Aims/hypothesisThe inflammatory milieu characteristic of insulitis affects translation fidelity and generates defective ribosomal products (DRiPs) that participate in autoimmune beta cell... Show moreAims/hypothesisThe inflammatory milieu characteristic of insulitis affects translation fidelity and generates defective ribosomal products (DRiPs) that participate in autoimmune beta cell destruction in type 1 diabetes. Here, we studied the role of early innate cytokines (IFNα) and late immune adaptive events (IFNɣ) in insulin DRiP-derived peptide presentation to diabetogenic CD8+ T cells.MethodsSingle-cell transcriptomics of human pancreatic islets was used to study the composition of the (immuno)proteasome. Specific inhibition of the immunoproteasome catalytic subunits was achieved using siRNA, and antigenic peptide presentation at the cell surface of the human beta cell line EndoC-βH1 was monitored using peptide-specific CD8 T cells.ResultsWe found that IFNγ induces the expression of the PSMB10 transcript encoding the β2i catalytic subunit of the immunoproteasome in endocrine beta cells, revealing a critical role in insulin DRiP-derived peptide presentation to T cells. Moreover, we showed that PSMB10 is upregulated in a beta cell subset that is preferentially destroyed in the pancreases of individuals with type 1 diabetes.Conclusions/interpretationOur data highlight the role of the degradation machinery in beta cell immunogenicity and emphasise the need for evaluation of targeted immunoproteasome inhibitors to limit beta cell destruction in type 1 diabetes. Show less
In this thesis we explore the Ubiquitin code using purification methods coupled with mass spectrometry. We overview the available methods and current knowledge of of Ubiquitin and SUMO... Show moreIn this thesis we explore the Ubiquitin code using purification methods coupled with mass spectrometry. We overview the available methods and current knowledge of of Ubiquitin and SUMO modifications with examples of substrates where the precise site of modification is important, and substrates where the modification site seems interchangeable.We show that the deubiquitinating enzymes regulate a separate subset of the ubiquitinome than the proteasome. The PARylating enzyme PARP1 show increased activity after ubiquitination, which is regulated by deubiquitinating enzymes.Furthermore, we developed an in-vivo tool to study SUMO dependent interaction using proximity labeling which can be used for microscopy or identification by mass spectrometry.Finally, we investigate binders of Ubiquitin and SUMO chains with specific linkages and elucidate a preference for some chain linkages based on biological pathway of the binder. We also explore possible binding domains and predict the structure of some chain binding complexes using protein docking. Show less
Proteins play an essential role in almost all the processes of a living organism, and post-translational modifications (PTM) can regulate their structure, location, function, and fate. Ubiquitin... Show moreProteins play an essential role in almost all the processes of a living organism, and post-translational modifications (PTM) can regulate their structure, location, function, and fate. Ubiquitin and ISG15 are two of the most versatile and common PTM modifiers in mammalian cells. Aberrant modification of Ubiquitin and ISG15 in cells results in various diseases, such as cancers and microbial infections. This dissertation introduces the development of small-molecule inhibitors against ISG15 deconjugating enzyme USP18 and ubiquitin deconjugating enzyme OTUB2 separately, and the identification of USP16 as a dual deconjugating enzyme that cleaves Ubiquitin and ISG15 from substrates. These research achievements are supposed to deepen the understanding of biology, regulation, and biochemical mechanisms of Ubiquitin and ISG15 deconjugating enzymes, thus paving the way for deconjugating enzymes-targeted therapeutics development in the future. Show less
Dit proefschrift bevat onderzoek over verschillende processen binnen het intracellulaire domein. Als eerst wordt er onderzocht hoe een cel zijn oplosbare eiwitten in de correcte compartimenten... Show moreDit proefschrift bevat onderzoek over verschillende processen binnen het intracellulaire domein. Als eerst wordt er onderzocht hoe een cel zijn oplosbare eiwitten in de correcte compartimenten krijgt na mitosis. Het tweede omschrijft een mechanisme dat verantwoordelijk is voor het structureren van het endoplasmatisch reticulum. Als derde werd onderzocht wat voorn rol het eiwit MOSPD2 vervult binnen contacten tussen het ER, Golgi apparatus en lysosomen. Show less
Large parts of the research described in this Thesis aims at the development of oligopeptide-masked toxins and their in situ immunoproteasome-mediated activation. Chapter 2 focuses on the... Show moreLarge parts of the research described in this Thesis aims at the development of oligopeptide-masked toxins and their in situ immunoproteasome-mediated activation. Chapter 2 focuses on the development of selective fluorogenic substrates for each of the iCP and cCP proteasome subunits. Chapter 3 describes the utilization of proteasome cleavable linkers in order to release a toxic entity in immunoproteasome expressing cells. By selecting oligopeptide sequences of previously described immunoproteasome-selective fluorogenic substrates and inhibitors, and linking these to doxorubicin via a cleavable linker, new constructs were obtained. Chapter 4 describes an immunoproteasome inhibitor-doxorubicin conjugate that targets multiple myeloma derived cells and releases doxorubicin upon low-dose photon irradiation. Chapter 5 describes how a trans-cyclooctene (TCO) is utilized for the release of a toxic payload via a click to release reaction in conjunction with selective proteasome targeting. TCOs were used in order to facilitate toxin activation via an inverse electron demanding Diels-Alder reaction with tetrazine as a dienophile. Chapter 6 gives insight in the development of pan-immuno subunit selective proteasome inhibitors based on P3 and P4 scaffold exchanges. Finally, the research described in this thesis is summarized in Chapter 7, and future prospects based the presented results are discussed. Show less
Spits, M.; Janssen, L.J.; Voortman, L.M.; Kooij, R.; Neefjes, A.C.M.; Ovaa, H.; Neefjes, J. 2019
Proteasomes are multi-protein, multi-catalytic complexes responsible for the degradation of 80-90% of the proteins inside eukaryotic cells. Proteasomes contain a cylindrical 20S core particle (CP)... Show moreProteasomes are multi-protein, multi-catalytic complexes responsible for the degradation of 80-90% of the proteins inside eukaryotic cells. Proteasomes contain a cylindrical 20S core particle (CP) and one or two 19S regulatory particles (RP). The constitutive proteasome core particle (cCP), which is expressed in all mammalian tissues, contains three catalytically active subunits, namely β1c, β2c and β5c. Lymphoid cells express another proteasome core particle known as the immunoproteasome (iCP). In iCPs, β1c, β2c and β5c are replaced by β1i, β2i and β5i. The research described in this thesis reports on the development of new subunit-selective inhibitors and activity-based probes, on the development of an assay to simultaneously monitor all cCP and iCP catalytic activities and on the development of a method that reports on CP catalytic active subunit composition. The tools that stem from the work described in this thesis can now be used to unravel the role of each individual catalytic subunit in a chemical genetics setting (selective and (near) complete inhibition of each subunit), and to clarify the role of mCPs, in, for instance, antigen presentation and cancer. Furthermore, these tools could possibly serve as leads in the discovery of agents for future treatment of cancer and autoimmune diseases. Show less
In this thesis, we studied the Diaphanous-Related Formins (DRFs) mDia1 and mDia2 for their actin-dependent and -independent roles in several cellular processes, including lamellipodia/ruffle... Show moreIn this thesis, we studied the Diaphanous-Related Formins (DRFs) mDia1 and mDia2 for their actin-dependent and -independent roles in several cellular processes, including lamellipodia/ruffle formation and cell migration, gene transcription, and proteasome-dependent protein homeostasis. In addition we systematically characterized a widely employed general Formin inhibitor SMFIH2. This thesis highlights actin-dependent and -independent functions of the DRFs mDia1 and mDia2, and sheds new light on novel mode of action for DRFs. Show less
Oliveira, C.C.; Sluijter, M.; Querido, B.; Ossendorp, F.; Burg, S.H. van der; Hall, T. van 2014
This Thesis aims at the development of novel subunit selective inhibitors of the proteasome. -Three vinyl sulfone analogues of three epoxyketone containing inhibitors described in literature are... Show moreThis Thesis aims at the development of novel subunit selective inhibitors of the proteasome. -Three vinyl sulfone analogues of three epoxyketone containing inhibitors described in literature are synthesised and characterised. The nature of the electrophile determines subunit selectivity of the inhibitor. -Ten Michael acceptors are coupled to three peptoid tails yielding thirty peptide-like compounds. None of the peptoid Michael acceptors are efficient proteasome inhibitors. Using the Staudinger-Bertozzi ligation followed by affinity purification, tryptic digestion of the isolated proteins and LC/MS/MS identification, the targets of two compounds in HEK293T and RAW264.7 cells are determined. -Syringolins are potent proteasome inhibitors found in nature. A syringolin structural motif was built in peptoid epoxyketones and vinyl sulfones yielding a 16-membered library of proteasome inhibitors. The distance between the urea and electrophile dictates subunit selectivity. -Three cyclooctynes are compared to the Staudinger-Bertozzi two-step labelling strategy. Cyclooctynes quantitatively convert azide labelled proteasomes at a lower concentration than the Staudinger-Bertozzi phosphane but cyclooctyne two-step labelling is associated with tremendous background labelling. -A library of peptoid vinyl sulfones with basic amino acid side chains is synthesised. A compound with two benzylamine residues is a potent and _2 selective proteasome inhibitor. Attachment of a BODIPY fluorophore yielded a _2 selective probe. Show less
This thesis describes the design, synthesis and application of chemical tools for the activity-based protein profiling of proteases, with the main focus on matrix metalloproteinases (MMPs) and the... Show moreThis thesis describes the design, synthesis and application of chemical tools for the activity-based protein profiling of proteases, with the main focus on matrix metalloproteinases (MMPs) and the proteasome. The use of photoaffinity labeling is described and the thesis starts with an extensive outline of the three most often used photoreactive groups and their application in (recently published) protein profiling studies. Targeting MMPs is performed by application of photoaffinity probes, while the proteasome is commonly targeted by so-called suicide inhibitors. The last experimental chapter deals with the creation of a novel chemoselective cleavable linker and its use in the pull-down of active proteasome subunits. Show less
In cells, proteins are continuously synthesized and degraded to control protein levels and thereby regulate a wide variety of biochemical processes. The proteasome is the main cellular degradation... Show moreIn cells, proteins are continuously synthesized and degraded to control protein levels and thereby regulate a wide variety of biochemical processes. The proteasome is the main cellular degradation machinery, responsible for the degradation of key proteins involved in the regulation of a wide range of cellular processes, including quality control, cell cycle progression, cell differentiation, signal transduction and apoptosis. Inhibition of the proteasome causes disruption of many regulatory processes, eventually leading to cell death. The observation that many cancer cells are more sensitive to proteasome inhibition than normal cells has led to the development of several proteasome inhibitors for the treatment of cancer. Proteasome activity in its broadest sense is the central theme of this thesis. The development and characterization of different chemical proteasome activity probes that can be used to study proteasome activity in a wide range of tissue types using a variety of assays are described. Subsequently, these probes are used to assess the effects of different proteasome inhibitors in preclinical and clinical studies and to purify proteasome and characterize its activity and composition. Finally, the molecular mechanism of proteasomal antigen splicing is studied. Show less
Glycoconjugates (a carbohydrate connected to a lipid, protein or other carbohydrate) play a key role in great variety of biological processes. The synthesis of these constructs is tightly regulated... Show moreGlycoconjugates (a carbohydrate connected to a lipid, protein or other carbohydrate) play a key role in great variety of biological processes. The synthesis of these constructs is tightly regulated by enzymes. Defects in these enzymes may result in an impaired degradation of the glycoconjugate. Consequently, the levels of glycoconjugates are increased and this may eventually lead to storage disorders such as Gaucher disease. The research described in this thesis focuses on the synthesis of chemical tools (activity-based probes, ABPs) to study the enzymes involved in the degradation of glycoconjugates. Using these probes, it was demonstrated that the activity of peptide N-glycanase (the enzyme that is responsible for the hydrolysis of N-linked glycoproteins)inhibitors is determined by its reactive group. Furthermore, the activity-based protein profiling strategy was used to study degradation of glycosy lated proteins. It appeared that deglycosylation of O-GlcNAclated proteins is not a prerequisite for proteasomal degradation. To study beta-glucosidases (enzymes that catalyze the hydrolysis of O-glycosidic linkages), ABPs based on cyclophellitol have been developed. Especially fluorescently labeled probes bind efficiently and selectively to beta-glucosidases. These probes have been used to investigate Gaucher disease. Both wild-type and mutant forms of the enzyme could be labeled in vitro and in living cells which allowed rapid identification activity of this glucosidase. Show less
Cytotoxic T cell epitopes are the targets for a T cell mediated immunotherapy of cancer. The thesis reports on their identification in the tumor associated proteins BCR-ABL and PRAME by the reverse... Show moreCytotoxic T cell epitopes are the targets for a T cell mediated immunotherapy of cancer. The thesis reports on their identification in the tumor associated proteins BCR-ABL and PRAME by the reverse immunology (prediction) strategy. An extended strategy is used, including the analysis of the C-terminal generation of potential epitopes by the proteasome. Novel HLA class I peptide binding assays were developed to enable further epitope discovery. Fundamental studies were performed to identify novel non-proteasomal cytosolic endopeptidases in the HLA class I antigen processing pathway. Nardilysin and thimet oligopeptidase were identified to generate in a concerted action an HLA-A3 restricted CTL epitope from PRAME. The general roles of nardilysin and TOP in class I processing were investigated. Show less
What makes plant shoots grow towards the light, and plant roots grow down into the soil? This was a question that Charles Darwin asked himself, and his experiments more than a century ago to find... Show moreWhat makes plant shoots grow towards the light, and plant roots grow down into the soil? This was a question that Charles Darwin asked himself, and his experiments more than a century ago to find the answer laid the basis for the identification of the growth hormone auxin. Auxin, or indole-3-acetic acid (IAA), directs plant growth and development through its polar cell-to-cell transport-driven asymmetric distribution. Cellular IAA concentrations determine cell division, -elongation and -differentiation by facilitating the degradation of the Aux/IAA repressor proteins and thus inducing gene expression. The presumed pathway for the programmed degradation of proteins involves the attachment of a protein called ubiquitin, leading to recognition and destruction by a molecular complex called the proteasome. Here we investigated the role of protein ubiquitination and degradation in auxin action. First, we provided evidence for the longstanding paradigm that Aux/IAA proteins are ubiquitinated prior to their proteasomal degradation. At the same time we showed that ubiquitin labeling is not necessarily required for proteasomal degradation of plant proteins. Moreover, we showed that a regulator of auxin transport polarity is also involved in fine tuning auxin responses through the ubiquitin pathway. Our results place protein ubiquitination at a central position in auxin biology and thus in the movement of plants. Show less
The synthesis of different tools to study protease activities are presented. Irreversible inhibitors of the proteasome or cathepsins were equipped with reporter groups and other functionalities to... Show moreThe synthesis of different tools to study protease activities are presented. Irreversible inhibitors of the proteasome or cathepsins were equipped with reporter groups and other functionalities to generate probes to study these proteases under different conditions. A two step labeling strategy allowed labeling of all proteasome subunits in living cells, and visualizing these activities after cell lysis. This strategy was employed further to visualize the subunit specificity of a newly developed proteasome inhibitor. An isotope coded tag was introduced in a cathepsin inhibitor in order to assess relative cathepsin activities. An crosslinking functionality or cell penetrating peptide sequence allowed active transport of cathepsin probes into cells, thereby shining a light on the uptake mechanism. Show less
Surgery is the most effective cancer therapy, followed by radiotherapy. These techniques usually target tumour specific tissue only, unlike most forms of chemotherapy as is best illustrated by the... Show moreSurgery is the most effective cancer therapy, followed by radiotherapy. These techniques usually target tumour specific tissue only, unlike most forms of chemotherapy as is best illustrated by the relatively moderate side effects of such treatments. When the immune system could find and destroy tumour cells, they (and their metastases) would be selectively destroyed without to many side effects as well. But then tumour cells have to be recognized and this requires presentation of tumour specific proteins to the immune system. This process called antigen presentation by the MHC class I molecules is studied here. Chapter 1 and 2 form an introduction to the ubiquitin proteasome system and the MHC class I antigen presentation route, which is operational in most cell types and is involved in presentation of antigens derived from degraded intracellular proteins (of self, tumour or viral origin). Proteins are not randomly degraded, but targeted for degradation by ubiquitin or ubiquitin-like post-translational modifications and subsequently degraded by the major cellular protease, the proteasome. Proteins are not only targeted for degradation because they are old, they may also be targeted for example in a cell cycle specific way or just because they have not been folded correctly during protein synthesis. Further trimming to free amino acids by other proteases follows degradation of cellular proteins by the proteasome. Only a minor pool of peptides that meets the requirements for antigen presentation may circumvent further degradation by binding to proteins involved in MHC class I presentation, like the transporter associated with antigen presentation (TAP), and MHC class I itself. Once the peptide is loaded onto MHC class I, the MHC class I-peptide complex can be transported to the plasma membrane. Here, the peptide is presented to cytotoxic T-cells (CTLs), which can in this way examine the intracellular protein content in their search for foreign content. The first step in antigen presentation by MHC class I is the decoration of target proteins with a degradation signal. The first discovered and best-studied degradation signal is a polymer of ubiquitin proteins. A ubiquitin polymer of more than four ubiquitin proteins can be recognized by the proteasome and subsequently unfolded, de-ubiquitylated and degraded by the proteasome. Free ubiquitin and mono- ubiquitylated proteins are not targets for degradation, but serve other functions. Most studies on ubiquitin have been of biochemical nature, but the introduction of the green fluorescent protein (GFP) allowed the study of ubiquitin behaviour in living cells. It was shown before that a GFP-ubiquitin construct could be stably expressed in human cells. In chapter 4, we have used this chimeric protein to study ubiquitin in living cells under normal cell culture conditions and during proteotoxic cell stress as the result of proteasome inhibition, and heat shock. In untreated cells we were able to confirm previous biochemical experiments showing that a large pool of ubiquitin molecules is coupled to histone 2A and 2B in the nucleus, whereas a small pool of ubiquitin is present as free monomers in both nucleus and cytosol. A third pool of ubiquitin was present in the form of ubiquitin polymers in both the nucleus and the cytosol. Manipulation of the cells with different proteotoxic stress conditions revealed a rapid de-ubiquitylation of the histone-bound ubiquitin pool in favour of poly-ubiquitin chains, which may even reach a size similar to the proteasome complex, which is at least one hundred times bigger as a single ubiquitin molecule. These rapid changes in the ubiquitin equilibrium do not only affect proteasomal degradation, but also induce chromatin condensation and altered gene transcription, thus establishing cross talk between these, at first sight unrelated, cellular processes. Alterations in the UPS are correlated with a variety of human pathologies, like cancer, immunological disorders, inflammation and neurodegenerative diseases. The exact role of the UPS in the pathophysiology of these diseases however, remains poorly understood. Because ubiquitin and the ubiquitin proteasome system are involved in several neurodegenerative diseases like Parkinson__s disease, Alzheimer__s disease and polyglutamine diseases like Huntington__s disease we set out our hypothesis of a sensitive ubiquitin equilibrium in the cell in chapter 5. Besides surgery, radiotherapy is one of the most effective ways of anticancer treatment. The main effects of radiotherapy on cells are induction of double-stranded DNA breaks and the formation of reactive radical species, which may lead to protein modifications like amino acid side-chain oxidation and breakage of di-sulphide bonds. These modifications will hopefully lead to DNA and protein damage, sufficient for cells to enter apoptosis or cell arrest. In chapter 6 we have shown that following exposure to g-irradiation, cell surface MHC class I-peptide complex expression is dose dependently upregulated in two phases. In the first phase of upregulation, proteins are degraded and presented that were directly damaged by the radiation and subsequent radical formation. The second phase is caused by a radiation driven activation of the mTOR pathway, which results in enhanced protein synthesis. This leads to the formation of malformed proteins called rapidly degraded proteins (RDPs) or defective ribosomal products (DRiPs) that are subsequently degraded by the proteasome and presented by MHC class I. The second phase does not only quantitatively alter MHC class I expression, but because of the mTOR pathway-specific protein expression also qualitatively. In addition, proteins may be upregulated to g-irradiation especially DNA repair proteins, resulting in more specific peptides. CTLs directed against these radiation-specific peptides were found in peripheral blood, but appeared in an anergic state. The existence of these CTLs and the expression of radiation-specific peptides may explain the inhibition of distant tumours after local radiotherapy if these CTLs could be activated. This effect is known as the abscopal effect of local radiotherapy. If these CTLs could be activated prior to irradiation in a combination therapy, these could induce a potent immune response against the irradiated cells. We show that prior radiation of a local tumour strongly improves the response to immunotherapy (adoptively transferred CTLs), showing the feasibility of a novel combination therapy: radio-immuno therapy. The majority of MHC class I loaded peptides is derived from cytosolic proteins. But it has been shown that MHC class I also presents peptides derived from extracellular sources like bacteria and proteins from neighbouring cells. This phenomenon is called cross-presentation and many pathways have been postulated to explain how proteins from extracellular sources may intersect with the MHC class I loading machinery. Examples are endosome to cytosol relocation, intercellular peptide transport through gap-junctions, exosomes and ER-phagosome fusion. In chapter 3, we have evaluated the evidence for and against the ER-phagosome theory and concluded that cross-presentation via fusion of phagosomes with the ER is very inefficient if at all possible. Our evaluation of the ER-phagosome theory was a commentary on a study by Touret et al, 2005. This study attempted to validate previous results leading to the ER-phagosome fusion theory, but failed to do so. We have also tried to show ER-phagosomal fusion in dendritic cells, but the best near-fusion event of the ER we could find was a close encounter of ribosome containing ER membranes with a mitochondrion. Also our calculations on the odds of presentation of phagosome-derived peptides were not in favour of antigen presentation via ER-phagosome fusion events. We conclude that cross-presentation to support vaccination should find a different route. Show less
In gene therapy, expression of a corrected gene leads to synthesis of proteins foreign to the immune system. Cells expressing these will therefore be recognized as aberrant and destructed. We used... Show moreIn gene therapy, expression of a corrected gene leads to synthesis of proteins foreign to the immune system. Cells expressing these will therefore be recognized as aberrant and destructed. We used a known immune evasion mechanism to "stealth" transgene products. We fused the coding sequence of the Gly-Ala repeats (GAr) of the Epstein-Barr Virus (EBV) nuclear antigen 1 (EBNA-1) with three different transgenes, i.e. E.coli LacZ, firefly Luciferase and herpes simplex virus 1 thymidine kinase (TK). We show that the EBV GAr system could well be used to prevent the immune system of reacting on transgenes. We could also show, that GAr-TK might be a good candidate to use in bone marrow transplantation protocols. In addition to the GAr, we used an alternative open reading frame found within the ENBA-1 sequence (GZr). We made a fusion of the GZr with the LacZ gene and show that, in contrast to a repeat deleted construct, the construct bearing repeats was protected for recognition by LacZ specific CTLs. This shows that the GZ repeats might be another candidate to shield transgenes for the immune system. The human herpes virus 8 (HHV-8) has a protein like EBNA-1, involved in establishing latency, latency-associated nuclear antigen-1 (LANA-1). We show that LANA-1, like EBNA-1, possesses an immune evasion effect. Show less
