1. Proximity-induced transfer of a mass tag enables direct profiling of active matrix metalloproteasesLomane Berthy, Ugo Pasco, Mylene Sejalon-Cipolla, Metka Novak, Barbara Breznik, 2026, original scientific article Abstract: Conventional activity-based probes in activity-based protein profiling (ABPP) require enrichment or reporter tags for detection, which limits sensitivity and multiplexing. Here, we present an enrichment-free chemoproteomic approach that enables direct mass spectrometric detection by Matrix-Assisted Laser Desorption/Ionization (MALDI) of active proteases. An active-site–directed affinity probe transfers, through a proximity-induced reaction, a MALDI-detectable α-cyano-4-hydroxycinnamic acid (CHCA) tag exclusively to catalytically active forms of matrix metalloproteases (MMPs). The CHCA label enhances ionization efficiency and markedly improves signal-to-noise ratios, allowing confident identification of CHCA-labelled peptides under discriminating analytical conditions. Each active metalloprotease is thereby, associated with a distinct set of CHCA signature peptides, defining its activity fingerprint. This workflow achieves multiplexed and quantitative activity profiling of MMPs, directly in complex proteomes. This design expands ABPP into the mass spectrometry domain and establishes a robust platform for activity-based enzyme detection.
Keywords: activity-based probes, chemoproteomic, mass tag, proximity-induced labelin
Published in DiRROS: 05.05.2026; Views: 144; Downloads: 83
 Full text (3,50 MB)
This document has many files! More... |
2. Meroslovna podpora za izboljšanje genomskega profiliranja v diangositki rakaMojca Milavec, Alexandra Bogožalec Košir, Metka Novak, Barbara Breznik, Carole A. Foy, Carla Divieto, 2025, published scientific conference contribution Keywords: tumorji, genomsko profiliranje, diagnostika raka, GenomeMET
Published in DiRROS: 11.03.2026; Views: 288; Downloads: 104
Full text (110,24 KB) |
3. Vrednotenje različnih metod ekstrakcije nukleinskih kislin iz humane celične 3D kulture rakaStefanija Ivanova, Alexandra Bogožalec Košir, Metka Novak, Barbara Breznik, Mojca Milavec, 2025, published scientific conference contribution Keywords: celične kulture, tumorji, molekularna diagnostika, ekstrakcijske metode, kontrola kakovosti, GenomeMET
Published in DiRROS: 11.03.2026; Views: 291; Downloads: 96
Full text (183,78 KB) |
4. Vpliv tehnoloških postopkov na uspešnost kompostiranja hmeljevineBarbara Čeh, Ana Karničnik Klančnik, 2025, professional article Abstract: V prispevku predstavljamo rezultate kompostiranja hmeljevine (listi in stebla hmelja, ki ostanejo po obiranju storžkov) na šestih hmeljarskih kmetijah. Kompostne kupe so postavili po obiranju hmelja (začetek septembra) v letih 2023 (štiri kmetije) in 2024 (šest kmetij). Kompostiranje naj bi potekalo po smernicah za kompostiranje hmeljevine, a so imeli na kmetijah med izvajanjem postopka različne težave. Le-te smo popisali in ocenili njihov vpliv na kakovost pridelanega komposta. Kompost smo vzorčili v aprilu v letih 2024 in 2025 in ugotovili, da je imel v vseh primerih temperaturo na nivoju okoliške in bil prijetnega vonja po zemlji. Največji negativen vpliv je imelo nezadostno mešanje – v primeru, ko je bil kup jeseni premešan le dvakrat, ni bila dosežena temperatura za higienizacijo (55 oC), material je bil slabo razgrajen, vsebnost hranil v kompostu je bila srednja, razmerje C:N pa neugodno. In le na teh vzorcih je bioindikatorski test kalivosti semen kitajskega kapusa pokazal možno fitotoksičnost komposta. Slabši rezultat je bil tudi v primeru, ko je bila za postavitev kupa uporabljena premajhna gmota biomase (le 7 ton) in je bila le-ta hkrati nekoliko presuha, ter v primeru, ko so kup prekrili s polprepustno ponjavo šele v sredini decembra namesto v novembru. Mešanje kupa v času dežja v primeru presuhe biomase jeseni je pozitivno vplivalo na parametre kakovosti komposta. Kompost z najboljšimi parametri je nastal v primeru, ko so izvajali kompostiranje dosledno po smernicah - pri rednem mešanju glede na meritve temperature, uporabljeni dovolj veliki gmoti hmeljevine (15 ton) in pravočasnem pokrivanju kupov. V tem primeru je bil test kalivosti 94 % (odličen kompost, ki vzpodbuja kalitev).
Keywords: hmeljevina, hmelj, Humulus lupulus L., kompost, organsko gnojilo
Published in DiRROS: 26.02.2026; Views: 238; Downloads: 178
Full text (507,59 KB)
This document has many files! More... |
5. MAGEA3/6 tumour antigens regulate glycolytic protein hexokinase to enhance pancreatic cancer cell survival under metabolic stressVesna Jurjevič, Jerneja Koren, Sima Tozandehjani, Sara Uhan, Lara Snoj, Barbara Breznik, Juan Solano, Klementina Fon Tacer, 2024, published scientific conference contribution abstract Keywords: pancreatic cancer, metabolism, MAGE, oncology
Published in DiRROS: 25.02.2026; Views: 331; Downloads: 93
Full text (85,16 KB) |
6. Imunosupresija pri glioblastomu : vloga cistatina F in vpliv na celice NKEmanuela Senjor, Ana Mitrović, Marko Jukič, Matic Proj, Stanislav Gobec, Barbara Breznik, Janko Kos, Milica Perišić, 2024, published scientific conference contribution Keywords: imunosupresija, glioblastom, celice NK, onkologija
Published in DiRROS: 25.02.2026; Views: 332; Downloads: 98
Full text (298,69 KB) |
7. Imunospresija pri glioblastomu : vloga cistatina F in vpliv na celice NKEmanuela Senjor, Ana Mitrović, Marko Jukič, Matic Proj, Stanislav Gobec, Barbara Breznik, Janko Kos, Milica Perišić, 2024, published scientific conference contribution Published in DiRROS: 25.02.2026; Views: 303; Downloads: 81
Full text (298,93 KB) |
8. Integrating computational fluid dynamics into organ-on-chip systems: a glioblastoma-centred design and validation frameworkHooman Taleban, Xinzhong Li, Zulfiqur Ali, Karunakaran Kalesh, Jai Prakash, Tugba Bagci-Onder, Barbara Breznik, 2026, review article Abstract: Glioblastoma GBM: Glioblastoma multiforme (GBM) remains one of the most lethal and treatment-resistant brain cancers, driven in part by the complexity of its tumour microenvironment (TME). While organ-on-chip (OoC) platforms offer more physiologically relevant models than traditional 2D or static 3D systems, their design remains largely empirical, lacking predictive control over flow conditions, biochemical gradients, and mechanical cues. Computational Fluid Dynamics (CFD) has emerged as a powerful tool to enhance the design, precision, and biological fidelity of OoC platforms. This comprehensive review highlights current limitations in replicating GBM’s biological complexity and technical constraints in device fabrication and maintenance, mapping them to specific CFD strategies. It synthesises current strategies into a structured workflow for integrating CFD into the design, optimisation, and validation of microfluidic tumour models—bridging engineering precision with biological complexity. In addition, validation frameworks reported in the literature are highlighted and mapped onto GBM-on-chip applications have been recommended, drawing on widely recognised international standards for engineering validation and regulatory modelling practices. Finally, this review positions CFD as a core component of GBM-on-chip development and explores how its integration with AI-based optimisation can advance the creation of more predictive, scalable, and biologically relevant in vitro tumour models.
Keywords: AI, computational fluid dynamics, glioblastoma, In silicosimulation, in vitro modelling, microfluidic perfusion, organ-on-chip, tumour microenvironment
Published in DiRROS: 13.02.2026; Views: 421; Downloads: 204
 Full text (716,80 KB)
This document has many files! More... |
9. Heterogenous mitochondrial ultrastructure and metabolism of human glioblastoma cells : differences between stem-like and differentiated cancer cells in response to chemotherapyUrban Bogataj, Metka Novak, Simona Katrin Galun, Klementina Fon Tacer, Miloš Vittori, Cornelis J. F. van Noorden, Barbara Breznik, 2025, original scientific article Abstract: Background[:] Glioblastoma stem-like cells (GSCs) contribute to the resistance of glioblastoma (GBM) tumors to standard therapies. The background of the resistance of GSCs to the chemotherapeutic agent temozolomide is not yet fully understood in the context of cellular metabolism and the role of mitochondria. The aim of this study was to perform a detailed ultrastructural characterization of the mitochondria of GSCs prior and post temozolomide exposure and to compare it to differentiated GBM cells. Materials and methods[:] Patient-derived and established GBM cell lines were used for the study. The ultrastructure of the mitochondria of the examined cell lines was assessed by transmission electron microscopy. The microscopic analysis was complemented and compared by an analysis of cell metabolism using Seahorse extracellular flux analysis. Results[:] We found that the metabolic profile of GSCs is quiescent and aerobic. Their elongated mitochondria with highly organized cristae are indicating increased biogenesis and mitochondrial fusion and corresponds to a more oxidative phosphorylation (OXPHOS)-dependent metabolism. The metabolism of GSCs is dependent on OXPHOS and there are no changes in defective mitochondria fraction after the treatment with temozolomide. In contrast, differentiated GBM cells with fragmented mitochondria, which have less organized cristae, are more energetic and glycolytic. Temozolomide treatment induced ultrastructural mitochondrial damage in differentiated GBM cells. Conclusions[:] We demonstrated differences in mitochondrial ultrastructure and cellular metabolism between GSCs and differentiated GBM cells in response to temozolomide, suggesting that mitochondria play an important role in the resistance of GSCs to temozolomide. This study provides a basis for further studies addressing GSC chemotherapy resistance in the context of mitochondrial structure and function.
Keywords: glioblastoma, mitochondria, metabolism, chemotherapy, stem cells
Published in DiRROS: 26.11.2025; Views: 405; Downloads: 315
Full text (1,35 MB)
This document has many files! More... |
10. Targeting cystatin F activation enhances NK cell cytotoxicity in glioblastoma modelsEmanuela Senjor, Anamarija Habič, Urban Švajger, Ana Mitrović, Matic Proj, Andrej Porčnik, Borut Prestor, Miha Jerala, Matic Bošnjak, Stanislav Gobec, Barbara Breznik, Janko Kos, Milica Perišić, 2025, original scientific article Abstract: Introduction: Glioblastoma (GBM) is a highly invasive brain tumor with limited treatment options and poor prognosis. Natural killer (NK) cells are key effectors of antitumor immunity, capable of eliminating cancer stem-like cells. However, GBM creates an immunosuppressive microenvironment that limits NK cell function. Here, we identify cystatin F as an immunosuppressive factor involved in regulating NK cell granule-mediated cytotoxicity. Methods: We analyzed cystatin F expression in GBM and its correlation with immune exhaustion markers. NK cell activity was compared between GBM patients and healthy donors. In vitro co-cultures of cystatin F-expressing microglial cells and glioblastoma stem-like cells were used to assess NK cell function. To block cystatin F activation from dimeric to active monomeric form, a small-molecule inhibitor of cathepsin V, the activating protease, was applied. Results: Cystatin F expression correlated with immune exhaustion and suppression markers in GBM. NK cells from patients showed reduced cytotoxicity compared to healthy donors. Co-cultures confirmed that cystatin F-expressing microglia impaired NK cell cytotoxicity, while inhibition of cathepsin V restored NK cell function in standard cytotoxicity assays, 3D spheroids, and microfluidic perfused models. Discussion: These results indicate that cystatin F mediates NK cell suppression in GBM. Targeting its activation enhances NK cell cytotoxicity, offering a potential strategy to improve NK-based immunotherapy for glioblastoma.
Keywords: glioblastoma, cystatin F, 3D models
Published in DiRROS: 26.11.2025; Views: 995; Downloads: 329
Full text (6,02 MB)
This document has many files! More... |
