Evaluation of Protein Profiles From Treated Xenograft Tumor Models Identifies an Antibody Panel for Formalin-fixed and Paraffin-embedded (FFPE) Tissue Analysis by Reverse Phase Protein Arrays (RPPA)

Reverse phase protein arrays (RPPA) are an established tool for measuring the expression and activation status of multiple proteins in parallel using only very small amounts of tissue. Several studies have demonstrated the value of this technique for signaling pathway analysis using proteins extracted from fresh frozen (FF) tissue in line with validated antibodies for this tissue type; however, formalin fixation and paraffin embedding (FFPE) is the standard method for tissue preservation in the clinical setting. Hence, we performed RPPA to measure profiles for a set of 300 protein markers using matched FF and FFPE tissue specimens to identify which markers performed similarly using the RPPA technique in fixed and unfixed tissues. Protein lysates were prepared from matched FF and FFPE tissue specimens of individual tumors taken from three different xenograft models of human cancer. Materials from both untreated mice and mice treated with either anti-HER3 or bispecific anti-IGF-1R/EGFR monoclonal antibodies were analyzed. Correlations between signals from FF and FFPE tissue samples were investigated. Overall, 60 markers were identified that produced comparable profiles between FF and FFPE tissues, demonstrating significant correlation between the two sample types. The top 25 markers also showed significance after correction for multiple testing. The panel of markers covered several clinically relevant tumor signaling pathways and both phosphorylated and nonphosphorylated proteins were represented. Biologically relevant changes in marker expression were noted when RPPA profiles from treated and untreated xenografts were compared. These data demonstrate that, using appropriately selected antibodies, RPPA analysis from FFPE tissue is well feasible and generates biologically meaningful information. The identified panel of markers that generate similar profiles in matched fixed and unfixed tissue samples may be clinically useful for pharmacodynamic studies of drug effect using FFPE tissues.Many human diseases are characterized by abnormalities in complex signaling pathways (1). The expression and activation status of proteins from these deregulated pathways has traditionally been analyzed using single marker techniques such as immunohistochemistry and Western blotting. Although these techniques have provided valuable information on the molecular abnormalities underlying human disease, they are labor intensive, have a low throughput, and often require high sample volume. Furthermore, techniques such as Western blotting are not applicable in the routine clinical setting. Miniaturized parallel immunoassay techniques have been developed in recent years and have played a pivotal role in biomarker discovery (2). Antibody arrays enable multiple potential disease markers to be investigated in a single sample in parallel (3). Beyond this, Reverse Phase Protein Arrays (RPPA)¹ are sensitive high throughput tools that can quantify protein expression levels and activation status (posttranslational modifications such as phosphorylation) in multiple experimental samples simultaneously. The technique requires only minute amounts of samples, printed as lysate arrays onto slides, and hundreds of markers of interest can be investigated, array by array, in a miniaturized dot blot manner. Numerous reports have demonstrated that RPPA can be applied to various sources of cells and tissues to analyze protein profiles, signaling pathway networks, and for the identification of biomarkers (4–13). A recently published workshop report reviews the full potential and advances of RPPA for use in clinical, translational, and basic research (11).In oncology, the parallel profiling of multiple protein markers is particularly desirable to study tumor initiation and progression, to classify tumor disease states on the molecular level, and to discover and monitor biomarkers that can predict therapeutic response or tumor recurrence (14–16). The study of signaling response and analysis of pharmacodynamic (PD) markers upon treatment using in vitro and in vivo test systems (e.g. cell line or patient derived xenograft tumor models) is an established component of preclinical and early clinical drug development. These techniques can provide evidence of target pathway modulation for new therapeutic lead candidate compounds and provide valuable information on the drug mode of action (17), especially in the translational phase. Multiplex analyses of PD biomarkers by RPPA have been performed in vitro using cancer cell lines (18, 19) as well as in patient-derived tumor tissue and blood samples (20, 21) to assess response to treatment and target inhibition. A combination of RPPA signaling pathway mapping and functional PET imaging has recently been successfully evaluated in xenograft models as an early response PD marker for anti-cancer drug efficacy (13).Translating miniaturized multiple protein analysis platforms-such as RPPA - from preclinical to clinical applicability is highly desirable; however, issues such as the limited amount of available clinical samples and tumor heterogeneity must first be addressed. Furthermore, most studies of RPPA in tumor tissue to date have been conducted using proteins extracted from fresh-frozen (FF) tissue specimens; whereas, formalin fixation and paraffin embedding (FFPE) is the standard method for tissue preservation used in clinical pathology laboratories. FFPE yields excellent tissue architecture for histological assessment and enables analysis of individual proteins in situ by techniques such as immunohistochemistry. However, formalin fixation leads to extensive protein–protein and protein–nucleic acid cross-linking (22), which can hamper protein extraction and reduce both the overall yield of extracted protein and the profile of proteins detectable by proteomic techniques (23, 24). Furthermore, formalin-induced cross-linking induces conformational changes in protein structure that can alter the immunoreactivity of some proteins in situ by hiding or altering peptide epitopes (25, 26). Such artifacts are absent from snap-frozen tissue; therefore, protein profiles obtained from FF tissue are likely to reflect the in vivo biology of the tumor more closely. However, FF tumor tissue is not widely available because it is costly to collect and maintain in the clinical setting. FFPE tissue samples are routinely archived by nearly every hospital and offer a unique opportunity to study thousands of samples retrospectively with extensive clinical records and follow-up information.Several groups have now established protocols for retrieving cross-linked proteins from fixed tissues (27–33). These methods are mainly based on the use of concentrated ionic detergents and high temperature protocols closely related to the antigen retrieval methods developed for immunohistochemistry. These studies show that obtaining nondegraded, full-length proteins from FFPE tissues for multiplex analyses is feasible (27–33). More recently, protein extraction techniques optimized for fixed samples have been used to successfully conduct RPPA using FFPE tissue biopsies from different cancer types (34–40). Guo et al. systematically investigated several protein extraction methods and demonstrated that RPPA of FFPE materials is feasible, reproducible and can generate biologically relevant protein profiles (41). Other studies have confirmed the validity of this approach and shown that data generated from RPPA analyses of FFPE tissue demonstrate good concordance with traditional immunohistochemistry markers such as HER2 protein in breast cancer (34, 40). However, to date, analyses have been performed only for a limited set of protein markers.To evaluate whether analysis of a broader panel of protein markers is feasible and generates meaningful data from FFPE tumor tissue sections, we conducted RPPA on matched samples of FF and FFPE tissues using a set of 300 markers, the largest panel reported to date. Our aim was to identify markers that performed similarly when comparing the protein profiles measured in protein extracts from matched FF and FFPE tissue, using RPPA assays established for use in frozen tissues. Correlating selected markers and assays in such a way should qualify RPPA for further use with FFPE tissues of clinical relevance, e.g. in PD marker studies. In this paper, we have specifically focused on the technical issues relevant for using the RPPA platform in a clinical setting, and did not address the biology of the test systems used in detail. However, the models used have been pre-characterized to identify key signaling parameters in context of targeted drug treatment (42). We conducted a systematic comparison of RPPA protein profiles in matched FF and FFPE tumor tissues resected from three different xenograft models of human cancer, each treated with targeted therapeutic antibodies that have previously been shown to achieve tumor growth inhibition. Furthermore, we investigated the effect of targeted drug treatment on protein expression and activation status, and the concordance of matched FF and FFPE tissue RPPA profiles. Finally, with one of the applied tumor models, we compared a set of protein profiles measured with two different multiple assay platforms - the RPPA and the Luminex Bio-Plex system, and discuss their relevance with respect to the analysis of FFPE tissue.     

Metabolic effects of intravenous LCT or MCT/LCT lipid emulsions in preterm infants

Most lipid emulsions for parenteral feeding of premature infants are based on long-chain triacylglycerols (LCTs), but inclusion of medium-chain triacylglycerols (MCTs) might provide a more readily oxidizable energy source. The influence of these emulsions on fatty acid composition and metabolism was studied in 12 premature neonates, who were randomly assigned to an LCT emulsion (control) or an emulsion with a mixture of MCT and LCT (1:1). On study day 7, all infants received [13C]linoleic (LA) and [13C]alpha-linolenic acid (ALA) tracers orally. Plasma phospholipid (PL) and triacylglycerol (TG) fatty acid composition and 13C enrichments of plasma PL fatty acids were determined on day 8. After 8 days of lipid infusion, plasma TGs in the MCT/LCT group had higher contents of C8:0 (0.50 +/- 0.60% vs. 0.10 +/- 0.12%; means +/- SD) and C10:0 (0.66 +/- 0.51% vs. 0.15 +/- 0.17%) than controls. LA content of plasma PLs was slightly lower in the MCT/LCT group (16.47 +/- 1.16% vs. 18.57 +/- 2.09%), whereas long-chain polyunsaturated derivatives (LC-PUFAs) of LA and ALA tended to be higher. The tracer distributions between precursors and products (LC-PUFAs) were not significantly different between groups. Both lipid emulsions achieve similar plasma essential fatty acid (EFA) contents and similar proportional conversion of EFAs to LC-PUFAs. The MCT/LCT emulsion seems to protect EFAs and LC-PUFAs from beta-oxidation.     

Aerial “flycatching”: non-predatory birds can catch small birds in flight

Aerial flycatching — the lightning-fast seizure of flying small birds in the beak of larger, not normally predatory birds, only a few cases of which are treated in the literature — is here described and discussed for white storks (Ciconia ciconia) and crows (Corvidae).Communicated by F. Bairlein     

Renal fibrosis and proteomics: current knowledge and still key open questions for proteomic investigation

Renal tubulo-interstitial fibrosis is a non-specific process, representing the final common pathway for all kidney diseases, irrespective of their initial cause, histological injury, or etiology, leading to gradual expansion of the fibrotic mass which destroys the normal structure of the tissue and results in organ dysfunction and, ultimately, in end-stage organ failure. Proteomic studies of the fibrotic pathophysiological mechanisms have been performed in cell cultures, animal models and human tissues, addressing some of the key issues. This article will review proteomic contribution to the raising current knowledge on renal fibrosis biology and also mention seminal open questions to which proteomic techniques and proteomists could fruitfully contribute.     

Über die tagesperiodischen Änderungen des Reaktionsvermögens von Keimpflanzen auf niedrige Temperatur

Ohne ZusammenfassungMit 40 Textabbildungen.     

Vergleichende Untersuchung von Jugendentwicklung und Zugverhalten bei Garten- und Hausrotschwanz,Phoenicurus phoenicurus undPh. ochruros

Zusammenfassung An je 12 handaufgezogenen Garten- und Hausrotschwänzen wurden Jugendmauser, Fettdeposition und Zugunruhe erfaßt und mit entsprechenden Daten freilebender Artgenossen verglichen. Die Daten stimmen gut mit denen freilebender Artgenossen überein. Beim Gartenrotschwanz setzt die Jugendmauser in frühem Alter ein und verläuft rasch, und Fettdeposition und Zugunruhe beginnen, ehe die Mauser beendet wird. Er zeigt das typische Bild eines frühwegziehenden Interkontinentalziehers. Beim Hausrotschwanz hingegen wird die Jugendmauser trotz ihrer großen Länge beendet, bevor Fettdeposition und Zugunruhe einsetzen, und beide haben geringeren Umfang. Er bietet das Bild eines weniger ausgeprägten Ziehers und eines Intrakontinentalziehers. Beide Arten zeigen ihre großen Unterschiede in Jugendentwicklung und Zugverhalten in weitgehend entsprechenden Versuchsbedingungen, vor allem unter ganz ähnlichen photoperiodischen Bedingungen. Das spricht dafür, daß diese Unterschiede einer stark endogenen, wahrscheinlich einer stark genetischen Kontrolle unterliegen. Der Gartenrotschwanz — als Weitstrekkenzieher — entwickelt viel, der Hausrotschwanz — als Kurz- bis Mittelstreckenzieher — weit weniger Nachtunruhe. Die Zeit, in der Nachtunruhe produziert wird, stimmt bei beiden Arten sehr gut mit der Zugzeit überein. Die Nachtunruhe ist daher bei beiden Arten typische Zugunruhe. Die verschiedenen gemessenen Zugunruhewerte stimmen z. T. sehr gut mit den zurückzulegenden Zugstrecken überein, z. T. zeigen sie erhebliche Abweichungen. Prinzipiell lassen sich die Daten jedoch alle gut im Sinne endogener Zug-Zeitprogramme interpretieren, wie sie früher für Sylviiden nachgewiesen wurden. Demnach lassen sich die Vorstellungen endogener Zug-Zeitprogramme nunmehr auf eine weitere Vogelgruppe, nämlich die kleinen Drosselvögel, ausdehnen.

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A comparative study of juvenile development, migratory restlessness and migratory behaviour in the Redstart and Black Redstart

Summary Juvenile development, migratory disposition and migratory activity were investigated in Redstarts and Black Redstarts. In each 12 hand-raised individuals, patterns of juvenile moult, fat deposition and migratory restlessness were determined and compared with corresponding data from freeliving conspecifics. There was good agreement between the data from hand-raised and feral birds. In the Redstart, juvenile moult starts early and proceeds rapidly and fat deposition and migratory restlessness start before the moult has ended. The Redstart is typical for an early departing intercontinental migrant. In the Black Redstart, however, the moult, despite its long duration was clearly separated from the migratory events, and fat deposition and migratory restlessness are both less pronounced than in the Redstart. The patterns of the Black Redstart were typical for a less pronounced or an intracontinental migrant. Both species produced the large differences in juvenile development and migratory behaviour in widely corresponding experimental conditions, above all in very similar photoperiodic conditions. This suggests that these differences were based to a high degree on endogenous, probably genetic factors. The Redstart, as a long-distance migrant, developed a lot, and the Black Redstart, a short- to middle-distance migrant, far less nocturnal restlessness. In both species the period in which nocturnal restlessness developed corresponded very well with the migratory season. Thus this restlessness was typical migratory restlessness. The various measurements of restlessness obtained corresponded in part with the distances covered during migration although there were substantial deviations. In principle, however, all the data can well be interpreted in terms of endogenous time programs for migration as they have been formerly demonstrated for Sylviid species. Thus the concept of these programs can now be extended to another bird group — to small Turdiid species.

     

Preparation and characterization of dinuclear palladium tetraamin-thiophenolate complexes coligated by bridging acetate and acetamidate units

The aromatic thioether (2,6-bis((2-(dimethylamino)ethylamino)methyl)phenyl)(tert-butyl)sulfane (6) reacts with [Pd(NCCH₃)₂Cl₂] under S-C bond cleavage to give the dinuclear palladium(II) complex [L³Pd₂(μ-Cl)]²⁺ (7), where (L³)⁻ = 2,6-bis((2-(dimethylamino)ethylamino)methyl)-thiophenolate. Complex 7 reacts readily with sodium acetate and sodium acetamide by the displacement of the bridging chloride group forming [L³Pd₂(μ-OAc)]²⁺ (8) and [L³Pd₂(μ-ONHCCH₃)]²⁺ (9), respectively. Complex 8 can also be prepared by the reaction of 6 with [Pd(OAc)₂]. All complexes were isolated as perchlorate salts and fully characterized by ESI-MS, IR, ¹H, and ¹³C NMR spectroscopy. The structures of 7[ClO₄] and 9[ClO₄]₂ have been determined by X-ray crystallography. The latter structure reveals a μ_1,3-bridging acetamidate unit showing that (L³)⁻ can alter its conformation sufficiently to accommodate a multi-atom bridging species between the two Pd atoms.     

Influence of FADS polymorphisms on tracking of serum glycerophospholipid fatty acid concentrations and percentage composition in children

Background

Tracking of fatty acid (FA) contribution to plasma or serum lipids over time was shown in children and adults. However, the potential role of FADS gene variants has not been investigated.

Methods and Principal Findings

Serum GP FA composition of 331 children aged 2 and 6 years, participating in an ongoing birth cohort study, was analyzed. Correlation coefficients were estimated to describe FA tracking over 4 years and to assess the influence of FADS variants on tracking. We found low to moderate tracking (r = 0.12–0.49) of FA compositions and concentration between 2 and 6 years. Concentration changes of total monounsaturated FA and total saturated FA over time correlated closely (r = 0.79) but percentage values were unrelated (r = −0.02). Tracking for n-6 long chain polyunsaturated fatty acid (LC-PUFA) concentrations was lower in subjects homozygous for the major allele of FADS variants and higher in carriers of at least one minor allele, whereas for total n-3 LC-PUFA concentrations and compositions this was vice versa. For individual n-3 PUFA inconsistent results were found.

Conclusions and Significance

Serum GP FA composition shows low to moderate tracking over 4 years with a higher tracking for LC-PUFA metabolites than for their precursor FA. Serum PUFA levels and their tracking seem to be more influenced by lipid and lipoprotein metabolism than by FA specific pathways.     

Effect of salt and pH on the activation of photoactive yellow protein and gateway mutants Y98Q and Y98F

We investigated the photocycle of mutants Y98Q and Y98F of the photoactive yellow protein (PYP) from Halorhodospira halophila. Y98 is located in the beta4-beta5 loop and is thought to interact with R52 in the alpha3-alpha4 loop thereby stabilizing this region. Y98 is conserved in all known PYP species, except in Ppr and Ppd where it is replaced by F. We find that replacement of Y98 by F has no significant effect on the photocycle kinetics. However, major changes were observed with the Y98Q mutant. Our results indicate a requirement for an aromatic ring at position 98, especially for recovery and a normal I1/I2 equilibrium. The ring of Y98 could stabilize the beta4-beta5 loop. Alternatively, the Y98 ring could transiently interact with the isomerized chromophore ring, thereby stabilizing the I2 intermediate in the I1/I2 equilibrium. For Y98Q, the decay of the signaling state I2' was slowed by a factor of approximately 40, and the rise of the I2 and I2' intermediates was slowed by a factor of 2-3. Moreover, the I1 intermediate is in a pH-dependent equilibrium with I2/I2' with the ratio of the I1 and I2 populations close to one at pH 7 and 50 mM KCl. From pH 5.5 to 8, the equilibrium shifts toward I1, with a pKa of approximately 6.3. Above pH 8, the populations of I1 and I2/I2' decrease due to an equilibrium between I1 and an additional species I1' which absorbs at approximately 425 nm (pKa approximately 9.8) and which we believe to be an I2-like form with a surface-exposed deprotonated chromophore. The I1/I2/I2' equilibrium was found to be strongly dependent on the KCl concentration, with salt stabilizing the signaling state I2' up to 600 mM KCl. This salt-induced transition to I2' was analyzed and interpreted as ion binding to a specific site. Moreover, from analysis of the amplitude spectra, we conclude that KCl exerts its major effect on the I2 to I2' transition, i.e., the global conformational change leading to the signaling state I2' and the exposure of a hydrophobic surface patch. In wild type and Y98F, the I1/I2 equilibrium is more on the side of I2/I2' as compared to Y98Q but is also salt-dependent at pH 7. The I2 to I2' transition appears to be controlled by an ionic lock, possibly involving the salt bridge between K110 on the beta-scaffold and E12 on the N-terminal cap. Salt binding would break the salt bridge and weaken the interaction between the two domains, facilitating the release of the N-terminal domain from the beta-scaffold in the formation of I2'.