Research Articles
- Research Article
The SARS-CoV2 envelope differs from host cells, exposes procoagulant lipids, and is disrupted in vivo by oral rinses
The lipid envelope of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an essential component of the virus; however, its molecular composition is undetermined. Addressing this knowledge gap could support the design of antiviral agents as well as further our understanding of viral-host protein interactions, infectivity, pathogenicity, and innate immune system clearance. Lipidomics revealed that the virus envelope comprised mainly phospholipids (PLs), with some cholesterol and sphingolipids, and with cholesterol/phospholipid ratio similar to lysosomes. - Research Article
Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia
Low levels of high density lipoprotein-cholesterol (HDL-C) are associated with an elevated risk of arteriosclerotic coronary heart disease. Heritability of HDL-C levels is high. In this research discovery study, we used whole-exome sequencing to identify damaging gene variants that may play significant roles in determining HDL-C levels. We studied 204 individuals with a mean HDL-C level of 27.8 ± 6.4 mg/dl (range: 4–36 mg/dl). Data were analyzed by statistical gene burden testing and by filtering against candidate gene lists. - Research Article
Sulfatide with ceramide composed of phytosphingosine (t18:0) and 2-hydroxy FAs in renal intercalated cells
Diverse molecular species of sulfatide with differences in FA lengths, unsaturation degrees, and hydroxylation statuses are expressed in the kidneys. However, the physiological functions of specific sulfatide species in the kidneys are unclear. Here, we evaluated the distribution of specific sulfatide species in the kidneys and their physiological functions. Electron microscopic analysis of kidneys of Cst-deficient mice lacking sulfatide showed vacuolar accumulation in the cytoplasm of intercalated cells in the collecting duct, whereas the proximal and distal tubules were unchanged. - Research Article
Genetic dissection in mice reveals a dynamic crosstalk between the delivery pathways of vitamin A
Vitamin A is distributed within the body to support chromophore synthesis in the eyes and retinoid signaling in most other tissues. Two pathways exist for the delivery of vitamin A: the extrinsic pathway transports dietary vitamin A in lipoproteins from intestinal enterocytes to tissues, while the intrinsic pathway distributes vitamin A from hepatic stores bound to serum retinol binding protein (RBP). Previously, the intestine-specific homeodomain transcription factor (ISX) and the RBP receptor STRA6 were identified as gatekeepers of these pathways; however, it is not clear how mutations in the corresponding genes affect retinoid homeostasis. - Research Article
Sortilin enhances secretion of apolipoprotein(a) through effects on apolipoprotein B secretion and promotes uptake of lipoprotein(a)
Elevated plasma lipoprotein(a) (Lp(a)) is an independent, causal risk factor for atherosclerotic cardiovascular disease and calcific aortic valve stenosis. Lp(a) is formed in or on hepatocytes from successive noncovalent and covalent interactions between apo(a) and apoB, although the subcellular location of these interactions and the nature of the apoB-containing particle involved remain unclear. Sortilin, encoded by the SORT1 gene, modulates apoB secretion and LDL clearance. We used a HepG2 cell model to study the secretion kinetics of apo(a) and apoB. - Research Article
Immune Checkpoint Blockade Augments Changes Within Oncolytic Virus-induced Cancer MHC-I Peptidome, Creating Novel Antitumor CD8 T Cell Reactivities
In Brief Immune checkpoint blockade augments changes within oncolytic virus-induced cancer MHC-I peptidome and contributes toward the therapy-induced novel antitumor CD8 T cell reactivities. - Research Article
Glutamine-Fructose-6-Phosphate Transaminase 2 (GFPT2) Is Upregulated in Breast Epithelial–Mesenchymal Transition and Responds to Oxidative Stress
In Brief Epithelial–mesenchymal transition (EMT) is a cellular process inherent to cancer cell metastasis. Metabolic reprogramming is a driver of EMT. We performed proteomic profiling of three isogenic cell lines from human breast epithelium representing the epithelial, mesenchymal, and “partial” mesenchymal states of EMT to identify metabolic vulnerabilities associated with cell invasion. Bioinformatic and functional analysis revealed that the metabolic enzyme GFPT2 is a marker of claudin-low breast cancer, responds to oxidative stress, and impacts EMT, cell growth, and cell invasion. - Research Article
DIA-Based Proteomics Identifies IDH2 as a Targetable Regulator of Acquired Drug Resistance in Chronic Myeloid Leukemia
In Brief To understand the underlying resistance mechanisms in response to imatinib (IMA) and adriamycin (ADR), we explored two unique drug resistance models of K562 cells. We applied an optimized DIA–MS method to quantify 98,232 peptides from 7082 proteotypic proteins from these samples using four DIA software tools including OpenSWATH, Spectronaut, DIA-NN, and EncyclopeDIA. The sirtuin signaling pathway was found significantly regulated in both models, and IDH2 was identified as a druggable regulator of acquired drug resistance. - Research Article
Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells
In Brief Quantitative LC-MS/MS analysis of AGR2 interactome has identified 15 potential partners in both T47D cells and H1299 cells stably transfected with AGR2. The most interesting partners, PDIA3 and PDIA6, belong to the protein disulfide isomerase family. Stronger PDIA3 interaction with AGR2 under ER stress further supports the existence of PDI reactive network in the cells. - Research Article
Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer
In Brief Metabolism is recognized as an important driver of complex diseases, but global metabolite profiling remains a challenge. Protein expression is a poor proxy because pathway enrichment models provide an incomplete mapping between the proteome and metabolism. We developed MOMENTA, a multiomic network approach for interrogating metabolic pathways from proteomics data. Analysis of data from cancer cell lines and human tumors reveals metabolic network rewiring and oncogene connections. The metabolic networks altered in cancer are linked to clinical outcomes. - Research Article
Dichotomous Responses to Chronic Fetal Hypoxia Lead to a Predetermined Aging Phenotype
In Brief Using bottom-up proteomics and the kidney as a paradigm, we report an integrative perspective of the cellular responses to chronic fetal hypoxia, uncovering fundamental mechanisms of the fetal programming of adult diseases theory that are principally applicable to all other organs in the body. The characteristic tissue and serum biomarker profile will promote the development of novel therapeutic approaches to counteract the premature aging phenotype that seems to be associated with the fetal programming of chronic diseases. - Research Article
Temporal Analysis of Protein Ubiquitylation and Phosphorylation During Parkin-Dependent Mitophagy
In Brief We used a quantitative proteomics approach to study dynamics of the mitochondrial proteome, ubiquitylome, and phosphoproteome during early (2–6 h) and late stages (12–18 h) of mitophagy. We focused on parkin-initiated ubiquitylation and the impact on the proteome level, which pointed to an outside–in progression of ubiquitylation and protein degradation of mitochondrial subcompartments. In addition, we validated the interplay of phosphorylation and ubiquitylation on VDAC2, which directly influenced its degradation over the course of mitophagy. - Research Article
Multidimensional Dynamics of the Proteome in the Neurodegenerative and Aging Mammalian Brain
In Brief Neurodegenerative diseases are characterized by the abnormal accumulation of aggregated proteins in the brain. Using in vivo pulse isotope labeling, we screened the proteome for changes in protein turnover and abundance in multiple mouse models of neurodegeneration. These data suggest that the disease state of pathologically affected tissue is characterized by a proteome-wide increase in protein turnover and repair. In contrast, in healthy wild-type mice, aging in the mammalian brain is associated with a global slowdown in protein turnover. - Research Article
Comparative Analysis of T-Cell Spatial Proteomics and the Influence of HIV Expression
In Brief Using HIV-1 as a model virus, we compared several published analytical tools for spatial proteomics to determine the effect of viral expression. We found that when using differential centrifugation to fractionate T cells, the accuracy of classifiers was organelle dependent with variable sensitivity to viral gene expression. Identification of protein translocations by the BANDLE pipeline showed the highest agreement with known HIV interactors and targets. These findings lay a foundation for future spatial proteomics studies of viral infection and expression. - Research Article
Interactome Analysis of Human Phospholipase D and Phosphatidic Acid-Associated Protein Network
In Brief Using a proteomic approach, Kattan et al. defined the protein interaction network for the human phospholipase D family of enzymes and their lipid product phosphatidic acid and revealed diverse cellular signaling events involving this important lipid metabolic pathway. - Research Article
Integrated Application of Multiomics Strategies Provides Insights Into the Environmental Hypoxia Response in Pelteobagrus vachelli Muscle
In Brief Aquatic ecosystems are increasingly stressed because of nutrient enrichment, pollutants, and global warming, which have seriously depleted oxygen concentrations. This sudden and significant lack of oxygen has resulted in persistent increase in fish mortality rates. Studying the molecular mechanisms involved in hypoxia adaptation in fishes will help researchers understand fish speciation and the evolution of the hypoxia-signaling pathway and guide the breeding of hypoxia-tolerant fish strains. - Research Article
Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis
In Brief Thuy-Boun et al. quantitatively compare the stool microbiomes of healthy and ulcerative colitis patients with label-free data-dependent LC-MS/MS proteomics. Their analyses identified 176 significantly enriched protein groups between the two cohorts, and serine-type endopeptidase activity was one such functionality overrepresented in UC patients. Pre-enrichment of the clinical samples with a biotinylated fluorophosphonate probe further demonstrated that serine endopeptidases are active within the patient fecal samples and that additional putative serine hydrolases were identified by this approach compared with unenriched profiling. - Research Article
A Dynamic and Combinatorial Histone Code Drives Malaria Parasite Asexual and Sexual Development
In Brief The complex combinatorial histone code of the malaria parasite is revealed through advanced, quantitative middle-down proteomics. Cross talk between histone PTMs (including novel PTMs) is dynamic and stage specific and includes arginine methylation. Chromatin proteomics show that the transcription factor AP2-G2 interacts with the combination of H3K18acK23ac to drive mature gametocyte transmissibility. The connectivity of the histone code in these parasites ultimately points toward a higher order of gene regulation involved in essential development processes than previously thought. - Research Article
Proteomics Profiling of Human Synovial Fluid Suggests Increased Protein Interplay in Early-Osteoarthritis (OA) That Is Lost in Late-Stage OA
In Brief This study presents data of the proteome in human synovial fluid from three groups representing early-stage knee OA, end-stage knee OA, and controls without knee OA. The early stage had an increased protein activity, while in end-stage OA, there was a loss of interplay between the proteins. These results highlight the importance of studying the early stage of OA progression and that the interplay between the proteins may be an additional key element in disentangling the complex OA pathogenesis. - Research Article
Mass Spectrometric and Glycan Microarray–Based Characterization of the Filarial Nematode Brugia malayi Glycome Reveals Anionic and Zwitterionic Glycan Antigens
In Brief While parasite glycans form the basis of highly successful diagnostic assays, filarial glycosylation is largely unexplored. Therefore, we conducted a comprehensive structural characterization of N-linked and GSL glycans of Brugia malayi. Our work revealed anionic and zwitterionic glycan motifs as major antibody targets. Glycan microarray analysis showed the induction of IgG and IgM to these glycans in a rhesus macaque infection model as well as a specific IgG response associated with infection in individuals from a Brugia malayi endemic area. - Research Article
Multiattribute Glycan Identification and FDR Control for Glycoproteomics
In Brief Glycoproteomics has seen rapid advances in methods for identifying glycopeptides, but challenges remain confidently determining the composition and structure of the attached glycan. We have developed a method using multiple sources of information from the mass spectrum to assign the composition of N-linked glycopeptides and an associated method for false discovery rate control. We show that this method is able to identify more glycopeptide spectra while also providing more accurate composition assignments than existing tools. - Research Article
Simple But Efficacious Enrichment of Integral Membrane Proteins and Their Interactions for In-Depth Membrane Proteomics
In Brief Membrane proteins, particularly integral membrane proteins, are barely detected in bottom–up proteomics because of their complex nature and abundant soluble proteins. We applied standard biochemical procedures to optimize the sample preparation method for membrane proteome. Membranes were precipitated by ultracentrifugation, followed by treatment with urea or alkaline solutions to remove contaminants. This enrichment was critical to obtain comprehensive membrane proteome data. Among the methods, washing membranes by urea distinctly revealed intricate membrane proteome with keeping protein–protein interactions. - Research Article
Integrated Liver and Plasma Proteomics in Obese Mice Reveals Complex Metabolic Regulation
In Brief Obesity leads to the development of type 2 diabetes and nonalcoholic fatty liver disease. To identify the underlying processes of obesity-induced metabolic dysfunction, we performed proteomics in liver and plasma of ob/ob mice. Peroxisomal biogenesis and dysregulation of the secretory machinery were apparent in the liver of obese mice, alongside substantial alterations to the plasma proteome. Integration of these datasets identified putatively liver-derived proteins that are systemically dysregulated in obesity, many of which are also altered in human metabolic diseases. - Research Article
Proteomics Uncovers Novel Components of an Interactive Protein Network Supporting RNA Export in Trypanosomes
In Brief This work was executed under full ethical compliance, and authorship is limited to those who have made significant contributions. The manuscript is original work, and works of others have been appropriately cited. We provide raw data for appropriate datasets at public databases. This work was performed standard compliant with community-acceptable guidelines and parameters. No known hazard was caused, nor any involvement of human subjects. Animal use for production of antibodies was performed under the institutional ethical guidelines. - Research Article
Multiple Reaction Monitoring-Mass Spectrometry Enables Robust Quantitation of Plasma Proteins Regardless of Whole Blood Processing Delays That May Occur in the Clinic
In Brief In the clinic, delays between blood collection and plasma generation are often unavoidable, possibly impacting intact protein-assay measurements, such as ELISA. Here we investigated the impact of plasma processing delays (0 to 40 h) on peptide-centric protein quantitation via validated LC/MRM-MS assays. From 159 LC/MRM-MS assays, 139 were ‘stable’ (RSD < 20%), 14 ‘semistable’ (RSD 20–30%), and 6 ‘unstable’ (RSD > 30%), demonstrating robustness and thus the potential for plasma-protein quantitation by validated LC/MRM-MS assays in a clinical setting.
