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1.
AAPS J ; 26(3): 60, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38730115

ABSTRACT

Subcutaneous (SC) administration of therapeutic proteins is perceived to pose higher risk of immunogenicity when compared with intravenous (IV) route of administration (RoA). However, systematic evaluations of clinical data to support this claim are lacking. This meta-analysis was conducted to compare the immunogenicity of the same therapeutic protein by IV and SC RoA. Anti-drug antibody (ADA) data and controlling variables for 7 therapeutic proteins administered by both IV and SC routes across 48 treatment groups were analyzed. RoA was the primary independent variable of interest while therapeutic protein, patient population, adjusted dose, and number of ADA samples were controlling variables. Analysis of variance was used to compare the ADA incidence between IV and SC RoA, while accounting for controlling variables and potential interactions. Subsequently, 10 additional therapeutic proteins with ADA data published for both IV and SC administration were added to the above 7 therapeutic proteins and were evaluated for ADA incidence. RoA had no statistically significant effect on ADA incidence for the initial dataset of 7 therapeutic proteins (p = 0.55). The only variable with a significant effect on ADA incidence was the therapeutic protein. None of the other controlling variables, including their interactions with RoA, was significant. When all data from the 17 therapeutic proteins were pooled, there was no statistically significant effect of RoA on ADA incidence (p = 0.81). In conclusion, there is no significant difference in ADA incidence between the IV and SC RoA, based on analysis of clinical ADA data from 17 therapeutic proteins.


Subject(s)
Administration, Intravenous , Humans , Injections, Subcutaneous , Antibodies/administration & dosage , Antibodies/immunology , Proteins/administration & dosage , Proteins/immunology
2.
Curr Opin Neurol ; 37(3): 305-315, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38667756

ABSTRACT

PURPOSE OF REVIEW: To provide an overview of the pathogenic mechanisms involved in autoimmune encephalitides mediated by antibodies against neuronal surface antigens, with a focus on NMDAR and LGI1 encephalitis. RECENT FINDINGS: In antibody-mediated encephalitides, binding of IgG antibodies to neuronal surface antigens results in different pathogenic effects depending on the type of antibody, IgG subclass and epitope specificity. NMDAR IgG1 antibodies cause crosslinking and internalization of the target, synaptic and brain circuitry alterations, as well as alterations of NMDAR expressing oligodendrocytes, suggesting a link with white matter lesions observed in MRI studies. LGI1 IgG4 antibodies, instead, induce neuronal dysfunction by disrupting the interaction with cognate proteins and altering AMPAR-mediated signaling. In-vitro findings have been corroborated by memory and behavioral changes in animal models obtained by passive transfer of patients' antibodies or active immunization. These models have been fundamental to identify targets for innovative therapeutic strategies, aimed at counteracting or preventing antibody effects, such as the use of soluble ephrin-B2, NMDAR modulators (e.g., pregnenolone, SGE-301) or chimeric autoantibody receptor T cells (CAART) in models of NMDAR encephalitis. SUMMARY: A deep understanding of the pathogenic mechanisms underlying antibody-mediated encephalitides is crucial for the development of new therapeutic approaches targeting brain autoimmunity.


Subject(s)
Autoantibodies , Encephalitis , Humans , Encephalitis/immunology , Animals , Autoantibodies/immunology , Receptors, N-Methyl-D-Aspartate/immunology , Receptors, N-Methyl-D-Aspartate/metabolism , Hashimoto Disease/immunology , Intracellular Signaling Peptides and Proteins/immunology , Intracellular Signaling Peptides and Proteins/metabolism , Proteins/immunology , Proteins/metabolism
3.
Nature ; 624(7992): 653-662, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37993717

ABSTRACT

Ameloblasts are specialized epithelial cells in the jaw that have an indispensable role in tooth enamel formation-amelogenesis1. Amelogenesis depends on multiple ameloblast-derived proteins that function as a scaffold for hydroxyapatite crystals. The loss of function of ameloblast-derived proteins results in a group of rare congenital disorders called amelogenesis imperfecta2. Defects in enamel formation are also found in patients with autoimmune polyglandular syndrome type-1 (APS-1), caused by AIRE deficiency3,4, and in patients diagnosed with coeliac disease5-7. However, the underlying mechanisms remain unclear. Here we show that the vast majority of patients with APS-1 and coeliac disease develop autoantibodies (mostly of the IgA isotype) against ameloblast-specific proteins, the expression of which is induced by AIRE in the thymus. This in turn results in a breakdown of central tolerance, and subsequent generation of corresponding autoantibodies that interfere with enamel formation. However, in coeliac disease, the generation of such autoantibodies seems to be driven by a breakdown of peripheral tolerance to intestinal antigens that are also expressed in enamel tissue. Both conditions are examples of a previously unidentified type of IgA-dependent autoimmune disorder that we collectively name autoimmune amelogenesis imperfecta.


Subject(s)
Amelogenesis Imperfecta , Autoantibodies , Celiac Disease , Polyendocrinopathies, Autoimmune , Humans , Amelogenesis Imperfecta/complications , Amelogenesis Imperfecta/immunology , Autoantibodies/immunology , Celiac Disease/complications , Celiac Disease/immunology , Immunoglobulin A/immunology , Polyendocrinopathies, Autoimmune/complications , Polyendocrinopathies, Autoimmune/immunology , Proteins/immunology , Proteins/metabolism , Ameloblasts/metabolism , Dental Enamel/immunology , Dental Enamel/metabolism , AIRE Protein/deficiency , Antigens/immunology , Antigens/metabolism , Intestines/immunology , Intestines/metabolism
4.
J Biol Chem ; 299(5): 104652, 2023 05.
Article in English | MEDLINE | ID: mdl-36990220

ABSTRACT

N-formyl methionine (fMet)-containing proteins are produced in bacteria, eukaryotic organelles mitochondria and plastids, and even in cytosol. However, Nα-terminally formylated proteins have been poorly characterized because of the lack of appropriate tools to detect fMet independently of downstream proximal sequences. Using a fMet-Gly-Ser-Gly-Cys peptide as an antigen, we generated a pan-fMet-specific rabbit polyclonal antibody called anti-fMet. The raised anti-fMet recognized universally and sequence context-independently Nt-formylated proteins in bacterial, yeast, and human cells as determined by a peptide spot array, dot blotting, and immunoblotting. We anticipate that the anti-fMet antibody will be broadly used to enable an understanding of the poorly explored functions and mechanisms of Nt-formylated proteins in various organisms.


Subject(s)
Antibodies , Antibody Specificity , N-Formylmethionine , Proteins , Animals , Humans , Rabbits , Antibodies/analysis , Antibodies/immunology , Bacteria/chemistry , Cytosol/metabolism , Immune Sera/analysis , Immune Sera/immunology , Immunoblotting , Mitochondria/metabolism , N-Formylmethionine/analysis , N-Formylmethionine/immunology , Proteins/analysis , Proteins/chemistry , Proteins/immunology , Proteins/metabolism , Saccharomyces cerevisiae/chemistry
5.
Front Immunol ; 14: 942849, 2023.
Article in English | MEDLINE | ID: mdl-36825005

ABSTRACT

Secretory pathway kinase or kinase-like proteins (SPKKPs) are effective in the lumen of the endoplasmic reticulum (ER), Golgi apparatus (GA), and extracellular space. These proteins are involved in secretory signaling pathways and are distinctive from typical protein kinases. Various reports have shown that SPKKPs regulate the tumorigenesis and progression of human cancer via the phosphorylation of various substrates, which is essential in physiological and pathological processes. Emerging evidence has revealed that the expression of SPKKPs in human cancers is regulated by multiple factors. This review summarizes the current understanding of the contribution of SPKKPs in tumorigenesis and the progression of immunity. With the epidemic trend of immunotherapy, targeting SPKKPs may be a novel approach to anticancer therapy. This study briefly discusses the recent advances regarding SPKKPs.


Subject(s)
Neoplasms , Phosphotransferases , Secretory Pathway , Humans , Carcinogenesis/immunology , Neoplasms/immunology , Phosphotransferases/immunology , Proteins/immunology , Secretory Pathway/immunology , Signal Transduction/immunology , Disease Progression
6.
CPT Pharmacometrics Syst Pharmacol ; 12(2): 139-143, 2023 02.
Article in English | MEDLINE | ID: mdl-36418887

ABSTRACT

Immunogenicity against therapeutic proteins frequently causes attrition owing to its potential impact on pharmacokinetics, pharmacodynamics, efficacy, and safety. Predicting immunogenicity is complex because of its multifactorial drivers, including compound properties, subject characteristics, and treatment parameters. To integrate these, the Immunogenicity Simulator was developed using published, predominantly late-stage trial data from 15 therapeutic proteins. This single-blinded evaluation with subject-level data from 10 further monoclonals assesses the Immunogenicity Simulator's credibility for application during the drug development process.


Subject(s)
Drug Development , Network Pharmacology , Humans , Proteins/immunology , Proteins/therapeutic use
7.
Nucleic Acids Res ; 50(W1): W36-W43, 2022 07 05.
Article in English | MEDLINE | ID: mdl-35640594

ABSTRACT

Proteins in food and personal care products can pose a risk for an immediate immunoglobulin E (IgE)-mediated allergic response. Bioinformatic tools can assist to predict and investigate the allergenic potential of proteins. Here we present AllerCatPro 2.0, a web server that can be used to predict protein allergenicity potential with better accuracy than other computational methods and new features that help assessors making informed decisions. AllerCatPro 2.0 predicts the similarity between input proteins using both their amino acid sequences and predicted 3D structures towards the most comprehensive datasets of reliable proteins associated with allergenicity. These datasets currently include 4979 protein allergens, 162 low allergenic proteins, and 165 autoimmune allergens with manual expert curation from the databases of WHO/International Union of Immunological Societies (IUIS), Comprehensive Protein Allergen Resource (COMPARE), Food Allergy Research and Resource Program (FARRP), UniProtKB and Allergome. Various examples of profilins, autoimmune allergens, low allergenic proteins, very large proteins, and nucleotide input sequences showcase the utility of AllerCatPro 2.0 for predicting protein allergenicity potential. The AllerCatPro 2.0 web server is freely accessible at https://allercatpro.bii.a-star.edu.sg.


Subject(s)
Allergens , Computers , Internet , Proteins , Software , Humans , Allergens/chemistry , Allergens/immunology , Amino Acid Sequence , Food Hypersensitivity/etiology , Food Hypersensitivity/immunology , Proteins/chemistry , Proteins/immunology , Cosmetics/adverse effects , Cosmetics/chemistry , Protein Conformation , Datasets as Topic
9.
PLoS Pathog ; 18(1): e1010249, 2022 01.
Article in English | MEDLINE | ID: mdl-35085371

ABSTRACT

Stress granules (SGs) are highly dynamic cytoplasmic foci that form in response to activation of the integrated stress response (ISR) that results in eIF2α phosphorylation and global translation shutdown. Stress granules, which are largely nucleated by G3BP1, serve as hubs for mRNA triage, but there is mounting evidence that they also perform cell signaling functions that are vital to cell survival, particularly during viral infection. We previously showed that SG formation leads to NFκB activation and JNK signaling and that this association may be due in part to G3BP1-dependent recruitment of PKR to SGs. Others have reported close associations between G3BP1 and various innate immune PRRs of the type 1 interferon signaling system, including RIG-I. We also reported SG assembly dynamics is dependent on the arginine-methylation status of G3BP1. Another protein that rapidly localizes to SGs, TDRD3, is a methyl reader protein that performs transcriptional activation and adaptor functions within the nucleus, but neither the mechanism nor its function in SGs is clear. Here, we present evidence that TDRD3 localizes to SGs partly based upon methylation potential of G3BP1. We also characterize granules that TDRD3 forms during overexpression and show that these granules can form in the absence of G3BP but also contain translation components found in canonical SGs. We also show for the first time that SGs recruit additional interferon effectors IRF3, IRF7, TBK1, and Sting, and provide evidence that TDRD3 may play a role in recruitment of these factors. We also present evidence that TDRD3 is a novel antiviral protein that is cleaved by enteroviral 2A proteinase. G3BP1 and TDRD3 knockdown in cells results in altered transcriptional regulation of numerous IFN effectors in complex modulatory patterns that are distinctive for G3BP1 and TDRD3. Overall, we describe a novel role of TDRD3 in innate immunity in which G3BP1 and TDRD3 may coordinate to play important roles in regulation of innate antiviral defenses.


Subject(s)
DNA Helicases/immunology , Immunity, Innate/immunology , Poly-ADP-Ribose Binding Proteins/immunology , Proteins/immunology , RNA Helicases/immunology , RNA Recognition Motif Proteins/immunology , Virus Diseases/immunology , Cell Line , Humans , Interferons/immunology , Signal Transduction/immunology , Stress Granules/immunology
10.
Front Immunol ; 12: 771826, 2021.
Article in English | MEDLINE | ID: mdl-34899723

ABSTRACT

Clostridium butyricum (CB) can enhance antioxidant capacity and alleviate oxidative damage, but the molecular mechanism by which this occurs remains unclear. This study used enterotoxigenic Escherichia coli (ETEC) K88 as a pathogenic model, and the p62-Keap1-Nrf2 signaling pathway and intestinal microbiota as the starting point to explore the mechanism through which CB alleviates oxidative damage. After pretreatment with CB for 15 d, mice were challenged with ETEC K88 for 24 h. The results suggest that CB pretreatment can dramatically reduce crypt depth (CD) and significantly increase villus height (VH) and VH/CD in the jejunum of ETEC K88-infected mice and relieve morphological lesions of the liver and jejunum. Additionally, compared with ETEC-infected group, pretreatment with 4.4×106 CFU/mL CB can significantly reduce malondialdehyde (MDA) level and dramatically increase superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) levels in the serum. This pretreatment can also greatly increase the mRNA expression levels of tight junction proteins and genes related to the p62-Keap1-Nrf2 signaling pathway in the liver and jejunum in ETEC K88-infected mice. Meanwhile, 16S rDNA amplicon sequencing revealed that Clostridium disporicum was significantly enriched after ETEC K88 challenge relative to the control group, while Lactobacillus was significantly enriched after 4.4×106 CFU/mL CB treatment. Furthermore, 4.4×106 CFU/mL CB pretreatment increased the short-chain fatty acid (SCFA) contents in the cecum of ETEC K88-infected mice. Moreover, we found that Lachnoclostridium, Roseburia, Lactobacillus, Terrisporobacter, Akkermansia, and Bacteroides are closely related to SCFA contents and oxidative indicators. Taken together, 4.4×106 CFU/mL CB pretreatment can alleviate ETEC K88-induced oxidative damage through activating the p62-Keap1-Nrf2 signaling pathway and remodeling the cecal microbiota community in mice.


Subject(s)
Antibiosis/immunology , Bacterial Infections/immunology , Cecum/microbiology , Clostridium butyricum/immunology , Enterotoxigenic Escherichia coli/immunology , Oxidative Stress/immunology , Proteins/immunology , Animals , Antibiosis/physiology , Bacterial Infections/genetics , Bacterial Infections/microbiology , Cecum/metabolism , Clostridium butyricum/physiology , Enterotoxigenic Escherichia coli/physiology , Gene Expression Regulation/immunology , Heme Oxygenase-1/genetics , Heme Oxygenase-1/immunology , Heme Oxygenase-1/metabolism , Jejunum/immunology , Jejunum/metabolism , Jejunum/microbiology , Kelch-Like ECH-Associated Protein 1/genetics , Kelch-Like ECH-Associated Protein 1/immunology , Kelch-Like ECH-Associated Protein 1/metabolism , Male , Mice , Microbiota/genetics , Microbiota/immunology , Microbiota/physiology , NF-E2-Related Factor 2/genetics , NF-E2-Related Factor 2/immunology , NF-E2-Related Factor 2/metabolism , Proteins/genetics , Proteins/metabolism , Sequestosome-1 Protein/genetics , Sequestosome-1 Protein/immunology , Sequestosome-1 Protein/metabolism , Signal Transduction/genetics , Signal Transduction/immunology , Superoxide Dismutase/genetics , Superoxide Dismutase/immunology , Superoxide Dismutase/metabolism , Swine
11.
PLoS One ; 16(12): e0262056, 2021.
Article in English | MEDLINE | ID: mdl-34972161

ABSTRACT

Characterization of protein complexes, i.e. sets of proteins assembling into a single larger physical entity, is important, as such assemblies play many essential roles in cells such as gene regulation. From networks of protein-protein interactions, potential protein complexes can be identified computationally through the application of community detection methods, which flag groups of entities interacting with each other in certain patterns. Most community detection algorithms tend to be unsupervised and assume that communities are dense network subgraphs, which is not always true, as protein complexes can exhibit diverse network topologies. The few existing supervised machine learning methods are serial and can potentially be improved in terms of accuracy and scalability by using better-suited machine learning models and parallel algorithms. Here, we present Super.Complex, a distributed, supervised AutoML-based pipeline for overlapping community detection in weighted networks. We also propose three new evaluation measures for the outstanding issue of comparing sets of learned and known communities satisfactorily. Super.Complex learns a community fitness function from known communities using an AutoML method and applies this fitness function to detect new communities. A heuristic local search algorithm finds maximally scoring communities, and a parallel implementation can be run on a computer cluster for scaling to large networks. On a yeast protein-interaction network, Super.Complex outperforms 6 other supervised and 4 unsupervised methods. Application of Super.Complex to a human protein-interaction network with ~8k nodes and ~60k edges yields 1,028 protein complexes, with 234 complexes linked to SARS-CoV-2, the COVID-19 virus, with 111 uncharacterized proteins present in 103 learned complexes. Super.Complex is generalizable with the ability to improve results by incorporating domain-specific features. Learned community characteristics can also be transferred from existing applications to detect communities in a new application with no known communities. Code and interactive visualizations of learned human protein complexes are freely available at: https://sites.google.com/view/supercomplex/super-complex-v3-0.


Subject(s)
Computational Biology/methods , Protein Interaction Maps , Proteins/immunology , Supervised Machine Learning , Viral Proteins/immunology , COVID-19/immunology , Humans , Protein Binding , Protein Interaction Mapping , SARS-CoV-2/immunology
12.
Microbiol Spectr ; 9(3): e0081421, 2021 12 22.
Article in English | MEDLINE | ID: mdl-34935429

ABSTRACT

The molecular details underlying differences in pathogenicity between Rickettsia species remain to be fully understood. Evidence points to macrophage permissiveness as a key mechanism in rickettsial virulence. Different studies have shown that several rickettsial species responsible for mild forms of rickettsioses can also escape macrophage-mediated killing mechanisms and establish a replicative niche within these cells. However, their manipulative capacity with respect to host cellular processes is far from being understood. A deeper understanding of the interplay between mildly pathogenic rickettsiae and macrophages and the commonalities and specificities of host responses to infection would illuminate differences in immune evasion mechanisms and pathogenicity. We used quantitative proteomics by sequential windowed data independent acquisition of the total high-resolution mass spectra with tandem mass spectrometry (SWATH-MS/MS) to profile alterations resulting from infection of THP-1 macrophages with three mildly pathogenic rickettsiae: Rickettsia parkeri, Rickettsia africae, and Rickettsia massiliae, all successfully proliferating in these cells. We show that all three species trigger different proteome signatures. Our results reveal a significant impact of infection on proteins categorized as type I interferon responses, which here included several components of the retinoic acid-inducible gene I (RIG-1)-like signaling pathway, mRNA splicing, and protein translation. Moreover, significant differences in protein content between infection conditions provide evidence for species-specific induced alterations. Indeed, we confirm distinct impacts on host inflammatory responses between species during infection, demonstrating that these species trigger different levels of beta interferon (IFN-ß), differences in the bioavailability of the proinflammatory cytokine interleukin 1ß (IL-1ß), and differences in triggering of pyroptotic events. This work reveals novel aspects and exciting nuances of macrophage-Rickettsia interactions, adding additional layers of complexity between Rickettsia and host cells' constant arms race for survival. IMPORTANCE The incidence of diseases caused by Rickettsia has been increasing over the years. It has long been known that rickettsioses comprise diseases with a continuous spectrum of severity. There are highly pathogenic species causing diseases that are life threatening if untreated, others causing mild forms of the disease, and a third group for which no pathogenicity to humans has been described. These marked differences likely reflect distinct capacities for manipulation of host cell processes, with macrophage permissiveness emerging as a key virulence trait. However, what defines pathogenicity attributes among rickettsial species is far from being resolved. We demonstrate that the mildly pathogenic Rickettsia parkeri, Rickettsia africae, and Rickettsia massiliae, all successfully proliferating in macrophages, trigger different proteome signatures in these cells and differentially impact critical components of innate immune responses by inducing different levels of beta interferon (IFN-ß) and interleukin 1ß (IL-1ß) and different timing of pyroptotic events during infection. Our work reveals novel nuances in rickettsia-macrophage interactions, offering new clues to understand Rickettsia pathogenicity.


Subject(s)
Inflammation , Macrophages/microbiology , Proteins/genetics , Proteome/genetics , Rickettsia Infections/immunology , Rickettsia/immunology , Humans , Immune Evasion , Macrophages/immunology , Proteins/immunology , Proteome/immunology , Rickettsia/classification , Rickettsia/genetics , Rickettsia/physiology , Rickettsia Infections/genetics , Rickettsia Infections/microbiology
13.
PLoS Negl Trop Dis ; 15(11): e0009949, 2021 11.
Article in English | MEDLINE | ID: mdl-34818332

ABSTRACT

Cryptosporidium is a life-threating protozoan parasite belonging to the phylum Apicomplexa, which mainly causes gastroenteritis in a variety of vertebrate hosts. Currently, there is a re-emergence of Cryptosporidium infection; however, no fully effective drug or vaccine is available to treat Cryptosporidiosis. In the present study, to better understand the detailed interaction between the host and Cryptosporidium parvum, a large-scale label-free proteomics study was conducted to characterize the changes to the proteome induced by C. parvum infection. Among 4406 proteins identified, 121 proteins were identified as differentially abundant (> 1.5-fold cutoff, P < 0.05) in C. parvum infected HCT-8 cells compared with uninfected cells. Among them, 67 proteins were upregulated, and 54 proteins were downregulated at 36 h post infection. Analysis of the differentially abundant proteins revealed an interferon-centered immune response of the host cells against C. parvum infection and extensive inhibition of metabolism-related enzymes in the host cells caused by infection. Several proteins were further verified using quantitative real-time reverse transcription polymerase chain reaction and western blotting. This systematic analysis of the proteomics of C. parvum-infected HCT-8 cells identified a wide range of functional proteins that participate in host anti-parasite immunity or act as potential targets during infection, providing new insights into the molecular mechanism of C. parvum infection.


Subject(s)
Cryptosporidiosis/genetics , Cryptosporidiosis/immunology , Cryptosporidium parvum/physiology , Cryptosporidiosis/parasitology , Cryptosporidium parvum/genetics , Host-Parasite Interactions , Humans , Proteins/genetics , Proteins/immunology , Proteomics
14.
Front Immunol ; 12: 749369, 2021.
Article in English | MEDLINE | ID: mdl-34745121

ABSTRACT

Ovarian cancer (OC) is one of the most malignant tumors whose mortality rate ranks first in gynecological tumors. Although immunotherapy sheds new light on clinical treatments, the low response still restricts its clinical use because of the unique characteristics of OC such as immunosuppressive microenvironment and unstable genomes. Further exploration on determining an efficient biomarker to predict the immunotherapy response of OC patients is of vital importance. In this study, integrative analyses were performed systematically using transcriptome profiles and somatic mutation data from The Cancer Genome Atlas (TCGA) based on the immune microenvironment and genomic instability of OC patients. Firstly, intersection analysis was conducted to identify immune-related differentially expressed genes (DEGs) and genomic instability-related DEGs. Secondly, Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3A (APOBEC3A) was recognized as a protective factor for OC, which was also verified through basic experiments such as quantitative reverse transcription PCR (RT-qPCR), immunohistochemistry (IHC), Cell Counting Kit-8 (CCK-8), and transwell assays. Thirdly, the correlation analyses of APOBEC3A expression with tumor-infiltrating immune cells (TICs), inhibitory checkpoint molecules (ICPs), Immunophenoscores (IPS), and response to anti-PD-L1 immunotherapy were further applied along with single-sample GSEA (ssGSEA), demonstrating APOBEC3A as a promising biomarker to forecast the immunotherapy response of OC patients. Last, the relationship between APOBEC3A expression with tumor mutation burden (TMB), DNA damage response (DDR) genes, and m6A-related regulators was also analyzed along with the experimental verification of immunofluorescence (IF) and RT-qPCR, comprehensively confirming the intimate association of APOBEC3A with genomic instability in OC. In conclusion, APOBEC3A was identified as a protective signature and a promising prognostic biomarker for forecasting the survival and immunotherapy effect of OC patients, which might accelerate the clinical application and improve immunotherapy effect.


Subject(s)
Cytidine Deaminase/genetics , Cytidine Deaminase/immunology , Ovarian Neoplasms/genetics , Ovarian Neoplasms/immunology , Proteins/genetics , Proteins/immunology , Tumor Microenvironment/genetics , Tumor Microenvironment/immunology , B7-H1 Antigen/antagonists & inhibitors , Biomarkers, Tumor/genetics , Biomarkers, Tumor/immunology , Cell Line, Tumor , Cell Movement , Cell Proliferation , Cell Survival , DNA Damage , Female , Gene Expression Regulation, Neoplastic , Genomic Instability , Humans , Immunotherapy , Middle Aged , Mutation , Ovarian Neoplasms/drug therapy , Prognosis
15.
Mol Cell Proteomics ; 20: 100155, 2021.
Article in English | MEDLINE | ID: mdl-34597790

ABSTRACT

Probing the human proteome in tissues and biofluids such as plasma is attractive for biomarker and drug target discovery. Recent breakthroughs in multiplex, antibody-based, proteomics technologies now enable the simultaneous quantification of thousands of proteins at as low as sub fg/ml concentrations with remarkable dynamic ranges of up to 10-log. We herein provide a comprehensive guide to the methodologies, performance, technical comparisons, advantages, and disadvantages of established and emerging technologies for the multiplexed ultrasensitive measurement of proteins. Gaining holistic knowledge on these innovations is crucial for choosing the right multiplexed proteomics tool for applications at hand to critically complement traditional proteomics methods. This can bring researchers closer than ever before to elucidating the intricate inner workings and cross talk that spans multitude of proteins in disease mechanisms.


Subject(s)
Antibodies/immunology , Proteome/analysis , Proteomics/methods , Humans , Immunoassay , Proteins/analysis , Proteins/immunology , Proteome/immunology
16.
Bioanalysis ; 13(19): 1459-1465, 2021 Oct.
Article in English | MEDLINE | ID: mdl-34605275

ABSTRACT

During the first half of 2021, and due to the SARS-CoV-2 pandemic preventing in-person meetings, the European Bioanalysis Forum organized four workshops as live interactive online meetings. The themes discussed at the workshops were carefully selected to match the cyberspace dynamics of the meeting format. The first workshop was a training day on challenges related to immunogenicity. The second one focused on biomarkers and continued the important discussion on integrating the principles of Context of Use (CoU) in biomarker research. The third workshop was dedicated to technology, that is, cutting-edge development in cell-based and ligand-binding assays and automation strategies. The fourth was on progress and the continued scientific and regulatory challenges related to peptide and protein analysis with MS. In all four workshops, the European Bioanalysis Forum included a mixture of scientific and regulatory themes, while reminding the audience of important strategic aspects and our responsibility toward the patient.


Subject(s)
Chemistry Techniques, Analytical , Mass Spectrometry , Proteins/analysis , Proteins/immunology , Automation , Biomarkers/analysis , Humans , Proteins/chemistry
17.
Immunology ; 164(2): 209-210, 2021 10.
Article in English | MEDLINE | ID: mdl-34523728

ABSTRACT

Neurodegenerative diseases place a devastating burden on affected individuals and their families, and new treatments are desperately needed for these common immune-mediated inflammatory conditions. While large aggregates of abnormal proteins in the brain cause significant damage, it is becoming clear that smaller soluble protein aggregates can also contribute to disease, by both direct and indirect mechanisms. These soluble protein oligomers can be found in patients' serum. Here, we describe recent research that identifies effects of model oligomer molecules on peripheral blood T cells, therefore providing an additional mechanism by which neurodegeneration may be worsened through amplification of peripheral adaptive immune responses.


Subject(s)
Brain/immunology , Neurodegenerative Diseases/immunology , Proteins/immunology , T-Lymphocytes/immunology , Adaptive Immunity/immunology , Humans , Inflammation/immunology
18.
Front Immunol ; 12: 661202, 2021.
Article in English | MEDLINE | ID: mdl-34557182

ABSTRACT

Protein S-palmitoylation is a covalent and reversible lipid modification that specifically targets cysteine residues within many eukaryotic proteins. In mammalian cells, the ubiquitous palmitoyltransferases (PATs) and serine hydrolases, including acyl protein thioesterases (APTs), catalyze the addition and removal of palmitate, respectively. The attachment of palmitoyl groups alters the membrane affinity of the substrate protein changing its subcellular localization, stability, and protein-protein interactions. Forty years of research has led to the understanding of the role of protein palmitoylation in significantly regulating protein function in a variety of biological processes. Recent global profiling of immune cells has identified a large body of S-palmitoylated immunity-associated proteins. Localization of many immune molecules to the cellular membrane is required for the proper activation of innate and adaptive immune signaling. Emerging evidence has unveiled the crucial roles that palmitoylation plays to immune function, especially in partitioning immune signaling proteins to the membrane as well as to lipid rafts. More importantly, aberrant PAT activity and fluctuations in palmitoylation levels are strongly correlated with human immunologic diseases, such as sensory incompetence or over-response to pathogens. Therefore, targeting palmitoylation is a novel therapeutic approach for treating human immunologic diseases. In this review, we discuss the role that palmitoylation plays in both immunity and immunologic diseases as well as the significant potential of targeting palmitoylation in disease treatment.


Subject(s)
Immune System Diseases/metabolism , Immune System/metabolism , Protein Processing, Post-Translational , Proteins/metabolism , Acyltransferases/metabolism , Adaptive Immunity , Animals , Humans , Immune System/immunology , Immune System Diseases/immunology , Immunity, Innate , Lipoylation , Proteins/immunology , Signal Transduction
19.
Clin Biochem ; 97: 11-24, 2021 Nov.
Article in English | MEDLINE | ID: mdl-34453894

ABSTRACT

OBJECTIVES: There is a need for precision medicine and an unspoken promise of an optimal approach for identification of the right patients for value-based medicine based on big data. However, there may be a misconception that measurement of proteins is more valuable than measurement of fewer selected biomarkers. In population-based research, variation may be somewhat eliminated by quantity. However, this fascination of numbers may limit the attention to and understanding of the single. This review highlights that protein measurements (with collagens as examples) may mean different things depending on the targeted epitope - formation or degradation of tissues, and even signaling potential of proteins. DESIGN AND METHODS: PubMed was searched for collagen, neo-epitope, biomarkers. RESULTS: Ample examples of assays with specific epitopes, either pathological such as HbA1c, or domain specific such as pro-peptides, which total protein arrays would not have identified were evident. CONCLUSIONS: We suggest that big data may be considered as the funnel of data points, in which most important parameters will be selected. If the technical precision is low or the biological accuracy is limited, and we include suboptimal quality of biomarkers, disguised as big data, we may not be able to fulfill the promise of helping patients searching for the optimal treatment. Alternatively, if the technical precision of the total protein quantification is high, but we miss the functional domains with the most considerable biological meaning, we miss the most important and valuable information of a given protein. This review highlights that measurements of the same protein in different ways may provide completely different meanings. We need to understand the pathological importance of each epitope quantified to maximize protein measurements.


Subject(s)
Cardiovascular Diseases/metabolism , Collagen/immunology , Epitopes , Proteins/analysis , Proteins/metabolism , Basement Membrane/metabolism , Bone Remodeling/immunology , Collagen/analysis , Collagen/metabolism , Gastrointestinal Diseases/metabolism , Humans , Kidney/metabolism , Liver Cirrhosis/metabolism , Neoplasms/immunology , Prognosis , Protein Domains , Protein Processing, Post-Translational , Proteins/immunology
20.
PLoS One ; 16(8): e0254628, 2021.
Article in English | MEDLINE | ID: mdl-34339430

ABSTRACT

Most current clinical vaccines work primarily by inducing the production of neutralizing antibodies against pathogens. Vaccine adjuvants that efficiently induce T cell responses to protein antigens need to be developed. In this study, we developed a new combination adjuvant consisting of 1,2-dioleoyl-3-trimethylammonium propane (DOTAP), D35, and an aluminum salt. Among the various combinations tested, the DOTAP/D35/aluminum salt adjuvant induced strong T cell and antibody responses against the model protein antigen with a single immunization. Adjuvant component and model antigen interaction studies in vitro also revealed that the strong mutual interactions among protein antigens and other components were one of the important factors for this efficient immune induction by the novel combination adjuvant. In addition, in vivo imaging of the antigen distribution suggested that the DOTAP component in the combination adjuvant formulation elicited transient antigen accumulation at the draining lymph nodes, possibly by antigen uptake DC migration. These results indicate the potential of the new combination adjuvant as a promising vaccine adjuvant candidate to treat infectious diseases and cancers.


Subject(s)
Adjuvants, Immunologic/pharmacology , Antigens/immunology , Proteins/immunology , T-Lymphocytes/immunology , Aluminum/pharmacology , Animals , Antibody Formation/immunology , Cell Movement/immunology , Fatty Acids, Monounsaturated/pharmacology , Humans , Immunity/immunology , Liposomes/immunology , Lymph Nodes/immunology , Mice , Quaternary Ammonium Compounds/pharmacology , T-Lymphocytes, Cytotoxic/drug effects , T-Lymphocytes, Cytotoxic/immunology , Vaccination/methods , Vaccines/immunology
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