Molecular Alterations in Pediatric Sarcomas: Potential Targets for Immunotherapy

Purpose/results/discussion. Recurrent chromosomal translocations are common features of many human malignancies. While such translocations often serve as diagnostic markers, molecular analysis of these breakpoint regions and the characterization of the affected genes is leading to a greater understanding of the causal role such translocations play in malignant transformation. A common theme that is emerging from the study of tumor-associated translocations is the generation of chimeric genes that, when expressed, frequently retain many of the functional properties of the wild-type genes from which they originated. Sarcomas, in particular, harbor chimeric genes that are often derived from transcription factors, suggesting that the resulting chimeric transcription factors contribute to tumorigenesis. The tumor-specific expression of the fusion proteins make them likely candidates for tumor-associated antigens (TAA) and are thus of interest in the development of new therapies. The focus of this review will be on the translocation events associated with Ewing's sarcomas/PNETs (ES), alveolar rhabdomyosarcoma (ARMS), malignant melanoma of soft parts (MMSP) (clear cell sarcoma), desmoplastic small round cell tumor (DSRCT), synovial sarcoma (SS), and liposarcoma (LS), and the potential for targeting the resulting chimeric proteins in novel immunotherapies

A phase I study of PankoMab-GEX, a humanised glyco-optimised monoclonal antibody to a novel tumour-specific MUC1 glycopeptide epitope in patients with advanced carcinomas

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Shared pooled mobility: expert review from nine disciplines and implications for an emerging transdisciplinary research agenda

Shared pooled mobility has been hailed as a sustainable mobility solution that uses digital innovation to efficiently bundle rides. Multiple disciplines have started investigating and analyzing shared pooled mobility systems. However, there is a lack of cross-community communication making it hard to build upon knowledge from other fields or know which open questions may be of interest to other fields. Here, we identify and review 9 perspectives: transdisciplinary social sciences, social physics, transport simulations, urban and energy economics, psychology, climate change solutions, and the Global South research and provide a common terminology. We identify more than 25 000 papers, with more than 100 fold variation in terms of literature count between research perspectives. Our review demonstrates the intellectual attractivity of this as a novel perceived mode of transportation, but also highlights that real world economics may limit its viability, if not supported with concordant incentives and regulation. We then sketch out cross-disciplinary open questions centered around (1) optimal configuration of ride-pooling systems, (2) empirical studies, and (3) market drivers and implications for the economics of ride-pooling. We call for researchers of different disciplines to actively exchange results and views to advance a transdisciplinary research agenda

Modification of EGF-Like Module 1 of Thrombospondin-1, an Animal Extracellular Protein, by O-Linked N-Acetylglucosamine

Thrombospondin-1 (TSP-1) is known to be subject to three unusual carbohydrate modifications: C-mannosylation, O-fucosylation, and O-glucosylation. We now describe a fourth: O-β-N-acetylglucosaminylation. Previously, O-β-N-acetylglucosamine (O-β-GlcNAc) was found on a threonine in the loop between the fifth and sixth cysteines of the 20th epidermal growth factor (EGF)-like module of Drosophila Notch. A BLAST search based on the Drosophila Notch loop sequence identified a number of human EGF-like modules that contain a similar sequence, including EGF-like module 1 of TSP-1 and its homolog, TSP-2. TSP-1, which has a potentially modifiable serine in the loop, reacted in immuno-blots with the CTD110.6 anti-O-GlcNAc antibody. Antibody reactivity was diminished by treatment of TSP-1 with β-N-acetylhexosaminidase. TSP-2, which lacks a potentially modifiable serine/threonine in the loop, did not react with CTD110.6. Analysis of tandem modules of TSP-1 localized reactivity of CTD110.6 to EGF-like module 1. Top-down mass spectrometric analysis of EGF-like module 1 demonstrated the expected modifications with glucose (+162 Da) and xylose (+132 Da) separately from modification with N-acetyl hexosamine (+203 Da). Mass spectrometric sequence analysis localized the +203-Da modification to Ser580 in the sequence 575CPPGYSGNGIQC586. These results demonstrate that O-β-N-acetylglucosaminylation can occur on secreted extracellular matrix proteins as well as on cell surface proteins

EEMlab: A graphical user-friendly interface for fluorimetry experiments based on the drEEM toolbox

[EN] Fluorescence has been widely employed for the characterization of organic matter. In particular, excitation emission matrixes (EEM) provide important qualitative information on its composition. However, the application of this technique is limited by the mathematical complexity involved, which requires the use of PARAFAC for deconvolution of the EEM in their components. To overcome the numerical problem specific MATLAB toolboxes for the PARAFAC deconvolution have been implemented (e.g. drEEM). This toolbox is widely used by the scientific community but its intrinsic complexity in terms of programming knowledge makes it difficult to use. In this regard and in order to facilitate the first approximation to the PARAFAC programming problem, this paper describes and offers to the community the EEMlab software application: a graphical user-firendly interface for fluorimetry experiments based on the drEEM toolbox. The interface is developed in order to facilitate not only the intuitive use of the drEEM (no previous MATLAB knowledge is needed) but also to automate many repetitive tasks (as the data load or the modeling loop) or even to manage the different formats of files being produced by all the devices involved in the process. In order to validate the EEMlab, the same experiment documented by the drEEM is reproduced. In addition, the EEMlab is tested again with conducting a new fluorimetry experiment and the results are presented at the end of the paper. Finally to appoint a reference to the public web site pabmitor.webs.upv.es/eemlab in where all the components of the EEMlab GUI (software, tutorial and datasets) are publicly available to the readers.The authors want to thank the financial support of the Generalitat Valenciana, Conselleria d'Educacio, Cultura i Esport (Spain) [GV/2015/074]. The authors want to thank the financial support of Ministerio de Educacion y Ciencia (Spain)(CTQ2015-69832-C4-4-R). Sara Garcia-Ballesteros would like to thank Ministerio de Economia y Competitividad (Spain) for her fellowship (BES-2013-066201). The authors want to thank Dr. F.S. García Einschlag who has independently tested the EEMlab and helped the authors to improve and validate the final version of the application.Micó Tormos, P.; García-Ballesteros, S.; Mora Carbonell, M.; Vicente Candela, R.; Amat Payá, AM.; Arqués Sanz, A. (2019). EEMlab: A graphical user-friendly interface for fluorimetry experiments based on the drEEM toolbox. Chemometrics and Intelligent Laboratory Systems. 188:6-13. https://doi.org/10.1016/j.chemolab.2019.03.001S61318

Binding patterns of DTR-specific antibodies reveal a glycosylation-conditioned tumor-specific epitope of the epithelial mucin (MUC1)

Glycosylation determines essential biological functions of epithelial mucins in health and disease. We report on the influence of glycosylation of the immunodominant DTR motif of MUC1 on its antigenicity. Sets of novel glycopeptides were synthesized that enabled us to examine sole and combined effects of peptide length (number of repeats) and O-glycosylation with GalNAc at the DTR motif on the binding patterns of 22 monoclonal antibodies recognizing this motif. In case of unglycosylated peptides almost all antibodies bound better to multiple MUC1 tandem repeats. Glycosylation at the DTR led to enhanced binding in 11 cases, whereas 10 antibodies were not influenced in binding, and one was inhibited. In nine of the former cases both length and DTR glycosylation were additive in their influence on antibody binding, suggesting that both effects are different. Improved binding to the glycosylated DTR motif was exclusively found with antibodies generated against tumor-derived MUC1. Based on these data a tumor-specific MUC1 epitope is defined comprising the ...PDTRP... sequence in a particular conformation essentially determined by O-glycosylation at its threonine with either GalNAcα1 or a related short glycan. The results can find application in the field of MUC1-based immunotherapy

Localization of O-glycosylation sites on glycopeptide fragments from lactation-associated MUC1. All putative sites within the tandem repeat are glycosylation targets in vivo

Since there is no consensus sequence directing the initial GalNAc incorporation into mucin peptides, O-glycosylation sites are not reliably predictable. We have developed a mass spectrometric sequencing strategy that allows the identification of in vivo O-glycosylation sites on mucin-derived glycopeptides. Lactation-associated MUC1 was isolated from human milk and partially deglycosylated by trifluoromethanesulfonic acid to the level of core GalNAc residues. The product was fragmented by the Arg-C-specific endopeptidase clostripain to yield tandem repeat icosapeptides starting with the PAP motif. PAP20 glycopeptides were subjected to sequencing by post-source decay matrix-assisted laser desorption ionization mass spectrometry or by solid phase Edman degradation to localize the glycosylation sites. The masses of C- or N-terminal fragments registered for the mono- to pentasubstituted PAP20 indicated that GalNAc was linked to the peptide at Ser5,Thr6 (GSTA) and Thr14 (VTSA) but contrary to previous in vitro glycosylation studies also at Thr19 and Ser15 located within the PDTR or VTSA motifs, respectively. Quantitative data from solid phase Edman sequencing revealed no preferential glycosylation of the threonines. These discrepancies between in vivo and in vitro glycosylation patterns may be explained by assuming that O-glycosylation of adjacent peptide positions is a dynamically regulated process that depends on changes of the substrate qualities induced by glycosylation at vicinal sites