Research Articles
- Research Article
Direct Proteomic Detection and Prioritization of 19 Onchocerciasis Biomarker Candidates in Humans
In BriefOnchocerca volvulus infects over 20 million people, causing severe disability. Diagnostic tests cannot reliably detect live adult worms, which is critical for disease elimination efforts. Plasma and urine samples from O. volvulus-infected individuals (and uninfected controls) were analyzed by MS proteomics to directly identify O. volvulus proteins in hosts. A total of 19 proteins were prioritized. This set of biomarker candidates is a valuable resource to further explore for the diagnosis of active O. volvulus infections. - Research Article
SKAP2 Modular Organization Differently Recognizes SRC Kinases Depending on Their Activation Status and Localization
In Brief SRC kinases play multiple functions in different metabolic pathways. To perform each of these functions, they interact specifically with other proteins. This work describes how the SKAP2 protein, an assembly platform, interacts with these kinases to better understand their combined action. New and more specific therapies could be developed from this type of work, particularly in oncology. - Research Article
Mass Spectrometry–Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease
In Brief We conducted an in-depth proteome analysis of human substantia nigra tissues from 15 Parkinson’s disease (PD) patients and 15 healthy control individuals to uncover dysregulated pathways in PD. We identified 10,040 proteins with 1140 differentially expressed proteins in the substantia nigra of PD patients, discovering mitoribosome proteins were the most dysregulated proteins, followed by ribosome, RNA splicing, and complement proteins. This study has discovered that mitoribosome dysfunction is potentially involved in the PD pathogenesis process for the first time. - Research Article
Proximity Labeling Facilitates Defining the Proteome Neighborhood of Photosystem II Oxygen Evolution Complex in a Model Cyanobacterium
In Brief An effective workflow for APEX2-based proximity labeling in the model cyanobacterium Synechocystis sp. PCC 6803 was developed. Proximity labeling of proteins proximal to the photosystem II oxygen evolution complex by PsbO-APEX2 resulted in proteomic identification of 38 integral thylakoid membrane proteins and 93 luminal proteins, thereby defining the proteome neighborhood of photosystem II in the luminal side. - Research Article
Multiple Layers of Complexity in O-Glycosylation Illustrated With the Urinary Glycoproteome
In Brief In this study, mass spectrometric data acquired on urinary O-glycopeptides were analyzed by four software packages. The results were compared, and the rate of misidentification was assessed. The major factors leading to data misinterpretation were identified, and software development suggestions aiming more reliable automated data interpretation were made. - Research Article
A comparative Proteomics Analysis Identified Differentially Expressed Proteins in Pancreatic Cancer–Associated Stellate Cell Small Extracellular Vesicles
In Brief In this article, we report that cancer-associated HPSC cells secreted more sEVs than primary stellate cells (HPaStec) and had no significant growth effects on the cancer cells. Intact membrane-associated proteins may be essential for sufficient uptake of sEVs by both normal and cancer cells. Comparative proteomics analysis between the 2 different sEVs revealed differentially expressed proteins. sEVs could potentially be targeted as a cargo vehicle for the safe delivery of drugs or other biological materials to the cancer cells. - Research Article
Red Blood Cells Protein Profile Is Modified in Breast Cancer Patients
In Brief This study demonstrates for the first time that the protein composition of red blood cells is different in the presence of a breast tumor, providing new information on the potential role of RBCs in the context of disseminated disease. In addition, it points to the value of red blood cell proteins in the prognosis and diagnosis of metastatic breast cancer in a non-invasive way. - Research Article
Glycoproteomics Landscape of Asymptomatic and Symptomatic Human Alzheimer’s Disease Brain
In Brief Glycosylation of proteins in human brains, especially those with Alzheimer’s disease (AD) is not well-known. We employed multi-lectin enrichment, HILIC, and mass spectrometry–based proteomics to profile N-glycoproteins in normal, asymptomatic, and symptomatic AD brains. Unlike other organs, the brain consists of mostly high-mannosidic glycans, notably the Man5 N-glycans and complex N-glycans that are fucosylated and bisected. We observed site-specific differences in glycosylation among different AD stages, such as the number of antennae or the frequency of fucosylation. - Research Article
Global Phosphoproteomics Unveils Kinase-Regulated Networks in Systemic Lupus Erythematosus
In Brief We established the global phosphoproteome landscape of peripheral blood mononuclear cells from healthy controls, systemic lupus erythematosus (SLE) patients (SLE_S, SLE_A), and rheumatoid arthritis by combining high-throughput phosphoproteomics with bioinformatics approaches. We validated some of the key phosphosites and kinases and then built kinase-regulated networks for SLE. The map of the global phosphoproteomic enables further understanding of the pathogenesis of this disease and will provide strategies for seeking potential therapeutic targets for SLE. - Research Article
Regio-Specific N-Glycome and N-Glycoproteome Map of the Elderly Human Brain With and Without Alzheimer’s Disease
In Brief Glycosylation plays an important role in brain development and function. The cell membrane–associated N-glycans and glycoproteins from the human brain were characterized using a nanoflow LC–MS/MS platform. The brain regions included the frontal, temporal, parietal, occipital, cingulate, lateral cerebellar and orbitofrontal cortex, posterior hippocampus, thalamus, caudate nucleus, and pons. We illustrate the utility of glycomic and glycoproteomic tools to define the general breadth and depth in glycans associated with the elderly human brain and some neuropathological conditions. - Research Article
In-Depth Characterization of the Clostridioides difficile Phosphoproteome to Identify Ser/Thr Kinase Substrates
In Brief An optimized workflow for phosphopeptide enrichment has been developed in Clostridioides difficile revealing extensive protein phosphorylation. Using kinase or phosphatase mutant strains and quantitative proteomics, 41 and 114 downstream targets of the kinases PrkC and CD2148, respectively, were identified in C. difficile. We confirmed the phosphorylation of PrkC and Spo0A in vitro and of FtsK in vivo. - Research Article
Proteomic Profiling of Intra-Islet Features Reveals Substructure-Specific Protein Signatures
In Brief Improved sample handling techniques have enabled us to go from studying the whole pancreas, to isolated whole islets, to islet sections, and now to islet substructures isolated from within islet sections. Using a microfluidic nanodroplet-based proteomics platform coupled with laser capture microdissection and field asymmetric waveform ion mobility spectrometry, we present an in-depth investigation of protein profiles from intra-islet features. The protein coverage and expression profiles obtained are sufficient to fully distinguish each of these features while presenting their own unique proteome signatures. - Research Article
Open Modification Searching of SARS-CoV-2–Human Protein Interaction Data Reveals Novel Viral Modification Sites
In Brief Public MS data were reanalyzed using open modification searching to investigate the presence of post-translational modifications during interaction of viral severe acute respiratory syndrome coronavirus 2 proteins and human host proteins. We examined several post-translational modifications, including phosphorylation, ubiquitination, and S-nitrosylation, in the context of the virus–host protein–protein interaction network to obtain novel hypotheses about the functional roles of these modifications during viral infection by severe acute respiratory syndrome coronavirus 2. - Research Article
Soluble ANPEP Released From Human Astrocytes as a Positive Regulator of Microglial Activation and Neuroinflammation: Brain Renin–Angiotensin System in Astrocyte–Microglia Crosstalk
In Brief Understanding the astrocyte secretome may provide insights into the regulatory mechanisms of neuroinflammation through astrocyte-mediated communication. In this study, we found that human astrocytes release the soluble form of aminopeptidase N as a component of the brain renin–angiotensin system, positively regulating microglial activation. Our findings suggest the diagnostic and therapeutic potential of soluble form of aminopeptidase N in neuroinflammatory diseases. - Research Article
Probing the sORF-Encoded Peptides of Deinococcus radiodurans in Response to Extreme Stress
In Brief To investigate the SEPs related to extreme stress, the integrated workflow consisting of multiple omics approaches were streamlined. The SEPome of Deinococcus radiodurans containing 109 novel SEPs was described. Among them, SEP068184 exhibited negative regulation of oxidative stress resistance in a comparative phenotypic assay of its mutants. Collectively, the SEPome dataset provides a rich resource for research on the molecular mechanisms of the response to extreme stress in organisms. - Research Article
A Complex Connection Between the Diversity of Human Gastric Mucin O-Glycans, Helicobacter pylori Binding, Helicobacter Infection and Fucosylation
In BriefHelicobacter pylori colonizes the gastric mucus layer of half the world population. Mucin glycans in this mucus layer govern pathogen virulence, growth, and adhesion. The 650 O-glycan structures identified in this study represent a reliable database of structures that are of putative importance for host–pathogen interactions. We further showed that both the enormous gastric O-glycan diversity and avidity for H. pylori are governed by fucosylation and infection-associated O-glycans. - Research Article
A New Monoclonal Antibody Enables BAR Analysis of Subcellular Importin β1 Interactomes
In Brief Proximity biotinylation with a new monoclonal antibody reveals subcellular importin β1 interactomes. - Research Article
The Mechano-Ubiquitinome of Articular Cartilage: Differential Ubiquitination and Activation of a Group of ER-Associated DUBs and ER Stress Regulators
In Brief Using ubiquitomics, we identified a unique ubiquitin signature of articular cartilage upon mechanical injury. A set of deubiquitinases (DUBs) and ER stress regulators including YOD1, ATXN3, RAD23B, VCP/p97, and Ubiquilin 1 were differentially ubiquitinated and their ubiquitination status was linked to enhanced DUB activity and upregulated ER stress response following injury. We observed a rapid increase in global DUB activity in injured and in human osteoarthritic cartilage. Data implicates DUBs as potential targets to modulate injury-induced tissue damage in osteoarthritis. - Research Article
Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays
In Brief The identification of biomarkers is an important challenge in oncology. In this study, we developed a liquid chromatography coupled to multiple reaction monitoring mass spectrometry assay that allows measuring the expression of target proteins in formalin-fixed paraffin-embedded tumor samples, the standard method for biopsy storage in clinical pathology. The method provided quantitative information on 185 proteins from three groups of breast tumors: triple-negative, HER2-overexpressing, and luminal A. In addition to markers such as HER2 or hormone receptors, we identified several proteins which are expressed differentially in triple-negative breast cancer samples. - Research Article
Quantitative Phosphoproteomics Analysis Uncovers PAK2- and CDK1-Mediated Malignant Signaling Pathways in Clear Cell Renal Cell Carcinoma
In Brief Senturk et al. (2022) identified >16,000 phosphopeptides in clear cell Renal Cell Carcinoma tumors, of which 600 were determined to be differentially regulated between tumor and normal adjacent tissues. Furthermore, several oncogenic pathways were determined to be enriched in the tumors such as RAC1 activation, MAPK and VEGF signaling, EGFR signaling, and cytokine signaling. Moreover, the kinase PAK2 was identified as one of the key drivers of tumor migration and invasion, having prognostic impact on the survival of ccRCC patients. - 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. - 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
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
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.
