Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anti-coagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay-based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches. This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.     

Synthesis and evaluation of bifunctional nitrocatechol inhibitors of pig liver catechol-O-methyltransferase

Bifunctional compounds were tested in vitro as potential inhibitors of pig liver catechol-O-methyltransferase (COMT) with respect to the catechol substrate 4-[(3,4-dihydroxyphenyl)azo]benzenesulfonate. The bifunctional compounds were a composite of either two nitrocatechols or one nitrocatechol and one phenol, linked by amide bonds to a spacer unit comprising two to five methylene groups. The unsymmetrical compounds N-[2-(4-hydroxybenzoylamine)ethyl]-3,4-dihydroxy-5-nitrobenzamide], N-[3-(4-hydroxybenzoyl-amine)propyl]-3,4-dihydroxy-5-nitrobenzamide] and N-[5-(4-hydroxybenzoylamine)pentyl]-3,4-dihydroxy-5-nitrobenzamide] demonstrated strong inhibitory action against COMT with K(i) values in the 100 nM range. In comparison, the monofunctional nitrocatechol analogues of these compounds had K(i) values that were significantly higher.     

CD8+ T lymphocytes in lung tissue from patients with idiopathic pulmonary fibrosis

Objective

To study the prevalence of respiratory and atopic symptoms in (young) adults born prematurely, differences between those who did and did not develop Bronchopulmonary Disease (BPD) at neonatal age and differences in respiratory health between males and females.

Methods

Design: Prospective cohort study. Setting: Nation wide follow-up study, the Netherlands. Participants: 690 adults (19 year old) born with a gestational age below 32 completed weeks and/or with a birth weight less than 1500 g. Controls were Dutch participants of the European Community Respiratory Health Survey (ECRHS). Main outcome measures: Presence of wheeze, shortness of breath, asthma, hay fever and eczema using the ECRHS-questionnaire

Results

The prevalence of doctor-diagnosed asthma was significantly higher in the ex-preterms than in the general population, whereas eczema and hay fever were significant lower. Women reported more symptoms than men. Preterm women vs controls: asthma 13% vs 5% (p < 0.001); hay fever 8% vs 20% (p < 0.001); eczema 10% vs 42% (p < 0.001). Preterm men vs controls: asthma 9% vs 4% (p = 0.007); hay fever 8% vs 17% (p = 0.005); eczema 9% vs 31% (p < 0.001) Preterm women reported more wheeze and shortness of breath during exercise (sob) than controls: wheeze 30% vs 22% (p = 0.009); sob 27% vs 16% (p < 0.001); 19-year-old women with BPD reported a higher prevalence of doctor diagnosed asthma compared to controls (24% vs 5% p < 0.001) and shortness of breath during exercise (43% vs 16% p = 0.008). The prevalence of reported symptoms by men with BPD were comparable with the controls.

Conclusion

Our large follow-up study shows a higher prevalence of asthma, wheeze and shortness of breath in the prematurely born young adults. 19-year-old women reported more respiratory symptoms than men. Compared to the general population atopic diseases as hay fever and eczema were reported less often.     

Inflammatory aetiology of human myometrial activation tested using directed graphs

There are three main hypotheses for the activation of the human uterus at labour: functional progesterone withdrawal, inflammatory stimulation, and oxytocin receptor activation. To test these alternatives we have taken information and data from the literature to develop causal pathway models for the activation of human myometrium. The data provided quantitative RT-PCR results on key genes from samples taken before and during labour. Principal component analysis showed that pre-labour samples form a homogenous group compared to those during labour. We therefore modelled the alternative causal pathways in non-laboring samples using directed graphs and statistically compared the likelihood of the different models using structural equations and D-separation approaches. Using the computer program LISREL, inflammatory activation as a primary event was highly consistent with the data (p = 0.925), progesterone withdrawal, as a primary event, is plausible (p = 0.499), yet comparatively unlikely, oxytocin receptor mediated initiation is less compatible with the data (p = 0.091). DGraph, a software program that creates directed graphs, produced similar results (p= 0.684, p= 0.280, and p = 0.04, respectively). This outcome supports an inflammatory aetiology for human labour. Our results demonstrate the value of directed graphs in determining the likelihood of causal relationships in biology in situations where experiments are not possible.     

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis

MS/MS and associated database search algorithms are essential proteomic tools for identifying peptides. Due to their widespread use, it is now time to perform a systematic analysis of the various algorithms currently in use. Using blood specimens used in the HUPO Plasma Proteome Project, we have evaluated five search algorithms with respect to their sensitivity and specificity, and have also accurately benchmarked them based on specified false-positive (FP) rates. Spectrum Mill and SEQUEST performed well in terms of sensitivity, but were inferior to MASCOT, X!Tandem, and Sonar in terms of specificity. Overall, MASCOT, a probabilistic search algorithm, correctly identified most peptides based on a specified FP rate. The rescoring algorithm, PeptideProphet, enhanced the overall performance of the SEQUEST algorithm, as well as provided predictable FP error rates. Ideally, score thresholds should be calculated for each peptide spectrum or minimally, derived from a reversed-sequence search as demonstrated in this study based on a validated data set. The availability of open-source search algorithms, such as X!Tandem, makes it feasible to further improve the validation process (manual or automatic) on the basis of "consensus scoring", i.e., the use of multiple (at least two) search algorithms to reduce the number of FPs. complement.     

The ionization state of the atmosphere as a function of the meteorological elements and of various sources of ions

The content of positive (N⁺) and negative (N^–) medium ions in the atmosphere, was measured during five periods. The influence of wind velocity and direction, humidity, rainfall and various sources of natural ionization on the N⁺ and N^– content and the relation N⁺/N^– were investigated. Emphasis was placed on the influence of a special kind of weather called chamsin in Israel. The amount of N⁺ and N^– and the relation N⁺/N^– began to increase about 10 hours before the meteorological instruments indicated the specific features of this kind of weather — increase in temperature and decrease in humidity. As some laboratory tests have shown that N^– has a beneficial physiological and biological influence, and N⁺ has the opposite effect, it is assumed that the above-mentioned changes in N⁺/N^– are the cause for persons who are sensitive to this kind of weather, feeling ill. The increase in N⁺ and N^– with the increase in radioactive emanation from the earth and the nuclear tests was established.

---

Zusammenfassung Der Gehalt der AtmosphÄre an positiven (N⁺) und negativen (N^–)mittleren Ionen wurde wÄhrend 5 Perioden gemessen. Es wurde nach dem Einfluss der Windgeschwindigkeit und Richtung, der Feuchtigkeit, des Regens und der verschiedenen Quellen der natürlichen Ionisation in der AtmosphÄre gesucht. Spezielle Interesse wurde der besonderen Wetterart, Chamsin, gewidmet. Die Mengen der N⁺ und N^– und das VerhÄltniss N⁺/N^– stieg ca. 10 Stunden bevor die besonderen charakteristischen Eigenschaften dieser Wetterart-steigende Temperatur und abnehmende Feuchtigkeit-sich anzeigten. Da Laboratoriumsversuche einen positiven physiologischen Einfluss der N^– und einen negativen der N⁺ gezeigt haben, mag es sein, dass die oben genannte Zunahme des N⁺/N^– der Grund der Beschwerden von Personen ist die besonders empfindlich auf diese Wetterart reagieren. Eine Zunahme in N⁺ und N^– mit Steigen der Emanation der Erde und der Atombomben Versuche wurde festgestelt.

---

Résumé Le contenu de l'atmosphère en ions moyens positifs (N⁺) et négatifs(N^–) a été mésuré pendant 5 periodes. L'influence de la vitesse du vent et de sa direction, de l'humidité, des pluies et de diverses sources d'ionisation naturelle sur le contenu en N⁺ et N^– et sur leur rapport N⁺/N^– a été étudiée. Une attention particulière a été attachée au climat appelé en Israel chamsin. Il a été trouvé que la quantité de N⁺ et de N^– ainsi que leur rapport N⁺/N^– commence à augmenter 10 heures avant que les instruments météorologiques indiquent les caractéristiques essentiels de ce climat(élévation de la température et diminution de l'humidité. Du fait que les essais de laboratoires ont montrés que N^– a un bon effet biologique alors que pour le N⁺ l'effet est opposé, noua pensons que les changements en N⁺/N^– sont a cause de ce que les personnes sensibles à ce genre de climat éprouvent un malaise. Ce genre de personne sent l'approche de ce climat 10 heures à l'avance ou davantage. L'augmentation du contenu en N⁺ et N^– avec l'émanation radioactive de la terre et des essais nucléaires a été établie.

     

Structural and functional characterization of the dimerization region of soluble guanylyl cyclase

Soluble guanylyl cyclase (sGC) is a ubiquitous enzyme that functions as a receptor for nitric oxide. Despite the obligate heterodimeric nature of sGC, the sequence segments mediating subunit association have remained elusive. Our initial screening for relevant interaction site(s) in the most common sGC isoenzyme, alpha(1) beta(1), identified two regions in each subunit, i.e. the regulatory domains and the central regions, contributing to heterodimer formation. To map the relevant segments in the beta(1) subunit precisely, we constructed multiple N- and C-terminal deletion variants and cotransfected them with full-length alpha(1) in COS cells. Immunoprecipitation revealed that a sequence segment spanning positions 204-408 mediates binding of beta(1) to alpha(1) The same region of beta(1)[204-408] was found to promote beta /beta(1) homodimerization. Fusion of [204 beta(1)-408] to enhanced green fluorescent protein conferred binding activity to the recipient protein. Coexpression of beta(1)[204-408] with alpha(1) or beta(1) targeted the sGC subunits for proteasomal degradation, suggesting that beta(1)[204-408] forms structurally deficient complexes with alpha(1) and beta(1). Analysis of deletion constructs lacking portions of the beta(1) dimerization region identified two distinct segments contributing to alpha(1) binding, i.e. an N-terminal site covering positions 204-244 and a C-terminal site at 379-408. Both sites are crucial for sGC function because deletion of either site rendered sGC dimerization-deficient and thus functionally inactive. We conclude that the dimerization region of beta(1) extends over 205 residues of its regulatory and central domains and that two discontinuous sites of 41 and 30 residues, respectively, facilitate binding of beta(1) to the alpha(1) subunit of sGC.     

Fine needle aspiration cytodiagnosis of liver tumors

OBJECTIVE: To present our experience with liver fine needle aspiration (FNA) diagnosis and the adjunctive use of cell blocks with reticulin stain. STUDY DESIGN: The authors reviewed the results of cytopathologic diagnosis obtained by FNA biopsy over a 1-year period, from January 2000 to December 2000, in patients who presented primarily with ultrasonographically suspected liver nodules. FNA smears from 936 patients and cell blocks from 796 patients were reviewed. RESULTS: Among the 936 aspirates studied, the most common malignancy was hepatocellular carcinoma (HCC), which was diagnosed in 427 cases (45.6%), followed by metastatic adenocarcinoma, with 52 cases (5.6%). The concurrent cell block was available in 796 cases. Among them, 574 (72.1%) contained sufficient tissue for diagnosis. Combining analysis of cytologic and histologic specimens, the sensitivity of ultrasound-guided FNA for diagnosis of liver tumors was 85.1% and the specificity 98.7%. The results were better than isolated cytologic analysis, which gave a sensitivity of 78.4% and specificity of 97.4%. The lower diagnostic accuracy of cytology resulted mainly from its lower ability to distinguish well-differentiated HCC from benign lesions. In the cell block sections with reticulin stain, all HCCs showed a decreased or absent reticulin pattern, whereas all the benign hepatocellular lesions usually had a normal trabecular reticulin framework. CONCLUSION: FNA cytology assisted by cell block examination can be an accurate and minimally invasive method for the definitive pathologic diagnosis of primary benign and malignant liver masses and for confirmation of tumors metastatic to the liver. In addition, reticulin staining should be part of the routine assessment of cell blocks. It enhances diagnostic accuracy, particularly for well-differentiated HCC.     

Immunological characteristics associated with the protective efficacy of antibodies to ricin

A/B toxins, produced by bacteria and plants, are among the deadliest molecules known. The B chain binds the cell, whereas the A chain exerts the toxic effect. Both anti-A chain and anti-B chain Abs can neutralize toxins in vivo and in vitro. B chain Abs block binding of the toxin to the cell. It is not known how anti-A chain Abs function. Working with ricin toxin, we demonstrate that immunization with A chain induces greater protection than immunization with B chain. A panel of mAbs, binding to A chain, B chain, or both chains, has been produced and characterized. Immunologic characteristics evaluated include isotype, relative avidity, and epitope specificity. The ability to inhibit ricin enzymatic or cell binding activity was studied, as was the ability to block ricin-mediated cellular cytotoxicity on human and murine cell lines. Finally, the in vivo protective efficacy of the Abs in mice was studied. The Ab providing the greatest in vivo protective efficacy was directed against the A chain. It had the greatest relative avidity and the greatest ability to block enzymatic function and neutralize cytotoxicity. Interestingly, we also obtained an anti-A chain Ab that bound with high avidity, blocked enzymatic activity, did not neutralize cytotoxicity, and actually enhanced the in vivo toxicity of ricin. Anti-A chain Abs with moderate avidity had no in vivo effect, nor did any anti-B chain Abs.