An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue

MALDI MS imaging (MSI) is a powerful analytical tool for spatial peptide detection in heterogeneous tissues. Proper sample preparation is crucial to achieve high quality, reproducible measurements. Here we developed an optimized protocol for spatially resolved proteolytic peptide detection with MALDI time-of-flight MSI of fresh frozen prostate tissue sections. The parameters tested included four different tissue washes, four methods of protein denaturation, four methods of trypsin digestion (different trypsin densities, sprayers, and incubation times), and five matrix deposition methods (different sprayers, settings, and matrix concentrations). Evaluation criteria were the number of detected and excluded peaks, percentage of high mass peaks, signal-to-noise ratio, spatial localization, and average intensities of identified peptides, all of which were integrated into a weighted quality evaluation scoring system. Based on these scores, the optimized protocol included an ice-cold EtOH+H₂O wash, a 5 min heating step at 95°C, tryptic digestion incubated for 17h at 37°C and CHCA matrix deposited at a final amount of 1.8 μg/mm². Including a heat-induced protein denaturation step after tissue wash is a new methodological approach that could be useful also for other tissue types. This optimized protocol for spatial peptide detection using MALDI MSI facilitates future biomarker discovery in prostate cancer and may be useful in studies of other tissue types.     

Modulation of the central carbon metabolism of Corynebacterium glutamicum improves malonyl-CoA availability and increases plant polyphenol synthesis

In recent years microorganisms have been engineered towards synthesizing interesting plant polyphenols such as flavonoids and stilbenes from glucose. Currently, the low endogenous supply of malonyl-CoA, indispensable for plant polyphenol synthesis, impedes high product titers. Usually, limited malonyl-CoA availability during plant polyphenol production is avoided by supplementing fatty acid synthesis-inhibiting antibiotics such as cerulenin, which are known to increase the intracellular malonyl-CoA pool as a side effect. Motivated by the goal of microbial polyphenol synthesis being independent of such expensive additives, we used rational metabolic engineering approaches to modulate regulation of fatty acid synthesis and flux into the tricarboxylic acid cycle (TCA cycle) in Corynebacterium glutamicum strains capable of flavonoid and stilbene synthesis. Initial experiments showed that sole overexpression of genes coding for the native malonyl-CoA-forming acetyl-CoA carboxylase is not sufficient for increasing polyphenol production in C. glutamicum. Hence, the intracellular acetyl-CoA availability was also increased by reducing the flux into the TCA cycle through reduction of citrate synthase activity. In defined cultivation medium, the constructed C. glutamicum strains accumulated 24 mg·L ⁻¹ (0.088 mM) naringenin or 112 mg·L ⁻¹ (0.49 mM) resveratrol from glucose without supplementation of phenylpropanoid precursor molecules or any inhibitors of fatty acid synthesis.     

Implementation of a Surgical Safety Checklist: Interventions to Optimize the Process and Hints to Increase Compliance

BackgroundA surgical safety checklist (SSC) was implemented and routinely evaluated within our hospital. The purpose of this study was to analyze compliance, knowledge of and satisfaction with the SSC to determine further improvements.MethodsThe implementation of the SSC was observed in a pilot unit. After roll-out into each operating theater, compliance with the SSC was routinely measured. To assess subjective and objective knowledge, as well as satisfaction with the SSC implementation, an online survey (N = 891) was performed.ResultsDuring two test runs in a piloting unit, 305 operations were observed, 175 in test run 1 and 130 in test run 2. The SSC was used in 77.1% of all operations in test run 1 and in 99.2% in test run 2. Within used SSCs, completion rates were 36.3% in test run 1 and 1.6% in test run 2. After roll-out, three unannounced audits took place and showed that the SSC was used in 95.3%, 91.9% and 89.9%. Within used SSCs, completion rates decreased from 81.7% to 60.6% and 53.2%. In 2014, 164 (18.4%) operating team members responded to the online survey, 160 of which were included in the analysis. 146 (91.3%) consultants and nursing staff reported to use the SSC regularly in daily routine.ConclusionThese data show that the implementation of new tools such as the adapted WHO SSC needs constant supervision and instruction until it becomes self-evident and accepted. Further efforts, consisting mainly of hands-on leadership and training are necessary.     

Targeting of anti-citrullinated protein/peptide antibodies in rheumatoid arthritis using peptides mimicking endogenously citrullinated fibrinogen antigens

IntroductionWe have previously identified endogenously citrullinated peptides derived from fibrinogen in rheumatoid arthritis (RA) synovial tissues. In this study, we have investigated the auto-antigenicity of four of those citrullinated peptides, and explored their feasibility to target anti-citrullinated protein/peptide antibodies (ACPA).MethodsThe autoantigenic potential of the fibrinogen peptides was investigated by screening 927 serum samples from the Epidemiological Investigation of RA (EIRA) cohort on a peptide microarray based on the ImmunoCAP ISAC® system. In order to assay for ACPA blocking, two independent pools of purified ACPA were incubated with the respective targeting peptide prior to binding to cyclic citrullinated peptide (CCP)2 using the CCPlus® ELISA kit.ResultsTwo peptides derived from the fibrinogen α chain, Arg573Cit (563-583) and Arg591Cit (580-600), referred to as Cit573 and Cit591, and two peptides from the fibrinogen β chain, Arg72Cit (62-81) and Arg74Cit (62-81) (Cit72 and Cit74), displayed 65 %, 15 %, 35 %, and 53 % of immune reactivity among CCP2-positive RA sera, respectively. In CCP2-negative RA sera, a positive reactivity was detected in 5 % (Cit573), 6 % (Cit591), 8 % (Cit72), and 4 % (Cit74). In the competition assay, Cit573 and Cit591 peptides reduced ACPA binding to CCP2 by a maximum of 84 % and 63 % respectively. An additive effect was observed when these peptides were combined. In contrast, Cit74 and Cit72 were less effective. Cyclization of the peptide structure containing Cit573 significantly increased the blocking efficiency.ConclusionsHere we demonstrate extensive autoantibody reactivity against in vivo citrullinated fibrinogen epitopes, and further show the potential use of these peptides for antagonizing ACPA.     

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

HLA class I molecules reflect the health state of cells to cytotoxic T cells by presenting a repertoire of endogenously derived peptides. However, the extent to which the proteome shapes the peptidome is still largely unknown. Here we present a high-throughput mass-spectrometry-based workflow that allows stringent and accurate identification of thousands of such peptides and direct determination of binding motifs. Applying the workflow to seven cancer cell lines and primary cells, yielded more than 22,000 unique HLA peptides across different allelic binding specificities. By computing a score representing the HLA-I sampling density, we show a strong link between protein abundance and HLA-presentation (p < 0.0001). When analyzing overpresented proteins – those with at least fivefold higher density score than expected for their abundance – we noticed that they are degraded almost 3 h faster than similar but nonpresented proteins (top 20% abundance class; median half-life 20.8h versus 23.6h, p < 0.0001). This validates protein degradation as an important factor for HLA presentation. Ribosomal, mitochondrial respiratory chain, and nucleosomal proteins are particularly well presented. Taking a set of proteins associated with cancer, we compared the predicted immunogenicity of previously validated T-cell epitopes with other peptides from these proteins in our data set. The validated epitopes indeed tend to have higher immunogenic scores than the other detected HLA peptides. Remarkably, we identified five mutated peptides from a human colon cancer cell line, which have very recently been predicted to be HLA-I binders. Altogether, we demonstrate the usefulness of combining MS-analysis with immunogenesis prediction for identifying, ranking, and selecting peptides for therapeutic use.The highly polymorphic Human Leukocyte Antigen class I (HLA-I)¹ genes are encoded by three loci (HLA-A, B, and C) in a gene-rich region on chromosome 6. They produce up to six unique cell surface receptors that bind and present the so-called HLA class I peptidome, which consists of peptides derived from proteolysis of intracellular proteins. Their function is to reflect the health state of the body''s cells to CD8+ cytotoxic T cells. During thymic maturation T cells that react to self-peptides are eliminated (1), leaving T cells with the capability to recognize peptides from viruses and bacteria. This recognition is interpreted as a danger signal, leading to removal of infected cells. Transformed, preneoplastic and cancer cells also tend to display atypical self-peptides from mutated or excessively expressed self-proteins, known as tumor associated antigens (TAAs). Although HLA-I molecules are indispensable in prevention of disease, they also pose a substantial health problem by causing allergies (2), life-threatening autoimmune diseases (3), and the often fatal rejection of donor organs because of recognition of both major and minor histocompatibility antigens (4).Finding the rules for peptide generation and selection is regarded as the most important open issue in the field of HLA-I biology by leading experts (5). Although the antigen presentation pathway is well characterized, it is still unclear how basic properties such as protein abundance, turnover, and subcellular localization influence and shape the HLA-I presented peptidome (6–10). One expectation is that protein abundance should correlate with presentation (11), but previous studies have reported conflicting and contradicting results that mostly argue against a strong link (6, 7, 10, 12, 13). It is also not fully understood why only some HLA-sampled self-peptides from cancer antigens spontaneously activate T cells, whereas others do not.The majority of HLA-I peptides are derived from proteasomal degradation (5). Although the proteasome generates an excess of peptides, only some have the required sequence motifs for HLA binding, resulting in a selective sampling of available peptides (14). The presented peptides are typically nine amino acids long, but the length can range from eight to 15. The high degree of genetic variance of HLA-I receptors translates into allele-specific peptide-binding motifs defined by anchor positions, which are usually the second and the last positions in a peptide (15). Each cell has around 200,000 cell-surface-expressed HLA complexes, which bind about 10,000 unique peptide sequences (16). The affinity of a peptide toward the presenting HLA molecule does not correlate strongly with its immunogenicity, and neither does the number of presented HLA complexes (17). Instead, the most robust predictor of peptide immunogenicity appears to be the number of potential reactive T-cell clones (17–19).The longer the source protein, the higher the chances it will contain sequences that fit to a certain HLA motif, which would inflate the representation of longer proteins regardless of biological role. Furthermore, some HLA-I peptide sequences can be mapped to multiple proteins, potentially causing a problem in determining the number of observed HLA peptides per protein (13). This illustrates that careful accounting of the potentially and actually presented HLA peptides is important in properly delineating trends in propensity of peptide presentation.In cancer immunotherapy, T cells can be directed against tumors, based on the pattern of cancer associated HLA peptides. Therefore, there is great interest in determining the identity of these immunogenic peptides. Bioinformatic methods that attempt to predict HLA peptides of cancer proteins of interest are easily accessible and most commonly used. They typically score sequences with respect to proteasomal degradation, transport into the ER via the transporter associate with antigen processing (TAP) and binding to different HLA-I alleles (20). However, their precision success is modest (21, 22). The second approach is to directly capture the naturally presented peptides using mass spectrometry; however, this requires the relevant biological sample and sophisticated instruments and workflows, which have become accessible only recently for large-scale work (23–28). Although identification of cancer associated HLA peptides by MS, if performed stringently, establish the in vivo existence of the peptide, it still does not guarantee that it will elicit a potent T-cell response, which is required for further development into therapeutics (29). Therefore, like in the case of in silico predicted peptides, the immunogenicity of the peptides must in any case be tested empirically.We here present a rich and high confidence HLA-I peptidome, established by applying state-of-the-art mass-spectrometric techniques on a collection of seven cell lines. We investigate how abundance affects the propensity of proteins to be presented as measurable HLA peptides and whether or not there are specific protein classes that are overrepresented even independent of abundance. Likewise, we explore how to use in silico immunogenicity tools on the set of identified HLA peptides from cancer-associated proteins, with a view to select vaccine candidates.     

Four-Dimensional Characterization of Thrombosis in a Live-Cell,Shear-Flow Assay: Development and Application to Xenotransplantation

Background

Porcine xenografts are a promising source of scarce transplantable organs, but stimulate intense thrombosis of human blood despite targeted genetic and pharmacologic interventions. Current experimental models do not enable study of the blood/endothelial interface to investigate adhesive interactions and thrombosis at the cellular level under physiologic conditions. The purpose of this study was to develop and validate a live-cell, shear-flow based thrombosis assay relevant to general thrombosis research, and demonstrate its potential in xenotransplantation applications.

Methodology/Principal Findings

Confluent wild-type (WT, n = 48) and Gal transferase knock-out (GalTKO, which resist hyperacute rejection; n = 11) porcine endothelia were cultured in microfluidic channels. To mimic microcirculatory flow, channels were perfused at 5 dynes/cm² and 37°C with human blood stained to fluorescently label platelets. Serial fluorescent imaging visualized percent surface area coverage (SA, for adhesion of labeled cells) and total fluorescence (a metric of clot volume). Aggregation was calculated by the fluorescence/SA ratio (FR). WT endothelia stimulated diffuse platelet adhesion (SA 65 ± 2%) and aggregation (FR 120 ± 1 a.u.), indicating high-grade thrombosis consistent with the rapid platelet activation and consumption seen in whole-organ lung xenotransplantation models. Experiments with antibody blockade of platelet aggregation, and perfusion of syngeneic and allo-incompatible endothelium was used to verify the biologic specificity and validity of the assay. Finally, with GalTKO endothelia thrombus volume decreased by 60%, due primarily to a 58% reduction in adhesion (P < 0.0001 each); importantly, aggregation was only marginally affected (11% reduction, P < 0.0001).

Conclusions/Significance

This novel, high-throughput assay enabled dynamic modeling of whole-blood thrombosis on intact endothelium under physiologic conditions, and allowed mechanistic characterization of endothelial and platelet interactions. Applied to xenogeneic thrombosis, it enables future studies regarding the effect of modifying the porcine genotype on sheer-stress-dependent events that characterize xenograft injury. This in-vitro platform is likely to prove broadly useful to study thrombosis and endothelial interactions under dynamic physiologic conditions.