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.Quantitative mass spectrometry is a powerful and widely used approach to identify differentially abundant proteins, e.g. for proteome profiling and biomarker discovery (1). Several tens of thousands of peptides and thousands of proteins can be routinely identified from a single sample injection in shotgun proteomics (2). Shotgun proteomics, however, is limited by low analytical reproducibility. This is due to the complexity of the samples that results in under sampling (supplemental Fig. 1) and to the fact that the acquisition of MS2 spectra is often triggered outside of the elution peak apex. As a result, only 17% of the detectable peptides are typically fragmented, and less than 60% of those are identified. This translates in reliable identification of only 10% of the detectable peptides (3). The overlap of peptide identification across technical replicates is typically 35–60% (4), which results in inconsistent peptide quantification. Alternatively to shotgun proteomics, selected reaction monitoring (SRM) enables quantification of up to 200–300 peptides at very high reproducibility, accuracy, and precision (5–8).Data-independent acquisition (DIA), a novel acquisition type, overcomes the semistochastic nature of shotgun proteomics (9–18). Spectra are acquired according to a predefined schema instead of dependent on the data. Targeted analysis of DIA data was introduced with SWATH-MS (19). For the originally published SWATH-MS, the mass spectrometer cycles through 32 predefined, contiguous, 25 Thomson wide precursor windows, and records high-resolution fragment ion spectra (19). This results in a comprehensive measurement of all detectable precursors of the selected mass range. The main novelty of SWATH-MS was in the analysis of the collected DIA data. Predefined fragment ions are extracted using precompiled spectrum libraries, which results in SRM-like data. Such targeted analyses are now enabled by several publicly available computational tools, in particular Spectronaut², Skyline (20), and OpenSWATH (21). The accuracy of peptide identification is evaluated based on the mProphet method (22).We introduce a novel SWATH-MS-type DIA workflow termed hyper reaction monitoring (HRM) (reviewed in (23)) implemented on a Thermo Scientific Q Exactive platform. It consists of comprehensive DIA acquisition and targeted data analysis with retention-time-normalized spectral libraries (24). Its high accuracy of peptide identification and quantification is due to three aspects. First, we developed a novel, improved DIA method. Second, we reimplemented the mProphet (22) approach in the software Spectronaut (www.spectronaut.org). Third, we developed large, optimized, and retention-time-normalized (iRT) spectral libraries.We compared HRM and state-of-the-art shotgun proteomics in terms of ability to discover differentially abundant proteins. For this purpose, we used a “profiling standard sample set” with 12 non-human proteins spiked at known absolute concentrations into a stable human cell line protein extract. This resulted in quasi complete data sets for HRM and the detection of a larger number of differentially abundant proteins as compared with shotgun proteomics. We utilized HRM to identify changes in the proteome in primary three-dimensional human liver microtissues after APAP exposure (25–27). These primary hepatocytes exhibit active drug metabolism. With a starting material of only 12,000 cells per sample, the abundance of 2,830 proteins was quantified over an APAP concentration range. Six novel NAPQI-cysteine proteins adducts that might be relevant for the toxicity of APAP were found and quantified mainly on mitochondrion-related proteins.     

Structural and functional studies of the first tripartite protein complex at the Trypanosoma brucei flagellar pocket collar

The flagellar pocket (FP) is the only endo- and exocytic organelle in most trypanosomes and, as such, is essential throughout the life cycle of the parasite. The neck of the FP is maintained enclosed around the flagellum via the flagellar pocket collar (FPC). The FPC is a macromolecular cytoskeletal structure and is essential for the formation of the FP and cytokinesis. FPC biogenesis and structure are poorly understood, mainly due to the lack of information on FPC composition. To date, only two FPC proteins, BILBO1 and FPC4, have been characterized. BILBO1 forms a molecular skeleton upon which other FPC proteins can, theoretically, dock onto. We previously identified FPC4 as the first BILBO1 interacting partner and demonstrated that its C-terminal domain interacts with the BILBO1 N-terminal domain (NTD). Here, we report by yeast two-hybrid, bioinformatics, functional and structural studies the characterization of a new FPC component and BILBO1 partner protein, BILBO2 (Tb927.6.3240). Further, we demonstrate that BILBO1 and BILBO2 share a homologous NTD and that both domains interact with FPC4. We have determined a 1.9 Å resolution crystal structure of the BILBO2 NTD in complex with the FPC4 BILBO1-binding domain. Together with mutational analyses, our studies reveal key residues for the function of the BILBO2 NTD and its interaction with FPC4 and evidenced a tripartite interaction between BILBO1, BILBO2, and FPC4. Our work sheds light on the first atomic structure of an FPC protein complex and represents a significant step in deciphering the FPC function in Trypanosoma brucei and other pathogenic kinetoplastids.     

Arterial remodeling and plasma volume expansion in caveolin-1-deficient mice

Caveolin-1 (Cav-1) is essential for the morphology of membrane caveolae and exerts a negative influence on a number of signaling systems, including nitric oxide (NO) production and activity of the MAP kinase cascade. In the vascular system, ablation of caveolin-1 may thus be expected to cause arterial dilatation and increased vessel wall mass (remodeling). This was tested in Cav-1 knockout (KO) mice by a detailed morphometric and functional analysis of mesenteric resistance arteries, shown to lack caveolae. Quantitative morphometry revealed increased media thickness and media-to-lumen ratio in KO. Pressure-induced myogenic tone and flow-induced dilatation were decreased in KO arteries, but both were increased toward wild-type (WT) levels following NO synthase (NOS) inhibition. Isometric force recordings following NOS inhibition showed rightward shifts of passive and active length-force relationships in KO, and the force response to alpha(1)-adrenergic stimulation was increased. In contrast, media thickness and force response of the aorta were unaltered in KO vs. WT, whereas lumen diameter was increased. Mean arterial blood pressure during isoflurane anesthesia was not different in KO vs. WT, but greater fluctuation in blood pressure over time was noted. Following NOS inhibition, fluctuations disappeared and pressure increased twice as much in KO (38 +/- 6%) compared with WT (17 +/- 3%). Tracer-dilution experiments showed increased plasma volume in KO. We conclude that NO affects blood pressure more in Cav-1 KO than in WT mice and that restructuring of resistance vessels and an increased responsiveness to adrenergic stimulation compensate for a decreased tone in Cav-1 KO mice.     

What is the Value of a Good Map? An Example Using High Spatial Resolution Imagery to Aid Riparian Restoration

Riparian areas contain structurally diverse habitats that are challenging to monitor routinely and accurately over broad areas. As the structural variability within riparian areas is often indiscernible using moderate-scale satellite imagery, new mapping techniques are needed. We used high spatial resolution satellite imagery from the QuickBird satellite to map harvested and intact forests in coastal British Columbia, Canada. We distinguished forest structural classes used in riparian restoration planning, each with different restoration costs. To assess the accuracy of high spatial resolution imagery relative to coarser imagery, we coarsened the pixel resolution of the image, repeated the classifications, and compared results. Accuracy assessments produced individual class accuracies ranging from 70 to 90% for most classes; whilst accuracies obtained using coarser scale imagery were lower. We also examined the implications of map error on riparian restoration budgets derived from our classified maps. To do so, we modified the confusion matrix to create a cost error matrix quantifying costs associated with misclassification. High spatial resolution satellite imagery can be useful for riparian mapping; however, errors in restoration budgets attributable to misclassification error can be significant, even when using highly accurate maps. As the spatial resolution of imagery increases, it will be used more routinely in ecosystem ecology. Thus, our ability to evaluate map accuracy in practical, meaningful ways must develop further. The cost error matrix is one method that can be adapted for conservation and planning decisions in many ecosystems.     

Characterization of the binding of cytosolic phospholipase A2 alpha and NOX2 NADPH oxidase in mouse macrophages

Molecular Biology Reports - Previous studies have demonstrated that cytosolic phospholipase A2α (cPLA2α) is required for NOX2 NADPH oxidase activation in human and mouse phagocytes....     

Expression of NLRP3 Inflammasomes in Neurogenic Niche Contributes to the Effect of Spatial Learning in Physiological Conditions but Not in Alzheimer’s Type Neurodegeneration

A common feature of neurodegenerative disorders, in particular Alzheimer's disease (AD), is a chronic neuroinflammation associated with aberrant neuroplasticity. Development of neuroinflammation affects efficacy of stem and progenitor cells proliferation, differentiation, migration, and integration of newborn cells into neural circuitry. However, precise mechanisms of neurogenesis alterations in neuroinflammation are not clear yet. It is well established that expression of NLRP3 inflammasomes in glial cells marks neuroinflammatory events, but less is known about contribution of NLRP3 to deregulation of neurogenesis within neurogenic niches and whether neural stem cells (NSCs), neural progenitor cells (NPCs) or immature neuroblasts may express inflammasomes in (patho)physiological conditions. Thus, we studied alterations of neurogenesis in rats with the AD model (intra-hippocampal injection of Aβ1-42). We found that in Aβ-affected brain, number of CD133+ cells was elevated after spatial training in the Morris water maze. The number of PSA-NCAM+ neuroblasts diminished by Aβ injection was completely restored by subsequent spatial learning. Spatial training leads to elevated expression of NLRP3 inflammasomes in the SGZ (subgranular zones): CD133+ and PSA-NCAM+ cells started to express NLRP3 in sham-operated, but not AD rats. Taken together, our data suggest that expression of NLRP3 inflammasomes in CD133+ and PSA-NCAM+ cells may contribute to stimulation of adult neurogenesis in physiological conditions, whereas Alzheimer’s type neurodegeneration abolishes stimuli-induced overexpression of NLRP3 within the SGZ neurogenic niche.

     

Oestrogen receptors interact with the α-catalytic subunit of AMP-activated protein kinase

Normal and pathological stressors engage the AMP-activated protein kinase (AMPK) signalling axis to protect the cell from energetic pressures. Sex steroid hormones also play a critical role in energy metabolism and significantly modify pathological progression of cardiac disease, diabetes/obesity and cancer. AMPK is targeted by 17β-oestradiol (E2), the main circulating oestrogen, but the mechanism by which E2 activates AMPK is currently unknown. Using an oestrogen receptor α/β (ERα/β) positive (T47D) breast cancer cell line, we validated E2-dependent activation of AMPK that was mediated through ERα (not ERβ) by using three experimental strategies. A series of co-immunoprecipitation experiments showed that both ERs associated with AMPK in cancer and striated (skeletal and cardiac) muscle cells. We further demonstrated direct binding of ERs to the α-catalytic subunit of AMPK within the βγ-subunit-binding domain. Finally, both ERs interacted with the upstream liver kinase B 1 (LKB1) kinase complex, which is required for E2-dependent activation of AMPK. We conclude that E2 activates AMPK through ERα by direct interaction with the βγ-binding domain of AMPKα.     

Nanostructuring of Continuous Gold Film by Laser Radiation Under Surface Plasmon Polariton Resonance Conditions

The physical mechanisms of metallic nanoparticles formation by laser technology were studied. The system air/Au film/glass was irradiated by laser at the conditions of surface plasmon resonance. A surface electromagnetic wave was excited in Kretchmann configuration by the fundamental and second harmonics of the Q-switched YAG/Nd⁺³ laser with pulse power density close to the threshold of melting. Nanostructuring of Au film was observed only for the second harmonic (λ = 0.532 μm) irradiation at the surface plasmon polariton resonance (SPR) conditions. Estimations were done using the interference model of the differently directed plasmon polariton waves excited by a surface electromagnetic wave on the metal surface. It was shown that a regular pattern of locally heated spots can be formed in a metallic film by pulsed laser irradiation. The spatial distribution of this pattern is close to the period of interference. The observed effect of laser nanofragmentation is explained by the self-organization of plasmon polariton subsystem in the process of Au nanoparticles formation at high laser intensity levels. These methods open new possibilities for nanostructured surfaces formation utilizing simple self-organization processes.