RESEARCH
The Institute of Cell Biology is a research institution with the longest tradition of cell biology-focused research in Slovenia. It combines state-of-the-art equipment with experts in the field of cell biology and microscopy. The Institute of Cell Biology is also chair of the Center of Electron Microscopy and the University infrastructural centre Biomedical Centre of Microscopy at the faculty of Medicine and the founder of Slovenian node of Eurobioimaging organisation as a European microscopy infrastructure consortium.
Basic and applicative research is focused on the epithelium of the urinary bladder – urothelium. Diverse experimental systems including several kinds of cell cultures and animal models are used to study the urothelial differentiation, proliferation, cell death and several lower urinary tract pathologies as carcinogenesis, bacterial and interstitial cystitis. A broad range of methods are employed: fluorescence microscopy, transmission and scanning electron microscopy, freeze-fracturing, immunofluorescence and immunoelectron microscopy, Western blotting, single cell analysis as well as transfection methods and cell and tissue culturing. These methods are employed to analyze the markers of urothelial differentiation, i.e. uroplakins, cytoskeleton, molecular components of cell-cell and cell-substrate adhesion. The traffic of endomembrane compartments in urothelial cells is studied by endocytic tracers and by immunolabelling.
The interdisciplinary approach to research is supported by numerous collaborations on the national and international level. On the national level the Institute of Cell Biology collaborates in projects with the Biotechnical faculty, Faculty of Electrical Engineering, Faculty of Pharmacy, Institute of Microbiology and Immunology at the Faculty of Medicine, University of Ljubljana, University Clinical centre of Ljubljana, Institute of Oncology and National Institute of Chemistry, Institute Jozef Stefan among others. Another successful collaboration is with the pharmaceutical company Lek, as part of Sandoz, the generic division of Novartis. On the international level the Institute of Cell Biology collaborates with the Eugenia Menni Research Center (Poliambulanza Foundation Hospital, Italy), the Telethon Institute of Genetics and Medicine (Italy), prof. Erik Manders (Advanced Microscopy, the Netherlands), Mathew Mulveys Lab (University of Utah, USA), David Križaj’s lab (University of Utah, USA), prof. Tung-Tien Sun (New York University School of Medicine, USA) and prof. Michael Winder, (Sahlgrenska Academy, Sweden).
RESEARCH TOPICS
Research Programme P3-0108 Cell Biology and Molecular Genetics in Biomedicine has been running continuously since 1999 and operates at the interface of cell biology, molecular genetics, and urology. Its central focus is the biology of the urinary bladder in health and disease, particularly the urothelium, the bladder’s epithelium, which forms a protective barrier between blood and urine. When urothelial recovery from environmental insult or injury is incomplete or uncontrolled, the result can be bladder cancer, bacterial cystitis or interstitial cystitis/bladder pain syndrome (IC/BPS). Compared with other biomedical fields, urological research remains comparatively underfunded, which slows progress in the prevention, diagnosis, and treatment of bladder diseases of substantial social and economic burden in Slovenia and worldwide.
Aim and scientific objectives. The programme aims to elucidate the cell biological and molecular genetic processes that maintain a functional and physiological urothelium, as well as those that drive urothelial dysfunction, pathology, and bladder disease. Specific objectives are: (i) integrative analysis of the cellular compartments and molecules contributing to functional and dysfunctional urothelium, including studies of cellular (ultra)structure and urothelial dynamics; (ii) analysis of bladder carcinogenesis and identification of new therapeutic targets and tools, exploring the potential of tunnelling nanotubes, macropinocytosis, retinoids, and human amniotic membrane in anticancer therapy, together with the role of nicotine and its metabolites in bladder carcinogenesis; (iii) analysis of the immune and inflammatory response of bladder urothelial cells in IC/BPS, including the role of oxidative stress and mitochondrial DNA, and therapeutic approaches with cannabidiol and retinoids; (iv) development of new methods, advancing cryo- and volume electron microscopy and developing patient-derived organoids through tissue engineering, together with advanced molecular genetic techniques applied to urothelial physiology and pathophysiology; and (v) dissemination of knowledge in cell biology and molecular genetics through conferences, workshops, and public communication.
Methodological strengths and broader expertise. A defining feature of the programme is its long-standing and internationally recognised expertise in cell biology and advanced microscopy. The group integrates high-resolution light, electron, cryo-, and volume electron microscopy with ultrastructural and morphometric analysis, biomimetic in vitro and in vivo models, patient-derived organoids and patient samples, tissue engineering, and a broad range of molecular genetics, biochemical, and immunological techniques. This methodological depth, particularly in cellular ultrastructure, membrane dynamics, and quantitative imaging, is the foundation on which the programme’s scientific output rests. It enables not only the bladder-focused research described above but also the programme’s most visible international achievements and collaborations beyond urology, including contributions to international consensus methodology in extracellular vesicle research and validation of human amniotic membrane use in regenerative medicine and to mechanistic studies of innate immunity and intercellular communication conducted jointly with leading international research groups in the respective fields.
Application areas and impact. By investigating basic cellular processes in in vitro and animal models that mimic the human urothelium, together with patient-derived samples, the programme generates a complex insight into the mechanisms of bladder diseases. Translational application areas include the identification of pharmacotherapeutic targets and innovative treatment strategies for bladder cancer and IC/BPS, the use of human amniotic membrane in antimicrobial, anticancer and related biomedical contexts, and the development of imaging and organoid technologies of broad biomedical utility. The programme’s societal, health-related, and socio-economic relevance stems from the high prevalence and burden of bladder cancer and IC/BPS, the relative underrepresentation of urological research, and the programme’s translational focus on the development of new diagnostic and therapeutic approaches. Academically, its core expertise in cell biology and microscopy positions the programme as a valuable and productive partner in interdisciplinary collaborations across the life sciences.
Current research projects and programmes funded by the Slovenian Research Agency:
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Linking prolonged oxidative stress to chronic inflammation in interstitial cystitis/bladder pain syndrome (Project No. Z3-50118), principal investigator: dr. Tadeja Kuret
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Inflammatory process in interstitial cystitis and evaluation of the influence of cannabinoid receptor agonists in urinary bladder - from cells to patients (project No. J3-2521), principal investigator dr. Peter Veranič
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The amniotic membrane as a novel multimodal therapy for bacterial cystitis and bladder cancer: unravelling its antimicrobial, immunomodulatory and anticancer activity (project No. J7-2594), principal investigator dr. Mateja Erdani Kreft
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Exploitation of the magneto-mechanical effect in the treatment of neurodegenerative diseases (project No. J2-3043) in collaboration with dr. Slavko Kralj
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Magnetically-controllable nanocarriers mimicking endogenous lipid particles for improved drug/nanoparticle delivery (project No. J2-3040) in collaboration with dr. Darko Makovec
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Bioactive, in situ modified, fibrous membranes based on bacterial cellulose: processing, characterisation and assessment of biomedical potential (project No. J2-2487) in collaboration with dr. Selestina Gorgieva
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Unravelling glioma stem cell niches for novel therapeutic targets in glioblastoma patients (project No. J3-2526) in collaboration with dr. Cornelis J.F. van Noorden
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Selective electroporation by distributed nanoelectrodes (project No. J2-3046) in collaboration with dr. Damijan Miklavčič
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Development of safe multifunctional surfaces for catheters to combat biofilms (DemoCat) (project No. L2-3163) in collaboration with dr. Alenka Vesel
AWARDS
2025
Excellence in Science 2025 Award (Slovenian Agency for Research and Innovation) for contributions to high-impact publications in Nature Communications (2025) and Journal of Extracellular Vesicles (2024):
WELSH, Joshua A., GOBERDHAN, Deborah CI, LENASSI, Metka, WITWER, Kenneth W, et al., HUDOKLIN, Samo (collaborator), ERDANI-KREFT, Mateja (collaborator), RESNIK, Nataša (collaborator), ROMIH, Rok (collaborator) et al. Minimal information for studies of extracellular vesicles (MISEV2023): from basic to advanced approaches. Journal of extracellular vesicles. Feb. 2024, vol. 13, iss. 2, e12404, ISSN 2001-3078.
BORŠIĆ, Elvira, ŽELEZNIK RAMUTA, Taja, OREHEK, Sara, ERDANI-KREFT, Mateja, GEYER, Matthias, JERALA, Roman, HAFNER BRATKOVIČ, Iva. Clustering of NLRP3 induced by membrane or protein scaffolds promotes inflammasome assembly. Nature communications. 2025, vol. 16, article no. 4887, ISSN 2041-1723.
2024
Researchers from the Institute of Cell Biology have actively contributed to the award-winning study on membrane nanostructures led by Prof. Dr. Veronika Kralj-Iglič. Their collaborative work and expertise helped secure the University of Ljubljana's Outstanding Research Achievement Award in 2024.
Dr. Dominika Peskar was awarded Krka's recognition with special praise for her doctoral dissertation, "Structural, functional and sensory properties of the urinary bladder in a model of interstitial cystitis". The doctoral thesis was prepared under the supervision of Assoc. Prof. Andreja Erman.
Špela Bernard was awarded Krka's recognition with special praise for her master’s thesis "The effect of cannabidiol on urinary bladder in mice with experimentally induced interstitial cystitis". The master’s thesis was prepared under the supervision of Assoc. Prof. Andreja Erman and Prof. Mojca Kerec Kos.
Luka Predojević’s doctoral dissertation, entitled “Uropathogenicity of Human Escherichia coli Strains Employing an In Vitro Biomimetic Model of Porcine Urothelium,” received the Krka Pharmaceutical Company Award with Special Commendation for 2024. The doctoral dissertation was prepared under the supervision of Prof. Marjanca Starčič Erjavec, PhD, and co-supervision of Prof. Mateja Erdani Kreft, PhD.
Nika Požun’s master’s thesis, entitled “Effect of Human Amniotic Membrane Homogenate and Defactinib on Autophagy in Urothelial Cancer Cells,” received the Krka Pharmaceutical Company Prize for 2024. The master’s thesis was prepared under the supervision of Prof. Mateja Erdani Kreft, PhD.
Research work of Žiga Sardoč, entitled "Effect of human amniotic membrane preparations on cancerous urothelial cells of the bladder in 2D and 3D models in vitro and ex vivo" was awarded with the Prešeren Award of Faculty of Medicine for 2024. The research work was prepared under the supervision of Prof. Mateja Erdani Kreft, PhD.
2022
Anja Emri received Prešeren Prize of the Medical faculty for her research thesis "Analysis of cell growth depending on different porosity (mechanical structure) of biocompatible membranes used in reconstructive surgery". The research was supervised by prof. dr. Uroš Ahčan and prof. dr. Mateja Erdani Kreft.
2021
Dr. Taja Železnik Ramuta was awarded the Krka Prize for post-graduates for her doctoral dissertation "Analysis of the effect of amniotic membrane-derived preparations in cancer urothelial cells and uropathogenic bacteria". The doctoral dissertation was prepared under the supervision of Prof. Mateja Erdani Kreft and Prof. Marjanca Starčič Erjavec.
Dr. Tadeja Kuret was awarded Krka's recognition with special praise for her doctoral dissertation"Cell and molecular markers of systemic vasculitis and autoantibodies against serum amyloid A as physiological regulators of the inflammatory response". The doctoral dissertation was prepared under the supervision of Prof. Snežna Sodin-Šemrl and Prof. Saša Čučnik.
Maja Vodlan received the Krka Prize and Prešeren Prize of the Medical faculty for her research thesis "The effect of metformin on biogenesis of mitochondria in in vitro breast cancer cells MDA-MB-231". The research was supervised by prof. dr. Peter Veranič and prof. dr. Maja Pavlin.
Valentina Vošner received Prešeren Prize of the Medical faculty for her research thesis "Analysis of molecular, morphological and physiological causes for premature rupture of fetal memebranes". The research thesis was prepared under the supervision of Prof. Andreja Trojner Bregar and Prof. Mateja Erdani Kreft.
2019
Excellence in Science award, 2019. Within the framework of the Excellent in Science project, the article Protein complexes from the fungal genus Pleurotus as new biopesticides for the control of Colorado potato beetle and corn beetle was included in the selection of achievements for 2019, in which Assist prof. Nataša Resnik and Prof. Peter Veranič from the Institute of Cell Biology of the Faculty of Medicine in Ljubljana. Excellent in science is a project implemented by the agency within the framework of the promotion of science. It is a selection of the most prominent achievements of the past year, which is proposed to the ARRS Scientific Council by the members of the Scientific Research Councils of individual sciences for approval. Selected achievements are presented every autumn in the form of short popular lectures at events accessible to the public. The article was published on 25/03/2019 in the journal Scientific reports and is available at: https://www.nature.com/articles/s41598-019-41450-4, and you can find more about the event at: http://www .arrs.si/sl/promocija/odlicni/odlicni-19.asp
Gaja Markovič was awarded Prešeren Prize of Faculty of Medicine for her research thesis "The role of focal adhesion kinase and its inhibitors in the formation of tunnel membrane nanotubes and the survival of cancer urothelial cells". The research was supervised by prof. dr. Mateja Erdani Kreft and doc. dr. Nataša Resnik.
2018
Research work of our undergraduate student Tina Šket was awarded with Prešeren Prize of Biotechnical Faculty.
Research work of our undergraduate student Irenej Kolšek was awarded with Prešeren Prize of Faculty of Medicine.
2017
Prof. Daša Zupančič was awarded EMBP 'Short Term Fellowship Award' for her work on the project »The role of retinoid signaling pathway in urothelial cancer transformation«. The project was carried out at hte Medical Faculty in Split, Croatia in collaboration with Prof. Janoš Terzić and Prof. Jelena Korać Prlić.
Urška Dragin Jerman was awarded the Krka Prize for post-graduates for doctoral dissertation “Interactions between cancer and normal urothelial cells and establishment of urothelial connective tissue equivalent on amniotic membrane scaffold”. The doctoral dissertation was prepared under the supervision of Prof. Mateja Erdani Kreft.
Polona Glažar received the Prešeren award of the Biotechnical faculty for the year 2017 for graduation thesis “Detection of motor proteins in tunneling nanotubes and their role in bacterial communication and dissemination”. The graduation thesis was prepared under the supervision of Prof. Mateja Erdani Kreft.
2016
Polona Glažar received the Prešeren award of the University of Ljubljana for the year 2016 for her research thesis “Carbohydrates of urothelial cells and the integrity of the basal lamina in urothelial neoplasia”. The research thesis was prepared under the supervision of Prof. Daša Zupančič.
Diana Baraga received the Prešeren award of the Biotechnical faculty for the year 2016 for her graduation thesis “Detection of membrane nanotubes between cancer cells and normal urothelial cells”. The graduation thesis was prepared under the supervision of Prof. Mateja Erdani Kreft.
2014
Matej Skočaj was awarded the Krka Prize for post-graduates for his doctoral dissertation “Labeling of cholesterol-enriched membrane microdomains with ostreolysin A”. The doctoral dissertation was prepared under the supervision of Prof. Kristina Sepčić, Ph.D, Biotechnical faculty, University of Ljubljana and Prof. Peter Veranič, Ph.D., Institute of Cell Biology.
Eva Ogorevc was awarded the Unesco L’Oreal For Women in Science Award for the year 2014. She prepared her doctoral dissertation “Membrane vesicles as biomarkers of homeostasis” under the supervision of Prof. Veronika Kralj-Iglič, Faculty of Health Sciences, University of Ljubljana, and Prof. Peter Veranič, Institute of Cell Biology.
Taja Železnik received the Prešeren award of the Biotechnical faculty for the year 2014 for graduation thesis “The use of amniotic membrane scaffold for inhibiting the growth of cancer urothelial cells”. The graduation thesis was prepared under the supervision of Prof. Mateja Erdani Kreft.
2011
The Senate of the Faculty of Medicine awarded the Lavrič teaching award for the year 2011 to Prof. Kristijan Jezernik, the lecturer and the head of the Institute of Cell Biology.
2010
Urška Dragin Jerman received the Prešeren award of the Biotechnical faculty for the year 2010 for graduation thesis “Amniotic membrane as a scaffold for urothelium and its role in differentiation of urothelial cells”. The graduation thesis was prepared under the supervision of Prof. Mateja Erdani Kreft.
2009
Larisa Tratnjek received the The Pomurje research award for best graduation thesis for the year 2009 rewarded for the graduation thesis “Endocitotic activity in urothelial cells: dependence on differentiation stage and microtubules”. The graduation thesis was prepared under the supervision of Prof. Mateja Erdani Kreft.