Spatial top-down proteomics for the functional characterization of human kidney.

Background: The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. Results: Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. Conclusions: We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.

Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform.

Conventional proteomic approaches measure the averaged signal from mixed cell populations or bulk tissues, leading to the dilution of signals arising from subpopulations of cells that might serve as important biomarkers. Recent developments in bottom-up proteomics have enabled spatial mapping of cellular heterogeneity in tissue microenvironments. However, bottom-up proteomics cannot unambiguously define and quantify proteoforms, which are intact (i.e., functional) forms of proteins capturing genetic variations, alternatively spliced transcripts and posttranslational modifications. Herein, we described a spatially resolved top-down proteomics (TDP) platform for proteoform identification and quantitation directly from tissue sections. The spatial TDP platform consisted of a nanodroplet processing in one pot for trace samples-based sample preparation system and an laser capture microdissection-based cell isolation system. We improved the nanodroplet processing in one pot for trace samples sample preparation by adding benzonase in the extraction buffer to enhance the coverage of nucleus proteins. Using ∼200 cultured cells as test samples, this approach increased total proteoform identifications from 493 to 700; with newly identified proteoforms primarily corresponding to nuclear proteins. To demonstrate the spatial TDP platform in tissue samples, we analyzed laser capture microdissection-isolated tissue voxels from rat brain cortex and hypothalamus regions. We quantified 509 proteoforms within the union of top-down mass spectrometry-based proteoform identification and characterization and TDPortal identifications to match with features from protein mass extractor. Several proteoforms corresponding to the same gene exhibited mixed abundance profiles between two tissue regions, suggesting potential posttranslational modification-specific spatial distributions. The spatial TDP workflow has prospects for biomarker discovery at proteoform level from small tissue sections.

Spatial Mapping of Plant N-Glycosylation Cellular Heterogeneity Inside Soybean Root Nodules Provided Insights Into Legume-Rhizobia Symbiosis.

Although ubiquitously present, information on the function of complex N-glycan posttranslational modification in plants is very limited and is often neglected. In this work, we adopted an enzyme-assisted matrix-assisted laser desorption/ionization mass spectrometry imaging strategy to visualize the distribution and identity of N-glycans in soybean root nodules at a cellular resolution. We additionally performed proteomics analysis to probe the potential correlation to proteome changes during symbiotic rhizobia-legume interactions. Our ion images reveal that intense N-glycosylation occurs in the sclerenchyma layer, and inside the infected cells within the infection zone, while morphological structures such as the cortex, uninfected cells, and cells that form the attachment with the root are fewer N-glycosylated. Notably, we observed different N-glycan profiles between soybean root nodules infected with wild-type rhizobia and those infected with mutant rhizobia incapable of efficiently fixing atmospheric nitrogen. The majority of complex N-glycan structures, particularly those with characteristic Lewis-a epitopes, are more abundant in the mutant nodules. Our proteomic results revealed that these glycans likely originated from proteins that maintain the redox balance crucial for proper nitrogen fixation, but also from enzymes involved in N-glycan and phenylpropanoid biosynthesis. These findings indicate the possible involvement of Lewis-a glycans in these critical pathways during legume-rhizobia symbiosis.

Online Hydrophilic Interaction Chromatography (HILIC) Enhanced Top-Down Mass Spectrometry Characterization of the SARS-CoV-2 Spike Receptor-Binding Domain.

SARS-CoV-2 cellular infection is mediated by the heavily glycosylated spike protein. Recombinant versions of the spike protein and the receptor-binding domain (RBD) are necessary for seropositivity assays and can potentially serve as vaccines against viral infection. RBD plays key roles in the spike protein's structure and function, and thus, comprehensive characterization of recombinant RBD is critically important for biopharmaceutical applications. Liquid chromatography coupled to mass spectrometry has been widely used to characterize post-translational modifications in proteins, including glycosylation. Most studies of RBDs were performed at the proteolytic peptide (bottom-up proteomics) or released glycan level because of the technical challenges in resolving highly heterogeneous glycans at the intact protein level. Herein, we evaluated several online separation techniques: (1) C2 reverse-phase liquid chromatography (RPLC), (2) capillary zone electrophoresis (CZE), and (3) acrylamide-based monolithic hydrophilic interaction chromatography (HILIC) to separate intact recombinant RBDs with varying combinations of glycosylations (glycoforms) for top-down mass spectrometry (MS). Within the conditions we explored, the HILIC method was superior to RPLC and CZE at separating RBD glycoforms, which differ significantly in neutral glycan groups. In addition, our top-down analysis readily captured unexpected modifications (e.g., cysteinylation and N-terminal sequence variation) and low abundance, heavily glycosylated proteoforms that may be missed by using glycopeptide data alone. The HILIC top-down MS platform holds great potential in resolving heterogeneous glycoproteins for facile comparison of biosimilars in quality control applications.

Proteomic Analysis Reveals Anti-Fibrotic Effects of Blue Light Photobiomodulation on Fibroblasts.

BACKGROUND AND OBJECTIVES: This study was aimed at determining the effects of blue light photobiomodulation on primary adult mouse dermal fibroblasts (AMDFs) and the associated signaling pathways. STUDY DESIGN/MATERIALS AND METHODS: Cultured AMDFs from adult C57BL/6 mice were irradiated by blue light from a light-emitting diode (wavelength = 463 ± 50 nm; irradiance = 5 mW/cm2 ; energy density = 4-8 J/cm2 ). The cells were analyzed using mass spectrometry for proteomics/phosphoproteomics, AlamarBlue assay for mitochondrial activity, time-lapse video for cell migration, quantitative polymerase chain reaction for gene expression, and immunofluorescence for protein expression. RESULTS: Proteomic/phosphoproteomic analysis showed inhibition of extracellular signal-regulated kinases/mammalian target of rapamycin and casein kinase 2 pathways, cell motility-related networks, and multiple metabolic processes, including carbon metabolism, biosynthesis of amino acid, glycolysis/gluconeogenesis, and the pentose phosphate pathway. Functional analysis demonstrated inhibition of mitochondrial activities, cell migration, and mitosis. Expression of growth promoting insulin-like growth factor 1 and fibrosis-related genes, including transforming growth factor ß1 (TGFß1) and collagen type 1 ɑ2 chain diminished. Protein expression of α-smooth muscle actin, an important regulator of myofibroblast functions, was also suppressed. CONCLUSIONS: Low-level blue light exerted suppressive effects on AMDFs, including suppression of mitochondrial activity, metabolism, cell motility, proliferation, TGFß1 levels, and collagen I production. Low-level blue light can be a potential treatment for the prevention and reduction of tissue fibrosis, such as hypertrophic scar and keloids. Lasers Surg. Med. © 2019 Wiley Periodicals, Inc.

Phosphoproteomics Reveals HMGA1, a CK2 Substrate, as a Drug-Resistant Target in Non-Small Cell Lung Cancer.

Although EGFR tyrosine kinase inhibitors (TKIs) have demonstrated good efficacy in non-small-cell lung cancer (NSCLC) patients harboring EGFR mutations, most patients develop intrinsic and acquired resistance. We quantitatively profiled the phosphoproteome and proteome of drug-sensitive and drug-resistant NSCLC cells under gefitinib treatment. The construction of a dose-dependent responsive kinase-substrate network of 1548 phosphoproteins and 3834 proteins revealed CK2-centric modules as the dominant core network for the potential gefitinib resistance-associated proteins. CK2 knockdown decreased cell survival in gefitinib-resistant NSCLCs. Using motif analysis to identify the CK2 core sub-network, we verified that elevated phosphorylation level of a CK2 substrate, HMGA1 was a critical node contributing to EGFR-TKI resistance in NSCLC cell. Both HMGA1 knockdown or mutation of the CK2 phosphorylation site, S102, of HMGA1 reinforced the efficacy of gefitinib in resistant NSCLC cells through reactivation of the downstream signaling of EGFR. Our results delineate the TKI resistance-associated kinase-substrate network, suggesting a potential therapeutic strategy for overcoming TKI-induced resistance in NSCLC.

dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation.

Given the increasing number of proteins reported to be regulated by S-nitrosylation (SNO), it is considered to act, in a manner analogous to phosphorylation, as a pleiotropic regulator that elicits dual effects to regulate diverse pathophysiological processes by altering protein function, stability, and conformation change in various cancers and human disorders. Due to its importance in regulating protein functions and cell signaling, dbSNO (http://dbSNO.mbc.nctu.edu.tw) is extended as a resource for exploring structural environment of SNO substrate sites and regulatory networks of S-nitrosylated proteins. An increasing interest in the structural environment of PTM substrate sites motivated us to map all manually curated SNO peptides (4165 SNO sites within 2277 proteins) to PDB protein entries by sequence identity, which provides the information of spatial amino acid composition, solvent-accessible surface area, spatially neighboring amino acids, and side chain orientation for 298 substrate cysteine residues. Additionally, the annotations of protein molecular functions, biological processes, functional domains and human diseases are integrated to explore the functional and disease associations for S-nitrosoproteome. In this update, users are allowed to search a group of interested proteins/genes and the system reconstructs the SNO regulatory network based on the information of metabolic pathways and protein-protein interactions. Most importantly, an endogenous yet pathophysiological S-nitrosoproteomic dataset from colorectal cancer patients was adopted to demonstrate that dbSNO could discover potential SNO proteins involving in the regulation of NO signaling for cancer pathways.

Obstacles delaying the prompt deployment of piston-type mechanical cardiopulmonary resuscitation devices during emergency department resuscitation: a video-recording and time-motion study.

BACKGROUND: The quality of cardiopulmonary resuscitation (CPR) is important to survival after cardiac arrest. Mechanical devices (MD) provide constant CPR, but their effectiveness may be affected by deployment timeliness. OBJECTIVES: To identify the timeliness of the overall and of each essential step in the deployment of a piston-type MD during emergency department (ED) resuscitation, and to identify factors associated with delayed MD deployment by video recordings. METHODS: Between December 2005 and December 2008, video clips from resuscitations with CPR sessions using a MD in the ED were reviewed using time-motion analyses. The overall deployment timeliness and the time spent on each essential step of deployment were measured. RESULTS: There were 37 CPR recordings that used a MD. Deployment of MD took an average 122.6 ± 57.8s. The 3 most time-consuming steps were: (1) setting the device (57.8 ± 38.3s), (2) positioning the patient (33.4 ± 38.0 s), and (3) positioning the device (14.7 ± 9.5s). Total no flow time was 89.1 ± 41.2s (72.7% of total time) and associated with the 3 most time-consuming steps. There was no difference in the total timeliness, no-flow time, and no-flow ratio between different rescuer numbers, time of day of the resuscitation, or body size of patients. CONCLUSIONS: Rescuers spent a significant amount of time on MD deployment, leading to long no-flow times. Lack of familiarity with the device and positioning strategy were associated with poor performance. Additional training in device deployment strategies are required to improve the benefits of mechanical CPR.

Programmable cellular retention of nanoparticles by replacing the synergistic anion of transferrin.

The ability to program the intracellular retention of nanoparticles (NPs) would increase their applicability for imaging and therapeutic applications. To date, there has been no efficient method developed to control the fate of NPs once they enter cells. Existing approaches to manipulate the intracellular retention of NPs are mostly "passive" and particle size-dependent. Different sized particles hold distinct cellular responses. The adverse effect of particle size may limit the utility of nanodelivery systems. Therefore, the development of tunable/"active" NP intracellular retention systems with fixed particle sizes remains a considerable challenge. By replacing the synergistic anions of transferrin (Tf) immobilized on quantum dots (Tf-QDs, ca. 25 nm), we have examined the feasibility of this concept. Substitution of synergistic anions of Tf from carbonate (holo-Tf) to oxalate (oxa-Tf) significantly increased the intracellular accumulation of the oxa-Tf-QDs as a result of (i) a delay in cellular removal triggered by oxalate (oxa-Tf)-induced endosomal Tf iron-release retardation and (ii) enhanced recycling of Tf-QD/TfR (Tf receptor) complexes from early endosomes to the plasma membrane. This accumulation extended the intracellular NP retention interval. The half-maximum fluorescence intensity of the oxa-Tf-QDs in vivo was 4 times higher than that of the holo-Tf-QDs. Programming of the intracellular NP retention time was accomplished through manipulation of the ratio of holo- and oxa-Tfs on the surfaces of the QDs. Using this simple and efficient approach, it was possible to readily achieve a desirable intracellular retention interval for the NPs.

Tracheal rapid ultrasound exam (T.R.U.E.) for confirming endotracheal tube placement during emergency intubation.

OBJECTIVES: This study aimed to assess the diagnostic accuracy and timeliness of using tracheal ultrasound to examine endotracheal tube placement during emergency intubation. METHODS: This was a prospective, observational study, conducted at the emergency department of a national university teaching hospital. Patients received emergency intubation because of impending respiratory failure, cardiac arrest, or severe trauma. The tracheal rapid ultrasound exam (T.R.U.E.) was performed during emergency intubation with the transducer placed transversely at the trachea over the suprasternal notch. Quantitative waveform capnography was used as the criterion standard for confirmation of tracheal intubation. The main outcome was the concordance between the T.R.U.E. and the capnography. RESULTS: A total of 112 patients were included in the analysis, and 17 (15.2%) had esophageal intubations. The overall accuracy of the T.R.U.E. was 98.2% (95% confidence interval [CI]: 93.7-99.5%). The kappa (κ) value was 0.93 (95% CI: 0.84-1.00), indicating a high degree of agreement between the T.R.U.E. and capnography. The sensitivity, specificity, positive predictive value, and negative predictive value of the T.R.U.E. were 98.9% (95% CI: 94.3-99.8%), 94.1% (95% CI: 73.0-99.0%), 98.9% (95% CI: 94.3-99.8%) and 94.1% (95% CI: 73.0-99.0%). The median operating time of the T.R.U.E. was 9.0s (interquartile range [IQR]: 6.0, 14.0). CONCLUSIONS: The application of the T.R.U.E. to examine endotracheal tube placement during emergency intubation is feasible, and can be rapidly performed.

Diversity in platinum-catalyzed hydrative cyclization of trialkyne substrates to form tetracyclic ketones.

We report a one-pot synthesis of tetracyclic ketones via PtI2-catalyzed hydrative cyclization of trialkyne functionalities. These triyne substrates bear an electron-rich aryl group at the outer alkyne to direct the initial hydration occurring at the adjacent alkynyl carbon. This tandem catalysis is proposed to comprise two alkyne hydrations, an alkyne insertion and an intramolecular aldol condensation.