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Adoptive T cell therapy using patient T cells redirected to recognize tumor-specific antigens by expressing genetically engineered high-affinity T-cell receptors (TCRs) has therapeutic potential for melanoma and other solid tumors. Clinical trials implementing genetically modified TCRs in melanoma patients have raised concerns regarding off-target toxicities resulting in lethal destruction of healthy tissue, highlighting the urgency of assessing which off-target peptides can be recognized by a TCR. As a model system we used the clinically efficacious NY-ESO-1-specific TCR C259, which recognizes the peptide epitope SLLMWITQC presented by HLA-A*02:01. We investigated which amino acids at each position enable a TCR interaction by sequentially replacing every amino acid position outside of anchor positions 2 and 9 with all 19 possible alternative amino acids, resulting in 134 peptides (133 altered peptides plus epitope peptide). Each peptide was individually evaluated using three different in vitro assays: binding of the NY-ESOc259 TCR to the peptide, peptide-dependent activation of TCR-expressing cells, and killing of peptide-presenting target cells. To represent the TCR recognition kernel, we defined Position Weight Matrices (PWMs) for each assay by assigning normalized measurements to each of the 20 amino acids in each position. To predict potential off-target peptides, we applied a novel algorithm projecting the PWM-defined kernel into the human proteome, scoring NY-ESOc259 TCR recognition of 336,921 predicted human HLA-A*02:01 binding 9-mer peptides. Of the 12 peptides with high predicted score, we confirmed 7 (including NY-ESO-1 antigen SLLMWITQC) strongly activate human primary NY-ESOc259-expressing T cells. These off-target peptides include peptides with up to 7 amino acid changes (of 9 possible), which could not be predicted using the recognition motif as determined by alanine scans. Thus, this replacement scan assay determines the "TCR fingerprint" and, when coupled with the algorithm applied to the database of human 9-mer peptides binding to HLA-A*02:01, enables the identification of potential off-target antigens and the tissues where they are expressed. This platform enables both screening of multiple TCRs to identify the best candidate for clinical development and identification of TCR-specific cross-reactive peptide recognition and constitutes an improved methodology for the identification of potential off-target peptides presented on MHC class I molecules.

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The (neo-) lacto series glycosphingolipids (nsGSLs) comprise of glycan epitopes that are present as blood group antigens, act as primary receptors for human pathogens and are also increasingly associated with malignant diseases. Beta-1, 3-N-acetyl-glucosaminyl-transferase 5 (B3GNT5) is suggested as the key glycosyltransferase for the biosynthesis of nsGSLs. In this study, we investigated the impact of CRISPR-Cas9 -mediated gene disruption of B3GNT5 (∆B3GNT5) on the expression of glycosphingolipids and N-glycoproteins by utilizing immunostaining and glycomics-based PGC-UHPLC-ESI-QTOF-MS/MS profiling. ∆B3GNT5 cells lost nsGSL expression coinciding with reduction of α2-6 sialylation on N-glycoproteins. In contrast, disruption of B4GALNT1, a glycosyltransferase for ganglio series GSLs did not affect α2-6 sialylation on N-glycoproteins. We further profiled all known α2-6 sialyltransferase-encoding genes and showed that the loss of α2-6 sialylation is due to silencing of ST6GAL1 expression in ∆B3GNT5 cells. These results demonstrate that nsGSLs are part of a complex network affecting N-glycosylation in ovarian cancer cells.

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Block copolymer vesicles can be turned into nanoreactors when a catalyst is encapsulated in these hollow nanostructures. However the membranes of these polymersomes are most often impermeable to small organic molecules, while applications as nanoreactor, as artificial organelles, or as drug-delivery devices require an exchange of substances between the outside and the inside of polymersomes. Here, a simple and versatile method is presented to render polymersomes semipermeable. It does not require complex membrane proteins or pose requirements on the chemical nature of the polymers. Vesicles made from three different amphiphilic block copolymers (α,ω-hydroxy-end-capped poly(2-methyl-2-oxazoline)-block-poly(dimethylsiloxane)-block-poly(2-methyl-2-oxazoline) (PMOXA-b-PDMS-b-PMOXA), α,ω-acrylate-end-capped PMOXA-b-PDMS-b-PMOXA, and poly(ethylene oxide)-block-poly(butadiene) (PEO-b-PB)) were reacted with externally added 2-hydroxy-4'-2-(hydroxyethoxy)-2-methylpropiophenone under UV-irradiation. The photoreactive compound incorporated into the block copolymer membranes independently of their chemical nature or the presence of double bonds. This treatment of polymersomes resulted in substantial increase in permeability for organic compounds while not disturbing the size and the shape of the vesicles. Permeability was assessed by encapsulating horseradish peroxidase into vesicles and measuring the accessibility of substrates to the enzyme. The permeability of photoreacted polymersomes for ABTS, AEC, pyrogallol, and TMB was determined to be between 1.9 and 38.2 nm s(-1). It correlated with the hydrophobicity of the compounds. Moreover, fluorescent dyes were released at higher rates from permeabilized polymersomes compared to unmodified ones. The permeabilized nanoreactors retained their ability to protect encapsulated biocatalysts from degradation by proteases.