Interactions of Gliotoxin with Protein Cysteines

<p>Gliotoxin is a secondary metabolite that is produced by several species of fungi, and is toxic to mammalian cells. It is immunosuppressive, affects antigen presentation by macrophages, and causes apoptosis of some cells. Gliotoxin is an epipolythiodioxopiperazine molecule and contains an internal disulfide bridge that is highly reactive and essential for its toxicity. Suggested mechanisms of action include modification of thiol groups of cysteine residues in target proteins by generating oxidative stress or through covalent modification. The goal of this project was to develop mass spectrometry methods to detect protein modification by gliotoxin. Creatine kinase was used as a model protein. The measured mass of creatine kinase from 45 spectra gave a mean of 42,944 ± 24 which was consistent with the predicted mass of creatine kinase. A tryptic digest of creatine kinase indicated ions consistent with the predicted masses of the four cys-containing peptides including abundant ions at m/z 794, 1130 and 2870 and an ion at low intensity at 4373. The reaction of creatine kinase with gliotoxin showed a time dependent reaction that after 14 h was consistent with formation of a gliotoxin adduct. Reduction of the product with dithiothreitol released creatine kinase. Analysis of the tryptic peptides using MALDI mass spectrometry indicated complex modification of cysteines possibly including formation of a mixed disulfide adduct, intramolecular disulfides of CK, and sulfur oxidation products. Further analysis using the ICAT (isotope-coded affinity tag) method suggested modification of Cys-254 and Cys-283 by gliotoxin. Preliminary experiments examined the effects of gliotoxin on HL-60 cells using ICAT. Proteins of gliotoxin-treated and untreated cells were labeled with Heavy and Light ICAT reagents. Potential ICAT pairs were detected in the mass spectrum as a preliminary search for proteins affected by gliotoxin. The results indicate that ICAT labeling should be an effective strategy for characterization of the protein targets of gliotoxin.</p>

Interactions of Gliotoxin with Protein Cysteines

<p>Gliotoxin is a secondary metabolite that is produced by several species of fungi, and is toxic to mammalian cells. It is immunosuppressive, affects antigen presentation by macrophages, and causes apoptosis of some cells. Gliotoxin is an epipolythiodioxopiperazine molecule and contains an internal disulfide bridge that is highly reactive and essential for its toxicity. Suggested mechanisms of action include modification of thiol groups of cysteine residues in target proteins by generating oxidative stress or through covalent modification. The goal of this project was to develop mass spectrometry methods to detect protein modification by gliotoxin. Creatine kinase was used as a model protein. The measured mass of creatine kinase from 45 spectra gave a mean of 42,944 ± 24 which was consistent with the predicted mass of creatine kinase. A tryptic digest of creatine kinase indicated ions consistent with the predicted masses of the four cys-containing peptides including abundant ions at m/z 794, 1130 and 2870 and an ion at low intensity at 4373. The reaction of creatine kinase with gliotoxin showed a time dependent reaction that after 14 h was consistent with formation of a gliotoxin adduct. Reduction of the product with dithiothreitol released creatine kinase. Analysis of the tryptic peptides using MALDI mass spectrometry indicated complex modification of cysteines possibly including formation of a mixed disulfide adduct, intramolecular disulfides of CK, and sulfur oxidation products. Further analysis using the ICAT (isotope-coded affinity tag) method suggested modification of Cys-254 and Cys-283 by gliotoxin. Preliminary experiments examined the effects of gliotoxin on HL-60 cells using ICAT. Proteins of gliotoxin-treated and untreated cells were labeled with Heavy and Light ICAT reagents. Potential ICAT pairs were detected in the mass spectrum as a preliminary search for proteins affected by gliotoxin. The results indicate that ICAT labeling should be an effective strategy for characterization of the protein targets of gliotoxin.</p>

Cellular effects of gliotoxin: Evaluation of a proteomic, isotope-based method to detect reactive cysteines

<p>Cysteinyl residues in proteins are important for many cellular processes and unregulated modification of the cysteine thiol group can have negative effects on cell vitality and viability. In this thesis, the potential for use of the isotope coded affinity tag (ICAT) method for detection of cysteine modification has been investigated. ICAT reagents label free cysteine thiols. The aim of this study was to use HL-60 cells treated with gliotoxin, a fungal metabolite with a reactive disulfide bridge, as a system to evaluate the performance of ICAT for identification of cysteine modification in a whole cell proteome. Gliotoxin has antimicrobial, antitumor, immunosuppressive and cytotoxic properties that have been related to cysteine modification in proteins. Cellular assays including viability using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, cell cycle analysis, and measurement of reactive oxygen species using dichlorofluorescin diacetate were used to establish conditions for measuring the effects of gliotoxin on HL-60 cells prior to large-scale cellular damage. Cells exposed to gliotoxin and control cells were then labeled with ICAT reagents and analysed by offline reversed phase liquid chromatography followed by matrix-assisted laser desorption/ionization tandem mass spectrometry. The pilot results identified tubulin, glyceraldehyde-3-phosphate dehydrogenase and peptidyl-prolyl cis-trans isomerase as putative targets of gliotoxin. Additionally, this study showed that ICAT can be used to detect modified cysteines from a highly complex sample, but further optimization is needed to unlock the full potential for detection of cysteine modification in complex samples.</p>

Cellular effects of gliotoxin: Evaluation of a proteomic, isotope-based method to detect reactive cysteines

<p>Cysteinyl residues in proteins are important for many cellular processes and unregulated modification of the cysteine thiol group can have negative effects on cell vitality and viability. In this thesis, the potential for use of the isotope coded affinity tag (ICAT) method for detection of cysteine modification has been investigated. ICAT reagents label free cysteine thiols. The aim of this study was to use HL-60 cells treated with gliotoxin, a fungal metabolite with a reactive disulfide bridge, as a system to evaluate the performance of ICAT for identification of cysteine modification in a whole cell proteome. Gliotoxin has antimicrobial, antitumor, immunosuppressive and cytotoxic properties that have been related to cysteine modification in proteins. Cellular assays including viability using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, cell cycle analysis, and measurement of reactive oxygen species using dichlorofluorescin diacetate were used to establish conditions for measuring the effects of gliotoxin on HL-60 cells prior to large-scale cellular damage. Cells exposed to gliotoxin and control cells were then labeled with ICAT reagents and analysed by offline reversed phase liquid chromatography followed by matrix-assisted laser desorption/ionization tandem mass spectrometry. The pilot results identified tubulin, glyceraldehyde-3-phosphate dehydrogenase and peptidyl-prolyl cis-trans isomerase as putative targets of gliotoxin. Additionally, this study showed that ICAT can be used to detect modified cysteines from a highly complex sample, but further optimization is needed to unlock the full potential for detection of cysteine modification in complex samples.</p>

Phostensin Enables Lymphocyte Integrin Activation and Population of Peripheral Lymphoid Organs

Rap1 GTPase drives assembly of the Mig10/RIAM/lamellipodin–Integrin–Talin (MIT) complex that enables integrin dependent lymphocyte functions. Here we used tandem affinity tag based proteomics to isolate and analyze the MIT complex and reveal that Phostensin (PTSN), a regulatory subunit of protein phosphatase 1, is a component of the complex. PTSN mediates dephosphorylation of Rap1 thereby preserving the activity and membrane localization of Rap1 to stabilize the MIT complex. CRISPR/Cas9-induced deletion of PPP1R18, which encodes PTSN, markedly suppresses integrin activation in Jurkat human T cells. We generated apparently healthy Ppp1r18 null mice that manifest lymphocytosis and reduced population of peripheral lymphoid tissues ascribable to defective activation of integrins. Ppp1r18 null T cells exhibit reduced capacity to induce colitis in a murine adoptive transfer model. Thus, PTSN enables lymphocyte integrin mediated functions by dephosphorylating Rap1 to stabilize the MIT complex. As a consequence, loss of PTSN ameliorates T cell mediated colitis.

Engineering of Recombinant Fortilin for Structure Activity Studies

Cardiovascular disease (CVD) is the leading cause of death worldwide affecting approximately 40% of all adults over the age of 20 and is responsible for an economic burden upwards of $3 billion annually. Treatments for CVD are limited to either hypertension medication to treat symptoms, and/or statin-based drugs to reduce low-density lipoprotein (LDL) cholesterol formation. However, recent studies suggest that approximately 50% of patients diagnosed with CVD have normal to low LDL cholesterol levels. Therefore, a critical need exists to develop new treatments for CVD that are independent of cholesterol lowering statins. Fortilin, also known as translationally controlled tumor protein (TCTP), is a 19kDa, 172 amino acid cytosolic protein ubiquitously expressed in all cell types, at all stages of life. Fortilin overexpression in arterial walls has been shown to propagate atherosclerotic plaque formation, a major component of CVD. Fortilin is therefore a promising target for the rational design of drugs to prevent formation of new plaques. For a structure-based drug development process, recombinant protein is required to characterize potential protein-drug interactions. Recombinant expression and purification of fortilin has proven to be effectual, provided any affinity tag used for purification is not cleaved. Here, we designed several constructs of recombinant fortilin fusion protein and were the first to successfully cleave the affinity tag, making structural activity studies more meaningful due to greater semblance to the native protein. Our new construct, GGS-fortilin, can be produced in high yield with greater than 85% tag cleavage, but still contains the three amino acid linkers at the N-terminus. To determine whether these three amino acids, Gly-Gly-Ser interfered with small molecule inhibitor (SMI) binding, loop constructs were designed, wherein the affinity tag, a Strep-Tactin peptide with the sequence WSHPQFEK, was placed at either the C terminal side of Arg37, Ser46 or Gly56 within the flexible loop of fortilin’s highly conserved structure and activity validated via calcium titration. Structural analysis and SMI binding studies were performed for the loop constructs using circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. NMR spectroscopy is a dynamic tool used in structure-based drug development to characterize the structure of recombinantly expressed protein and to determine binding sites for SMIs. The results presented here portend to the development of novel fortilin constructs and structural studies with SMIs. Structural integrity was validated for the loop constructs using CD and NMR, and activity validated with an NMR calcium binding assay. Binding studies were also attempted using differential scanning fluorimetry (DSF) and NMR.

Affinity Tag Coating Enables Reliable Detection of Antigen-Specific B Cells in Immunospot Assays

Assessment of humoral immunity to SARS-CoV-2 and other infectious agents is typically restricted to detecting antigen-specific antibodies in the serum. Rarely does immune monitoring entail assessment of the memory B-cell compartment itself, although it is these cells that engage in secondary antibody responses capable of mediating immune protection when pre-existing antibodies fail to prevent re-infection. There are few techniques that are capable of detecting rare antigen-specific B cells while also providing information regarding their relative abundance, class/subclass usage and functional affinity. In theory, the ELISPOT/FluoroSpot (collectively ImmunoSpot) assay platform is ideally suited for antigen-specific B-cell assessments since it provides this information at single-cell resolution for individual antibody-secreting cells (ASC). Here, we tested the hypothesis that antigen-coating efficiency could be universally improved across a diverse set of viral antigens if the standard direct (non-specific, low affinity) antigen absorption to the membrane was substituted by high-affinity capture. Specifically, we report an enhancement in assay sensitivity and a reduction in required protein concentrations through the capture of recombinant proteins via their encoded hexahistidine (6XHis) affinity tag. Affinity tag antigen coating enabled detection of SARS-CoV-2 Spike receptor binding domain (RBD)-reactive ASC, and also significantly improved assay performance using additional control antigens. Collectively, establishment of a universal antigen-coating approach streamlines characterization of the memory B-cell compartment after SARS-CoV-2 infection or COVID-19 vaccinations, and facilitates high-throughput immune-monitoring efforts of large donor cohorts in general.

Deciphering the tumor-specific immunopeptidome in vivo with genetically engineered mouse models

Effective immunosurveillance of cancer requires the presentation of peptide antigens on major histocompatibility complex Class I (MHC-I). Recent developments in proteomics have improved the identification of peptides that are naturally presented by MHC-I, collectively known as the “immunopeptidome”. Current approaches to profile tumor immunopeptidomes have been limited to in vitro investigation, which fails to capture the in vivo repertoire of MHC-I peptides, or bulk tumor lysates, which are obscured by the lack of tumor-specific MHC-I isolation. To overcome these limitations, we report here the engineering of a Cre recombinase-inducible affinity tag into the endogenous mouse MHC-I gene and targeting of this allele to the KrasLSL-G12D/+; p53fl/fl (KP) mouse model (KP; KbStrep). This novel approach has allowed us to isolate tumor-specific MHC-I peptides from autochthonous pancreatic ductal adenocarcinoma (PDAC) and lung adenocarcinoma (LUAD) in vivo. With this powerful analytical tool, we were able to profile the evolution of the LUAD immunopeptidome through tumor progression and show that in vivo MHC-I presentation is shaped by post-translational mechanisms. We also uncovered novel, putative LUAD tumor associated antigens (TAAs). Many peptides that were recurrently presented in vivo exhibited very low expression of the cognate mRNA, provoking reconsideration of antigen prediction pipelines that triage peptides according to transcript abundance. Beyond cancer, the KbStrep allele is compatible with a broad range of Cre-driver lines to explore antigen presentation in vivo in the pursuit of understanding basic immunology, infectious disease, and autoimmunity.

Engineering of Bio-Adhesive Ligand Containing Recombinant RGD and PHSRN Fibronectin Cell-Binding Domains in Fusion with a Colored Multi Affinity Tag: Simple Approach for Fragment Study from Expression to Adsorption

Engineering of biomimetic motives have emerged as promising approaches to improving cells’ binding properties of biomaterials for tissue engineering and regenerative medicine. In this study, a bio-adhesive ligand including cell-binding domains of human fibronectin (FN) was engineered using recombinant protein technology, a major extracellular matrix (ECM) protein that interacts with a variety of integrins cell-surface’s receptors and other ECM proteins through specific binding domains. 9th and 10th fibronectin type III repeat containing Arginine-Glycine-Aspartic acid (RGD) and Pro-His-Ser-Arg-Asn (PHSRN) synergic site (FNIII9-10) were expressed in fusion with a Colored Multi Affinity Tag (CMAT) to develop a simplified production and characterization process. A recombinant fragment was produced in the bacterial system using E. coli with high yield purified protein by double affinity chromatography. Bio-adhesive surfaces were developed by passive coating of produced fragment onto non adhesive surfaces model. The recombinant fusion protein (CMAT-FNIII9/10) demonstrated an accurate monitoring capability during expression purification and adsorption assay. Finally, biological activity of recombinant FNIII9/10 was validated by cellular adhesion assay. Binding to α5β1 integrins were successfully validated using a produced fragment as a ligand. These results are robust supports to the rational development of bioactivation strategies for biomedical and biotechnological applications.