Differential Content of Proteins, mRNAs, and miRNAs Suggests that MDSC and Their Exosomes May Mediate Distinct Immune Suppressive Functions

Myeloid-derived suppressor cells (MDSC) are immature myeloid cells that accumulate in the circulation and the tumor microenvironment of most cancer patients. There, MDSC suppress both adaptive and innate immunity, hindering immunotherapies. The inflammatory milieu often present in cancers facilitates MDSC suppressive activity, causing aggressive tumor progression and metastasis. MDSC from tumor-bearing mice release exosomes, which carry biologically active proteins and mediate some of the immunosuppressive functions characteristic of MDSC. Studies on other cell types have shown that exosomes may also carry RNAs which can be transferred to local and distant cells, yet the mRNA and microRNA cargo of MDSC-derived exosomes has not been studied to date. Here, the cargo of MDSC and their exosomes was interrogated with the goal of identifying and characterizing molecules that may facilitate MDSC suppressive potency. Because inflammation is an established driving force for MDSC suppressive activity, we used the well-established 4T1 mouse mammary carcinoma system, which includes "conventional" as well as "inflammatory" MDSC. We provide evidence that MDSC-derived exosomes carry proteins, mRNAs, and microRNAs with different quantitative profiles than those of their parental cells. Several of these molecules have known or predicted functions consistent with MDSC suppressive activity, suggesting a potential mechanistic redundancy.

Evaluation of Spectral Counting for Relative Quantitation of Proteoforms in Top-Down Proteomics

Spectral counting is a straightforward label-free quantitation strategy used in bottom-up proteomics workflows. The application of spectral counting in label-free top-down proteomics workflows can be similarly straightforward but has not been applied as widely as quantitation by chromatographic peak areas or peak intensities. In this study, we evaluate spectral counting for quantitative comparisons in label-free top-down proteomics workflows by comparison with chromatographic peak areas and intensities. We tested these quantitation approaches by spiking standard proteins into a complex protein background and comparing relative quantitation by spectral counts with normalized chromatographic peak areas and peak intensities from deconvoluted extracted ion chromatograms of the spiked proteins. Ratio estimates and statistical significance of differential abundance from each quantitation technique are evaluated against the expected ratios and each other. In this experiment, spectral counting was able to detect differential abundance of spiked proteins for expected ratios ≥2, with comparable or higher sensitivity than normalized areas and intensities. We also found that while ratio estimates using peak areas and intensities are usually more accurate, the spectral-counting-based estimates are not substantially worse. Following the evaluation and comparison of these label-free top-down quantitation strategies using spiked proteins, spectral counting, along with normalized chromatographic peak areas and intensities, were used to analyze the complex protein cargo of exosomes shed by myeloid-derived suppressor cells collected under high and low conditions of inflammation, revealing statistically significant differences in abundance for several proteoforms, including the active pro-inflammatory proteins S100A8 and S100A9.

Structural characterization of product ions by electrospray ionization and quadrupole time-of-flight mass spectrometry to support regulatory analysis of veterinary drug residues in foods. Part 2: Benzimidazoles, nitromidazoles, phenothiazines, and mectins

RATIONALE

Analysis for identification and quantification of regulated veterinary drug residues in foods is usually achieved by liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS). The instrumental method requires the selection of characteristic ions, but structural elucidation is seldom performed to help ensure accuracy. This study is a continuation of previous work to characterize selected product ions in support of regulatory monitoring programs.

METHODS

The tandem mass spectra of 28 veterinary drugs from a previously published LC/MS/MS method were acquired with a high-resolution quadrupole time-of-flight (Q-TOF) mass spectrometer using electrospray ionization (ESI) in positive mode. The TOF analyzer was calibrated to achieve a mass accuracy error <5 ppm for the MS and MS/MS modes, and samples were infused for data acquisition.

RESULTS

The high mass accuracy achieved in Q-TOF allowed elucidation of the formulae of the product ions previously selected for qualitative identification. Rational interpretation of results was made and compared with the published literature, and the structure for the MS/MS product ions of four classes of regulated drugs (mectins, benzimidazoles, nitroimidazoles, and phenothiazines), totaling 28 compounds, were examined leading to the report of new structures or confirmation of published structures using low-resolution MS.

CONCLUSIONS

Structural characterization of the product ions selected for identification and quantification of veterinary drug residues is important information for regulatory monitoring programs in defense of regulatory enforcement actions. This study has allowed structural elucidation of 84 MS/MS product ions previously selected for the LC/MS/MS analysis of 28 drug analytes.

Top-down analysis of low mass proteins in exosomes shed by murine myeloid-derived suppressor cells

Top-down analysis is reported for a portion of the protein cargo of exosomes shed by myeloid-derived suppressor cells that participate in intracellular signaling in the tumor microenvironment. Instrument mass resolution limited the study to proteins of molecular masses below 30 kDa. A two-step fractionation strategy was used, including open tubular gel electrophoresis and C3 reverse phase high performance liquid chromatography. Twenty-one unique proteins were identified among more than 200 proteoforms, and comprising primarily two functionally important protein families: the S100 proinflammatory mediators and an abundance of histones. Fifty-six percent of the total protein in these exosomes was determined to comprise histones, of which H2B variants contribute 42 %.

Structural characterization of product ions by electrospray ionization and quadrupole time-of-flight mass spectrometry to support regulatory analysis of veterinary drug residues in foods

RATIONALE

Monitoring of veterinary drug residues in foods is often conducted using liquid chromatography/tandem mass spectrometry (LC/MS/MS). Results have high economic stakes for producers, but the ions monitored are usually selected due to signal intensities without structural interpretation. In this study, the ion transitions were characterized by high-resolution mass spectrometry.

METHODS

The 62 veterinary drugs from the LC/MS/MS method consisted of sulfonamides, β-lactams, phenicols, macrolides, tetracyclines, fluoroquinolones, non-steroidal anti-inflammatory drugs (NSAIDs), and corticosteroids. They were individually infused into a quadrupole time-of-flight (Q-TOF) mass spectrometer using electrospray ionization (ESI) operated in positive mode. The MS and collision-induced dissociation (CID) MS/MS spectra for each analyte were obtained for structural elucidation. The Q-TOF instrument was calibrated to obtain a mass accuracy error <5 ppm for the MS and MS/MS spectra.

RESULTS

The use of high-resolution ESI-Q-TOF-MS for the generation of the MS/MS product ions allowed for the determination of chemical formulae for the analytes, some of which led to new findings. Assigned structures were based on rational interpretation of the most stable possible products with comparison with the scientific literature. In difficult cases, isotopically labeled drugs or hydrogen/deuterium (H/D) exchange experiments were used to help confirm the structures of the product ions.

CONCLUSIONS

The use of ESI-Q-TOF-MS in this study has allowed structure elucidation of 186 MS/MS product ions previously selected for the LC/MS/MS analysis of 62 veterinary drugs. This serves to reduce the chances of false positives and negatives in the monitoring program, and provides justification and defense in regulatory enforcement actions.

Cytotoxic, virucidal, and antiviral activity of South American plant and algae extracts

Herpes simplex virus type 1 (HSV-1) infection has a prevalence of 70% in the human population. Treatment is based on acyclovir, valacyclovir, and foscarnet, three drugs that share the same mechanism of action and of which resistant strains have been isolated from patients. In this aspect, innovative drug therapies are required. Natural products offer unlimited opportunities for the discovery of antiviral compounds. In this study, 28 extracts corresponding to 24 plant species and 4 alga species were assayed in vitro to detect antiviral activity against HSV-1. Six of the methanolic extracts inactivated viral particles by direct interaction and 14 presented antiviral activity when incubated with cells already infected. Most interesting antiviral activity values obtained are those of Limonium brasiliense, Psidium guajava, and Phyllanthus niruri, which inhibit HSV-1 replication in vitro with 50% effective concentration (EC(50)) values of 185, 118, and 60 μg/mL, respectively. For these extracts toxicity values were calculated and therefore selectivity indexes (SI) obtained. Further characterization of the bioactive components of antiviral plants will pave the way for the discovery of new compounds against HSV-1.

Transfer of pesticides to the brew during mate drinking process and their relationship with physicochemical properties

In order to evaluate the extraction of pesticide residues that are transferred to the brew during mate drinking process of P.U.1 yerba mate leaves (Ilex paraguariensis), a special device to simulate the way in which mate is drunk in Uruguay was developed. The transfer to the brew of 12 organophosphates, 5 synthethic pyrethroids and one organochlorine pesticide from spiked samples was studied. The relationship between the transfer data thus obtained and physicochemical properties like water solubility (Ws), octanol-water coefficient (Kow) and Henry's constant (H) was evaluated. The extractability of the pesticide residues from yerba mate can be correlated with log Ws and log Kow. These transfer values allowed the calculation of ARLs (acceptable residue level) for the pesticides following Food and Agriculture Organization (FAO), World Health Organizaion (WHO) guidelines. These results can help the future establishment of maximum residue levels (MRLs).