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Multiple myeloma (MM) is tightly dependent on inflammatory bone marrow microenvironment. IL-17 producing CD4+ T cells (Th17) sustain MM cells growth and osteoclasts-dependent bone damage. In turn, Th17 differentiation relies on inflammatory stimuli. Here, we investigated the role of miR-21 in Th17-mediated MM tumor growth and bone disease. We found that early inhibition of miR-21 in naive T cells (miR-21i-T cells) impaired Th17 differentiation in vitro and abrogated Th17-mediated MM cell proliferation and osteoclasts activity. We validated these findings in NOD/SCID-g-NULL mice, intratibially injected with miR-21i-T cells and MM cells. A Pairwise RNAseq and proteome/phosphoproteome analysis in Th17 cells demonstrated that miR-21 inhibition led to upregulation of STAT-1/-5a-5b, STAT-3 impairment and redirection of Th17 to Th1/Th2 like activated/polarized cells. Our findings disclose the role of miR-21 in pathogenic Th17 activity and open the avenue to the design of miR-21-targeting strategies to counteract microenvironment dependence of MM growth and bone disease.

MS-based proteomics is expanding its role as a routine tool for biological discovery. Nevertheless, the task of accurately and precisely quantifying thousands of analytes in a single experiment remains challenging. In this study, the diagnostic accuracy of three popular data-dependent methods for protein relative quantification (label-free [LF], dimethyl labelling [DML] and tandem mass tags [TMT]) has been assessed using a mixed species proteome (three species) and five experimental replicates per condition. Data were produced using a quadrupole-Orbitrap mass spectrometer and analysed using a single platform (the MaxQuant/Perseus software suite). The whole comparative analysis was repeated three times over a period of 6 months, in order to assess the consistency of the reported findings. As expected, label-based methods reproducibly provided a lower false positives rate, whereas TMT and LF performed similarly, and significantly better than DML, in terms of proteome coverage using the same instrument time. Although parameters like proteome coverage and precision were consistent in between replicates, other parameters like sensitivity, intended as the capacity of correctly classifying true positives (regulated proteins), were found to be less reproducible, especially at challenging fold-changes (1.5). Collectively, data suggest that an increased interest in data reproducibility would be desirable in the quantitative proteomics field., (© 2020 John Wiley & Sons, Ltd.)

Although the concepts of somatic cell reprogramming and human-induced pluripotent stem cells (hiPSCs) generation have undergone several analyses to validate the usefulness of these cells in research and clinic, it remains still controversial whether the hiPSCs are equivalent to human embryonic stem cells (hESCs), pointing to the need of further characterization for a more comprehensive understanding of pluripotency. Most of the experimental evidence comes from the transcriptome analysis, while a little is available on protein data, and even less is known about the post-translational modifications. Here, we report a combined strategy of mass spectrometry and gene expression profiling for proteogenomic analysis of reprogrammed and embryonic stem cells. The data obtained through this integrated, multi-"omics" approach indicate that a small, but still significant, number of distinct pathways is enriched in reprogrammed versus embryonic stem cells, supporting the view that pluripotency is an extremely complex, multifaceted phenomenon, with peculiarities that are characteristic of each cell type., (© 2019 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.)

Purpose: The application of a methodology for quantitative protein analysis from formalin-fixed and paraffin-embedded (FFPE) tissue by using hydrogels. Miniaturized polymeric gels are placed onto histologically defined tissue regions in order to perform localized digestion for bottom-up proteomics. Hydrogel-extracted peptides are then labeled with tandem mass tags (TMT) reagents for relative protein quantification. A cardiac myxoma biopsy is used., Experimental Design: Multiple hydrogels, incorporating the proteolytic enzyme trypsin, are placed on serial tissue sections, and processed for digestion and TMT derivatization. SCX fractionation before LC-MS/MS analysis and bioinformatics analysis are carried out., Results: Two histologically different areas on both FFPE and frozen sections of the same cardiac myxoma biopsy are compared. In total, 1949 (FFPE) and 2491 (frozen) proteins are identified, with a total overlap of 56%. The quantitative comparison highlighted 15 (FFPE) and 138 (frozen) differentially expressed proteins between myxoma regions., Conclusion: The methodology successfully detects numerous protein signals from FFPE and frozen specimens and is able to differentiate between tissue regions. A fast and reliable tissue preparation for quantitative protein analysis by minimum sample manipulation is developed. This offers an option for on-tissue proteomics analysis while preserving the inherent spatial information on the tissue., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A series of isatin-dihydropyrazole hybrids have been synthesized in order to assess their potential as anticancer agents. In particular, 12 compounds were evaluated for their antiproliferative activity toward A549, IGR39, U87, MDA-MB-231, MCF-7, BT474, BxPC-3, SKOV-3, and H1299 cell lines, and human foreskin fibroblasts. Four compounds exhibited interesting antiproliferative activity and were further examined to determine their EC 50 values toward a panel of selected tumor cell lines. The best compounds were then investigated for their induced mechanism of cell death. Preliminary structure-activity relationship indicates that the presence of a substituent such as a chlorine atom or a methyl moiety in position 5 of the isatin nucleus is beneficial for the antitumor activity. EMAC4001 proved the most promising compound within the studied series with EC 50 values ranging from 0.01 to 0.38 μM., Competing Interests: The authors declare no competing financial interest.

A novel series of of 4-[(3-phenyl-4-aryl-2,3-dihydro-1,3-thiazol-2-ylidene)amino]benzene-1-sulfonamides ( EMAC10111a-g ) was synthesized and assayed toward both human carbonic anhydrase isozymes I, II, IX, and XII and cyclooxygenase isoforms. The majority of these derivatives preferentially inhibit hCA isoforms II and XII and hCOX-2 isozyme, indicating that 2,3,4-trisubstituted 2,3-dihydrothiazoles are a promising scaffold for the inhibition of hCA isozymes and of hCOX-2 enzyme. The nature of the substituent at the dihydrothiazole ring position 4 influenced the activity and selectivity toward both enzyme families. EMAC10111g resulted as the best performing compound toward both enzyme families and exhibited preferential activity toward hCA XII and hCOX-2 isozymes., Competing Interests: The authors declare no competing financial interest.

A small library of psoralen carboxylic acids and their corresponding benzenesulfonamide derivatives were designed and synthesized to evaluate their activity and selectivity toward tumor associated human carbonic anhydrase (hCA) isoforms IX and XII. Both psoralen acids and sulfonamides exhibited potent inhibition of IX and XII isozymes in the nanomolar concentration range. However, psoralen acids resulted as the most selective in comparison with the corresponding benzenesulfonamide derivatives. Our data indicate that the psoralen scaffold is a promising starting point for the design of highly selective tumor associated hCA inhibitors., Competing Interests: The authors declare no competing financial interest.

This work compares the composition at different temperatures of gaseous phase of bergamot essential oil at equilibrium with the liquid phase. A new GC-MS methodology to determine quantitatively the volatile aroma compounds was developed. The adopted methodology involved the direct injection of headspace gas into injection port of GC-MS system and of known amounts of the corresponding authentic volatile compounds. The methodology was validated. This study showed that gaseous phase composition is different from that of the liquid phase at equilibrium with it.

A rapid analytical approach for the assay of resveratrol in red wines, based on Paper Spray Mass Spectrometry (PS-MS) and Multiple Reaction Monitoring (MRM) is described. The assay involves the use of the stable isotope dilution method. The analytical parameters calculated analyzing fortified samples confirm the reliability of the proposed approach, with accuracy values about 100%, and LOD and LOQ values calculated at 0.5 and 0.8μg/mL, respectively. Furthermore, both the recovery, which was quantitative for the analyte, and the reproducibility (RSD%), checked on different days on the same wine, always below 7%, highlighted the consistency of the methodology., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

A series of N -acylbenzenesulfonamide dihydro-1,3,4-oxadiazole hybrids ( EMAC8000a-m ) was designed and synthesized with the aim to target tumor associated carbonic anhydrase (hCA) isoforms IX and XII. Most of the compounds were selective inhibitors of the tumor associated hCA XII. Moreover, resolution of EMAC8000d racemic mixture led to the isolation of the levorotatory eutomer exhibiting an increase of hCA XII inhibition potency and selectivity with respect to hCA II. Computational studies corroborated these data. Overall our data indicate that both substitution pattern and stereochemistry of dihydro-1,3,4-oxadiazole could be considered as key factors to determine activity and selectivity toward hCA isozymes. These results can provide further indication for the design and optimization of selective hCA inhibitors.

An optimized workflow for multiplexed and spatially localized on-tissue quantitative protein analysis is here presented. The method is based on the use of an enzyme delivery platform, a polymeric hydrogel disc, allowing for a localized digestion directly onto the tissue surface coupled with an isobaric mass tag strategy for peptide labeling and relative quantification. The digestion occurs within such hydrogels, followed by peptide solvent extraction and identification by liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/MS). Since this is a histology-directed on-tissue analysis, multiple hydrogels were placed onto morphologically and spatially different regions of interest (ROIs) within the tissue surface, e.g., cardiac myxoma tumor vascularized region and the adjacent hypocellular area. After a microwave digestion step (2 min), enzymatically cleaved peptides were labeled using TMT reagents with isobaric mass tags, enabling analysis of multiple samples per experiment. Thus, N = 8 hydrogel-digested samples from cardiac myxoma serial tissue sections (N = 4 from the vascularized ROIs and N = 4 from the adjacent hypocellular areas) were processed and then combined before a single LC-MS/MS analysis. Regulated proteins from both cardiac myxoma regions were assayed in a single experiment. Graphical abstract The workflow for histology-guided on-tissue localized protein digestion followed by isobaric mass tagging and LC-MS/MS analysis for proteins quantification is here summarized.

The spatiotemporal analysis of the proteomic profile during human wound healing is a critical investigative step that can establish the complex interplay of molecular events that comprise the local response to burn injury. Partial-thickness wound samples with adjacent "normal" skin were collected from twenty-one patients with burn wounds and examined across a time spectrum ranging from the acute injury period at 3, 6, 11 days to the later hypertrophic scar period at 7 and 15 months. The techniques used for histology-directed tissue analyses highlighted inflammatory protein markers at the early time points after injury with diminished expression as burn wounds progressed into the proliferative phase. The datasets show the usefulness of MALDI MS and imaging mass spectrometry as discovery approaches to identify and map the cutaneous molecular sequence that is activated in response to the unique systemic inflammatory response following burn trauma. This information has the potential to define the unique factors that predispose human burn victims to disfiguring hypertrophic scar formation., (© 2016 by the Wound Healing Society.)

A novel approach for the rapid discrimination of bergamot essential oil from other citrus fruits oils is presented. The method was developed using paper spray mass spectrometry (PS-MS) allowing for a rapid molecular profiling coupled with a statistic tool for a precise and reliable discrimination between the bergamot complex matrix and other similar matrices, commonly used for its reconstitution. Ambient mass spectrometry possesses the ability to record mass spectra of ordinary samples, in their native environment, without sample preparation or pre-separation by creating ions outside the instrument. The present study reports a PS-MS method for the determination of oxygen heterocyclic compounds such as furocoumarins, psoralens and flavonoids present in the non-volatile fraction of citrus fruits essential oils followed by chemometric analysis. The volatile fraction of Bergamot is one of the most known and fashionable natural products, which found applications in flavoring industry as ingredient in beverages and flavored foodstuff. The development of the presented method employed bergamot, sweet orange, orange, cedar, grapefruit and mandarin essential oils. PS-MS measurements were carried out in full scan mode for a total run time of 2 min. The capability of PS-MS profiling to act as marker for the classification of bergamot essential oils was evaluated by using multivariate statistical analysis. Two pattern recognition techniques, linear discriminant analysis and soft independent modeling of class analogy, were applied to MS data. The cross-validation procedure has shown excellent results in terms of the prediction ability because both models have correctly classified all samples for each category. Copyright © 2016 John Wiley & Sons, Ltd., (Copyright © 2016 John Wiley & Sons, Ltd.)

A simple and fast method based on paper spray mass spectrometry for the determination of caffeine in commercial beverages and drugs has been developed; the analyses were carried out in MRM mode, monitoring the transitions m/z 195 → m/z 138 for caffeine and m/z 198 → m/z 140 for the labeled internal standard. To verify the reliability of the proposed approach, a spiked sample (soda drink and paracetamol tablet) with a known amount of caffeine has been prepared and analyzed by PS-MS, providing accuracy values about 100 %; the LOQ and LOD values were calculated at 1.2 and 1.6 μg/mL, respectively. Both beverages and drugs were also analyzed with the classic analytical method based on LC-UV measurements, showing consistent results between the two approaches, thus confirming the reliability of the developed ambient MS determination. Graphical Abstract The assay of caffeine by paper mass spectrometry.

Herein we present a simple, reproducible and versatile approach for in situ protein digestion and identification on formalin-fixed and paraffin-embedded (FFPE) tissues. This adaptation is based on the use of an enzyme delivery platform (hydrogel discs) that can be positioned on the surface of a tissue section. By simultaneous deposition of multiple hydrogels over select regions of interest within the same tissue section, multiple peptide extracts can be obtained from discrete histological areas. After enzymatic digestion, the hydrogel extracts are submitted for LC-MS/MS analysis followed by database inquiry for protein identification. Further, imaging mass spectrometry (IMS) is used to reveal the spatial distribution of the identified peptides within a serial tissue section. Optimization was achieved using cutaneous tissue from surgically excised pressure ulcers that were subdivided into two prime regions of interest: the wound bed and the adjacent dermal area. The robust display of tryptic peptides within these spectral analyses of histologically defined tissue regions suggests that LC-MS/MS in combination with IMS can serve as useful exploratory tools., (© 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

A method for the determination and quantification of ketosteroid hormones in meat by mass spectrometry, based on the derivatization of the carbonyl moiety of steroids by O-methylhydroxylamine, is presented. The quantitative assay is performed by means of multiple-reaction-monitoring (MRM) scan mode and using the corresponding labelled species, obtained by reaction with d 3-methoxylamine, as internal standard. The accuracy of the method was established by evaluating artificially spiked samples, obtaining values in the range 90-110%. Recovery tests were performed on blank matrix samples spiked with non-natural steroids including trenbolone and melengestrol acetate. The latter experiment revealed that the yield of the extraction processes was approximately 60%. Good values of LOQ and LOD were achieved, making this method competitive with current hormone assay methods.

The present study was designed to demonstrate the potential of an optimized histology directed protein identification combined with imaging mass spectrometry technology to reveal and identify molecules associated to ectopic calcification in human tissue. As a proof of concept, mineralized and non-mineralized areas were compared within the same dermal tissue obtained from a patient affected by Pseudoxanthoma elasticum, a genetic disorder characterized by calcification only at specific sites of soft connective tissues. Data have been technically validated on a contralateral dermal tissue from the same subject and compared with those from control healthy skin. Results demonstrate that this approach 1) significantly reduces the effects generated by techniques that, disrupting tissue organization, blend data from affected and unaffected areas; 2) demonstrates that, abolishing differences due to inter-individual variability, mineralized and non-mineralized areas within the same sample have a specific protein profile and have a different distribution of molecules; and 3) avoiding the bias of focusing on already known molecules, reveals a number of proteins that have been never related to the disease nor to the calcification process, thus paving the way for the selection of new molecules to be validated as pathogenic or as potential pharmacological targets., (Copyright © 2015. Published by Elsevier Inc.)

Imaging mass spectrometry (IMS) was employed for the analysis of frozen skin biopsies to investigate the differences between stage IV pressure ulcers that remain stalled, stagnant, and unhealed versus those exhibiting clinical and histological signs of improvement. Our data reveal a rich diversity of proteins that are dynamically modulated, and we selectively highlight a family of calcium binding proteins (S-100 molecules) including calcyclin (S100-A6), calgranulins A (S100-A8) and B (S100-A9), and calgizzarin (S100-A11). IMS allowed us to target three discrete regions of interest: the wound bed, adjacent dermis, and hypertrophic epidermis. Plots derived using unsupervised principal component analysis of the global protein signatures within these three spatial niches indicate that these data from wound signatures have potential as a prognostic tool since they appear to delineate wounds that are favorably responding to therapeutic interventions versus those that remain stagnant or intractable in their healing status. Our discovery-based approach with IMS augments current knowledge of the molecular signatures within pressure ulcers while providing a rationale for a focused examination of the role of calcium modulators within the context of impaired wound healing.

This study presents on-tissue proteolytic digestion using a microwave irradiation and peptide extraction method for in situ analysis of proteins from spatially defined regions of a tissue section. The methodology utilizes hydrogel discs (1 mm diameter) embedded with trypsin solution. The enzyme-laced hydrogel discs are applied to a tissue section, directing enzymatic digestion to a spatially confined area of the tissue. By applying microwave radiation, protein digestion is performed in 2 min on-tissue, and the extracted peptides are then analyzed by matrix assisted laser desorption/ionization mass spectrometry (MALDI MS) and liquid chromatography tandem mass spectrometry (LC-MS/MS). The reliability and reproducibility of the microwave assisted hydrogel mediated on-tissue digestion is demonstrated by the comparison with other on-tissue digestion strategies, including comparisons with conventional heating and in-solution digestion. LC-MS/MS data were evaluated considering the number of identified proteins as well as the number of protein groups and distinct peptides. The results of this study demonstrate that rapid and reliable protein digestion can be performed on a single thin tissue section while preserving the relationship between the molecular information obtained and the tissue architecture, and the resulting peptides can be extracted in sufficient abundance to permit analysis using LC-MS/MS. This approach will be most useful for samples that have limited availability but are needed for multiple analyses, especially for the correlation of proteomics data with histology and immunohistochemistry.

Introduction: Vegetables contain a variety of phytochemicals that have the ability to modify enzymatic and chemical reactions, and therefore may have a positive influence on human health. In particular kaempferol is known to possess anti-carcinogenic activity., Objective: The purpose of this work was to determine the structure of glycosylated kaempferol derivatives, acylated with malonic acid on the sugar portion., Methods: A methanolic extract of the leaves of Allium porrum L. was submitted to fractionation procedures through semi-preparative HPLC/UV-MS techniques. The collected fractions were evaluated by accurate tandem mass spectrometry experiments using an electrospray ionisation (ESI) quadrupole time-of-flight instrument. Isolated compounds were hydrolysed in order to obtain information on the ester moieties., Results: The structures of five compounds not previously reported in leek were determined. The molecules are mono-hexose, di-hexose and coumaroyl, feruloyl and caffeoyl acylated di-hexose derivatives of kaempferol. The common characteristic of the structures relies on the presence of the malonyl moiety on the primary alcoholic function of the sugar immediately linked to the aglycone. Accurate tandem MS experiments and basic hydrolysis treatments revealed a sequence of the acylated glycosidic moieties., Conclusion: A set of secondary metabolites of the aerial part of Allium porrum L. (leek) was identified and characterised by ESI/MS(2) . Knowledge of the presence of these first-reported compounds in leek could provide the means for fully understanding of the metabolism of this plant in relation to the biosynthesis of the phenolics., (Copyright © 2013 John Wiley & Sons, Ltd.)

Flavanones, a class of flavonoids present in large amounts in fruits and vegetables, have been assayed by LC-MS/MS and derivatization chemistry using d0/d3-labelled derivatized internal standards obtained by simple reaction procedures which involves d0/d3 methoxyamine. The assay method considers 13 flavanones including aglycones, neohesperidosides, rutinosides and 3-hydroxy-3-methyl glutaryl derivatives. The strengths of the method consist in a relative short analysis time (16 min) and good repeatability and reproducibility values which are in most cases under 10% (RSD%). The accuracy values range from 95.4% to 111.3% whilst the LOQ values ranges from 0.05 to 0.29 mg/L depending on the analyte., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

A high-throughput mass spectrometric method is presented for the simultaneous detection of Sudan I, II, III, IV and Para-Red azo-dyes in foodstuff. The method is based on the use of paper spray mass spectrometry (MS) and deuterium-labeled internal standards on a triple-quadrupole instrument. A detailed assay of each azo-dye was performed by the isotope dilution method, through the precursor ion scan approach, using deuterium-labeled internal standards. The gas-phase breakdown pattern of each labeled and unlabeled analogue displays the naphthoic moiety as a common fragment. Sudan dyes can be determined above the threshold of 1 ppm. Paper spray allows for a wide range of analytes and samples to be investigated by MS in the open air and without sample preparation and bypassing chromatography., (Copyright © 2013 John Wiley & Sons, Ltd.)

Clementine is a citrus fruit that has found a peculiar habitat in specific areas of Calabria, a region located in southern Italy. Due to its peculiar characteristics it was recently awarded with protected geographical indications (PGI) from the European Union. In this work, stepwise linear discriminant analysis (S-LDA), soft independent modeling of class analogy (SIMCA), and partial least-squares discriminant analysis (PLS-DA) were used to build chemometric models able to protect PGI Clementine from others of different origin. Accordingly, the concentration of 24-26 elements was determined in peel and juice samples, respectively, obtained from Calabrian PGI clementine and from fruits cultivated in Algeria, Tunisia, and Spain. A cross-validation procedure has shown very satisfactory values of prediction ability for both S-LDA (96.6% for juice samples and 100% for peel samples) and SIMCA (100% for both peel and juice samples). PLS-DA models also yielded satisfactory results.

The pathogenesis of impaired healing within pressure ulcers remains poorly characterized and rarely examined. We describe the results of a pilot study that applies matrix-assisted laser desorption/ionization imaging mass spectrometry technology for direct tissue analysis to evaluate proteomic signatures ranging from 2 to 20 kDa and phospholipids from 300-1,200 Da in focal regions within the wound microenvironment. Distinguishing molecular differences were apparent between upper vs. lower regions of ulcers and further contrasted against adjacent dermis and epidermal margins using protein profiles, ion density maps, principal component analysis and significant analysis of microarrays. Several proteins previously uncharacterized in pressure ulcers, the α-defensins (human neutrophil peptide [HNP]-1, -2, -3), are potential markers indicating whether the wound status is improving or being prolonged in a deleterious, chronic state. Thymosin β4 appears to be a favorable protein marker showing higher relative levels in adjacent dermis and maturing areas of the wound bed. Lipidomic examination revealed the presence of major lipid classes: glycerophosphocholines, glycerophosphoglycerols, glycerophosphoinositols, and triacylglycerols. Our pilot data examined from either a global perspective using proteomic or lipidomic signatures or as individual distributions reveal that imaging mass spectrometry technology can be effectively used for discovery and spatial mapping of molecular disturbances within the microenvironment of chronic wounds., (2011 by the Wound Healing Society.)

Investigations into the human skin proteome by classical analytical procedures have not addressed spatial molecular distributions in whole-skin biopsies. The aim of this study was to develop methods for the detection of protein signatures and their spatial disposition in human skin using advanced molecular imaging technology based on mass spectrometry technologies. This technology allows for the generation of protein images at specific molecular weight values without the use of antibody while maintaining tissue architecture. Two experimental approaches were employed: MALDI-MS profiling, where mass spectra were taken from discrete locations based on histology, and MALDI-IMS imaging, where complete molecular images were obtained at various MW values. In addition, proteins were identified by in situ tryptic digestion, sequence analysis of the fragment peptides and protein database searching. We have detected patterns of protein differences that exist between epidermis and dermis as well as subtle regional differences between the papillary and reticular dermis. Furthermore, we were able to detect proteins that are constitutive features of human skin as well as those associated with unique markers of individual variability., (© 2011 John Wiley & Sons A/S.)

The 3-hydroxy-3-methylglutaryl neohesperidosides of hesperetin (brutieridin, 1) and naringenin (melitidin, 2) were isolated and detected from the fruits of bergamot (Citrus bergamia). The structures of these compounds were determined by spectroscopic and chemical methods.

A set of minor constituents of Olea europaea L. leaves have been identified and characterized by electrospray ionization tandem mass spectrometry (ESI-MS/MS) and high-resolution measurements (HRMS). Most of them are modified hydroxytyrosol species conjugated to a hexose unit. When possible, the structures of the new phenolic compounds present in Olea europaea L. have been confirmed by matching their MS/MS spectra with those of authentic standards isolated from other plants of the oleaceae family. The knowledge of the presence of new phenolic species in Olea europaea L. could provide tools for a full understanding of the secondary metabolism of this plant in relation to the biosynthesis of the phenolic species., (Copyright 2007 John Wiley & Sons, Ltd.)