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
Proteomic Analysis Uncovers Measles Virus Protein C Interaction With p65–iASPP Protein Complex
In Brief Control of measles virus infection and measles-based oncolytic therapy are possible, thanks to the existence of a safe and efficient live attenuated vaccine. Molecular mechanisms that make this vaccine to be so efficient are yet to be determined. We show that the measles C protein is responsible for the establishment of complex networks of interactions with the host cell. We suggest that the C protein binding to the p65–iASPP protein complex controls the host cell death and innate immunity pathways. - Research Article
Dynamic Changes to the Skeletal Muscle Proteome and Ubiquitinome Induced by the E3 Ligase, ASB2β
In Brief The E3 ubiquitin ligase ASB2β has been identified as a regulator of skeletal muscle mass. To gain insights into potential mechanisms of action, mouse muscles expressing a Flag-tagged ASB2β were investigated using quantitative proteomic methods. The results identified ASB2β-induced changes in the abundance and ubiquitination of proteins associated with mitochondria, the sarcomere, and the cytoskeleton. Additional in vitro studies identified novel putative ASB2β target substrates. The results highlight the complex relationship between protein abundance and ubiquitination in ASB2β-mediated muscle adaptation. - Research Article
New Proteomic Signatures to Distinguish Between Zika and Dengue Infections
In Brief Differentiation between the mosquito-borne Zika and dengue Flavivirus infections is clinically important for correct treatment, but remains challenging. We used mass spectrometry to quantify expression levels for 277 proteins measured in serum samples from 62 patients, providing a resource to the community. We identified 13 proteins with significant differential expression between the closely related types of infections. Most of the proteins link to pregnancy and brain function. We also identified expression signatures that mark ambiguous infections with respect to temporal differences. - Research Article
Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling
In Brief Analysis of protein phosphorylation in isolated nerve terminals (synaptosomes) treated with C. botulinum neurotoxins (BoNT) to inhibit synaptic vesicle (SV) cycling reveals phosphorylation events that are primarily dependent on depolarization-induced Ca2+ influx and those that also require active SV-cycling machinery. In particular, SV-cycling-dependent phosphorylation sites on synaptobrevin (Vamp2), syntaxin-1 (Stx1a), and cannabinoid receptor-1 (Cnr1) are capable of changing the rate of exo- and endocytosis in cultured hippocampal neurons. - Research Article
Quantitative Proteomics and Phosphoproteomics Support a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis
In Brief The MUT9-like kinases are a family of plant-specific nuclear-localized kinases with roles in diverse signaling pathways, including light sensing, phytohormone perception, and the circadian clock. The proteome and phosphoproteome of compound mlk mutant seedlings have been determined under light and dark conditions. These experiments identify new roles for these kinases regulating secondary plant metabolism and stress responses, tested through metabolite analysis and assaying seedling sensitivity to DNA damaging agents. - Research Article
Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner
In Brief A proximity interaction network for the androgen receptor (AR) was obtained from androgen-responsive prostate cancer cells. A total of 267 candidates were identified, most associating following ligand stimulation, including Krüppel-like factor 4 (KLF4). KLF4 and AR were found to colocalize genome-wide on 4097 genes including PSA (KLK3), for which KLF4 acts as a repressor, without regulating the expression of AR. These results are instrumental to further dissect the molecular mechanisms underlying androgen signaling in prostate cells. - Technological Innovation and Resources
Stable Isotope Labeling of Amino Acids in Flies (SILAF) Reveals Differential Phosphorylation of Mitochondrial Proteins Upon Loss of OXPHOS Subunits
In Brief We advanced a fully composed food source for Drosophila melanogaster into a highly efficient, versatile, and cheap labeling method, termed SILAF. The larval proteome incorporates more than 99% heavy lysine-6 label within 6 days, while the adult fly metabolism allows protein turnover studies. We obtained a phosphoproteome with site-specific occupancy in a fly model of mitochondrial metabolic disease, highlighting the regulation of two novel conserved phosphosites on subunits of the electron transport chain. - Research Article
Secretome and Comparative Proteomics of Yersinia pestis Identify Two Novel E3 Ubiquitin Ligases That Contribute to Plague Virulence
In Brief Rapid adaption to the environments is critical for microbes to establish infection. Quantitative proteome and secretome analyses of Y. pestis grown under conditions mimicking its two typical natural niches were performed to understand the adaption strategies of this deadly pathogen. We identified three secreted proteins that can be translocated into host cells and further demonstrated that two of them show strong E3 ubiquitin ligase activity and contribute significantly to the virulence of Y. pestis. - Research Article
Proteomic Profiling of Gastric Signet Ring Cell Carcinoma Tissues Reveals Characteristic Changes of the Complement Cascade Pathway
In Brief This study took advantages of LCM and DIA-MS, generating a data set in the context of different subtypes of gastric tumors, globally and precisely. It was discovered for the first time that the complement cascade in SRCC tumors was specifically activated compared with AC. - Research Article
Quantitative Proteomics Reveals that the OGT Interactome Is Remodeled in Response to Oxidative Stress
In Brief The goal of these studies was to provide insight into the regulation of the O-GlcNAc transferase (OGT) basally and in response to oxidative stress, as well as the role that O-GlcNAc plays in promoting cytoprotection. Using quantitative proteomics, the basal and injury-induced interactome of OGT has been defined and validated. Protein interactors are anticipated to regulate either the activity or substrate targeting of OGT, or to be substrates of OGT, thus affecting cytoprotection. - Research Article
Integrative Proteomic and Metabolomic Analysis Reveals Metabolic Phenotype in Mice With Cardiac-Specific Deletion of Natriuretic Peptide Receptor A
In Brief Metabolomic analysis in mice revealed that natriuretic peptide receptor A (NPRA) is mainly involved in nucleotide biosynthesis and histidine metabolism in cardiac tissues, and in creatine metabolism, TCA cycle and pentose phosphate pathway in the plasma. Furthermore, proteomics revealed that Cox7c, Cox7b, ATP5J2, Uqcr10, and Myh7 play a vital role in the regulation of metabolic pathway. Together, deterioration of NPRA results in metabolic dysfunction involved with a protein and metabolite-interacting pathway. - Research Article
Integrated Redox Proteomic Analysis Highlights New Mechanisms of Sensitivity to Silver Nanoparticles
In Brief Silver nanoparticles (AgNPs) are widely used nanomaterials, but the molecular mechanisms underlying their activity remain elusive. Here, we show using time course studies that AgNP-sensitive lung cells experience broader and more pronounced changes in protein abundance and protein oxidation impacting protein translation and modification, lipid metabolism, bioenergetics, and mitochondrial dynamics. The findings are further validated by imaging of mitochondria using confocal microscopy and transmission electron microscopy. - Research Article
Domain Mapping of Chondroitin/Dermatan Sulfate Glycosaminoglycans Enables Structural Characterization of Proteoglycans
In Brief Glycosaminoglycans (GAGs) remain one of the most challenging posttranslational modifications to study, much due to their structural complexity and heterogeneity, and new methods for analysis are therefore required. We have developed a protocol for enrichment and structural characterization of GAGs of proteoglycans using nLC-MS/MS. We provide detailed information on the nonreducing end, internal, and linkage region GAG domains and use the data to determine an overall GAG structure of chromogranin-A of rat INS-1832/13 cells. - Research Article
Mapping Isoform Abundance and Interactome of the Endogenous TMPRSS2-ERG Fusion Protein by Orthogonal Immunoprecipitation–Mass Spectrometry Assays
In Brief Orthogonal immunoprecipitation-mass spectrometry assays quantified TMPRSS2-ERG fusion protein (∼27,000 copies/cell) and its four distinct isoforms, and revealed that T1E4-ERG isoform accounted for 52 ± 3% of the total ERG in VCaP cells and 50 ± 11% in FFPE prostate cancer tissues. Methionine-truncated and N-acetylated peptide TASSSSDYGQTSK unique for T1/E4 TMPRSS2-ERG fusion was identified. Unlike the N-terminal antibodies, C-terminal antibodies identified 29 ERG-interacting proteins, including mutually exclusive BRG1- and BRM-associated canonical SWI/SNF chromatin remodeling complexes. Clinical perspectives of assays were discussed. - Research Article
In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease
In Brief An exploratory glycosylation-based biomarker study has been conducted for in-depth mapping of an overall glycosylation landscape and site-specific alteration in glycoproteome collected from cerebrospinal fluids (CSF) in healthy control and Alzheimer’s disease (AD) subjects. The comparison will shed light on the glycoproteome profile, dominant glycosylation differences and similarities, and some of the interesting glycoprotein candidates with specific glycosylation pattern alterations in AD. - Research Article
Feature Selection Methods for Protein Biomarker Discovery from Proteomics or Multiomics Data
In Brief Untargeted mass spectrometry–based proteomics provides a powerful platform for protein biomarker discovery, but clinical translation depends on the selection of a small number of proteins for verification and validation. We present feature selection methods for protein biomarker selection from proteomics or multiomics data. The algorithms show good performance, enable functional interpretation of the identified markers, and provide alternative choices for each identified marker to facilitate a robust transition to the verification and validation platforms. - Technological Innovation and Resources
Enabling Photoactivated Cross-Linking Mass Spectrometric Analysis of Protein Complexes by Novel MS-Cleavable Cross-Linkers
In Brief Although photochemistry complements residue-specific chemistry through labeling amino acids nonspecifically, existing photo-cross-linking reagents are thus far inapplicable to multisubunit protein complexes owing to low yields and high complexities of photo-cross-linked products. The development of the three sulfoxide-containing MS-cleavable photoreactive SDASO cross-linkers permits MSn-based analytical workflow for accurate identification of photo-cross-linked peptides, enabling complex PPI profiling for the first time. This work has established a solid foundation for future applications of photo-cross-linking in complex XL-MS studies. - Research Article
Calculating Sample Size Requirements for Temporal Dynamics in Single-Cell Proteomics
In Brief Cellular development and disease progression are gradual transitions between phenotypic stages. Time-course measurements that explicitly measure this transition are important to discover proteome dynamics. Single-cell measurements are a powerful tool for understanding heterogeneity, especially during phenotypic transitions. Single-cell proteomics measurements are emerging as an available tool to characterize the cellular state. We created a statistical method that predicts the success of an experimental design for temporal dynamics. - Research Article
TMEM67, TMEM237, and Embigin in Complex With Monocarboxylate Transporter MCT1 Are Unique Components of the Photoreceptor Outer Segment Plasma Membrane
In Brief The plasma membrane which envelopes the light-sensitive outer segment organelle of vertebrate photoreceptor cells plays diverse roles in supporting photoreceptor function and health. Protein correlation profiling of this membrane revealed a surprisingly small number of unique protein components. Among them are TMEM67 and TMEM237, whose mutations are associated with various syndromic ciliopathies, and embigin found to be associated with the monocarboxylate transporter MCT1. The MCT1–embigin complex likely facilitates lactate transport through this cellular compartment. - Research Article
HLA Class II Presentation Is Specifically Altered at Elevated Temperatures in the B-Lymphoblastic Cell Line JY
In Brief Here the cellular response in a “fever-mimicking state” was investigated by sampling in parallel the proteome and the HLA class I and II ligandomes. Using quantitative proteomics and immunopeptidomics, we found that a proteomic “fever response” is initiated in B-cells after growing the cells for only 3 days at 40 °C and that it is largely mediated by adaptation in the HLA class II rather than HLA class I system. - Research Article
Structural Investigations of Human A2M Identify a Hollow Native Conformation That Underlies Its Distinctive Protease-Trapping Mechanism
In Brief The native conformation of the protease inhibitor A2M was investigated using negative stain electron microscopy, small-angle X-ray scattering, and cross-linking mass spectrometry. The low-resolution model built from these data describes a hollow tubular configuration that explains several aspects of A2M’s unique trapping mechanism. This model was further validated by two recombinantly expressed A2M mutants, which probed the location of the bait region and demonstrated the existence of a critical interface between A2M’s disulfide-bridged dimers. - Research Article
The Expression of NTAL and Its Protein Interactors Is Associated With Clinical Outcomes in Acute Myeloid Leukemia
In Brief Here, we demonstrated that the knockdown of non–T cell activation linker (NTAL) in acute myeloid leukemia (AML) cells was linked to reduced cell proliferation and survival in vitro and in vivo. In addition, we identified NTAL interactors in AML using label-free protein quantification. NTAL interactors presented a high expression in patients with AML, being associated with a leukemic granulocyte–macrophage progenitor-like state. Finally, NTAL interactors were capable to predict survival in a large subset of patients with AML. These data provide evidence that NTAL and its interactors could represent potential therapeutic targets for granulocyte–macrophage progenitor-like leukemias. - Research Article
The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development
In Brief We identified ADAMTS16 as a target protein for C-mannosylation and showed that this modification is needed for proper secretion of ADAMTS16. Targeting a distinct C-mannosyltransferase by CRISPR–Cas9 in medaka fish embryos caused defects in eye development. We conclude that these developmental defects are caused by reduced secretion of ADAMTS16 when C-mannosylation is missing. - Technological Innovation and Resources
GAGrank: Software for Glycosaminoglycan Sequence Ranking Using a Bipartite Graph Model
In Brief We demonstrate GAGrank, an algorithm that uses a bipartite graph model for sequencing glycosaminoglycans from EDD or NETD tandem mass spectra. The process involves first assigning glycosaminoglycan product ions using the GAGfinder algorithm. The second step is to rank possible sequences using GAGrank. We show GAGrank’s ability to sequence isomeric mixtures. - Research Article
Reverse Phase Protein Array Reveals Correlation of Retinoic Acid Metabolism With Cardiomyopathy in Friedreich's Ataxia
In Brief We conducted a sensitive and high-throughput reverse phase protein array to attain protein expression profiles of primary fibroblasts from patients with Friedreich's ataxia (FRDA) and unaffected controls using a pool of 217 validated antibodies. Our extensive bioinformatics analyses correlated differentially expressed (DE) proteins with critical disease parameters. Expression levels of several integrin proteins specifically associated with hearing loss in FRDA. Also, reverse phase protein array data integrated with transcriptome data uncovered defects in retinoic acid metabolism in FRDA samples. - Research Article
Adipose Triglyceride Lipase Loss Promotes a Metabolic Switch in A549 Non–Small Cell Lung Cancer Cell Spheroids
In Brief We here demonstrate that loss of adipose triglyceride lipase (ATGL) in an in-vitro model of 3D lung carcinoma cell (A549) culture leads to a metabolic switch supporting larger spheroid growth and better adaptation to hypoxia. Cancer spheroids lacking ATGL show a higher abundance of glucose transporters, increased glucose uptake and lactate production, and use alternative lipid metabolic pathways. Overall, our data suggest consideration of ATGL as potentially relevant target in lung cancer. - Research Article
Increased Wheat Protein Content via Introgression of an HMW Glutenin Selectively Reshapes the Grain Proteome
In Brief The differences between the grain proteome of three wheat cultivars and corresponding Ay HMW-GS–introgressed near-isogenic lines have been determined. In addition to increased abundance of 1Ay HMW-GS, 115 differentially expressed proteins were also discovered. This revealed that introgression of the 1Ay21∗ HMW-GS increases wheat grain protein content and improves bread-making quality in association with a wider reshaping of the grain proteome network. - Research Article
Revealing the Dynamic Allosteric Changes Required for Formation of the Cysteine Synthase Complex by Hydrogen-Deuterium Exchange MS
In Brief We have used hydrogen/deuterium exchange MS to unveil the allosteric changes occurring during complex formation of CysE and CysK, the last two enzymes of cysteine biosynthetic pathway in bacteria. Significant changes in conformation and dynamics occur in each protein upon complex formation, including long distance intraprotein and interprotein communication. Being absent in mammals, both CysE and CysK represent potential targets for new antibacterial drugs, and our results on the formation and allostery of the complex could help guide drug development. - Research Article
Proteogenomic Assessment of Intraspecific Venom Variability: Molecular Adaptations in the Venom Arsenal of Conus purpurascens
In Brief Cone snail venom is an extensive source of active molecules that have potential pharmacological and biotechnological applications. We employed a top-down functional proteogenomic approach to assess the injected venom of Conus purpurascens. The two distinct venom profiles found will interact differently to target neural pathways aimed to immobilize prey. These venom expression patterns will aid target prediction and the development of conotoxins into drug leads or neural probes. - Research Article
Normothermic Ex-vivo Kidney Perfusion in a Porcine Auto-Transplantation Model Preserves the Expression of Key Mitochondrial Proteins: An Unbiased Proteomics Analysis
In Brief The molecular changes associated with normothermic ex-vivo kidney perfusion (NEVKP) compared with static cold storage were studied using discovery proteomics in a porcine model. NEVKP resulted in increased expression of mitochondrial proteins (ETFB, CPT2) responsible for critical metabolic steps of ATP-synthesis. PPARGC1A, PPARA/D, and RXRA were computationally predicted as upstream regulators of proteins increased in NEVKP and showed increased mRNA expression in NEVKP-treated kidneys. PPAR-family members and their target proteins may represent new therapeutic targets to ameliorate ischemia-reperfusion injury. - Research Article
Nuclear Phosphatidylinositol 3,4,5-Trisphosphate Interactome Uncovers an Enrichment in Nucleolar Proteins
In Brief The polyphosphoinositide (PPIn) phosphatidylinositol 3,4,5 trisphosphate (PtdIns(3,4,5)P3) localizes to the nucleus and nucleolus. Using an affinity enrichment MS approach, the nuclear PtdIns(3,4,5)P3 interactome identified new interaction partners associated with the nucleolus. Among these, the DNA repair PARP1 protein, colocalized to the nucleolus with PtdIns(3,4,5)P3 and showed direct interaction to PPIn via three polybasic regions. The nuclear PtdIns(3,4,5)P3 interactome reported here will serve as a resource to further investigate the molecular mechanisms underlying PtdIns(3,4,5)P3-mediated interactions in the nucleus and nucleolus. - Research Article
Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs
In Brief This study proposed a new and effective strategy for the improved discovery and identification of novel SEPs, including the construction of databases maximally collecting all putative small ORFs from human and mouse lncRNA transcripts in NONCODE and the effective enrichment of polypeptides based on 30-kDa molecular weight cutoff (MWCO) membrane and C8 solid-phase extraction column. This effort led to the discovery of 762 novel lncRNA-encoded SEPs from multiple cell lines and tissues. - Research Article
Proteome Profiling of Recombinant DNase Therapy in Reducing NETs and Aiding Recovery in COVID-19 Patients
In Brief Neutrophils contribute to the extracellular DNA pool by forming neutrophil extracellular traps (NETs), which cause sputum thickening, pulmonary inflammation, and hindrance to gaseous exchange during infections. Here, we demonstrate the presence of NETs in sputum from severe COVID-19 patients using mass spectrometry and immunofluorescence analyses. Treatment with clinically approved recombinant human DNase reduced NETs and was associated with improved recovery and reduced inflammation. Targeting NETs using DNase may have significant therapeutic implications in COVID-19 disease and warrants further studies. - Research Article
Age-Associated Proteomic Signatures and Potential Clinically Actionable Targets of Colorectal Cancer
In Brief The incidence of early-onset colorectal cancer (CRC) has been increasing since 1990s, whereas the overall CRC frequency is declining. The underlying mechanisms of age-related clinical differences remain unknown. Here, we reported the proteomic signatures of CRC across age groups. Lots of proteins with adjusted intensities significantly correlated with age. Some proteins were verified as potential clinically actionable targets. This study identifies age-associated proteomic signatures and potential therapeutic targets of CRC and helps to make a precise decision on CRC treatment. - Research Article
Proteome Characterization of Glaucoma Aqueous Humor
In Brief Liu et al. characterized the proteome of aqueous humor from three types of glaucoma. Fifty-seven primary acute angle-closure glaucoma (PAACG), 50 primary chronic angle-closure glaucoma (PCACG), 35 neovascular glaucoma (NVG), and 33 cataract patient samples were analyzed using data-independent analysis and parallel reaction monitoring. Lipid metabolism, immune response, and cell death pathways showed different degrees of activation among the three types of glaucoma but were all higher relative to cataract. SERPIND1 was discovered as a vital protein in glaucoma. - Research Article
A Reductionist Approach Using Primary and Metastatic Cell–Derived Extracellular Vesicles Reveals Hub Proteins Associated with Oral Cancer Prognosis
In Brief A multi-omics strategy was used to map the proteome, miRNA, metabolome, and lipidome of EVs derived from human primary tumor (SCC-9) cells and matched lymph node metastatic (LN1) cells. Differentially abundant molecules associated with the metastatic phenotype were enriched for key processes and pathways. An integrative analysis revealed 11 ‘hub proteins’ that are correlated with reduced survival and tumor aggressiveness in patients with cancer according to public databases. These EV molecules are candidates as prognostic markers in oral cancer. - Research Article
Comparative Host Interactomes of the SARS-CoV-2 Nonstructural Protein 3 and Human Coronavirus Homologs
In Brief SARS-CoV-2 nonstructural protein 3 (nsp3) facilitates virion biogenesis and modulates host ubiquitinylation/ISGylation. The SARS-CoV-2 nsp3 host interactome has not been fully characterized. Using affinity purification–mass spectrometry, we identify interactors of SARS-CoV-2 nsp3 and homologs from four CoV strains. We show the N-terminus of SARS-CoV-2 nsp3 interacts with the transcription factor ATF6 and suppresses its stress response. This work examines the interface between a key CoV protein and host cells, highlighting potential dependencies for antiviral therapeutics. - Research Article
Proteomic Landscape of Exosomes Reveals the Functional Contributions of CD151 in Triple-Negative Breast Cancer
In Brief Using a quantitative proteomics approach, Li et al. characterized the proteomes of triple-negative breast cancer (TNBC) patient–derived serum exosomes and found the tetraspanin CD151 to be significantly enriched. Proteomic analysis of CD151-deleted exosomes and cells showed regulation of ribosomal and complement protein secretion. CD151-deleted exosomes were shown to significantly decrease the migration and invasion of TNBC cells, indicating that exosomal CD151 may be a potential therapeutic target for TNBC. - Research Article
Unbiased Proteomic and Phosphoproteomic Analysis Identifies Response Signatures and Novel Susceptibilities After Combined MEK and mTOR Inhibition in BRAFV600E Mutant Glioma
In Brief BRAFV600E is a key oncogenic driver in glioma, melanoma, and colon cancer. These tumors escape mitogen-activated protein kinase pathway inhibition by upregulating mammalian target of rapamycin signaling. Using comprehensive unbiased proteomic and phosphoproteomic analysis of an in vivo BRAFV600E mutant glioma model treated with inhibitors of both these key pathways, we characterize the tumor and stromal response and suggest additional therapeutic targets for BRAF-driven cancers, including epidermal growth factor receptor and class 1 histone deacetylases. - Research Article
Affinity Proteomics and Deglycoproteomics Uncover Novel EDEM2 Endogenous Substrates and an Integrative ERAD Network
In Brief Various pathologies including neurodegenerative diseases and cancers result from disruptions to or stress of ER homeostasis. One key protein proposed to act in quality control processes maintaining ER homeostasis is EDEM2. Using affinity proteomics and sucrose-density sedimentation, we identified several new EDEM2 partners involved in quality control. Moreover, we defined novel endogenous candidates for EDEM2-dependent degradation by combining glycoproteomics and SILAC-based proteomics. Our data suggest that EDEM2 is involved in ER homeostasis to a greater extent than previously thought. - Research Article
Proteomics, Lipidomics, Metabolomics, and 16S DNA Sequencing of Dental Plaque From Patients With Diabetes and Periodontal Disease
In Brief The human oral cavity houses a complex ecosystem of microbes, some of which have pathogenic influence on the host. Multi-omics analysis of oral plaques revealed key players in microbial communities derived from diabetic and periodontal disease patients. With cross-omic correlation analysis, we found host-specific proteins and associated lipids that were elevated in plaques from periodontal disease patients. Furthermore, this multi-omic approach leads to the finding that oral community member Lautropia mirabilis synthesizes monomethyl phosphatidylethanolamine, an uncommon lipid in oral microbiota. - Research Article
Quantitative Proteomic and Metabolomic Profiling Reveals Altered Mitochondrial Metabolism and Folate Biosynthesis Pathways in the Aging Drosophila Eye
In Brief Hall et al. profiled the proteome, transcriptome, and metabolome of the aging Drosophila eye. The integrated analysis revealed changes in metabolism, potentially due to decreases in availability of B vitamins, together with chronic activation of immune response. - Research Article
Region-Specific Cell Membrane N-Glycome of Functional Mouse Brain Areas Revealed by nanoLC-MS Analysis
In Brief We have characterized the cell-membrane N-glycome of two major developmental divisions of the brain, the forebrain and hindbrain, and three functional derivatives from them, including the cerebral cortex, hippocampus, and cerebellum, revealing an extraordinary diversity of N-glycans expressed in a global and functional region-specific manner in the adult mouse. Furthermore, we identified +25 N-glycans able to differentiate the forebrain and hindbrain N-glycome. Additionally, over 35 N-glycans distinguished the cortex, hippocampus, and cerebellum N-glycomes and may serve as region-specific glycan biomarkers. - Research Article
Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities With Malignancy-Associated EMT
In Brief EMT can play a role in retinal diseases. Here, we present a comprehensive proteomic analysis aimed at defining the temporal protein expression changes associated with EMT of stem cell–derived retinal pigment epithelial cells. Tandem mass tag and direct data-independent acquisition MS approaches were performed after inducing RPE-EMT by enzymatic dissociation. We present integration of our proteomic data with prior transcriptomic (RNA-Seq) data to provide additional insights into the RPE-EMT progression. - Research Article
Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes
In Brief We present a pipeline that streamlines cross-linking mass spectrometry (XL-MS) data collection, data analysis, and integrative modeling of host–pathogen complexes. Using XL-MS, known atomic structures, and functional genetic data, we determined an integrative structure of the HIV-human A3G-CRL5-Vif-CBFβ complex. This structure illustrates HIV-1 Vif interaction with A3G and captures the structural dynamics and flexibility of the entire A3G-CRL5-Vif-CBFβ complex.
