Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.

The data-independent acquisition (DIA) approach has recently been introduced as a novel mass spectrometric method that promises to combine the high content aspect of shotgun proteomics with the reproducibility and precision of selected reaction monitoring. Here, we evaluate, whether SWATH-MS type DIA effectively translates into a better protein profiling as compared with the established shotgun proteomics. We implemented a novel DIA method on the widely used Orbitrap platform and used retention-time-normalized (iRT) spectral libraries for targeted data extraction using Spectronaut. We call this combination hyper reaction monitoring (HRM). Using a controlled sample set, we show that HRM outperformed shotgun proteomics both in the number of consistently identified peptides across multiple measurements and quantification of differentially abundant proteins. The reproducibility of HRM in peptide detection was above 98%, resulting in quasi complete data sets compared with 49% of shotgun proteomics. Utilizing HRM, we profiled acetaminophen (APAP)(1)-treated three-dimensional human liver microtissues. An early onset of relevant proteome changes was revealed at subtoxic doses of APAP. Further, we detected and quantified for the first time human NAPQI-protein adducts that might be relevant for the toxicity of APAP. The adducts were identified on four mitochondrial oxidative stress related proteins (GATM, PARK7, PRDX6, and VDAC2) and two other proteins (ANXA2 and FTCD). Our findings imply that DIA should be the preferred method for quantitative protein profiling.

Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.

To understand the structure and function of large molecular machines, accurate knowledge of their stoichiometry is essential. In this study, we developed an integrated targeted proteomics and super-resolution microscopy approach to determine the absolute stoichiometry of the human nuclear pore complex (NPC), possibly the largest eukaryotic protein complex. We show that the human NPC has a previously unanticipated stoichiometry that varies across cancer cell types, tissues and in disease. Using large-scale proteomics, we provide evidence that more than one third of the known, well-defined nuclear protein complexes display a similar cell type-specific variation of their subunit stoichiometry. Our data point to compositional rearrangement as a widespread mechanism for adapting the functions of molecular machines toward cell type-specific constraints and context-dependent needs, and highlight the need of deeper investigation of such structural variants.

Using iRT, a normalized retention time for more targeted measurement of peptides.

Multiple reaction monitoring (MRM) has recently become the method of choice for targeted quantitative measurement of proteins using mass spectrometry. The method, however, is limited in the number of peptides that can be measured in one run. This number can be markedly increased by scheduling the acquisition if the accurate retention time (RT) of each peptide is known. Here we present iRT, an empirically derived dimensionless peptide-specific value that allows for highly accurate RT prediction. The iRT of a peptide is a fixed number relative to a standard set of reference iRT-peptides that can be transferred across laboratories and chromatographic systems. We show that iRT facilitates the setup of multiplexed experiments with acquisition windows more than four times smaller compared to in silico RT predictions resulting in improved quantification accuracy. iRTs can be determined by any laboratory and shared transparently. The iRT concept has been implemented in Skyline, the most widely used software for MRM experiments.

Induction of ER Stress by an AAV5 BDD FVIII Construct Is Dependent on the Strength of the Hepatic-Specific Promoter.

Adeno-associated virus 5 (AAV5)-human factor VIII-SQ (hFVIII-SQ; valoctocogene roxaparvovec) is an AAV-mediated product under evaluation for treatment of severe hemophilia A, which contains a B-domain-deleted hFVIII (hFVIII-SQ) transgene and a hybrid liver-specific promotor (HLP). To increase FVIII-SQ expression and reduce the vector dose required, a stronger promoter may be considered. However, because FVIII-SQ is a protein known to be difficult to fold and secrete, this could potentially induce endoplasmic reticulum (ER) stress. We evaluated the effect of two AAV5-hFVIII-SQ vectors with different liver-specific promoter strength (HLP << 100ATGB) on hepatic ER stress in mice. Five weeks after receiving vehicle or vector, the percentage of transduced hepatocytes and levels of liver hFVIII-SQ DNA and RNA increased dose dependently for both vectors. At lower doses, plasma hFVIII-SQ protein levels were higher for 100ATGB. This difference was attenuated at the highest dose. For 100ATGB, liver hFVIII-SQ protein accumulated dose dependently, with increased expression of ER stress markers at the highest dose, suggesting hepatocytes reached or exceeded their capacity to fold/secrete hFVIII-SQ. These data suggest that weaker promoters may require relatively higher doses to distribute expression load across a greater number of hepatocytes, whereas relatively stronger promoters may produce comparable levels of FVIII in fewer hepatocytes, with potential for ER stress.

Transcriptomic, Proteomic, and Functional Long-Term Characterization of Multicellular Three-Dimensional Human Liver Microtissues.

Three-Dimensional (3D) liver microtissues, specifically prepared from primary human hepatocytes (PHH) in coculture with nonparenchymal cells (NPCs), have been shown to be a valuable tool for in vitro toxicology. However, a lack of thorough characterization on a functional, transcriptomic, and proteomic level of such models during long-term cultivation is evident. By integrating multiple omics technologies, we provide in this study an in-depth long-term characterization of 3D microtissues composed of PHH from three different donors cocultured with primary NPCs. The 3D human liver microtissues (hLiMTs) exhibited stable adenosine triphosphate (ATP) content and albumin secretion over 5 weeks. Histological analysis indicated a healthy liver tissue with polarized expression of bile salt export pump (BSEP) and multidrug resistance protein 2 (MRP2) in a structure reminiscent of bile canaliculi. The 3D microtissues exhibited stable basal and inducible cytochrome P450 activities up to 5 weeks in culture. Analysis of 40,716 transcripts using RNA arrays revealed distinct similarities to native human liver gene expression. Long-term culture showed a stable phenotype up to 5 weeks, with differences in liver gene expression primarily attributed to individual donors. Proteomic profiling of 2200 unique proteins by label-free LC-MS/MS revealed a relatively stable protein expression where only 7.3% were up- or downregulated more than twofold from day 7 to 35 in culture. Taken together, these results suggest that hLiMTs represent a responsive and physiologically relevant in vitro liver model that maintains stable function over 5 weeks and is therefore well suited for repeated-dose toxicity testing.

Estrogenic activity of pharmaceuticals and pharmaceutical mixtures in a yeast reporter gene system.

Pharmaceuticals enter aquatic environments in unchanged form or as metabolites. Little is known about their potential hormonal activity, which is of particular interest due to potential long-term effects on fertility and reproduction in aquatic organisms. Moreover, there is a need to assess the combined activity of pharmaceutical mixtures. In this study, 37 pharmaceuticals have been analysed in vitro for estrogenic activity using a recombinant yeast system expressing the human estrogen receptor alpha. Six pharmaceuticals belonging to different therapeutic classes, cimetidine, fenofibrate, furosemide, paracetamol, phenazone and tamoxifen, exhibited weak estrogenic activity. Furosemide showed an almost full concentration-response curve, whereas the other compounds showed low efficacy. The half-maximal activities of the pharmaceuticals were in the range of 0.66-25.53 mM. Furthermore, binary mixtures of furosemide and 17beta-estradiol (E2), and furosemide and phenazone, and mixtures of up to five active pharmaceuticals were assessed for their combinatory activity at different equipotent concentrations. The estrogenic activity of binary mixtures of furosemide with E2 and phenazone, respectively, followed the model of concentration addition (CA). Mixtures of other pharmaceuticals often deviated from the CA model, because extrapolations become inaccurate with only partial and non-parallel concentration-response curves having low efficacy. This demonstrates that full and parallel concentration-response curves are a prerequisite for accurate predictions of mixture activity. Our study demonstrates for the first time weak estrogenic activity in vitro of some common pharmaceuticals and their mixtures.

Cytotoxicity of pharmaceuticals found in aquatic systems: comparison of PLHC-1 and RTG-2 fish cell lines.

There is need for a better understanding of the ecotoxicity of pharmaceuticals present in aquatic systems as only little is known about their potential acute and chronic toxicity to aquatic organisms. In our work, we evaluate the in vitro cytotoxicity of 34 common pharmaceuticals from different classes and with different modes of action using the mitochondrial MTT reduction and neutral red uptake assays in the two fish cell lines, PLHC-1 and RTG-2. Cytotoxicity was found for 21 pharmaceuticals with EC50-values ranging from 2.1microM (1.14mgl(-1)) (doxorubicin) to 8.66mM (1200mgl(-1)) (salicylic acid). There was no significant difference between the MTT and NR assays except for an increase in absorption observed with four pharmaceuticals at low concentrations in the MTT assay with PLHC-1 cells indicating a hormesis effect. The comparison of the cell lines revealed that the PLHC-1 cell line was slightly more sensitive than the RTG-2 cell line, showing cytotoxicity at smaller concentrations. The cytotoxicity of pharmaceuticals showed a correlation with their Log D-values at physiological conditions (pH 7.0). A correlation between the in vitro data and in vivo data was found for Daphnia, but not for fish due to insufficient and heterogeneous data. Our work provides an indication that in vitro cytotoxicity assays with fish cell lines could be suited for the first screening of the acute in vivo toxicity of pharmaceuticals, thereby contributing to the reduction of in vivo experiments. Further investigations with a larger set of pharmaceuticals are needed to strengthen the reliability of the assays and to validate the correlation with in vivo data.

Generation of recombinant antibody fragments for membrane protein crystallization.

Membrane proteins are challenging targets for crystallization and structure determination by X-ray crystallography. Hurdles can be overcome by antibody-mediated crystallization. More than 25 unique structures of membrane protein:antibody complexes have already been determined. In the majority of cases, hybridoma-derived antibody fragments either in Fab or Fv fragment format were employed for these complexes. We will briefly introduce the background and current status of the strategy and describe in detail the current protocols of well-established methods for the immunization, the selection, and the characterization of antibodies, as well as the cloning, the production, and the purification of recombinant antibodies useful for structural analysis of membrane proteins.

Reverse protein arrays as novel approach for protein quantification in muscular dystrophies.

The definite molecular diagnosis in patients with muscular dystrophies often requires the assessment of muscular expression of multiple proteins in small amounts of muscle tissue. The sample material obtained in muscle biopsies is limited and the measurement of multiple proteins is often restricted to conventional, non-quantitative assays, i.e. immunohistochemistry and immunoblotting. Here, we demonstrate that reverse protein arrays are a novel and excellent material-saving method for the measurement and quantification of changes in protein expression between healthy and diseased muscle tissue as well as cultured primary myotubes. We evaluated a set of antibodies and found reproducible differences between Duchenne muscular dystrophy/limb-girdle muscular dystrophy patients and control samples for dystrophin, the sarcoglycans and the dystroglycans. As little as 10 mg of tissue is sufficient for the analysis of all diagnostically relevant proteins. The average coefficient of variation calculated for the sample signals confirmed that the method is highly reproducible. Thus, our experiments provide strong evidence that quantitative protein detection from very small amounts of muscle tissue is possible using reverse protein arrays. This technology may not only be of interest for diagnostic purposes, but also for protein quantification of multiple, follow-up biopsies during clinical trials when protein expression in muscle is considered an important outcome measure or biomarker.

Two GxxxG-like motifs facilitate promiscuous interactions of the human ErbB transmembrane domains.

Members of the ErbB/HER family of epidermal growth factor receptor tyrosine kinases cross a membrane with a single transmembrane (TM) helix. ErbB receptors form diverse homo- and heterodimers, which substantially increases the signaling potential of ErbB receptors. The involvement of the ErbB TM domains in homo- and heterodimerization is largely enigmatic. In this study, we experimentally analyzed the potential role of two conserved GxxxG-like motifs for mediating and/or stabilizing homo- and hetero-oligomeric interactions of the human ErbB TM domains. Both motifs appear to be critical for homo- and hetero-oligomeric TM helix interactions. Consequently, multiple TM structures are possible for the various ErbB homo- and heterodimers, which might be critical for the formation and TM signaling of specific ErbB pairs in vivo.

The single transmembrane domains of human receptor tyrosine kinases encode self-interactions.

Transmembrane signaling by receptor tyrosine kinases typically involves a dynamic receptor monomer-dimer equilibrium in which ligand binding to soluble extracellular domains triggers receptor dimerization and subsequent signaling events. Although the role in signal transduction of the single transmembrane helices of individual receptors, which connect the extracellular with the intracellular protein domains, is not understood in detail, we show here that the single transmembrane domains of all 58 human receptor tyrosine kinases alone have an intrinsic propensity to form stable dimeric structures within a membrane. Thus, defined interactions of the transmembrane domains are most likely generally involved in signaling by all human receptor tyrosine kinases.