Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment.

Circulating extracellular matrix (ECM) proteins are serological biomarkers of interest due to their association with pathologies involving disease processes such as fibrosis and cancers. In this study, we investigate the potential for serum biomarker research using differential protease specificity (DPS), leveraging alternate protease specificity as a targeting mechanism to selectively digest circulating ECM protein serum proteins. A proof-of-concept study is presented using serum from patients with cirrhotic liver or hepatocellular carcinoma. The approach uses collagenase DPS for digestion of deglycosylated serum and liquid-chromatography-trapped ion mobility-tandem mass spectrometry (LC-TIMS-MS/MS) to enhance the detection of ECM proteins in serum. It requires no sample enrichment and minimizes the albumin average precursor intensity readout to less than 1.2%. We further demonstrate the capabilities for using the method as a high-throughput matrix-assisted laser/desorption ionization mass spectrometry (MALDI-MS) assay coupled with reference library searching. A goal is to improve the depth and breadth of biofluid proteomics for noninvasive assays.

Stochastic assembly of biomacromolecular complexes: impact and implications on charge interpretation in native mass spectrometry.

Native mass spectrometry is a potent method for characterizing biomacromolecular assemblies. A critical aspect to extracting accurate mass information is the correct inference of the ion ensemble charge states. While a variety of experimental strategies and algorithms have been developed to facilitate this, virtually all approaches rely on the implicit assumption that any peaks in a native mass spectrum can be directly attributed to an underlying charge state distribution. Here, we demonstrate that this paradigm breaks down for several types of macromolecular protein complexes due to the intrinsic heterogeneity induced by the stochastic nature of their assembly. Utilizing several protein assemblies of adeno-associated virus capsids and ferritin, we demonstrate that these particles can produce a variety of unexpected spectral appearances, some of which appear superficially similar to a resolved charge state distribution. When interpreted using conventional charge inference strategies, these distorted spectra can lead to substantial errors in the calculated mass (up to ∼5%). We provide a novel analytical framework to interpret and extract mass information from these spectra by combining high-resolution native mass spectrometry, single particle Orbitrap-based charge detection mass spectrometry, and sophisticated spectral simulations based on a stochastic assembly model. We uncover that these mass spectra are extremely sensitive to not only mass heterogeneity within the subunits, but also to the magnitude and width of their charge state distributions. As we postulate that many protein complexes assemble stochastically, this framework provides a generalizable solution, further extending the usability of native mass spectrometry in the characterization of biomacromolecular assemblies.

Methodology-related pseudohyperkalemia associated with marked muscle enzyme leakage in a dog.

BACKGROUND: As hyperkalemia may be life-threatening, it is critical to recognize artifactually increased potassium concentrations. Pseudohyperkalemia may occur in myopathies when using the VetScan2 analyzer (VS2), but the degree of pseudohyperkalemia and relationships relative to creatine kinase activity (CK) are unknown. OBJECTIVES: We aimed to determine what degree of muscle enzyme leakage, as reflected by increased serum CK activity, results in cases with falsely elevated potassium concentrations when measured by the VS2. We also sought to establish if a linear relationship exists between potassium concentrations measured by the VS2 and CK activity. METHODS: Serum samples from dogs with increased CK activity and with CK activity within the reference interval and without clinically relevant biochemical alterations were used to create diluted samples having various CK activities. Potassium concentrations and CK activities were determined on VS2 and Cobas c501 (Cobas) analyzers. Wilcoxon signed rank, Bland-Altman, and Passing-Bablok analyses were used to compare potassium concentrations generated by the VS2 and Cobas analyzers. Least squares regression analysis was performed to evaluate if a linear relationship exists between VS2 potassium concentrations and Cobas CK activities. RESULTS: Potassium concentrations from the VS2 were higher (median and standard deviation (SD) = 5.2 +/- 0.46 mmol/L) than those from the Cobas analyzer (4.4 +/- 0.35 mmol/L; P < 0.000), and a positive mean bias was found (mean difference = 0.774 mmol/L; 95% Confidence Interval (CI) = 0.706-0.842; limits of agreement = 0.21-1.34). Passing-Bablok regression showed a positive proportional bias for potassium concentrations on the VS2 compared with paired Cobas results (Slope = 1.328; 95% CI = 1.100-1.500) but did not reveal systematic bias (Intercept = -0.714; 95% CI = -1.46-0.265). Least squares regression analysis showed a poor non-significant relationship (R2 = 0.19) between potassium measured by the VS2 and CK measured by the Cobas analyzer. CONCLUSIONS: A defined threshold value of CK activity at which potassium concentration begins to falsely increase when measured on the VS2 was not established as data widely varied. A poor non-significant relationship between potassium concentrations and CK activities did not allow prediction of the threshold at which falsely increased potassium concentrations would be expected on the VS2.

Perspectives on pediatric congenital aortic valve stenosis: Extracellular matrix proteins, post translational modifications, and proteomic strategies.

In heart valve biology, organization of the extracellular matrix structure is directly correlated to valve function. This is especially true in cases of pediatric congenital aortic valve stenosis (pCAVS), in which extracellular matrix (ECM) dysregulation is a hallmark of the disease, eventually leading to left ventricular hypertrophy and heart failure. Therapeutic strategies are limited, especially in pediatric cases in which mechanical and tissue engineered valve replacements may not be a suitable option. By identifying mechanisms of translational and post-translational dysregulation of ECM in CAVS, potential drug targets can be identified, and better bioengineered solutions can be developed. In this review, we summarize current knowledge regarding ECM proteins and their post translational modifications (PTMs) during aortic valve development and disease and contributing factors to ECM dysregulation in CAVS. Additionally, we aim to draw parallels between other fibrotic disease and contributions to ECM post-translational modifications. Finally, we explore the current treatment options in pediatrics and identify how the field of proteomics has advanced in recent years, highlighting novel characterization methods of ECM and PTMs that may be used to identify potential therapeutic strategies relevant to pCAVS.

Defining the Tumor Microenvironment by Integration of Immunohistochemistry and Extracellular Matrix Targeted Imaging Mass Spectrometry.

Breast stroma plays a significant role in breast cancer risk and progression yet remains poorly understood. In breast stroma, collagen is the most abundantly expressed protein and its increased deposition and alignment contributes to progression and poor prognosis. Collagen post-translation modifications such as hydroxylated-proline (HYP) control deposition and stromal organization. The clinical relevance of collagen HYP site modifications in cancer processes remains undefined due to technical issues accessing collagen from formalin-fixed, paraffin-embedded (FFPE) tissues. We previously developed a targeted approach for investigating collagen and other extracellular matrix proteins from FFPE tissue. Here, we hypothesized that immunohistochemistry staining for fibroblastic markers would not interfere with targeted detection of collagen stroma peptides and could reveal peptide regulation influenced by specific cell types. Our initial work demonstrated that stromal peptide peak intensities when using MALD-IMS following IHC staining (αSMA, FAP, P4HA3 and PTEN) were comparable to serial sections of nonstained tissue. Analysis of histology-directed IMS using PTEN on breast tissues and TMAs revealed heterogeneous PTEN staining patterns and suggestive roles in stromal protein regulation. This study sets the foundation for investigations of target cell types and their unique contribution to collagen regulation within extracellular matrix niches.

Methemoglobin concentrations in three salmonid species following exposure to benzocaine or tricaine methanesulfonate.

Methemoglobin is hemoglobin containing ferric iron rather than ferrous iron which renders it incapable of binding to oxygen. Blood sampling of fish is done under sedation or general anesthesia. Tricaine methanesulfonate (TMS) or benzocaine is commonly used but both can cause oxidation of hemoglobin to methemoglobin. Our objective was to determine if methemoglobin concentrations in healthy rainbow trout (Oncorhynchus mykiss), brook trout (Salvelinus fontinalis), or Atlantic salmon (Salmo salar) increase during sedation with 25 mg/L of a 10% benzocaine solution or with repeated short anesthetizations by 65 mg/L of 10% benzocaine solution or 65 mg/L of TMS. Sedation by benzocaine caused a significant increase in methemoglobin in all species over time (P < 0.05). The methemoglobin percentage in brook trout increased by 129%, rainbow trout by 42%, and Atlantic salmon by 49%. The methemoglobin in brook trout was significantly greater than the other species at multiple time points. Repeated brief anesthetizing by benzocaine and TMS caused significant methemoglobin by 60 (P < 0.05), 90 (P < 0.01), and 120 min (P < 0.001) in brook trout but no significant change in methemoglobin in rainbow trout or Atlantic salmon except at 120 min in Atlantic salmon (P < 0.05) repeatedly anesthetized with benzocaine. For example, following multiple anesthetizations with benzocaine, the methemoglobin percentage in brook trout increased by 140%, whereas the rise in methemoglobin in rainbow trout and Atlantic salmon was more modest (37% increase in Rainbow trout and 53% increase in Atlantic salmon). Following multiple anesthetizations with TMS, the methemoglobin increased by 90%, 5%, and 1% in brook trout, rainbow trout, and Atlantic salmon, respectively. Methemoglobin may increase significantly over time in fish immersed in a sedating dose of benzocaine or repeatedly anesthetized with benzocaine or TMS. The susceptibility varies with the individual and species with brook trout being more susceptible than Atlantic salmon or rainbow trout.

An in vivo platform to select and evolve aggregation-resistant proteins.

Protein biopharmaceuticals are highly successful, but their utility is compromised by their propensity to aggregate during manufacture and storage. As aggregation can be triggered by non-native states, whose population is not necessarily related to thermodynamic stability, prediction of poorly-behaving biologics is difficult, and searching for sequences with desired properties is labour-intensive and time-consuming. Here we show that an assay in the periplasm of E. coli linking aggregation directly to antibiotic resistance acts as a sensor for the innate (un-accelerated) aggregation of antibody fragments. Using this assay as a directed evolution screen, we demonstrate the generation of aggregation resistant scFv sequences when reformatted as IgGs. This powerful tool can thus screen and evolve 'manufacturable' biopharmaceuticals early in industrial development. By comparing the mutational profiles of three different immunoglobulin scaffolds, we show the applicability of this method to investigate protein aggregation mechanisms important to both industrial manufacture and amyloid disease.

Stakeholder Requirements for an Ethical Framework to Sustain Multiple Research Projects in an Emerging Living Lab Involving Older Adults.

Living Lab (LL) research should follow clear ethical guidelines and principles. While these exist in specific disciplinary contexts, there is a lack of tailored and specific ethical guidelines for the design, development, and implementation of LL projects. As well as the complexity of these dynamic and multi-faceted contexts, the engagement of older adults, and adults with reducing cognitive and physical capacity in LL research, poses additional ethical challenges. Semi-structured interviews were undertaken with 26 participants to understand multistakeholder experiences related to user engagement and related ethical issues in emerging LL research. The participants' experiences and concerns are reported and translated into an ethical framework to guide future LL research initiatives.

A Rapid Array-Based Approach to N-Glycan Profiling of Cultured Cells.

Typically, N-glycosylation studies done on cultured cells require up to millions of cells followed by lengthy preparation to release, isolate, and profile N-glycans. To overcome these limitations, we report a rapid array-based workflow for profiling N-glycan signatures from cells, adapted from imaging mass spectrometry used for on-tissue N-glycan profiling. Using this approach, N-glycan profiles from a low-density array of eight cell chambers could be reported within 4 h of completing cell culture. Approaches are demonstrated that account for background N-glycans due to serum media. Normalization procedures are shown. The method is robust and reproducible, requiring as few as 3000 cells per replicate with a 3-20% coefficient of variation to capture label-free profiles of N-glycans. Quantification by stable isotopic labeling of N-glycans in cell culture is demonstrated and adds no additional time to preparation. Utility of the method is demonstrated by measurement of N-glycan turnover rates due to induction of oxidative stress in human primary aortic endothelial cells. The developed method and ancillary tools serve as a foundational launching point for rapid profiling of N-glycans ranging from high-density arrays down to single cells in culture.

An exploratory study of barriers to inclusion in the European workplace.

BACKGROUND: The European Disability Strategy (2010-2020) seeks to significantly raise the proportion of people with disabilities working in the open labour market. The ERGO WORK project is a collaboration of academic and industrial partners in six European countries, focused on understanding and tackling barriers to workplace inclusion for workers with disabilities. METHODS: This study sought to explore the perceptions and needs of stakeholders in terms of workplace adaptation to the needs of employees with disabilities. An exploratory online survey was completed by 480 participants across six countries. RESULTS: The analysis suggests that workplaces could be further improved to meet the needs of employees with considerable scope for training within companies to raise awareness about employees' needs, employers' obligations and workplace adaptation. CONCLUSIONS: This snapshot suggests there is still a gap between intent and reality in workplace inclusion and further strategies are needed to improve the opportunities for employees with disabilities. The paper argues that ergonomics may have a key role to play in tackling these challenges and adapting the workplace environment and job design to suit the needs of individual employees. Implications for rehabilitation This study suggests there is considerable scope for workplace adaptation and improvements to meet the needs of employees with disabilities. Employers need and want further specialist practitioner guidance to facilitate workplace inclusion and support adaptation to individual needs. Organisations would benefit from training to raise awareness about potential solutions and approaches that would support more widespread employment of people with disabilities.

An in vivo platform for identifying inhibitors of protein aggregation.

Protein aggregation underlies an array of human diseases, yet only one small-molecule therapeutic targeting this process has been successfully developed to date. Here, we introduce an in vivo system, based on a ß-lactamase tripartite fusion construct, that is capable of identifying aggregation-prone sequences in the periplasm of Escherichia coli and inhibitors that prevent their aberrant self-assembly. We demonstrate the power of the system using a range of proteins, from small unstructured peptides (islet amyloid polypeptide and amyloid ß) to larger, folded immunoglobulin domains. Configured in a 48-well format, the split ß-lactamase sensor readily differentiates between aggregation-prone and soluble sequences. Performing the assay in the presence of 109 compounds enabled a rank ordering of inhibition and revealed a new inhibitor of islet amyloid polypeptide aggregation. This platform can be applied to both amyloidogenic and other aggregation-prone systems, independent of sequence or size, and can identify small molecules or other factors able to ameliorate or inhibit protein aggregation.

ESI-IMS-MS: A method for rapid analysis of protein aggregation and its inhibition by small molecules.

Electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is a powerful method for the study of conformational changes in protein complexes, including oligomeric species populated during protein self-aggregation into amyloid fibrils. Information on the mass, stability, cross-sectional area and ligand binding capability of each transiently populated intermediate, present in the heterogeneous mixture of assembling species, can be determined individually in a single experiment in real-time. Determining the structural characterisation of oligomeric species and alterations in self-assembly pathways observed in the presence of small molecule inhibitors is of great importance, given the urgent demand for effective therapeutics. Recent studies have demonstrated the capability of ESI-IMS-MS to identify small molecule modulators of amyloid assembly and to determine the mechanism by which they interact (positive, negative, non-specific binding, or colloidal) in a high-throughput format. Here, we demonstrate these advances using self-assembly of Aß40 as an example, and reveal two new inhibitors of Aß40 fibrillation.

Insights into the consequences of co-polymerisation in the early stages of IAPP and Aß peptide assembly from mass spectrometry.

The precise molecular mechanisms by which different peptides and proteins assemble into highly ordered amyloid deposits remain elusive. The fibrillation of human amylin (also known as islet amyloid polypeptide, hIAPP) and the amyloid-beta peptide (Aß-40) are thought to be pathogenic factors in Type 2 diabetes mellitus (T2DM) and Alzheimer's disease (AD), respectively. Amyloid diseases may involve co-aggregation of different protein species, in addition to the self-assembly of single precursor sequences. Here we investigate the formation of heterogeneous pre-fibrillar, oligomeric species produced by the co-incubation of hIAPP and Aß-40 using electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS)-based methods. Conformational properties and gas-phase stabilities of amyloid oligomers formed from hIAPP or Aß40 alone, and from a 1 : 1 mixture of hIAPP and Aß40 monomers, were determined and compared. We show that co-assembly of the two sequences results in hetero-oligomers with distinct properties and aggregation kinetics properties compared with the homo-oligomers present in solution. The observations may be of key significance to unravelling the mechanisms of amyloid formation in vivo and elucidating how different sequences and/or assembly conditions can result in different fibril structures and/or pathogenic outcomes.

Screening and classifying small-molecule inhibitors of amyloid formation using ion mobility spectrometry-mass spectrometry.

The search for therapeutic agents that bind specifically to precursor protein conformations and inhibit amyloid assembly is an important challenge. Identifying such inhibitors is difficult because many protein precursors of aggregation are partially folded or intrinsically disordered, which rules out structure-based design. Furthermore, inhibitors can act by a variety of mechanisms, including specific or nonspecific binding, as well as colloidal inhibition. Here we report a high-throughput method based on ion mobility spectrometry-mass spectrometry (IMS-MS) that is capable of rapidly detecting small molecules that bind to amyloid precursors, identifying the interacting protein species and defining the mode of inhibition. Using this method we have classified a variety of small molecules that are potential inhibitors of human islet amyloid polypeptide (hIAPP) aggregation or amyloid-beta 1-40 aggregation as specific, nonspecific, colloidal or non-interacting. We also demonstrate the ability of IMS-MS to screen for inhibitory small molecules in a 96-well plate format and use this to discover a new inhibitor of hIAPP amyloid assembly.

Characterization of functionally distinct mitochondrial subpopulations.

Mitochondrial stress results in changes in mitochondrial function, morphology and homeostasis (biogenesis, fission/fusion, mitophagy) and may lead to changes in mitochondrial subpopulations. While flow cytometric techniques have been developed to quantify features of individual mitochondria related to volume, Ca(2+) concentration, mtDNA content, respiratory capacity and oxidative damage, less information is available concerning the identification and characterization of mitochondrial subpopulations, particularly in epithelial cells. Mitochondria from rabbit kidneys were stained with molecular probes for cardiolipin content (nonyl acridine orange, NAO) and membrane potential (tetramethylrhodamine, TMRM) and analyzed using flow cytometry. We validated that side scatter was a better indicator of volume and that as side scatter (SSC) decreased mitochondrial volume increased. Furthermore, those mitochondria with the highest NAO content had greater side scattering and were most highly charged. Mitochondria with average NAO content were of average side scattering and maintained an intermediate charge. Those mitochondria with low NAO content had minimal side scattering and exhibited minimal charge. Upon titration with the uncoupler carbonylcyanide-4-(trifluoromethoxy)-phenylhydrazone (FCCP), it was found that the high NAO content subpopulations were more resistant to uncoupling than lower NAO content populations. Ca(2+)-induced swelling of mitochondria was evaluated using probability binning (PB) analyses of SSC. Interestingly, only 30% of the mitochondria showed changes in response to Ca(2+), which was blocked by cyclosporine A. In addition, the small, high NAO content mitochondria swelled differentially in response to Ca(2+) over time. Our results demonstrate that flow cytometry can be used to identify mitochondrial subpopulations based on high, mid and low NAO content and/or volume/complexity. These subpopulations showed differences in membrane potential, volume, and responses to uncoupling and Ca(2+)-induced swelling.

Comparison of NADH-dependent cytochrome b5 reductase activity and in vitro methemoglobin induction by sodium nitrite in Oncorhynchus mykiss, Salmo salar, and Salvelinus fontinalis.

Methemoglobin is hemoglobin containing ferric iron. Methemoglobin cannot bind to oxygen and at high concentrations causes tissue hypoxia. Brook trout (Salvelinus fontinalis) develop significantly greater methemoglobinemia than Atlantic salmon (Salmo salar) or rainbow trout (Oncorhynchus mykiss) following general anesthesia with benzocaine or tricaine methanesulfonate. The objective of this study was to compare the activity of the major methemoglobin reducing enzyme, NADH-dependent cytochrome b5 reductase (CB5R), in brook trout erythrocytes to the activity of CB5R in Atlantic salmon and rainbow trout erythrocytes. Methemoglobin levels were compared using co-oximetry following in vitro incubation of erythrocytes with sodium nitrite (NaNO(2)). The CB5R activity was measured using a ferricyanide assay. There was significantly greater methemoglobin at time 0 in brook trout erythrocytes than in rainbow trout or Atlantic salmon erythrocytes (2.79 ± 0.29 %, 2.19 ± 0.23 %, 2.08 ± 0.14 %), (P < 0.001). There was significantly greater methemoglobin induction by NaNO(2) in brook trout erythrocytes (33.14 ± 3.32 %) than in rainbow trout or Atlantic salmon erythrocytes (28.73 ± 2.92 % and 24.85 ± 1.40 %, respectively), (P < 0.001). The CB5R activity was significantly less in brook trout erythrocytes (median of 3.05 µmol/min/µl) than in rainbow trout erythrocytes (median of 6.73 µmol/min/µl). The CB5R activity in Atlantic salmon erythrocytes (median 4.09 µmol/min/µl) was not significantly different than in brook or rainbow trout erythrocytes. Total methemoglobin at any one time is a balance between induction by oxidants and reduction by antioxidants. Lower CB5R activity in brook trout erythrocytes may contribute to a species-specific sensitivity to methemoglobin induction; however, there are likely additional factors.

Evaluation of co-oximetry for the measurement of methemoglobin in rainbow trout (Oncorhynchus mykiss) and values in 3 salmonid species.

BACKGROUND: Methemoglobin (metHb) is oxidized hemoglobin that cannot reversibly bind oxygen, and concentrations in healthy fish have been reported to be 0.6-24.8% compared with 0-3% in healthy mammals. In fish, metHb has been measured using spectrophotometric methods using potassium cyanide (KCN), but not using co-oximetry, which is the preferred method for human samples. OBJECTIVES: The aims of this study were to evaluate co-oximetry as a method for measuring metHb in Oncorhynchus mykiss, compare co-oximetry with a KCN spectrophotometric method, and establish reference values for metHb concentrations as measured using co-oximetry in O mykiss, Salmo salar, and Salvelinus fontinalis. METHODS: Blood samples from healthy female O mykiss, female S salar, and female and male S fontinalis were prepared by separation and washing of erythrocytes in Tris/NaCl/EDTA buffer followed by lysis in Tris/EDTA buffer. MetHb concentrations were measured using an IL-682 co-oximeter. Moderate and high metHb concentrations were produced in vitro using NaNO(2). RESULTS: At low concentrations of methemoglobin, CVs for intraday precision were 10.3% and 53.9% using co-oximetry and the KCN spectrophotometric method, respectively. The CV for interday precision using co-oximetry was 11.9%. MetHb concentrations were stable in whole blood stored at 4°C for 7 days. MetHb concentrations were linear up to 58.2% (r = .99) using co-oximetry and 27.5% (r = .94) using the KCN method. The lower limit of detection for metHb was 0.02 g/dL using co-oximetry. Reference values for metHb concentrations using co-oximetry in O mykiss, S salar, and S fontinalis (n = 40 of each species) were 0.6-1.8%, 1.1-1.9%, and 1.1-4.0%, respectively. CONCLUSIONS: Co-oximetry can be used to measure methemoglobin in blood from fish, in particular in O mykiss, and is better than the KCN spectrophotometric method. Reference values for methemoglobin concentrations in O mykiss, S salar, and S fontinalis are similar to those in mammals.