Marko Fonović

Marko Fonović
Jožef Stefan Institute | IJS · Department of Biochemistry, Molecular and Structural Biology

PhD

About

66
Publications
9,308
Reads
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2,458
Citations
Citations since 2016
35 Research Items
1339 Citations
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
2016201720182019202020212022050100150200
Additional affiliations
September 2007 - present
Jožef Stefan Institute
Position
  • Institut Jozef Stefan
November 2004 - September 2007
Stanford University
February 1999 - May 1999
Icahn School of Medicine at Mount Sinai
Position
  • Researcher
Education
October 1999 - October 2004
University of Ljubljana
Field of study
  • Biochemistry and Molecular Biology
October 1991 - April 1998
University of Ljubljana
Field of study
  • Chemistry

Publications

Publications (66)
Article
Full-text available
Circular RNAs (circRNAs) have been shown to play an important role in the pathogenesis of hepatocellular carcinoma (HCC). By implementing available transcriptomic analyses of HCC patients, we identified an upregulated circRNA hsa_circ_0062682. Stable perturbations of hsa_circ_0062682 in Huh-7 and SNU-449 cell lines influenced colony formation, migr...
Article
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Background High temperature requirement A (HtrA) is an active serine protease secreted by the group-I carcinogen Helicobacter pylori ( H. pylori ). The human cell adhesion protein and tumor suppressor E-cadherin (hCdh1) expressed on the surface of gastric epithelial cells was identified as the first HtrA substrate. HtrA-mediated hCdh1 cleavage and...
Article
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Modulated electro-hyperthermia (mEHT) is a selective cancer treatment used in human oncology complementing other therapies. During mEHT, a focused electromagnetic field (EMF) is generated within the tumor inducing cell death by thermal and nonthermal effects. Here we investigated molecular changes elicited by mEHT using multiplex methods in an aggr...
Article
Full-text available
(1) Background: Lipopolysaccharide (LPS)-induced systemic inflammation is associated with septic acute kidney injury (AKI). We investigated the time-dependent miRNA expression changes in the kidney caused by LPS. (2) Methods: Male outbred NMRI mice were injected with LPS and sacrificed at 1.5 and 6 h (40 mg/kg i.p., early phase, EP) or at 24 and 48...
Article
Full-text available
Helicobacter pylori (H. pylori) secretes the chaperone and serine protease high temperature requirement A (HtrA) that cleaves gastric epithelial cell surface proteins to disrupt the epithelial integrity and barrier function. First inhibitory lead structures have demonstrated the essential role of HtrA in H. pylori physiology and pathogenesis. Compr...
Article
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Porphyromonas gingivalis, the main etiologic agent of periodontitis, secretes cysteine proteases named gingipains. HRgpA and RgpB gingipains have Arg-specificity, while Kgp gingipain is Lys-specific. Together they can cleave an array of proteins and importantly contribute to the development of periodontitis. In this study we focused on gingipain-ex...
Article
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(1) Background: Sepsis-induced acute kidney injury (AKI) is the most common form of acute kidney injury (AKI). We studied the temporal profile of the sepsis-induced renal proteome changes. (2) Methods: Male mice were injected intraperitoneally with bacterial lipopolysaccharide (LPS) or saline (control). Renal proteome was studied by LC-MS/MS (Prote...
Article
The vital role of proteases in the progression of various diseases has been increasingly recognized. Proteolytically generated proteoforms are secreted into body fluids, such as blood, urine, and cerebrospinal fluid which enables their utilisation in biomarker discovery. Degradomic methodologies can be applied for the initial identification and val...
Article
The upregulation of protease expression and proteolytic activity is implicated in numerous pathological conditions such as neurodegeneration, cancer, cardiovascular and autoimmune diseases, and bone degeneration. During disease progression, various proteases form characteristic patterns of cleaved proteins and peptides, which can affect disease sev...
Article
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Legumain or asparagine endopeptidase is a unique cysteine endopeptidase with a distinctive specificity for the hydrolysis of peptide bonds after asparagine and to a lesser extent after aspartate. It is ubiquitously expressed in various tissues and besides its involvement in immune response and other physiological processes, it was also shown to pla...
Article
The GGGGCC (G4C2) repeat expansion mutation in the C9ORF72 gene is the most common genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Transcription of the repeat and formation of nuclear RNA foci, which sequester specific RNA-binding proteins, is one of the possible pathological mechanisms. Here, we show that (G...
Article
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Macropinocytosis and phagocytosis are evolutionarily conserved forms of bulk endocytosis used by cells to ingest large volumes of fluid and solid particles, respectively. Both processes are regulated by Ras signaling, which is precisely controlled by mechanisms involving Ras GTPase activating proteins (RasGAPs) responsible for terminating Ras activ...
Article
Proteases are considered of major importance in biomedical research because of their crucial roles in health and disease. Their ability to hydrolyze their protein and peptide substrates at single or multiple sites, depending on their specificity, makes them unique among the enzymes. Understanding protease specificity is therefore crucial to underst...
Article
Cysteine cathepsins have been for a long time considered to execute mainly nonspecific bulk proteolysis in the endolysosomal system. However, this view has been changing profoundly over the last decade as cathepsins were found in the cytoplasm, nucleus and in the extracellular milieu. Cathepsins are currently gaining increased attention largely bec...
Chapter
The discovery of the protein targets of small molecule probes is a crucial aspect of activity-based protein profiling and chemical biology. Mass spectrometry is the primary method for target identification, and in the last decade, cleavable linkers have become a popular strategy to facilitate protein enrichment and identification. In this chapter,...
Article
Determination of protease specificity is of crucial importance for understanding protease function. We have developed the first gel-based label-free proteomic approach (DIPPS-direct in-gel profiling of protease specificity) that enables quick and reliable determination of protease cleavage specificities under large variety of experimental condition...
Article
Full-text available
To ensure successful feeding tick saliva contains a number of inhibitory proteins that interfere with the host immune response and help to create a permissive environment for pathogen transmission. Among the potential targets of the salivary cystatins are two host cysteine proteases, cathepsin S, which is essential for antigen- and invariant chain-...
Article
Full-text available
Cysteine cathepsins are proteases that, in addition to their important physiological functions, have been associated with multiple pathologies, including cancer. Cystatin C (CstC) is a major endogenous inhibitor that regulates the extracellular activity of cysteine cathepsins. We investigated the role of cystatin C in mammary cancer using CstC knoc...
Chapter
Profiling of protease specificity is crucial for characterization of these important enzymes that play numerous roles in health and disease. In the past, several proteomic methods have been developed that enable profiling of protease specificities. Although able to identify thousands of protease cleavage events, these degradomics approaches are oft...
Article
Full-text available
Background Omics approaches have significantly increased our understanding of biological systems. However, they have had limited success in explaining the dramatically increased productivity of commercially important natural products by industrial high-producing strains, such as the erythromycin-producing actinomycete Saccharopolyspora erythraea. F...
Article
ELISA (Enzyme-linked ImmunoSorbent Assay), as one possible application of antibody-based methods, has proved to be a good candidate for the determination of proteins in works of art due to the low limit of detection, high sensitivity (in the nanogram range), specificity and micro invasiveness of required sampling. Despite the advantages of this met...
Article
Proteolytic cleavage is a ubiquitous, irreversible, posttranslational modification that changes protein structure and function and plays an important role in numerous physiological and pathological processes. Over the last decade, proteases have become increasingly important clinical targets because many of their inhibitors are already used in the...
Conference Paper
Full-text available
Analysing the materials present in artworks presents unique challenges, due to their chemical complexity, interactions between the components of the mixture, alteration, exposure to human intervention, etc. Among materials present in art objects, proteins have been widely used, generally in the form of adhesives, coatings, but especially as binding...
Article
Full-text available
Extracellular cysteine cathepsins are known to drive cancer progression, but besides degradation of extracellular matrix proteins little is known about their physiological substrates and thus the molecular mechanisms they deploy. One of the major mechanisms used by other extracellular proteases to facilitate cancer progression is proteolytic releas...
Article
Proteases are important effectors of numerous physiological and pathological processes. Reliable determination of a protease's specificity is crucial to understand protease function and to develop activity-based probes and inhibitors. During the last decade, various proteomic approaches for profiling protease substrate specificities were reported....
Article
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Cathepsin B (CtsB) is a lysosomal cysteine proteinase that is specifically translocated to the extracellular milieu during cancer progression. The development of a lipidated CtsB inhibitor incorporated into the envelope of a liposomal nanocarrier (LNC-NS-629) is described. Ex vivo and in vivo studies confirmed selective targeting and internalizatio...
Article
Full-text available
Cathepsin B (CtsB) is a lysosomal cysteine proteinase that is specifically translocated to the extracellular milieu during cancer progression. The development of a lipidated CtsB inhibitor incorporated into the envelope of a liposomal nanocarrier (LNC-NS-629) is described. Ex vivo and in vivo studies confirmed selective targeting and internalizatio...
Article
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Ein neues Wirkstofftransportsystem mit Krebs-assoziiertem extrazellulärem Cathepsin-B als Zielstruktur wird von B. Turk, O. Vasiljeva et al. in ihrer Zuschrift auf S. 10241 ff. vorgestellt. Das entwickelte System basiert auf einem lipidierten, Cathepsin-B-spezifischen, in die Hülle der liposomalen Nanoträger eingebauten Inhibitor, mit dem selektiv...
Article
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Alternative functions, apart from cathepsins inhibition, are being discovered for stefin B. Here, we investigate its role in vesicular trafficking and autophagy. Astrocytes isolated from stefin B knock-out (KO) mice exhibited an increased level of protein aggregates scattered throughout the cytoplasm. Addition of stefin B monomers or small oligomer...
Article
Background: Erythromycin is a medically important antibiotic, biosynthesized by the actinomycete Saccharopolyspora erythraea. Genes encoding erythromycin biosynthesis are organized in a gene cluster, spanning over 60 kbp of DNA. Most often, gene clusters encoding biosynthesis of secondary metabolites contain regulatory genes. In contrast, the eryth...
Article
Since their discovery, cysteine cathepsins were generally considered to be involved mainly in the nonspecific bulk protein degradation that takes place within the lysosomes. However, it has become clear that their proteolytical activity can also influence various specific pathological processes such as cancer, arthritis and atherosclerosis. Further...
Conference Paper
Full-text available
Proteins have been widely used, generally in the forms of adhesives, coatings but especially of binding media for colouring materials, where the most commonly used were casein (milk), ovalbumin (egg white), or collagen (bone, skin). Analysing the binding media in artworks presents unique challenges, due to their chemical complexity, interactions be...
Article
Full-text available
Erythromycin is a medically important antibiotic, biosynthesized by the actinomycete Saccharopolyspora erythraea. Genes encoding erythromycin biosynthesis are organized in a gene cluster, spanning over 60 kbp of DNA. Most often, gene clusters encoding biosynthesis of secondary metabolites contain regulatory genes. In contrast, the erythromycin gene...
Article
Abstract Human stefins and cystatins are physiologically important cysteine proteinase inhibitors, acting as a first line of defense against undesirable proteolysis. Mutations in the cystatin B gene cause a rare form of epilepsy EPM1. Its two missense mutants, G50E and Q71P, lack the inhibitory activity and are partially unfolded, which leads to ch...
Article
Full-text available
Cathepsin X has been reported to be a tumor promotion factor in various types of cancer; however, the molecular mechanisms linking its activity with malignant processes are not understood. Here we present profilin 1, a known tumor suppressor, as a target for cathepsin X carboxypeptidase activity in prostate cancer PC-3 cells. Profilin 1 co-localize...
Data
Co-localization of cathepsin X with α-enolase, γ-enolase and β2-integrin in PC-3 cells. All proteins were visualized by immunofluorescence staining using antibodies to cathepsin X, α-enolase, γ-enolase or β2-integrin, followed by Alexa Fluor conjugated secondary antibodies, Alexa Fluor 488 (green) for cathepsin X and Alexa Fluor 555 (red) for α-eno...
Data
Cathepsin X silencing in PC-3 cells. PC-3 cells were transfected with control or cathepsin X specific siRNA using Lipofectamine. After 24, 48 and 72 hours, cell lysates were prepared and cathepsin X activity measured using Abz-FEK(Dnp)-OH substrate (A) and the amount of cathepsin X (ng/ml) determined with ELISA (B). Mean values of three (control an...
Data
Cathepsin X action on control octapeptides. Octapeptides LFPITSVL (A) and AMEDASVL (B) (both 800 µM) were digested with recombinant cathepsin X (4.62 µM) at 37°C for 60 minutes and separated on a C18 Gemini column (5 µm, 110 Å, 150×4.6 mm) (Phenomenex). (TIF)
Article
Full-text available
Actin filaments are key components of the eukaryotic cytoskeleton that provide mechanical structure and generate forces during cell shape changes, growth, and migration. Actin filaments are dynamically assembled into higher-order structures at specified locations to regulate diverse functions. The Rab family of small guanosine triphosphatases is ev...
Article
Traditional proteomics methodology allows global analysis of protein abundance but does not provide information on the regulation of protein activity. Proteases, in particular, are known for their multilayered post-translational activity regulation that can lead to a significant difference between protease abundance levels and their enzyme activity...
Article
The field of activity-based proteomics makes use of small molecule active site probes to monitor distinct subsets of enzymatic proteins. While a number of reactive functional groups have been applied to activity-based probes (ABPs) that target diverse families of proteases, there remains a continual need for further evaluation of new probe scaffold...
Article
Newly replicated Plasmodium falciparum parasites escape from host erythrocytes through a tightly regulated process that is mediated by multiple classes of proteolytic enzymes. However, the identification of specific proteases has been challenging. We describe here a forward chemical genetic screen using a highly focused library of more than 1,200 c...
Article
Activity-based probes (ABPs) that specifically target subsets of related enzymatic proteins are finding increasing use in proteomics research. One of the main applications for these reagents is affinity isolation of probe-labeled targets. However, the use of cheap and efficient biotin affinity tags on ABPs can be problematic due to difficulty in re...
Article
Full-text available
Activity-Based Probes (ABPs) are small molecules that form stable covalent bonds with active enzymes thereby allowing detection and quantification of their activities in complex proteomes. A number of ABPs that target proteolytic enzymes have been designed based on well-characterized mechanism-based inhibitors. We describe here the evaluation of a...
Article
(Chemical Equation Presented) An amicable split: Small-molecule probes can be applied for the enrichment of specific protein targets from a complex proteome. A cleavable linker system, which prevents the release of unwanted, nonspecifically bound proteins, can be used for a very mild and highly selective cleavage of probe-labeled proteins.
Article
Full-text available
Recent advances in global genomic and proteomic methods have lead to a greater understanding of how genes and proteins function in complex networks within a cell. One of the major limitations in these methodologies is their inability to provide information on the dynamic, post-translational regulation of enzymatic proteins. In particular proteases...
Article
Recent characterization of multiple classes of functionalized azapeptides as effective covalent inhibitors of cysteine proteases prompted us to investigate O-acyl hydroxamates and their azapeptide analogues for use as activity-based probes (ABPs). We report here a new class of azaglycine-containing O-acylhydroxamates that form stable covalent adduc...