from 261 yeast two-hybrid screens. Here we roughly double the number of previously published interactions using an ORFeome-based, proteome-wide yeast two-hybrid screening strategy. We identified a total of 1515 protein-protein interactions, of which 1461 are new. The integration of all the interactions reported in H. pylori results in 3004 unique interactions that connect about 70% of its proteome. Excluding interactions of promiscuous proteins we derived from our new data a core network consisting of 908 interactions. We compared our data set to several other bacterial interactomes and experimentally benchmarked the conservation of interactions using 365 protein pairs (interologs) of E. coli of which one third turned out to be conserved in both species.

The Rbf1, Hfl1 and Dbp4 of Candida albicans regulate common as well as transcription factor-specific mitochondrial and other cell activities

BACKGROUND

Our interest in Candida albicans mitochondria began with the identification of GOA1. We demonstrated its role in cell energy production, cross-talk among mitochondria and peroxisomes, non-glucose energy metabolism, maintenance of stationary phase growth, and prevention of premature apoptosis. Its absence results in avirulence. However, what regulated transcription of GOA1 was unknown.

RESULTS

To identify transcriptional regulators (TRs) of GOA1, we screened a C. albicans TF knockout library (TRKO) and identified Rbf1p, Hfl1p, and Dpb4p as positive TRs of GOA1. The phenotypes of each mutant (reduced respiration, inability to grow on glycerol, reduced ETC CI and CIV activities) are reasonable evidence for their required roles especially in mitochondrial functions. While the integration of mitochondria with cell metabolic activities is presumed to occur, there is minimal information on this subject at the genome level. Therefore, microarray analysis was used to provide this information for each TR mutant. Transcriptional profiles of Rbf1p and Hfl1p are more similar than that of Dpn4p. Our data demonstrate common and also gene-specific regulatory functions for each TR. We establish their roles in carbon metabolism, stress adaptation, cell wall synthesis, transporter efflux, peroxisomal metabolism, phospholipid synthesis, rRNA processing, and nuclear/mtDNA replication.

CONCLUSIONS

The TRs regulate a number of common genes but each also regulates specific gene transcription. These data for the first time create a genome roadmap that can be used to integrate mitochondria with other cell processes. Of interest, the TRs are fungal-specific, warranting consideration as antifungal drug targets.

Studying protein complexes by the yeast two-hybrid system

Protein complexes are typically analyzed by affinity purification and subsequent mass spectrometric analysis. However, in most cases the structure and topology of the complexes remains elusive from such studies. Here we investigate how the yeast two-hybrid system can be used to analyze direct interactions among proteins in a complex. First we tested all pairwise interactions among the seven proteins of Escherichia coli DNA polymerase III as well as an uncharacterized complex that includes MntR and PerR. Four and seven interactions were identified in these two complexes, respectively. In addition, we review Y2H data for three other complexes of known structure which serve as "gold-standards", namely Varicella Zoster Virus (VZV) ribonucleotide reductase (RNR), the yeast proteasome, and bacteriophage lambda. Finally, we review an Y2H analysis of the human spliceosome which may serve as an example for a dynamic mega-complex.

Oxidative fabrication of patterned, large, non-flaking CuO nanowire arrays

We report a simple and fast approach to fabricate large, non-flaking arrays of CuO nanowires by oxidizing thin copper substrates in air. Oxidative CuO nanowire growth is commonly accompanied by oxide layer flaking due to stress at the copper-copper oxide interface. Using thin substrates is shown to prevent this flaking by introducing favourable material thickness ratios in the samples after oxidation. Additionally, thin foils allow larger scale topographic patterns to be transferred from an underlying mould to realize non-flat, nanowire-decorated surfaces. Further patterning is possible by electrodeposition of a nickel layer, which restricts nanowire growth to specific areas of the sample.

A bio-originated porous template for the fabrication of very long, inorganic nanotubes and nanowires

A biopolymer-based template assembly constructed around the spines of the bristle worm Aphrodita aculeata (sea mouse) was used to fabricate very high aspect ratio nanowires and nanotubes using established methods adopted from nanofabrication in porous membranes. The easily available bio-originated template contains more than 100 000 highly ordered, very high aspect ratio nanochannels, each about 150 to 200 nm in diameter but up to a centimetre in length. Their parallel, hexagonal arrangement in the spine constitutes a photonic crystal, which gives the animal its colourful, iridescent appearance. Around the nanochannels, the spines consist of a chitin/protein composite material, which has been shown to withstand the chemical and thermal conditions needed for established template-assisted nanofabrication strategies. A template preparation procedure was developed and the template was used to fabricate copper and nickel nanowires by electrodeposition and aluminium oxide nanotubes by atomic layer deposition. Due to their high thermal and chemical stability, decomposition of the filled templates proved to be difficult, and different approaches to obtain separated nanostructures are described and discussed. Alongside this, the presented system of parallel nanowires or nanotubes in a biopolymer matrix might be utilized in applications, where such separated structures are not needed. Comparing to porous membranes, the presented template allows us to increase the maximum length of nanotubes and nanowires produced using nanochannel-based templates by at least one order of magnitude.

Optical image correlator realized with a hybrid liquid-crystal-photoconducting polymer structure

A joint Fourier-transform optical correlator for image recognition based on a novel hybrid photoconducting polymer-nematic liquid-crystal structure is described. The optically addressed active element that we have designed is capable of performing real-time image processing 20 times/s, at light-intensity levels of 10mW/cm(2) with dc operating voltage of the order of 10 V. We present the results of correlation of simple objects as well as complicated photographs. The sensitivity, durability, and reliability of the presented system open possibilities for many applications.