Research Articles
- Research Article
Larval Exposure to Parasitic Varroa destructor Mites Triggers Specific Immune Responses in Different Honey Bee Castes and Species
In Brief We used three honey bee genotypes and investigated their attractiveness and physiological responses to parasitic Varroa destructor mites. Mites preferred 6-day-old larvae, irrespective of their species/castes. Comparing larval hemolymph proteomes revealed physiological responses to mite exposure in all genotypes and castes, but tolerant larvae responded more pronounced by increasing the abundance of proteins linked to immune and stress responses. We provide key insights into the complex involvement of the honey bee immune system against mite infestations, which could be used for future breeding purposes. - Research Article
A Single-Cell Atlas of Tumor-Infiltrating Immune Cells in Pancreatic Ductal Adenocarcinoma
In Brief Here, we employed mass cytometry to characterize the immune composition of PDAC microenvironment. We identified cell clusters with aberrant frequencies in tumors and observed elevated levels of immune markers, for example, PD-1, CD137L, and CD69. Moreover, TCGA PDAC tumors were stratified into three immune subtypes with different prognosis and distinct mechanisms of immune exclusion. Taken together, the data depicted a cell atlas of PDAC immune microenvironment and revealed useful cell phenotypes and targets for immunotherapy development. - Research Article
Comparative Proteome and Cis-Regulatory Element Analysis Reveals Specific Molecular Pathways Conserved in Dog and Human Brains
In Brief We generated the first spatiotemporal brain proteomes of domestic dogs. By comparison of brain proteomes together with genome-wide cis-regulatory elements frequency between dog, human, and mouse, we identified specific pathways involved in myelination, hippocampus, and neurological diseases conserved between dog and human; the conserved pathways between the two species may help understand their shared social cognitive abilities. The dog brain proteome we generated provides an invaluable resource for comparative studies of brain development, function, and disorder. - Research Article
Multiomic Analysis Reveals Disruption of Cholesterol Homeostasis by Cannabidiol in Human Cell Lines
In Brief The nonpsychoactive cannabinoid, cannabidiol (CBD) has been Food and Drug Administration approved for treatment of two drug-resistant epileptic disorders and is seeing widespread supplemental use by the public. The mechanisms that underly the therapeutic effects of CBD are not well understood. We took a systematic multiomics approach to profile the intracellular pathway changes that occur following CBD treatment. From this effort, we identified a response centered in the disruption of cholesterol homeostasis and membrane fluidity that could impact clinical outcomes. - Research Article
Phosphoproteomic Analysis of FLCN Inactivation Highlights Differential Kinase Pathways and Regulatory TFEB Phosphoserines
In Brief Comprehensive phosphoproteomics (pY + pSTY) of FLCNPOS and FLCNNEG human renal cells in conjunction with INKA and with posttranslational modification–based signature enrichment analyses identified FLCN phosphorylation dependencies. FLCN-dependent kinase pathways were investigated through drug experiments and validated in a BHD tumor cell line. This pinpointed RTK-MAPK1/3-RPS6K1/3 as a key axis downstream of FLCN loss. In addition, we show that FLCN loss induces ROS and modulates localization of the TFEB transcription factor by dephosphorylation of specific serines. - Research Article
Limited Evidence for Protein Products of Noncoding Transcripts in the HEK293T Cellular Cytosol
In Brief The discrepancy between the number of novel proteins predicted from ribosomal profiling and detected novel protein products by proteomics remains a matter of debate. We here applied an N-terminal proteogenomics strategy on a HEK293T cytosolic extract to find translational evidence for novel proteins. Our stringent downstream filtering and curation workflow provides limited evidence for the existence of novel proteins and highlights the importance of curation of proteomics data to confidently report novel proteins. - Research Article
Effect of Environmental Temperatures on Proteome Composition of Salmonella enterica Serovar Typhimurium
In Brief We performed systematic proteome analyses of Salmonella enterica serovar Typhimurium (STM) grown at human host body temperature (37 °C) compared to environmental temperatures relevant of agriculture (20, 16, 12, 8 °C). Altered abundance of members of various gene ontology classes reveal global adaptation of environmental temperatures. Virulence proteins for interaction with mammalian hosts were increased at 37 °C, while metabolic proteins were increased at lower temperatures. During growth at 12 °C, STM build functional flagella and showed altered motility. - Research Article
MS2Rescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates
In Brief The integration of newly trained immunopeptide MS2PIP models, DeepLC, and Percolator into one software package called MS2Rescore allows for a significant boost in immunopeptide identification rate as well as a substantial increase in specificity. MS2Rescore is search engine-agnostic and unbiased toward HLA types. MS2Rescore, therefore, shows great promise to extend the current neo- and xeno-epitope landscape in existing and future immunopeptidomics experiments. - Research Article
Single-Cell Quantitative Proteomic Analysis of Human Oocyte Maturation Revealed High Heterogeneity in In Vitro–Matured Oocytes
In Brief Here, we performed single-cell quantitative proteomic analysis of human germinal vesicle (GV), in vivo (IVO), and in vitro matured (IVM) oocytes and found low correlation between protein and mRNA levels. IVM oocytes showed higher heterogeneity in protein expression, which is related to the levels of estradiol per mature follicle on trigger day. This study provides a rich resource to characterize the mechanisms of oocyte maturation and to evaluate the quality heterogeneity of IVM oocytes at protein level. - Research Article
A Proteomic Approach Identifies Isoform-Specific and Nucleotide-Dependent RAS Interactions
In Brief Miller et al. presents a comprehensive and quantitative interactome of RAS, a protein found to be a driver of many human cancers. This resource identifies interactors of the active form of RAS (nucleotide-dependent) as well as isoform-specific (KRAS, HRAS, and NRAS) interactors of RAS. Several of the proteins identified were confirmed as being important for cancer cell viability or senescence. Exploring these proteins for further studies may lead to new strategies to treat cancers caused by RAS mutations. - Research Article
Normics: Proteomic Normalization by Variance and Data-Inherent Correlation Structure
In Brief Normalization of proteomic data is necessary for quantitative comparison and to improve statistical power. Share, extent, and direction of differential expression are usually unknown. Normalizing with unbalanced or high shares of differential expression can distort the data. Normics computes a ranking list for the selection of a likely invariant protein subset for normalization. It increases sensitivity, specificity, and quantitative accuracy compared to standard normalization alone. Its reversed ranking list provides a filter for highly variant proteins for downstream bioinformatic analyses. - Research Article
Quantitative Proteomics Identifies Proteins Enriched in Large and Small Extracellular Vesicles
In Brief The proteome of large and small extracellular vesicles has been determined with quantitative mass spectrometry. Tetraspanins, ADAMs, and ESCRT proteins, as well as SNAREs and Rab proteins associated with endosomes were enriched in small EVs, whereas ribosomal, mitochondrial, and nuclear proteins, as well as proteins involved in cytokinesis, were enriched in large EVs. Several proteins previously suggested to be enriched in either small or large EVs were validated, and several additional novel protein markers were suggested. - Research Article
Cardiac Myosin Filaments are Maintained by Stochastic Protein Replacement
In Brief To examine the mechanisms of myosin filament replacement in mouse hearts, we labeled proteins with D3-leucine and a GFP-tag in vivo. We used a combination of high-resolution mass spectrometry, analytical modeling, biochemical fractionations, and fluorescence imaging to demonstrate that individual molecules are stochastically replaced from within these large macromolecular filamentous complexes. - Research Article
Quantitative Acetylomics Reveals Dynamics of Protein Lysine Acetylation in Mouse Livers During Aging and Upon the Treatment of Nicotinamide Mononucleotide
In Brief Li et al. have performed label-free quantification of the acetylomes in mouse livers with age and upon the treatment of nicotinamide mononucleotide (NMN), revealing previously unknown acetylation events. The datasets characterize not just the dynamics of acetylation with age but also specific acetylation sites as new aging biomarkers. The investigation indicates that the life-beneficial effect of NMN could be partially reflected by the changes in age-related protein acetylation. NMN has mild effects on acetylation previously reported as substrates of Sirtuins. - Research Article
Early Prediction of COVID-19 Patient Survival by Targeted Plasma Multi-Omics and Machine Learning
In Brief During times of hospital admission overload, triage may be required to maximize the number of survivors. Mass spectometry–based proteomic and metabolomic analysis of COVID patients’ blood, collected at the time of admission to the ICU, enabled a prediction of survival versus nonsurvival with 92% accuracy. These analyses, which can be performed on widely available mass spectrometers, have the potential to assist physicians with these difficult decisions. - Research Article
Spatial Proteomics Reveals Differences in the Cellular Architecture of Antibody-Producing CHO and Plasma Cell–Derived Cells
In Brief We used state-of-the-art protein spatial profiling together with MS-based protein expression analysis and subsequent bioinformatics analysis to elucidate the subcellular proteome organization and organelle architecture of two antibody-secreting cell lines, a CHO and a murine plasma derived cell line (MPC-11). Characterization of differentially expressed and localized proteins and their associated biological pathways allowed a systematic comparison of both cell lines and implicates further targets for CHO cell line engineering. - Research Article
Temporal and Sex-Linked Protein Expression Dynamics in a Familial Model of Alzheimer’s Disease
In Brief Alzheimer’s disease still lacks effective therapies. In this study, we provide a longitudinal proteomic characterization of 5XFAD mice hippocampus hoping to identify new clinical intervention targets. Our proteomics approach reveals a striking increase in protein expression in 5XFAD mice overtime, which includes 23 proteins here newly associated with Alzheimer’s disease. Globally, our data reveals initial temporal signatures of DNA damage and senescence transitioning into neuroinflammatory signatures concurrent with disease progression. - Research Article
Functional Diversity and Evolution of the Drosophila Sperm Proteome
In Brief Fertilization is the sine qua non of animal and plant reproduction, a process conserved across the tree of life. During fertilization, a specific subset of male-derived proteins, many of unknown function, enter and are present in the developing egg and zygote. We therefore reinterrogated previous published sperm proteomes using improved purification and fractionation methods and identified >3000 proteins in sperm including a novel exchange of paralogous ribosomal proteins suggesting complex patterns of paralog switching and selectivity during spermatogenesis. - Research Article
Mass Spectrometry Identification of Biomarkers in Extracellular Vesicles From Plasmodium vivax Liver Hypnozoite Infections
In Brief Human malaria caused by Plasmodium vivax represents a major barrier to achieve the goal of malaria elimination as this species evolved a dormant liver form called a hypnozoite that can remain latent after the initial infection. Current diagnostic tools are unable to detect asymptomatic patients harboring hypnozoites. We have used a MS proteomics approach to discover biomarkers of latent liver infections associated with circulating extracellular vesicles in an in vivo model of P. vivax liver hypnozoite infections. - Research Article
High-Throughput Human Complement C3 N-Glycoprofiling Identifies Markers of Early Onset Type 1 Diabetes Mellitus in Children
In Brief Changes in glycosylation are known to modulate inflammatory responses, so glycans are more and more being considered as biomarkers of various diseases. Little is known about complement component C3 N-glycome as proper methods for its analysis are lacking, so we developed a novel high-throughput LC-MS method for C3 plasma enrichment and subsequent glycome analysis. We demonstrated that C3 N-glycan profile is stable in a healthy individual, and results showed that C3 N-glycosylation profile is significantly changed in type 1 diabetes. - Research Article
Comparative Proteomic Analysis Identifies Key Metabolic Regulators of Gemcitabine Resistance in Pancreatic Cancer
In Brief For pancreatic cancer (PDAC) patients, gemcitabine resistance (GemR) represents a major clinical problem. Global quantitative differential proteomic analysis of highly GemR PDAC cells developed from relatively Gem-sensitive PDAC cell lines identified multiple networks within the thousands of quantified proteins that support adaptation to Gem-induced stress, and reveal the complexity of GemR. Drug metabolism pathways were key contributors to GemR, and expression changes in Gem-metabolizing enzymes suggest both their influence upon Gem responsiveness, and drug-targetable vulnerabilities to improve clinical Gem efficacy. - Research Article
Ionizing Radiation Drives Key Regulators of Antigen Presentation and a Global Expansion of the Immunopeptidome
In-Brief It has been known that cancer treatment using radiation therapy activates the immune system. Here, we show that radiation increases a signaling component of the immune system called the major histocompatibility complex on tumor cells. This increase makes the tumor more recognizable to T cells whose roles are to specifically find and kill defective or mutated cells. These findings could give physicians a reason to combine radiation therapy with immunotherapies to use the immune effect of radiation for therapeutic benefits. - Research Article
The in vivo Interaction Landscape of Histones H3.1 and H3.3
In Brief Proximity-dependent (BioID) interactome analysis of the histone H3 variants H3.1 and H3.3 identified 608 interaction partners and expanded the characterized H3 interaction landscape. Among the most significant findings were that the chaperone chromatin assembly factor 1, previously thought to be H3.1-specific, interacts with H3.3 throughout the cell cycle. Preferential binding was identified between H3.1 and components of the mitotic machinery and between H3.3 and transcription factors, notably MYC interactors. - Research Article
Improving Statistical Certainty of Glycosylation Similarity between Influenza A Virus Variants Using Data-Independent Acquisition Mass Spectrometry
In Brief It is necessary to sample glycoprotein glycoforms deeply for biological studies. DDA is limited by missing values that result from limited scan speed and stochastic precursor ion selection. DIA samples all glycopeptide glycoforms, but duty cycle is reduced compared with DDA. DIA outperforms DDA for confident assignment of glycopeptides provided target glycoproteins are relatively pure. - Research Article
Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones
In Brief A wide range of proteins can prevent amyloid formation in vitro and in vivo, but the exact nature of these interactions is unclear. By combining machine learning–based structure prediction of protein complexes with mass spectrometry, we can discern the molecular determinants of specific and nonspecific chaperone–client interactions.
