A data analysis framework for combining multiple batches increases the power of isobaric proteomics experiments

We present a framework for the analysis of multiplexed mass spectrometry proteomics data that reduces estimation error when combining multiple isobaric batches. Variations in the number and quality of observations have long complicated the analysis of isobaric proteomics data. Here we show that the power to detect statistical associations is substantially improved by utilizing models that directly account for known sources of variation in the number and quality of observations that occur across batches.In a multibatch benchmarking experiment, our open-source software (msTrawler) increases the power to detect changes, especially in the range of less than twofold changes, while simultaneously increasing quantitative proteome coverage by utilizing more low-signal observations. Further analyses of previously published multiplexed datasets of 4 and 23 batches highlight both increased power and the ability to navigate complex missing data patterns without relying on unverifiable imputations or discarding reliable measurements.

Exercise plasma boosts memory and dampens brain inflammation via clusterin

Physical exercise is generally beneficial to all aspects of human and animal health, slowing cognitive ageing and neurodegeneration¹. The cognitive benefits of physical exercise are tied to an increased plasticity and reduced inflammation within the hippocampus^2-4, yet little is known about the factors and mechanisms that mediate these effects. Here we show that 'runner plasma', collected from voluntarily running mice and infused into sedentary mice, reduces baseline neuroinflammatory gene expression and experimentally induced brain inflammation. Plasma proteomic analysis revealed a concerted increase in complement cascade inhibitors including clusterin (CLU). Intravenously injected CLU binds to brain endothelial cells and reduces neuroinflammatory gene expression in a mouse model of acute brain inflammation and a mouse model of Alzheimer's disease. Patients with cognitive impairment who participated in structured exercise for 6 months had higher plasma levels of CLU. These findings demonstrate the existence of anti-inflammatory exercise factors that are transferrable, target the cerebrovasculature and benefit the brain, and are present in humans who engage in exercise.

An Integrated Genomic, Proteomic, and Immunopeptidomic Approach to Discover Treatment-Induced Neoantigens

All nucleated mammalian cells express major histocompatibility complex (MHC) proteins that present peptides on cell surfaces for immune surveillance. These MHC-presented peptides (pMHC) are necessary for directing T-cell responses against cells harboring non-self antigens derived from pathogens or from somatic mutations. Alterations in tumor-specific antigen repertoires — particularly novel MHC presentation of mutation-bearing peptides (neoantigens) — can be potent targets of anti-tumor immune responses. Here we employed an integrated genomic and proteomic antigen discovery strategy aimed at measuring how interferon gamma (IFN-γ) alters antigen presentation, using a human lymphoma cell line, GRANTA-519. IFN-γ treatment resulted in 126 differentially expressed proteins (2% of all quantified proteins), which included components of antigen presentation machinery and interferon signaling pathways, and MHC molecules themselves. In addition, several proteasome subunits were found to be modulated, consistent with previous reports of immunoproteasome induction by IFN-γ exposure. This finding suggests that a modest proteomic response to IFN-γ could create larger alteration to cells’ antigen/epitope repertoires. Accordingly, MHC immunoprecipitation followed by mass spectrometric analysis of eluted peptide repertoires revealed exclusive signatures of IFN-γ induction, with 951 unique peptides reproducibly presented by MHC-I and 582 presented by MHC-II. Furthermore, an additional set of pMHCs including several candidate neoantigens, distinguished control and the IFN-γ samples by their altered relative abundances. Accordingly, we developed a classification system to distinguish peptides which are differentially presented due to altered expression from novel peptides resulting from changes in antigen processing. Taken together, these data demonstrate that IFN-γ can re-shape antigen repertoires by identity and by abundance. Extending this approach to models with greater clinical relevance could help develop strategies by which immunopeptide repertoires are intentionally reshaped to improve endogenous or vaccine-induced anti-tumor immune responses and potentially anti-viral immune responses.

Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice

Performing large-scale plasma proteome profiling is challenging due to limitations imposed by lengthy preparation and instrument time. We present a fully automated multiplexed proteome profiling platform (AutoMP3) using the Hamilton Vantage liquid handling robot capable of preparing hundreds to thousands of samples. To maximize protein depth in single-shot runs, we combined 16-plex Tandem Mass Tags (TMTpro) with high-field asymmetric waveform ion mobility spectrometry (FAIMS Pro) and real-time search (RTS). We quantified over 40 proteins/min/sample, doubling the previously published rates. We applied AutoMP3 to investigate the naked mole-rat plasma proteome both as a function of the circadian cycle and in response to ultraviolet (UV) treatment. In keeping with the lack of synchronized circadian rhythms in naked mole-rats, we find few circadian patterns in plasma proteins over the course of 48 h. Furthermore, we quantify many disparate changes between mice and naked mole-rats at both 48 h and one week after UV exposure. These species differences in plasma protein temporal responses could contribute to the pronounced cancer resistance observed in naked mole-rats. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD022891.

Physiological blood-brain transport is impaired with age by a shift in transcytosis

The vascular interface of the brain, known as the blood-brain barrier (BBB), is understood to maintain brain function in part via its low transcellular permeability^1-3. Yet, recent studies have demonstrated that brain ageing is sensitive to circulatory proteins^4,5. Thus, it is unclear whether permeability to individually injected exogenous tracers-as is standard in BBB studies-fully represents blood-to-brain transport. Here we label hundreds of proteins constituting the mouse blood plasma proteome, and upon their systemic administration, study the BBB with its physiological ligand. We find that plasma proteins readily permeate the healthy brain parenchyma, with transport maintained by BBB-specific transcriptional programmes. Unlike IgG antibody, plasma protein uptake diminishes in the aged brain, driven by an age-related shift in transport from ligand-specific receptor-mediated to non-specific caveolar transcytosis. This age-related shift occurs alongside a specific loss of pericyte coverage. Pharmacological inhibition of the age-upregulated phosphatase ALPL, a predicted negative regulator of transport, enhances brain uptake of therapeutically relevant transferrin, transferrin receptor antibody and plasma. These findings reveal the extent of physiological protein transcytosis to the healthy brain, a mechanism of widespread BBB dysfunction with age and a strategy for enhanced drug delivery.

Abstract B121: An oncogene-linked prodrug strategy in lung cancer

KEAP1-mutant non-small cell lung cancer is a high prevalence indication that responds poorly to conventional chemotherapy owing to constitutive activation of NRF2 and its associated drug metabolism target genes. Using an approach to identify compounds that selectively kill cancer cell lines in a biomarker-driven manner, we identify BRD-K19050021 (K1905), a compound displaying strong toxicity in cells expressing CYP4F11 - a cytochrome p450 family member and NRF2 transcriptional target. Using genome-wide pooled CRISPR screens, we show that CYP4F11 activity is necessary and sufficient for response to K1905, and in acquired resistance models developed from multiple cell lines, we show a minor subpopulation of cells mechanistically converge on suppressed CYP4F11 expression to bypass K1905 response. CYP4F11 converts K1905 from a prodrug into a covalent active metabolite that alkylates several cellular targets, triggering all three canonical arms of the unfolded protein response pathway and culminating in cell death. We propose that CYP4F11 and similar metabolic enzyme activities promoted by oncogenic drivers represent a unique opportunity to restrict prodrug activation within tumors, provided that normal tissue expression of such prodrug-converting enzymes do not diminish therapeutic index.

Citation Format: Aaron Boudreau, Jennifer Roth, James Rong, Niclas Olsson, Chris Mader, Jordan Byran, Jordan Rossen, Li Wang, Kevin Larpenteur, Amy Goodale, Colin Trepicchio, Samantha Bender, Aviad Tsherniak, Aravind Subramanian, Mustafa Kocak, Federica Piccioni, Josh Bittker, Cong Zhu, Frank Li, Nick Eriksson, Daphne Koller, Fiona McAllister, Todd Golub, Jeff Settleman, Ari Firestone, David Stokoe. An oncogene-linked prodrug strategy in lung cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B121. doi:10.1158/1535-7163.TARG-19-B121

Predicting HLA class II antigen presentation through integrated deep learning

Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II molecules would be valuable for vaccine development and cancer immunotherapies. Current computational methods trained on in vitro binding data are limited by insufficient training data and algorithmic constraints. Here we describe MARIA (major histocompatibility complex analysis with recurrent integrated architecture; https://maria.stanford.edu/ ), a multimodal recurrent neural network for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles. In addition to in vitro binding measurements, MARIA is trained on peptide HLA ligand sequences identified by mass spectrometry, expression levels of antigen genes and protease cleavage signatures. Because it leverages these diverse training data and our improved machine learning framework, MARIA (area under the curve = 0.89-0.92) outperformed existing methods in validation datasets. Across independent cancer neoantigen studies, peptides with high MARIA scores are more likely to elicit strong CD4+ T cell responses. MARIA allows identification of immunogenic epitopes in diverse cancers and autoimmune disease.

Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin

Somatic mutations in cancer are a potential source of cancer specific neoantigens. Acute myeloid leukemia (AML) has common recurrent mutations shared between patients in addition to private mutations specific to individuals. We hypothesized that neoantigens derived from recurrent shared mutations would be attractive targets for future immunotherapeutic approaches. Here we sought to study the HLA Class I and II immunopeptidome of thirteen primary AML tumor samples and two AML cell lines (OCI-AML3 and MV4-11) using mass spectrometry to evaluate for endogenous mutation-bearing HLA ligands from common shared AML mutations. We identified two endogenous, mutation-bearing HLA Class I ligands from nucleophosmin (NPM1). The ligands, AVEEVSLRK from two patient samples and C(cys)LAVEEVSL from OCI-AML3, are predicted to bind the common HLA haplotypes, HLA-A*03:01 and HLA-A*02:01 respectively. Since NPM1 is mutated in approximately one-third of patients with AML, the finding of endogenous HLA ligands from mutated NPM1 supports future studies evaluating immunotherapeutic approaches against this shared target, for this subset of patients with AML.

TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets

Although mass spectrometry is well suited to identifying thousands of potential protein post-translational modifications (PTMs), it has historically been biased towards just a few. To measure the entire set of PTMs across diverse proteomes, software must overcome the dual challenges of covering enormous search spaces and distinguishing correct from incorrect spectrum interpretations. Here, we describe TagGraph, a computational tool that overcomes both challenges with an unrestricted string-based search method that is as much as 350-fold faster than existing approaches, and a probabilistic validation model that we optimized for PTM assignments. We applied TagGraph to a published human proteomic dataset of 25 million mass spectra and tripled confident spectrum identifications compared to its original analysis. We identified thousands of modification types on almost 1 million sites in the proteome. We show alternative contexts for highly abundant yet understudied PTMs such as proline hydroxylation, and its unexpected association with cancer mutations. By enabling broad characterization of PTMs, TagGraph informs as to how their functions and regulation intersect.

Multiple Click-Selective tRNA Synthetases Expand Mammalian Cell-Specific Proteomics

Bioorthogonal tools enable cell-type-specific proteomics, a prerequisite to understanding biological processes in multicellular organisms. Here we report two engineered aminoacyl-tRNA synthetases for mammalian bioorthogonal labeling: a tyrosyl ( ScTyr_Y43G) and a phenylalanyl ( MmPhe_T413G) tRNA synthetase that incorporate azide-bearing noncanonical amino acids specifically into the nascent proteomes of host cells. Azide-labeled proteins are chemoselectively tagged via azide-alkyne cycloadditions with fluorophores for imaging or affinity resins for mass spectrometric characterization. Both mutant synthetases label human, hamster, and mouse cell line proteins and selectively activate their azido-bearing amino acids over 10-fold above the canonical. ScTyr_Y43G and MmPhe_T413G label overlapping but distinct proteomes in human cell lines, with broader proteome coverage upon their coexpression. In mice, ScTyr_Y43G and MmPhe_T413G label the melanoma tumor proteome and plasma secretome. This work furnishes new tools for mammalian residue-specific bioorthogonal chemistry, and enables more robust and comprehensive cell-type-specific proteomics in live mammals.

T-Cell Immunopeptidomes Reveal Cell Subtype Surface Markers Derived From Intracellular Proteins

Immunopeptidomes promise novel surface markers as ideal immunotherapy targets, but their characterization by mass spectrometry (MS) remains challenging. Until recently, cell numbers exceeding 10⁹ were needed to survey thousands of HLA ligands. Such limited analytical sensitivity has historically constrained the types of clinical specimens that can be evaluated to cell cultures or bulk tissues. Measuring immunopeptidomes from purified cell subpopulations would be preferable for many applications, particularly those evaluating rare, primary hematopoietic cell lineages. Here, we test the feasibility of immunopeptidome profiling from limited numbers of primary purified human regulatory T cells (T_Reg ), conventional T cells (T_conv ), and activated T cells. The combined T cell immunopeptide dataset reported here contains 13 804 unique HLA ligands derived from 5049 proteins. Of these, more than 700 HLA ligands were derived from 82 proteins that we exclusively identified from T_Reg -enriched cells. This study 1) demonstrates that primary, lineage-enriched T cell subpopulations recovered from single donors are compatible with immunopeptidome analysis; 2) presents new T_Reg -biased ligand candidates; and 3) supports immunopeptidome surveys' value for revealing T cell biology that may not be apparent from expression data alone. Taken together, these findings open up new avenues for targeting T_Reg and abrogating their suppressive functions to treat cancer.

Immuno-proteomic interrogation of antigen presentation during Dengue and Zika infections reveals novel targets for the design of broad acting T-cell vaccines

The recent outbreak of Zika virus (ZIKV) infection across the Americas has raised dire concerns about its potential long-term health effects including its negative impact on neuronal, psychological and motor development in affected individuals. Emerging evidence pointing to Alzheimer’s-like damage to the adult brain further highlights the urgent need for efficacious prophylactic measures. Zika-affected regions are often endemic to the related Dengue virus (DENV). Antibodies against the two viruses are crossreactive and cause antibody-mediated enhancement (ADE) of infection. This confounds the design of traditional vaccines that elicit humoral antibody-mediated responses. T cell vaccines mediated by cytotoxic CD8+ T cells that recognize conserved viral epitopes presented on the major histocompatibility complex (MHC-I) of infected cells are unencumbered by ADE and can supplement or substitute traditional vaccines. In order to identify robust T cell vaccine candidates, we first used an immunoproteomic approach and isolated over 100 novel DENV and ZIKA epitopes presented by infected B lymphocytes in vitro. These viral peptides were not predicted to be epitopes by computational programs typically used for epitope discovery, which discard >95% of all predictions. Focussing on epitopes derived from polyprotein regions strictly conserved between the two viruses, we validated the presentation of these epitopes in primary dendritic cells and assayed their ability to stimulate robust T cell responses in ex vivo ELISpot assays. Together these discoveries let us assay the immunogenic potentials of an unprecedented range of DENV and ZIKV antigens which have the potential to serve as broad acting and effective Zika vaccine candidates.

Antigen presentation profiling reveals T-cell recognition of lymphoma immunoglobulin neoantigens

Presentation of novel antigenic peptides (neoantigens) that distinguish malignant from normal cells by major histocompatibility complexes (MHC) can serve as potent substrates for specific anti-tumor immune responses. We sought to identify mantle cell lymphoma (MCL) neoantigens by taking an integrated genomic and proteomic strategy that interrogates antigen peptides presented by MHC-class I and class II. Peptides bound to MHC were purified via immunoprecipitation followed by identification using mass spectrometry. Mass spectra were searched against patient-specific proteome databases generated by whole exome sequencing and targeted immunoglobulin gene sequencing. This approach was applied to systematically characterize over 36,000 immunopeptides from 17 patients’ tumor specimens. Interestingly, 52 neoantigenic peptides were derived from the lymphoma immunoglobulin (Ig) heavy or light chain variable regions. Although we identified MHC presentation of private germline polymorphic alleles, no mutated peptides were recovered from non-Ig somatically mutated genes. Furthermore, somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC-II. T-cells specific for Ig-derived neoantigens were found in two patients. Following ex vivo activation and expansion, the T-cells were remarkably able to mediate killing of autologous lymphoma cells. These results demonstrate that combining MHC isolation, peptide identification and exome sequencing is an effective platform to uncover tumor neoantigens. Application of this strategy to MCL implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.

Immuno-proteomic interrogation of antigen presentation during Dengue infection reveals novel and HLA haplotype-specific MHC-I antigens

Dengue (DEN) virus infection is a leading cause of hospitalization and death in the developing world and broadly effective vaccines and therapies remain elusive. Identifying infection-specific peptide antigens would open new avenues for developing T cell based interventions. Past efforts towards mapping viral antigens used computational predictions that only partially reflect actual antigens presented by the major histocompatibility complex (MHC). To identify DEN-specific antigens without relying on error prone predictions, we developed an immuno-proteomics approach for interrogating antigen presentation in DEN infected B-lymphocytes. This approach enabled three fundamental findings; First, we identified 86 viral MHC-I antigens (59 novel), and mapped them to presentation hotspots in the DEN genome. Second, we discovered post-translationally modified viral and host antigens and antigens derived from alternate reading frames. Predicting these antigens using computational methods alone would be infeasible. Third, we found antigens responsible for HLA-haplotype dependent immune responses against DEN infection: we genetically engineered B-lymphocytes to express HLA alleles associated with either strong or weak DEN-immune responses and identified corresponding allele specific antigens. Together these discoveries let us assay the immunogenic potentials of an unprecedented range of DEN-specific antigens. Ex-vivo assays including ELISPOT and HLA tetramer staining supported our identification of immunogenic antigens in DEN-specific CD8+ T cells. These antigens have potential as both diagnostic tools to characterize DEN-specific T cell immunity, and serve as candidates for designing effective DEN vaccines.

AFFIRM--a multiplexed immunoaffinity platform that combines recombinant antibody fragments and LC-SRM analysis

Targeted measurements of low abundance proteins in complex mixtures are in high demand in many areas, not the least in clinical applications measuring biomarkers. We here present the novel platform AFFIRM (AFFInity sRM) that utilizes the power of antibody fragments (scFv) to efficiently enrich for target proteins from a complex background and the exquisite specificity of SRM-MS based detection. To demonstrate the ability of AFFIRM, three target proteins of interest were measured in a serum background in single-plexed and multiplexed experiments in a concentration range of 5-1000 ng/mL. Linear responses were demonstrated down to low ng/mL concentrations with high reproducibility. The platform allows for high throughput measurements in 96-well format, and all steps are amendable to automation and scale-up. We believe the use of recombinant antibody technology in combination with SRM MS analysis provides a powerful way to reach sensitivity, specificity, and reproducibility as well as the opportunity to build resources for fast on-demand implementation of novel assays.

Grading breast cancer tissues using molecular portraits

Tumor progression and prognosis in breast cancer patients are difficult to assess using current clinical and laboratory parameters, where a pathological grading is indicative of tumor aggressiveness. This grading is based on assessments of nuclear grade, tubule formation, and mitotic rate. We report here the first protein signatures associated with histological grades of breast cancer, determined using a novel affinity proteomics approach. We profiled 52 breast cancer tissue samples by combining nine antibodies and label-free LC-MS/MS, which generated detailed quantified proteomic maps representing 1,388 proteins. The results showed that we could define in-depth molecular portraits of histologically graded breast cancer tumors. Consequently, a 49-plex candidate tissue protein signature was defined that discriminated between histological grades 1, 2, and 3 of breast cancer tumors with high accuracy. Highly biologically relevant proteins were identified, and the differentially expressed proteins indicated further support for the current hypothesis regarding remodeling of the tumor microenvironment during tumor progression. The protein signature was corroborated using meta-analysis of transcriptional profiling data from an independent patient cohort. In addition, the potential for using the markers to estimate the likelihood of long-term metastasis-free survival was also indicated. Taken together, these molecular portraits could pave the way for improved classification and prognostication of breast cancer.

Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties

Protein-peptide interactions are a common occurrence and essential for numerous cellular processes, and frequently explored in broad applications within biology, medicine, and proteomics. Therefore, understanding the molecular mechanism(s) of protein-peptide recognition, specificity, and binding interactions will be essential. In this study, we report the first detailed analysis of antibody-peptide interaction characteristics, by combining large-scale experimental peptide binding data with the structural analysis of eight human recombinant antibodies and numerous peptides, targeting tryptic mammalian and eukaryote proteomes. The results consistently revealed that promiscuous peptide-binding interactions, that is, both specific and degenerate binding, were exhibited by all antibodies, and the discovery was corroborated by orthogonal data, indicating that this might be a general phenomenon for low-affinity antibody-peptide interactions. The molecular mechanism for the degenerate peptide-binding specificity appeared to be executed through the use of 2-3 semi-conserved anchor residues in the C-terminal part of the peptides, in analogue to the mechanism utilized by the major histocompatibility complex-peptide complexes. In the long-term, this knowledge will be instrumental for advancing our fundamental understanding of protein-peptide interactions, as well as for designing, generating, and applying peptide specific antibodies, or peptide-binding proteins in general, in various biotechnical and medical applications.

Ability to perform a single heel-rise is significantly related to patient-reported outcome after Achilles tendon rupture

This study evaluated the short-term recovery of function after an acute Achilles tendon rupture, measured by a single-legged heel-rise test, with main emphasis on the relation to the patient-reported outcomes and fear of physical activity and movement (kinesiophobia). Eighty-one patients treated surgically or non-surgically with early active rehabilitation after Achilles tendon rupture were included in the study. Patient's ability to perform a single-legged heel-rise, physical activity level, patient-reported symptoms, general health, and kinesiophobia was evaluated 12 weeks after the injury. The heel-rise test showed that 40 out of 81 (49%) patients were unable to perform a single heel-rise 12 weeks after the injury. We found that patients who were able to perform a heel-rise were significantly younger, more often of male gender, reported a lesser degree of symptoms, and also had a higher degree of physical activity at 12 weeks. There was also a significant negative correlation between kinesiophobia and all the patient-reported outcomes and the physical activity level. The heel-rise ability appears to be an important early achievement and reflects the general level of healing, which influences patient-reported outcome and physical activity. Future treatment protocols focusing on regaining strength early after the injury therefore seem to be of great importance. Kinesiophobia needs to be addressed early during the rehabilitation process.

Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry

The development of high-performance technology platforms for generating detailed protein expression profiles, or protein atlases, is essential. Recently, we presented a novel platform that we termed global proteome survey, where we combined the best features of affinity proteomics and mass spectrometry, to probe any proteome in a species independent manner while still using a limited set of antibodies. We used so called context-independent-motif-specific antibodies, directed against short amino acid motifs. This enabled enrichment of motif-containing peptides from a digested proteome, which then were detected and identified by mass spectrometry. In this study, we have demonstrated the quantitative capability, reproducibility, sensitivity, and coverage of the global proteome survey technology by targeting stable isotope labeling with amino acids in cell culture-labeled yeast cultures cultivated in glucose or ethanol. The data showed that a wide range of motif-containing peptides (proteins) could be detected, identified, and quantified in a highly reproducible manner. On average, each of six different motif-specific antibodies was found to target about 75 different motif-containing proteins. Furthermore, peptides originating from proteins spanning in abundance from over a million down to less than 50 copies per cell, could be targeted. It is worth noting that a significant set of peptides previously not reported in the PeptideAtlas database was among the profiled targets. The quantitative data corroborated well with the corresponding data generated after conventional strong cation exchange fractionation of the same samples. Finally, several differentially expressed proteins, with both known and unknown functions, many relevant for the central carbon metabolism, could be detected in the glucose- versus ethanol-cultivated yeast. Taken together, the study demonstrated the potential of our immunoaffinity-based mass spectrometry platform for reproducible quantitative proteomics targeting classes of motif-containing peptides.

Proteomic analysis and discovery using affinity proteomics and mass spectrometry

Antibody-based microarrays are a rapidly evolving affinity-proteomic methodology that recently has shown great promise in clinical applications. The resolution of these proteomic analyses is, however, directly related to the number of data-points, i.e. antibodies, included on the array. Currently, this is a key bottleneck because of limited availability of numerous highly characterized antibodies. Here, we present a conceptually new method, denoted global proteome survey, opening up the possibility to probe any proteome in a species-independent manner while still using a limited set of antibodies. We use context-independent-motif-specific antibodies directed against short amino acid motifs, where each motif is present in up to a few hundred different proteins. First, the digested proteome is exposed to these antibodies, whereby motif-containing peptides are enriched, which then are detected and identified by mass spectrometry. In this study, we profiled extracts from human colon tissue, yeast cells lysate, and mouse liver tissue to demonstrate proof-of-concept.

Cellular expansion and gene expression in the developing grape (Vitis vinifera L.)

Expression profiles of genes involved in cell wall metabolism and water transport were compared with changes in grape (Vitis vinifera L.) berry growth, basic chemical composition, and the shape, size, and wall thickness of cells within tissues of the berry pericarp. Expression of cell wall-modifying and aquaporin genes in berry pericarp tissues generally followed a bimodal expression profile with high levels of expression coinciding with the two periods of rapid berry growth, stages I and III, and low levels of expression corresponding to the slow-growth period, stage II. Cellular expansion was observed throughout all tissues during stage I, and only mesocarp cellular expansion was observed during stage III. Expansion of only exocarp cells was evident during transition between stages II and III. Cell wall-modifying and aquaporin gene expression profiles followed similar trends in exocarp and mesocarp tissues throughout berry development, with the exception of the up-regulation of pectin methylesterase, pectate lyase, two aquaporin genes (AQ1 and AQ2), and two expansin genes (EXP3 and EXPL) during stage II, which was delayed in the exocarp tissue compared with mesocarp tissue. Exocarp endo-(1-->3)-beta-glucanase and expansin-like gene expression was concurrent with increases in epidermal and hypodermal cell wall thickness. These results indicate a potential role of the grape berry skin in modulating grape berry growth.

Update on Anti-Saccharomyces cerevisiae antibodies, anti-nuclear associated anti-neutrophil antibodies and antibodies to exocrine pancreas detected by indirect immunofluorescence as biomarkers in chronic inflammatory bowel diseases: Results of a multicenter study

AIM: Anti-Saccharomyces cerevisiae antibodies (ASCA), anti-nuclear associated anti-neutrophil antibodies (NANA) and antibodies to exocrine pancreas (PAB), are serological tools for discriminating Crohn’s disease (CrD) and ulcerative colitis (UC). Like CrD, coeliac disease (CoD) is an inflammatory bowel disease (IBD) associated with (auto) antibodies. Performing a multicenter study we primarily aimed to determine the performance of ASCA, NANA and PAB tests for IBD diagnosis in children and adults, and secondarily to evaluate the prevalence of these markers in CoD.

METHODS: Sera of 109 patients with CrD, 78 with UC, 45 with CoD and 50 healthy blood donors were retrospectively included. ASCA, NANA and PAB were detected by indirect immunofluorescence (IIF).

RESULTS: ASCA+/NANA- profile displayed a positive predictive value of 94.2% for CrD. Detection of ASCA was correlated with a more severe clinical profile of CrD and treatment of the disease did not influence their serum levels. ASCA positivity was found in 37.9% of active CoD. PAB were found in 36.7% CrD and 13.3% CoD patients and were not correlated with clinical features of CrD, except with an early onset of the disease. Fifteen CrD patients were ASCA negative and PAB positive.

CONCLUSION: ASCA and PAB detected by IIF are specific markers for CrD although their presence does not rule out a possible active CoD. The combination of ASCA, NANA and PAB tests improves the sensitivity of immunological markers for CrD. Repeating ASCA, NANA, and PAB testing during the course of CrD has no clinical value.

Light charged-particle production in 96 MeV neutron-induced reactions on carbon and oxygen

In recent years, an increasing number of applications involving fast neutrons have been developed or are under consideration, e.g. radiation treatment of cancer, neutron dosimetry at commercial aircraft altitudes, soft-error effects in computer memories, accelerator-driven transmutation of nuclear waste and energy production and determination of the response of neutron detectors. Data on light-ion production in light nuclei such as carbon, nitrogen and oxygen are particularly important in calculations of dose distributions in human tissue for radiation therapy at neutron beams, and for dosimetry of high-energy neutrons produced by high-energy cosmic radiation interacting with nuclei (nitrogen and oxygen) in the atmosphere. When studying neutron dose effects, it is especially important to consider carbon and oxygen, since they are, by weight, the most abundant elements in human tissue. Preliminary experimental double-differential cross sections of inclusive light-ion (p, d, t, (3)He and alpha) production in carbon induced by 96-MeV neutrons have been presented. Energy spectra were measured at eight laboratory angles: 20, 40, 60, 80, 100, 120, 140 and 160 degrees. Measurements were performed at The Svedberg Laboratory (TSL), Uppsala, using the dedicated MEDLEY experimental setup. The authors have earlier reported experimental double-differential cross sections of inclusive light-ion production in oxygen. In this paper, the deduced kerma coefficients for oxygen has been presented and compared with reaction model calculations.

An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development

BACKGROUND

Accuracy in quantitative real-time RT-PCR is dependent on high quality RNA, consistent cDNA synthesis, and validated stable reference genes for data normalization. Reference genes used for normalization impact the results generated from expression studies and, hence, should be evaluated prior to use across samples and treatments. Few statistically validated reference genes have been reported in grapevine. Moreover, success in isolating high quality RNA from grapevine tissues is typically limiting due to low pH, and high polyphenolic and polysaccharide contents.

RESULTS

We describe optimization of an RNA isolation procedure that compensates for the low pH found in grape berries and improves the ability of the RNA to precipitate. This procedure was tested on pericarp and seed developmental series, as well as steady-state leaf, root, and flower tissues. Additionally, the expression stability of actin, AP47 (clathrin-associated protein), cyclophilin, EF1-alpha (elongation factor 1-alpha), GAPDH (glyceraldehyde 3-phosphate dehydrogenase), MDH (malate dehydrogenase), PP2A (protein phosphatase), SAND, TIP41, alpha-tubulin, beta-tubulin, UBC (ubiquitin conjugating enzyme), UBQ-L40 (ubiquitin L40) and UBQ10 (polyubiquitin) were evaluated on Vitis vinifera cv. Cabernet Sauvignon pericarp using three different statistical approaches. Although several of the genes proved to be relatively stable, no single gene outperformed all other genes in each of the three evaluation methods tested. Furthermore, the effect of using one reference gene versus normalizing to the geometric mean of several genes is presented for the expression of an aquaporin and a sucrose transporter over a developmental series.

CONCLUSION

In order to quantify relative transcript abundances accurately using real-time RT-PCR, we recommend that combinations of several genes be used for normalization in grape berry development studies. Our data support GAPDH, actin, EF1-alpha and SAND as the most relevant reference genes for this purpose.

CCL17 and CCL22 attenuate CCL5-induced mast cell migration

BACKGROUND

Mast cells (MCs) accumulate at sites of allergic mucosal inflammation where they act as central effectors and regulatory cells. Chemokines are believed to be crucial for the recruitment of MCs to sites of inflammation. We recently reported that human umbilical cord blood MCs (CBMCs) expresses the CC chemokine receptors, CCR1 and CCR4. We found a unique response profile to ligands of the respective receptors in which, of all tested ligands, only CCL5/RANTES-induced migration.

OBJECTIVE

To further investigate the function of CCR4 in MCs.

METHODS

CBMCs were used for competition binding experiments, migration, and intracellular calcium mobilization and release response studies.

RESULTS

The natural ligands for CCR4, CCL17/TARC and CCL22/MDC could both compete for binding with radiolabelled CCL5. Further, both CCL17 and CCL22 act as CCR4 antagonists by inhibiting CCL5-induced migration. Although both CCL17 and CCL22 caused mobilization of intracellular calcium, none of them induced migration or histamine release.

CONCLUSIONS

These results suggest that CCL5-induced migration of MCs via CCR4 can be regulated by the natural agonists CCL17 and CCL22, which are up-regulated at sites of allergic inflammation.

Measurement of the absolute n p scattering differential cross section at 194 MeV

We describe a double-scattering experiment with a novel tagged neutron beam to measure differential cross sections for np backscattering to better than +/-2% absolute precision. The measurement focuses on angles and energies where the cross section magnitude and angle dependence constrain the charged pion-nucleon coupling constant, but existing data show serious discrepancies among themselves and with energy-dependent partial-wave analyses. The present results are in good accord with the partial-wave analyses, but deviate systematically from other recent measurements.

Regulation of mast cell migration by T and T cytokines: identification of tumour necrosis factor-alpha and interleukin-4 as mast cell chemotaxins

Mast cells act as central effector and regulatory cells in many inflammatory disorders, including T helper 1 (T(H1))-mediated inflammations such as autoimmunity and T(H2)-mediated inflammations such as allergy and parasite infections. One characteristic for mast cell-mediated inflammations is the accumulation of mast cells in the inflamed tissue. The factors regulating mast cell recruitment in these inflammations are still not fully characterized. We have investigated the potency of T(H1)- and T(H2)-secreted cytokines to mediate mast cell migration. Supernatants from six different T(H1) and T(H2) clones were tested for mast cell-chemotactic activity using the human mast cell line (HMC-1) as a responder cell. All six clones produced factors that induced mast cell migration. Using blocking antibodies to a broad range of cytokines, we found that anti-tumour necrosis factor-alpha (anti-TNF-alpha) reduced the migration of mast cells to supernatants from T(H1) clones. In contrast, the main mast cell chemoattractants secreted by T(H2) clones were found to be interleukin-4 (IL-4) and IL-8. The potency of these cytokines to act as mast cell chemoattractants was confirmed by using recombinant IL-4, IL-8 and TNF-alpha. Our results suggest that TNF-alpha can be involved in the recruitment of mast cells in T(H1)-mediated inflammations, whereas IL-4 and IL-8 might play a similar role in T(H2)-mediated inflammations.

Expression of CCL5/RANTES by Hodgkin and Reed-Sternberg cells and its possible role in the recruitment of mast cells into lymphomatous tissue

HL is a malignant lymphoma characterized by a small number of malignant HRS cells among a major population of infiltrating reactive cells, e.g., lymphocytes and eosinophils. We previously reported that mast cells are present in HL-affected lymph nodes and therein are the predominant CD30L-expressing cells. The CD30L expressed on mast cells is functionally active and can provide stimulatory signals to HRS cells. Thus, mast cells constitute an important portion of the infiltrating reactive cells that contribute to tumor progression in HL. Control of the recruitment of this previously unrecognized cell and its interactions with tumor cells are essentially unknown. To elucidate if mast cells might be specifically attracted to the tumor area by chemokines produced by HRS cells, we investigated chemokine expression in HL cell lines and in vivo. By RNase protection assay, mRNA expression of several chemokines could be detected in the cell lines. Despite the heterogeneous expression profile exhibited by the cell lines, 4 of 5 expressed CCL5 (RANTES) mRNA. RT-PCR and immunohistochemistry confirmed expression of CCL5 in vivo. Furthermore, secreted CCL5 was detected in conditioned media from 3 of the cell lines. In a migration assay, we found that CCL5 present in conditioned medium could induce mast cell migration. Taken together, our results suggest that CCL5 produced by HRS cells is one mechanism by which mast cells can be attracted into the tumor tissue in HL.

Beyond kerma--neutron data for biomedical applications

Presently, many new applications of fast neutrons are emerging or under development, like dose effects due to cosmic-ray neutrons for airplane crew, fast-neutron cancer therapy, studies of electronics failures induced by cosmic-ray neutrons, and accelerator-driven incineration of nuclear waste and energy production technologies. All these areas would benefit from improved neutron dosimetry. In this paper, the present rapid progress on measurements of double-differential neutron-induced nuclear reaction data are described. With such data at hand, the full response of, in principle, any system, including human tissue, can be calculated in detail. This could potentially revolutionise our understanding of biological effects in tissue due to fast neutrons.

Selective CCL5/RANTES-induced mast cell migration through interactions with chemokine receptors CCR1 and CCR4

Mast cells (MCs) accumulate at sites of allergic mucosal inflammation where they act as central effector and regulatory cells. Because chemokines are of vital importance in directing inflammatory leukocytes to the sites of inflammations, we have investigated the expression and function of CC-chemokine receptor (CCR) on human MCs. Two previously unrecognized MC-chemokine receptors, CCR1 and CCR4, could be identified on cord blood-derived MCs (CBMCs). CCR1 and CCR4 expressed on CBMCs exhibited a unique response profile. Of seven CCR1 and CCR4 agonists tested, only CCL5/RANTES act as an agonist inducing chemotaxis. The migration could be partially blocked by specific antibodies against CCR1 or CCR4, while a complete inhibition was achieved when both CCR1 and CCR4 were blocked. These results demonstrate that both CCR1 and CCR4 are functional receptors on human mast cells with capacity to mediate migration towards CCL5.

Stem cell factor-induced migration of mast cells requires p38 mitogen-activated protein kinase activity

Stem cell factor (SCF) can be considered a cardinal cytokine in mast cell biology as it affects mast cell differentiation, survival, and migration. The objective of this study was to investigate the role of two mitogen-activated protein (MAP) kinases, extracellular signal-regulated kinase (ERK) and p38, in SCF-induced cell migration. This was examined in mouse mast cells by using PD 098059 and SB203580, which are specific inhibitors of mitogen-induced extracellular kinase (MEK) and p38 MAP kinase, respectively. SCF induced a rapid and transient activation of ERK and p38 in a dose-dependent manner. Inhibition of p38 activity by SB203580 was paralleled with a marked reduction of migration toward SCF, whereas the effect of the MEK inhibitor was less pronounced. This is the first report of a physiological function of SCF-dependent activation of p38. Whether p38-mediated mast cell migration is a possible target for suppression of mast cell hyperplasia remains to be determined.

Transforming growth factor-beta-mediated mast cell migration depends on mitogen-activated protein kinase activity

Transforming growth factor-beta (TGF-beta) isoforms regulate numerous cellular functions through binding to receptors with intrinsic serine/threonine kinase activity that transduce the intracellular signals via activation of Smad proteins. In this study, we examined the signalling pathways involved in TGF-beta1-mediated growth inhibition and migration in a human mast cell line, HMC-1. TGF-beta1 evoked optimal migration at 40 fM, whereas maximal growth inhibition was obtained at 400 pM. Protein tyrosine kinase inhibitors completely inhibited TGF-beta1-mediated migration, without affecting the antimitogenic response. Smad2 was phosphorylated upon TGF-beta1 treatment, both in the absence and presence of genistein. The mitogen-induced extracellular kinase (MEK) inhibitor, PD98059, blocked the migratory response without affecting growth inhibition. In contrast, the p38 MAP kinase inhibitor, SB203580, had no significant effect on either migration or growth inhibition. These results indicate that different signalling pathways mediate TGF-beta1-induced migration and growth inhibition in HMC-1 cells, where the migration involves MEK activity.

Demonstration of mast cell chemotactic activity in synovial fluid from rheumatoid patients

OBJECTIVES

The significance of the mast cell in the pathogenesis of rheumatic diseases has become more evident. Although mast cell hyperplasia is a feature of rheumatoid arthritis, the nature of mast cell chemoattractants involved in the recruitment of mast cells in joint diseases has not been studied in any detail. In this study the presence of mast cell chemotactic activity in synovial fluids was examined.

METHODS

Synovial fluids from seven rheumatoid patients were tested in a modified Boyden chamber, where a human mast cell line was used as responder. The presence of stem cell factor (SCF) and transforming growth factor beta (TGFbeta) was measured by enzyme linked immunosorbent assay (ELISA).

RESULTS

Six of the seven synovial fluids tested exhibited mast cell chemotactic activity. Two characterised human mast cell chemotaxins, SCF and TGFbeta, were highly expressed in the synovium. Soluble SCF could be detected in all fluids analysed. Blocking antibodies against SCF or TGFbeta almost completely blocked the activity in one fluid, partially blocked the activity in three, and did not affect the activity in two. Treatment of the responder cells with pertussis toxin reduced the migratory response against seven fluids, indicating the presence of chemoattractants mediating their effect through G(i) coupled receptors.

CONCLUSION

These data demonstrate the presence of multiple factors in synovial fluid acting as mast cell chemoattractants, two of which are SCF and TGFbeta that contribute to the effect. These findings may be of importance for developing new strategies to inhibit mast cell accumulation in rheumatic diseases.

The chemokine receptor CXCR4 is expressed within the mast cell lineage and its ligand stromal cell-derived factor-1alpha acts as a mast cell chemotaxin

In this study we provide evidence that the chemokine stromal cell-derived factor-1alpha (SDF-1alpha) acts as a mast cell chemoattractant through interactions with its receptor CXCR4 expressed on mast cell progenitors in the blood as well as on in vitro-developed and leukemic mast cells. We found expression of CXCR4 on cord blood-derived mast cells (CBMC) and on the human mast cell line HMC-1, analyzed by RNAse protection assay and flow cytometry. SDF-1alpha induced intracellular calcium mobilization in HMC-1 cells and was chemotactic for both HMC-1 cells and CBMC. The activity of SDF-1alpha was completely blocked by treating the cells with pertussis toxin, indicating the involvement of Gi-proteins in the signaling. By applying a transwell assay we could show that SDF-1alpha induces migration of a cell population in peripheral blood that is enriched for cells with the capacity to differentiate into mast cells. These findings thus suggest a mechanism by which human mast cell progenitors may be recruited from circulation into the tissue.

A comparison of correlation, calibration, and diagnosticity as measures of the confidence-accuracy relationship in witness identification

The relationship between witness confidence and accuracy (CA) has traditionally been measured by the point-biserial correlation (rpb). Recently, 2 alternative indices for measuring the CA relation have been proposed, namely calibration and diagnosticity analyses (e.g., P. Juslin, N. Olsson, & A. Winman, 1996). In this study, the 3 measures were compared quantitatively using 52 independent data sets. The measures rpb and calibration were weakly correlated, whether computed across earwitness data sets, eyewitness data sets, or all data. Thus, when applied to the same data, these 2 measures sometimes yield different conclusions. A modest relation was observed between the rpb and the diagnosticity of confidence. Finally, calibration and degree of over- and underconfidence covaried with task difficulty, consistent with K. A. Deffenbachers' (1980) optimality hypothesis.

Human mast cell migration in response to members of the transforming growth factor-beta family

Mast cells are known to accumulate at sites of inflammation, however, the chemotaxins involved remain largely undefined. Transforming growth factor-beta (TGF-beta) isoforms regulate numerous cellular functions, including cell growth and differentiation, formation of extracellular matrix, and the immune response. In this study we have compared the potency of different members of the TGF-beta family as human mast cell chemotaxins, and analyzed the expression of TGF-beta binding proteins on human mast cells. We were able to demonstrate that the maximal chemotactic response was attained at approximately 40 fM for the three TGF-beta isoforms, with TGF-beta3 being more effective than TGF-beta1 and TGF-beta2 at this concentration. This effect was observed in both the HMC-1 human mast cell line and in cultured primary mast cells. In addition, TGF-beta1, TGF-beta2, and less efficiently, TGF-beta3 inhibited the proliferation of HMC-1 cells. The migratory response is probably mediated through interaction with the TGF-beta serine/threonine type I and II receptors that were found to be expressed on the cells. No expression of TGF-beta type III receptor, endoglin, or the endothelial TGF-beta type I receptor ALK-1 could be detected. These results provide evidence that TGF-beta isoforms are highly potent chemotaxins for human mast cells and can play an important role in the recruitment of mast cells in inflammatory reactions.

Demonstration of mast cell chemotactic activity in bronchoalveolar lavage fluid collected from asthmatic patients before and during pollen season

BACKGROUND

Mast cells are versatile effector cells of primary importance in asthma and airway inflammation. During inflammation mast cells accumulate in the bronchial epithelium. The mechanism for this increase in mast cell number has not been defined.

OBJECTIVES

The aim of this study was to examine the presence of mast cell chemotactic activity in bronchoalveolar lavage (BAL) fluid taken before and at the end of 2 pollen seasons from patients with allergic asthma.

METHODS

To measure mast cell chemotactic activity, we used a modified Boyden chamber and the human mast cell line HMC-1 or in vitro-developed mast cells as responder cells.

RESULTS

A total of 27 patients were investigated, of which 8 exhibited mast cell chemotactic activity in their BAL fluid collected before season. A significant increase in the activity was found in 18 of 27 BAL fluids sampled at the end of the pollen season. No difference was found between patients treated with immunotherapy or placebo. The presence of stem cell factor could be detected in all BAL fluids analyzed. Blocking antibodies against stem cell factor or transforming growth factor-beta partially blocked the activity in some of the BAL fluids. Treatment of the responder cells with pertussis toxin reduced the migratory activity in 13 of 14 BAL fluids collected during pollen season.

CONCLUSION

This study demonstrates the presence of mast cell chemotactic activity in BAL fluids from patients with allergic asthma, with a significant increase in activity during pollen season. The major part of this activity consisted of factors mediating their effect through G(i)-protein coupled receptors. This activity may be responsible for the mast cell accumulation in the intraepithelial layer seen in allergic asthmatic patients.

Can self-reported encoding strategy and recognition skill be diagnostic of performance in eyewitness identifications?

The relationship between 3 witness factors and identification accuracy, as well as calibration and diagnosticity of confidence, was investigated. A total of 384 participants in an eyewitness experiment rated their facial recognition skill, general memory skill, and self-reported encoding strategy on a questionnaire presented after the photo-confrontation. Participants who rated themselves to be good face recognizers showed a slightly higher overall accuracy with a more diagnostic confidence-accuracy relation. Participants who reported that they relied on a holistic encoding strategy were associated with more accurate identifications and a stronger confidence-accuracy relation than those who reported an analytic encoding strategy. Degree of self-reported general memory skill was not diagnostic of identification performance.

Serum amyloid A induces chemotaxis of human mast cells by activating a pertussis toxin-sensitive signal transduction pathway

Serum amyloid A (SAA) is an acute-phase protein and its concentration increases in the blood up to 1000 times during an inflammatory response. Mast cells are known to accumulate in various inflammatory processes, some of which are associated with increased levels of acute-phase reactants such as SAA. We report here that SAA can act as a mast cell chemoattractant. Recombinant SAA at concentrations corresponding to those found during the acute phase induced directional migration of human mast cells. No chemokinetic effect was observed. Preincubation of the cells with pertussis toxin inhibited SAA chemotaxis, suggesting that the effect is mediated by G proteins of the Gi class. Furthermore, chemotaxis was diminished after pretreatment with genistein, a tyrosine kinase inhibitor, or bisindolylmaleimide I, a protein kinase C inhibitor. We suggest that SAA may participate in the migration of mast cells to inflamed tissues during an acute-phase response, acting through a pertussis toxin-sensitive signaling pathway.